Bin Zhao Edison Ong Yongqun He (Oliver) Yu Lin (Asiyah) OHPI is a biomedical ontology in the area of host-pathogen interactions. OHPI is developed by following the OBO Foundry Principles (e.g., openness and collaboration). OWL-DL A biomedical ontology in the area of host-pathogen interactions. OHPI: Ontology of Host-Pathogen Interactions http://creativecommons.org/licenses/by/4.0/ BFO OWL specification label BFO OWL规范标签 Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification. 将本体中的实体关联到用于在代码中表示它的变量的名称，这些代码从lispy规范生成BFO OWL 文件。 Really of interest to developers only 只对开发人员感兴趣 BFO OWL specification label BFO OWL specification label BFO OWL规范标签 BFO OWL规范标签 BFO CLIF specification label BFO CLIF规范标签 Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 将本体中的实体关联到用于在BFO2 CLIF规范中表示它的术语上。 Person:Alan Ruttenberg Person:Alan Ruttenberg Really of interest to developers only 只对开发人员感兴趣 BFO CLIF specification label BFO CLIF specification label BFO CLIF规范标签 BFO CLIF规范标签 An annotation property that represents an ID used in the NIH LINCS project. An annotation property that represents an LINCS ID of a cell line. 表示细胞系的LINCS ID的注释属性。 Oliver He, Jiangan Xie Oliver He, Jiangan Xie Oliver He, Jiangan Xie, Jie Zheng Cell line LINCS ID LINCS ID 细胞系LINCS ID 细胞系LINCS ID editor preferred label editor preferred label editor preferred term editor preferred term editor preferred term~editor preferred label 编辑首选术语 编辑首选标签 The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) 对于一类或属性的简洁的、有意义的、与人类友好的名称由本体开发商首选。 （美国英语） PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> editor preferred label editor preferred label editor preferred term editor preferred term editor preferred term~editor preferred label editor preferred term~editor preferred label 编辑首选术语 编辑首选术语 编辑首选术语~编辑首选标签 编辑首选标签 编辑首选标签 example example of usage 例子 用法示例 A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. 短语描述一个类的名字应该如何使用。也可包括其他类型有助于直接理解类的语义的例子，如广为人知的类的原型子类或实例。虽然高水平的术语必不可少，对于低级别术语的示例（例如，Affymetrix HU133阵列）不 PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> IAO:0000112 uberon example_of_usage true example_of_usage example of usage example of usage 用法示例 用法示例 has curation status 有管理状态 PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot OBI_0000281 has curation status has curation status 有管理状态 有管理状态 definition definition textual definition textual definition 定义 OBI的官方定义，解释类或属性的含义。应该是亚里士多德式的，形式化和规范化的。 可以通过口语定义进行扩充。 The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. 官方的定义，解释类或属性的含义。应该是亚里士多德式的，形式化和规范化的。 可以通过口语定义进行扩充。 2012-04-05: Barry Smith OBI的官方定义解释了一个类或属性的含义：'应该是亚里士多德式的，形式化和规范化的。可以用口语定义'是糟糕的。 您能解决这样的问题吗？ 解释关于类或属性的表达含义的必要和充分条件的陈述。 Alan Ruttenberg 您提出的定义是一个合理的备选，除非它很常见，没有给出必要和充分的条件。大多数情况下它们是必要的，偶尔是必要的，充分的或者仅仅仅充分的。它们通常使用不是自己定义的术语，因此它们实际上不能通过这些标准进行评估。 关于拟议定义的具体内容： 我们没有“含义”，或“表达”或“属性”的定义。对于在预期意义上的“参考”，我认为我们使用术语“指示”。对于'表达'，我认为我们和你的意思是符号，或标识符。对于“含义”，它不同于类和属性。对于类，我们希望文档能够让读者确定一个实体是否是该类的实例。对于属性，让我们的目标读者决定，给定一对潜在的关系，判断关系成立的断言正确与否。 “目标读者”部分表明我们也指定了我们期望的能够理解定义的人，并且概括了人类和计算机读者以包含文本和逻辑定义。 就我个人而言，我更愿意削弱对文档的定义，并指出什么是可取的。 我们还有一个悬而未决的问题，就是如何针对不同的受众定位不同的定义。临床读者阅读chebi需要来自受过化学训练的受众的不同类型的定义文档/定义，同样需要一个适合本体工作者的定义。 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition definition textual definition textual definition 定义 定义 文本定义 文本定义 editor note 编者注 An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. 管理者注释用于其编辑器。它可能不包含在本体的出版版本中，所以它应该不包含最终用户了解本体所需的信息。 PERSON:Daniel Schober GROUP:OBI:<http://purl.obfoundry.org/obo/obi> IAO:0000116 IAO:0000116 uberon uberon editor_note editor_note 编辑_注释 true editor_note editor_note 编辑_注释 IAO:0000116 IAO:0000116 uberon uberon editor_note editor_note 1 true editor_note editor_note editor note editor note 编者注 编者注 definition editor term editor 术语编辑者 Name of editor entering the definition in the file. The definition editor is a point of contact for information regarding the term. The definition editor may be, but is not always, the author of the definition, which may have been worked upon by several people Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people 输入文件中术语编辑者的名称。术语编辑者是有关术语的信息交汇点。术语编辑者可以是，但并不总是，定义的作者，这可能是由几个人完成 20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115. 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. 20110707，MC：术语编辑和定义进行相应的修改。见http://code.google.com/p/information-artifact-ontology/issues/detail?id=115。 PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition editor definition editor term editor term editor 术语编辑者 术语编辑者 alternative term 替代术语 An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) 一类或属性的替代名称，这意味着与所述首选名称同样的事物（语义上等价） PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> alternative term alternative term 替代术语 替代术语 definition source 定义来源 Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007. formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 正式引用，例如在外部数据库中的标识符，用于表示/定义的属性源（S）。自由文本表示/为定义属性源（S）。实例：在2007年1月31日的作者姓名，URI，MeSH术语C04，PUBMEDID，维基uri PERSON:Daniel Schober Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> 论OBO-讨论邮件-列表，请参阅http://bit.ly/hgm99w definition source definition source 定义来源 定义来源 Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007. url:http://purl.obolibrary.org/obo/iao.owl has obsolescence reason Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. PERSON:Alan Ruttenberg PERSON:Melanie Courtot has obsolescence reason curator note 管理者注释 An administrative note of use for a curator but of no use for a user 管理者注释对管理者有用对用户无用 PERSON:Alan Ruttenberg IAO:0000232 IAO:0000232 uberon uberon curator_notes curator_notes 管理者_注释 true curator_notes curator_notes 管理者_注释 IAO:0000232 uberon curator_notes 1 true curator_notes curator note curator note curator notes curator notes 管理者注释 管理者注释 term tracker item the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ An IRI or similar locator for a request or discussion of an ontology term. Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg The 'tracker item' can associate a tracker with a specific ontology term. term tracker item The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg The 'term requester' can credit the person, organization or project who request the ontology term. ontology term requester expand expression to ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones Chris Mungall expand expression to expand expression to OBO foundry unique label An alternative name for a class or property which is unique across the OBO Foundry. The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . PERSON:Alan Ruttenberg PERSON:Bjoern Peters PERSON:Chris Mungall PERSON:Melanie Courtot GROUP:OBO Foundry <http://obofoundry.org/> OBO foundry unique label elucidation 说明 person:Alan Ruttenberg Person:Barry Smith Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms 在最高级别的本体中的原始术语如BFO是对我们理解现实最基本，以至于无法以非循环的方式来定义它们的术语。对于这些，因此，我们只能提供说明，通过例子和公理进行补充 elucidation elucidation 说明 说明 has associated axiom(nl) 具有相关联的公理（nl） Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom associated with a term expressed using natural language 与一个使用自然语言表达的术语相关的公理 has associated axiom(nl) has associated axiom(nl) 具有相关联的公理（nl） 具有相关联的公理（nl） has associated axiom(fol) 具有相关联的公理（fol） Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom expressed in first order logic using CLIF syntax 使用CLIF语法在第一逻辑进行表达的公理 has associated axiom(fol) has associated axiom(fol) 具有相关联的公理（fol） 具有相关联的公理（fol） has axiom id Person:Alan Ruttenberg Person:Alan Ruttenberg A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI axiom id has axiom label term replaced by Add as annotation triples in the granting ontology Use on obsolete terms, relating the term to another term that can be used as a substitute Person:Alan Ruttenberg Person:Alan Ruttenberg term replaced by term replaced by an annotation property that lists keyword(s) useful for literature tagging and retrieval of sentences containing the type (or kind) of entity (e.g., interaction) as shown by the ontology term label and definition. Yongqun He has literature mining keywords the symbol assigned by the nomenclature authority Oliver He, Yue Liu symbol from nomenclature authority the full name assigned by the nomenclature authority Oliver He, Yue Liu full name from nomenclature authority A GeneID in the NCBI Gene database Oliver He, Yue Liu NCBI GeneID the NCBI LocusTag name of a gene Oliver He, Yue Liu NCBI LocusTag the map location of a gene Oliver He, Yue Liu gene map location a date of content modification Oliver He, Yue Liu modification date The NCBITaxon ontology ID of an organism. Oliver He, Yue Liu organism NCBITaxon ID A chromosome ID where a gene is located. Oliver He chromosome ID of gene an annotation property that specifies the type of a gene Oliver He type of gene an annotation property that specifies a nomenclature status Oliver He nomenclature status an annotation property that shows the GO information associated with a specific gene. Yongqun He YH: use the convention: GO_ID (EC: xx; Qualifier: xx; PMID: xxxxx;) where GO_ID is a GO ID, EC is the Evidence Code, Qualifier is a specific association type, and PMID is a PubMed ID of a paper that supports the gene-GO association. has GO association An annotation property that represents a gene's association with PubMed publication(s). Yongqun He YH: use the format: PMID: pmid1, pmid2, ... where pmid1 and pmid2 are specfic PubMed IDs (PMIDs). has PubMed association The annotation of the gene as a virulence factor stored in the Victors database (http://www.phidias.us/victors/). Edison Ong; Yongqun He; Yu Lin has Victors annotation The idenfier of the entity stored in the Victors database (http://www.phidias.us/victors/). Edison Ong; Yongqun He; Yu Lin has Victors id An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. temporal interpretation https://code.google.com/p/obo-relations/wiki/ROAndTime https://github.com/oborel/obo-relations/wiki/ROAndTime S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T. https://orcid.org/0000-0002-6601-2165 RO:0002174 uberon dubious_for_taxon true true dubious_for_taxon This relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take ongoing coordinated effort to resolve. Example: metencephalon in teleost this relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take time to resolve. Example: metencephalon in teleost dubious for taxon dubious_for_taxon S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T. S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S https://orcid.org/0000-0002-6601-2165 RO:0002175 applicable for taxon uberon present_in_taxon true true present_in_taxon present in taxon present_in_taxon S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S defined by inverse Used to annotate object properties to describe a logical meta-property or characteristic of the object property. logical macro assertion on an object property logical macro assertion on an annotation property relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y The general property hierarchy is: "directly P" SubPropertyOf "P" Transitive(P) Where we have an annotation assertion "directly P" "is direct form of" "P" If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q' Chris Mungall is direct form of If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL is a defining property chain axiom If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R. is a defining property chain axiom where second argument is reflexive cjm 2018-03-14T00:03:16Z is positive form of cjm 2018-03-14T00:03:24Z is negative form of part-of is homeomorphic for independent continuants. R is homemorphic for C iff (1) there exists some x,y such that x R y, and x and y instantiate C and (2) for all x, if x is an instance of C, and there exists some y some such that x R y, then it follows that y is an instance of C. cjm 2018-10-21T19:46:34Z R homeomorphic-for C expands to: C SubClassOf R only C. Additionally, for any class D that is disjoint with C, we can also expand to C DisjointWith R some D, D DisjointWith R some C. is homeomorphic for An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class. UBPROP:0000001 uberon external_definition true external_definition This annotation property may be replaced with an annotation property from an external ontology such as IAO external_definition An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class. A textual description of an axiom loss in this ontology compared to an external ontology. UBPROP:0000002 uberon axiom_lost_from_external_ontology true axiom_lost_from_external_ontology This annotation property may be replaced with an annotation property from an external ontology such as IAO axiom_lost_from_external_ontology A textual description of an axiom loss in this ontology compared to an external ontology. Notes on the homology status of this class. UBPROP:0000003 uberon homology_notes true homology_notes This annotation property may be replaced with an annotation property from an external ontology such as IAO homology_notes Notes on the homology status of this class. An alternate comment for a class taken unmodified from an external source. Note that obo format only allows a single comment for a class, and does not provide a structured means of adding provenance info. UBPROP:0000005 uberon external_comment true external_comment This annotation property may be replaced with an annotation property from an external ontology such as IAO external_comment An alternate comment for a class taken unmodified from an external source. Note that obo format only allows a single comment for a class, and does not provide a structured means of adding provenance info. UBPROP:0000006 uberon implements_design_pattern true implements_design_pattern implements_design_pattern Used to connect a class to an adjectival form of its label. For example, a class with label 'intestine' may have a relational adjective 'intestinal'. UBPROP:0000007 uberon has_relational_adjective true has_relational_adjective has_relational_adjective Notes on the how instances of this class vary across species. UBPROP:0000008 uberon taxon_notes true taxon_notes taxon_notes Notes on the how instances of this class vary across species. Notes on the evolved function of instances of this class. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000009 uberon function_notes true function_notes function_notes Notes on the evolved function of instances of this class. Notes on the structure, composition or histology of instances of this class. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000010 uberon structure_notes true structure_notes structure_notes Notes on the structure, composition or histology of instances of this class. Notes on the ontogenic development of instances of this class. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000011 uberon development_notes true development_notes development_notes Notes on the ontogenic development of instances of this class. Notes on how similar or equivalent classes are represented in other ontologies. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000012 uberon external_ontology_notes true external_ontology_notes external_ontology_notes Notes on how similar or equivalent classes are represented in other ontologies. Notes on how lexical conventions regarding this class, in particular any issues that may arise due to homonyny or synonymy. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000013 uberon terminology_notes true terminology_notes terminology_notes Notes on how lexical conventions regarding this class, in particular any issues that may arise due to homonyny or synonymy. UBPROP:0000100 uberon is_count_of true is_count_of is count of A property used in conjunction with repeated_element_number to indicate an axis and directionality along that axis. If P preceding_element_is R, and P is_count_of S, and X P N, and X' P N+1, then it follows that every X R some X', and the class expression [S and R some X' and inv(R) some X] is empty (i.e. X is followed by X', with no intermediates) UBPROP:0000101 uberon preceding_element_is true preceding_element_is preceding element is A property used in conjunction with repeated_element_number to indicate an axis and directionality along that axis. If P preceding_element_is R, and P is_count_of S, and X P N, and X' P N+1, then it follows that every X R some X', and the class expression [S and R some X' and inv(R) some X] is empty (i.e. X is followed by X', with no intermediates) x pharyngeal_arch_number N if and only if (i) x is a pharyngeal arch, and (ii) x is ancestrally pharyngeal arch number N in a series of pharyngeal arches repeated along a antero-posterior axis, with arch_number 1 being the mandibular arch. gill arch N = PA N-2. the term branchial_arch is ambiguous. UBPROP:0000103 uberon pharyngeal_arch_number true pharyngeal_arch_number pharyngeal arch number x pharyngeal_arch_number N if and only if (i) x is a pharyngeal arch, and (ii) x is ancestrally pharyngeal arch number N in a series of pharyngeal arches repeated along a antero-posterior axis, with arch_number 1 being the mandibular arch. FMA has terms like 'set of X'. In general we do not include set-of terms in uberon, but provide a mapping between the singular form and the FMA set term UBPROP:0000202 uberon fma_set_term true fma_set_term fma_set_term FMA has terms like 'set of X'. In general we do not include set-of terms in uberon, but provide a mapping between the singular form and the FMA set term FMA IUPAC NAME Manually annotated by ChEBI Team DO_AGR_slim DO_FlyBase_slim DO_MGI_slim DO_cancer_slim DO_rare_slim NCIthesaurus TopNodes_DOcancerslim Term not to be used for direct annotation Term not to be used for direct manual annotation AGR slim Aspergillus GO slim Candida GO slim ChEMBL protein targets summary FlyBase Drosophila GO ribbon slim Generic GO slim Metagenomics GO slim Mouse GO slim PIR GO slim Plant GO slim Fission yeast GO slim Yeast GO slim A metadata relation between a class and its taxonomic rank (eg species, family) ncbi_taxonomy has_rank Label appended to organism-specific terms in place of scientific name Unique short label for PRO terms for display purposes; based on orthology eco subset abbreviation A historic synonym, no longer encouraged dubious or contested synonym preferred term when talking about an instance of this class in Homo sapiens indicates that a synonym is used in an inconsistent or confusing way, typically between species latin term expert consultation and attribution required plural term taxonomic disambiguation CUMBO developmental_classification A class that represents an early developmental structure, like a blastocyst. This part of the ontology is undergoing review to remove inappropriate grouping classes. EFO slim derived from the union of EHDAA2 and EMAPA - still to be checked functional_classification Subset consisting of classes creating for grouping purposes A grouping class that depends on an assumption of homology between subclasses classes that have some inconsistency with FMA somewhat fuzzy grouping for analysis purposes, currently composed of something like: liver, heart, skeletal, kidney, bladder, brain, skin, mouth, esophagus, stomach, small intestine, large intestines, trachea nose, lungs, brain, spinal cord, peripheral nerves, kidneys, ureters, bladder, urethra, gonads abstract class brought in to group ontology classes but not informative organs, excluding individual muscles and skeletal elements Phenotype slim A subset specifically created for the 2012 Phenotype RCN meeting. Includes some human-specific terms that may eventually be removed when they are adequately represented with part of relationships in FMA Uberon slim - subset that excludes obscure terms and deep compositional terms abstract upper-level terms not directly useful for analysis core classes typically found across vertebrates. one purpose is to create a rough set of terms that could be used to start a new vertebrate AO Examples of a Contributor include a person, an organisation, or a service. Typically, the name of a Contributor should be used to indicate the entity. uberon dc-contributor true dc-contributor An entity responsible for making contributions to the content of the resource. Contributor Contributor contributor Examples of a Creator include a person, an organisation, or a service. Typically, the name of a Creator should be used to indicate the entity. uberon dc-creator true dc-creator An entity primarily responsible for making the content of the resource. Creator Creator creator Typically, Date will be associated with the creation or availability of the resource. Recommended best practice for encoding the date value is defined in a profile of ISO 8601 [W3CDTF] and follows the YYYY-MM-DD format. A date associated with an event in the life cycle of the resource. Date Date dc:date Description may include but is not limited to: an abstract, table of contents, reference to a graphical representation of content or a free-text account of the content. uberon dc-description true dc-description An account of the content of the resource. Description Description description Typically, Format may include the media-type or dimensions of the resource. Format may be used to determine the software, hardware or other equipment needed to display or operate the resource. Examples of dimensions include size and duration. Recommended best practice is to select a value from a controlled vocabulary (for example, the list of Internet Media Types [MIME] defining computer media formats). The physical or digital manifestation of the resource. Format Format The present resource may be derived from the Source resource in whole or in part. Recommended best practice is to reference the resource by means of a string or number conforming to a formal identification system. uberon dc-source true dc-source A reference to a resource from which the present resource is derived. Source Source derived from resource Typically, a Subject will be expressed as keywords, key phrases or classification codes that describe a topic of the resource. Recommended best practice is to select a value from a controlled vocabulary or formal classification scheme. The topic of the content of the resource. Subject and Keywords Subject and Keywords Typically, a Title will be a name by which the resource is formally known. uberon dc-title true dc-title A name given to the resource. Title Title title Type includes terms describing general categories, functions, genres, or aggregation levels for content. Recommended best practice is to select a value from a controlled vocabulary (for example, the DCMI Type Vocabulary [DCMITYPE]). To describe the physical or digital manifestation of the resource, use the Format element. The nature or genre of the content of the resource. Resource Type Resource Type Mark Miller 2018-05-11T13:47:29Z license created_by creation_date has_alternative_id has_broad_synonym database_cross_reference database_cross_reference 数据库_交叉_引用 数据库_交叉_引用 has_exact_synonym has_narrow_synonym disease_ontology has_obo_namespace has_obo_namespace 有_obo_命名空间 有_obo_命名空间 has_related_synonym has_scope has_synonym_type id in_subset shorthand shorthand is defined by is defined by This is an experimental annotation label label label 标签 uberon foaf-homepage true foaf-homepage homepage uberon foaf-page true foaf-page page is part of my brain is part of my body (continuant parthood, two material entities) my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) this day is part of this year (occurrent parthood) a core relation that holds between a part and its whole Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. part_of BFO:0000050 external protein uberon part_of part_of part of part of part_of part_of http://www.obofoundry.org/ro/#OBO_REL:part_of has part my body has part my brain (continuant parthood, two material entities) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has_part BFO:0000051 chebi_ontology external protein uberon has_part false has_part has part has part has_part inheres-in_at inheresInAt b inheres_in c at t =Def. b is a dependent continuant & c is an independent continuant that is not a spatial region & b s-depends_on c at t. (axiom label in BFO2 Reference: [051-002]) Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'inheres in at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'inheres in@en(x,y,t)'. BFO 2 Reference: Inherence is a subrelation of s-depends_on which holds between a dependent continuant and an independent continuant that is not a spatial region. Since dependent continuants cannot migrate from one independent continuant bearer to another, it follows that if b s-depends_on independent continuant c at some time, then b s-depends_on c at all times at which a exists. Inherence is in this sense redundantly time-indexed.For example, consider the particular instance of openness inhering in my mouth at t as I prepare to take a bite out of a donut, followed by a closedness at t+1 when I bite the donut and start chewing. The openness instance is then shortlived, and to say that it s-depends_on my mouth at all times at which this openness exists, means: at all times during this short life. Every time you make a fist, you make a new (instance of the universal) fist. (Every time your hand has the fist-shaped quality, there is created a new instance of the universal fist-shaped quality.) BFO2 Reference: independent continuant that is not a spatial region BFO2 Reference: specifically dependent continuant (iff (inheresInAt a b t) (and (DependentContinuant a) (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))) // axiom label in BFO2 CLIF: [051-002] inheres in at all times b inheres_in c at t =Def. b is a dependent continuant & c is an independent continuant that is not a spatial region & b s-depends_on c at t. (axiom label in BFO2 Reference: [051-002]) (iff (inheresInAt a b t) (and (DependentContinuant a) (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))) // axiom label in BFO2 CLIF: [051-002] bearer-of_st bearerOfAt b bearer_of c at t =Def. c s-depends_on b at t & b is an independent continuant that is not a spatial region. (axiom label in BFO2 Reference: [053-004]) Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'bearer of at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'bearer of@en'(x,y,t) BFO2 Reference: independent continuant that is not a spatial region BFO2 Reference: specifically dependent continuant (iff (bearerOfAt a b t) (and (specificallyDependsOnAt b a t) (IndependentContinuant a) (not (SpatialRegion a)) (existsAt b t))) // axiom label in BFO2 CLIF: [053-004] bearer of at some time b bearer_of c at t =Def. c s-depends_on b at t & b is an independent continuant that is not a spatial region. (axiom label in BFO2 Reference: [053-004]) (iff (bearerOfAt a b t) (and (specificallyDependsOnAt b a t) (IndependentContinuant a) (not (SpatialRegion a)) (existsAt b t))) // axiom label in BFO2 CLIF: [053-004] realized-in realizedIn realized in this disease is realized in this disease course this fragility is realized in this shattering this investigator role is realized in this investigation is realized by realized_in [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) if a realizable entity b is realized in a process p, then p stands in the has_participant relation to the bearer of b. (axiom label in BFO2 Reference: [106-002]) (forall (x y z t) (if (and (RealizableEntity x) (Process y) (realizesAt y x t) (bearerOfAt z x t)) (hasParticipantAt y z t))) // axiom label in BFO2 CLIF: [106-002] Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realized in if a realizable entity b is realized in a process p, then p stands in the has_participant relation to the bearer of b. (axiom label in BFO2 Reference: [106-002]) (forall (x y z t) (if (and (RealizableEntity x) (Process y) (realizesAt y x t) (bearerOfAt z x t)) (hasParticipantAt y z t))) // axiom label in BFO2 CLIF: [106-002] realizes realizes realizes this disease course realizes this disease this investigation realizes this investigator role this shattering realizes this fragility to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) (forall (x y t) (if (realizesAt x y t) (and (Process x) (or (Disposition y) (Role y)) (exists (z) (and (MaterialEntity z) (hasParticipantAt x z t) (bearerOfAt z y t)))))) // axiom label in BFO2 CLIF: [059-003] Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realizes to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) (forall (x y t) (if (realizesAt x y t) (and (Process x) (or (Disposition y) (Role y)) (exists (z) (and (MaterialEntity z) (hasParticipantAt x z t) (bearerOfAt z y t)))))) // axiom label in BFO2 CLIF: [059-003] participates-in_st participatesInAt [copied from inverse property 'has participant at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'has participant at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'has participant@en'(x,y,t) [copied from inverse property 'has participant at some time'] BFO 2 Reference: Spatial regions do not participate in processes. [copied from inverse property 'has participant at some time'] BFO2 Reference: independent continuant that is not a spatial region, specifically dependent continuant, generically dependent continuant [copied from inverse property 'has participant at some time'] BFO2 Reference: process [copied from inverse property 'has participant at some time'] has_participant is an instance-level relation between a process, a continuant, and a temporal region at which the continuant participates in some way in the process. (axiom label in BFO2 Reference: [086-003]) BFO:0000056 uberon participates_in participates_in participates in participates in at some time preceded by X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X) x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by http://www.obofoundry.org/ro/#OBO_REL:preceded_by BFO:0000062 is preceded by takes place after uberon preceded_by preceded_by preceded by preceded_by is preceded by SIO:000249 takes place after Allen:precedes precedes x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. BFO:0000063 uberon precedes precedes precedes precedes occurs-in occursIn occurs in b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t [XXX-001 occurs_in unfolds in unfolds_in BFO:0000066 external occurs_in occurs_in Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant occurs in occurs in contains-process containsProcess site of [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t [XXX-001 BFO:0000067 uberon contains_process contains_process Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant contains process contains process s-depends-on_at specificallyDependsOn A pain s-depends_on the organism that is experiencing the pain a gait s-depends_on the walking object. (All at some specific time.) a shape s-depends_on the shaped object one-sided s-dependence of a dependent continuant on an independent continuant: an instance of headache s-depends_on some head one-sided s-dependence of a dependent continuant on an independent continuant: an instance of temperature s-depends_on some organism one-sided s-dependence of a process on something: a process of cell death s-depends_on a cell one-sided s-dependence of a process on something: an instance of seeing (a relational process) s-depends_on some organism and on some seen entity, which may be an occurrent or a continuant one-sided s-dependence of one occurrent on another: a process of answering a question is dependent on a prior process of asking a question one-sided s-dependence of one occurrent on another: a process of obeying a command is dependent on a prior process of issuing a command one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of hitting a ball with a cricket bat one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of paying cash to a merchant in exchange for a bag of figs reciprocal s-dependence between occurrents: a process of buying and the associated process of selling reciprocal s-dependence between occurrents: a process of increasing the volume of a portion of gas while temperature remains constant and the associated process of decreasing the pressure exerted by the gas reciprocal s-dependence between occurrents: in a game of chess the process of playing with the white pieces is mutually dependent on the process of playing with the black pieces the one-sided dependence of an occurrent on an independent continuant: football match on the players, the ground, the ball the one-sided dependence of an occurrent on an independent continuant: handwave on a hand the three-sided reciprocal s-dependence of the hue, saturation and brightness of a color [45 the three-sided reciprocal s-dependence of the pitch, timbre and volume of a tone [45 the two-sided reciprocal s-dependence of the roles of husband and wife [20 Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'specifically depends on at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'specifically depends on@en(x,y,t)'. BFO 2 Reference: An entity – for example an act of communication or a game of football – can s-depends_on more than one entity. Complex phenomena for example in the psychological and social realms (such as inferring, commanding and requesting) or in the realm of multi-organismal biological processes (such as infection and resistance), will involve multiple families of dependence relations, involving both continuants and occurrents [1, 4, 28 BFO 2 Reference: S-dependence is just one type of dependence among many; it is what, in the literature, is referred to as ‘existential dependence’ [87, 46, 65, 20 BFO 2 Reference: the relation of s-depends_on does not in every case require simultaneous existence of its relata. Note the difference between such cases and the cases of continuant universals defined historically: the act of answering depends existentially on the prior act of questioning; the human being who was baptized or who answered a question does not himself depend existentially on the prior act of baptism or answering. He would still exist even if these acts had never taken place. BFO2 Reference: specifically dependent continuant\; process; process boundary To say that b s-depends_on a at t is to say that b and c do not share common parts & b is of its nature such that it cannot exist unless c exists & b is not a boundary of c and b is not a site of which c is the host [64 If b is s-depends_on something at some time, then b is not a material entity. (axiom label in BFO2 Reference: [052-001]) If b s-depends_on something at t, then there is some c, which is an independent continuant and not a spatial region, such that b s-depends_on c at t. (axiom label in BFO2 Reference: [136-001]) If occurrent b s-depends_on some independent continuant c at t, then b s-depends_on c at every time at which b exists. (axiom label in BFO2 Reference: [015-002]) an entity does not s-depend_on any of its (continuant or occurrent) parts or on anything it is part of. (axiom label in BFO2 Reference: [013-002]) if b s-depends_on c at t & c s-depends_on d at t then b s-depends_on d at t. (axiom label in BFO2 Reference: [054-002]) (forall (x y t) (if (and (Entity x) (or (continuantPartOfAt y x t) (continuantPartOfAt x y t) (occurrentPartOf x y) (occurrentPartOf y x))) (not (specificallyDependsOnAt x y t)))) // axiom label in BFO2 CLIF: [013-002] (forall (x y t) (if (and (Occurrent x) (IndependentContinuant y) (specificallyDependsOnAt x y t)) (forall (t_1) (if (existsAt x t_1) (specificallyDependsOnAt x y t_1))))) // axiom label in BFO2 CLIF: [015-002] (forall (x y t) (if (specificallyDependsOnAt x y t) (exists (z) (and (IndependentContinuant z) (not (SpatialRegion z)) (specificallyDependsOnAt x z t))))) // axiom label in BFO2 CLIF: [136-001] (forall (x y z t) (if (and (specificallyDependsOnAt x y t) (specificallyDependsOnAt y z t)) (specificallyDependsOnAt x z t))) // axiom label in BFO2 CLIF: [054-002] (forall (x) (if (exists (y t) (specificallyDependsOnAt x y t)) (not (MaterialEntity x)))) // axiom label in BFO2 CLIF: [052-001] specifically depends on at all times If b is s-depends_on something at some time, then b is not a material entity. (axiom label in BFO2 Reference: [052-001]) If b s-depends_on something at t, then there is some c, which is an independent continuant and not a spatial region, such that b s-depends_on c at t. (axiom label in BFO2 Reference: [136-001]) If occurrent b s-depends_on some independent continuant c at t, then b s-depends_on c at every time at which b exists. (axiom label in BFO2 Reference: [015-002]) an entity does not s-depend_on any of its (continuant or occurrent) parts or on anything it is part of. (axiom label in BFO2 Reference: [013-002]) if b s-depends_on c at t & c s-depends_on d at t then b s-depends_on d at t. (axiom label in BFO2 Reference: [054-002]) (forall (x y t) (if (and (Entity x) (or (continuantPartOfAt y x t) (continuantPartOfAt x y t) (occurrentPartOf x y) (occurrentPartOf y x))) (not (specificallyDependsOnAt x y t)))) // axiom label in BFO2 CLIF: [013-002] (forall (x y t) (if (and (Occurrent x) (IndependentContinuant y) (specificallyDependsOnAt x y t)) (forall (t_1) (if (existsAt x t_1) (specificallyDependsOnAt x y t_1))))) // axiom label in BFO2 CLIF: [015-002] (forall (x y t) (if (specificallyDependsOnAt x y t) (exists (z) (and (IndependentContinuant z) (not (SpatialRegion z)) (specificallyDependsOnAt x z t))))) // axiom label in BFO2 CLIF: [136-001] (forall (x y z t) (if (and (specificallyDependsOnAt x y t) (specificallyDependsOnAt y z t)) (specificallyDependsOnAt x z t))) // axiom label in BFO2 CLIF: [054-002] (forall (x) (if (exists (y t) (specificallyDependsOnAt x y t)) (not (MaterialEntity x)))) // axiom label in BFO2 CLIF: [052-001] f-of_at functionOfAt a function_of b at t =Def. a is a function and a inheres_in b at t. (axiom label in BFO2 Reference: [067-001]) Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'function of at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'function of@en(x,y,t)'. (iff (functionOf a b t) (and (Function a) (inheresInAt a b t))) // axiom label in BFO2 CLIF: [067-001] function of at all times a function_of b at t =Def. a is a function and a inheres_in b at t. (axiom label in BFO2 Reference: [067-001]) (iff (functionOf a b t) (and (Function a) (inheresInAt a b t))) // axiom label in BFO2 CLIF: [067-001] q-of_at qualityOfAt b quality_of c at t = Def. b is a quality & c is an independent continuant that is not a spatial region & b s-depends_on c at t. (axiom label in BFO2 Reference: [056-002]) Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'quality of at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'quality of@en(x,y,t)'. (iff (qualityOfAt a b t) (and (Quality a) (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))) // axiom label in BFO2 CLIF: [056-002] quality of at all times b quality_of c at t = Def. b is a quality & c is an independent continuant that is not a spatial region & b s-depends_on c at t. (axiom label in BFO2 Reference: [056-002]) (iff (qualityOfAt a b t) (and (Quality a) (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))) // axiom label in BFO2 CLIF: [056-002] r-of_at roleOfAt a role_of b at t =Def. a is a role and a inheres_in b at t. (axiom label in BFO2 Reference: [065-001]) Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'role of at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'role of@en(x,y,t)'. (iff (roleOfAt a b t) (and (Role a) (inheresInAt a b t))) // axiom label in BFO2 CLIF: [065-001] role of at all times a role_of b at t =Def. a is a role and a inheres_in b at t. (axiom label in BFO2 Reference: [065-001]) (iff (roleOfAt a b t) (and (Role a) (inheresInAt a b t))) // axiom label in BFO2 CLIF: [065-001] located-in_at locatedInAt Mary located_in Salzburg the Empire State Building located_in New York. this portion of cocaine located_in this portion of blood this stem cell located_in this portion of bone marrow your arm located_in your body b located_in c at t = Def. b and c are independent continuants, and the region at which b is located at t is a (proper or improper) continuant_part_of the region at which c is located at t. (axiom label in BFO2 Reference: [045-001]) Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'located in at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'located in@en(x,y,t)'. BFO2 Reference: independent continuant Located_in is transitive. (axiom label in BFO2 Reference: [046-001]) for all independent continuants b, c, and d: if b continuant_part_of c at t & c located_in d at t, then b located_in d at t. (axiom label in BFO2 Reference: [048-001]) for all independent continuants b, c, and d: if b located_in c at t & c continuant_part_of d at t, then b located_in d at t. (axiom label in BFO2 Reference: [049-001]) (forall (x y z t) (if (and (IndependentContinuant x) (IndependentContinuant y) (IndependentContinuant z) (continuantPartOfAt x y t) (locatedInAt y z t)) (locatedInAt x z t))) // axiom label in BFO2 CLIF: [048-001] (forall (x y z t) (if (and (IndependentContinuant x) (IndependentContinuant y) (IndependentContinuant z) (locatedInAt x y t) (continuantPartOfAt y z t)) (locatedInAt x z t))) // axiom label in BFO2 CLIF: [049-001] (forall (x y z t) (if (and (locatedInAt x y t) (locatedInAt y z t)) (locatedInAt x z t))) // axiom label in BFO2 CLIF: [046-001] (iff (locatedInAt a b t) (and (IndependentContinuant a) (IndependentContinuant b) (exists (r_1 r_2) (and (occupiesSpatialRegionAt a r_1 t) (occupiesSpatialRegionAt b r_2 t) (continuantPartOfAt r_1 r_2 t))))) // axiom label in BFO2 CLIF: [045-001] located in at all times b located_in c at t = Def. b and c are independent continuants, and the region at which b is located at t is a (proper or improper) continuant_part_of the region at which c is located at t. (axiom label in BFO2 Reference: [045-001]) Located_in is transitive. (axiom label in BFO2 Reference: [046-001]) for all independent continuants b, c, and d: if b continuant_part_of c at t & c located_in d at t, then b located_in d at t. (axiom label in BFO2 Reference: [048-001]) for all independent continuants b, c, and d: if b located_in c at t & c continuant_part_of d at t, then b located_in d at t. (axiom label in BFO2 Reference: [049-001]) (forall (x y z t) (if (and (IndependentContinuant x) (IndependentContinuant y) (IndependentContinuant z) (continuantPartOfAt x y t) (locatedInAt y z t)) (locatedInAt x z t))) // axiom label in BFO2 CLIF: [048-001] (forall (x y z t) (if (and (IndependentContinuant x) (IndependentContinuant y) (IndependentContinuant z) (locatedInAt x y t) (continuantPartOfAt y z t)) (locatedInAt x z t))) // axiom label in BFO2 CLIF: [049-001] (forall (x y z t) (if (and (locatedInAt x y t) (locatedInAt y z t)) (locatedInAt x z t))) // axiom label in BFO2 CLIF: [046-001] (iff (locatedInAt a b t) (and (IndependentContinuant a) (IndependentContinuant b) (exists (r_1 r_2) (and (occupiesSpatialRegionAt a r_1 t) (occupiesSpatialRegionAt b r_2 t) (continuantPartOfAt r_1 r_2 t))))) // axiom label in BFO2 CLIF: [045-001] located-at-r_st occupiesSpatialRegionAt Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'occupies spatial region at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'occupies spatial region@en'(x,y,t) BFO2 Reference: independent continuant BFO2 Reference: spatial region b occupies_spatial_region r at t means that r is a spatial region in which independent continuant b is exactly located (axiom label in BFO2 Reference: [041-002]) every region r is occupies_spatial_region r at all times. (axiom label in BFO2 Reference: [042-002]) if b occupies_spatial_region r at t & b continuant_part_of b at t, then there is some r which is continuant_part_of r at t such that b occupies_spatial_region r at t. (axiom label in BFO2 Reference: [043-001]) (forall (r t) (if (Region r) (occupiesSpatialRegionAt r r t))) // axiom label in BFO2 CLIF: [042-002] (forall (x r t) (if (occupiesSpatialRegionAt x r t) (and (SpatialRegion r) (IndependentContinuant x)))) // axiom label in BFO2 CLIF: [041-002] (forall (x y r_1 t) (if (and (occupiesSpatialRegionAt x r_1 t) (continuantPartOfAt y x t)) (exists (r_2) (and (continuantPartOfAt r_2 r_1 t) (occupiesSpatialRegionAt y r_2 t))))) // axiom label in BFO2 CLIF: [043-001] occupies spatial region at some time b occupies_spatial_region r at t means that r is a spatial region in which independent continuant b is exactly located (axiom label in BFO2 Reference: [041-002]) every region r is occupies_spatial_region r at all times. (axiom label in BFO2 Reference: [042-002]) if b occupies_spatial_region r at t & b continuant_part_of b at t, then there is some r which is continuant_part_of r at t such that b occupies_spatial_region r at t. (axiom label in BFO2 Reference: [043-001]) (forall (r t) (if (Region r) (occupiesSpatialRegionAt r r t))) // axiom label in BFO2 CLIF: [042-002] (forall (x r t) (if (occupiesSpatialRegionAt x r t) (and (SpatialRegion r) (IndependentContinuant x)))) // axiom label in BFO2 CLIF: [041-002] (forall (x y r_1 t) (if (and (occupiesSpatialRegionAt x r_1 t) (continuantPartOfAt y x t)) (exists (r_2) (and (continuantPartOfAt r_2 r_1 t) (occupiesSpatialRegionAt y r_2 t))))) // axiom label in BFO2 CLIF: [043-001] has-f_st hasFunctionAt a has_function b at t =Def. b function_of a at t. (axiom label in BFO2 Reference: [070-001]) Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'has function at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'has function@en'(x,y,t) (iff (hasFunctionAt a b t) (functionOf b a t)) // axiom label in BFO2 CLIF: [070-001] has function at some time a has_function b at t =Def. b function_of a at t. (axiom label in BFO2 Reference: [070-001]) (iff (hasFunctionAt a b t) (functionOf b a t)) // axiom label in BFO2 CLIF: [070-001] has-q_st has quality at some time has-r_st hasRoleAt a has_role b at t =Def. b role_of a at t. (axiom label in BFO2 Reference: [068-001]) Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'has role at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'has role@en'(x,y,t) (iff (hasRoleAt a b t) (roleOfAt b a t)) // axiom label in BFO2 CLIF: [068-001] has role at some time a has_role b at t =Def. b role_of a at t. (axiom label in BFO2 Reference: [068-001]) (iff (hasRoleAt a b t) (roleOfAt b a t)) // axiom label in BFO2 CLIF: [068-001] has-g-dep_st [copied from inverse property 'generically depends on at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'generically depends on at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'generically depends on@en'(x,y,t) [copied from inverse property 'generically depends on at some time'] BFO2 Reference: generically dependent continuant [copied from inverse property 'generically depends on at some time'] BFO2 Reference: independent continuant [copied from inverse property 'generically depends on at some time'] b g-depends on c at t1 means: b exists at t1 and c exists at t1 & for some type B it holds that (c instantiates B at t1) & necessarily, for all t (if b exists at t then some instance_of B exists at t) & not (b s-depends_on c at t1). (axiom label in BFO2 Reference: [072-002]) has generic dependent at some time d-of_at dispositionOfAt a disposition_of b at t =Def. a is a disposition and a inheres_in b at t. (axiom label in BFO2 Reference: [066-001]) Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'disposition of at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'disposition of@en(x,y,t)'. (iff (dispositionOf a b t) (and (Disposition a) (inheresInAt a b t))) // axiom label in BFO2 CLIF: [066-001] disposition of at all times a disposition_of b at t =Def. a is a disposition and a inheres_in b at t. (axiom label in BFO2 Reference: [066-001]) (iff (dispositionOf a b t) (and (Disposition a) (inheresInAt a b t))) // axiom label in BFO2 CLIF: [066-001] exists-at existsAt BFO2 Reference: entity BFO2 Reference: temporal region b exists_at t means: b is an entity which exists at some temporal region t. (axiom label in BFO2 Reference: [118-002]) exists at b exists_at t means: b is an entity which exists at some temporal region t. (axiom label in BFO2 Reference: [118-002]) has-d_st hasDispositionAt a has_disposition b at t =Def. b disposition_of a at t. (axiom label in BFO2 Reference: [069-001]) Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'has disposition at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'has disposition@en'(x,y,t) (iff (hasDispositionAt a b t) (dispositionOf b a t)) // axiom label in BFO2 CLIF: [069-001] has disposition at some time a has_disposition b at t =Def. b disposition_of a at t. (axiom label in BFO2 Reference: [069-001]) (iff (hasDispositionAt a b t) (dispositionOf b a t)) // axiom label in BFO2 CLIF: [069-001] has-material-basis_at hasMaterialBasisAt the material basis of John’s disposition to cough is the viral infection in John’s upper respiratory tract the material basis of the disposition to wear unevenly of John’s tires is the worn suspension of his car. Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has material basis at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has material basis@en(x,y,t)'. b has_material_basis c at t means: b is a disposition & c is a material entity & there is some d bearer_of b at t& c continuant_part_of d at t& d has_disposition b at t because c continuant_part_of d at t. (axiom label in BFO2 Reference: [071-002]) (forall (x y t) (if (hasMaterialBasisAt x y t) (and (Disposition x) (MaterialEntity y) (exists (z) (and (bearerOfAt z x t) (continuantPartOfAt y z t) (exists (w) (and (Disposition w) (if (hasDisposition z w) (continuantPartOfAt y z t))))))))) // axiom label in BFO2 CLIF: [071-002] has material basis at all times b has_material_basis c at t means: b is a disposition & c is a material entity & there is some d bearer_of b at t& c continuant_part_of d at t& d has_disposition b at t because c continuant_part_of d at t. (axiom label in BFO2 Reference: [071-002]) (forall (x y t) (if (hasMaterialBasisAt x y t) (and (Disposition x) (MaterialEntity y) (exists (z) (and (bearerOfAt z x t) (continuantPartOfAt y z t) (exists (w) (and (Disposition w) (if (hasDisposition z w) (continuantPartOfAt y z t))))))))) // axiom label in BFO2 CLIF: [071-002] o-has-part hasOccurrentPart [copied from inverse property 'part of occurrent'] Mary’s 5th birthday occurrent_part_of Mary’s life [copied from inverse property 'part of occurrent'] The process of a footballer’s heart beating once is an occurrent part but not a temporal_part of a game of football. [copied from inverse property 'part of occurrent'] the first set of the tennis match occurrent_part_of the tennis match. b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001]) [copied from inverse property 'part of occurrent'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion. [copied from inverse property 'part of occurrent'] BFO2 Reference: occurrent [copied from inverse property 'part of occurrent'] b occurrent_part_of c =Def. b is a part of c & b and c are occurrents. (axiom label in BFO2 Reference: [003-002]) (iff (hasOccurrentPart a b) (occurrentPartOf b a)) // axiom label in BFO2 CLIF: [007-001] has occurrent part b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001]) (iff (hasOccurrentPart a b) (occurrentPartOf b a)) // axiom label in BFO2 CLIF: [007-001] o-has-ppart hasProperOccurrentPart [copied from inverse property 'proper part of occurrent'] b proper_occurrent_part_of c =Def. b occurrent_part_of c & b and c are not identical. (axiom label in BFO2 Reference: [005-001]) b has_proper_occurrent_part c = Def. c proper_occurrent_part_of b. [XXX-001 has proper occurrent part has-profile has profile has-t-part [copied from inverse property 'temporal part of'] the 4th year of your life is a temporal part of your life\. The first quarter of a game of football is a temporal part of the whole game\. The process of your heart beating from 4pm to 5pm today is a temporal part of the entire process of your heart beating.\ The 4th year of your life is a temporal part of your life [copied from inverse property 'temporal part of'] the process boundary which separates the 3rd and 4th years of your life. [copied from inverse property 'temporal part of'] your heart beating from 4pm to 5pm today is a temporal part of the process of your heart beating [copied from inverse property 'temporal part of'] b proper_temporal_part_of c =Def. b temporal_part_of c & not (b = c). (axiom label in BFO2 Reference: [116-001]) [copied from inverse property 'temporal part of'] b temporal_part_of c =Def.b occurrent_part_of c & & for some temporal region t, b occupies_temporal_region t & for all occurrents d, t (if d occupies_temporal_region t & t? occurrent_part_of t then (d occurrent_part_of a iff d occurrent_part_of b)). (axiom label in BFO2 Reference: [078-003]) has temporal part r-location-of_st [copied from inverse property 'occupies spatial region at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'occupies spatial region at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'occupies spatial region@en'(x,y,t) [copied from inverse property 'occupies spatial region at some time'] BFO2 Reference: independent continuant [copied from inverse property 'occupies spatial region at some time'] BFO2 Reference: spatial region [copied from inverse property 'occupies spatial region at some time'] b occupies_spatial_region r at t means that r is a spatial region in which independent continuant b is exactly located (axiom label in BFO2 Reference: [041-002]) has spatial occupant at some time has-s-dep_st [copied from inverse property 'specifically depends on at some time'] A pain s-depends_on the organism that is experiencing the pain [copied from inverse property 'specifically depends on at some time'] a gait s-depends_on the walking object. (All at some specific time.) [copied from inverse property 'specifically depends on at some time'] a shape s-depends_on the shaped object [copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of a dependent continuant on an independent continuant: an instance of headache s-depends_on some head [copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of a dependent continuant on an independent continuant: an instance of temperature s-depends_on some organism [copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of a process on something: a process of cell death s-depends_on a cell [copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of a process on something: an instance of seeing (a relational process) s-depends_on some organism and on some seen entity, which may be an occurrent or a continuant [copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of one occurrent on another: a process of answering a question is dependent on a prior process of asking a question [copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of one occurrent on another: a process of obeying a command is dependent on a prior process of issuing a command [copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of hitting a ball with a cricket bat [copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of paying cash to a merchant in exchange for a bag of figs [copied from inverse property 'specifically depends on at some time'] reciprocal s-dependence between occurrents: a process of buying and the associated process of selling [copied from inverse property 'specifically depends on at some time'] reciprocal s-dependence between occurrents: a process of increasing the volume of a portion of gas while temperature remains constant and the associated process of decreasing the pressure exerted by the gas [copied from inverse property 'specifically depends on at some time'] reciprocal s-dependence between occurrents: in a game of chess the process of playing with the white pieces is mutually dependent on the process of playing with the black pieces [copied from inverse property 'specifically depends on at some time'] the one-sided dependence of an occurrent on an independent continuant: football match on the players, the ground, the ball [copied from inverse property 'specifically depends on at some time'] the one-sided dependence of an occurrent on an independent continuant: handwave on a hand [copied from inverse property 'specifically depends on at some time'] the three-sided reciprocal s-dependence of the hue, saturation and brightness of a color [45 [copied from inverse property 'specifically depends on at some time'] the three-sided reciprocal s-dependence of the pitch, timbre and volume of a tone [45 [copied from inverse property 'specifically depends on at some time'] the two-sided reciprocal s-dependence of the roles of husband and wife [20 [copied from inverse property 'specifically depends on at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'specifically depends on at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'specifically depends on@en'(x,y,t) [copied from inverse property 'specifically depends on at some time'] BFO 2 Reference: An entity – for example an act of communication or a game of football – can s-depends_on more than one entity. Complex phenomena for example in the psychological and social realms (such as inferring, commanding and requesting) or in the realm of multi-organismal biological processes (such as infection and resistance), will involve multiple families of dependence relations, involving both continuants and occurrents [1, 4, 28 [copied from inverse property 'specifically depends on at some time'] BFO 2 Reference: S-dependence is just one type of dependence among many; it is what, in the literature, is referred to as ‘existential dependence’ [87, 46, 65, 20 [copied from inverse property 'specifically depends on at some time'] BFO 2 Reference: the relation of s-depends_on does not in every case require simultaneous existence of its relata. Note the difference between such cases and the cases of continuant universals defined historically: the act of answering depends existentially on the prior act of questioning; the human being who was baptized or who answered a question does not himself depend existentially on the prior act of baptism or answering. He would still exist even if these acts had never taken place. [copied from inverse property 'specifically depends on at some time'] BFO2 Reference: specifically dependent continuant\; process; process boundary [copied from inverse property 'specifically depends on at some time'] To say that b s-depends_on a at t is to say that b and c do not share common parts & b is of its nature such that it cannot exist unless c exists & b is not a boundary of c and b is not a site of which c is the host [64 has specific dependent at some time occupied-by [copied from inverse property 'occupies spatiotemporal region'] BFO 2 Reference: The occupies_spatiotemporal_region and occupies_temporal_region relations are the counterpart, on the occurrent side, of the relation occupies_spatial_region. [copied from inverse property 'occupies spatiotemporal region'] p occupies_spatiotemporal_region s. This is a primitive relation between an occurrent p and the spatiotemporal region s which is its spatiotemporal extent. (axiom label in BFO2 Reference: [082-003]) has spatiotemporal occupant material-basis-of_st material basis of at some time member-part-of_st memberPartOfAt each piece in a chess set is a member part of the chess set; each Beatle in the collection called The Beatles is a member part of The Beatles. each tree in a forest is a member_part of the forest b member_part_of c at t =Def. b is an object & there is at t a mutually exhaustive and pairwise disjoint partition of c into objects x1, …, xn (for some n &gt; 1) with b = xi for some 1 ? i ? n. (axiom label in BFO2 Reference: [026-004]) Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'member part of at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'member part of@en'(x,y,t) BFO2 Reference: object BFO2 Reference: object aggregate if b member_part_of c at t then b continuant_part_of c at t. (axiom label in BFO2 Reference: [104-001]) (forall (x y t) (if (memberPartOfAt x y t) (continuantPartOfAt x y t))) // axiom label in BFO2 CLIF: [104-001] member part of at some time b member_part_of c at t =Def. b is an object & there is at t a mutually exhaustive and pairwise disjoint partition of c into objects x1, …, xn (for some n &gt; 1) with b = xi for some 1 ? i ? n. (axiom label in BFO2 Reference: [026-004]) if b member_part_of c at t then b continuant_part_of c at t. (axiom label in BFO2 Reference: [104-001]) (forall (x y t) (if (memberPartOfAt x y t) (continuantPartOfAt x y t))) // axiom label in BFO2 CLIF: [104-001] occupies occupiesSpatiotemporalRegion BFO 2 Reference: The occupies_spatiotemporal_region and occupies_temporal_region relations are the counterpart, on the occurrent side, of the relation occupies_spatial_region. p occupies_spatiotemporal_region s. This is a primitive relation between an occurrent p and the spatiotemporal region s which is its spatiotemporal extent. (axiom label in BFO2 Reference: [082-003]) occupies spatiotemporal region p occupies_spatiotemporal_region s. This is a primitive relation between an occurrent p and the spatiotemporal region s which is its spatiotemporal extent. (axiom label in BFO2 Reference: [082-003]) o-part-of occurrentPartOf Mary’s 5th birthday occurrent_part_of Mary’s life The process of a footballer’s heart beating once is an occurrent part but not a temporal_part of a game of football. the first set of the tennis match occurrent_part_of the tennis match. [copied from inverse property 'has occurrent part'] b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001]) BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion. BFO2 Reference: occurrent b occurrent_part_of c =Def. b is a part of c & b and c are occurrents. (axiom label in BFO2 Reference: [003-002]) occurrent_part_of is antisymmetric. (axiom label in BFO2 Reference: [123-001]) occurrent_part_of is reflexive (every occurrent entity is an occurrent_part_of itself). (axiom label in BFO2 Reference: [113-002]) occurrent_part_of is transitive. (axiom label in BFO2 Reference: [112-001]) occurrent_part_of satisfies unique product. (axiom label in BFO2 Reference: [125-001]) occurrent_part_of satisfies weak supplementation. (axiom label in BFO2 Reference: [124-001]) (forall (x y t) (if (and (occurrentPartOf x y t) (not (= x y))) (exists (z) (and (occurrentPartOf z y t) (not (exists (w) (and (occurrentPartOf w x t) (occurrentPartOf w z t)))))))) // axiom label in BFO2 CLIF: [124-001] (forall (x y t) (if (and (occurrentPartOf x y t) (occurrentPartOf y x t)) (= x y))) // axiom label in BFO2 CLIF: [123-001] (forall (x y t) (if (exists (v) (and (occurrentPartOf v x t) (occurrentPartOf v y t))) (exists (z) (forall (u w) (iff (iff (occurrentPartOf w u t) (and (occurrentPartOf w x t) (occurrentPartOf w y t))) (= z u)))))) // axiom label in BFO2 CLIF: [125-001] (forall (x y z) (if (and (occurrentPartOf x y) (occurrentPartOf y z)) (occurrentPartOf x z))) // axiom label in BFO2 CLIF: [112-001] (forall (x) (if (Occurrent x) (occurrentPartOf x x))) // axiom label in BFO2 CLIF: [113-002] part of occurrent b occurrent_part_of c =Def. b is a part of c & b and c are occurrents. (axiom label in BFO2 Reference: [003-002]) occurrent_part_of is antisymmetric. (axiom label in BFO2 Reference: [123-001]) occurrent_part_of is reflexive (every occurrent entity is an occurrent_part_of itself). (axiom label in BFO2 Reference: [113-002]) occurrent_part_of is transitive. (axiom label in BFO2 Reference: [112-001]) occurrent_part_of satisfies unique product. (axiom label in BFO2 Reference: [125-001]) occurrent_part_of satisfies weak supplementation. (axiom label in BFO2 Reference: [124-001]) (forall (x y t) (if (and (occurrentPartOf x y t) (not (= x y))) (exists (z) (and (occurrentPartOf z y t) (not (exists (w) (and (occurrentPartOf w x t) (occurrentPartOf w z t)))))))) // axiom label in BFO2 CLIF: [124-001] (forall (x y t) (if (and (occurrentPartOf x y t) (occurrentPartOf y x t)) (= x y))) // axiom label in BFO2 CLIF: [123-001] (forall (x y t) (if (exists (v) (and (occurrentPartOf v x t) (occurrentPartOf v y t))) (exists (z) (forall (u w) (iff (iff (occurrentPartOf w u t) (and (occurrentPartOf w x t) (occurrentPartOf w y t))) (= z u)))))) // axiom label in BFO2 CLIF: [125-001] (forall (x y z) (if (and (occurrentPartOf x y) (occurrentPartOf y z)) (occurrentPartOf x z))) // axiom label in BFO2 CLIF: [112-001] (forall (x) (if (Occurrent x) (occurrentPartOf x x))) // axiom label in BFO2 CLIF: [113-002] profile-of processProfileOf process profile of t-ppart-of properTemporalPartOf proper temporal part of c-ppart-of_at properContinuantPartOfAt b proper_continuant_part_of c at t =Def. b continuant_part_of c at t & b and c are not identical. (axiom label in BFO2 Reference: [004-001]) Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'proper part of continuant at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'proper part of continuant@en(x,y,t)'. (iff (properContinuantPartOfAt a b t) (and (continuantPartOfAt a b t) (not (= a b)))) // axiom label in BFO2 CLIF: [004-001] proper part of continuant at all times b proper_continuant_part_of c at t =Def. b continuant_part_of c at t & b and c are not identical. (axiom label in BFO2 Reference: [004-001]) (iff (properContinuantPartOfAt a b t) (and (continuantPartOfAt a b t) (not (= a b)))) // axiom label in BFO2 CLIF: [004-001] o-ppart-of properOccurrentPartOf [copied from inverse property 'has proper occurrent part'] b has_proper_occurrent_part c = Def. c proper_occurrent_part_of b. [XXX-001 b proper_occurrent_part_of c =Def. b occurrent_part_of c & b and c are not identical. (axiom label in BFO2 Reference: [005-001]) (iff (properOccurrentPartOf a b) (and (occurrentPartOf a b) (not (= a b)))) // axiom label in BFO2 CLIF: [005-001] proper part of occurrent b proper_occurrent_part_of c =Def. b occurrent_part_of c & b and c are not identical. (axiom label in BFO2 Reference: [005-001]) (iff (properOccurrentPartOf a b) (and (occurrentPartOf a b) (not (= a b)))) // axiom label in BFO2 CLIF: [005-001] t-part-of temporalPartOf the 4th year of your life is a temporal part of your life\. The first quarter of a game of football is a temporal part of the whole game\. The process of your heart beating from 4pm to 5pm today is a temporal part of the entire process of your heart beating.\ The 4th year of your life is a temporal part of your life the process boundary which separates the 3rd and 4th years of your life. your heart beating from 4pm to 5pm today is a temporal part of the process of your heart beating b proper_temporal_part_of c =Def. b temporal_part_of c & not (b = c). (axiom label in BFO2 Reference: [116-001]) b temporal_part_of c =Def.b occurrent_part_of c & & for some temporal region t, b occupies_temporal_region t & for all occurrents d, t (if d occupies_temporal_region t & t? occurrent_part_of t then (d occurrent_part_of a iff d occurrent_part_of b)). (axiom label in BFO2 Reference: [078-003]) if b proper_temporal_part_of c, then there is some d which is a proper_temporal_part_of c and which shares no parts with b. (axiom label in BFO2 Reference: [117-002]) (forall (x y) (if (properTemporalPartOf x y) (exists (z) (and (properTemporalPartOf z y) (not (exists (w) (and (temporalPartOf w x) (temporalPartOf w z)))))))) // axiom label in BFO2 CLIF: [117-002] (iff (properTemporalPartOf a b) (and (temporalPartOf a b) (not (= a b)))) // axiom label in BFO2 CLIF: [116-001] (iff (temporalPartOf a b) (and (occurrentPartOf a b) (exists (t) (and (TemporalRegion t) (occupiesSpatioTemporalRegion a t))) (forall (c t_1) (if (and (Occurrent c) (occupiesSpatioTemporalRegion c t_1) (occurrentPartOf t_1 r)) (iff (occurrentPartOf c a) (occurrentPartOf c b)))))) // axiom label in BFO2 CLIF: [078-003] temporal part of b proper_temporal_part_of c =Def. b temporal_part_of c & not (b = c). (axiom label in BFO2 Reference: [116-001]) b temporal_part_of c =Def.b occurrent_part_of c & & for some temporal region t, b occupies_temporal_region t & for all occurrents d, t (if d occupies_temporal_region t & t? occurrent_part_of t then (d occurrent_part_of a iff d occurrent_part_of b)). (axiom label in BFO2 Reference: [078-003]) if b proper_temporal_part_of c, then there is some d which is a proper_temporal_part_of c and which shares no parts with b. (axiom label in BFO2 Reference: [117-002]) (forall (x y) (if (properTemporalPartOf x y) (exists (z) (and (properTemporalPartOf z y) (not (exists (w) (and (temporalPartOf w x) (temporalPartOf w z)))))))) // axiom label in BFO2 CLIF: [117-002] (iff (properTemporalPartOf a b) (and (temporalPartOf a b) (not (= a b)))) // axiom label in BFO2 CLIF: [116-001] (iff (temporalPartOf a b) (and (occurrentPartOf a b) (exists (t) (and (TemporalRegion t) (occupiesSpatioTemporalRegion a t))) (forall (c t_1) (if (and (Occurrent c) (occupiesSpatioTemporalRegion c t_1) (occurrentPartOf t_1 r)) (iff (occurrentPartOf c a) (occurrentPartOf c b)))))) // axiom label in BFO2 CLIF: [078-003] st-projects-onto-s_st projects onto spatial region at some time s-projection-of-st_st spatial projection of spatiotemporal at some time st-projects-onto-t projects onto temporal region t-projection-of-st temporal projection of spatiotemporal spans occupiesTemporalRegion p occupies_temporal_region t. This is a primitive relation between an occurrent p and the temporal region t upon which the spatiotemporal region p occupies_spatiotemporal_region projects. (axiom label in BFO2 Reference: [132-001]) occupies temporal region p occupies_temporal_region t. This is a primitive relation between an occurrent p and the temporal region t upon which the spatiotemporal region p occupies_spatiotemporal_region projects. (axiom label in BFO2 Reference: [132-001]) span-of spanOf [copied from inverse property 'occupies temporal region'] p occupies_temporal_region t. This is a primitive relation between an occurrent p and the temporal region t upon which the spatiotemporal region p occupies_spatiotemporal_region projects. (axiom label in BFO2 Reference: [132-001]) has temporal occupant during-which-exists [copied from inverse property 'exists at'] BFO2 Reference: entity [copied from inverse property 'exists at'] BFO2 Reference: temporal region [copied from inverse property 'exists at'] b exists_at t means: b is an entity which exists at some temporal region t. (axiom label in BFO2 Reference: [118-002]) during which exists bearer-of_at bearerOfAt b bearer_of c at t =Def. c s-depends_on b at t & b is an independent continuant that is not a spatial region. (axiom label in BFO2 Reference: [053-004]) Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'bearer of at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'bearer of@en(x,y,t)'. BFO2 Reference: independent continuant that is not a spatial region BFO2 Reference: specifically dependent continuant (iff (bearerOfAt a b t) (and (specificallyDependsOnAt b a t) (IndependentContinuant a) (not (SpatialRegion a)) (existsAt b t))) // axiom label in BFO2 CLIF: [053-004] bearer of at all times b bearer_of c at t =Def. c s-depends_on b at t & b is an independent continuant that is not a spatial region. (axiom label in BFO2 Reference: [053-004]) (iff (bearerOfAt a b t) (and (specificallyDependsOnAt b a t) (IndependentContinuant a) (not (SpatialRegion a)) (existsAt b t))) // axiom label in BFO2 CLIF: [053-004] has-q_at has quality at all times has-f_at hasFunctionAt a has_function b at t =Def. b function_of a at t. (axiom label in BFO2 Reference: [070-001]) Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has function at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has function@en(x,y,t)'. (iff (hasFunctionAt a b t) (functionOf b a t)) // axiom label in BFO2 CLIF: [070-001] has function at all times a has_function b at t =Def. b function_of a at t. (axiom label in BFO2 Reference: [070-001]) (iff (hasFunctionAt a b t) (functionOf b a t)) // axiom label in BFO2 CLIF: [070-001] has-r_at hasRoleAt a has_role b at t =Def. b role_of a at t. (axiom label in BFO2 Reference: [068-001]) Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has role at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has role@en(x,y,t)'. (iff (hasRoleAt a b t) (roleOfAt b a t)) // axiom label in BFO2 CLIF: [068-001] has role at all times a has_role b at t =Def. b role_of a at t. (axiom label in BFO2 Reference: [068-001]) (iff (hasRoleAt a b t) (roleOfAt b a t)) // axiom label in BFO2 CLIF: [068-001] has-d_at hasDispositionAt a has_disposition b at t =Def. b disposition_of a at t. (axiom label in BFO2 Reference: [069-001]) Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has disposition at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has disposition@en(x,y,t)'. (iff (hasDispositionAt a b t) (dispositionOf b a t)) // axiom label in BFO2 CLIF: [069-001] has disposition at all times a has_disposition b at t =Def. b disposition_of a at t. (axiom label in BFO2 Reference: [069-001]) (iff (hasDispositionAt a b t) (dispositionOf b a t)) // axiom label in BFO2 CLIF: [069-001] material-basis-of_at material basis of at all times participates-in_at participatesInAt participates in at all times has-s-dep_at has specific dependent at all times s-depends-on_st specificallyDependsOn A pain s-depends_on the organism that is experiencing the pain a gait s-depends_on the walking object. (All at some specific time.) a shape s-depends_on the shaped object one-sided s-dependence of a dependent continuant on an independent continuant: an instance of headache s-depends_on some head one-sided s-dependence of a dependent continuant on an independent continuant: an instance of temperature s-depends_on some organism one-sided s-dependence of a process on something: a process of cell death s-depends_on a cell one-sided s-dependence of a process on something: an instance of seeing (a relational process) s-depends_on some organism and on some seen entity, which may be an occurrent or a continuant one-sided s-dependence of one occurrent on another: a process of answering a question is dependent on a prior process of asking a question one-sided s-dependence of one occurrent on another: a process of obeying a command is dependent on a prior process of issuing a command one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of hitting a ball with a cricket bat one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of paying cash to a merchant in exchange for a bag of figs reciprocal s-dependence between occurrents: a process of buying and the associated process of selling reciprocal s-dependence between occurrents: a process of increasing the volume of a portion of gas while temperature remains constant and the associated process of decreasing the pressure exerted by the gas reciprocal s-dependence between occurrents: in a game of chess the process of playing with the white pieces is mutually dependent on the process of playing with the black pieces the one-sided dependence of an occurrent on an independent continuant: football match on the players, the ground, the ball the one-sided dependence of an occurrent on an independent continuant: handwave on a hand the three-sided reciprocal s-dependence of the hue, saturation and brightness of a color [45 the three-sided reciprocal s-dependence of the pitch, timbre and volume of a tone [45 the two-sided reciprocal s-dependence of the roles of husband and wife [20 Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'specifically depends on at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'specifically depends on@en'(x,y,t) BFO 2 Reference: An entity – for example an act of communication or a game of football – can s-depends_on more than one entity. Complex phenomena for example in the psychological and social realms (such as inferring, commanding and requesting) or in the realm of multi-organismal biological processes (such as infection and resistance), will involve multiple families of dependence relations, involving both continuants and occurrents [1, 4, 28 BFO 2 Reference: S-dependence is just one type of dependence among many; it is what, in the literature, is referred to as ‘existential dependence’ [87, 46, 65, 20 BFO 2 Reference: the relation of s-depends_on does not in every case require simultaneous existence of its relata. Note the difference between such cases and the cases of continuant universals defined historically: the act of answering depends existentially on the prior act of questioning; the human being who was baptized or who answered a question does not himself depend existentially on the prior act of baptism or answering. He would still exist even if these acts had never taken place. BFO2 Reference: specifically dependent continuant\; process; process boundary To say that b s-depends_on a at t is to say that b and c do not share common parts & b is of its nature such that it cannot exist unless c exists & b is not a boundary of c and b is not a site of which c is the host [64 If b is s-depends_on something at some time, then b is not a material entity. (axiom label in BFO2 Reference: [052-001]) If b s-depends_on something at t, then there is some c, which is an independent continuant and not a spatial region, such that b s-depends_on c at t. (axiom label in BFO2 Reference: [136-001]) If occurrent b s-depends_on some independent continuant c at t, then b s-depends_on c at every time at which b exists. (axiom label in BFO2 Reference: [015-002]) an entity does not s-depend_on any of its (continuant or occurrent) parts or on anything it is part of. (axiom label in BFO2 Reference: [013-002]) if b s-depends_on c at t & c s-depends_on d at t then b s-depends_on d at t. (axiom label in BFO2 Reference: [054-002]) (forall (x y t) (if (and (Entity x) (or (continuantPartOfAt y x t) (continuantPartOfAt x y t) (occurrentPartOf x y) (occurrentPartOf y x))) (not (specificallyDependsOnAt x y t)))) // axiom label in BFO2 CLIF: [013-002] (forall (x y t) (if (and (Occurrent x) (IndependentContinuant y) (specificallyDependsOnAt x y t)) (forall (t_1) (if (existsAt x t_1) (specificallyDependsOnAt x y t_1))))) // axiom label in BFO2 CLIF: [015-002] (forall (x y t) (if (specificallyDependsOnAt x y t) (exists (z) (and (IndependentContinuant z) (not (SpatialRegion z)) (specificallyDependsOnAt x z t))))) // axiom label in BFO2 CLIF: [136-001] (forall (x y z t) (if (and (specificallyDependsOnAt x y t) (specificallyDependsOnAt y z t)) (specificallyDependsOnAt x z t))) // axiom label in BFO2 CLIF: [054-002] (forall (x) (if (exists (y t) (specificallyDependsOnAt x y t)) (not (MaterialEntity x)))) // axiom label in BFO2 CLIF: [052-001] specifically depends on at some time If b is s-depends_on something at some time, then b is not a material entity. (axiom label in BFO2 Reference: [052-001]) If b s-depends_on something at t, then there is some c, which is an independent continuant and not a spatial region, such that b s-depends_on c at t. (axiom label in BFO2 Reference: [136-001]) If occurrent b s-depends_on some independent continuant c at t, then b s-depends_on c at every time at which b exists. (axiom label in BFO2 Reference: [015-002]) an entity does not s-depend_on any of its (continuant or occurrent) parts or on anything it is part of. (axiom label in BFO2 Reference: [013-002]) if b s-depends_on c at t & c s-depends_on d at t then b s-depends_on d at t. (axiom label in BFO2 Reference: [054-002]) (forall (x y t) (if (and (Entity x) (or (continuantPartOfAt y x t) (continuantPartOfAt x y t) (occurrentPartOf x y) (occurrentPartOf y x))) (not (specificallyDependsOnAt x y t)))) // axiom label in BFO2 CLIF: [013-002] (forall (x y t) (if (and (Occurrent x) (IndependentContinuant y) (specificallyDependsOnAt x y t)) (forall (t_1) (if (existsAt x t_1) (specificallyDependsOnAt x y t_1))))) // axiom label in BFO2 CLIF: [015-002] (forall (x y t) (if (specificallyDependsOnAt x y t) (exists (z) (and (IndependentContinuant z) (not (SpatialRegion z)) (specificallyDependsOnAt x z t))))) // axiom label in BFO2 CLIF: [136-001] (forall (x y z t) (if (and (specificallyDependsOnAt x y t) (specificallyDependsOnAt y z t)) (specificallyDependsOnAt x z t))) // axiom label in BFO2 CLIF: [054-002] (forall (x) (if (exists (y t) (specificallyDependsOnAt x y t)) (not (MaterialEntity x)))) // axiom label in BFO2 CLIF: [052-001] located-in_st locatedInAt Mary located_in Salzburg the Empire State Building located_in New York. this portion of cocaine located_in this portion of blood this stem cell located_in this portion of bone marrow your arm located_in your body b located_in c at t = Def. b and c are independent continuants, and the region at which b is located at t is a (proper or improper) continuant_part_of the region at which c is located at t. (axiom label in BFO2 Reference: [045-001]) Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'located in at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'located in@en'(x,y,t) BFO2 Reference: independent continuant Located_in is transitive. (axiom label in BFO2 Reference: [046-001]) for all independent continuants b, c, and d: if b continuant_part_of c at t & c located_in d at t, then b located_in d at t. (axiom label in BFO2 Reference: [048-001]) for all independent continuants b, c, and d: if b located_in c at t & c continuant_part_of d at t, then b located_in d at t. (axiom label in BFO2 Reference: [049-001]) (forall (x y z t) (if (and (IndependentContinuant x) (IndependentContinuant y) (IndependentContinuant z) (continuantPartOfAt x y t) (locatedInAt y z t)) (locatedInAt x z t))) // axiom label in BFO2 CLIF: [048-001] (forall (x y z t) (if (and (IndependentContinuant x) (IndependentContinuant y) (IndependentContinuant z) (locatedInAt x y t) (continuantPartOfAt y z t)) (locatedInAt x z t))) // axiom label in BFO2 CLIF: [049-001] (forall (x y z t) (if (and (locatedInAt x y t) (locatedInAt y z t)) (locatedInAt x z t))) // axiom label in BFO2 CLIF: [046-001] (iff (locatedInAt a b t) (and (IndependentContinuant a) (IndependentContinuant b) (exists (r_1 r_2) (and (occupiesSpatialRegionAt a r_1 t) (occupiesSpatialRegionAt b r_2 t) (continuantPartOfAt r_1 r_2 t))))) // axiom label in BFO2 CLIF: [045-001] located in at some time b located_in c at t = Def. b and c are independent continuants, and the region at which b is located at t is a (proper or improper) continuant_part_of the region at which c is located at t. (axiom label in BFO2 Reference: [045-001]) Located_in is transitive. (axiom label in BFO2 Reference: [046-001]) for all independent continuants b, c, and d: if b continuant_part_of c at t & c located_in d at t, then b located_in d at t. (axiom label in BFO2 Reference: [048-001]) for all independent continuants b, c, and d: if b located_in c at t & c continuant_part_of d at t, then b located_in d at t. (axiom label in BFO2 Reference: [049-001]) (forall (x y z t) (if (and (IndependentContinuant x) (IndependentContinuant y) (IndependentContinuant z) (continuantPartOfAt x y t) (locatedInAt y z t)) (locatedInAt x z t))) // axiom label in BFO2 CLIF: [048-001] (forall (x y z t) (if (and (IndependentContinuant x) (IndependentContinuant y) (IndependentContinuant z) (locatedInAt x y t) (continuantPartOfAt y z t)) (locatedInAt x z t))) // axiom label in BFO2 CLIF: [049-001] (forall (x y z t) (if (and (locatedInAt x y t) (locatedInAt y z t)) (locatedInAt x z t))) // axiom label in BFO2 CLIF: [046-001] (iff (locatedInAt a b t) (and (IndependentContinuant a) (IndependentContinuant b) (exists (r_1 r_2) (and (occupiesSpatialRegionAt a r_1 t) (occupiesSpatialRegionAt b r_2 t) (continuantPartOfAt r_1 r_2 t))))) // axiom label in BFO2 CLIF: [045-001] member-part-of_at memberPartOfAt each piece in a chess set is a member part of the chess set; each Beatle in the collection called The Beatles is a member part of The Beatles. each tree in a forest is a member_part of the forest b member_part_of c at t =Def. b is an object & there is at t a mutually exhaustive and pairwise disjoint partition of c into objects x1, …, xn (for some n &gt; 1) with b = xi for some 1 ? i ? n. (axiom label in BFO2 Reference: [026-004]) Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'member part of at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'member part of@en(x,y,t)'. BFO2 Reference: object BFO2 Reference: object aggregate if b member_part_of c at t then b continuant_part_of c at t. (axiom label in BFO2 Reference: [104-001]) (forall (x y t) (if (memberPartOfAt x y t) (continuantPartOfAt x y t))) // axiom label in BFO2 CLIF: [104-001] member part of at all times b member_part_of c at t =Def. b is an object & there is at t a mutually exhaustive and pairwise disjoint partition of c into objects x1, …, xn (for some n &gt; 1) with b = xi for some 1 ? i ? n. (axiom label in BFO2 Reference: [026-004]) if b member_part_of c at t then b continuant_part_of c at t. (axiom label in BFO2 Reference: [104-001]) (forall (x y t) (if (memberPartOfAt x y t) (continuantPartOfAt x y t))) // axiom label in BFO2 CLIF: [104-001] c-ppart-of_st properContinuantPartOfAt [copied from inverse property 'has proper continuant part at some time'] b has_proper_continuant_part c at t = Def. c proper_continuant_part_of b at t. [XXX-001 b proper_continuant_part_of c at t =Def. b continuant_part_of c at t & b and c are not identical. (axiom label in BFO2 Reference: [004-001]) Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'proper part of continuant at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'proper part of continuant@en'(x,y,t) [copied from inverse property 'has proper continuant part at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'has proper continuant part at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'has proper continuant part@en'(x,y,t) (iff (properContinuantPartOfAt a b t) (and (continuantPartOfAt a b t) (not (= a b)))) // axiom label in BFO2 CLIF: [004-001] proper part of continuant at some time b proper_continuant_part_of c at t =Def. b continuant_part_of c at t & b and c are not identical. (axiom label in BFO2 Reference: [004-001]) (iff (properContinuantPartOfAt a b t) (and (continuantPartOfAt a b t) (not (= a b)))) // axiom label in BFO2 CLIF: [004-001] c-part-of_st continuantPartOfAt Mary’s arm continuant_part_of Mary in the time of her life prior to her operation the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists. [copied from inverse property 'has continuant part at some time'] b has_continuant_part c at t = Def. c continuant_part_of b at t. (axiom label in BFO2 Reference: [006-001]) Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'part of continuant at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'part of continuant@en'(x,y,t) BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001]) BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion. BFO2 Reference: continuant BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region. [copied from inverse property 'has continuant part at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'has continuant part at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'has continuant part@en'(x,y,t) b continuant_part_of c at t =Def. b is a part of c at t & t is a time & b and c are continuants. (axiom label in BFO2 Reference: [002-001]) continuant_part_of is antisymmetric. (axiom label in BFO2 Reference: [120-001]) continuant_part_of is reflexive (every continuant entity is a continuant_part_of itself). (axiom label in BFO2 Reference: [111-002]) continuant_part_of is transitive. (axiom label in BFO2 Reference: [110-001]) continuant_part_of satisfies unique product. (axiom label in BFO2 Reference: [122-001]) continuant_part_of satisfies weak supplementation. (axiom label in BFO2 Reference: [121-001]) if b continuant_part_of c at t and b is an independent continuant, then b is located_in c at t. (axiom label in BFO2 Reference: [047-002]) (forall (x t) (if (Continuant x) (continuantPartOfAt x x t))) // axiom label in BFO2 CLIF: [111-002] (forall (x y t) (if (and (continuantPartOfAt x y t) (IndependentContinuant x)) (locatedInAt x y t))) // axiom label in BFO2 CLIF: [047-002] (forall (x y t) (if (and (continuantPartOfAt x y t) (continuantPartOfAt y x t)) (= x y))) // axiom label in BFO2 CLIF: [120-001] (forall (x y t) (if (and (continuantPartOfAt x y t) (not (= x y))) (exists (z) (and (continuantPartOfAt z y t) (not (exists (w) (and (continuantPartOfAt w x t) (continuantPartOfAt w z t)))))))) // axiom label in BFO2 CLIF: [121-001] (forall (x y t) (if (exists (v) (and (continuantPartOfAt v x t) (continuantPartOfAt v y t))) (exists (z) (forall (u w) (iff (iff (continuantPartOfAt w u t) (and (continuantPartOfAt w x t) (continuantPartOfAt w y t))) (= z u)))))) // axiom label in BFO2 CLIF: [122-001] (forall (x y z t) (if (and (continuantPartOfAt x y t) (continuantPartOfAt y z t)) (continuantPartOfAt x z t))) // axiom label in BFO2 CLIF: [110-001] (iff (ImmaterialEntity a) (and (IndependentContinuant a) (not (exists (b t) (and (MaterialEntity b) (continuantPartOfAt b a t)))))) // axiom label in BFO2 CLIF: [028-001] part of continuant at some time BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001]) b continuant_part_of c at t =Def. b is a part of c at t & t is a time & b and c are continuants. (axiom label in BFO2 Reference: [002-001]) continuant_part_of is antisymmetric. (axiom label in BFO2 Reference: [120-001]) continuant_part_of is reflexive (every continuant entity is a continuant_part_of itself). (axiom label in BFO2 Reference: [111-002]) continuant_part_of is transitive. (axiom label in BFO2 Reference: [110-001]) continuant_part_of satisfies unique product. (axiom label in BFO2 Reference: [122-001]) continuant_part_of satisfies weak supplementation. (axiom label in BFO2 Reference: [121-001]) if b continuant_part_of c at t and b is an independent continuant, then b is located_in c at t. (axiom label in BFO2 Reference: [047-002]) (forall (x t) (if (Continuant x) (continuantPartOfAt x x t))) // axiom label in BFO2 CLIF: [111-002] (forall (x y t) (if (and (continuantPartOfAt x y t) (IndependentContinuant x)) (locatedInAt x y t))) // axiom label in BFO2 CLIF: [047-002] (forall (x y t) (if (and (continuantPartOfAt x y t) (continuantPartOfAt y x t)) (= x y))) // axiom label in BFO2 CLIF: [120-001] (forall (x y t) (if (and (continuantPartOfAt x y t) (not (= x y))) (exists (z) (and (continuantPartOfAt z y t) (not (exists (w) (and (continuantPartOfAt w x t) (continuantPartOfAt w z t)))))))) // axiom label in BFO2 CLIF: [121-001] (forall (x y t) (if (exists (v) (and (continuantPartOfAt v x t) (continuantPartOfAt v y t))) (exists (z) (forall (u w) (iff (iff (continuantPartOfAt w u t) (and (continuantPartOfAt w x t) (continuantPartOfAt w y t))) (= z u)))))) // axiom label in BFO2 CLIF: [122-001] (forall (x y z t) (if (and (continuantPartOfAt x y t) (continuantPartOfAt y z t)) (continuantPartOfAt x z t))) // axiom label in BFO2 CLIF: [110-001] (iff (ImmaterialEntity a) (and (IndependentContinuant a) (not (exists (b t) (and (MaterialEntity b) (continuantPartOfAt b a t)))))) // axiom label in BFO2 CLIF: [028-001] c-part-of_at continuantPartOfAt Mary’s arm continuant_part_of Mary in the time of her life prior to her operation the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists. [copied from inverse property 'has continuant part at all times that part exists'] forall(t) exists_at(y,t) -> exists_at(x,t) and 'has continuant part'(x,y,t) Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'part of continuant at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'part of continuant@en(x,y,t)'. BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001]) BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion. BFO2 Reference: continuant BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region. [copied from inverse property 'has continuant part at all times that part exists'] This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'part of continuant at all times' b continuant_part_of c at t =Def. b is a part of c at t & t is a time & b and c are continuants. (axiom label in BFO2 Reference: [002-001]) continuant_part_of is antisymmetric. (axiom label in BFO2 Reference: [120-001]) continuant_part_of is reflexive (every continuant entity is a continuant_part_of itself). (axiom label in BFO2 Reference: [111-002]) continuant_part_of is transitive. (axiom label in BFO2 Reference: [110-001]) continuant_part_of satisfies unique product. (axiom label in BFO2 Reference: [122-001]) continuant_part_of satisfies weak supplementation. (axiom label in BFO2 Reference: [121-001]) if b continuant_part_of c at t and b is an independent continuant, then b is located_in c at t. (axiom label in BFO2 Reference: [047-002]) (forall (x t) (if (Continuant x) (continuantPartOfAt x x t))) // axiom label in BFO2 CLIF: [111-002] (forall (x y t) (if (and (continuantPartOfAt x y t) (IndependentContinuant x)) (locatedInAt x y t))) // axiom label in BFO2 CLIF: [047-002] (forall (x y t) (if (and (continuantPartOfAt x y t) (continuantPartOfAt y x t)) (= x y))) // axiom label in BFO2 CLIF: [120-001] (forall (x y t) (if (and (continuantPartOfAt x y t) (not (= x y))) (exists (z) (and (continuantPartOfAt z y t) (not (exists (w) (and (continuantPartOfAt w x t) (continuantPartOfAt w z t)))))))) // axiom label in BFO2 CLIF: [121-001] (forall (x y t) (if (exists (v) (and (continuantPartOfAt v x t) (continuantPartOfAt v y t))) (exists (z) (forall (u w) (iff (iff (continuantPartOfAt w u t) (and (continuantPartOfAt w x t) (continuantPartOfAt w y t))) (= z u)))))) // axiom label in BFO2 CLIF: [122-001] (forall (x y z t) (if (and (continuantPartOfAt x y t) (continuantPartOfAt y z t)) (continuantPartOfAt x z t))) // axiom label in BFO2 CLIF: [110-001] (iff (ImmaterialEntity a) (and (IndependentContinuant a) (not (exists (b t) (and (MaterialEntity b) (continuantPartOfAt b a t)))))) // axiom label in BFO2 CLIF: [028-001] part of continuant at all times BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001]) b continuant_part_of c at t =Def. b is a part of c at t & t is a time & b and c are continuants. (axiom label in BFO2 Reference: [002-001]) continuant_part_of is antisymmetric. (axiom label in BFO2 Reference: [120-001]) continuant_part_of is reflexive (every continuant entity is a continuant_part_of itself). (axiom label in BFO2 Reference: [111-002]) continuant_part_of is transitive. (axiom label in BFO2 Reference: [110-001]) continuant_part_of satisfies unique product. (axiom label in BFO2 Reference: [122-001]) continuant_part_of satisfies weak supplementation. (axiom label in BFO2 Reference: [121-001]) if b continuant_part_of c at t and b is an independent continuant, then b is located_in c at t. (axiom label in BFO2 Reference: [047-002]) (forall (x t) (if (Continuant x) (continuantPartOfAt x x t))) // axiom label in BFO2 CLIF: [111-002] (forall (x y t) (if (and (continuantPartOfAt x y t) (IndependentContinuant x)) (locatedInAt x y t))) // axiom label in BFO2 CLIF: [047-002] (forall (x y t) (if (and (continuantPartOfAt x y t) (continuantPartOfAt y x t)) (= x y))) // axiom label in BFO2 CLIF: [120-001] (forall (x y t) (if (and (continuantPartOfAt x y t) (not (= x y))) (exists (z) (and (continuantPartOfAt z y t) (not (exists (w) (and (continuantPartOfAt w x t) (continuantPartOfAt w z t)))))))) // axiom label in BFO2 CLIF: [121-001] (forall (x y t) (if (exists (v) (and (continuantPartOfAt v x t) (continuantPartOfAt v y t))) (exists (z) (forall (u w) (iff (iff (continuantPartOfAt w u t) (and (continuantPartOfAt w x t) (continuantPartOfAt w y t))) (= z u)))))) // axiom label in BFO2 CLIF: [122-001] (forall (x y z t) (if (and (continuantPartOfAt x y t) (continuantPartOfAt y z t)) (continuantPartOfAt x z t))) // axiom label in BFO2 CLIF: [110-001] (iff (ImmaterialEntity a) (and (IndependentContinuant a) (not (exists (b t) (and (MaterialEntity b) (continuantPartOfAt b a t)))))) // axiom label in BFO2 CLIF: [028-001] has-t-ppart has proper temporal part history-of historyOf [copied from inverse property 'has history'] b has_history c iff c history_of b [XXX-001 b history_of c if c is a material entity or site and b is a history that is the unique history of cAxiom: if b history_of c and b history_of d then c=d [XXX-001 history of has-history hasHistory b has_history c iff c history_of b [XXX-001 [copied from inverse property 'history of'] b history_of c if c is a material entity or site and b is a history that is the unique history of cAxiom: if b history_of c and b history_of d then c=d [XXX-001 has history c-part-of-object_at [copied from inverse property 'has continuant part at all times'] b has_continuant_part c at t = Def. c continuant_part_of b at t. (axiom label in BFO2 Reference: [006-001]) forall(t) exists_at(y,t) -> exists_at(x,t) and 'part of continuant'(x,y,t) This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'has continuant part at all times' [copied from inverse property 'has continuant part at all times'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has continuant part at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has continuant part@en(x,y,t)'. part of continuant at all times that whole exists forall(t) exists_at(y,t) -> exists_at(x,t) and 'part of continuant'(x,y,t) This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'has continuant part at all times' x anterior_to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail: bearer cjm 2009-07-31T02:15:46Z BSPO:0000096 uberon anterior_to anterior_to anterior_to x anterior_to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail: bearer x distal_to y iff x is further along the proximo-distal axis than y, towards the appendage tip. A proximo-distal axis extends from tip of an appendage (distal) to where it joins the body (proximal). BSPO:0000097 uberon distal_to distal_to distal_to x distal_to y iff x is further along the proximo-distal axis than y, towards the appendage tip. A proximo-distal axis extends from tip of an appendage (distal) to where it joins the body (proximal). x dorsal_to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly). BSPO:0000098 uberon dorsal_to dorsal_to dorsal_to x dorsal_to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly). x posterior_to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail. BSPO:0000099 caudal_to uberon posterior_to posterior_to posterior_to x posterior_to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail. x proximal_to y iff x is closer to the point of attachment with the body than y. BSPO:0000100 uberon proximal_to proximal_to proximal_to x proximal_to y iff x is closer to the point of attachment with the body than y. x ventral_to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly). BSPO:0000102 uberon ventral_to ventral_to ventral_to x ventral_to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly). Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines. BSPO:0000107 uberon deep_to deep_to deep_to Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines. Near the outer surface of the organism. Thus, skin is superficial to the muscle layer. BSPO:0000108 uberon superficial_to superficial_to superficial_to Near the outer surface of the organism. Thus, skin is superficial to the muscle layer. X in_left_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the left portion. BSPO:0000120 uberon in_left_side_of in_left_side_of in_left_side_of https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern X in_left_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the left portion. BSPO:PATO_mtg_2009 X in_right_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the right portion. BSPO:0000121 uberon in_right_side_of in_right_side_of in_right_side_of https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern X in_right_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the right portion. BSPO:PATO_mtg_2009 X posterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the posterior portion. BSPO:0000122 uberon in_posterior_side_of in_posterior_side_of in_posterior_side_of X posterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the posterior portion. BSPO:PATO_mtg_2009 X anterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the anterior portion. BSPO:0000123 uberon in_anterior_side_of in_anterior_side_of in_anterior_side_of X anterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the anterior portion. BSPO:PATO_mtg_2009 X proximal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the proximal portion. BSPO:0000124 uberon in_proximal_side_of in_proximal_side_of in_proximal_side_of X proximal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the proximal portion. BSPO:PATO_mtg_2009 X distal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the distal portion. BSPO:0000125 uberon in_distal_side_of in_distal_side_of in_distal_side_of X distal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the distal portion. BSPO:PATO_mtg_2009 X in_lateral_side_of Y <=> if X is in_left_side_of Y or X is in_right_side_of Y. X is often, but not always a paired structure BSPO:0000126 uberon in_lateral_side_of in_lateral_side_of in_lateral_side_of https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern X in_lateral_side_of Y <=> if X is in_left_side_of Y or X is in_right_side_of Y. X is often, but not always a paired structure X proximalmost_part_of Y <=> X is part_of Y and X is adjacent_to the proximal boundary of Y BSPO:0001106 uberon proximalmost_part_of proximalmost_part_of proximalmost_part_of X proximalmost_part_of Y <=> X is part_of Y and X is adjacent_to the proximal boundary of Y This relation holds when both the deep_to and ajdacent_to relationship similarly hold. BSPO:0001107 uberon immediately_deep_to immediately_deep_to immediately_deep_to This relation holds when both the deep_to and ajdacent_to relationship similarly hold. X distalmost_part_of Y <=> X is part_of Y and X is adjacent_to the distal boundary of Y BSPO:0001108 uberon distalmost_part_of distalmost_part_of distalmost_part_of X distalmost_part_of Y <=> X is part_of Y and X is adjacent_to the distal boundary of Y derives from patient having disease has disease is in cell line repository is disease model for derived from anatomic part This document is about information artifacts and their representations is_about is a (currently) primitive relation that relates an information artifact to an entity. 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. person:Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy is about A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named. denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically 2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. g denotes r =def r is a portion of reality there is some c that is a concretization of g every c that is a concretization of g specifically denotes r person:Alan Ruttenberg Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan denotes inverse of the relation 'denotes' Person: Jie Zheng, Chris Stoeckert, Mike Conlon denoted by has material basis in has_material_basis_in is_specified_input_of some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters is_specified_input_of is_specified_output_of is_specified_output_of A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters is_specified_output_of achieves_planned_objective A cell sorting process achieves the objective specification 'material separation objective' This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process. BP, AR, PPPB branch PPPB branch derived modified according to email thread from 1/23/09 in accordince with DT and PPPB branch achieves_planned_objective has grain the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car. Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. Definition take from the definition of granular parthood in the cited paper. Needs work to put into standard form PERSON: Alan Ruttenberg PAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349 has grain objective_achieved_by This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. OBI OBI objective_achieved_by a 'part of continuant at some time' relation that incides a genome belongs to a organism. Yongqun He, Bin Zhao is genome of organism a relation between a gene and the organism where this gene belongs to the organism in nature. It does not include a foreign gene that is transferred to an organism by a genetic engineering method. Oliver He, Yue Liu is gene of organism An object property that represents a relation between a gene and an organism, where the gene comes from a pathogen and the organism is a host, and the mutant of the gene for the pathogen is attenuated in the host organism. Edison Ong; Yongqun He; Yu Lin gene mutant attenuated in host organism An object property that represents a relation between a gene and an organism, where the gene is a virulence factor and the organism is a pathogen, and the mutant of the gene for the pathogen is attenuated in the host. Edison Ong; Yongqun He gene as virulence factor in pathogen An object property that represents a relation between a gene and a cell line cell, where the gene comes from a pathogen and the cell line cell comes from a host, and the mutant of the gene for the pathogen is attenuated inside the cell line cell. Edison Ong; Yongqun He gene mutant attenuated in host cell line cell An object property that represents a relation between a gene and a cell, where the gene comes from a pathogen and the cell comes from a host, and the mutant of the gene for the pathogen is attenuated inside the cell. Edison Ong; Yongqun He; Yu Lin gene mutant attenuated in host cell An object property that represents a relation between a gene and a host, where the gene comes from a pathogen, and the mutant of the gene for the pathogen is attenuated in the host. Edison Ong; Yongqun He; Yu Lin gene mutant attenuated in host Edison Ong; Yongqun He; Yu Lin has microbe mutated gene An object property that represents a relation between a host-pathogen interaction process and an organism (or tissue or cell as part of the organism, or cell line cell derived from organism) which serves as the host that participates in the process. Edison Ong; Yongqun He has HPI host An object property that represents a relation between a host-pathogen interaction process and an organism (or virus) which serves as the pathgen that participates in the process. Edison Ong; Yongqun He has HPI pathogen Edison Ong; Yongqun He has HPI host organism Edison Ong; Yongqun He has HPI host cell Edison Ong; Yongqun He has HPI host cell line cell Edison Ong gene encoding antigen inheres in this fragility inheres in this vase this red color inheres in this apple a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence A dependent inheres in its bearer at all times for which the dependent exists. inheres_in inheres in bearer of this apple is bearer of this red color this vase is bearer of this fragility a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. bearer_of is bearer of RO:0000053 uberon bearer_of bearer_of bearer of bearer of participates in this blood clot participates in this blood coagulation this input material (or this output material) participates in this process this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process participates_in RO:0000056 protein participates_in false participates_in participates in participates_in has participant this blood coagulation has participant this blood clot this investigation has participant this investigator this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. is concretized as A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. concretizes this catalysis function is a function of this enzyme a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. function_of is function of function of this investigator role is a role of this person a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. is role of role_of role of this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. has_function has function a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence has disposition inverse of has disposition disposition of derives from this cell derives from this parent cell (cell division) this nucleus derives from this parent nucleus (nuclear division) a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. derives_from This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations. RO:0001000 protein derives_from derives_from derives from derives_from derives_from this parent cell derives into this cell (cell division) this parent nucleus derives into this nucleus (nuclear division) a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. derives_into derives into is location of my head is the location of my brain this cage is the location of this rat a relation between two independent continuants, the location and the target, in which the target is entirely within the location Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime location_of RO:0001015 uberon location_of location_of location of location_of contained in Containment is location not involving parthood, and arises only where some immaterial continuant is involved. Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition): Intended meaning: domain: material entity range: spatial region or site (immaterial continuant) contained_in contained in contains RO:0001019 uberon contains contains contains contains located in my brain is located in my head this rat is located in this cage a relation between two independent continuants, the target and the location, in which the target is entirely within the location Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime located_in http://www.obofoundry.org/ro/#OBO_REL:located_in RO:0001025 protein uberon located_in located_in located in located_in This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. the surface of my skin is a 2D boundary of my body a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. 2D_boundary_of boundary of is 2D boundary of is boundary of RO:0002000 uberon boundary_of boundary_of 2D boundary of boundary of my body has 2D boundary the surface of my skin a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. David Osumi-Sutherland has boundary has_2D_boundary RO:0002002 uberon has_boundary has_boundary has 2D boundary has boundary David Osumi-Sutherland http://www.ncbi.nlm.nih.gov/pubmed/22402613 RO:0002005 nerve supply uberon innervated_by innervated_by http://code.google.com/p/obo-relations/issues/detail?id=6 innervated_by innervated_by nerve supply FMA:85999 X outer_layer_of Y iff: . X :continuant that bearer_of some PATO:laminar . X part_of Y . exists Z :surface . X has_boundary Z . Z boundary_of Y has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000 David Osumi-Sutherland RO:0002007 uberon bounding_layer_of bounding_layer_of A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. bounding layer of bounding layer of A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. dos 2017-05-24T09:30:46Z has regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. dos 2017-05-24T09:31:01Z By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. has negative regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. dos 2017-05-24T09:31:17Z By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. has positive regulatory component activity dos 2017-05-24T09:44:33Z A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. has component activity w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. dos 2017-05-24T09:49:21Z has component process A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. dos 2017-07-19T17:30:36Z has ligand dos 2017-09-17T13:52:24Z Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. directly regulated by Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. GOC:dos Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. dos 2017-09-17T13:52:38Z directly negatively regulated by Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. GOC:dos Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. dos 2017-09-17T13:52:47Z directly positively regulated by Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. GOC:dos A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. dos 2017-09-22T14:14:36Z This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. has effector activity A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. GOC:dos David Osumi-Sutherland X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) David Osumi-Sutherland starts_at_end_of A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]. RO:0002087 directly preceded by is directly preceded by is immediately preceded by starts_at_end_of uberon immediately_preceded_by immediately_preceded_by X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately preceded by immediately_preceded_by A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]. SIO:000251 is immediately preceded by SIO:000251 David Osumi-Sutherland ends_at_start_of meets X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) immediately precedes A overlaps B if they share some part in common. x overlaps y if and only if there exists some z such that x has part z and z part of y BFO_0000051 some (BFO_0000050 some ?Y) http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) RO:0002131 uberon overlaps overlaps overlaps overlaps true Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. T innervates some R Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. David Osumi-Sutherland <http://purl.obolibrary.org/obo/RO_0002132> some (<http://purl.obolibrary.org/obo/GO_0043005> that (<http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) RO:0002134 uberon innervates innervates http://code.google.com/p/obo-relations/issues/detail?id=6 innervates innervates X continuous_with Y if and only if X and Y share a fiat boundary. David Osumi-Sutherland connected to The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint) RO:0002150 uberon continuous_with continuous_with continuous with continuous_with FMA:85972 A is spatially_disjoint_from B if and only if they have no parts in common There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. Chris Mungall Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy BFO_0000051 exactly 0 (BFO_0000050 some ?Y) spatially disjoint from https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). Binary relationship: x connected_to y if and only if there exists some z such that z connects x and y in a ternary connected_to(x,y,z) relationship. a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b RO:0002170 uberon connected_to connected_to Connection does not imply overlaps. connected to connected to https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern Binary relationship: x connected_to y if and only if there exists some z such that z connects x and y in a ternary connected_to(x,y,z) relationship. The M8 connects Glasgow and Edinburgh a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). Binary relationship: z connects x if and only if there exists some y such that z connects x and y in a ternary connected_to(x,y,z) relationship. c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system. this is currently used for both structural relationships (such as between a valve and the chamber it connects) and abstract relationships (anatomical lines and the entities they connect) RO:0002176 uberon connects connects connects connects https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern Binary relationship: z connects x if and only if there exists some y such that z connects x and y in a ternary connected_to(x,y,z) relationship. a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. attached to part of (anatomical structure to anatomical structure) RO:0002177 uberon attaches_to_part_of attaches_to_part_of attached to part of attaches_to_part_of true true Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy. relation between an artery and the structure is supplies with blood. Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure RO:0002178 arterial supply of uberon supplies supplies source: FMA supplies supplies arterial supply of FMA:86003 Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure. Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure RO:0002179 drains blood from drains from uberon drains drains source: Wikipedia drains drains w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. RO:0002180 protein uberon has_component false has_component has component has component has_component x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y Chris Mungall David Osumi-Sutherland Melissa Haendel Terry Meehan RO:0002202 uberon develops_from develops_from This is the transitive form of the develops from relation develops from develops_from inverse of develops from Chris Mungall David Osumi-Sutherland Terry Meehan RO:0002203 uberon develops_into develops_into develops into develops_into Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y. Chris Mungall David Osumi-Sutherland has developmental precursor FBbt RO:0002207 uberon directly_develops_from directly_develops_from TODO - add child relations from DOS directly develops from directly_develops_from inverse of directly develops from developmental precursor of directly develops into process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit Chris Mungall David Hill Tanya Berardini GO Regulation precludes parthood; the regulatory process may not be within the regulated process. regulates (processual) false RO:0002211 external regulates regulates regulates regulates Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. Chris Mungall negatively regulates (process to process) RO:0002212 external negatively_regulates negatively_regulates negatively regulates negatively regulates Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. Chris Mungall positively regulates (process to process) RO:0002213 external positively_regulates positively_regulates positively regulates positively regulates mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) osteoclast SubClassOf 'capable of' some 'bone resorption' A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. Chris Mungall has function realized in For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". RO_0000053 some (RO_0000054 only ?Y) RO:0002215 protein uberon capable_of false capable_of capable of capable of capable_of c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. Chris Mungall has function in RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y)) RO:0002216 uberon capable_of_part_of capable_of_part_of capable of part of capable of part of true x actively participates in y if and only if x participates in y and x realizes some active role Chris Mungall agent in actively participates in 'heart development' has active participant some Shh protein x has participant y if and only if x realizes some active role that inheres in y This may be obsoleted and replaced by the original 'has agent' relation Chris Mungall has agent obsolete has active participant true surrounded by x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x x surrounded_by y if and only if x is adjacent to y and for every region r that is adjacent to x, r overlaps y x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y Chris Mungall RO:0002219 uberon surrounded_by surrounded_by surrounded by surrounded_by x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. The epidermis layer of a vertebrate is adjacent to the dermis. The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies. The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used. x adjacent to y if and only if x and y share a boundary. x adjacent_to y iff: x and y share a boundary This relation acts as a join point with BSPO Chris Mungall RO:0002220 uberon adjacent_to adjacent_to adjacent to adjacent to adjacent_to A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. inverse of surrounded by inverse of surrounded_by Chris Mungall RO:0002221 uberon surrounds surrounds surrounds surrounds inverse of surrounded_by move to BFO? Chris Mungall Allen Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporal relation temporally related to Relation between occurrents, shares a start boundary with. inverse of starts with Chris Mungall Allen RO:0002223 uberon starts starts starts starts Relation between occurrents, shares a start boundary with. Allen:starts Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. Chris Mungall started by RO:0002224 uberon starts_with starts_with starts with starts with x develops from part of y if and only if there exists some z such that x develops from z and z is part of y Chris Mungall RO:0002225 uberon develops_from_part_of develops_from_part_of develops from part of develops_from_part_of x develops_in y if x is located in y whilst x is developing Chris Mungall EHDAA2 Jonathan Bard, EHDAA2 RO:0002226 uberon develops_in develops_in This relation take from EHDAA2 - precise semantics yet to be defined develops in develops_in Relation between occurrents, shares an end boundary with. inverse of ends with Chris Mungall RO:0002229 finishes uberon ends ends ends ends Relation between occurrents, shares an end boundary with. Allen:starts ZFS:finishes x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. Chris Mungall finished by RO:0002230 uberon ends_with ends_with ends with ends with x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y Chris Mungall starts with process that occurs in has start location x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y Chris Mungall ends with process that occurs in has end location p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. Chris Mungall consumes has input p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p. Chris Mungall produces has output Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y Chris Mungall RO:0002254 uberon has_developmental_contribution_from has_developmental_contribution_from has developmental contribution from has developmental contribution from inverse of has developmental contribution from Chris Mungall RO:0002255 uberon developmentally_contributes_to developmentally_contributes_to developmentally contributes to developmentally_contributes_to t1 developmentally_induced_by t2 if there is a process of organ induction (GO:0001759) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor tissue type T to T', where T' develops_from T. t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor anatomical structure type T to T', where T' develops_from T Chris Mungall David Osumi-Sutherland Melissa Haendel induced by Developmental Biology, Gilbert, 8th edition, figure 6.5(F) GO:0001759 We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm] RO:0002256 uberon developmentally_induced_by developmentally_induced_by sources for developmentally_induced_by relationships in Uberon: Developmental Biology, Gilbert, 8th edition, figure 6.5(F) developmentally induced by developmentally_induced_by t1 developmentally_induced_by t2 if there is a process of organ induction (GO:0001759) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor tissue type T to T', where T' develops_from T. GO:0001759 Inverse of developmentally induced by Chris Mungall developmentally induces Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p false Chris Mungall In general you should not use this relation to make assertions - use one of the more specific relations below this one RO:0002258 uberon developmentally_preceded_by developmentally_preceded_by This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from developmentally preceded by developmentally preceded by A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. acts upstream of A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. affects acts upstream of or within x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage Chris Mungall replaces RO:0002285 uberon developmentally_replaces developmentally_replaces developmentally replaces developmentally_replaces Inverse of developmentally preceded by Chris Mungall developmentally succeeded by 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue Chris Mungall part of developmental precursor of p results in the developmental progression of s iff p is a developmental process and s is an anatomical structure and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. Chris Mungall results_in_developmental_progression_of results in developmental progression of an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) Chris Mungall GOC:mtg_berkeley_2013 results_in_formation_of results in formation of cjm holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect cjm holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y causally upstream of, negative effect q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w. Because part_of is transitive, inheres in is a sub-relation of inheres in part of Chris Mungall inheres in part of true A mereological relationship or a topological relationship Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships mereotopologically related to A relationship that holds between entities participating in some developmental process (GO:0032502) Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development developmentally related to a particular instances of akt-2 enables some instance of protein kinase activity Chris Mungall catalyzes executes has is catalyzing is executing This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. enables A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. Chris Mungall This is a grouping relation that collects relations used for the purpose of connecting structure and function RO:0002328 uberon functionally_related_to functionally_related_to functionally related to functionally related to this relation holds between c and p when c is part of some c', and c' is capable of p. Chris Mungall false RO:0002329 uberon part_of_structure_that_is_capable_of part_of_structure_that_is_capable_of part of structure that is capable of part of structure that is capable of true c involved_in p if and only if c enables some process p', and p' is part of p Chris Mungall actively involved in enables part of RO:0002331 protein involved_in false involved_in involved in involved_in inverse of enables Chris Mungall enabled by inverse of regulates Chris Mungall regulated by (processual) regulated by inverse of negatively regulates Chris Mungall negatively regulated by inverse of positively regulates Chris Mungall positively regulated by An organism that is a member of a population of organisms is member of is a mereological relation between a item and a collection. is member of member part of SIO RO:0002350 uberon member_of member_of member of member of has member is a mereological relation between a collection and an item. SIO RO:0002351 uberon has_member has_member has member has member inverse of has input Chris Mungall RO:0002352 uberon input_of input_of input of input of inverse of has output Chris Mungall RO:0002353 protein uberon output_of false output_of output of output of output_of Chris Mungall formed as result of a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a Chris Mungall attached to (anatomical structure to anatomical structure) RO:0002371 uberon attaches_to attaches_to attached to attaches_to m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. Chris Mungall Wikipedia:Insertion_(anatomy) RO:0002373 uberon has_muscle_insertion has_muscle_insertion The insertion is the point of attachment of a muscle that moves the most when the muscle shortens, or the most distal end of limb muscles has muscle insertion has_muscle_insertion We need to import uberon muscle into RO to use as a stricter domain constraint m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network. Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves) in branching relationship with https://github.com/obophenotype/uberon/issues/170 Deschutes River tributary_of Columbia River inferior epigastric vein tributary_of external iliac vein x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein. Chris Mungall drains into drains to tributary channel of http://en.wikipedia.org/wiki/Tributary http://www.medindia.net/glossary/venous_tributary.htm This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries) RO:0002376 uberon drains into tributary_of tributary_of tributary of tributary_of http://en.wikipedia.org/wiki/Tributary drains into dbpowl:drainsTo A lump of clay and a statue x spatially_coextensive_with y if and inly if x and y have the same location Chris Mungall This relation is added for formal completeness. It is unlikely to be used in many practical scenarios spatially coextensive with x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y we need to check if FMA branch_of implies part_of. the relation we intend to use here should - for example, see vestibulocochlear nerve Chris Mungall RO:0002380 uberon branching_part_of branching_part_of branching part of branching_part_of FMA:85994 x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). Chris Mungall has developmental potential involving x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y Chris Mungall RO:0002385 uberon has_potential_to_developmentally_contribute_to has_potential_to_developmentally_contribute_to has potential to developmentally contribute to has potential to developmentally contribute to x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y Chris Mungall has potential to developmentally induce x has the potential to develop into y iff x develops into y or if x is capable of developing into y x has the potential to develop into y iff x develops into y or if x is capable of developing into y Chris Mungall RO:0002387 uberon has_potential_to_develop_into has_potential_to_develop_into has potential to develop into has potential to develop into x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y Chris Mungall RO:0002388 uberon has_potential_to_directly_develop_into has_potential_to_directly_develop_into has potential to directly develop into has potential to directly develop into inverse of upstream of Chris Mungall causally downstream of Chris Mungall immediately causally downstream of This relation groups causal relations between material entities and causal relations between processes This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causally related to p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain Chris Mungall causally upstream of p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. Chris Mungall immediately causally upstream of p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 Chris Mungall influences (processual) affects causally upstream of or within inverse of causally upstream of or within Chris Mungall causally downstream of or within c involved in regulation of p if c is involved in some p' and p' regulates some p Chris Mungall involved in regulation of c involved in regulation of p if c is involved in some p' and p' positively regulates some p Chris Mungall involved in positive regulation of c involved in regulation of p if c is involved in some p' and p' negatively regulates some p Chris Mungall involved in negative regulation of c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p OWL does not allow defining object properties via a Union Chris Mungall involved in or reguates involved in or involved in regulation of A protein that enables activity in a cytosol. c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. Chris Mungall executes activity in enables activity in is active in true c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. GOC:cjm GOC:dos p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm. Chris Mungall RO:0002433 uberon contributes_to_morphology_of contributes_to_morphology_of contributes to morphology of A relationship that holds between two entities in which the processes executed by the two entities are causally connected. Considering relabeling as 'pairwise interacts with' This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. Chris Mungall Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. in pairwise interaction with interacts with http://purl.obolibrary.org/obo/MI_0914 https://github.com/oborel/obo-relations/wiki/InteractionRelations An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. Chris Mungall binds molecularly binds with molecularly interacts with http://purl.obolibrary.org/obo/MI_0915 Axiomatization to GO to be added later Chris Mungall An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. phosphorylates Holds between molecular entities A and B where A can physically interact with B and in doing so regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. Chris Mungall molecularly controls activity directly regulates activity of Holds between molecular entities A and B where A can physically interact with B and in doing so negatively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. Chris Mungall inhibits molecularly decreases activity of activity directly negatively regulates activity of Holds between molecular entities A and B where A can physically interact with B and in doing so positively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. Chris Mungall activates molecularly increases activity of activity directly positively regulates activity of Chris Mungall This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. helper property (not for use in curation) Chris Mungall is symbiosis 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. x composed_primarily_of y iff: more than half of the mass of x is made from parts of y Chris Mungall RO:0002473 uberon composed_primarily_of composed_primarily_of composed primarily of p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. Chris Mungall has part that occurs in true Chris Mungall is kinase activity Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage. relation between structure and stage Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s. x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y). Chris Mungall RO:0002488 begins_to_exist_during uberon existence_starts_during existence_starts_during existence starts during existence starts during Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s. Relation between continuant and occurrent, such that c comes into existence at the start of p. x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y). Chris Mungall RO:0002489 uberon existence_starts_with existence_starts_with existence starts with Relation between continuant and occurrent, such that c comes into existence at the start of p. x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y)) Chris Mungall The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence overlaps Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely. x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y). Chris Mungall RO:0002492 ceases_to_exist_during uberon existence_ends_during existence_ends_during The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends during Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely. Relation between continuant and occurrent, such that c ceases to exist at the end of p. x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y). Chris Mungall RO:0002493 uberon existence_ends_with existence_ends_with The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends with Relation between continuant and occurrent, such that c ceases to exist at the end of p. x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships Chris Mungall RO:0002494 transforms from uberon transformation_of transformation_of transformation of transforms from SIO:000657 x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t Chris Mungall RO:0002495 direct_transformation_of immediately transforms from uberon immediate_transformation_of immediate_transformation_of immediate transformation of direct_transformation_of immediately transforms from SIO:000658 x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y). Chris Mungall RO:0002496 uberon existence_starts_during_or_after existence_starts_during_or_after The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence starts during or after x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends. Chris Mungall RO:0002497 uberon existence_ends_during_or_before existence_ends_during_or_before The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends during or before A relationship between a material entity and a process where the material entity has some causal role that influences the process causal agent in process p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between processes Chris Mungall depends on The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between material entities Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. A relation between a subdivision of an organism and the single subdivision of skeleton that provides structural support for that subdivision. Chris Mungall has supporting framework The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell). RO:0002551 uberon has sekeletal support has supporting framework has_skeleton has_skeleton has skeleton This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional. A relation between a subdivision of an organism and the single subdivision of skeleton that provides structural support for that subdivision. Chris Mungall causally influenced by (material entity to material entity) causally influenced by Chris Mungall interaction relation helper property https://github.com/oborel/obo-relations/wiki/InteractionRelations Chris Mungall molecular interaction relation helper property Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b Chris Mungall causally influences (material entity to material entity) causally influences A relation that holds between elements of a musculoskeletal system or its analogs. Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. biomechanically related to inverse of branching part of Chris Mungall RO:0002569 uberon has_branching_part has_branching_part has branching part x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. Chris Mungall GOC:cjm RO:0002571 uberon lumen_of lumen_of lumen of s is luminal space of x iff s is lumen_of x and s is an immaterial entity Chris Mungall RO:0002572 uberon luminal_space_of luminal_space_of luminal space of inverse of has skeleton Chris Mungall RO:0002576 uberon skeleton_of skeleton_of skeleton of Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. Chris Mungall directly regulates (processual) directly regulates gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p Chris Mungall has part structure that is capable of A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. Chris Mungall causal relation between material entity and a process pyrethroid -> growth Holds between c and p if and only if c is capable of some activity a, and a regulates p. capable of regulating Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. capable of negatively regulating renin -> arteriolar smooth muscle contraction Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. capable of positively regulating Inverse of 'causal agent in process' process has causal agent A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. obsolete related via dependence to true Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. directly positively regulates (process to process) directly positively regulates Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. directly negatively regulates (process to process) directly negatively regulates a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. Melissa Haendel RO:0003000 uberon produces produces Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. produces produces a produced_by b iff some process that occurs_in b has_output a. Melissa Haendel RO:0003001 uberon produced_by produced_by produced by produced_by A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M. cjm 2017-12-26T19:45:49Z realized in response to stimulus Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. cjm 2018-01-25T23:20:13Z enables subfunction cjm 2018-01-26T23:49:30Z acts upstream of or within, positive effect cjm 2018-01-26T23:49:51Z acts upstream of or within, negative effect c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive cjm 2018-01-26T23:53:14Z acts upstream of, positive effect c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative cjm 2018-01-26T23:53:22Z acts upstream of, negative effect cjm 2018-03-13T23:55:05Z causally upstream of or within, negative effect cjm 2018-03-13T23:55:19Z causally upstream of or within, positive effect A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions. An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut) Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph. r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r. Austin Meier Chris Mungall David Osumi-Sutherland Marie Angelique Laporte triggered by process realized in response to https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit triggered by process RO:cjm Genetic information generically depend on molecules of DNA. The novel *War and Peace* generically depends on this copy of the novel. The pattern shared by chess boards generically depends on any chess board. The score of a symphony g-depends on a copy of the score. This pdf file generically depends on this server. A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*. [072-ISO] g-depends on generically depends on Molecules of DNA are carriers of genetic information. This copy of *War and Peace* is carrier of the novel written by Tolstoy. This hard drive is carrier of these data items. *b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t* [072-ISO] is carrier of vaccine immunization for host vaccine immunization against microbe Type of tissue or cell/the source of the material. disease_ontology derives_from derives_from Type of tissue or cell/the source of the material. DO:lh x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y. uberon anteriorly_connected_to anteriorly connected to x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y. carries uberon channel_for channel for uberon channels_from channels_from uberon channels_into channels_into x is a conduit for y iff y passes through the lumen of x. uberon conduit_for conduit for x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y. uberon distally_connected_to distally connected to x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y. uberon existence_starts_and_ends_during existence starts and ends during uberon extends_fibers_into extends_fibers_into Relationship between a fluid and a material entity, where the fluid is the output of a realization of a filtration role that inheres in the material entity. uberon filtered_through Relationship between a fluid and a filtration barrier, where the portion of fluid arises as a transformation of another portion of fluid on the other side of the barrier, with larger particles removed filtered through a indirectly_supplies s iff a has a branch and the branch supplies or indirectly supplies s add to RO uberon indirectly_supplies indirectly_supplies x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y. uberon posteriorly_connected_to posteriorly connected to x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y. uberon protects protects x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y. uberon proximally_connected_to proximally connected to x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y. uberon subdivision_of placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B subdivision of . uberon transitively_anteriorly_connected_to transitively anteriorly connected to . uberon transitively_connected_to transitively_connected to . uberon transitively_distally_connected_to transitively distally connected to . . uberon transitively_proximally_connected_to transitively proximally connected to . has_disease_location has_disease_location entity entity 实体 Entity Entity 实体 entity 实体 Julius Caesar Verdi’s Requiem the Second World War your body mass index 你的身体质量指数 凯撒大帝 威尔第年代安魂曲 第二次世界大战 BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 BFO 2参考：在经验性总结分析的所有领域，我们遇到两种一般术语。首先是指共相或类型的一般术语：animaltuberculosissurgical proceduredisease其次，是用来指以下实例组的一般术语，这些实例组实例化一个给定共性但对应于该共相的任何子共相的扩展，因为没有实体的内在本质讨论因为他们-只有他们-被视为属于给定的群体。例子是：对斯德哥尔摩病人进行的周三手术过程中诊断出结核分枝杆菌而购买的动物，被确定为临床试验的候选人＃2056-555根据莱昂纳多·达·芬奇（Leonardo da Vinci）条款制定的656-PPV表格的签名人。这些术语代表所谓的“专业化'[81 Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf 实体不具有闭合公理，因为子类不一定丧失所有可能性。例如，Werner Ceusters的“现实的部分”包括4类，实体（当BFO构造它们时）、普遍性、配置和关系。这是一个开放性的问题，即在BFO中所解释的实体是否会在某个时候也包含这些其他的现实部分。参见，例如“如何完全追踪所有事物”在http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) 一个实体是存在或已经存在或将存在的任何事物。 （BFO2公理标签参考：[001-001]） entity entity 实体 Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf per discussion with Barry Smith An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) continuant continuant 常体 Continuant Continuant 常体 continuant 常体 An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. 一个在任何时候都存在的实体，它持续存在，在维持其特性的同时且没有暂时的部分。 BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 BFO 2参考：持续实体是可以被分割的实体，只能沿着空间维度分割成部分，例如产生您的桌子的部分，我们称之为它的腿、顶部、指甲。 “我的桌子从窗户延伸到门口。它有空间部分，可以在空间切成两半。不过，就时间而言，一个事物是连续的。“[60，p。 240 Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants 常体不具有闭合公理，因为子类不一定丧失所有可能性。例如，在涉及引入一些Ceuster的实体的其他部分的扩展中，提出了普遍性是否是连续性的问题 A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) 一个常体是一个持续、持久或持续存在且同时保持其身份的实体。 （BFO2中的公理标签参考：[008-002]） if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) 如果b是一个常体，并且如果对于某个t，c在t时刻具有_常体_部分b，则c是一个常体。 （BFO2公理标签参考：[126-001]） 如果b是一个常体，并且如果，对于某个t，c是在t时刻的b的常体_部分，则c是一个常体。 （BFO2公理标签参考：[009-002]） 如果b是物质实体，则在b存在期间有一些时间间隔（以下称为一维时间区域）。 （BFO2公理标签：[011-002]） (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] continuant continuant 常体 Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] occurrent Occurrent An entity that has temporal parts and that happens, unfolds or develops through time. BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] occurrent Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. per discussion with Barry Smith Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] ic IndependentContinuant a chair a heart a leg a molecule a spatial region an atom an orchestra. an organism the bottom right portion of a human torso the interior of your mouth A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] independent continuant 独立常体 b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] s-region SpatialRegion BFO 2 Reference: Spatial regions do not participate in processes. Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] spatial region Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. per discussion with Barry Smith A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] t-region TemporalRegion Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] temporal region Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional per discussion with Barry Smith A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] 2d-s-region TwoDimensionalSpatialRegion an infinitely thin plane in space. the surface of a sphere-shaped part of space A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] two-dimensional spatial region A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] st-region SpatiotemporalRegion the spatiotemporal region occupied by a human life the spatiotemporal region occupied by a process of cellular meiosis. the spatiotemporal region occupied by the development of a cancer tumor A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) Every spatiotemporal region occupies_spatiotemporal_region itself. Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] spatiotemporal region A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] process Process a process of cell-division, \ a beating of the heart a process of meiosis a process of sleeping the course of a disease the flight of a bird the life of an organism your process of aging. An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] bfo BFO:0000015 process process p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] realizable realizable 可实现的 RealizableEntity RealizableEntity 可实现实体(RealizableEntity) realizable entity 可实现实体 the disposition of this piece of metal to conduct electricity. the disposition of your blood to coagulate the function of your reproductive organs the role of being a doctor the role of this boundary to delineate where Utah and Colorado meet 作为医生的角色 你的生殖器官的功能 你的血液的凝结倾向 这个边界角色描绘了犹他州和科罗拉多州的交汇点 这块金属的导电倾向。 A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. 一个特定依赖性常体，在常体实体中存在，并且在每个实体或一组实体中都不会全部展现出来。可实现实体的展示或实现是在特定情况下发生的特定表现、功能或过程。 To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) 要说b是一个可实现实体，就是说b是一个特定依赖性常体，它存在于某些依赖常体中，这个连续体不是一个空间区域，而是一个在相关类型的过程中实现的类型实例。 （BFO2公理标签参考：[058-002]） All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) 所有可实现依赖常体都有独立常体，这些独立常体不是空间区域作为承载。 （BFO2公理标签参考：[060-002]） (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] realizable entity 可实现实体 To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] 0d-s-region ZeroDimensionalSpatialRegion A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] zero-dimensional spatial region A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] quality Quality the ambient temperature of this portion of air the color of a tomato the length of the circumference of your waist the mass of this piece of gold. the shape of your nose the shape of your nostril a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] bfo BFO:0000019 quality quality 性质 a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] sdc sdc SpecificallyDependentContinuant SpecificallyDependentContinuant 特定依赖性常体(SpecificallyDependentContinuant) specifically dependent continuant 特定依赖性常体 Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key of one-sided specifically dependent continuants: the mass of this tomato of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. the disposition of this fish to decay the function of this heart: to pump blood the mutual dependence of proton donors and acceptors in chemical reactions [79 the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction the pink color of a medium rare piece of grilled filet mignon at its center the role of being a doctor the shape of this hole. the smell of this portion of mozzarella 交互特定依赖性常体：这个键的功能打开这个锁和这个锁的相互依赖的配置：被这个键打开 作为医生的角色 关系独立常体（对个载体）：约翰对玛丽的爱，约翰与这座雕像之间的所有关系，以及约翰与他的下属之间的权力关系。 在它中心的一块四分熟烤菲力牛排的粉色 局部特定依赖性常体：这个番茄的性质 捕食者角色和猎物角色的相互依赖由两个生物体在给定的相互作用中扮演 质子供体和受体在化学反应中的相互依赖[79 这个洞的形状。 这条鱼的腐烂倾向 这部分马苏里拉奶酪的气味 这颗心的功能：抽血 A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) b是一个关系特定依赖性常体 = Def. b是特定依赖性常体并且有n &gt;1个独立常体c1，... cn不是空间区域且是这样的，即对于全部1个 i&lt;j n，ci和cj没有共同的部分，对于每个1 i n，在b存在的过程中每个时间t，b s-依赖_于 ci（BFO2中的公理标号：[131-004]） b是一个特定依赖性常体 = Def. b是一个常体& 存在一些独立常体c，c不是一个空间区域且是这样的，在b的存在过程地每个时间t，b s-依赖_于c。 （BFO2公理标签参考：[050-003]） 一个在其他实体中存在或由其他实体承担的常体。 A的每个实例都需要一些特定的B实例，这些B实例必须始终相同。 Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. 具体而言，相关常体不具有闭合公理，因为子类不一定丧失所有可能性。我们不确定在这里会发生什么，但是会有如什么是承诺，义务等等的问题。 (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] specifically dependent continuant 特定依赖性常体 b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. per discussion with Barry Smith (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] role Role John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. the priest role the role of a boundary to demarcate two neighboring administrative territories the role of a building in serving as a military target the role of a stone in marking a property boundary the role of subject in a clinical trial the student role A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] role 角色 b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] fiat-object fiat-object-part FiatObjectPart or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29 the FMA:regional parts of an intact human body. the Western hemisphere of the Earth the division of the brain into regions the division of the planet into hemispheres the dorsal and ventral surfaces of the body the upper and lower lobes of the left lung BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] bfo BFO:0000024 fiat object fiat object part fiat object part b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] 1d-s-region OneDimensionalSpatialRegion an edge of a cube-shaped portion of space. A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] one-dimensional spatial region A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] object-aggregate ObjectAggregate a collection of cells in a blood biobank. a swarm of bees is an aggregate of members who are linked together through natural bonds a symphony orchestra an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team) defined by fiat: the aggregate of members of an organization defined through physical attachment: the aggregate of atoms in a lump of granite defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container defined via attributive delimitations such as: the patients in this hospital the aggregate of bearings in a constant velocity axle joint the aggregate of blood cells in your body the nitrogen atoms in the atmosphere the restaurants in Palo Alto your collection of Meissen ceramic plates. An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee). ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] object aggregate An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] 3d-s-region ThreeDimensionalSpatialRegion a cube-shaped region of space a sphere-shaped region of space, A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] three-dimensional spatial region A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] site Site Manhattan Canyon) a hole in the interior of a portion of cheese a rabbit hole an air traffic control region defined in the airspace above an airport the Grand Canyon the Piazza San Marco the cockpit of an aircraft the hold of a ship the interior of a kangaroo pouch the interior of the trunk of your car the interior of your bedroom the interior of your office the interior of your refrigerator the lumen of your gut your left nostril (a fiat part – the opening – of your left nasal cavity) b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] site b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] object Object atom cell cells and organisms engineered artifacts grain of sand molecule organelle organism planet solid portions of matter star BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting. BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below). BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47 BFO 2 Reference: an object is a maximal causally unified material entity BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74 b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) bfo BFO:0000030 object object b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) gdc GenericallyDependentContinuant The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. the pdf file on your laptop, the pdf file that is a copy thereof on my laptop the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] generically dependent continuant 普遍依赖性常体 b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] function Function the function of a hammer to drive in nails the function of a heart pacemaker to regulate the beating of a heart through electricity the function of amylase in saliva to break down starch into sugar BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] function A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] p-boundary ProcessBoundary the boundary between the 2nd and 3rd year of your life. p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] process boundary p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] 1d-t-region OneDimensionalTemporalRegion the temporal region during which a process occurs. BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks). A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] one-dimensional temporal region A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] material MaterialEntity a flame a forest fire a human being a hurricane a photon a puff of smoke a sea wave a tornado an aggregate of human beings. an energy wave an epidemic the undetached arm of a human being An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] bfo BFO:0000040 material entity material entity A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] cf-boundary ContinuantFiatBoundary b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions. BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29 Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. Every continuant fiat boundary is located at some spatial region at every time at which it exists (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] continuant fiat boundary b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] immaterial ImmaterialEntity BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10 immaterial entity 1d-cf-boundary OneDimensionalContinuantFiatBoundary The Equator all geopolitical boundaries all lines of latitude and longitude the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin. the median sulcus of your tongue a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] one-dimensional continuant fiat boundary a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] process-profile ProcessProfile On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance. The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on. b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] process profile b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] 2 r-quality RelationalQuality John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. a marriage bond, an instance of love, an obligation between one person and another. a marriage bond, an instance of requited love, an obligation between one person and another. b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] relational quality 2 b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] 2d-cf-boundary TwoDimensionalContinuantFiatBoundary a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] two-dimensional continuant fiat boundary a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] 0d-cf-boundary ZeroDimensionalContinuantFiatBoundary the geographic North Pole the point of origin of some spatial coordinate system. the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] zero-dimensional continuant fiat boundary zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. requested by Melanie Courtot a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] 0d-t-region ZeroDimensionalTemporalRegion a temporal region that is occupied by a process boundary right now the moment at which a child is born the moment at which a finger is detached in an industrial accident the moment of death. temporal instant. A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] zero-dimensional temporal region A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] history History A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) history A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) anatomical entity connected anatomical structure material anatomical entity immaterial anatomical entity multi-cell-part structure neuron projection bundle multicellular anatomical structure biological entity molecular entity Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well molecular entity chebi_ontology entidad molecular entidades moleculares entite moleculaire molecular entities molekulare Entitaet CHEBI:23367 molecular entity Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. fake:2 molecular entity IUPAC entidad molecular IUPAC entidades moleculares IUPAC entite moleculaire IUPAC molecular entities IUPAC molekulare Entitaet ChEBI A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances. chemical entity chebi_ontology CHEBI:24431 chemical entity chemical entity UniProt a maintaining cell culture process that keeps cell line cell alive and actively cultured. a maintaining cell culture process that keeps cell line cell alive and actively cultured. 维持细胞株存活和活跃培养的细胞培养过程。 YH YH cell line cell culturing cell line cell culturing 细胞系细胞培养 cell line cell cell line cell 细胞系细胞 A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture 一个培养细胞，它是一个细胞株（一个稳定的，同质的细胞群，具有共同的生物学起源和增殖史）的一部分 一个培养细胞，它是一个细胞株（一个稳定的，同质的细胞群，具有共同的生物学起源和增殖史）的一部分 Yongqun He, Matthew Brush, Sirarat Sarntivijai, Alexander Diehl, Jie Zheng, Yu Lin, Bjoern Peters Yongqun He, Matthew Brush, Sirarat Sarntivijai, Alexander Diehl, Jie Zheng, Yu Lin, Bjoern Peters A 'cell line cell' is a part of a cell line established through the passaging/selection of a primary cultured cells or the experimental modification of an existing cell line. New types of cell line cells are established after sufficient passaging of a primary culture to establish a stable and homogenous population that qualifies as a line (typically 1-20 passages), or following some spontaneous or experimental modification that confers novel characteristics to an existing line. A cell line cell typically has mutations of five or more genes compared to the original cell that derives the cell line cell. Some gene mutations may turn on some oncogenes. Cell line cells can be in active culture, stored in a quiescent state for future use (e.g. frozen in liquid nitrogen), or applied in experimental procedures. A 'cell line cell' is a part of a cell line established through the passaging/selection of a primary cultured cells or the experimental modification of an existing cell line. New types of cell line cells are established after sufficient passaging of a primary culture to establish a stable and homogenous population that qualifies as a line (typically 1-20 passages), or following some spontaneous or experimental modification that confers novel characteristics to an existing line. A cell line cell typically has mutations of five or more genes compared to the original cell that derives the cell line cell. Some gene mutations may turn on some oncogenes. Cell line cells can be in active culture, stored in a quiescent state for future use (e.g. frozen in liquid nitrogen), or applied in experimental procedures. “细胞系细胞”是通过原代培养细胞的传代/选择或现有细胞系的实验性修饰而建立的细胞系的一部分。新类型的细胞系细胞的建立过程是原代培养物充分传代后以建立符合条件（典型地1-20代）的稳定且同质的群体，或者在某些自发或实验性修饰之后赋予现有细胞系新的特征。与产生细胞系细胞的原始细胞相比，细胞系细胞通常具有5个或更多个基因的突变。 一些基因突变可能会开启一些致癌基因。 细胞系细胞可处于活性培养物中，以静止状态储存以供将来使用（例如在液氮中冷冻），或者在实验程序使用。 cell line cell cell line cell 细胞系细胞 suspension cell line culturing is a cell line culturing method where cells do not require a surface for growth and differentiation. This method is appropriate for cells that are adapted to suspension culture or cells that are non-adhesive (e.g. hematopoietic cells) suspension cell line culturing is a cell line culturing method where cells do not require a surface for growth and differentiation. This method is appropriate for cells that are adapted to suspension culture or cells that are non-adhesive (e.g. hematopoietic cells) 悬浮细胞系培养是其中细胞不需要生长和分化表面的细胞系培养方法。 该方法适用于适合悬浮培养的细胞或非贴壁细胞（如造血细胞） suspension cell line culturing suspension cell line culturing 悬浮细胞培养 adherent cell line culturing is a cell line culturing method where cells require a surface for growth and differentiation. adherent cell line culturing is a cell line culturing method where cells require a surface for growth and differentiation. 贴壁细胞系培养是一种细胞系培养方法，其中细胞需要一个表面进行生长和分化。 adherent cell line culturing adherent cell line culturing 贴壁细胞系培养 a role that inheres in a cell line repository organization. a role that inheres in a cell line repository organization. 一个细胞系资源组织中所起的作用 SS, YH SS, YH cell line repository role cell line repository role 细胞库角色 an organization that serves as a repository of cell lines. an organization that serves as a repository of cell lines. 一个作为细胞系存储库的组织。 SS, YH SS, YH cell line repository cell line repository 细胞库 adherent on coated surface cell line culturing is an adherent cell line culturing method that the surface is coated with extracellular matrix component to increase adhesion properties and provide other signals needed for growth and differentiation. adherent on coated surface cell line culturing adherent on feeder cells cell line culturing adherent on feeder cells cell line culturing 在饲养细胞上贴壁培养细胞系 adherent-patchy cell line culturing adherent-patchy cell line culturing 贴壁斑片状细胞培养 loosely adherent cell line culturing loosely adherent cell line culturing 松散贴壁细胞培养 immortal cell line cell immortal cell line cell 永生细胞系细胞 A cell line cell that is expected to be capable of an unlimited number of divisions, and is thus able to support indefinite propagation in vitro as part of an immortal cell line. A cell line cell that is expected to be capable of an unlimited number of divisions, and is thus able to support indefinite propagation in vitro as part of an immortal cell line. 预期能够进行无限次分裂的细胞系细胞，作为永生细胞系一部分，能够支持体外无限增殖。 Yongqun He, Matthew Brush, Allen Xiang, Asiyah Yu Lin, Sirarat Sarntivijai, James Malone, Jie Zheng, Tomasz Adamusiak Yongqun He, Matthew Brush, Allen Xiang, Asiyah Yu Lin, Sirarat Sarntivijai, James Malone, Jie Zheng, Tomasz Adamusiak continuous cell line cell continuous cell line cell permanent cell line cell permanent cell line cell 永久细胞系细胞 连续细胞系细胞 immortal cell line cell immortal cell line cell 永生细胞系细胞 a cell culture growth mode that indicates a cell needs to adhere to a cell culture plate to grow. a cell culture growth mode that indicates a cell needs to adhere to a cell culture plate to grow. 一种细胞培养生长模式：细胞需要粘附在细胞培养板上生长 YH YH adherent cell culture growth mode adherent cell culture growth mode 贴壁细胞培养生长模式 a cell culture growth mode that indicates a cell can grow when the cell is suspended in cell culture medium. a cell culture growth mode that indicates a cell can grow when the cell is suspended in cell culture medium. 一种细胞培养生长模式：当细胞悬浮在细胞培养基中时，细胞可以生长 YH YH suspension cell culture growth mode suspension cell culture growth mode 悬浮细胞培养生长模式 a disposition that represents a mode of cell culture growth, i.e., the cell will grow at a specific cell culture mode. For example, an adherent cell culture growh mode means that the cell will grow when the cell is adhere to a cell culture plate. a disposition that represents a mode of cell culture growth, i.e., the cell will grow at a specific cell culture mode. For example, an adherent cell culture growh mode means that the cell will grow when the cell is adhere to a cell culture plate. 一种代表细胞培养生长模式的配置，即细胞将以特定细胞培养模式生长。 例如，贴壁细胞培养生长模式意味着当细胞粘附于细胞培养板时细胞将生长。 YH YH cell culture growth mode cell culture growth mode 细胞培养生长模式 cell line A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture). A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture). cell line 细胞系 mixed adherent and suspension cell line culturing mixed adherent and suspension cell line culturing 混合贴壁悬浮细胞培养 mixed suspension clusters in suspension cell line culturing clusters in suspension cell line culturing 在悬浮细胞系培养中的成簇细胞 suspension with feeder cells cell line culturing suspension-multicell aggregates cell line culturing a immortal cell line that is dervied from mouse tissue. a immortal cell line that is dervied from mouse tissue. 从老鼠组织中得到的一种永生细胞系。 Yue Liu, Yongqun He Yue Liu, Yongqun He immortal mouse cell line 永生的小鼠细胞系 immortal mouse cell line cell immortal mouse cell line cell 永生的小鼠细胞系细胞 YH a immortal cell line that is dervied from mouse macrophage. immortal mouse macrophage cell line a cell line that is derived from motile cell a cell line that is derived from motile cell 源自运动细胞的细胞系 ZX, YH ZX, YH immortal motile cell line immortal motile cell line 永生的游动细胞系 immortal motile cell line cell immortal motile cell line cell 永生的游动细胞系细胞 a immortal motile cell line that is derived from leukocyte a immortal motile cell line that is derived from leukocyte 源自白细胞的永生游动细胞系 ZX, YH ZX, YH immortal leukocyte cell line immortal leukocyte cell line 永生的白细胞系 immortal leukocyte cell line cell immortal leukocyte cell line cell 永生的白细胞系细胞 a immortal leukocyte cell line that is derived from myeloid leukocyte a immortal leukocyte cell line that is derived from myeloid leukocyte 源自髓系白细胞的永生白细胞系 ZX, YH ZX, YH immortal myeloid leukocyte cell line immortal myeloid leukocyte cell line 永生的髓样白血球细胞系 immortal myeloid leukocyte cell line cell immortal myeloid leukocyte cell line cell 永生的髓样白血球细胞系细胞 a immortal myeloid leukocyte cell line that is derived from monocyte a immortal myeloid leukocyte cell line that is derived from monocyte 源自单核细胞的永生髓系白细胞系 ZX, YH ZX, YH immortal monocyte cell line immortal monocyte cell line 永生的单核细胞系 immortal monocyte cell line cell immortal monocyte cell line cell 永生的单核细胞系细胞 a immortal leukocyte cell line that is derived from nongranular leukocyte a immortal leukocyte cell line that is derived from nongranular leukocyte 源自无粒白细胞的永生白细胞细胞系 ZX, YH ZX, YH immortal nongranular leukocyte cell line immortal nongranular leukocyte cell line 永生的无颗粒白细胞细胞系 immortal nongranular leukocyte cell line cell immortal nongranular leukocyte cell line cell 永生的无颗粒白细胞细胞系细胞 a immortal cell line cell that is derived from eukaryotic cell a immortal cell line cell that is derived from eukaryotic cell 源自真核细胞的永生细胞系细胞 ZX, YH ZX, YH immortal eukaryotic cell line cell immortal eukaryotic cell line cell 永生的真核细胞系细胞 a immortal eukaryotic cell line that is derived from animal cell a immortal eukaryotic cell line that is derived from animal cell 源自动物细胞的永生真核细胞系 ZX, YH ZX, YH immortal animal cell line immortal animal cell line 永生的动物细胞系 immortal animal cell line cell immortal animal cell line cell 永生的动物细胞系细胞 a immortal animal cell line that is derived from epithelial cell a immortal animal cell line that is derived from epithelial cell 源自上皮细胞的永生动物细胞系 ZX, YH ZX, YH immortal epithelial cell line cell immortal epithelial cell line cell 永生的上皮细胞系细胞 a immortal animal cell line that is derived from hematopoietic cell a immortal animal cell line that is derived from hematopoietic cell 源自造血细胞的永生动物细胞系 ZX, YH ZX, YH immortal hematopoietic cell line immortal hematopoietic cell line 永生的造血细胞系 immortal hematopoietic cell line cell immortal hematopoietic cell line cell 永生的造血细胞系细胞 a immortal hematopoietic cell line that is derived from myeloid cell a immortal hematopoietic cell line that is derived from myeloid cell 源自骨髓细胞的永生造血细胞系 ZX, YH ZX, YH immortal myeloid cell line immortal myeloid cell line 永生的骨髓细胞系 immortal myeloid cell line cell immortal myeloid cell line cell 永生的骨髓细胞系细胞 a cell line that is derived from somatic cell a cell line that is derived from somatic cell 源自体细胞的细胞系 ZX, YH ZX, YH immortal somatic cell line cell immortal somatic cell line cell 永生的体细胞系细胞 An immortal cell line cell that derives from pair of lungs. An immortal cell line cell that derives from pair of lungs. 源自一对肺的永生细胞系细胞。 Yue Liu, Yongqun He Yue Liu, Yongqun He immortal lung-derived cell line cell immortal lung-derived cell line cell 永生化的肺衍生细胞系细胞 An immortal cell line cell that derives from kidney. An immortal cell line cell that derives from kidney. 源自肾的永生细胞系细胞。 Yue Liu, Yongqun He Yue Liu, Yongqun He immortal kidney-derived cell line cell immortal kidney-derived cell line cell 永生化的肾衍生细胞系细胞 An immortal cell line cell that derives from colon. An immortal cell line cell that derives from colon. 源自结肠的永生细胞系细胞。 Yue Liu, Yongqun He Yue Liu, Yongqun He immortal colon-derived cell line cell immortal colon-derived cell line cell 永生的结肠衍生细胞系细胞 An immortal cell line cell that derives from female gonad. An immortal cell line cell that derives from female gonad. 源自雌性性腺的永生细胞系细胞。 Yue Liu, Yongqun He Yue Liu, Yongqun He immortal female gonad-derived cell line cell immortal female gonad-derived cell line cell 永生的雌性性腺衍生细胞系细胞 An immortal cell line cell that derives from stomach. An immortal cell line cell that derives from stomach. 源自胃的永生细胞系细胞。 Yue Liu, Yongqun He Yue Liu, Yongqun He immortal stomach-derived cell line cell immortal stomach-derived cell line cell 永生化的胃衍生细胞系细胞 An immortal epithelial cell line cell that derives from uterine cervix. An immortal epithelial cell line cell that derives from uterine cervix. 源自子宫颈的永生上皮细胞系细胞。 Yue Liu, Yongqun He Yue Liu, Yongqun He immortal uterine cervix-derived epithelial cell line cell immortal uterine cervix-derived epithelial cell line cell 永生的宫颈衍生上皮细胞系细胞 An immortal lung-derived cell line cell that derives from human. An immortal lung-derived cell line cell that derives from human. 源自人的永生肺衍生细胞系细胞。 Yue Liu, Yongqun He Yue Liu, Yongqun He immortal human lung-derived cell line cell immortal human lung-derived cell line cell 永生的人肺衍生细胞系细胞 An immortal cell line cell that derives from human. An immortal cell line cell that derives from human. 源自人的永生细胞系细胞。 Yue Liu, Yongqun He Yue Liu, Yongqun He immortal human cell line cell immortal human cell line cell 永生的人细胞系细胞 An immortal colon-derived cell line cell that derives from human. An immortal colon-derived cell line cell that derives from human. 源自人的永生结肠衍生细胞系细胞。 Yue Liu, Yongqun He Yue Liu, Yongqun He immortal human colon-derived cell line cell immortal human colon-derived cell line cell 永生化的人结肠衍生细胞系细胞 An immortal kidney-derived cell line cell that derives from vervet monkey. An immortal kidney-derived cell line cell that derives from vervet monkey. 源自黑长尾猴的永生肾衍生细胞系细胞。 Yue Liu, Yongqun He Yue Liu, Yongqun He immortal vervet monkey kidney-derived cell line cell immortal vervet monkey kidney-derived cell line cell 永生的黑长尾猴肾衍生细胞系细胞 An immortal stomach-derived cell line cell that derives from human. An immortal stomach-derived cell line cell that derives from human. 源自人的永生胃衍生细胞系细胞。 Yue Liu, Yongqun He Yue Liu, Yongqun He immortal human stomach-derived cell line cell immortal human stomach-derived cell line cell 永生的人胃衍生细胞系细胞 An immortal epithelial cell line cell that derives from human. An immortal epithelial cell line cell that derives from human. 源自人的永生上皮细胞系细胞。 Yue Liu, Yongqun He Yue Liu, Yongqun He immortal human epithelial cell line cell immortal human epithelial cell line cell 永生的人上皮细胞系细胞 An immortal uterine cervix-derived epithelial cell line cell that derives from human. An immortal uterine cervix-derived epithelial cell line cell that derives from human. 源自人的永生子宫颈衍生上皮细胞系细胞。 Yue Liu, Yongqun He Yue Liu, Yongqun He immortal human uterine cervix-derived epithelial cell line cell immortal human uterine cervix-derived epithelial cell line cell 永生的人宫颈衍生上皮细胞系细胞 An immortal monocyte cell line cell that derives from human. An immortal monocyte cell line cell that derives from human. 源自人的永生单核细胞系细胞。 Yue Liu, Yongqun He Yue Liu, Yongqun He immortal human monocyte cell line cell immortal human monocyte cell line cell 永生的人单核细胞系细胞 LCL-1601 LCL-1601 A549 A549 A549 cell A549 cell A549 细胞 ATCC: CCL-185 ATCC: CCL-185 CHEMBL: CHEMBL3307651 CHEMBL: CHEMBL3307651 CVCL: CVCL_0023 CVCL: CVCL_0023 EFO: EFO_0001086 EFO: EFO_0001086 HyperCLDB: cl207 HyperCLDB: cl207 LCL-1893 LCL-1893 AGS AGS AGS cell AGS cell AGS 细胞 ATCC: CRL-1739 ATCC: CRL-1739 CHEMBL: CHEMBL3308078 CHEMBL: CHEMBL3308078 CVCL: CVCL_0139 CVCL: CVCL_0139 EFO: EFO_0002109 EFO: EFO_0002109 LCL-1170 LCL-1170 Caco-2 Caco-2 disease: colorectal adenocarcinoma disease: colorectal adenocarcinoma 疾病：结肠直肠腺癌 Caco-2 cell Caco-2 cell Caco-2 细胞 ATCC: HTB-37 ATCC: HTB-37 CHEMBL: CHEMBL3307519 CHEMBL: CHEMBL3307519 CVCL: CVCL_0025 CVCL: CVCL_0025 EFO: EFO_0001099 EFO: EFO_0001099 HyperCLDB: cl618 HyperCLDB: cl618 MeSH: D018938 MeSH: D018938 CHO CHO Chinese Hamster Ovary cell Chinese Hamster Ovary cell 中国仓鼠卵巢细胞 CHO cell CHO cell CHO 细胞 HyperCLDB: cl721 HyperCLDB: cl721 MeSH: D016466 MeSH: D016466 LCL-1226 Detroit 562 https://www.atcc.org/products/all/CCL-138.aspx disease: carcinoma (pharynx primary) Detroit 562 cell ATCC: CCL-138 CHEMBL: CHEMBL3308486 CVCL: CVCL_1171 ECACC: 87042205 EFO: EFO_0002170 LCL-1512 LCL-1512 HeLa HeLa WEB: http://en.wikipedia.org/wiki/HeLa WEB: http://en.wikipedia.org/wiki/HeLa WEB: http://www.atcc.org/products/all/CCL-2.aspx WEB: http://www.atcc.org/products/all/CCL-2.aspx WEB: https://www.ncbi.nlm.nih.gov/pubmed/12001993 WEB: https://www.ncbi.nlm.nih.gov/pubmed/12001993 1951年2月8日从一位于1951年10月4日因癌症死亡的病人Henrietta Lacks中获取的宫颈腺癌癌细胞衍生的永生人类子宫颈衍生上皮细胞系。 an immortal human uterine cervix-derived epithelial cell line that was derived from cervical adenocarcinoma cancer cells taken on February 8, 1951 from Henrietta Lacks, a patient who died of her cancer on October 4, 1951. an immortal human uterine cervix-derived epithelial cell line that was derived from cervical adenocarcinoma cancer cells taken on February 8, 1951 from Henrietta Lacks, a patient who died of her cancer on October 4, 1951. HeLa cell HeLa cell HeLa 细胞 ATCC: CCL-2 ATCC: CCL-2 CHEMBL: CHEMBL3308376 CHEMBL: CHEMBL3308376 EFO: EFO_0001185 EFO: EFO_0001185 HyperCLDB: cl1601 HyperCLDB: cl1601 MeSH: D006367 MeSH: D006367 RRID:CVCL_0030 RRID:CVCL_0030 HEp-2 HEp-2 cell ATCC: CCL-23 INT 407 INT 407 cell HyperCLDB: cl2897 J774A.1 J774A.1 J 774A.1 J774A.1 cell J774A.1 cell J774A.1 细胞 ATCC: TIB-67 ATCC: TIB-67 HyperCLDB: cl2928 HyperCLDB: cl2928 LS 174T LS 174T disease: colorectal adenocarcinoma disease: colorectal adenocarcinoma 疾病：大肠腺癌 LS 174T cell LS 174T cell LS 174T 细胞 ATCC: CL-188 ATCC: CL-188 NCI-H292 NCI-H292 disease: mucoepidermoid pulmonary carcinoma disease: mucoepidermoid pulmonary carcinoma 疾病：黏液表皮样肺癌 NCI-H292 cell NCI-H292 cell NCI-H292 细胞 ATCC: CRL-1848 ATCC: CRL-1848 LCL-1072 LCL-1072 THP-1 THP-1 THP1 THP1 THP-1 cell THP-1 cell THP-1 细胞 ATCC: TIB-202 ATCC: TIB-202 CHEMBL: CHEMBL3307574 CHEMBL: CHEMBL3307574 CVCL: CVCL_0006 CVCL: CVCL_0006 EFO: EFO_0001253 EFO: EFO_0001253 HyperCLDB: cl4514 HyperCLDB: cl4514 Vero Vero Vero cell Vero cell Vero 细胞 ATCC: CCL-81 ATCC: CCL-81 HyperCLDB: cl4644 HyperCLDB: cl4644 MeSH: D014709 MeSH: D014709 LCL-1601 A immortal human cell line cell that has the characteristics: Lung carcinoma, refer to ATCC CCL185 RIKEN Cell bank Team Yongqun He A549 RCB0098 Derived from tissue: lung in animal: human. Originator: Giard, D. J. Register: Abe, Shin-ichiro RCB0098 cell ATCC: CCL-185 cell cell PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .." A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. CALOHA:TS-2035 FMA:68646 GO:0005623 KUPO:0000002 VHOG:0001533 WBbt:0004017 XAO:0003012 cell The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). cell cell cell type cell type 细胞 细胞类型 primary cultured cell A cultured cell that is freshly isolated from a organismal source, or derives in culture from such a cell prior to the culture being passaged. primary cultured cell primary cultured cell 原代培养细胞 native cell A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment). CARO:0000013 cell in vivo cell To accommodate unicellular organisms better, 'cell in vivo' has been re-labeled 'native cell' to better represent its intended meaning - that is, that it is a cell in the context of a multicellular organism or in a natural environment. 'Native' is intended to contrast with 'in vitro', which refers to cells or other biological entities that have been intentionally placed in a controlled, non-natural setting for the purpose of study or manipulation. (MAH 1.12.12). native cell cultured cell A cell in vitro that is or has been maintained or propagated as part of a cell culture. cell Note that this class was re-labeled to 'cultured cell' instead of 'cell line cell', as it intent was clarified to cover any cultured cells of multicellular and unicellular organisms. This includes cells actively being cultured, or cells that have been cultured but are stored in a quiescent state for future use. In having been cultured, cells must establish homeostasis and often replicate in a foreign environment. Accomodation of this stress initiates a selection of cells fit for such challenges, wherein necessary adaptive biochemical and.or genetic changes can occur. These changes can set them apart from the in vivo cells from which they derive, and such changes will typically accumulate and change over increasing time in culture. cultured cell epithelial cell A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina. BTO:0000414 CALOHA:TS-2026 CARO:0000077 FBbt:00000124 FMA:66768 WBbt:0003672 epitheliocyte cell epithelial cell epithelial cell 上皮细胞 A cell found predominately in the blood. FMA:62844 cell blood cell blood cell 血细胞 An endothelial cell comprises the outermost layer or lining of anatomical structures and can be squamous or cuboidal. In mammals, endothelial cell has vimentin filaments and is derived from the mesoderm. BTO:0001176 CALOHA:TS-0278 FMA:66772 endotheliocyte cell From FMA: 9.07.2001: Endothelial cell has always been classified as a kind of epithelial cell, specifically a squamous cell but that is not true. First, endothelial cell can either be squamous or cuboidal (e.g. high-endothelial cell) and secondly, it has different embryological derivation (mesodermal) than a true epithelial cell (ectodermal and endodermal). The basis for present classification is the fact that it comprises the outermost layer or lining of anatomical structures (location-based) but a better structural basis for the differentia is the cytoskeleton of the cell. Endothelial cell has vimentin filaments while an epithelial cell has keratin filaments. [Onard]. endothelial cell A cell that moves by its own activities. cell motile cell motile cell 游动细胞 macrophage A mononuclear phagocyte present in variety of tissues, typically differentiated from monocytes, capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells. BTO:0000801 CALOHA:TS-0587 FMA:63261 FMA:83585 histiocyte cell Morphology: Diameter 30_M-80 _M, abundant cytoplasm, low N/C ratio, eccentric nucleus. Irregular shape with pseudopods, highly adhesive. Contain vacuoles and phagosomes, may contain azurophilic granules; markers: Mouse & Human: CD68, in most cases CD11b. Mouse: in most cases F4/80+; role or process: immune, antigen presentation, & tissue remodelling; lineage: hematopoietic, myeloid. macrophage macrophage 巨噬细胞 B cell A lymphocyte of B lineage with the phenotype CD19-positive, CD20-positive, and capable of B cell mediated immunity. B cell cell eukaryotic cell eukaryotic cell 真核细胞 lymphocyte A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin. BTO:0000775 CALOHA:TS-0583 FMA:62863 VHOG:0001535 cell Editors note: consider adding taxon constraint to vertebrata (PMID:18025161) lymphocyte cell animal cell animal cell 动物细胞 Myeloid mononuclear recirculating leukocyte that can act as a precursor of tissue macrophages, osteoclasts and some populations of tissue dendritic cells. BTO:0000876 CALOHA:TS-0638 FMA:62864 cell Morphology: Mononuclear cell, diameter, 14 to 20 _M, N/C ratio 2:1-1:1. Nucleus may appear in variety of shapes: round, kidney, lobulated, or convoluted. Fine azurophilic granules present; markers: CD11b (shared with other myeloid cells), human: CD14, mouse: F4/80-mid,GR1-low; location: Blood, but can be recruited into tissues; role or process: immune & tissue remodelling; lineage: hematopoietic, myeloid. monocyte monocyte 单核细胞 experimentally modified cell in vitro A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure. experimentally modified cell in vitro An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue. BTO:0000751 CALOHA:TS-0549 FMA:62852 immune cell leucocyte white blood cell cell leukocyte leukocyte 白血球 A cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage. BTO:0001441 CALOHA:TS-0647 cell myeloid cell myeloid cell 骨髓细胞 A cell of the monocyte, granulocyte, or mast cell lineage. cell myeloid leukocyte myeloid leukocyte 骨髓白细胞 mononuclear cell A leukocyte with a single non-segmented nucleus in the mature form. mononuclear cell A cell of a hematopoietic lineage. BTO:0000574 CALOHA:TS-2017 FMA:70366 FMA:83598 haematopoietic cell haemopoietic cell hemopoietic cell cell hematopoietic cell hematopoietic cell 造血干细胞 A leukocyte that lacks granules. tmeehan 2010-07-22T11:30:33Z FMA:62855 agranular leukocyte cell nongranular leukocyte nongranular leukocyte 无颗粒白细胞 An epithelial cell of the bronchus. tmeehan 2010-09-20T02:00:00Z BTO:0002922 cell bronchial epithelial cell A large nucleated basophilic erythrocyte found in mammalian embryos. This cell type arises from the blood islands of yolk sacs and expresses different types of hemoglobins (beta-H1, gamma-1 and zeta) than adult erythrocytes. Considered a type of erythroblast as this cell type can enucleate in circulation. tmeehan 2010-09-22T09:27:05Z primitive erythroblast primitive erythrocyte primitive erythroid cell cell primitive red blood cell A cell of an organism that does not pass on its genetic material to the organism's offspring (i.e. a non-germ line cell). tmeehan 2010-09-24T09:44:42Z BTO:0001268 FMA:72300 WBbt:0008378 cell somatic cell somatic cell 体细胞 An epithelial cell of the intestine. tmeehan 2011-03-01T05:18:31Z cell intestinal epithelial cell Cell of the nasopharyngeal epithelium. CALOHA:TS-2398 nasopharynx respiratory epithelial cells nasopharyngeal epithelial cell Any blood vessel endothelial cell that is part of a microvascular endothelium. TermGenie 2014-06-04T15:07:42Z cell CL:2000008 microvascular endothelial cell A nervous system disease which is located in a part of the nervous system responsible for processing sensory information that consists of sensory receptors, neural pathways, and parts of the brain involved in sensory perception. Commonly recognized sensory systems are those for vision, hearing, somatic sensation (touch), taste and olfaction (smell). disease_ontology DOID:0050155 sensory system disease A nervous system disease which is located in a part of the nervous system responsible for processing sensory information that consists of sensory receptors, neural pathways, and parts of the brain involved in sensory perception. Commonly recognized sensory systems are those for vision, hearing, somatic sensation (touch), taste and olfaction (smell). url:http://en.wikipedia.org/wiki/Sensory_system A respiratory system disease which involves the lower respiratory tract. ICD9CM:478.1 ICD9CM:478.19 UMLS_CUI:C0029581 disease_ontology DOID:0050161 lower respiratory tract disease A respiratory system disease which involves the lower respiratory tract. url:http://en.wikipedia.org/wiki/lower_respiratory_tract An organ system cancer located_in the respiratory system that is characterized by uncontrolled cellular proliferation in the respiratory tract. disease_ontology DOID:0050615 respiratory system cancer An organ system cancer located_in the respiratory system that is characterized by uncontrolled cellular proliferation in the respiratory tract. url:http://en.wikipedia.org/wiki/Respiratory_tract_neoplasm A cancer that is classified based on the organ it starts in. snadendla 2011-06-13T03:28:33Z MESH:D009371 disease_ontology DOID:0050686 organ system cancer A cancer that is classified based on the organ it starts in. url:http://cancerguide.org/basic.html A cancer that is classified by the type of cell from which it is derived. snadendla 2011-06-13T03:28:50Z disease_ontology DOID:0050687 cell type cancer A cancer that is classified by the type of cell from which it is derived. url:http://cancerguide.org/basic.html url:http://en.wikipedia.org/wiki/Cancer A large intestine cancer that is located_in the terminal part of the large intestine. snadendla 2011-06-14T01:34:36Z disease_ontology DOID:0050688 anal canal cancer A large intestine cancer that is located_in the terminal part of the large intestine. url:http://en.wikipedia.org/wiki/Anal_canal An eye and adnexa disease that is located_in the adnexa of the eye. lschriml 2013-12-05T12:55:42Z disease_ontology DOID:0050815 eye adnexa disease An eye and adnexa disease that is located_in the adnexa of the eye. url:http://en.wikipedia.org/wiki/Accessory_visual_structures A heart disease that is located_in the innermost layer of tissue that lines the chambers of the heart. lschriml 2014-02-12T01:53:42Z disease_ontology DOID:0050825 endocardium disease A heart disease that is located_in the innermost layer of tissue that lines the chambers of the heart. url:http://en.wikipedia.org/wiki/Endocardium url:http://people.upei.ca/lmiller/2009_CV_Endocardial_Pathology/ENDOCARDIUM-2009.pdf A vascular disease that is located_in an artery. lschriml 2014-02-12T03:08:35Z disease_ontology DOID:0050828 artery disease A vascular disease that is located_in an artery. url:http://en.wikipedia.org/wiki/Artery#Pathology An organ system cancer located_in the muscular and skeletal organs and characterized by uncontrolled cellular proliferation of the musculoskeletal organs. lschriml 2011-07-15T02:30:51Z DOID:0060124 skeletal system cancer disease_ontology DOID:0060100 musculoskeletal system cancer An organ system cancer located_in the muscular and skeletal organs and characterized by uncontrolled cellular proliferation of the musculoskeletal organs. url:http://en.wikipedia.org/wiki/Musculoskeletal_system#Diseases_and_disorders A connective tissue tumor that can be a benign chondroma or a maligannt chondrosarcoma. lschriml 2011-07-20T01:40:49Z disease_ontology DOID:0060102 cartilage cancer A connective tissue tumor that can be a benign chondroma or a maligannt chondrosarcoma. url:https://en.wikipedia.org/wiki/Cartilage_tumor A nervous system cancer that is located in the sensory system. lschriml 2011-07-25T01:51:56Z disease_ontology DOID:0060116 sensory system cancer A nervous system cancer that is located in the sensory system. url:http://en.wikipedia.org/wiki/Sensory_system A disease of anatomical entity that is located_in the thoracic cavity. lschriml 2011-07-25T02:23:47Z disease_ontology DOID:0060118 thoracic disease A disease of anatomical entity that is located_in the thoracic cavity. url:http://en.wikipedia.org/wiki/Thoracic_cavity A gastrointestinal system cancer that is located_in the pharynx. lschriml 2011-07-27T01:26:34Z MESH:D010610 NCI:C3325 SNOMEDCT_US_2018_03_01:95001001 UMLS_CUI:C0031347 pharyngeal neoplasm pharynx neoplasm disease_ontology pharyngeal cancer DOID:0060119 pharynx cancer A gastrointestinal system cancer that is located_in the pharynx. url:http://en.wikipedia.org/wiki/Pharynx An organ system cancer that is located_in the skin, hair and nails. lschriml 2011-07-27T02:31:34Z disease_ontology DOID:0060122 integumentary system cancer An organ system cancer that is located_in the skin, hair and nails. url:http://en.wikipedia.org/wiki/Integumentary_system A musculoskeletal system disease that affects the muscles. disease_ontology DOID:0080000 muscular disease A musculoskeletal system disease that affects the muscles. url:http://www.nlm.nih.gov/medlineplus/muscledisorders.html A connective tissue disease that affects the structure or development of bone or causes an impairment of normal bone function. DOID:1290 ICD10CM:M89.9 MESH:D001847 SNOMEDCT_US_2018_03_01:76069003 UMLS_CUI:C0005940 disease_ontology skeletal disease DOID:0080001 bone disease A connective tissue disease that affects the structure or development of bone or causes an impairment of normal bone function. url:http://en.wikipedia.org/wiki/Bone_disease An eye disease that affects the cornea, which is the transparent surface of the eye that assists in light refraction. DOID:2284 ICD10CM:H18.9 ICD9CM:371.9 MESH:D003316 NCI:C26731 SNOMEDCT_US_2018_03_01:15250008 UMLS_CUI:C0010034 disease_ontology DOID:10124 corneal disease An eye disease that affects the cornea, which is the transparent surface of the eye that assists in light refraction. url:https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&ns=ncit&code=C26731 A gastrointestinal system cancer that is located_in the intestine. ICD10CM:C26.0 ICD9CM:159.0 MESH:D007414 NCI2004_11_17:C4572 NCI:C4572 SNOMEDCT_US_2018_03_01:93838000 UMLS_CUI:C0346627 malignant intestinal tumors malignant neoplasm of intestine disease_ontology DOID:10155 intestinal cancer A gastrointestinal system cancer that is located_in the intestine. url:http://en.wikipedia.org/wiki/Intestine A gastrointestinal system cancer that is located_in the stomach. DOID:10539 DOID:10542 DOID:10543 DOID:4713 GARD:7704 ICD10CM:C16 ICD10CM:C16.2 ICD10CM:C16.5 ICD10CM:C16.6 ICD10CM:C16.9 ICD9CM:151 ICD9CM:151.4 ICD9CM:151.5 ICD9CM:151.6 ICD9CM:151.9 MESH:D013274 NCI:C3387 NCI:C9331 OMIM:137215 OMIM:613659 SNOMEDCT_US_2018_03_01:93717002 SNOMEDCT_US_2018_03_01:93818001 SNOMEDCT_US_2018_03_01:93867004 SNOMEDCT_US_2018_03_01:94074003 UMLS_CUI:C0024623 UMLS_CUI:C0038356 UMLS_CUI:C0153421 UMLS_CUI:C0153422 UMLS_CUI:C0153423 Ca body - stomach Ca lesser curvature - stomach ca greater curvature of stomach gastric cancer gastric neoplasm malignant neoplasm of body of stomach malignant neoplasm of lesser curve of stomach malignant tumor of body of stomach malignant tumor of greater curve of stomach malignant tumor of lesser curve of stomach disease_ontology DOID:10534 OMIM mapping confirmed by DO. [SN]. stomach cancer A gastrointestinal system cancer that is located_in the stomach. url:http://cancergenome.nih.gov/cancersselected/stomach-esophagealcancer url:http://en.wikipedia.org/wiki/Stomach An eye disease that affects the lens of the eye, which is the transparent disc that focuses light to the photosensors in the back of the eye. ICD10CM:H25-H28 ICD10CM:H27.9 MESH:D007905 NCI:C26812 SNOMEDCT_US_2018_03_01:10810001 UMLS_CUI:C0023308 disease_ontology DOID:110 lens disease An eye disease that affects the lens of the eye, which is the transparent disc that focuses light to the photosensors in the back of the eye. url:https://en.wikipedia.org/wiki/Lens_(anatomy) A female reproductive system disease that is located_in the ovary. MESH:D010049 NCI:C26841 SNOMEDCT_US_2018_03_01:5552004 UMLS_CUI:C0029928 disease_ontology DOID:1100 ovarian disease A female reproductive system disease that is located_in the ovary. url:https://medlineplus.gov/ovariandisorders.html An urinary system cancer that results_in malignant growth located_in the urinary bladder. DOID:5428 GARD:12210 ICD10CM:C67 ICD10CM:C67.9 ICD9CM:188 ICD9CM:188.9 KEGG:05219 MESH:D001749 NCI2004_11_17:C2901 NCI:C2901 NCI:C9334 OMIM:109800 SNOMEDCT_US_2018_03_01:93689003 UMLS_CUI:C0005684 UMLS_CUI:C0005695 bladder cancer tumor of the bladder disease_ontology DOID:11054 OMIM mapping confirmed by DO. [SN]. urinary bladder cancer An urinary system cancer that results_in malignant growth located_in the urinary bladder. url:http://en.wikipedia.org/wiki/Bladder_cancer A cardiovascular system disease that involves the heart. ICD10CM:I51.9 ICD9CM:429.9 MESH:D006331 NCI:C3079 SNOMEDCT_US_2018_03_01:56265001 UMLS_CUI:C0018799 disease_ontology DOID:114 heart disease A cardiovascular system disease that involves the heart. url:http://en.wikipedia.org/wiki/Heart_disease A female reproductive system disease characterized by the growth of endometrial tissue that is located_in the fallopian tube. ICD10CM:N80.2 ICD9CM:617.2 ICD9CM_2006:617.2 NCI:C26763 SNOMEDCT_US_2018_03_01:22611009 UMLS_CUI:C0014177 Endometriosis of fallopian tube disease_ontology DOID:11424 fallopian tube endometriosis A female reproductive system disease characterized by the growth of endometrial tissue that is located_in the fallopian tube. url:https://en.wikipedia.org/wiki/Endometriosis A female reproductive system disease characterized by the growth of endometrial tissue that is located_in the intestine. ICD10CM:N80.5 ICD9CM:617.5 SNOMEDCT_US_2018_03_01:5562006 UMLS_CUI:C0156347 disease_ontology DOID:11428 endometriosis of intestine A female reproductive system disease characterized by the growth of endometrial tissue that is located_in the intestine. url:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2653346/ A female reproductive system disease characterized by the growth of endometrial tissue that is located_in the ovary. DOID:11426 ICD10CM:N80.1 ICD9CM:617.1 NCI:C27628 SNOMEDCT_US_2018_03_01:31007005 UMLS_CUI:C0156344 ovarian endometriosis disease_ontology DOID:11432 endometriosis of ovary A female reproductive system disease characterized by the growth of endometrial tissue that is located_in the ovary. url:https://en.wikipedia.org/wiki/Endometriosis A cardiovascular cancer located_in the heart. DOID:9918 GARD:2619 ICD10CM:C38.0 ICD9CM:164.1 MESH:D006338 NCI2004_11_17:C3081 NCI2004_11_17:C3548 NCI:C3081 NCI:C3548 SNOMEDCT_US_2018_03_01:93825008 UMLS_CUI:C0018809 UMLS_CUI:C0153500 Cardiac tumor Tumour of heart malignant Cardiac tumor malignant neoplasm of heart disease_ontology DOID:117 heart cancer A cardiovascular cancer located_in the heart. url:http://en.wikipedia.org/wiki/Heart_cancer ICD10CM:C67.5 ICD9CM:188.5 SNOMEDCT_US_2018_03_01:94124002 UMLS_CUI:C0153613 malignant neoplasm of urinary bladder neck malignant tumor of bladder neck disease_ontology DOID:11809 bladder neck cancer A urinary system cancer that is located_in the ureter. ICD10CM:C66 ICD9CM:189.2 MESH:D014516 NCI2004_11_17:C7543 NCI:C7543 OMIM:191600 SNOMEDCT_US_2018_03_01:94121005 UMLS_CUI:C0153619 malignant tumour of ureter malignant ureteral tumor disease_ontology DOID:11819 OMIM mapping confirmed by DO. [SN]. ureter cancer A urinary system cancer that is located_in the ureter. url:http://en.wikipedia.org/wiki/Ureter_cancer A female reproductive system cancer that is located_in the vagina. DOID:1902 CSP2005:2016-2004 GARD:9348 ICD10CM:C52 ICD9CM:184.0 ICD9CM_2006:184.0 MESH:D014625 NCI2004_11_17:C3437 NCI2004_11_17:C7410 NCI:C3437 NCI:C7410 UMLS_CUI:C0042237 UMLS_CUI:C0042258 malignant neoplasm of vagina malignant tumor of vagina malignant vaginal tumor neoplasm of vagina vagina neoplasm vaginal tumor disease_ontology DOID:119 vaginal cancer A female reproductive system cancer that is located_in the vagina. url:http://www.cancer.gov/dictionary?CdrID=523460 A respiratory system cancer that is located_in the trachea. ICD10CM:C33 ICD9CM:162.0 MTH:NOCODE NCI2004_11_17:C9346 NCI:C9346 UMLS_CUI:C0153489 disease_ontology DOID:11920 tracheal cancer A respiratory system cancer that is located_in the trachea. url:http://en.wikipedia.org/wiki/Lung_cancer An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx. CSP2005:2005-4325 GARD:12425 MESH:D006258 MTH:NOCODE NCI:C3077 UMLS_CUI:C0018671 head and neck neoplasm head and neck tumours head/neck neoplasm tumor of head and neck disease_ontology DOID:11934 head and neck cancer An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx. url:http://apps.who.int/bookorders/anglais/detart1.jsp?sesslan=1&codlan=1&codcol=70&codcch=9 url:http://en.wikipedia.org/wiki/Head_and_neck_cancer url:http://www.cancer.gov/cancertopics/factsheet/Sites-Types/head-and-neck url:http://www.cancer.gov/dictionary?CdrID=257519 url:http://www.iarc.fr/en/publications/pdfs-online/pat-gen/bb9/index.php A reproductive organ cancer that is manifested in the female genitals. This includes organs such as the ovaries, fallopian tubes, uterus, cervix, vagina and vulva. DOID:1244 DOID:1281 ICD10CM:C57 ICD9CM:184 MESH:D005833 NCI2004_11_17:C4913 NCI:C3053 NCI:C4913 UMLS_CUI:C0017416 UMLS_CUI:C0153585 UMLS_CUI:C0699889 female reproductive cancer malignant Gynecologic tumor malignant neoplasm of female genital organ disease_ontology DOID:120 female reproductive organ cancer A reproductive organ cancer that is manifested in the female genitals. This includes organs such as the ovaries, fallopian tubes, uterus, cervix, vagina and vulva. url:http://en.wikipedia.org/wiki/Template:Female_genital_neoplasia url:http://www.wrongdiagnosis.com/g/genital_system_cancer/intro.htm A female reproductive system disease that is located_in the vagina. MESH:D014623 NCI:C26910 SNOMEDCT_US_2018_03_01:25658005 UMLS_CUI:C0042251 disease_ontology DOID:121 vaginal disease A female reproductive system disease that is located_in the vagina. url:https://en.wikipedia.org/wiki/Vaginal_disease ICD10CM:C18.7 ICD9CM:153.3 MESH:D012811 SNOMEDCT_US_2018_03_01:94006002 UMLS_CUI:C0153436 Ca sigmoid colon malignant tumor of sigmoid colon disease_ontology DOID:12192 sigmoid colon cancer A cancer that affects the blood or bone marrow characterized by an abnormal proliferation of blood cells. DOID:9145 ICD10CM:C95 ICD10CM:C95.9 ICD10CM:C95.90 ICD9CM:208 ICD9CM:208.9 MESH:D007938 NCI:C3161 SNOMEDCT_US_2018_03_01:87163000 SNOMEDCT_US_2018_03_01:93143009 UMLS_CUI:C0023418 disease_ontology DOID:1240 leukemia A cancer that affects the blood or bone marrow characterized by an abnormal proliferation of blood cells. url:http://en.wikipedia.org/wiki/Leukemia url:http://www.cancer.gov/dictionary?CdrID=45343 An eye disease that involves the globe of the eye. ICD10CM:H44.39 ICD9CM:360.29 UMLS_CUI:C0154780 disease_ontology DOID:1242 globe disease An eye disease that involves the globe of the eye. url:https://en.wikipedia.org/wiki/Globe_(human_eye) A vascular disease that is located_in the capillaries. ICD10CM:I78 ICD10CM:I78.9 ICD9CM:448 SNOMEDCT_US_2018_03_01:57223003 SNOMEDCT_US_2018_03_01:58729003 UMLS_CUI:C0155765 disease of capillaries disease_ontology DOID:1271 capillary disease A vascular disease that is located_in the capillaries. url:http://en.wikipedia.org/wiki/Capillary#Pathophysiology DOID:12760 ICD10CM:C69.3 ICD9CM:190.6 MESH:D002830 NCI2004_11_17:C2949 NCI2004_11_17:C3566 NCI:C2949 NCI:C3566 SNOMEDCT_US_2018_03_01:93755007 UMLS_CUI:C0008523 UMLS_CUI:C0153630 Choroidal tumor choroid neoplasm malignant tumor of choroid malignant tumor of the Choroid neoplasm of choroid disease_ontology DOID:12759 choroid cancer MESH:D012002 SNOMEDCT_US_2018_03_01:5964004 UMLS_CUI:C0034882 disease_ontology DOID:1285 rectal disease A disease of anatomical entity which occurs in the blood, heart, blood vessels or the lymphatic system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells or lymph to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis. DOID:73 ICD9CM:429.2 MESH:D002318 NCI:C2931 SNOMEDCT_US_2018_03_01:49601007 UMLS_CUI:C0007222 disease of subdivision of hemolymphoid system disease_ontology DOID:1287 cardiovascular system disease A disease of anatomical entity which occurs in the blood, heart, blood vessels or the lymphatic system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells or lymph to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis. url:http://en.wikipedia.org/wiki/Circulatory_system A hematologic cancer located_in the central nervous system. NCI2004_11_17:C5440 NCI:C5440 UMLS_CUI:C1332884 Leukemia of the CNS disease_ontology DOID:12969 central nervous system leukemia A hematologic cancer located_in the central nervous system. url:http://www.springerlink.com/content/gl61tx644217n938/ A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain. DOID:2125 DOID:2126 DOID:3543 DOID:6649 DOID:911 CSP2005:2006-2736 ICD10CM:C71 ICD10CM:C71.9 ICD9CM:191 ICD9CM:191.9 ICD9CM:239.6 MESH:D001932 NCI2004_11_17:C2907 NCI2004_11_17:C3568 NCI2004_11_17:C4952 NCI2004_11_17:C4954 NCI2004_11_17:C5115 NCI2004_11_17:C7710 NCI:C2907 NCI:C3568 NCI:C4952 NCI:C4954 NCI:C5115 NCI:C7710 SNOMEDCT_US_2018_03_01:93727008 UMLS_CUI:C0006118 UMLS_CUI:C0153633 UMLS_CUI:C0220624 UMLS_CUI:C0750974 UMLS_CUI:C0750979 UMLS_CUI:C1334557 BT - Brain tumour adult brain tumor adult malignant brain neoplasm brain neoplasm brain neoplasm, adult malignant brain tumour malignant primary brain neoplasm malignant primary brain tumor malignant tumor of Brain malignant tumor of adult brain neoplasm of brain primary brain neoplasm primary brain tumor primary malignant neoplasm of brain tumor of the Brain disease_ontology DOID:1319 brain cancer A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain. url:http://www.cancer.gov/dictionary?CdrID=387264 A respiratory system cancer that is located_in the lung. DOID:13075 DOID:1322 DOID:9881 ICD10CM:C34.1 ICD10CM:C34.2 ICD10CM:C34.3 ICD9CM:162.3 ICD9CM:162.4 ICD9CM:162.5 ICD9CM:162.8 OMIM:211980 OMIM:608935 OMIM:612571 OMIM:612593 OMIM:614210 UMLS_CUI:C0024624 UMLS_CUI:C0153491 UMLS_CUI:C0153492 UMLS_CUI:C0153493 disease_ontology lung neoplasm DOID:1324 lung cancer A respiratory system cancer that is located_in the lung. url:http://en.wikipedia.org/wiki/Lung_cancer A uterine cancer that is located_in tissues lining the uterus. DOID:5654 EFO:0004230 GARD:11981 ICD10CM:C54.1 KEGG:05213 MESH:D016889 NCI2004_11_17:C27815 NCI2004_11_17:C3012 NCI:C27815 NCI:C3012 OMIM:608089 UMLS_CUI:C0007103 UMLS_CUI:C0014170 endometrial Ca endometrial neoplasm malignant endometrial neoplasm malignant neoplasm of endometrium neoplasm of endometrium primary malignant neoplasm of endometrium tumor of Endometrium disease_ontology DOID:1380 endometrial cancer A uterine cancer that is located_in tissues lining the uterus. url:http://www.cancer.gov/dictionary?CdrID=444987 A large intestine cancer that is located_in the anus. DOID:12240 GARD:9300 ICD10CM:C21.0 ICD10CM:C21.1 ICD9CM:154.2 ICD9CM:154.3 NCI2004_11_17:C7379 NCI:C7379 SNOMEDCT_US_2018_03_01:93669004 SNOMEDCT_US_2018_03_01:93676009 UMLS_CUI:C0153445 UMLS_CUI:C0153446 anal cancer malignant anal tumor disease_ontology DOID:14110 anus cancer A large intestine cancer that is located_in the anus. url:http://en.wikipedia.org/wiki/Anus ICD10CM:H31.9 ICD9CM:363.9 MESH:D015862 NCI:C34468 UMLS_CUI:C0008521 disease_ontology DOID:1417 choroid disease A urinary system disease that is located_in the ureter. MESH:D014515 NCI:C27148 UMLS_CUI:C0041954 disease_ontology DOID:1426 ureteral disease A urinary system disease that is located_in the ureter. url:http://www.nlm.nih.gov/medlineplus/ureteraldisorders.html A disease that is characterized by abnormally rapid cell division. DOID:0000818 cell process disease neoplasm disease_ontology DOID:14566 disease of cellular proliferation A disease that is characterized by abnormally rapid cell division. url:http://en.wikipedia.org/w/index.php?title=Cell_proliferation A sensory system disease that is located_in the eye or the adnexa of the eye. ICD10CM:H35.00 ICD9CM:362.10 SNOMEDCT_US_2018_03_01:31411005 SNOMEDCT_US_2018_03_01:42873008 UMLS_CUI:C0004608 disease_ontology DOID:1492 eye and adnexa disease A sensory system disease that is located_in the eye or the adnexa of the eye. url:http://en.wikipedia.org/wiki/Category:Diseases_of_the_eye_and_adnexa A disease of anatomical entity that is located_in reproductive system organs. DOID:6309 NCI:C27613 UMLS_CUI:C1335037 genital system disease disease_ontology DOID:15 reproductive system disease A disease of anatomical entity that is located_in reproductive system organs. url:http://en.wikipedia.org/wiki/Reproductive_system A colon cancer that has_material_basis_in abnormally proliferating cells derives_from epithelial cells. NCI2004_11_17:C4910 NCI:C4910 UMLS_CUI:C0699790 Colonic carcinoma carcinoma of colon disease_ontology DOID:1520 OMIM mapping confirmed by DO. [SN]. colon carcinoma A colon cancer that has_material_basis_in abnormally proliferating cells derives_from epithelial cells. url:http://en.wikipedia.org/wiki/Carcinoma A disease of anatomical entity that located_in the respiratory system which extends from the nasal sinuses to the diaphragm. DOID:3226 ICD10CM:J96-J99 ICD10CM:J98 ICD9CM:510-519.99 ICD9CM:519 UMLS_CUI:C0029582 disease_ontology DOID:1579 respiratory system disease A disease of anatomical entity that located_in the respiratory system which extends from the nasal sinuses to the diaphragm. url:http://en.wikipedia.org/wiki/File:Respiratory_system_complete_en.svg url:http://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=respiratory%20system A disease of anatomical entity that is located_in the integumentary system comprising the skin and its appendages. disease_ontology DOID:16 integumentary system disease A disease of anatomical entity that is located_in the integumentary system comprising the skin and its appendages. url:http://en.wikipedia.org/wiki/Integumentary_system A disease of cellular proliferation that is malignant and primary, characterized by uncontrolled cellular proliferation, local cell invasion and metastasis. ICD10CM:C80 ICD10CM:C80.1 ICD9CM:199 ICDO:M8000/3 MESH:D009369 NCI:C9305 SNOMEDCT_US_2018_03_01:38807002 UMLS_CUI:C0006826 malignant neoplasm malignant tumor primary cancer disease_ontology DOID:162 Updating out dated UMLS CUI. cancer A disease of cellular proliferation that is malignant and primary, characterized by uncontrolled cellular proliferation, local cell invasion and metastasis. url:http://en.wikipedia.org/wiki/cancer url:http://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=cancer A disease of anatomical entity that occurs in the muscular and/or skeletal system. MESH:D009140 NCI:C107377 SNOMEDCT_US_2018_03_01:928000 UMLS_CUI:C0026857 disease_ontology DOID:17 musculoskeletal system disease A disease of anatomical entity that occurs in the muscular and/or skeletal system. url:http://en.wikipedia.org/wiki/Human_musculoskeletal_system#Diseases_and_disorders An organ system cancer located_in endocrine system that is characterized by uncontrolled cellular proliferation of the hormone producing glands of the endocrine system. DOID:10009 CSP2005:2009-5861 ICD10CM:C75.9 ICD9CM:194.9 MESH:D004701 NCI2004_11_17:C3010 NCI2004_11_17:C3575 NCI:C3010 NCI:C3575 SNOMEDCT_US_2018_03_01:93780007 UMLS_CUI:C0014132 UMLS_CUI:C0153658 Endocrine tumor endocrine neoplasm malignant Endocrine tumor malignant neoplasm of endocrine gland malignant tumour of endocrine gland neoplasm of endocrine gland neoplasm of endocrine system disease_ontology DOID:170 endocrine gland cancer An organ system cancer located_in endocrine system that is characterized by uncontrolled cellular proliferation of the hormone producing glands of the endocrine system. url:http://en.wikipedia.org/wiki/Endocrine_system A cardiovascular cancer that is located_in blood vessels. DOID:3339 DOID:5454 DOID:5548 DOID:7019 DOID:7020 DOID:7392 CSP2005:2007-0683 MESH:D019043 NCI2004_11_17:C5380 NCI2004_11_17:C5383 NCI2004_11_17:C5388 NCI2004_11_17:C7387 NCI2004_11_17:C7388 NCI2004_11_17:C7390 NCI:C5348 NCI:C5380 NCI:C5383 NCI:C5388 NCI:C7388 NCI:C7390 SNOMEDCT_US_2018_03_01:93817006 UMLS_CUI:C0282607 UMLS_CUI:C0346845 UMLS_CUI:C1290407 UMLS_CUI:C1334616 UMLS_CUI:C1334617 UMLS_CUI:C1334630 UMLS_CUI:C1335753 Blood Vessel neoplasm Blood vessel tumor Blood vessel tumors Blood vessel tumour disorder Haemangiomatous tumour blood vessel neoplasm leiomyosarcoma of the renal Vein malignant great vessel tumor malignant tumor of pulmonary Vein malignant tumor of pulmonary artery malignant vascular neoplasm malignant vascular tumor neoplasm of great vessel pulmonary artery malignant neoplasm pulmonary vein malignant neoplasm renal vein leiomyosarcoma vascular tissue neoplasm vascular tumors disease_ontology DOID:175 vascular cancer A cardiovascular cancer that is located_in blood vessels. url:http://en.wikipedia.org/wiki/Vascular An organ system cancer that located_in the heart and blood vessels. CSP2005:2007-0683 NCI2004_11_17:C4784 NCI:C4784 UMLS_CUI:C0497243 Cardiovascular tumors cardiovascular neoplasm disease_ontology DOID:176 cardiovascular cancer An organ system cancer that located_in the heart and blood vessels. url:http://www.cancer.gov/dictionary?CdrID=44005 url:http://www.healthcentral.com/heart-disease/h/cardiovascular-cancer.html A cardiovascular system disease that primarily affects the blood vessels which includes the arteries, veins and capillaries that carry blood to and from the heart. DOID:0000405 DOID:2403 DOID:2869 DOID:324 DOID:325 DOID:45 ICD10CM:I72.9 ICD9CM:442.9 MESH:D000783 MESH:D014652 MESH:D020758 MESH:D020760 NCI:C26693 NCI:C35117 SNOMEDCT_US_2018_03_01:27550009 SNOMEDCT_US_2018_03_01:85659009 UMLS_CUI:C0002940 UMLS_CUI:C0042373 UMLS_CUI:C0752127 UMLS_CUI:C0752130 vascular tissue disease disease_ontology DOID:178 vascular disease A cardiovascular system disease that primarily affects the blood vessels which includes the arteries, veins and capillaries that carry blood to and from the heart. url:http://en.wikipedia.org/wiki/Vascular_disease A disease of anatomical entity that is located_in kidney, ureter, bladder and urethra. DOID:579 NCI2004_11_17:C27599 NCI:C27599 UMLS_CUI:C1335051 Non-neoplastic urinary tract disease urinary tract disease disease_ontology DOID:18 urinary system disease A disease of anatomical entity that is located_in kidney, ureter, bladder and urethra. url:http://en.wikipedia.org/wiki/Urinary_system A connective tissue cancer that is located_in bone and is characterized by uncontrolled cellular proliferation that destroys normal bone tissue. DOID:3348 CSP2005:2019-1041 MESH:D001859 NCI2004_11_17:C4016 NCI2004_11_17:C9343 NCI:C9343 UMLS_CUI:C0005967 CA - bone cancer bone neoplasm bone tumour malignant bone neoplasm malignant bone tumour malignant neoplasm of bone malignant osseous tumor neoplasm of bone osseous tumor disease_ontology DOID:184 bone cancer A connective tissue cancer that is located_in bone and is characterized by uncontrolled cellular proliferation that destroys normal bone tissue. url:http://www.cancer.gov/cancertopics/factsheet/Sites-Types/bone url:http://www.cancer.gov/cancertopics/types/bone url:http://www.wrongdiagnosis.com/b/bone_cancer/intro.htm A bone cancer and jaw disease that is located in the jaw and results in a swollen jaw, results in numbness or a tingling sensation in jaw, and results in an abnormal growth of the jaw bone. MESH:D007573 UMLS_CUI:C0022364 neoplasm of jaw disease_ontology jaw neoplasm DOID:1862 jaw cancer A bone cancer and jaw disease that is located in the jaw and results in a swollen jaw, results in numbness or a tingling sensation in jaw, and results in an abnormal growth of the jaw bone. url:http://www.buzzle.com/articles/jaw-cancer-symptoms.html MESH:D012888 NCI:C3375 UMLS_CUI:C0037305 disease_ontology DOID:1863 skull cancer An organ system cancer that is manifested in the reproductive organs. DOID:1900 NCI2004_11_17:C3674 NCI:C3674 UMLS_CUI:C0178830 Reproductive tumor malignant reproductive system neoplasm disease_ontology cancer of reproductive system DOID:193 reproductive organ cancer An organ system cancer that is manifested in the reproductive organs. url:http://en.wikipedia.org/wiki/Reproductive_system#Examples_of_cancers A female reproductive system disease that is located_in the fallopian tube. MESH:D005184 NCI:C26771 UMLS_CUI:C0015556 disease_ontology DOID:1962 fallopian tube disease A female reproductive system disease that is located_in the fallopian tube. url:https://www.ncbi.nlm.nih.gov/pubmed/21415195 A female reproductive organ cancer that is located_in fallopian tube. DOID:1961 GARD:9162 ICD10CM:C57.0 ICD9CM:183.2 MESH:D005185 MTHICD9_2006:183.2 NCI2004_11_17:C3032 NCI2004_11_17:C7480 NCI:C3032 NCI:C7480 SNOMEDCT_US_2018_03_01:93794008 UMLS_CUI:C0015558 UMLS_CUI:C0153579 fallopian tube neoplasm malignant neoplasm of uterine tube malignant tumor of fallopian tube malignant tumour of fallopian tube neoplasm of fallopian tube tumor of the fallopian tube tumor, fallopian tube, malignant disease_ontology DOID:1964 fallopian tube cancer A female reproductive organ cancer that is located_in fallopian tube. url:http://en.wikipedia.org/wiki/Fallopian_tube_cancer A colorectal cancer that is located_in the rectum. DOID:1989 ICD10CM:C20 ICD9CM:154.1 MESH:D012004 NCI2004_11_17:C7418 NCI2004_11_17:C9382 NCI:C7418 NCI:C9382 SNOMEDCT_US_2018_03_01:93984006 UMLS_CUI:C0007113 UMLS_CUI:C0949022 carcinoma of rectum carcinoma of the rectum malignant Rectal tumor malignant neoplasm of rectum malignant rectum tumor malignant tumor of rectum rectal cancer disease_ontology cancer of rectum DOID:1993 rectum cancer A colorectal cancer that is located_in the rectum. url:http://www.cancer.gov/dictionary?CdrID=529764 A musculoskeletal system cancer that is located_in connective tissue. CSP2005:2008-3809 MESH:D009372 UMLS_CUI:C0027656 Tumour of connective tissue connective tissue neoplasm neoplasm of connective tissues disease_ontology DOID:201 connective tissue cancer A musculoskeletal system cancer that is located_in connective tissue. url:http://en.wikipedia.org/wiki/Connective_tissue A sensory system cancer located_in the eye that is characterized by uncontrolled cellular proliferation in the eye. DOID:9985 CSP2005:2018-3273 ICD9CM:190.8 MESH:D005134 NCI2004_11_17:C3030 NCI:C3030 UMLS_CUI:C0015414 UMLS_CUI:C0153632 Ocular tumor eye neoplasm malignant eye neoplasm neoplasm of eye neoplasm of eye proper disease_ontology DOID:2174 ocular cancer A sensory system cancer located_in the eye that is characterized by uncontrolled cellular proliferation in the eye. url:http://en.wikipedia.org/wiki/Eye url:http://en.wikipedia.org/wiki/Eye_neoplasm A colorectal cancer that is located_in the colon. ICD10CM:C18 ICD10CM:C18.9 ICD9CM:153 ICD9CM:153.9 MESH:D003110 NCI:C9242 SNOMEDCT_US_2018_03_01:93761005 UMLS_CUI:C0007102 disease_ontology DOID:219 colon cancer A colorectal cancer that is located_in the colon. url:http://www.cancer.gov/dictionary?CdrID=44237 A uterine disease that is located_in the cervix. MESH:D002577 NCI:C40241 SNOMEDCT_US_2018_03_01:63339007 UMLS_CUI:C0007867 disease_ontology DOID:2253 cervix disease A uterine disease that is located_in the cervix. url:https://www.mdedge.com/obgmanagement/article/136739/gynecology/2017-update-cervical-disease An endocrine system disease that is located_in the gonads. MESH:D006058 NCI:C26786 UMLS_CUI:C0018050 disease_ontology DOID:2277 gonadal disease An endocrine system disease that is located_in the gonads. url:https://www.nature.com/subjects/gonadal-disorders A reproductive system disease that impairs the ability to reproduce and is located in the uterus, vagina, cervix, ovaries or fallopian tubes. ICD9CM:629.9 MESH:D005831 SNOMEDCT_US_2018_03_01:38233001 UMLS_CUI:C0017411 disease_ontology DOID:229 female reproductive system disease A reproductive system disease that impairs the ability to reproduce and is located in the uterus, vagina, cervix, ovaries or fallopian tubes. url:http://en.wikipedia.org/wiki/Female_reproductive_system url:http://en.wikipedia.org/wiki/Reproductive_system_disease A colon carcinoma that derives_from epithelial cells of glandular origin. NCI2004_11_17:C4349 NCI:C4349 UMLS_CUI:C0338106 Colonic adenocarcinoma adenocarcinoma of colon disease_ontology adenocarcinoma of the colon DOID:234 colon adenocarcinoma colon adenocarcinoma 结肠腺癌 A colon carcinoma that derives_from epithelial cells of glandular origin. url:http://en.wikipedia.org/wiki/Adenocarcinoma ICD9CM:593.81 ICD9CM_2006:593.81 NCI:C35338 SNOMEDCT_US_2018_03_01:16934004 UMLS_CUI:C0268790 renal vascular disease vascular disorder of kidney disease_ontology DOID:2388 renal artery disease A female reproductive organ cancer that is located_in the ovary. DOID:0060070 DOID:2144 DOID:9595 CSP2005:2016-1387 GARD:7295 ICD10CM:C56 ICD9CM:183.0 MESH:D010051 MTH:NOCODE NCI2004_11_17:C4984 NCI2004_11_17:C7431 NCI:C4984 NCI:C7431 OMIM:167000 OMIM:607893 ORDO:213500 ORDO:213517 SNOMEDCT_US_2018_03_01:93934004 UMLS_CUI:C0919267 UMLS_CUI:C1140680 UMLS_CUI:C1299247 malignant Ovarian tumor malignant tumour of ovary ovarian neoplasm ovary neoplasm primary ovarian cancer tumor of the Ovary disease_ontology DOID:2394 Xref MGI. OMIM mapping confirmed by DO. [SN]. ovarian cancer A female reproductive organ cancer that is located_in the ovary. url:http://www.cancer.gov/dictionary?CdrID=445074 MESH:D007499 NCI:C34737 SNOMEDCT_US_2018_03_01:85478004 UMLS_CUI:C0022078 disease_ontology DOID:240 iris disease CSP2005:1114-7471 NCI:C35170 SNOMEDCT_US_2018_03_01:57534004 UMLS_CUI:C0154833 retina circulation disorder disease_ontology DOID:2462 retinal vascular disease An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes. DOID:1034 DOID:2532 CSP2005:2004-0139 MESH:D019337 NCI2004_11_17:C27134 NCI:C27134 UMLS_CUI:C0376544 Hematologic malignancy Hematologic neoplasm Hematological tumors blood cancer hematopoietic and lymphoid system tumor hematopoietic cancer hematopoietic neoplasm hematopoietic tumors malignant hematopoietic neoplasm disease_ontology DOID:2531 hematologic cancer An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes. url:http://en.wikipedia.org/wiki/Blood_cancer url:http://www.cancer.gov/dictionary/?CdrID=45708 A urinary system cancer that is located_in the kidney. DOID:11834 DOID:3676 ICD10CM:C64 ICD9CM:189.0 MESH:D007680 NCI:C120456 NCI:C3150 NCI:C7548 SNOMEDCT_US_2018_03_01:93849006 UMLS_CUI:C0022665 UMLS_CUI:C0494158 UMLS_CUI:C0740457 malignant neoplasm of kidney except pelvis malignant tumour of kidney renal cancer disease_ontology DOID:263 kidney cancer A urinary system cancer that is located_in the kidney. url:http://en.wikipedia.org/wiki/Kidney_cancer NCI2004_11_17:C6531 NCI:C6531 UMLS_CUI:C1334624 malignant tumor of Synovium disease_ontology DOID:2706 synovium cancer A disease of anatomical entity that is located_in endocrine glands which secretes a type of hormone directly into the bloodstream to regulate the body. ICD10CM:E34.9 ICD9CM:259.9 MESH:D004700 NCI:C3009 SNOMEDCT_US_2018_03_01:67432001 UMLS_CUI:C0014130 disease_ontology DOID:28 endocrine system disease A disease of anatomical entity that is located_in endocrine glands which secretes a type of hormone directly into the bloodstream to regulate the body. url:http://en.wikipedia.org/wiki/Endocrine_system A female reproductive system disease characterized by the growth of endometrial tissue outside the uterine body. EFO:0001065 ICD10CM:N80 ICD10CM:N80.9 ICD9CM:617 ICD9CM:617.9 MESH:D004715 NCI:C3014 SNOMEDCT_US_2018_03_01:11871002 UMLS_CUI:C0014175 disease_ontology DOID:289 endometriosis A female reproductive system disease characterized by the growth of endometrial tissue outside the uterine body. url:https://en.wikipedia.org/?title=Endometriosis url:https://www.ncbi.nlm.nih.gov/pubmed/20574791 A cervical cancer that is located_in the cervix uteri or located_in the cervical area and that has_material_basis_in abnormally proliferating cells derives_from epithelial cells. MTH:166 NCI2004_11_17:C9039 NCI:C9039 SNOMEDCT_US_2018_03_01:93752005 UMLS_CUI:C0302592 cancer of cervix carcinoma OF CERVIX carcinoma cervix uteri carcinoma of cervix carcinoma of the Cervix Uteri disease_ontology DOID:2893 OMIM mapping confirmed by DO. [SN]. cervix carcinoma A cervical cancer that is located_in the cervix uteri or located_in the cervical area and that has_material_basis_in abnormally proliferating cells derives_from epithelial cells. url:http://en.wikipedia.org/wiki/Cervical_cancer A carcinoma that has_material_basis_in abnormally proliferating cells, derives_from epithelial cells, which originate in glandular tissue. MESH:D000230 NCI:C2852 SNOMEDCT_US_2018_03_01:35917007 UMLS_CUI:C0001418 adenocarcinomas disease_ontology DOID:299 adenocarcinoma adenocarcinoma 腺癌 A carcinoma that has_material_basis_in abnormally proliferating cells, derives_from epithelial cells, which originate in glandular tissue. url:http://en.wikipedia.org/wiki/Adenocarcinoma An adenocarcinoma that derives_from epithelial cells originating in glandular tissue, which produce mucin. DOID:4532 MESH:D002288 NCI2004_11_17:C26712 NCI2004_11_17:C27379 NCI2004_11_17:C27825 NCI:C26712 NCI:C27379 NCI:C27825 SNOMEDCT_US_2018_03_01:72495009 SNOMEDCT_US_2018_03_01:900006 UMLS_CUI:C0007130 UMLS_CUI:C0334368 Mucin-Secreting adenocarcinoma Mucin-Secreting carcinoma Mucin-producing adenocarcinoma Mucous carcinoma Pseudomyxoma peritonei with unknown primary site mucin-producing adenocarcinoma disease_ontology DOID:3030 mucinous adenocarcinoma An adenocarcinoma that derives_from epithelial cells originating in glandular tissue, which produce mucin. url:http://coloncancer.about.com/od/typesofcancer/a/Mucinous_Tumor.htm url:http://medical-dictionary.thefreedictionary.com/mucinous+carcinoma A cell type cancer that has_material_basis_in abnormally proliferating cells derives_from epithelial cells. DOID:2428 DOID:6570 CSP2005:2000-5801 MESH:D002277 MESH:D009375 NCI2004_11_17:C6927 NCI:C2916 NCI:C3709 SNOMEDCT_US_2018_03_01:68453008 SNOMEDCT_US_2018_03_01:71298006 UMLS_CUI:C0007097 UMLS_CUI:C0553707 UMLS_CUI:C1368683 epithelial cancer epithelioma malignant Epithelioma disease_ontology DOID:305 carcinoma carcinoma 癌 A cell type cancer that has_material_basis_in abnormally proliferating cells derives_from epithelial cells. url:http://en.wikipedia.org/wiki/Carcinoma An organ system cancer located_in the nervous system that affects the central or peripheral nervous system. DOID:1193 DOID:3195 DOID:4695 CSP2005:2012-5157 ICD9CM:192 ICD9CM:192.9 MESH:D009380 NCI2004_11_17:C3268 NCI2004_11_17:C35562 NCI:C35562 UMLS_CUI:C0027665 UMLS_CUI:C0153643 UMLS_CUI:C1334956 malignant neoplasm of nervous system neoplasm of nervous system nervous system neoplasm neural neoplasm neural tumor tumor of the nervous system disease_ontology DOID:3093 nervous system cancer An organ system cancer located_in the nervous system that affects the central or peripheral nervous system. url:http://emedicine.medscape.com/oncology url:http://en.wikipedia.org/wiki/Nervous_system_disease An organ system cancer located_in gastrointestinal tract that is manifested in organs of the gastrointestinal system. DOID:4945 DOID:8377 ICD10CM:C26.9 ICD9CM:239.0 MESH:D004067 MESH:D005770 NCI2004_11_17:C3052 NCI2004_11_17:C4890 NCI:C3052 NCI:C4890 SNOMEDCT_US_2018_03_01:93811007 UMLS_CUI:C0012243 UMLS_CUI:C0017185 UMLS_CUI:C0685938 GI tumor digestive system cancer gastrointestinal tract cancer disease_ontology DOID:3119 gastrointestinal system cancer An organ system cancer located_in gastrointestinal tract that is manifested in organs of the gastrointestinal system. url:http://en.wikipedia.org/wiki/Human_gastrointestinal_tract DOID:11479 DOID:11993 MESH:D001004 MTHICD9_2006:565.0 NCI:C26695 SNOMEDCT_US_2018_03_01:32110003 UMLS_CUI:C0003462 Nontraumatic tear of anus Solitary anal ulcer Ulcer of anus anal disease anal fissure anal fissure and fistula anal ulcer fissure in ano disease_ontology DOID:3128 anus disease ICD10CM:G95.9 ICD9CM:336.9 MESH:D013118 NCI:C97110 SNOMEDCT_US_2018_03_01:48522003 SNOMEDCT_US_2018_03_01:95648003 UMLS_CUI:C0037928 disease_ontology myelopathy DOID:319 spinal cord disease ICD10CM:S12.8 MESH:D014133 NCI:C35079 SNOMEDCT_US_2018_03_01:47125007 UMLS_CUI:C0040580 disease_ontology DOID:3225 tracheal disease A nervous system disease that affects either the spinal cord (myelopathy) or brain (encephalopathy) of the central nervous system. ICD10CM:G96.9 MESH:D002493 NCI:C2934 SNOMEDCT_US_2018_03_01:23853001 UMLS_CUI:C0007682 disease_ontology DOID:331 central nervous system disease A nervous system disease that affects either the spinal cord (myelopathy) or brain (encephalopathy) of the central nervous system. url:http://en.wikipedia.org/wiki/Central_nervous_system_disease MESH:D002340 NCI:C84476 UMLS_CUI:C0007273 disorder of carotid artery disease_ontology DOID:3407 carotid artery disease A female reproductive system disease that is located_in the uterus. ICD10CM:N85.9 ICD9CM:621.9 MESH:D014591 NCI:C26907 SNOMEDCT_US_2018_03_01:12337004 UMLS_CUI:C0042131 disease_ontology DOID:345 uterine disease A female reproductive system disease that is located_in the uterus. url:http://www.merriam-webster.com/dictionary/uterus DOID:6353 MESH:D015811 NCI2004_11_17:C3142 NCI2004_11_17:C4554 NCI:C3142 NCI:C4554 UMLS_CUI:C0022079 UMLS_CUI:C0346372 malignant neoplasm of the Iris malignant tumor of iris tumor of the Iris disease_ontology DOID:3478 iris cancer DOID:12754 MESH:D014604 NCI2004_11_17:C3436 NCI2004_11_17:C6105 NCI:C3436 NCI:C6105 UMLS_CUI:C0042162 UMLS_CUI:C1334629 Uveal tumor malignant Uveal tumor malignant uvea neoplasm disease_ontology DOID:3479 uveal cancer An eye disease affecting the uvea, which are the pigmented layers of the eye consisting of the iris, ciliary body, and choroid. GARD:8192 MESH:D014603 NCI:C26908 SNOMEDCT_US_2018_03_01:95678007 UMLS_CUI:C0042161 disease_ontology DOID:3480 uveal disease An eye disease affecting the uvea, which are the pigmented layers of the eye consisting of the iris, ciliary body, and choroid. url:https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&ns=ncit&code=C26908 A skin disease where there is a diffuse infection of connective tissue with severe inflammation of dermal and subcutaneous layers of the skin. Cellulitis can be caused by normal skin flora or by exogenous bacteria, and often occurs where the skin has previously been broken: cracks in the skin, cuts, blisters, burns, insect bites, surgical wounds, or sites of intravenous catheter insertion. DOID:2472 ICD10CM:L03.90 MESH:D002481 NCI:C26715 NCI:C34454 SNOMEDCT_US_2018_03_01:62837005 SNOMEDCT_US_2018_03_01:74276003 UMLS_CUI:C0007642 UMLS_CUI:C0007646 disease_ontology DOID:3488 cellulitis A skin disease where there is a diffuse infection of connective tissue with severe inflammation of dermal and subcutaneous layers of the skin. Cellulitis can be caused by normal skin flora or by exogenous bacteria, and often occurs where the skin has previously been broken: cracks in the skin, cuts, blisters, burns, insect bites, surgical wounds, or sites of intravenous catheter insertion. url:http://en.wikipedia.org/wiki/Cellulitis A nervous system cancer that is located_in the central nervous system. DOID:0060093 DOID:1318 CSP2005:2012-5421 EFO:0000326 ICD10CM:C72.9 MESH:D016543 NCI2004_11_17:C4627 NCI2004_11_17:C9293 NCI:C4627 NCI:C9293 SNOMEDCT_US_2018_03_01:93744007 UMLS_CUI:C0085136 UMLS_CUI:C0348374 CNS neoplasm central nervous system tumor central nervous system tumors malignant neoplasm of central nervous system malignant tumor of CNS neoplasm of central nervous system disease_ontology DOID:3620 central nervous system cancer A nervous system cancer that is located_in the central nervous system. url:http://en.wikipedia.org/wiki/Central_nervous_system A female reproductive organ cancer that is located_in the uterus. DOID:4363 CSP2005:2016-1566 ICD10CM:C55 ICD9CM:179 MESH:D014594 NCI2004_11_17:C3435 NCI2004_11_17:C3552 NCI:C3435 NCI:C3552 SNOMEDCT_US_2018_03_01:93718007 SNOMEDCT_US_2018_03_01:94127009 UMLS_CUI:C0042138 UMLS_CUI:C0153567 CA - cancer of uterus Tumour of uterus malignant neoplasm of uterus malignant uterine tumor neoplasm of uterus uterine tumor uterus neoplasm disease_ontology DOID:363 uterine cancer A female reproductive organ cancer that is located_in the uterus. url:http://www.cancer.gov/dictionary?CdrID=445094 A urinary system disease that is located_in the bladder. ICD10CM:N32.9 ICD9CM:596.9 MESH:D001745 NCI:C2900 SNOMEDCT_US_2018_03_01:42643001 UMLS_CUI:C0005686 Urinary Bladder Disease disease_ontology DOID:365 bladder disease A urinary system disease that is located_in the bladder. url:http://www.nlm.nih.gov/medlineplus/bladderdiseases.html An integumentary system disease that is located_in skin. DOID:1576 DOID:1698 DOID:187 DOID:6486 DOID:8948 ICD9CM:702 MESH:D012871 MESH:D012873 NCI:C27554 NCI:C3371 SNOMEDCT_US_2018_03_01:5613003 SNOMEDCT_US_2018_03_01:80659006 SNOMEDCT_US_2018_03_01:95320005 UMLS_CUI:C0029574 UMLS_CUI:C0037274 UMLS_CUI:C0037277 Genodermatosis skin and subcutaneous tissue disease disease_ontology DOID:37 skin disease An integumentary system disease that is located_in skin. url:http://en.wikipedia.org/wiki/Skin_disease A cervix carcinoma that derives_from epithelial cells of glandular origin. NCI2004_11_17:C4029 NCI:C4029 UMLS_CUI:C0279672 adenocarcinoma cervix uteri adenocarcinoma of cervix adenocarcinoma of the uterine Cervix disease_ontology DOID:3702 cervical adenocarcinoma cervical adenocarcinoma 子宫颈腺癌 A cervix carcinoma that derives_from epithelial cells of glandular origin. url:http://en.wikipedia.org/wiki/Adenocarcinoma A stomach carcinoma that derives_from epithelial cells of glandular origin. NCI2004_11_17:C4004 NCI:C4004 UMLS_CUI:C0278701 adenocarcinoma of stomach stomach adenocarcinoma disease_ontology DOID:3717 gastric adenocarcinoma gastric adenocarcinoma 胃腺癌 A stomach carcinoma that derives_from epithelial cells of glandular origin. url:http://en.wikipedia.org/wiki/Adenocarcinoma A lung cancer that has_material_basis_in abnormally proliferating cells derives_from epithelial cells and is located_in the lungs and has_symptom cough and has_symptom chest discomfort or pain and has_symptom weight loss and has_symptom hemoptysis. EFO:0001071 ICD10CM:C34.90 NCI2004_11_17:C4878 NCI:C4878 UMLS_CUI:C0684249 cancer of lung disease_ontology carcinoma of lung DOID:3905 OMIM mapping confirmed by DO. [SN]. lung carcinoma A lung cancer that has_material_basis_in abnormally proliferating cells derives_from epithelial cells and is located_in the lungs and has_symptom cough and has_symptom chest discomfort or pain and has_symptom weight loss and has_symptom hemoptysis. url:https://merck.com/mmpe/sec05/ch062/ch062b.html A lung carcinoma that is characterized as any type of epithelial lung cancer other than small cell lung carcinoma. EFO:0003060 KEGG:05223 MESH:D002289 NCI:C2926 UMLS_CUI:C0007131 NSCLC Non-small cell lung cancer non-small cell lung carcinoma disease_ontology DOID:3908 lung non-small cell carcinoma non-small cell lung carcinoma non-small cell lung carcinoma 非小细胞肺癌 A lung carcinoma that is characterized as any type of epithelial lung cancer other than small cell lung carcinoma. url:http://en.wikipedia.org/wiki/Non-small-cell_lung_carcinoma An organ system cancer that is located_in the kidneys, ureteres, bladder or urethra. ICD10CM:C68.9 ICD9CM:189.9 UMLS_CUI:C0348371 disease_ontology DOID:3996 urinary system cancer An organ system cancer that is located_in the kidneys, ureteres, bladder or urethra. url:http://en.wikipedia.org/wiki/Urinary_system A disease is a disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. MESH:D004194 NCI:C2991 SNOMEDCT_US_2018_03_01:64572001 UMLS_CUI:C0012634 disease_ontology DOID:4 disease A disease is a disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. url:http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf A gastrointestinal system disease that is located_in the mouth. MESH:D009059 NCI:C27641 NCI:C3240 UMLS_CUI:C0026636 disease_ontology DOID:403 mouth disease A gastrointestinal system disease that is located_in the mouth. url:http://en.wikipedia.org/wiki/Oral_and_maxillofacial_pathology NCI2004_11_17:C6516 NCI:C6516 UMLS_CUI:C1334619 malignant tumor of Skeletal Muscle disease_ontology DOID:4043 skeletal muscle cancer A musculoskeletal system cancer that is located_in muscle. DOID:4046 ICD10CM:C49 MESH:D009217 MESH:D019042 NCI2004_11_17:C4883 NCI:C4883 SNOMEDCT_US_2018_03_01:20667008 SNOMEDCT_US_2018_03_01:93913006 UMLS_CUI:C0027095 UMLS_CUI:C0684743 malignant neoplasm of muscle malignant tumor of muscle malignant tumor of the Muscle myosarcoma disease_ontology DOID:4045 muscle cancer A musculoskeletal system cancer that is located_in muscle. url:http://en.wikipedia.org/wiki/Muscle An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells. GARD:10421 MESH:D012878 MTH:NOCODE NCI2004_11_17:C2920 NCI:C2920 SNOMEDCT_US_2018_03_01:94047004 UMLS_CUI:C0007114 CA - skin cancer malignant neoplasm of skin melanoma and Non-melanoma skin cancer disease_ontology cancer of skin DOID:4159 skin cancer An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells. url:http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0002414/ DOID:13974 DOID:4204 DOID:4208 GARD:8244 ICD10CM:C71.7 ICD9CM:191.7 MESH:D020295 NCI:C3570 NCI:C4869 NCI:C4975 NCI:C5967 SNOMEDCT_US_2018_03_01:93726004 UMLS_CUI:C0153641 UMLS_CUI:C0677866 UMLS_CUI:C0751886 UMLS_CUI:C1332192 malignant neoplasm of brain stem malignant neoplasm of brainstem neoplasm of adult brain stem neoplasm of brain stem primary brain Stem tumor primary brain stem neoplasm disease_ontology DOID:4203 brain stem cancer NCI2004_11_17:C6511 NCI:C6511 UMLS_CUI:C1334620 malignant tumor of Smooth Muscle disease_ontology DOID:4230 smooth muscle cancer DOID:6352 ICD10CM:C69.4 NCI2004_11_17:C4364 NCI2004_11_17:C4766 NCI:C4364 NCI:C4766 SNOMEDCT_US_2018_03_01:93756008 UMLS_CUI:C0339349 UMLS_CUI:C0496833 malignant neoplasm of ciliary body malignant tumor of ciliary body malignant tumor of the Ciliary body neoplasm of ciliary body tumor of the Ciliary body disease_ontology DOID:4352 ciliary body cancer NCI:C35775 SNOMEDCT_US_2018_03_01:68575007 UMLS_CUI:C0271100 disease_ontology DOID:4353 ciliary body disease A female reproductive organ cancer that is located_in the cervix. DOID:4361 CSP2005:2016-1746 ICD10CM:C53 ICD10CM:C53.9 ICD9CM:180 ICD9CM:180.9 MESH:D002583 NCI2004_11_17:C2940 NCI:C2940 NCI:C9311 OMIM:603956 SNOMEDCT_US_2018_03_01:93752005 UMLS_CUI:C0007847 UMLS_CUI:C0007873 cervical neoplasm cervix cancer cervix uteri cancer neoplasm of uterine cervix tumor of the Cervix Uteri uterine cervical neoplasm disease_ontology DOID:4362 cervical cancer A female reproductive organ cancer that is located_in the cervix. url:http://cancergenome.nih.gov/cancersselected/cervicalcancer url:http://en.wikipedia.org/wiki/Cervical_cancer url:http://www.cancer.gov/dictionary?CdrID=444973 DOID:770 ICD10CM:C69.2 ICD9CM:190.5 MESH:D019572 NCI2004_11_17:C3216 NCI2004_11_17:C4800 NCI:C3216 NCI:C4800 SNOMEDCT_US_2018_03_01:93987004 UMLS_CUI:C0024622 UMLS_CUI:C0524801 Retinal tumor malignant Retinal neoplasm malignant neoplasm of retina malignant tumor of retina neoplasm of retina disease_ontology DOID:4645 retinal cancer A brain cancer that is located_in the infratentorial region. DOID:4789 ICD10CM:C71.7 MESH:D015192 NCI2004_11_17:C3139 NCI2004_11_17:C4966 NCI:C3139 NCI:C4966 UMLS_CUI:C0021432 UMLS_CUI:C0751593 brain neoplasm, Infratentorial malignant Infratentorial tumors disease_ontology DOID:4706 infratentorial cancer A brain cancer that is located_in the infratentorial region. url:http://en.wikipedia.org/wiki/Tentorium_cerebelli url:http://www.ncbi.nlm.nih.gov/mesh/68015192 DOID:12343 ICD10CM:C65 ICD9CM:189.1 NCI2004_11_17:C6142 NCI2004_11_17:C7525 NCI:C6142 NCI:C7525 SNOMEDCT_US_2018_03_01:93985007 UMLS_CUI:C0153618 UMLS_CUI:C1335749 carcinoma of kidney Pelvis malignant neoplasm of renal pelvis malignant renal Pelvis neoplasm malignant tumor of renal pelvis renal pelvis cancer disease_ontology DOID:4919 renal pelvis carcinoma An organ system cancer located_in the thoracic cavity that develops in the different types of cells within the lungs, as well as less common cancers of the esophagus, the trachea, or the chest wall. DOID:3937 CSP2005:2005-5041 ICD10CM:C76.1 ICD9CM:195.1 MESH:D013899 NCI2004_11_17:C3406 NCI:C3406 NCI:C3576 UMLS_CUI:C0039981 UMLS_CUI:C0153661 Thoracic tumor thorax cancer thorax neoplasm tumor of thorax disease_ontology DOID:5093 thoracic cancer An organ system cancer located_in the thoracic cavity that develops in the different types of cells within the lungs, as well as less common cancers of the esophagus, the trachea, or the chest wall. url:http://www.advocatehealth.com/cmc/body.cfm?id=203 An artery disease that is characterized by degeneration of the cells composing the aortic wall. CSP2005:0571-0627 MESH:D001018 NCI:C101253 SNOMEDCT_US_2018_03_01:47040006 UMLS_CUI:C0003493 aortic disorder disorder of the aorta disease_ontology DOID:520 aortic disease An artery disease that is characterized by degeneration of the cells composing the aortic wall. url:http://www.hopkinsmedicine.org/heart_vascular_institute/conditions_treatments/conditions/aorta.html NCI2004_11_17:C4574 NCI:C4574 UMLS_CUI:C0346811 malignant neoplasm of Dermis malignant tumor of dermis disease_ontology DOID:5274 malignant dermis tumor A gastrointestinal system disease that is located_in the intestine. DOID:10759 DOID:11222 DOID:11789 DOID:8531 DOID:8558 DOID:8591 ICD10CM:K63.9 ICD9CM:569.9 MESH:D007410 NCI:C26801 SNOMEDCT_US_2018_03_01:85919009 UMLS_CUI:C0021831 disease_ontology DOID:5295 intestinal disease A gastrointestinal system disease that is located_in the intestine. url:http://en.wikipedia.org/wiki/Human_gastrointestinal_tract DOID:10758 CSP2005:1248-3971 MESH:D003108 UMLS_CUI:C0009373 colon disorder disease_ontology DOID:5353 colonic disease A stomach cancer that is located_in the stomach. EFO:0000178 NCI2004_11_17:C4911 NCI:C4911 UMLS_CUI:C0699791 cancer of the stomach carcinoma of stomach gastric carcinoma disease_ontology DOID:5517 stomach carcinoma A stomach cancer that is located_in the stomach. url:http://en.wikipedia.org/wiki/Stomach_cancer A urinary system disease that is located_in the kidney. EFO:0003086 ICD10CM:N08 ICD10CM:N28.9 MESH:D007674 NCI:C3149 NCI:C34843 SNOMEDCT_US_2018_03_01:90708001 UMLS_CUI:C0022658 nephropathy disease_ontology DOID:557 kidney disease A urinary system disease that is located_in the kidney. url:http://www.nlm.nih.gov/medlineplus/kidneydiseases.html A central nervous system cancer that is located_in the spinal cord. It is mostly formed from metastases from primary cancers elsewhere (commonly breast, prostate, and lung cancer). DOID:3638 DOID:7225 ICD10CM:C72.0 ICD9CM:192.2 MESH:D013120 MESH:D013125 NCI2004_11_17:C3381 NCI2004_11_17:C3382 NCI2004_11_17:C3572 NCI:C3381 NCI:C3572 SNOMEDCT_US_2018_03_01:94068003 UMLS_CUI:C0037930 UMLS_CUI:C0037939 UMLS_CUI:C0153646 Intraspinal tumor malignant tumor of the Spinal Cord spinal cord cancer spinal cord neoplasm tumor of the Spinal Cord disease_ontology spinal neoplasm DOID:5612 spinal cancer A central nervous system cancer that is located_in the spinal cord. It is mostly formed from metastases from primary cancers elsewhere (commonly breast, prostate, and lung cancer). url:http://en.wikipedia.org/wiki/Spinal_tumor An eye and adnexa disease that is located_in the eye. DOID:2933 ICD10CM:H44 ICD10CM:H44.9 ICD9CM:360 ICD9CM:360.9 ICD9CM:379.90 MESH:D005128 NCI:C26767 SNOMEDCT_US_2018_03_01:79517001 UMLS_CUI:C0015397 disease_ontology DOID:5614 eye disease An eye and adnexa disease that is located_in the eye. url:http://en.wikipedia.org/wiki/Eye_disease An intestinal cancer that effects the long, tube-like organ that is connected to the small intestine at one end and the anus at the other. DOID:1994 DOID:1997 ICD10CM:C18.9 MESH:D015179 NCI:C2955 NCI:C4978 NCI:C5105 SNOMEDCT_US_2018_03_01:93854002 UMLS_CUI:C0009402 UMLS_CUI:C0346629 UMLS_CUI:C1319315 disease_ontology DOID:5672 large intestine cancer An intestinal cancer that effects the long, tube-like organ that is connected to the small intestine at one end and the anus at the other. url:http://en.wikipedia.org/wiki/Large_intestine An eye disease that is located_in the retina. ICD10CM:H35.9 ICD9CM:362.9 MESH:D012164 NCI:C26875 NCI:C62601 SNOMEDCT_US_2018_03_01:29555009 SNOMEDCT_US_2018_03_01:35426003 UMLS_CUI:C0035309 disease_ontology DOID:5679 retinal disease An eye disease that is located_in the retina. url:http://en.wikipedia.org/wiki/Retina#Diseases_and_disorders A nervous system disease that affects the peripheral nervous system. DOID:13069 CSP2005:2042-6617 ICD10CM:G64 ICD9CM:350-359.99 MESH:D010523 MTH:516 NCI:C119734 NCI:C27580 NCI:C27587 SNOMEDCT_US_2018_03_01:42658009 UMLS_CUI:C0031117 UMLS_CUI:C1335029 disease_ontology peripheral nerve disease peripheral neuropathy DOID:574 peripheral nervous system disease A nervous system disease that affects the peripheral nervous system. url:http://en.wikipedia.org/w/index.php?title=Peripheral_neuropathy&redirect=no peripheral nerve disease MTH:516 A hematologic cancer and central nervous system neoplasm that is located_in the central nervous system. NCI2004_11_17:C5503 NCI:C5503 UMLS_CUI:C1332882 CNS hematopoietic tumor disease_ontology hematopoietic neoplasm of central nervous system DOID:5772 central nervous system hematologic cancer A hematologic cancer and central nervous system neoplasm that is located_in the central nervous system. url:http://www.oncologystat.com/journals/ew/YSONC/Central_Nervous_System_Disease_in_Hematologic_Malignancies_Historical_Perspective_and_Practical_Applications.html DOID:14538 NCI2004_11_17:C4570 NCI:C4570 NCI:C5346 SNOMEDCT_US_2018_03_01:93778001 UMLS_CUI:C0346612 UMLS_CUI:C1290401 malignant Endocardial tumor malignant neoplasm of endocardium malignant tumor of endocardium disease_ontology DOID:5877 endocardium cancer An artery disease that is located in the lungs. disease_ontology DOID:60001 pulmonary artery disease An artery disease that is located in the lungs. url:https://www.ncbi.nlm.nih.gov/pubmed/23737196 DOID:12757 ICD10CM:C69.1 ICD9CM:190.4 NCI2004_11_17:C3565 NCI2004_11_17:C4361 NCI:C3565 NCI:C4361 SNOMEDCT_US_2018_03_01:93766000 UMLS_CUI:C0153629 UMLS_CUI:C0339304 Corneal tumor malignant Corneal tumor malignant neoplasm of cornea malignant tumor of cornea neoplasm of cornea disease_ontology DOID:6199 cornea cancer A musculoskeletal system disease that affects tissues such as skin, tendons, and cartilage. CSP2005:0729-7208 MESH:D003240 NCI:C26729 UMLS_CUI:C0009782 connective tissue disorder disorder of connective tissue disease_ontology DOID:65 connective tissue disease A musculoskeletal system disease that affects tissues such as skin, tendons, and cartilage. url:http://www.niams.nih.gov/Health_Info/Scleroderma/default.asp An vascular disease that is characterized by dysfunction of the blood vessels supplying the brain. DOID:12214 DOID:3455 DOID:8231 CSP2005:0617-5539 EFO:0000712 ICD10CM:I60-I69 ICD10CM:I63.9 ICD10CM:I67.9 ICD9CM:430-438.99 ICD9CM:437.9 MESH:D002561 MESH:D020521 NCI:C2938 NCI:C3390 SNOMEDCT_US_2018_03_01:62914000 SNOMEDCT_US_2018_03_01:82797006 UMLS_CUI:C0007820 UMLS_CUI:C0038454 CVA Cerebrovascular accident cerebrovascular accident cerebrovascular disorder stroke disease_ontology DOID:6713 OMIM mapping confirmed by DO. [SN]. cerebrovascular disease An vascular disease that is characterized by dysfunction of the blood vessels supplying the brain. url:http://en.wikipedia.org/wiki/Cerebrovascular_disease url:http://www.ncbi.nlm.nih.gov/books/NBK378/ A disease that manifests in a defined anatomical structure. DOID:1 DOID:2 DOID:5 DOID:71 DOID:72 DOID:8 disease_ontology DOID:7 disease of anatomical entity A disease that manifests in a defined anatomical structure. url:http://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=anatomic A urinary system disease that is located_in the urethra. ICD10CM:N36.9 MESH:D014522 NCI2004_11_17:C26903 NCI:C26903 SNOMEDCT_US_2018_03_01:4985009 UMLS_CUI:C0041969 urethra disease disease_ontology DOID:732 urethral disease A urinary system disease that is located_in the urethra. url:http://www.nlm.nih.gov/medlineplus/urethraldisorders.html An urinary tract cancer that derives_from the tissues of the urethra. DOID:737 GARD:9390 ICD10CM:C68.0 ICD9CM:189.3 MESH:D014523 NCI2004_11_17:C7507 NCI:C7507 NCI:C9106 SNOMEDCT_US_2018_03_01:94123008 UMLS_CUI:C0153620 UMLS_CUI:C0700101 malignant tumour of urethra malignant urethral neoplasm urethral Ca disease_ontology cancer of urethra DOID:734 urethra cancer An urinary tract cancer that derives_from the tissues of the urethra. url:http://www.cancer.gov/cancertopics/pdq/treatment/urethral/Patient A disease of anatomical entity that has_material_basis_in hematopoietic cells. CSP2005:0427-3600 ICD10CM:D75.9 ICD9CM:280-289.99 ICD9CM:289.9 ICD9CM_2006:280-289.99 MESH:D006402 MTH:NOCODE MTHICD9_2006:289.9 NCI:C26323 SNOMEDCT_US_2018_03_01:34093004 UMLS_CUI:C0018939 Blood disease Blood dyscrasia DISEASE OF THE BLOOD AND BLOOD-FORMING ORGANS Hematological disease blood disorder disease of hematopoietic system disease_ontology DOID:74 hematopoietic system disease A disease of anatomical entity that has_material_basis_in hematopoietic cells. url:http://en.wikipedia.org/wiki/Hematopathology url:https://www.ncbi.nlm.nih.gov/books/NBK1741/ A gastrointestinal system disease that is located_in the stomach. MESH:D013272 NCI2004_11_17:C26886 NCI:C26886 SNOMEDCT_US_2018_03_01:29384001 UMLS_CUI:C0038354 Gastropathy stomach disorder disease_ontology gastric disease DOID:76 stomach disease A gastrointestinal system disease that is located_in the stomach. url:http://en.wikipedia.org/wiki/Stomach_disease A disease of anatomical entity that is located_in the gastrointestinal tract. DOID:27 DOID:944 CSP2005:1248-3545 ICD10CM:K92.9 ICD9CM:520-579.99 MESH:D004066 SNOMEDCT_US_2018_03_01:53619000 UMLS_CUI:C0012242 GIT disease Gastroenteropathy alimentary system disease digestive system disorder gastrointestinal disease gastrointestinal disorder disease_ontology DOID:77 gastrointestinal system disease A disease of anatomical entity that is located_in the gastrointestinal tract. url:http://en.wikipedia.org/wiki/Human_gastrointestinal_tract A lower respiratory tract disease in which the function of the lungs is adversely affected by narrowing or blockage of the airways resulting in poor air flow, a loss of elasticity in the lungs that produces a decrease in the total volume of air that the lungs are able to hold, and clotting, scarring, or inflammation of the blood vessels that affect the ability of the lungs to take up oxygen and to release carbon dioxide. DOID:11894 DOID:11895 DOID:29 DOID:766 ICD10CM:J98.4 MESH:D008171 NCI:C3198 SNOMEDCT_US_2018_03_01:19829001 UMLS_CUI:C0024115 disease_ontology DOID:850 Updating out dated CUI and removing lung abscess as a synonym. lung disease A lower respiratory tract disease in which the function of the lungs is adversely affected by narrowing or blockage of the airways resulting in poor air flow, a loss of elasticity in the lungs that produces a decrease in the total volume of air that the lungs are able to hold, and clotting, scarring, or inflammation of the blood vessels that affect the ability of the lungs to take up oxygen and to release carbon dioxide. url:http://www.niehs.nih.gov/health/topics/conditions/lung-disease/index.cfm url:http://www.nlm.nih.gov/medlineplus/ency/article/000066.htm A myeloid leukemia that is characterized by a dominance of monocytes in the marrow. DOID:8526 DOID:8809 DOID:8884 DOID:8935 DOID:9151 CSP2005:2004-2820 ICD10CM:C93 ICD9CM:206.8 UMLS_CUI:C0153903 Schilling's leukemia disease_ontology DOID:8527 monocytic leukemia A myeloid leukemia that is characterized by a dominance of monocytes in the marrow. url:https://en.wikipedia.org/wiki/Monocytic_leukemia DOID:8563 DOID:8605 DOID:8975 DOID:9031 DOID:9135 ICD10CM:C00 ICD10CM:C00.9 ICD9CM:140 ICD9CM:140.6 ICD9CM:140.8 MESH:D008048 MTHICD9_2006:140.4 MTHICD9_2006:140.5 MTHICD9_2006:140.6 MTHICD9_2006:140.9 NCI2004_11_17:C7485 NCI:C7485 SNOMEDCT_US_2018_03_01:93762003 SNOMEDCT_US_2018_03_01:93869001 UMLS_CUI:C0153340 UMLS_CUI:C0153346 UMLS_CUI:C0153347 malignant neoplasm of commissure of lip malignant neoplasm of external Lip, not specified as upper or lower malignant neoplasm of labial commissure of lip malignant neoplasm of lip malignant neoplasm of lip, external malignant neoplasm of lip, inner aspect malignant neoplasm of lip, vermilion border malignant neoplasm of lower lip, buccal aspect malignant neoplasm of lower lip, inner aspect malignant neoplasm of lower lip, mucosa malignant neoplasm of lower lip, oral aspect malignant neoplasm of oral aspect of lip, not specified whether upper or lower malignant neoplasm of other sites of lip malignant neoplasm of vermilion border of lip malignant tumor of commissure of lip malignant tumor of labial mucosa malignant tumor of lip malignant tumor of lower labial mucosa malignant tumor of the Lip malignant tumour of labial commissure malignant tumour of lip disease_ontology DOID:8564 lip cancer A gastrointestinal system cancer that is located_in the oral cavity. DOID:0050627 DOID:8617 DOID:9049 DOID:9055 GARD:9360 ICD10CM:C04 ICD10CM:C04.0 ICD10CM:C04.1 ICD10CM:C04.9 ICD9CM:144 ICD9CM:144.0 ICD9CM:144.1 ICD9CM:144.9 MTH:NOCODE MTH:U001372 NCI2004_11_17:C9318 NCI:C9318 SNOMEDCT_US_2018_03_01:93672006 SNOMEDCT_US_2018_03_01:93802007 SNOMEDCT_US_2018_03_01:93860002 UMLS_CUI:C0153368 UMLS_CUI:C0153369 UMLS_CUI:C0496758 malignant neoplasm of anterior portion of floor of mouth malignant neoplasm of floor of mouth malignant neoplasm of lateral floor of mouth malignant neoplasm of lateral portion of floor of mouth malignant tumor of anterior floor of mouth malignant tumor of lateral floor of mouth malignant tumor of the Floor of the Mouth disease_ontology DOID:8618 oral cavity cancer A gastrointestinal system cancer that is located_in the oral cavity. url:http://en.wikipedia.org/wiki/Oral_cancer A disease of anatomical entity that is located_in the central nervous system or located_in the peripheral nervous system. ICD10CM:G00-G99 ICD10CM:G98 ICD10CM:G98.8 ICD9CM:349.9 MESH:D009422 NCI:C26835 UMLS_CUI:C0027765 disease_ontology DOID:863 nervous system disease A disease of anatomical entity that is located_in the central nervous system or located_in the peripheral nervous system. url:http://en.wikipedia.org/wiki/Nervous_system A vascular disease that is located_in a vein. ICD10CM:I82 ICD9CM:453 UMLS_CUI:C0155774 disease_ontology DOID:866 vein disease A vascular disease that is located_in a vein. url:http://en.wikipedia.org/wiki/Vein#Venous_diseases A leukemia that is located_in myeloid tissue. DOID:8878 DOID:8879 DOID:8910 DOID:9066 DOID:9126 CSP2005:2004-4431 GARD:8226 ICD10CM:C92 ICD10CM:C92.9 ICD10CM:C92.90 ICD9CM:205 ICD9CM:205.9 MESH:D007951 MTH:NOCODE NCI2004_11_17:C3172 NCI:C3172 SNOMEDCT_US_2018_03_01:37810007 SNOMEDCT_US_2018_03_01:94717009 UMLS_CUI:C0023470 Non-Lymphocytic Leukemia leukemia myelogenous myeloid granulocytic leukemia disease_ontology DOID:8692 myeloid leukemia A leukemia that is located_in myeloid tissue. url:http://en.wikipedia.org/wiki/Myeloid_leukemia A monocytic leukemia where the majority of monocytic cells are promonocytes. DOID:9208 GARD:525 ICD9CM:206.0 MESH:D007948 NCI2004_11_17:C7318 OMIM:151380 SNOMEDCT_US_2018_03_01:22331004 SNOMEDCT_US_2018_03_01:91859000 UMLS_CUI:C0023465 acute Monoblastic Leukemia and acute Monocytic Leukemia acute monocytic leukemia without mention of remission acute monocytic leukemia, FAB M5 acute monocytic leukemia, morphology disease_ontology DOID:8864 OMIM mapping confirmed by DO. [SN]. acute monocytic leukemia acute monocytic leukemia 急性单核细胞性白血病 A monocytic leukemia where the majority of monocytic cells are promonocytes. url:https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=18.09d&ns=ncit&code=C4861 ICD10CM:C00.1 ICD9CM:140.1 SNOMEDCT_US_2018_03_01:94136008 UMLS_CUI:C0432520 disease_ontology DOID:8883 lower lip cancer A large intestine cancer that is located_in the colon and/or located_in the rectum. KEGG:05210 MESH:D015179 OMIM:114500 UMLS_CUI:C1527249 disease_ontology DOID:9256 Xref MGI. OMIM mapping confirmed by DO. [SN]. colorectal cancer A large intestine cancer that is located_in the colon and/or located_in the rectum. url:http://www.cancer.gov/dictionary?CdrID=444983 ICD10CM:K13.0 ICD9CM:528.5 ICD9CM_2006:528.5 MESH:D008047 NCI:C26818 SNOMEDCT_US_2018_03_01:90678009 UMLS_CUI:C0023760 disease of lips disease_ontology DOID:9297 lip disease DOID:14536 NCI2004_11_17:C4569 NCI2004_11_17:C5349 NCI:C4569 NCI:C5349 SNOMEDCT_US_2018_03_01:93914000 UMLS_CUI:C0346611 UMLS_CUI:C1290402 malignant Myocardial tumor malignant neoplasm of myocardium tumor of Myocardium disease_ontology DOID:9299 myocardium cancer An adnexa disease that is located_in the eye socket. ICD10CM:H05 ICD10CM:H05.9 ICD9CM:376 ICD9CM:376.9 MESH:D009916 SNOMEDCT_US_2018_03_01:11270005 UMLS_CUI:C0029182 disease_ontology DOID:930 orbital disease An adnexa disease that is located_in the eye socket. url:http://www.hopkinsmedicine.org/wilmer/services/oculofacial_plastic_surgery/reconstructive/orbital_disease.html A central nervous system disease that is located_in the brain. DOID:8510 ICD10CM:G93.40 ICD10CM:G93.9 ICD9CM:348.3 ICD9CM:348.30 ICD9CM:348.9 MESH:D001927 NCI:C26920 NCI:C96413 SNOMEDCT_US_2018_03_01:76011009 SNOMEDCT_US_2018_03_01:81308009 UMLS_CUI:C0006111 UMLS_CUI:C0085584 encephalopathy disease_ontology DOID:936 brain disease A central nervous system disease that is located_in the brain. url:https://medlineplus.gov/braindiseases.html A hematopoietic system disease that is located_in white blood cells. ICD10CM:D72.9 ICD9CM:288 ICD9CM:288.9 MESH:D007960 SNOMEDCT_US_2018_03_01:54097007 UMLS_CUI:C0023510 disease_ontology DOID:9500 leukocyte disease A hematopoietic system disease that is located_in white blood cells. url:https://rarediseases.org/rare-diseases/leukocyte-adhesion-deficiency-syndromes/ A respiratory system disease which involves the upper respiratory tract. ICD9CM:478.1 ICD9CM:478.19 UMLS_CUI:C0029581 disease_ontology DOID:974 upper respiratory tract disease A respiratory system disease which involves the upper respiratory tract. url:http://en.wikipedia.org/wiki/Category:Upper_respiratory_tract_diseases url:http://www.who.int/topics/respiratory_tract_diseases/en/ Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats. Wikipedia:Immune_system biological_process GO:0002376 Note that this term is a direct child of 'biological_process ; GO:0008150' because some immune system processes are types of cellular process (GO:0009987), whereas others are types of multicellular organism process (GO:0032501). This term was added by GO_REF:0000022. immune system process Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats. GOC:add GOC:mtg_15nov05 GO_REF:0000022 Any process that modulates the frequency, rate, or extent of an immune system process. biological_process GO:0002682 regulation of immune system process Any process that modulates the frequency, rate, or extent of an immune system process. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of an immune system process. down regulation of immune system process down-regulation of immune system process downregulation of immune system process inhibition of immune system process biological_process GO:0002683 negative regulation of immune system process Any process that stops, prevents, or reduces the frequency, rate, or extent of an immune system process. GOC:add Any process that activates or increases the frequency, rate, or extent of an immune system process. up regulation of immune system process up-regulation of immune system process upregulation of immune system process activation of immune system process stimulation of immune system process biological_process GO:0002684 positive regulation of immune system process Any process that activates or increases the frequency, rate, or extent of an immune system process. GOC:add molecular_function A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. molecular process GO:0005554 molecular function molecular_function GO:0003674 Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. GO:molecular_function molecular_function A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. GOC:pdt catalytic activity Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. Wikipedia:Enzyme enzyme activity molecular_function GO:0003824 catalytic activity Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. GOC:vw ISBN:0198506732 enzyme activity GOC:dph GOC:tb true Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function. receptor binding Wikipedia:Ligand_(biochemistry) receptor ligand molecular_function receptor-associated protein activity GO:0005102 Where appropriate, also consider annotating to 'receptor agonist activity ; GO:0048018'. signaling receptor binding Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function. GOC:bf GOC:ceb ISBN:0198506732 The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule. Wikipedia:Binding_(molecular) ligand molecular_function GO:0005488 Note that this term is in the subset of terms that should not be used for direct, manual gene product annotation. Please choose a more specific child term, or request a new one if no suitable term is available. For ligands that bind to signal transducing receptors, consider the molecular function term 'receptor binding ; GO:0005102' and its children. binding The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule. GOC:ceb GOC:mah ISBN:0198506732 Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules). GO:0001948 GO:0045308 MIPS_funcat:16.01 MIPS_funcat:18.01.07 Reactome:R-HSA-170835 Reactome:R-HSA-170846 protein amino acid binding glycoprotein binding molecular_function GO:0005515 protein binding Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules). GOC:go_curators Reactome:R-HSA-170835 An anchoring protein, ZFYVE9 (SARA), recruits SMAD2/3 Reactome:R-HSA-170846 TGFBR2 recruits TGFBR1 The chemical reactions and pathways involving the nonmetallic element phosphorus or compounds that contain phosphorus, usually in the form of a phosphate group (PO4). phosphorus metabolism biological_process GO:0006793 phosphorus metabolic process The chemical reactions and pathways involving the nonmetallic element phosphorus or compounds that contain phosphorus, usually in the form of a phosphate group (PO4). GOC:ai The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid. MIPS_funcat:01.04 phosphate metabolism biological_process phosphate metabolic process GO:0006796 phosphate-containing compound metabolic process The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid. GOC:ai immune response Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. MIPS_funcat:36.25.16 biological_process GO:0006955 This term was improved by GO_REF:0000022. It was redefined and moved. immune response Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. GOC:add GOC:mtg_15nov05 GO_REF:0000022 Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. Wikipedia:Cell_signaling biological_process GO:0007154 cell communication Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. GOC:mah The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. GO:0023033 MIPS_funcat:30 Wikipedia:Signal_transduction signaling cascade signalling cascade biological_process signaling pathway signalling pathway GO:0007165 Note that signal transduction is defined broadly to include a ligand interacting with a receptor, downstream signaling steps and a response being triggered. A change in form of the signal in every step is not necessary. Note that in many cases the end of this process is regulation of the initiation of transcription. Note that specific transcription factors may be annotated to this term, but core/general transcription machinery such as RNA polymerase should not. signal transduction The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. GOC:go_curators GOC:mtg_signaling_feb11 signalling pathway GOC:mah biological_process A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end. janelomax 2012-09-19T15:05:24Z GO:0000004 GO:0007582 GO:0044699 Wikipedia:Biological_process biological process physiological process biological_process single organism process single-organism process GO:0008150 Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this. biological_process A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. GOC:pdt The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. janelomax 2012-10-17T15:46:40Z GO:0044236 GO:0044710 MIPS_funcat:01 Wikipedia:Metabolism metabolism metabolic process resulting in cell growth metabolism resulting in cell growth multicellular organism metabolic process biological_process single-organism metabolic process GO:0008152 Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions. metabolic process The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. GOC:go_curators ISBN:0198547684 Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GO:0044252 down regulation of metabolic process down-regulation of metabolic process downregulation of metabolic process negative regulation of metabolism negative regulation of organismal metabolism inhibition of metabolic process inhibition of organismal metabolic process negative regulation of multicellular organismal metabolic process biological_process GO:0009892 negative regulation of metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GO:0044253 positive regulation of metabolism up regulation of metabolic process up-regulation of metabolic process upregulation of metabolic process activation of metabolic process positive regulation of multicellular organismal metabolic process positive regulation of organismal metabolism stimulation of metabolic process stimulation of organismal metabolic process up-regulation of organismal metabolic process biological_process GO:0009893 positive regulation of metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GOC:go_curators Any process that modulates the frequency, rate or extent of signal transduction. GO:0035466 biological_process regulation of signaling pathway regulation of signalling pathway GO:0009966 regulation of signal transduction Any process that modulates the frequency, rate or extent of signal transduction. GOC:sm regulation of signalling pathway GOC:mah Any process that activates or increases the frequency, rate or extent of signal transduction. GO:0035468 up regulation of signal transduction up-regulation of signal transduction upregulation of signal transduction activation of signal transduction stimulation of signal transduction biological_process positive regulation of signaling pathway positive regulation of signalling pathway GO:0009967 positive regulation of signal transduction Any process that activates or increases the frequency, rate or extent of signal transduction. GOC:sm positive regulation of signalling pathway GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction. GO:0035467 down regulation of signal transduction down-regulation of signal transduction downregulation of signal transduction inhibition of signal transduction biological_process negative regulation of signaling pathway negative regulation of signalling pathway GO:0009968 negative regulation of signal transduction Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction. GOC:sm negative regulation of signalling pathway GOC:mah cellular process Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. janelomax 2012-12-11T16:56:55Z GO:0008151 GO:0044763 GO:0050875 cell physiology cellular physiological process cell growth and/or maintenance biological_process single-organism cellular process GO:0009987 cellular process Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GOC:go_curators GOC:isa_complete Any process that modulates the frequency, rate or extent of a signaling receptor activity. Receptor activity is when a molecule combines with an extracellular or intracellular messenger to initiate a change in cell activity. regulation of receptor activity biological_process GO:0010469 regulation of signaling receptor activity Any process that modulates the frequency, rate or extent of a signaling receptor activity. Receptor activity is when a molecule combines with an extracellular or intracellular messenger to initiate a change in cell activity. GOC:dph GOC:tb Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus. biological_process GO:0010562 positive regulation of phosphorus metabolic process Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus. GOC:dph GOC:tb Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus. biological_process GO:0010563 negative regulation of phosphorus metabolic process Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus. GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. biological_process GO:0010646 regulation of cell communication Any process that modulates the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. GOC:dph GOC:tb Any process that increases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. biological_process GO:0010647 positive regulation of cell communication Any process that increases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. GOC:dph GOC:tb Any process that decreases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. biological_process GO:0010648 negative regulation of cell communication Any process that decreases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. GOC:dph GOC:tb true Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. Reactome:R-HSA-6788855 Reactome:R-HSA-6788867 phosphokinase activity molecular_function GO:0016301 Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term. kinase activity Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. ISBN:0198506732 Reactome:R-HSA-6788855 FN3KRP phosphorylates PsiAm, RibAm Reactome:R-HSA-6788867 FN3K phosphorylates ketosamines The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide. Wikipedia:Phosphorylation biological_process GO:0016310 phosphorylation The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide. ISBN:0198506732 Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. EC:2 Reactome:R-HSA-1483089 Reactome:R-HSA-1483186 Reactome:R-HSA-5668414 Reactome:R-HSA-6787403 Reactome:R-HSA-8868783 molecular_function GO:0016740 transferase activity Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. ISBN:0198506732 Reactome:R-HSA-1483089 PE is converted to PS by PTDSS2 Reactome:R-HSA-1483186 PC is converted to PS by PTDSS1 Reactome:R-HSA-5668414 TRAF2 ubiquitinates cIAP1,2 in cIAP1,2:TRAF1:TRAF2:TRAF3:NIK Reactome:R-HSA-6787403 GTPBP3 and MTO1 transform uridine-34 yielding 5-taurinomethyluridine-34 in tRNA Reactome:R-HSA-8868783 TSR3 transfers aminocarboxypropyl group from S-adenosylmethionine to N(1)-methylpseudouridine-1248 of 18SE rRNA yielding N(1)-methyl-N(3)-aminocarboxypropylpseudouridine-1248 Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor). EC:2.7 molecular_function GO:0016772 Note that this term encompasses all kinase activities, as well as activities that transfer other phosphorus-containing groups such as diphosphate or nucleotides. transferase activity, transferring phosphorus-containing groups Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor). GOC:jl ISBN:0198506732 Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphates. regulation of phosphate metabolism biological_process GO:0019220 regulation of phosphate metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphates. GOC:go_curators Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GO:0044246 regulation of metabolism regulation of multicellular organismal metabolic process regulation of organismal metabolic process biological_process GO:0019222 regulation of metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GOC:go_curators regulation of organismal metabolic process GOC:tb The attachment of a cell or organism to a substrate, another cell, or other organism. Biological adhesion includes intracellular attachment between membrane regions. biological_process GO:0022610 biological adhesion The attachment of a cell or organism to a substrate, another cell, or other organism. Biological adhesion includes intracellular attachment between membrane regions. GOC:isa_complete Any process that modulates the frequency, rate or extent of a signaling process. 2010-02-16T09:30:50Z biological_process regulation of signaling process regulation of signalling process GO:0023051 regulation of signaling Any process that modulates the frequency, rate or extent of a signaling process. GOC:mtg_signal regulation of signaling process GOC:bf regulation of signalling process GOC:mah The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered. janelomax 2010-02-16T09:30:50Z GO:0023046 GO:0044700 biological signaling signaling process signalling biological_process signalling process single organism signaling GO:0023052 Note that a signal is any variable property or parameter that serves to convey information, and may be a physical entity such as a gene product or small molecule, a photon, or a change in state such as movement or voltage change. signaling The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered. GOC:mtg_signal GOC:mtg_signaling_feb11 GOC:signaling signalling process GOC:mah Any process that activates, maintains or increases the frequency, rate or extent of a signaling process. 2010-02-16T09:30:50Z positive regulation of signalling process biological_process positive regulation of signaling process GO:0023056 positive regulation of signaling Any process that activates, maintains or increases the frequency, rate or extent of a signaling process. GOC:mtg_signal positive regulation of signalling process GOC:mah positive regulation of signaling process GOC:bf Any process that stops, prevents, or reduces the frequency, rate or extent of a signaling process. 2010-02-16T09:30:50Z biological_process negative regulation of signaling process negative regulation of signalling process GO:0023057 negative regulation of signaling Any process that stops, prevents, or reduces the frequency, rate or extent of a signaling process. GOC:mtg_signal negative regulation of signaling process GOC:bf negative regulation of signalling process GOC:mah The function of interacting (directly or indirectly) with receptors such that the proportion of receptors in the active form is changed. MIPS_funcat:18.02.07 molecular_function GO:0030545 receptor regulator activity The function of interacting (directly or indirectly) with receptors such that the proportion of receptors in the active form is changed. GOC:ceb The function of interacting (directly or indirectly) with receptors such that the proportion of receptors in the active form is increased. receptor activator activity molecular_function GO:0030546 signaling receptor activator activity The function of interacting (directly or indirectly) with receptors such that the proportion of receptors in the active form is increased. GOC:ceb Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. regulation of cellular metabolism biological_process GO:0031323 regulation of cellular metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. down regulation of cellular metabolic process down-regulation of cellular metabolic process downregulation of cellular metabolic process negative regulation of cellular metabolism inhibition of cellular metabolic process biological_process GO:0031324 negative regulation of cellular metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. GOC:mah Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. positive regulation of cellular metabolism up regulation of cellular metabolic process up-regulation of cellular metabolic process upregulation of cellular metabolic process activation of cellular metabolic process stimulation of cellular metabolic process biological_process GO:0031325 positive regulation of cellular metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of protein binding. down regulation of protein binding down-regulation of protein binding downregulation of protein binding inhibition of protein binding biological_process GO:0032091 negative regulation of protein binding Any process that stops, prevents, or reduces the frequency, rate or extent of protein binding. GOC:mah Any process that activates or increases the frequency, rate or extent of protein binding. up regulation of protein binding up-regulation of protein binding upregulation of protein binding activation of protein binding stimulation of protein binding biological_process GO:0032092 positive regulation of protein binding Any process that activates or increases the frequency, rate or extent of protein binding. GOC:mah Any process that modulates the frequency, rate or extent of any process in which a cell, a substance, or a cellular entity is transported to, or maintained in, a specific location. regulation of localisation biological_process GO:0032879 regulation of localization Any process that modulates the frequency, rate or extent of any process in which a cell, a substance, or a cellular entity is transported to, or maintained in, a specific location. GOC:mah regulation of localisation GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. down regulation of kinase activity down-regulation of kinase activity downregulation of kinase activity inhibition of kinase activity kinase inhibitor biological_process GO:0033673 negative regulation of kinase activity Any process that stops, prevents, or reduces the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. GOC:mah Any process that activates or increases the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. up regulation of kinase activity up-regulation of kinase activity upregulation of kinase activity kinase activator stimulation of kinase activity biological_process GO:0033674 positive regulation of kinase activity Any process that activates or increases the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. GOC:mah Receiving a signal and transmitting it in the cell to initiate a change in cell activity. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response. rfoulger 2011-08-01T02:45:27Z GO:0004872 GO:0019041 receptor activity receptor activity involved in signal transduction molecular_function GO:0038023 signaling receptor activity Receiving a signal and transmitting it in the cell to initiate a change in cell activity. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response. GOC:bf GOC:signaling receptor activity involved in signal transduction GOC:bf Any process that modulates the frequency, rate or extent of addition of phosphate groups into a molecule. biological_process GO:0042325 regulation of phosphorylation Any process that modulates the frequency, rate or extent of addition of phosphate groups into a molecule. GOC:jl Any process that stops, prevents or decreases the rate of addition of phosphate groups to a molecule. down regulation of phosphorylation down-regulation of phosphorylation downregulation of phosphorylation inhibition of phosphorylation biological_process GO:0042326 negative regulation of phosphorylation Any process that stops, prevents or decreases the rate of addition of phosphate groups to a molecule. GOC:jl Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to a molecule. up regulation of phosphorylation up-regulation of phosphorylation upregulation of phosphorylation activation of phosphorylation stimulation of phosphorylation biological_process GO:0042327 positive regulation of phosphorylation Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to a molecule. GOC:jl Any process that activates or increases the activity of an enzyme. GO:0048554 MIPS_funcat:18.02.01.01 positive regulation of enzyme activity up regulation of enzyme activity up-regulation of enzyme activity upregulation of enzyme activity activation of enzyme activity activation of metalloenzyme activity positive regulation of metalloenzyme activity stimulation of enzyme activity stimulation of metalloenzyme activity up regulation of metalloenzyme activity up-regulation of metalloenzyme activity upregulation of metalloenzyme activity biological_process GO:0043085 positive regulation of catalytic activity Any process that activates or increases the activity of an enzyme. GOC:ebc GOC:jl GOC:tb GOC:vw positive regulation of enzyme activity GOC:tb Any process that stops or reduces the activity of an enzyme. GO:0048553 down regulation of enzyme activity down-regulation of enzyme activity down-regulation of metalloenzyme activity downregulation of enzyme activity negative regulation of enzyme activity down regulation of metalloenzyme activity downregulation of metalloenzyme activity inhibition of enzyme activity inhibition of metalloenzyme activity negative regulation of metalloenzyme activity biological_process GO:0043086 negative regulation of catalytic activity Any process that stops or reduces the activity of an enzyme. GOC:ebc GOC:jl GOC:tb GOC:vw negative regulation of enzyme activity GOC:tb Any process that modulates the frequency, rate or extent of protein binding. biological_process GO:0043393 regulation of protein binding Any process that modulates the frequency, rate or extent of protein binding. GOC:go_curators Any process that modulates the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. biological_process GO:0043549 regulation of kinase activity Any process that modulates the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. GOC:bf Any process that modulates the frequency, rate or extent of a multi-organism process, a process in which an organism has an effect on another organism of the same or different species. biological_process GO:0043900 regulation of multi-organism process Any process that modulates the frequency, rate or extent of a multi-organism process, a process in which an organism has an effect on another organism of the same or different species. GOC:jl Any process that stops, prevents, or reduces the frequency, rate or extent of a multi-organism process, a process in which an organism has an effect on another organism of the same or different species. biological_process GO:0043901 negative regulation of multi-organism process Any process that stops, prevents, or reduces the frequency, rate or extent of a multi-organism process, a process in which an organism has an effect on another organism of the same or different species. GOC:jl Any process that activates or increases the frequency, rate or extent of a multi-organism process, a process in which an organism has an effect on another organism of the same or different species. biological_process GO:0043902 positive regulation of multi-organism process Any process that activates or increases the frequency, rate or extent of a multi-organism process, a process in which an organism has an effect on another organism of the same or different species. GOC:jl Any process that modulates the frequency, rate or extent of symbiosis, an interaction between two organisms living together in more or less intimate association. biological_process GO:0043903 regulation of symbiosis, encompassing mutualism through parasitism Any process that modulates the frequency, rate or extent of symbiosis, an interaction between two organisms living together in more or less intimate association. GOC:jl Any process that stops or reduces the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. jane 2009-04-21T04:07:27Z biological_process GO:0044092 negative regulation of molecular function Any process that stops or reduces the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. GO:jl Any process that activates or increases the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. jane 2009-04-21T04:11:06Z biological_process GO:0044093 positive regulation of molecular function Any process that activates or increases the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. GO:jl The chemical reactions and pathways by which individual cells transform chemical substances. cellular metabolism biological_process intermediary metabolism GO:0044237 cellular metabolic process The chemical reactions and pathways by which individual cells transform chemical substances. GOC:go_curators intermediary metabolism GOC:mah true A process carried out by symbiont gene products that enables the interaction between two organisms living together in more or less intimate association. The various forms of symbiosis include parasitism, in which the association is disadvantageous or destructive to one of the organisms; mutualism, in which the association is advantageous, or often necessary to one or both and not harmful to either; and commensalism, in which one member of the association benefits while the other is not affected. However, mutualism, parasitism, and commensalism are often not discrete categories of interactions and should rather be perceived as a continuum of interaction ranging from parasitism to mutualism. In fact, the direction of a symbiotic interaction can change during the lifetime of the symbionts due to developmental changes as well as changes in the biotic/abiotic environment in which the interaction occurs. Microscopic symbionts are often referred to as endosymbionts. GO:0043298 GO:0044404 GO:0072519 GO:0085031 commensalism host-pathogen interaction parasitism biological_process symbiosis symbiosis, encompassing mutualism through parasitism symbiotic interaction symbiotic interaction between host and organism symbiotic interaction between organisms symbiotic interaction between species GO:0044403 Changed term, definition see https://github.com/geneontology/go-ontology/issues/14807 symbiosis, encompassing mutualism through parasitism symbiotic process A process carried out by symbiont gene products that enables the interaction between two organisms living together in more or less intimate association. The various forms of symbiosis include parasitism, in which the association is disadvantageous or destructive to one of the organisms; mutualism, in which the association is advantageous, or often necessary to one or both and not harmful to either; and commensalism, in which one member of the association benefits while the other is not affected. However, mutualism, parasitism, and commensalism are often not discrete categories of interactions and should rather be perceived as a continuum of interaction ranging from parasitism to mutualism. In fact, the direction of a symbiotic interaction can change during the lifetime of the symbionts due to developmental changes as well as changes in the biotic/abiotic environment in which the interaction occurs. Microscopic symbionts are often referred to as endosymbionts. GOC:cc https://study.com/academy/lesson/symbiont-definition-lesson-quiz.html The attachment of a symbiont to its host via adhesion molecules, general stickiness etc., either directly or indirectly. The host is defined as the larger of the organisms involved in a symbiotic interaction. GO:0051825 GO:0051856 adhesion to other organism involved in symbiotic interaction adhesion to host adhesion to symbiont host adhesion biological_process adhesion to other organism during symbiotic interaction GO:0044406 This term can be used to annotate both symbiont and host organisms. Consider also annotating to interaction with host ; GO:0051702, or interaction with symbiont ; GO:0051702. adhesion of symbiont to host The attachment of a symbiont to its host via adhesion molecules, general stickiness etc., either directly or indirectly. The host is defined as the larger of the organisms involved in a symbiotic interaction. GOC:bf GOC:cc GOC:dos GOC:jl adhesion to other organism during symbiotic interaction GOC:dph Any process in which an organism has an effect on an organism of a different species. interaction with another species interspecies interaction interspecies interaction with other organisms biological_process GO:0044419 interspecies interaction between organisms Any process in which an organism has an effect on an organism of a different species. GOC:cc Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving phosphates. down regulation of phosphate metabolic process down-regulation of phosphate metabolic process downregulation of phosphate metabolic process negative regulation of phosphate metabolism inhibition of phosphate metabolic process biological_process GO:0045936 negative regulation of phosphate metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving phosphates. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving phosphates. positive regulation of phosphate metabolism up regulation of phosphate metabolic process up-regulation of phosphate metabolic process upregulation of phosphate metabolic process activation of phosphate metabolic process stimulation of phosphate metabolic process biological_process GO:0045937 positive regulation of phosphate metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving phosphates. GOC:go_curators The activity of a gene product that interacts with a receptor to effect a change in the activity of the receptor. Ligands may be produced by the same, or different, cell that expresses the receptor. Ligands may diffuse extracellularly from their point of origin to the receiving cell, or remain attached to an adjacent cell surface (e.g. Notch ligands). midori 2010-09-13T04:51:59Z GO:0071884 receptor agonist activity signaling molecule signaling receptor ligand activity vitamin D receptor activator activity molecular_function GO:0048018 Definition discussed in https://github.com/geneontology/go-ontology/issues/14220 receptor ligand activity The activity of a gene product that interacts with a receptor to effect a change in the activity of the receptor. Ligands may be produced by the same, or different, cell that expresses the receptor. Ligands may diffuse extracellularly from their point of origin to the receiving cell, or remain attached to an adjacent cell surface (e.g. Notch ligands). GOC:kv GOC:molecular_function_refactoring GOC:pdt receptor agonist activity GOC:molecular_function_refactoring Any process that activates or increases the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. GO:0043119 positive regulation of physiological process up regulation of biological process up-regulation of biological process upregulation of biological process activation of biological process stimulation of biological process biological_process GO:0048518 positive regulation of biological process Any process that activates or increases the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. GOC:jid Any process that stops, prevents, or reduces the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. GO:0043118 down regulation of biological process down-regulation of biological process downregulation of biological process negative regulation of physiological process inhibition of biological process biological_process GO:0048519 negative regulation of biological process Any process that stops, prevents, or reduces the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. GOC:jid Any process that activates or increases the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GO:0051242 positive regulation of cellular physiological process up regulation of cellular process up-regulation of cellular process upregulation of cellular process activation of cellular process stimulation of cellular process biological_process GO:0048522 positive regulation of cellular process Any process that activates or increases the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GOC:jid Any process that stops, prevents, or reduces the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GO:0051243 down regulation of cellular process down-regulation of cellular process downregulation of cellular process negative regulation of cellular physiological process inhibition of cellular process biological_process GO:0048523 negative regulation of cellular process Any process that stops, prevents, or reduces the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GOC:jid Any process that modulates the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. biological_process GO:0048583 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. regulation of response to stimulus Any process that modulates the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. GOC:jid Any process that activates, maintains or increases the rate of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. up regulation of response to stimulus up-regulation of response to stimulus upregulation of response to stimulus activation of response to stimulus stimulation of response to stimulus biological_process GO:0048584 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. positive regulation of response to stimulus Any process that activates, maintains or increases the rate of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. GOC:jid Any process that stops, prevents, or reduces the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. down regulation of response to stimulus down-regulation of response to stimulus downregulation of response to stimulus inhibition of response to stimulus biological_process GO:0048585 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. negative regulation of response to stimulus Any process that stops, prevents, or reduces the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. GOC:jid Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus. biological_process GO:0050776 regulation of immune response Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus. down regulation of immune response down-regulation of immune response downregulation of immune response inhibition of immune response biological_process GO:0050777 negative regulation of immune response Any process that stops, prevents, or reduces the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus. GOC:ai Any process that activates or increases the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus. up regulation of immune response up-regulation of immune response upregulation of immune response stimulation of immune response biological_process GO:0050778 positive regulation of immune response Any process that activates or increases the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus. GOC:ai Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. GO:0050791 regulation of physiological process biological_process GO:0050789 regulation of biological process Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. GOC:ai GOC:go_curators Any process that modulates the activity of an enzyme. GO:0048552 MIPS_funcat:18.02.01 regulation of enzyme activity regulation of metalloenzyme activity biological_process GO:0050790 regulation of catalytic activity Any process that modulates the activity of an enzyme. GOC:ai GOC:ebc GOC:vw Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GO:0051244 regulation of cellular physiological process biological_process GO:0050794 regulation of cellular process Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GOC:go_curators response to stimulus Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism. GO:0051869 MIPS_funcat:34.11 physiological response to stimulus biological_process GO:0050896 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. response to stimulus Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism. GOC:ai GOC:bf Any process that modulates the frequency, rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule. biological_process GO:0051098 regulation of binding Any process that modulates the frequency, rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule. GOC:ai Any process that activates or increases the rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule. up regulation of binding up-regulation of binding upregulation of binding activation of binding stimulation of binding biological_process GO:0051099 positive regulation of binding Any process that activates or increases the rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule. GOC:ai Any process that stops or reduces the rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule. down regulation of binding down-regulation of binding downregulation of binding inhibition of binding biological_process GO:0051100 negative regulation of binding Any process that stops or reduces the rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule. GOC:ai Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus. regulation of phosphorus metabolism biological_process GO:0051174 regulation of phosphorus metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus. GOC:ai Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation. jl 2013-12-18T13:51:04Z GO:1902578 establishment and maintenance of localization establishment and maintenance of position localisation establishment and maintenance of cellular component location establishment and maintenance of substance location establishment and maintenance of substrate location biological_process single organism localization single-organism localization GO:0051179 localization Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation. GOC:ai GOC:dos localisation GOC:mah single organism localization GOC:TermGenie Any process that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation. Gene Ontology: http://purl.obolibrary.org/obo/go.owl establishment of localisation biological_process GO:0051234 establishment of localization Any process that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation. GOC:ai GOC:dos establishment of localisation GOC:mah Any process that modulates the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. transferase regulator biological_process GO:0051338 This term is useful for grouping, but is too general for manual annotation. Please use a child term instead. regulation of transferase activity Any process that modulates the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. EC:2.-.-.- GOC:ai Any process that activates or increases the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor. transferase activator up regulation of transferase activity up-regulation of transferase activity upregulation of transferase activity activation of transferase activity stimulation of transferase activity biological_process GO:0051347 This term is useful for grouping, but is too general for manual annotation. Please use a child term instead. positive regulation of transferase activity Any process that activates or increases the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor. GOC:ai Any process that stops or reduces the rate of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor. down regulation of transferase activity down-regulation of transferase activity downregulation of transferase activity transferase inhibitor inhibition of transferase activity biological_process GO:0051348 This term is useful for grouping, but is too general for manual annotation. Please use a child term instead. negative regulation of transferase activity Any process that stops or reduces the rate of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor. GOC:ai A biological process which involves another organism of the same or different species. GO:0051706 interaction between organisms physiological interaction between organisms physiological interaction with other organism biological_process GO:0051704 multi-organism process A biological process which involves another organism of the same or different species. GOC:jl Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus by a cell and ends with a change in state or activity or the cell. biological_process GO:0051716 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. cellular response to stimulus Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus by a cell and ends with a change in state or activity or the cell. GOC:bf GOC:jl A compound molecular function in which an effector function is controlled by one or more regulatory components. molecular_function GO:0060089 molecular transducer activity A compound molecular function in which an effector function is controlled by one or more regulatory components. GOC:dos GOC:pdt Any process that modulates a measurable attribute of any biological process, quality or function. regulation biological_process GO:0065007 biological regulation Any process that modulates a measurable attribute of any biological process, quality or function. GOC:dph GOC:isa_complete GOC:mah GOC:pr GOC:vw Any process that modulates the frequency, rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. regulation of a molecular function biological_process GO:0065009 regulation of molecular function Any process that modulates the frequency, rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. GOC:isa_complete A molecular function that modulates the activity of a gene product or complex. Examples include enzyme regulators and channel regulators. molecular_function GO:0098772 molecular function regulator A molecular function that modulates the activity of a gene product or complex. Examples include enzyme regulators and channel regulators. GOC:dos GOC:pt Any process that modulates the frequency, rate or extent of a protein or other molecule binding to a receptor. bf 2012-02-22T11:40:53Z regulation of receptor ligand biological_process GO:1900120 regulation of receptor binding Any process that modulates the frequency, rate or extent of a protein or other molecule binding to a receptor. GOC:TermGenie GOC:signaling regulation of receptor ligand GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of a protein or other molecule binding to a receptor. bf 2012-02-22T11:40:57Z down regulation of receptor binding down-regulation of receptor binding downregulation of receptor binding inhibition of receptor binding inhibition of receptor ligand biological_process down regulation of receptor-associated protein activity GO:1900121 negative regulation of receptor binding Any process that stops, prevents or reduces the frequency, rate or extent of a protein or other molecule binding to a receptor. GOC:TermGenie GOC:signaling down regulation of receptor binding GOC:TermGenie down-regulation of receptor binding GOC:TermGenie downregulation of receptor binding GOC:TermGenie inhibition of receptor binding GOC:TermGenie inhibition of receptor ligand GOC:TermGenie down regulation of receptor-associated protein activity GOC:TermGenie Any process that activates or increases the frequency, rate or extent of a protein or other molecule binding to a receptor. bf 2012-02-22T11:41:00Z up regulation of receptor binding upregulation of receptor binding activation of receptor binding biological_process GO:1900122 positive regulation of receptor binding Any process that activates or increases the frequency, rate or extent of a protein or other molecule binding to a receptor. GOC:TermGenie GOC:signaling up regulation of receptor binding GOC:TermGenie upregulation of receptor binding GOC:TermGenie activation of receptor binding GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of a signaling receptor activity. rfoulger 2010-12-02T09:28:47Z negative regulation of receptor activity biological_process GO:2000272 negative regulation of signaling receptor activity Any process that stops, prevents or reduces the frequency, rate or extent of a signaling receptor activity. GOC:obol Any process that activates or increases the frequency, rate or extent of signaling receptor activity. rfoulger 2010-12-02T09:28:50Z biological_process GO:2000273 positive regulation of signaling receptor activity Any process that activates or increases the frequency, rate or extent of signaling receptor activity. GOC:obol measurement unit label Examples of measurement unit labels are liters, inches, weight per volume. A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure. 2009-03-16: provenance: a term measurement unit was proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and Cristian Cocos, and subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definition of this, different, term. 2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. PERSON: Alan Ruttenberg PERSON: Melanie Courtot measurement unit label objective specification In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction. a directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed." 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that. Answers the question, why did you do this experiment? PERSON: Alan Ruttenberg PERSON: Barry Smith PERSON: Bjoern Peters PERSON: Jennifer Fostel goal specification OBI Plan and Planned Process/Roles Branch OBI_0000217 objective specification Pour the contents of flask 1 into flask 2 a directive information entity that describes an action the bearer will take Alan Ruttenberg OBI Plan and Planned Process branch action specification datum label A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n GROUP: IAO 9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum. datum label software Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit. see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178 PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Chris Stoeckert PERSON: Melanie Courtot GROUP: OBI software information carrier In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case. A quality of an information bearer that imparts the information content 12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'. 2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it. PERSON: Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy information carrier data item Data items include counts of things, analyte concentrations, and statistical summaries. a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief PERSON: Alan Ruttenberg PERSON: Chris Stoeckert PERSON: Jonathan Rees data data item information content entity Examples of information content entites include journal articles, data, graphical layouts, and graphs. A generically dependent continuant that is about some thing. An information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ). information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. PERSON: Chris Stoeckert OBI_0000142 information content entity An information content entity whose concretizations indicate to their bearer how to realize them in a process. 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it. 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan PERSON: Alan Ruttenberg PERSON: Bjoern Peters directive information content entity directive information entity dot plot Dot plot of SSC-H and FSC-H. A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions. person:Allyson Lister person:Chris Stoeckert OBI_0000123 group:OBI dot plot graph A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way. PERSON: Lawrence Hunter person:Alan Ruttenberg person:Allyson Lister OBI_0000240 group:OBI graph algorithm PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies. A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata. Philippe Rocca-Serra PlanAndPlannedProcess Branch OBI_0000270 adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg) algorithm curation status specification The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) PERSON:Bill Bug GROUP:OBI:<http://purl.obolibrary.org/obo/obi> OBI_0000266 curation status specification data format specification A data format specification is the information content borne by the document published defining the specification. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file 2009-03-16: provenance: term imported from OBI_0000187, which had original definition "A data format specification is a plan which organizes information. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file" PERSON: Alan Ruttenberg PlanAndPlannedProcess Branch OBI branch derived OBI_0000187 data format specification data set Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction. person:Allyson Lister person:Chris Stoeckert OBI_0000042 group:OBI data set image An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface. person:Alan Ruttenberg person:Allyson person:Chris Stoeckert OBI_0000030 group:OBI image data about an ontology part is a data item about a part of an ontology, for example a term Person:Alan Ruttenberg data about an ontology part plan specification PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice. A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. 2014-03-31: A plan specification can have other parts, such as conditional specifications. Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved Alan Ruttenberg OBI Plan and Planned Process branch OBI_0000344 2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them plan specification material information bearer A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier. a brain a hard drive A material entity in which a concretization of an information content entity inheres. GROUP: IAO material information bearer histogram A histogram is a report graph which is a statistical description of a distribution in terms of occurrence frequencies of different event classes. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot GROUP:OBI histogram heatmap A heatmap is a report graph which is a graphical representation of data where the values taken by a variable(s) are shown as colors in a two-dimensional map. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot GROUP:OBI heatmap dendrogram Dendrograms are often used in computational biology to illustrate the clustering of genes. A dendrogram is a report graph which is a tree diagram frequently used to illustrate the arrangement of the clusters produced by a clustering algorithm. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot WEB: http://en.wikipedia.org/wiki/Dendrogram dendrogram scatter plot Comparison of gene expression values in two samples can be displayed in a scatter plot A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot scattergraph WEB: http://en.wikipedia.org/wiki/Scatterplot scatter plot obsolescence reason specification The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. PERSON: Alan Ruttenberg PERSON: Melanie Courtot obsolescence reason specification figure Any picture, diagram or table An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something. PERSON: Lawrence Hunter figure diagram A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space. A figure that expresses one or more propositions PERSON: Lawrence Hunter diagram document A journal article, patent application, laboratory notebook, or a book A collection of information content entities intended to be understood together as a whole PERSON: Lawrence Hunter document The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. A denotator type indicates how a term should be interpreted from an ontological perspective. Alan Ruttenberg Barry Smith, Werner Ceusters denotator type A role borne by an infectious agent when contained in a host in which its infectious disposition can be realized. Albert Goldfain Alexander Diehl Lindsay Cowell infectious agent role A role borne by pathogen in virtue of the fact that it or one of its products is sufficiently close to an organism towards which it has the pathogenic disposition to allow realization of the pathogenic disposition. Albert Goldfain Alexander Diehl Lindsay Cowell Clostridium botulinum is an example of an entity with the capability to bear the pathogen role but that does not have the capability to bear the infectious agent role or the parasite role. The influenza viruses are examples of organisms that can bear both the infectious agent and pathogen roles. pathogen role A disposition borne by a biological macromolecule produced by a pathogen that is a disposition to undergo processes that increase the pathogen's virulence. Albert Goldfain Alexander Diehl Lindsay Cowell The virulence factor disposition is typically realized in processes that improve survival of the pathogen in a host, increase the likelihood of transmission to a host, or cause pathological processes in a host. virulence factor disposition A role borne by an infectious disorder in virtue of the fact that (1) the host has at least two distinct infectious disorders, where neither arose from the other through metastasis, (2) at the time the infectious disorder was established in the host, the host had no infectious disorder, and (3) the infectious disorder increases the host's susceptibility to infectious disorders. Albert Goldfain Alexander Diehl Lindsay Cowell The role is realized in a process by which the infectious disorder is established in the host. primary infection role A role borne by an infectious disorder in virtue of the fact that (1) the host has at least two distinct infectious disorders, where neither arose from the other through metastasis, (2) at the time the infectious disorder was established in the host, the host had a primary infectious disorder, and (3) establishment of the infectious disorder occurs because of increased susceptibility to infectious disorders conferred by the primary infectious disorder. Albert Goldfain Alexander Diehl Lindsay Cowell The role is realized in a process by which the infectious disorder is established in the host. secondary infection role A disease whose physical basis is an infectious disorder. Albert Goldfain Alexander Diehl Lindsay Cowell tranmissible disease The disposition is realized in an infectious disease course. infectious disease A disposition borne by a biological macromolecule that is the disposition to participate in adherence to a host. Albert Goldfain Alexander Diehl Lindsay Cowell The disposition is realized in an adherence to host process. adhesion disposition A disposition to initiate processes that result in a disorder. Albert Goldfain Alexander Diehl Lindsay Cowell pathogenicity A pathogenic disposition is realized in processes that create a disorder. The use of 'initiates' is intended to convey that a pathogenic disposition is realized when processes resulting in a disorder begin because of some action on the part of the bearer of the disposition. By this interpretation of 'initiates', disorder-causing entities such as glass, UV light, and toxins do not have a pathogenic disposition. pathogenic disposition A pathogenic disposition that inheres in an organism and is a disposition for that organism (1) to be transmitted to a host, (2) to establish itself in the host, (3) to initiate processes that result in a disorder in the host, and (4) to become part of that disorder. Albert Goldfain Alexander Diehl Lindsay Cowell The disposition is realized in a process that has as part a transmission process, an establishment in host process, a process that results in a disorder, and a process in which the bearer of the disposition becomes part of that disorder. The infectious disposition has a complementary disposition that inheres in an organism and is the capability to be host to an organism with an infectious disposition and to undergo processes initiated by that infectious organism that result in a disorder. infectious disposition A quality that inheres in an entity and is the degree to which it can be harmed by another entity. Albert Goldfain Alexander Diehl Lindsay Cowell Low susceptibility is often referred to as resistance. In this sense, resistance is a quality. susceptibility A susceptibility that inheres in an organism and is the degree to which it can be harmed by an infectious agent. Albert Goldfain Alexander Diehl Lindsay Cowell susceptibility to infectious agent An infection comprised of infectious organisms from different Species. Albert Goldfain Alexander Diehl Lindsay Cowell mixed infection polymicrobial infection complex infection An infection for which the infectious agents that are part of the infection persist in the extracellular space of the host. Albert Goldfain Alexander Diehl Lindsay Cowell extracellular infection An infection for which the infectious agents that are part of the infection persist inside host cells. Albert Goldfain Alexander Diehl Lindsay Cowell intracellular infection An infection for which the infectious agents that are part of the infection are distributed throughout the host. Albert Goldfain Alexander Diehl Lindsay Cowell systemic infection An infection for which the infectious agents that are part of the infection are limited to a relatively small area of the host's body. Albert Goldfain Alexander Diehl Lindsay Cowell local infection A local infection for which symptoms are observed in parts of the host's extended organism that are distant from the infection. Albert Goldfain Alexander Diehl Lindsay Cowell focal infection An infectious disease course that begins soon after infection is established and progresses rapidly to severe stages. Albert Goldfain Alexander Diehl Lindsay Cowell acute infectious disease course A disease course that is the realization of an infectious disease. Albert Goldfain Alexander Diehl Lindsay Cowell infectious disease course An infection that is clinically abnormal. Albert Goldfain Alexander Diehl Lindsay Cowell infectious disorder An infection that has as part virus particles located in the blood. Albert Goldfain Alexander Diehl Lindsay Cowell viremia An infection that has as part bacteria located in the blood. Albert Goldfain Alexander Diehl Lindsay Cowell bacteremia A material entity with a pathogenic disposition. Albert Goldfain Alexander Diehl Lindsay Cowell pathogen An organism bearing a host role. Albert Goldfain Alexander Diehl Lindsay Cowell host A biological macromolecule produced by a pathogen and that has a virulence factor disposition. Albert Goldfain Alexander Diehl Lindsay Cowell virulence factor A biological macromolecule that has an adhesion disposition. Albert Goldfain Alexander Diehl Lindsay Cowell adhesin adhesion molecule adhesion factor An infection bearing the primary infection role. Albert Goldfain Alexander Diehl Lindsay Cowell primary infection An infection bearing the secondary infection role. Albert Goldfain Alexander Diehl Lindsay Cowell secondary infection An infection that is part of an asymptomatic host. Albert Goldfain Alexander Diehl Lindsay Cowell subclinical infection infection A part of an extended organism that itself has as part a population of one or more infectious agents and that (1) exists as a result of processes initiated by members of the infectious agent population and is (2) clinically abnormal in virtue of the presence of this infectious agent population, or (3) has a disposition to bring clinical abnormality to immunocompetent organisms of the same Species as the host (the organism corresponding to the extended organism) through transmission of a member or offspring of a member of the infectious agent population. Albert Goldfain Alexander Diehl Lindsay Cowell The organism corresponding to the extended organism is host to the infectious agents. By this definition, parts of the host can be considered part of the infection. infection An organism that has an infectious disposition. Albert Goldfain Alexander Diehl Lindsay Cowell infectious agent An establishment of localization process in which a material entity reaches a site in an organism in which it can survive, grow, multiply, or mature. Requested addition of this term to the GO. Albert Goldfain Alexander Diehl Lindsay Cowell An organism begins bearing a particular host role as soon as the extended organism contains the relevant material entity, regardless of that entity's location in the extended organism. An establishment process is any process by which the entity reaches a location in the extended organism in which it can persist and continue its lifecycle. For example, an organism is host to a virus as soon as any part of the extended organism is occupied by virus particles. During an establishment process, virus particles enter host cells of the relevant type, and viral DNA is integrated into host DNA. establishment of localization in host A process by which a disorder comes into existence. Albert Goldfain Alexander Diehl Lindsay Cowell appearance of disorder An infectious disorder that is the physical basis for an unfolding acute infectious disease course. Albert Goldfain Alexander Diehl Lindsay Cowell acute infection An infection that persists for an extended period of time. Albert Goldfain Alexander Diehl Lindsay Cowell persistent infection chronic infection A role borne by an organism in virtue of the fact that it's extended organism contains a material entity other than the organism. Albert Goldfain Alexander Diehl Lindsay Cowell host role An infection resulting from a transmission process that unfolds in a hospital. Albert Goldfain Alexander Diehl Lindsay Cowell nosocomial infection hospital-acquired infection An infection resulting from a transmission process that did not unfold in a health care facility. Albert Goldfain Alexander Diehl Lindsay Cowell community-acquired infection An infection established as a result of spread from another infection in a non-adjacent location in the extended organism of the host. Albert Goldfain Alexander Diehl Lindsay Cowell metatstatic infection An infection resulting from a transmission process that unfolds in a nursing home. Albert Goldfain Alexander Diehl Lindsay Cowell nursing-home acquired infection An infection comprised of infectious organisms all of the same Species. Albert Goldfain Alexander Diehl Lindsay Cowell simple infection An infection that has as part organisms of the Genus Candida. Albert Goldfain Alexander Diehl Lindsay Cowell candidiasis An infection that has as part organisms of the Species Trichomonas vaginalis. Albert Goldfain Alexander Diehl Lindsay Cowell trichomoniasis An infection that has as part organisms of the Genus Leptospira. Albert Goldfain Alexander Diehl Lindsay Cowell leptospirosis An infection located in the bowel and that has as part organisms of the Genus Shigella. Albert Goldfain Alexander Diehl Lindsay Cowell Shigellosis An infection located in the colon and that has as part organisms of the Species Entamoeba histolytica Albert Goldfain Alexander Diehl Lindsay Cowell amebiasis Interaction is a processual entity that has two or more participants (i.e., interactors) that have an effect upon one another. YH, ZX interact, interacted, interacting, interaction, interaction, interactor, interactors, interacts, participates; plays a role, contribute, contributed, contributes, contributing, engagement, engagements, engages, engaging, involve, involved, involves, involving, act, acted, acting, acts interaction an regulator role that is borne by a material entity that regulates an interaction. YH regulator role an interactor role that is borne by a material entity that acts as an input of an interaction. YH, ZX interaction input role input interactor role an interactor role that is borne by a material entity that acts as an output of an interaction. YH, ZX interaction output role output interactor role a positive regulator role that is borne by a material entity that activates an interaction. YH activator role a role that is borne by a material entity to act as a participant in an interaction process. YH, ZX interactor role an interactor role that is played by a material entity that starts or speeds up a chemical reaction while undergoing no permanent change itself. YH chemical reaction catalyst role an interactor role that is borne by a material entity that positively regulates an interaction. YH positive regulator role an interactor role that is borne by a material entity that negatively regulates an interaction. YH negative regulator role a negative regulator role that is borne by a material entity that deactivates, inhibits, blocks, or disrupts the action of a biological agent (e.g., enzyme). YH deactivator role an input interactor role that is borne by a material entity that motivates a process. Oliver He https://en.wikipedia.org/wiki/Motivation#Herzberg's_two-factor_theory motivator role an input interactor role that is borne by a material entity (e.g. status, job security, salary and fringe benefits) that do not motivate if present, but, if absent, result in demotivation. Oliver He https://en.wikipedia.org/wiki/Motivation#Herzberg's_two-factor_theory hygiene factor role GC_ID:1 hamsters ncbi_taxonomy Cricetinae ncbi_taxonomy Cgri- Chinese hamster NCBITaxon:10029 Cricetulus griseus Cricetulus griseus 灰仓鼠 Cgri- PRO:DAN Chinese hamster golden hamster ncbi_taxonomy NCBITaxon:10036 Mesocricetus auratus golden hamster GC_ID:1 gerbils ncbi_taxonomy Gerbillinae GC_ID:1 Mongolian gerbil Mongolian jird ncbi_taxonomy Meriones unguiculatus GC_ID:1 PMID:15371245 ncbi_taxonomy Muridae GC_ID:1 Mus mice mouse ncbi_taxonomy Mus <mouse, genus> Mus musculus house mouse mouse NCBITaxon:85055 GC_ID:1 house mouse mouse ncbi_taxonomy Mus muscaris m mice C57BL/6xCBA/CaJ hybrid mouse NCBITaxon:10090 Mus musculus Mus musculus 小家鼠 m PRO:DAN mouse GC_ID:1 rat rats ncbi_taxonomy Rattus GC_ID:1 chinchillas chinchillas and viscachas ncbi_taxonomy Chinchillidae Viruses GC_ID:1 Viruses ncbi_taxonomy Vira Viridae viral- viruses NCBITaxon:10239 Viruses virus viral- PRO:DAN GC_ID:1 ncbi_taxonomy Chordopoxvirinae GC_ID:1 ncbi_taxonomy Orthopoxvirus CPXV GC_ID:1 ncbi_taxonomy cowpox virus CPV Cowpox virus GC_ID:1 ncbi_taxonomy vaccinia virus VV Vaccinia virus GC_ID:1 ncbi_taxonomy Vaccinia virus (strain Tian Tan) Vaccinia virus Tian Tan GC_ID:1 ncbi_taxonomy Vaccinia virus (strain WR) NCBITaxon:10254 Vaccinia virus WR GC_ID:1 ncbi_taxonomy Contagious pustular dermatitis virus orf virus OV Orf virus SPPV GC_ID:1 ncbi_taxonomy sheep pox virus Sheeppox virus GC_ID:1 ncbi_taxonomy Leporipoxvirus SFV GC_ID:1 ncbi_taxonomy Shope fibroma virus Shope fibroma virus SFV Rabbit fibroma virus GC_ID:1 ncbi_taxonomy myxoma virus MYX Myxoma virus GC_ID:1 ncbi_taxonomy H5N1 H5N1 subtype Herpesviridae GC_ID:1 ncbi_taxonomy Herpesviridae GC_ID:1 ncbi_taxonomy Alphaherpesvirinae GC_ID:1 ncbi_taxonomy Simplexvirus HSV-1 HSV1 GC_ID:1 Herpes simplex virus type 1 ncbi_taxonomy Herpes simplex virus 1 Human Herpesvirus-1 Human herpesvirus 1 Human herpesvirus type 1 herpes simplex virus 1 HSV-1 herpes simplex virus HSV-1 herpes simplex virus type 1 HSV-1 herpes simplex virus type 1 HSV1 herpes simplex virus type-1 HSV-1 NCBITaxon:10298 Human alphaherpesvirus 1 Human herpesvirus 1 HSV1 GC_ID:1 HSV1(17) ncbi_taxonomy NCBITaxon:10299 Herpes simplex virus (type 1 / strain 17) Herpes simplex virus type 1 strain 17 HSV1(17) PRO:DAN HSV2 GC_ID:1 ncbi_taxonomy Herpes simplex virus (type 2) Herpes simplex virus 2 Herpes simplex virus type 2 herpes simplex virus type 2 HSV-2 Human herpesvirus 2 GC_ID:1 ncbi_taxonomy Varicellovirus NCBITaxon:11265 NCBITaxon:12738 BoHV-1 GC_ID:1 ncbi_taxonomy Bovine herpesvirus 1 Bovine herpesvirus type 1 Bovine herpesvirus-1 Bovine rhinotracheitis virus Infectious bovine rhinotracheitis virus bovine herpesvirus 1 BHV 1 bovine herpesvirus 1 BHV-1 bovine herpesvirus 1 BHV1 bovine herpesvirus BHV-1 bovine herpesvirus type 1 BHV-1 bovine herpesvirus type-1 BHV-1 infectious bovine rhinotracheitis virus BHV-1 Bovine alphaherpesvirus 1 Bovine herpesvirus 1 EHV-1 GC_ID:1 Equine herpesvirus 1 ncbi_taxonomy Equid herpesvirus 1 Equine herpesvirus type 1 Equine herpesvirus-1 equine abortion virus equine herpesvirus 1 EHV-1 equine herpesvirus type 1 EHV-1 equine herpesvirus type 1 EVH-1 equine herpesvirus type-1 Equid alphaherpesvirus 1 Equid herpesvirus 1 GC_ID:1 ncbi_taxonomy Felid herpesvirus 1 Feline herpesvirus 1 Feline herpesvirus type 1 Feline viral rhinotracheitis virus feline herpesvirus feline herpesvirus type 1 FHV-1 feline herpesvirus-1 feline herpesvirus-1 FHV-1 NCBITaxon:10334 Felid alphaherpesvirus 1 Felid herpesvirus 1 HHV-3 VZV GC_ID:1 Varicella-zoster virus ncbi_taxonomy Human alphaherpesvirus 3 Varicella Zoster Virus varicella zoster virus VZV varicella-zoster virus VZV Human herpesvirus 3 NCBITaxon:44156 PRV GC_ID:1 Pseudorabies virus ncbi_taxonomy Alphaherpesvirus pseudorabies virus PRV Aujeszky's disease virus Pseudorabies Virus PRV Pseudorabies virus Suid herpesvirus 1 Suid herpesvirus type 1 Suid alphaherpesvirus 1 Suid herpesvirus 1 NCBITaxon:10342 NCBITaxon:12743 NCBITaxon:46620 GaHV-1 ILTV GC_ID:1 ncbi_taxonomy Avian infectious laryngotracheitis virus Gallid herpesvirus 1 Gallid herpesvirus type 1 Infectious laryngotracheitis virus Laryngotracheitis virus infectious laryngotracheitis virus ILTV Gallid alphaherpesvirus 1 Gallid herpesvirus 1 NCBITaxon:38013 NCBITaxon:39111 NCBITaxon:43684 GaHV-2 MDV1 GC_ID:1 Marek disease virus type 1 ncbi_taxonomy Gallid herpesvirus 1 (serotype 1) Gallid herpesvirus type 2 Marek disease virus Marek's disease herpesvirus Marek's disease herpesvirus 1 Marek's disease virus Marek's disease virus (MDV) Marek's disease virus MDV Marek's disease virus MDV1 Marek's disease virus serotype 1 MDV-1 Marek's disease virus type 1 Marek's disease virus type 1 MDV1 Gallid herpesvirus 2 GC_ID:1 ncbi_taxonomy Obtectomera ASFV GC_ID:1 ncbi_taxonomy African swine fever virus ASF African swine fever virus ASFV African swine fever virus, ASFV African swine fever virus PPV GC_ID:1 ncbi_taxonomy porcine parvovirus PPV Porcine parvovirus GC_ID:1 ncbi_taxonomy Rotaviruses Rotavirus GC_ID:1 arboviruses group A ncbi_taxonomy Alphaviridae Alphavirus RRV GC_ID:1 ncbi_taxonomy Ross River virus GC_ID:1 ncbi_taxonomy Sindbis virus dsSIN Sindbis virus VEE VEEV GC_ID:1 ncbi_taxonomy Venezuelan equine encephalitis VEE Venezuelan equine encephalitis virus VEE Venezuelan equine encephalomyelitis virus Venezuelan equine encephalitis virus GC_ID:1 ncbi_taxonomy Western equine encephaliomyelitis virus Western equine encephalitis virus Western equine encephalomyelitis virus Western equine encephalitis virus Western equine encephalomyelitis virus GC_ID:1 ncbi_taxonomy Flavivirus (arbovirus group B) Flaviviridae GC_ID:1 arboviruses group B ncbi_taxonomy Flavivirus WNV GC_ID:1 ncbi_taxonomy WNV- NCBITaxon:11082 West Nile virus WNV- PRO:DAN TBEV GC_ID:1 ncbi_taxonomy FSME virus tick-borne encephalitis virus TBE virus tick-borne encephalitis virus TBEV Tick-borne encephalitis virus YFV GC_ID:1 ncbi_taxonomy Flavivirus febricis yellow fever virus YFV Yellow fever virus NCBITaxon:12625 NCBITaxon:54314 GC_ID:1 PMID:7747470 ncbi_taxonomy Hog cholera virus Pestivirus type 2 classical swine fever virus CSFV hog cholera virus HCV swine fever virus Classical swine fever virus GC_ID:1 ncbi_taxonomy Hog cholera virus (strain Brescia) Hog cholera virus - Brescia Classical swine fever virus - Brescia FIPV GC_ID:1 FIPV ncbi_taxonomy Feline infectious peritonitis virus GC_ID:1 ncbi_taxonomy porcine respiratory coronavirus PRCV porcine respiratory virus Porcine respiratory coronavirus GC_ID:11 PMID:11155970 ncbi_taxonomy Bartonella birtlesii GC_ID:11 ncbi_taxonomy pseudomallei group GC_ID:1 negative-sense genome single-stranded RNA viruses ncbi_taxonomy Mononegavirales GC_ID:1 ncbi_taxonomy Paramyxoviridae GC_ID:1 ncbi_taxonomy Paramyxovirinae NDV GC_ID:1 ncbi_taxonomy Avian paramyxovirus type 1 Newcastle disease virus NDV avian paramyxovirus 1 Newcastle disease virus NCBITaxon:11202 GC_ID:1 ncbi_taxonomy Human parainfluenza 3 virus Human parainfluenza virus type 3 Parainfluenza virus type 3 human parainfluenza virus 3 HPIV3 human parainfluenza virus type 3 PIV3 parainfluenza virus type 3 PIV-3 Human parainfluenza virus 3 NCBITaxon:11230 GC_ID:1 ncbi_taxonomy Cell-associated subacute sclerosing panencephalitis Measles virus Subacute sclerosing panencephalitis virus measles virus MV rougeole virus rubeola virus subacute sclerose panencephalitis virus subacute sclerosing panencephalitis virus, SSPEV Measles morbillivirus Measles virus GC_ID:1 ncbi_taxonomy Pneumovirinae Pneumoviridae Pneumovirinae GC_ID:1 ncbi_taxonomy Pneumovirus NCBITaxon:12604 BRS BRSV GC_ID:1 ncbi_taxonomy Bovine respiratory syncytial virus bovine RSV bovine respiratory syncytial virus BRSV Bovine orthopneumovirus Bovine respiratory syncytial virus HRSV GC_ID:1 ncbi_taxonomy Human respiratory syncytial virus human RSV Human orthopneumovirus GC_ID:1 ncbi_taxonomy Human respiratory syncytial virus (strain A2) Human respiratory syncytial virus A2 GC_ID:1 PMID:16186241 ncbi_taxonomy Rhabdoviridae IHNV GC_ID:1 ncbi_taxonomy Infectious haematopoietic necrosis virus Infectious hematopoietic necrosis virus GC_ID:1 ncbi_taxonomy Rabies virus Rabies lyssavirus Rabies virus GC_ID:1 ncbi_taxonomy Influenza virus Influenza virus sp. Influenzavirus avian influenza virus unidentified influenza virus FLUAV GC_ID:1 ncbi_taxonomy Influenza virus type A influenza A virus INF A NCBITaxon:11320 Influenza A virus GC_ID:1 ncbi_taxonomy Bunyaviridae GC_ID:11 PMID:10192388 PMID:10871362 ncbi_taxonomy Chlamydia pneumoniae CWL029 Chlamydophila pneumoniae CWL029 GC_ID:1 ncbi_taxonomy Bunyavirus la crosse La Crosse virus RVFV GC_ID:1 ncbi_taxonomy Rift Valley fever virus GC_ID:1 ncbi_taxonomy Korean hemorrhagic fever virus Hantaan virus GC_ID:1 ncbi_taxonomy Lentivirinae Lentivirus Primate lentivirus group GC_ID:1 ncbi_taxonomy Primate immunodeficiency viruses Primate lentivirus group FIV GC_ID:1 ncbi_taxonomy feline immunodeficiency virus FIV Feline immunodeficiency virus Human immunodeficiency virus 1 HIV HIV-1 HIV1 LAV-1 GC_ID:1 ncbi_taxonomy AIDS virus Human immundeficiency virus type 1 Human immunodeficiencey virus type 1 Human immunodeficiency virus type 1 human immunodeficiency virus 1 HIV-1 human immunodeficiency virus HIV-1 human immunodeficiency virus type 1 ,HIV-1 human immunodeficiency virus type 1 HIV 1 human immunodeficiency virus type 1 HIV-1 human immunodeficiency virus type 1 HIV1 human immunodeficiency virus type 1, HIV-1 human immunodeficiency virus type I HIV-1 human immunodeficiency virus type-1 HIV-1 human immunodeficiency virus-1 HIV-1 Human immunodeficiency virus 1 NCBITaxon:11677 NCBITaxon:11739 NCBITaxon:11740 CIV SIV GC_ID:1 ncbi_taxonomy Chimpanzee immunodeficiency virus Chimpanzee immunodeficiency virus (SIV(CPZ)) Simian immunodeficiency virus SIVcpz simian immunodeficiency virus SIV simian immunodeficiency virus, SIV simian immunodeficiency viruses SIV Simian immunodeficiency virus GC_ID:1 fish fishes ncbi_taxonomy Agnatha Hyperotreti Euteleostomi bony vertebrates NCBITaxon:40673 GC_ID:1 bony vertebrates ncbi_taxonomy Euteleostomi ncbi_taxonomy NCBITaxon:118882 Brucellaceae GC_ID:11 PMID:16280474 ncbi_taxonomy Legionellaceae group Legionellales Garrity et al. 2005 Legionellales GC_ID:11 PMID:5462048 ncbi_taxonomy Francisella tularensis var. palaearctica Francisella tularensis subsp. holarctica Ecdysozoa GC_ID:1 ncbi_taxonomy Ecdysozoa EMCV GC_ID:1 ncbi_taxonomy encephalomyocarditis virus EMCV encephalomyocarditis virus, EMCV Encephalomyocarditis virus GC_ID:1 ncbi_taxonomy NCBITaxon:121791 Nipah henipavirus Nipah virus GC_ID:11 PMID:11321122 PMID:11542017 PMID:11837318 PMID:16280474 PMID:26654112 purple bacteria purple bacteria and relatives purple non-sulfur bacteria purple photosynthetic bacteria purple photosynthetic bacteria and relatives ncbi_taxonomy Alphaproteobacteraeota proteobacteria Proteobacteria GC_ID:11 PMID:10710307 ncbi_taxonomy Neisseria meningitidis serogroup B strain MC58 NCBITaxon:122586 Neisseria meningitidis MC58 GC_ID:11 ncbi_taxonomy Neisseria meningitidis serogroup A strain Z2491 Neisseria meningitidis Z2491 GC_ID:11 PMID:16280474 PMID:23334881 ncbi_taxonomy Gammaproteobacteria Garrity et al. 2005 Proteobacteria gamma subdivision Purple bacteria, gamma subdivision g-proteobacteria gamma proteobacteria gamma subdivision gamma subgroup Gammaproteobacteria NCBITaxon:31968 GC_ID:11 PMID:10555317 PMID:11034484 PMID:11542017 PMID:15143038 PMID:25403554 PMID:26654112 Gram-positive bacteria low G+C Gram-positive bacteria low GC Gram+ ncbi_taxonomy Bacillaeota Bacillus/Clostridium group Clostridium group firmicutes Firmacutes Gram positive bacteria Low G+C firmicutes clostridial firmicutes firmicutes Firmicutes CAV GC_ID:1 ncbi_taxonomy Chicken anaemia virus Chicken infectious anemia virus chicken anaemia agent CAA chicken anaemia agent virus CAA chicken anemia virus CAV chicken anemia virus, CAV chiken anemia agent virus Chicken anemia virus GC_ID:1 ncbi_taxonomy Ectromelia mousepox virus mousepox mousepox virus Ectromelia virus HIV GC_ID:1 ncbi_taxonomy AIDS virus Human immunodeficiency virus NCBITaxon:325213 GC_ID:11 PMID:8573498 ncbi_taxonomy Micrococcus aureus Micrococcus pyogenes Staph- Staphilococcus aureus Staphlococcus pyogenes citreus Staphylococcus pyogenes aureus Staphylococus aureus Streptococcus aureus NCBITaxon:1280 Staphylococcus aureus Staph- PRO:DAN GC_ID:11 PMID:10555340 PMID:14657115 PMID:1720654 PMID:19620365 PMID:19880633 PMID:7537076 PMID:8995803 ncbi_taxonomy Streptococcus NCBITaxon:76757 GC_ID:11 PMID:15774692 PMID:8995807 ncbi_taxonomy Streptoccocus de la mammite Streptococcus agalactiae contagiosae Streptococcus difficile Streptococcus difficilis Streptococcus mastitidis Streptococcus agalactiae GC_ID:11 ncbi_taxonomy Diplococcus pneumoniae Micrococcus pneumoniae Streptococcus pneumoniae GC_ID:11 ncbi_taxonomy Micrococcus scarlatinae Streptococcus erysipelatos Streptococcus hemolyticus Streptococcus pyrogenes Streptococcus scarlatinae Streptococcus pyogenes GC_ID:11 ncbi_taxonomy Streptococcus equi GC_ID:11 PMID:12734250 PMID:1283774 PMID:16558776 ncbi_taxonomy Acinetobacter mallei Actinobacillus mallei Bacillus mallei Loefferella mallei Malleomyces mallei Pfeifferella mallei Pseudomonas mallei Burkholderia mallei GC_ID:11 PMID:8427810 PMID:9103648 ncbi_taxonomy Enterococcus NCBITaxon:1219670 GC_ID:11 ncbi_taxonomy Enterococcus feacalis Enterococcus proteiformis Enterocoque Micrococcus ovalis Micrococcus zymogenes Streptococcus faecalis Streptococcus glycerinaceus Streptococcus liquefaciens NCBITaxon:1351 Enterococcus faecalis GC_ID:11 ncbi_taxonomy Streptococcus faecium NCBITaxon:1352 Enterococcus faecium GC_ID:11 ncbi_taxonomy Neisseria meningitidis (serogroup C) Neisseria meningitidis serogroup C GC_ID:11 PMID:11075904 PMID:11542017 PMID:16558735 PMID:1917844 ncbi_taxonomy spirochetes Spirochaetales GC_ID:11 ncbi_taxonomy Bacillus/Staphylococcus group Bacillales GC_ID:11 PMID:10871362 ncbi_taxonomy Chlamydia pneumoniae (strain J138) Chlamydophila pneumoniae J138 GC_ID:11 PMID:1380285 PMID:1503971 PMID:24744012 PMID:7699027 PMID:7981102 PMID:8995796 PMID:9336916 Borrelia burgdorferi sensu stricto Lyme disease spirochete ncbi_taxonomy Borrelia burdorferi Borrelia burgdorferi Borrelia burgdorffragment Borrelia burgdorferi Borreliella burgdorferi NCBITaxon:1494525 NCBITaxon:1494531 NCBITaxon:1494577 GC_ID:11 PMID:8123566 anthrax anthrax bacterium ncbi_taxonomy Bacillus cereus var. anthracis Bacteridium anthracis anthrax- NCBITaxon:1392 Bacillus anthracis anthrax- PRO:DAN GC_ID:1 PMID:11743200 PMID:11791233 ncbi_taxonomy Boreotheria Boreoeutheria NCBITaxon:147540 GC_ID:1 ncbi_taxonomy Loculoascomycetes Plectomycetes bitunicate ascomycetes Eurotiomycetes NCBITaxon:69207 GC_ID:11 PMID:26643615 PMID:27488356 ncbi_taxonomy Anaerobacter Clostridium NCBITaxon:29368 GC_ID:11 PMID:10028279 PMID:15244052 ncbi_taxonomy Bacillus botulinus Bacillus putrificus Botulobacillus botulinus Clostridium putrificum Ermengemillus botulinus Pacinia putrifica Clostridium botulinum NCBITaxon:1440055 NCBITaxon:1581190 GC_ID:11 PMID:23834245 PMID:27370902 PMID:27902176 Clostridium difficile [Clostridium] difficile ncbi_taxonomy Bacillus difficilis Clostridium difficile Clostridium difficle Peptoclostridium difficile Clostridioides difficile [Clostridium] difficile GC_ID:11 PMID:11043982 ncbi_taxonomy Yersinia enterocolitica subsp. enterocolitica NCBITaxon:1683536 GC_ID:11 PMID:1374625 PMID:184898 ncbi_taxonomy 'Clostridium plagarum' Bacillus perfringens Bacterium welchii Clostridium plagarum NCBITaxon:1502 Clostridium perfringens GC_ID:11 Escherichia coli O157:H7 EDL933 Escherichia coli O157:H7 strain EDL933 ncbi_taxonomy Escherichia coli 0157:H7 EDL933 Escherichia coli O157:H7 str. EDL933 GC_ID:11 PMID:11418146 ncbi_taxonomy Staphylococcus aureus (strain Mu50 / ATCC 700699) NCBITaxon:158878 Staphylococcus aureus subsp. aureus Mu50 GC_ID:11 PMID:11418146 ncbi_taxonomy Staphylococcus aureus (strain N315) NCBITaxon:158879 Staphylococcus aureus subsp. aureus N315 GC_ID:11 PMID:11296296 Streptococcus pyogenes (serotype 1 / M1 GAS) ncbi_taxonomy Streptococcus pyogenes ATCC 700294 Streptococcus pyogenes SF370 Streptococcus pyogenes strain SF370 Streptococcus pyogenes M1 GAS GC_ID:11 PMID:17012393 Streptococcus pyogenes Manfredo Streptococcus pyogenes strain Manfredo ncbi_taxonomy Streptococcus pyogenes (serotype 5 / Manfredo) Streptococcus pyogenes str. Manfredo HMPV GC_ID:1 ncbi_taxonomy Human metapneumovirus NCBITaxon:5072 GC_ID:1 ncbi_taxonomy A. nidulans Aspergillus nidulans Aspergillus nidulellus Aspergilus nidulans Emericella nidulans GC_ID:1 oriental rat flea ncbi_taxonomy Xenopsylla cheopis NCBITaxon:1634566 GC_ID:11 PMID:17773427 PMID:1906732 PMID:8782698 ncbi_taxonomy Bacterium monocytogenes Bacterium monocytogenes hominis Corynebacterium infantisepticum Corynebacterium parvulum Erysipelothrix monocytogenes Listerella hepatolytica Listeria momocytogenes Lysteria monocytogenes Listeria monocytogenes GC_ID:11 ncbi_taxonomy Yersinia pseudotuberculosis complex GC_ID:11 PMID:11679669 Listeria monocytogenes EGDe Listeria monocytogenes str. EGD-e Listeria monocytogenes strain EGD-e ncbi_taxonomy Listeria monocytogenes ATCC BAA-679 Listeria monocytogenes EGD-e GC_ID:11 PMID:11463916 ncbi_taxonomy NCBITaxon:170187 Streptococcus pneumoniae TIGR4 NCBITaxon:29512 NCBITaxon:29514 NCBITaxon:29516 GC_ID:11 PMID:10425768 PMID:1581182 PMID:19868121 PMID:9103653 ncbi_taxonomy Ancona Canela Jequitaia Leptospira GC_ID:11 PMID:11544234 ncbi_taxonomy Streptococcus pneumoniae (strain ATCC BAA-255 / R6) Streptococcus pneumoniae str. R6 NCBITaxon:171101 Streptococcus pneumoniae R6 GC_ID:11 PMID:7729671 ncbi_taxonomy Bacillus diphtheriae Bacterium diphtheriae Microsporon diphthericum Microsporon diphtheriticum Mycobacterium diphtheriae Pacinia loeffleri Corynebacterium diphtheriae GC_ID:11 PMID:1380284 PMID:1581193 PMID:16014496 PMID:1883713 PMID:2275850 PMID:29497402 PMID:7547284 PMID:7547304 PMID:7907223 PMID:8863452 ncbi_taxonomy Mycobacterium Lehmann and Neumann 1896 Mycobacterium GC_ID:11 PMID:2397193 PMID:8347508 ncbi_taxonomy Bacillus tuberculosis gallinarum Mycobacterium tuberculosis avium Mycobacterium tuberculosis typus gallinaceus Tuberculose des oiseaux Mycobacterium avium GC_ID:11 PMID:29205127 ncbi_taxonomy Bacillus tuberculosis Bacterium tuberculosis Mtub- Mycobacterium tuberculosis typus humanus Mycobacterium tuberculosis var. hominis NCBITaxon:1773 Mycobacterium tuberculosis Mtub- PRO:DAN GC_ID:11 Francisella tularensis subsp. tularensis str. SCHU S4 Francisella tularensis subsp. tularensis strain SCHU S4 ncbi_taxonomy Francisella tularensis Biovar A str. SCHU S4 Francisella tularensis Biovar A str. Schu 4 Francisella tularensis subsp. tularensis Schu 4 Francisella tularensis subsp. tularensis SCHU S4 GC_ID:1 ncbi_taxonomy WEEV complex GC_ID:11 PMID:18988685 PMID:23851394 ncbi_taxonomy Terrabacteria group NCBITaxon:427679 GC_ID:1 ncbi_taxonomy Cryptococcus neoformans A Cryptococcus neoformans serotype A Filobasidiella neoformans serotype A Filobasidiella neoformans var. grubii Cryptococcus neoformans var. grubii GC_ID:11 ncbi_taxonomy Chlamydia pneumoniae TW-183 Chlamydia pneumoniae TW183 Chlamydophila pneumoniae TW183 Chlamydophila pneumoniae TW-183 GC_ID:1 ncbi_taxonomy Trypanosoma brucei strain TREU927 NCBITaxon:185431 Trypanosoma brucei TREU927 Trypanosoma brucei brucei TREU927 GC_ID:11 PMID:11917108 ncbi_taxonomy Streptococcus pyogenes (serotype 18 / MGAS8232) Streptococcus pyogenes MGAS8232 ZEBOV GC_ID:1 ncbi_taxonomy Zaire Ebola virus Zaire ebolavirus GC_ID:1 ncbi_taxonomy Clupeocephala GC_ID:11 PMID:16558750 PMID:24480908 ncbi_taxonomy Eubacteriales Clostridiales GC_ID:1 ncbi_taxonomy Orthopneumovirus GC_ID:11 PMID:20212322 ncbi_taxonomy Lactobacillales GC_ID:11 PMID:12142430 Yersinia pestis str. KIM10+ Yersinia pestis strain KIM10+ ncbi_taxonomy Yersinia pestis KIM Yersinia pestis KIM 10 Yersinia pestis KIM 10+ Yersinia pestis KIM10+ GC_ID:11 PMID:12712204 ncbi_taxonomy NCBITaxon:189518 Leptospira interrogans serovar Lai str. 56601 GC_ID:11 Bacillus anthracis A2012 Bacillus anthracis strain A2012 ncbi_taxonomy Bacillus anthracis str. A2012 GC_ID:11 PMID:10688204 Campylobacter jejuni subsp. jejuni ATCC 700819 = NCTC 11168 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 ncbi_taxonomy Campylobacter jejuni subsp. jejuni ATCC 700819 Campylobacter jejuni subsp. jejuni NCTC 11168 NCBITaxon:192222 Campylobacter jejuni subsp. jejuni NCTC 11168 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 GC_ID:11 Streptococcus pyogenes str. SSI-1 ncbi_taxonomy Streptococcus pyogenes SSI-1 GC_ID:11 PMID:15660156 PMID:16943349 Campylobacter jejuni str. RM1221 Campylobacter jejuni strain RM1221 ncbi_taxonomy Campylobacter jejuni RM1221 GC_ID:11 PMID:11792842 Clostridium perfringens 13 ncbi_taxonomy Clostridium perfringens str. 13 GC_ID:11 PMID:16825665 Clostridium perfringens str. ATCC 13124 Clostridium perfringens strain ATCC 13124 ncbi_taxonomy Clostridium perfringens ATCC 13124 GC_ID:11 PMID:12044378 ncbi_taxonomy Staphylococcus aureus (strain MW2) Staphylococcus aureus subsp. aureus str. MW2 NCBITaxon:196620 Staphylococcus aureus subsp. aureus MW2 GC_ID:11 PMID:11321120 ncbi_taxonomy Ampylobacter jejuni Campylobacter fetus subsp. jejuni Vibrio hepaticus Vibrio jejuni Campylobacter jejuni Pancrustacea Pancrustacea ncbi_taxonomy FluA- NCBITaxon:197911 Influenzavirus A FluA- PRO:DAN GC_ID:11 PMID:12721629 Bacillus anthracis (strain Ames) Bacillus anthracis Ames Bacillus anthracis strain Ames ncbi_taxonomy Bacillus anthracis str. Ames GC_ID:11 PMID:12384590 ncbi_taxonomy Shigella flexneri serotype 2a str. 301 Shigella flexneri 2a str. 301 GC_ID:11 PMID:12704152 Shigella flexneri 2a strain 2457T Shigella flexneri serotype 2a str. 2457T ncbi_taxonomy Shigella flexneri 2a str. 2457T GC_ID:11 Streptococcus pyogenes str. MGAS315 ncbi_taxonomy Streptococcus pyogenes MGAS315 GC_ID:1 ncbi_taxonomy Coccidioides posadasii GC_ID:11 Escherichia coli str. CFT073 Escherichia coli strain CFT073 ncbi_taxonomy NCBITaxon:199310 Escherichia coli CFT073 Bacteria eubacteria GC_ID:11 PMID:10425795 PMID:10425796 PMID:10425797 PMID:10490293 PMID:10843050 PMID:10939651 PMID:10939673 PMID:10939677 PMID:11211268 PMID:11321083 PMID:11321113 PMID:11411719 PMID:11540071 PMID:11542017 PMID:11542087 PMID:11760965 PMID:12054223 PMID:2112744 PMID:270744 PMID:8123559 PMID:8590690 PMID:9103655 PMID:9336922 Bacteria <prokaryote> eubacteria ncbi_taxonomy Monera Procaryotae Prokaryota Prokaryotae bact- bacteria not Bacteria Haeckel 1894 prokaryote prokaryotes NCBITaxon:2 Bacteria bact- PRO:DAN GC_ID:11 PMID:11837318 PMID:25288668 PMID:26654112 ncbi_taxonomy Spirochaetes Spirochaetia GC_ID:11 PMID:12271122 Brucella suis biovar 1 (strain 1330) Brucella suis str. 1330 ncbi_taxonomy Brucella melitensis biovar Suis str. 1330 Brucella suis ATCC 23444 Brucella suis NCTC 10316 Bsuis1330- NCBITaxon:204722 Brucella suis 1330 Brucella suis biovar 1 (strain 1330) PRO:CNA Bsuis1330- PRO:DAN NCBITaxon:11268 GC_ID:1 ncbi_taxonomy Ebola virus EBO unidentified Ebola virus Ebola virus sp. GC_ID:11 ncbi_taxonomy Streptococcus agalactiae str. A909 Streptococcus agalactiae A909 GC_ID:11 PMID:12200547 Streptococcus agalactiae str. 2603V/R ncbi_taxonomy Streptococcus agalactiae 2603VR NCBITaxon:208435 Streptococcus agalactiae 2603V/R GC_ID:11 ncbi_taxonomy Pseudomonas aeruginosa str. UCBPP-PA14 Pseudomonas aeruginosa UCBPP-PA14 GC_ID:11 PMID:10984043 ncbi_taxonomy Pseudomonas aeruginosa PA01 Pseudomonas aeruginosa str. PA01 Pseudomonas aeruginosa str. PAO1 NCBITaxon:208964 Pseudomonas aeruginosa PAO1 GC_ID:11 PMID:12644504 Salmonella enterica subsp. enterica serovar Typhi strain Ty2 ncbi_taxonomy Salmonella enterica subsp. enterica serovar Typhi Ty2 Salmonella enterica subsp. enterica serovar Typhi str. Ty2 GC_ID:4 ncbi_taxonomy Mycoplasma gallisepticum NCBITaxon:219 GC_ID:11 PMID:11931154 PMID:1995031 PMID:8186097 PMID:8494747 ncbi_taxonomy Campylobacter pylori Campylobacter pylori subsp. pylori Campylobacter pyloridis Helicobacter nemestrinae Helicobacter pylori NCBITaxon:11455 NCBITaxon:197769 NCBITaxon:228930 NCBITaxon:382824 NCBITaxon:384491 NCBITaxon:385648 GC_ID:1 ncbi_taxonomy Influenza A virus ( A/Puerto Rico/8/1934(H1N1)) Influenza A virus (A/PR 8/34 (H1N1)) Influenza A virus (A/PR/8/1934(H1N1)) Influenza A virus (A/PR/8/34(H0N1)) Influenza A virus (A/PR/8/34(H1N1)) Influenza A virus (A/PR/8/34(HON1)) Influenza A virus (A/PR8/1934(H1N1)) Influenza A virus (A/Puerto Rico/8/1934(H0N1)) Influenza A virus (A/Puerto Rico/8/34(H1N1)) Influenza A virus (A/Puerto Rico/8/34) Influenza A virus (STRAIN A/PUERTO RICO/8/34) nfluenza A virus (A/PR 8/34(H1N1)) NCBITaxon:211044 Influenza A virus (A/Puerto Rico/8/1934(H1N1)) GC_ID:11 PMID:12354221 ncbi_taxonomy Streptococcus agalactiae str. NEM316 Streptococcus agalactiae NEM316 GC_ID:11 PMID:12552129 ncbi_taxonomy Clostridium tetani str. E88 NCBITaxon:212717 Clostridium tetani E88 GC_ID:11 PMID:16403855 ncbi_taxonomy 'Campylobacterales' Campylobacterales GC_ID:11 PMID:11586360 Yersinia pestis str. CO92 Yersinia pestis strain CO92 ncbi_taxonomy Yersinia pestis CO92 GC_ID:1 Cryptococcus neoformans JEC21 Cryptococcus neoformans var. neoformans strain JEC21 ncbi_taxonomy Cryptococcus neoformans var. neoformans serotype D JEC21 Filobasidiella neoformans var. neoformans strain JEC21 Cryptococcus neoformans var. neoformans JEC21 Archaea ncbi_taxonomy arch- NCBITaxon:2157 Archaea arch- PRO:DAN GC_ID:11 PMID:11677608 Salmonella enterica subsp. enterica serovar Typhi CT18 Salmonella enterica subsp. enterica serovar Typhi strain CT18 Salmonella typhi CT18 ncbi_taxonomy Salmonella enterica subsp. enterica serovar Typhi str. CT18 GC_ID:11 PMID:9403685 ncbi_taxonomy Borrelia burgdorferi str. B31 NCBITaxon:224326 Borrelia burgdorferi B31 Borreliella burgdorferi B31 GC_ID:11 PMID:11756688 Brucella melitensis biotype 1 (strain 16m / atcc 23456 / nctc 10094) ncbi_taxonomy Bmel16M- Brucella melitensis 16M Brucella melitensis ATCC 23456 Brucella melitensis str. 16M Brucella melitensis str. ATCC 23456 NCBITaxon:224914 Brucella melitensis bv. 1 str. 16M Brucella melitensis biotype 1 (strain 16m / atcc 23456 / nctc 10094) PRO:CNA Bmel16M- PRO:DAN GC_ID:11 PMID:12663927 Enterococcus faecalis str. V583 Enterococcus faecalis strain V583 ncbi_taxonomy NCBITaxon:226185 Enterococcus faecalis V583 GC_ID:1 ncbi_taxonomy Emericella nidulans FGSC A4 Aspergillus nidulans FGSC A4 GC_ID:11 PMID:12704232 ncbi_taxonomy Coxiella burnetii str. RSA 493 NCBITaxon:227377 Coxiella burnetii RSA 493 GC_ID:11 PMID:15262951 PMID:15368893 Yersinia pestis biovar Microtus 91001 Yersinia pestis biovar Microtus strain 91001 ncbi_taxonomy Yersinia pestis biovar Mediaevails str. 91001 Yersinia pestis biovar Medievalis str. 91001 Yersinia pestis bv. Microtus str. 91001 Yersinia pestis biovar Microtus str. 91001 GC_ID:11 PMID:28066370 PMID:8573514 ncbi_taxonomy Bru- Brucella Meyer and Shaw 1920 NCBITaxon:234 Brucella Bru- PRO:DAN GC_ID:11 Brucella melitensis bv. Abortus ncbi_taxonomy Bacterium abortus Brucella melitensis biovar Abortus Brucella abortus ncbi_taxonomy NCBITaxon:235443 Cryptococcus neoformans var. grubii H99 GC_ID:12 ncbi_taxonomy NCBITaxon:237561 Candida albicans SC5314 GC_ID:11 Burkholderia mallei str. ATCC 23344 ncbi_taxonomy NCBITaxon:243160 Burkholderia mallei ATCC 23344 GC_ID:11 PMID:10952301 Vibrio cholerae El Tor N16961 Vibrio cholerae serotype O1 biotype El Tor strain N16961 Vibrio cholerae serotype O1 biotype ElTor strain N16961 ncbi_taxonomy Vchol- Vibrio cholerae O1 biovar eltor str. N16961 NCBITaxon:243277 Vibrio cholerae O1 biovar El Tor str. N16961 Vchol- PRO:DAN GC_ID:11 PMID:14602910 Corynebacterium diphtheriae NCTC13129 ncbi_taxonomy Corynebacterium diphtheriae NCTC 13129 GC_ID:11 PMID:12910271 ncbi_taxonomy Bordetella bronchiseptica RB50 GC_ID:11 PMID:12910271 ncbi_taxonomy NCBITaxon:257313 Bordetella pertussis Tohama I GC_ID:11 Bacillus anthracis (strain Sterne) Bacillus anthracis Sterne ncbi_taxonomy Bacillus anthracis str. Sterne GC_ID:11 PMID:18952800 Bacillus anthracis Ames "Ancestor" Bacillus anthracis str. Ames Ancestor Bacillus anthracis strain 'Ames Ancestor' ncbi_taxonomy Bacillus anthracis str. Ames 0581 Bacillus anthracis str. 'Ames Ancestor' NCBITaxon:164623 OpMNPV GC_ID:1 ncbi_taxonomy Orgya pseudotsugata MNPV Orgya pseudotsugata nucleopolyhedrovirus Orgyia pseudotsugata multicapsid nuclear polyhedrosis virus Orgyia pseudotsugata multicapsid nuclear polyhedrosis virus OpMNPV Orgyia pseudotsugata multicapsid nucleopolyhedrovirus Orgyia pseudotsugata multicapsid polyhedrosis virus Orgyia pseudotsugata multinucleocapsid nuclear polyhedrosis virus Orgyia pseudotsugata multiple nucleopolyhedrovirus Orgyia pseudotsugata MNPV GC_ID:11 PMID:16116077 PMID:20870759 Mycobacterium avium subsp. paratuberculosis str. K-10 Mycobacterium avium subsp. paratuberculosis strain K-10 ncbi_taxonomy Mycobacterium avium subsp. paratuberculosis K10 Mycobacterium avium subsp. paratuberculosis K-10 GC_ID:11 ncbi_taxonomy Bacterium tularense Brucella tularensis Francisella tularense Pasteurella tularensis Francisella tularensis GC_ID:11 Listeria monocytogenes serotype 4b strain F2365 ncbi_taxonomy Listeria monocytogenes str. 4b F2365 Listeria monocytogenes serotype 4b str. F2365 GC_ID:1 ncbi_taxonomy Pneumonia virus of mice J3666 NCBITaxon:10458 BmNPV BmSNPV GC_ID:1 ncbi_taxonomy Bombyx mori S nuclear polyhedrosis virus Bombyx mori nuclear polyhedrosis virus Bombyx mori nuclear polyhedrosis virus BmNPV Bombyx mori nuclear polyhedrosis virus, BmSNPV Bombyx mori nucleopolyhedrosis virus Bombyx mori nucleopolyhedrovirus Bombyx mori NPV GC_ID:11 Burkholderia pseudomallei str. K96243 Burkholderia pseudomallei strain K96243 ncbi_taxonomy NCBITaxon:272560 Burkholderia pseudomallei K96243 GC_ID:11 Chlamydia trachomatis str. D/UW-3/CX Chlamydia trachomatis strain D/UW-3/CX ncbi_taxonomy NCBITaxon:272561 Chlamydia trachomatis D/UW-3/CX GC_ID:11 Clostridium difficile 630 (epidemic type X) Clostridium difficile str. 630 Clostridium difficile strain 630 ncbi_taxonomy NCBITaxon:272563 Clostridioides difficile 630 Clostridium difficile 630 GC_ID:11 PMID:15448271 Legionella pneumophila subsp. pneumophila 'Philadelphia 1' Legionella pneumophila subsp. pneumophila strain Philadelphia 1 ncbi_taxonomy Legionella pneumophila subsp. pneumophila str. Philadelphia 1 GC_ID:11 Neisseria meningitidis str. FAM18 Neisseria meningitidis strain FAM18 ncbi_taxonomy Neisseria meningitidis FAM18 GC_ID:11 Pasteurella multocida subsp. multocida Pm70 Pasteurella multocida subsp. multocida strain Pm70 ncbi_taxonomy Pasteurella multocida subsp. multocida str. Pm70 GC_ID:11 PMID:9823893 Rickettsia prowazekii 'Madrid E' Rickettsia prowazekii strain Madrid E ncbi_taxonomy Rickettsia prowazekii str. Madrid E GC_ID:11 Staphylococcus aureus str. RF122 Staphylococcus aureus strain RF122 ncbi_taxonomy NCBITaxon:273036 Staphylococcus aureus RF122 GC_ID:11 Yersinia pseudotuberculosis IP32953 Yersinia pseudotuberculosis str. IP 32953 Yersinia pseudotuberculosis strain IP 32953 ncbi_taxonomy NCBITaxon:273123 Yersinia pseudotuberculosis IP 32953 Eukaryota eucaryotes eukaryotes GC_ID:1 PMID:23020233 eucaryotes eukaryotes ncbi_taxonomy Eucarya Eucaryotae Eukarya Eukaryotae euk- eukaryotes NCBITaxon:2759 Eukaryota euk- PRO:DAN GC_ID:11 PMID:15968074 Haemophilus influenzae str. 86-028NP Haemophilus influenzae strain 86-028NP ncbi_taxonomy Haemophilus influenzae 86-028NP GC_ID:11 PMID:11541974 PMID:11837318 PMID:16166687 PMID:16403855 PMID:19060069 ncbi_taxonomy "Alphabacteria" Cavalier-Smith 1992 Alphabacteria Alphabacteria Cavalier-Smith 2002 Alphaproteobacteria Garrity et al. 2006 Proteobacteria alpha subdivision Purple bacteria, alpha subdivision a-proteobacteria alpha proteobacteria alpha subdivision alpha subgroup Alphaproteobacteria GC_ID:11 PMID:16403855 PMID:28581923 ncbi_taxonomy 'Betaproteobacteria' Proteobacteria beta subdivision Purple bacteria, beta subdivision b-proteobacteria beta proteobacteria beta subdivision beta subgroup Betaproteobacteria GC_ID:11 PMID:15213324 Staphylococcus aureus subsp. aureus str. MRSA252 Staphylococcus aureus subsp. aureus strain MRSA252 ncbi_taxonomy NCBITaxon:282458 Staphylococcus aureus subsp. aureus MRSA252 GC_ID:11 PMID:15210978 Bartonella henselae strain Houston-1 ncbi_taxonomy Bartonella henselae ATCC 49882 Bartonella henselae str. ATCC 49882 Bartonella henselae strain ATCC 49882 Bartonella henselae str. Houston-1 NCBITaxon:12796 NCBITaxon:70172 PRRSV GC_ID:1 ncbi_taxonomy Porcine reproductive and respiratory syndrome virus (PRRSV) Porcine respiratory and reproductive syndrome virus porcine reproductive and respiratory syndrome virus PRRSV porcine reproductive and respiratory syndrome virus, PRRSV Porcine reproductive and respiratory syndrome virus GC_ID:1 ncbi_taxonomy NCBITaxon:283643 Cryptococcus neoformans var. neoformans B-3501A GC_ID:1 ncbi_taxonomy Influenza A virus (A/Vietnam/1203/04(H5N1)) Influenza A virus (A/Vietnam/1203/2004) Influenza A virus (A/Viet Nam/1203/2004(H5N1)) NCBITaxon:1435366 NCBITaxon:1435368 NCBITaxon:1435988 NCBITaxon:1439853 NCBITaxon:1487954 NCBITaxon:1487955 GC_ID:11 PMID:12734250 PMID:1283774 ncbi_taxonomy Bacillus pseudomallei Bacterium whitmori Burkholderia pseudomallai Burkholderia pseudomallei MSHR4009 Burkholderia pseudomallei MSHR4018 Burkholderia pseudomallei MSHR44 Burkholderia pseudomallei MSHR7839 Burkholderia sp. MSHR7839 Loefflerella pseudomallei Malleomyces pseudomallei Pseudomonas pseudomallei Burkholderia pseudomallei GC_ID:1 Candida glabrata ATCC 2001 Candida glabrata ATCC2001 Candida glabrata CBS138 ncbi_taxonomy Candida glabrata CBS 138 GC_ID:1 ncbi_taxonomy Eurotiaceae Trichocomaceae GC_ID:11 PMID:15272401 Streptococcus pyogenes str. MGAS10394 Streptococcus pyogenes strain MGAS10394 ncbi_taxonomy Streptococcus pyogenes MGAS10394 NCBITaxon:1224290 NCBITaxon:1437768 NCBITaxon:1437769 NCBITaxon:1437770 NCBITaxon:1508364 NCBITaxon:1683559 NCBITaxon:1683561 NCBITaxon:1851858 NCBITaxon:1851865 NCBITaxon:1860124 NCBITaxon:665948 NCBITaxon:931955 NCBITaxon:931956 NCBITaxon:931957 NCBITaxon:931958 NCBITaxon:932477 GC_ID:11 ncbi_taxonomy Bacillus aeruginosus Bacillus pyocyaneus Bacterium aeruginosum Bacterium pyocyaneum Micrococcus pyocyaneus Peudomonas aeruginosa Pseudomonas polycolor Pseudomonas pyocyanea Pseudomonas sp. 2_1_26 probable synonym or variety: "Pseudomonas polycolor" Clara 1930 NCBITaxon:287 Pseudomonas aeruginosa NCBITaxon:10973 NCBITaxon:183404 GC_ID:1 ncbi_taxonomy Group A rotaviruses Rotavirus group A group A rotavirus Rotavirus A GC_ID:11 PMID:16825665 Clostridium perfringens str. SM101 Clostridium perfringens strain SM101 ncbi_taxonomy Clostridium perfringens SM101 GC_ID:11 ncbi_taxonomy Streptococcus pyogenes MGAS5005 GC_ID:1 ncbi_taxonomy Entamoeba histolytica HM-1:IMSS GC_ID:11 PMID:8573514 ncbi_taxonomy Micrococcus melitensis Streptococcus Miletensis Brucella melitensis GC_ID:11 ncbi_taxonomy Yersinia ruckeri GC_ID:11 ncbi_taxonomy Salmonella enterica subsp. enterica serovar Paratypi A str. ATCC 9150 Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150 GC_ID:11 ncbi_taxonomy Legionella pneumophila Lens Legionella pneumophila str. Lens GC_ID:11 ncbi_taxonomy Legionella pneumophila Paris Legionella pneumophila str. Paris GC_ID:11 Shigella dysenteriae str. Sd197 Shigella dysenteriae strain Sd197 ncbi_taxonomy NCBITaxon:300267 Shigella dysenteriae Sd197 GC_ID:11 Shigella boydii str. Sb227 Shigella boydii strain Sb227 ncbi_taxonomy Shigella boydii Sb227 GC_ID:11 Shigella sonnei str. Ss046 Shigella sonnei strain Ss046 ncbi_taxonomy Shigella sonnei Ss046 GC_ID:11 ncbi_taxonomy NCBITaxon:301447 Streptococcus pyogenes serotype M1 GC_ID:11 Streptococcus pyogenes (serotype M3) ncbi_taxonomy Streptococcus pyogenes serotype M3 GC_ID:1 PMID:11214318 PMID:11214319 PMID:12878460 ncbi_taxonomy Laurasiatheria Euarchontoglires GC_ID:1 PMID:11214319 PMID:12082125 PMID:12878460 PMID:15522813 ncbi_taxonomy Euarchontoglires GC_ID:1 PMID:11214319 PMID:12082125 PMID:15522813 Rodents and rabbits ncbi_taxonomy Glires GC_ID:1 ncbi_taxonomy Anthropoidea Simiiformes GC_ID:11 PMID:18245285 Escherichia coli DH10B Escherichia coli str. K12 substr. DH10B Escherichia coli strain K12 substrain DH10B ncbi_taxonomy Escherichia coli str. K-12 substr. DH10B GC_ID:11 PMID:20802035 Escherichia coli ETEC str. H10407 Escherichia coli ETEC strain H10407 ncbi_taxonomy Escherichia coli H10407 Escherichia coli strain H10407 Escherichia coli ETEC H10407 GC_ID:11 Streptococcus pyogenes str. MGAS6180 Streptococcus pyogenes strain MGAS6180 ncbi_taxonomy Streptococcus pyogenes MGAS6180 GC_ID:11 PMID:11321120 Campylobacter jejuni jejuni ncbi_taxonomy Campylobacter jejuni subsp. jejuni GC_ID:11 Burkholderia pseudomallei str. 1710b Burkholderia pseudomallei strain 1710b ncbi_taxonomy Burkholderia pseudomallei 1710b GC_ID:11 Burkholderia pseudomallei str. 668 Burkholderia pseudomallei strain 668 ncbi_taxonomy Burkholderia pseudomallei 668 GC_ID:11 Burkholderia mallei str. SAVP1 Burkholderia mallei strain SAVP1 ncbi_taxonomy Burkholderia mallei SAVP1 GC_ID:11 Burkholderia mallei str. NCTC 10247 Burkholderia mallei strain NCTC 10247 ncbi_taxonomy Burkholderia mallei NCTC 10247 GC_ID:11 Salmonella enterica subsp. enterica serovar Choleraesuis SC-B67 Salmonella enterica subsp. enterica serovar Choleraesuis strain SC-B67 ncbi_taxonomy Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67 Tetrapoda tetrapods Tetrapoda Amniota amniotes GC_ID:1 amniotes ncbi_taxonomy Amniota GC_ID:1 ncbi_taxonomy NCBITaxon:330879 Aspergillus fumigatus Af293 ncbi_taxonomy plant- NCBITaxon:33090 Viridiplantae plant- PRO:DAN GC_ID:11 PMID:18676672 Escherichia coli str. E24377A Escherichia coli strain E24377A ncbi_taxonomy Escherichia coli E24377A GC_ID:11 PMID:18676672 Escherichia coli str. HS Escherichia coli strain HS ncbi_taxonomy Escherichia coli HS Opisthokonta GC_ID:1 ncbi_taxonomy Fungi/Metazoa group opisthokonts NCBITaxon:33154 Opisthokonta NCBITaxon:259362 NCBITaxon:36053 NCBITaxon:5102 GC_ID:1 PMID:17486980 ncbi_taxonomy Gymnoascales Onygenales ncbi_taxonomy metazoan- NCBITaxon:33208 Metazoa metazoan- PRO:DAN Bilateria GC_ID:1 ncbi_taxonomy Bilateria GC_ID:1 ncbi_taxonomy Endopterygota Holometabola GC_ID:11 Mycobacterium tuberculosis str. F11 Mycobacterium tuberculosis strain F11 ncbi_taxonomy Mycobacterium tuberculosis F11 NCBITaxon:10348 GC_ID:1 ncbi_taxonomy Pseudorabies virus (STRAIN KA) Pseudorabies virus (strain Kaplan) Suid herpesvirus 1 (strain KA) Suid herpesvirus 1 (strain Kaplan) Suid herpesvirus 1 strain Kaplan GC_ID:1 PMID:15019624 PMID:15371245 ncbi_taxonomy Muroidea GC_ID:11 ncbi_taxonomy Actinobacillus pleuropneumoniae 2 Actinobacillus pleuropneumoniae serotype 2 Actinobacillus pleuropneumoniae serovar 2 GC_ID:11 ncbi_taxonomy Streptococcus pyogenes serotype M12 GC_ID:11 Shigella boydii str. CDC 3083-94 Shigella boydii strain CDC 3083-94 ncbi_taxonomy Shigella boydii BS512 Shigella boydii CDC 3083-94 GC_ID:1 ncbi_taxonomy SARS coronavirus ZJ0301 GC_ID:11 Vibrio cholerae str. O395 Vibrio cholerae strain O395 ncbi_taxonomy Vibrio cholerae O395 LmjF GC_ID:1 ncbi_taxonomy Leishmania major MHOM/IL/81/Friedlin Leishmania major strain Friedlin GC_ID:11 PMID:20061468 Yersinia pestis str. Angola Yersinia pestis strain Angola ncbi_taxonomy Yersinia pestis Angola O.Pe.3 Yersinia pestis Angola GC_ID:11 Yersinia pseudotuberculosis str. IP 31758 Yersinia pseudotuberculosis strain IP 31758 ncbi_taxonomy Yersinia pseudotuberculosis IP 31758 GC_ID:1 ncbi_taxonomy dsDNA viruses dsDNA viruses, no RNA stage NCBITaxon:12593 NCBITaxon:36349 BoHV-5 GC_ID:1 ncbi_taxonomy Bovine encephalitis herpesvirus Bovine herpesvirus type 5 Bovine herpesvirus 5 Retro-transcribing viruses Retro-transcribing viruses GC_ID:1 ncbi_taxonomy ssRNA positive-strand viruses, no DNA stage GC_ID:1 ncbi_taxonomy Plasmodium yoelii yoelii str. 17XNL Plasmodium yoelii yoelii 17XNL GC_ID:1 ncbi_taxonomy ssRNA negative-strand viruses GC_ID:1 ncbi_taxonomy Cryptosporidium parvum strain Iowa type II Cryptosporidium parvum Iowa II GC_ID:1 ncbi_taxonomy NCBITaxon:353153 Trypanosoma cruzi strain CL Brener GC_ID:11 Campylobacter jejuni subsp. jejuni str. 81-176 Campylobacter jejuni subsp. jejuni strain 81-176 ncbi_taxonomy Campylobacter jejuni subsp. jejuni 81-176 GC_ID:11 PMID:16403855 PMID:1854635 rhizobacteria ncbi_taxonomy 'Rhizobiales' Rhizobiaceae group alpha-2 proteobacteria Rhizobiales GC_ID:1 ncbi_taxonomy Dictyochales GC_ID:11 Burkholderia pseudomallei str. 1106a Burkholderia pseudomallei strain 1106a ncbi_taxonomy Burkholderia pseudomallei 1106a GC_ID:11 PMID:16299333 PMID:20462421 Brucella melitensis biovar Abortus str. 2308 Brucella melitensis biovar Abortus strain 2308 ncbi_taxonomy BmelAbo2308- NCBITaxon:359391 Brucella abortus 2308 Brucella melitensis biovar Abortus 2308 BmelAbo2308- PRO:DAN GC_ID:11 Bartonella bacilliformis str. KC583 Bartonella bacilliformis strain KC583 ncbi_taxonomy Bartonella bacilliformis KC583 GC_ID:11 Yersinia pestis str. Antiqua Yersinia pestis strain Antiqua ncbi_taxonomy Yersinia pestis Antiqua GC_ID:11 Campylobacter jejuni subsp. doylei str. 269.97 Campylobacter jejuni subsp. doylei strain 269.97 ncbi_taxonomy Campylobacter jejuni subsp. doylei 362.97 Campylobacter jejuni subsp. doylei 269.97 GC_ID:11 Bordetella avium str. 197N Bordetella avium strain 197N ncbi_taxonomy Bordetella avium 197N GC_ID:11 PMID:16912116 Escherichia coli str. 536 Escherichia coli strain 536 ncbi_taxonomy Escherichia coli 536 GC_ID:1 ncbi_taxonomy PLASMODIUM FALCIPARUM (ISOLATE 3D7). Plasmodium falciparum (isolate 3D7) NCBITaxon:36329 Plasmodium falciparum 3D7 GC_ID:11 Escherichia coli str. UTI89 Escherichia coli strain UTI89 ncbi_taxonomy Escherichia coli UTI89 NCBITaxon:10977 NCBITaxon:28878 GC_ID:1 ncbi_taxonomy Group C rotaviruses Rotavirus group C group C rotavirus Rotavirus C NCBITaxon:381766 NCBITaxon:548158 GC_ID:1 Cryptococcus bacillisporus VGI WM276 Cryptococcus bacillisporus WM276 Cryptococcus neoformans WM276 ncbi_taxonomy Cryptococcus gattii WM276 GC_ID:11 PMID:8863443 ncbi_taxonomy Clostridium botulinum A GC_ID:11 PMID:16636287 Streptococcus pyogenes str. MGAS9429 Streptococcus pyogenes strain MGAS9429 ncbi_taxonomy Streptococcus pyogenes MGAS9429 GC_ID:11 PMID:16636287 Streptococcus pyogenes str. MGAS10270 Streptococcus pyogenes strain MGAS10270 ncbi_taxonomy Streptococcus pyogenes MGAS10270 GC_ID:11 PMID:16636287 Streptococcus pyogenes str. MGAS2096 Streptococcus pyogenes strain MGAS2096 ncbi_taxonomy Streptococcus pyogenes MGAS2096 GC_ID:11 PMID:16636287 Streptococcus pyogenes str. MGAS10750 Streptococcus pyogenes strain MGAS10750 ncbi_taxonomy Streptococcus pyogenes MGAS10750 GC_ID:11 Streptococcus pneumoniae str. D39 Streptococcus pneumoniae strain D39 ncbi_taxonomy NCBITaxon:373153 Streptococcus pneumoniae D39 GC_ID:11 PMID:16822325 ncbi_taxonomy Shigella flexneri 5 strain 8401 Shigella flexneri 5 str. 8401 GC_ID:11 Neisseria meningitidis str. 053442 Neisseria meningitidis strain 053442 ncbi_taxonomy Neisseria meningitidis 053442 GC_ID:11 Francisella tularensis subsp. holarctica str. LVS Francisella tularensis subsp. holarctica strain LVS ncbi_taxonomy Francisella tularensis subsp. holarctica LVS GC_ID:11 ncbi_taxonomy Escherichia coli O26:H- GC_ID:11 Yersinia pestis str. Nepal516 Yersinia pestis strain Nepal516 ncbi_taxonomy Yersinia pestis Nepal516 GC_ID:11 PMID:18801193 Aeromonas salmonicida subsp. salmonicida str. A449 Aeromonas salmonicida subsp. salmonicida strain A449 ncbi_taxonomy Aeromonas salmonicida subsp. salmonicida A449 GC_ID:11 Bartonella tribocorum str. CIP 105476 Bartonella tribocorum strain CIP 105476 ncbi_taxonomy Bartonella tribocorum CIP 105476 NCBITaxon:806 GC_ID:11 PMID:1371515 PMID:8240958 ncbi_taxonomy Rochalimaea henselae Bartonella henselae GC_ID:1 Leishmania ncbi_taxonomy Leishmania <subgenus> GC_ID:1 ncbi_taxonomy Leishmania donovani species complex GC_ID:11 Escherichia coli O157:H7 strain Sakai ncbi_taxonomy Escherichia coli O157:H7 str. Sakai GC_ID:11 PMID:17966401 Yersinia pestis str. Pestoides F Yersinia pestis strain Pestoides F ncbi_taxonomy Yersinia pestis Pestoides F NCBITaxon:56147 GC_ID:1 alfalfa lucerne ncbi_taxonomy Medicago sativa subsp. sativa alfalfa NCBITaxon:3879 Medicago sativa alfalfa Murinae NCBITaxon:109679 GC_ID:1 ncbi_taxonomy Murinae GC_ID:11 Yersinia enterocolitica subsp. enterocolitica str. 8081 Yersinia enterocolitica subsp. enterocolitica strain 8081 ncbi_taxonomy NCBITaxon:393305 Yersinia enterocolitica subsp. enterocolitica 8081 GC_ID:1 ncbi_taxonomy Circoviridae GC_ID:11 Legionella pneumophila 'Corby' Legionella pneumophila strain Corby ncbi_taxonomy Legionella pneumophila str. Corby NCBITaxon:135857 GC_ID:1 ncbi_taxonomy Cryptococcus neoformans serotype D Filobasidiella neoformans var. neoformans Cryptococcus neoformans var. neoformans GC_ID:11 PMID:17293413 Escherichia coli str. APEC O1 Escherichia coli strain APEC O1 ncbi_taxonomy Escherichia coli APEC O1 Mammalia mammals mammal ncbi_taxonomy mammal- NCBITaxon:40674 Mammalia mammal mammal- PRO:DAN GC_ID:11 PMID:17873037 Campylobacter jejuni subsp. jejuni str. 81116 Campylobacter jejuni subsp. jejuni strain 81116 ncbi_taxonomy Campylobacter jejuni subsp. jejuni NCTC 11828 Campylobacter jejuni subsp. jejuni 81116 GC_ID:11 Escherichia coli str. SE11 Escherichia coli strain SE11 ncbi_taxonomy Escherichia coli SE11 NCBITaxon:320386 GC_ID:11 Burkholderia mallei str. 10229 Burkholderia mallei strain 10229 ncbi_taxonomy Burkholderia mallei 10229 Burkholderia mallei NCTC 10229 GC_ID:11 Yersinia pestis str. CA88-4125 Yersinia pestis strain CA88-4125 ncbi_taxonomy Yersinia pestis CA88-4125 GC_ID:11 Escherichia coli B (REL606 strain) Escherichia coli B strain REL606 Escherichia coli str. B substr. REL606 ncbi_taxonomy Escherichia coli B str. Bc251 Escherichia coli B str. REL606 GC_ID:11 PMID:18065534 Actinobacillus pleuropneumoniae serovar 5b strain L20 ncbi_taxonomy Actinobacillus pleuropneumoniae L20 Actinobacillus pleuropneumoniae serovar 5b str. L20 GC_ID:1 ncbi_taxonomy Vinckeia Plasmodium (Vinckeia) GC_ID:11 Staphylococcus aureus subsp. aureus str. Mu3 Staphylococcus aureus subsp. aureus strain Mu3 ncbi_taxonomy NCBITaxon:418127 Staphylococcus aureus subsp. aureus Mu3 GC_ID:11 Mycobacterium tuberculosis str. H37Ra Mycobacterium tuberculosis strain H37Ra ncbi_taxonomy Mycobacterium tuberculosis ATCC 25177 Mycobacterium tuberculosis H37Ra GC_ID:1 ncbi_taxonomy Eimeriorina GC_ID:11 Legionella pneumophila str. 2300/99 Alcoy Legionella pneumophila strain 2300/99 Alcoy ncbi_taxonomy Legionella pneumophila 2300/99 Legionella pneumophila 2300/99 Alcoy GC_ID:12 ncbi_taxonomy Candida dubliniensis GC_ID:11 PMID:17951380 Staphylococcus aureus subsp. aureus strain Newman ncbi_taxonomy Staphylococcus aureus subsp. aureus Newman NCBITaxon:426430 Staphylococcus aureus subsp. aureus str. Newman GC_ID:11 ncbi_taxonomy Shigella flexneri serotype 2a Shigella flexneri 2a GC_ID:11 ncbi_taxonomy Actinobacillus pleuropneumoniae serovar 3 str. JL03 GC_ID:1 ncbi_taxonomy ssRNA viruses GC_ID:11 PMID:18708504 Escherichia coli str. SMS-3-5 Escherichia coli strain SMS-3-5 ncbi_taxonomy Escherichia coli SECEC SMS-3-5 Escherichia coli SMS-3-5 GC_ID:11 Clostridium botulinum A ATCC 19397 Clostridium botulinum A strain ATCC 19397 ncbi_taxonomy Clostridium botulinum A str. ATCC 19397 GC_ID:11 Clostridium botulinum A strain Hall ncbi_taxonomy NCBITaxon:441771 Clostridium botulinum A str. Hall GC_ID:11 ncbi_taxonomy Escherichia coli O157:H7 str. EC4115 GC_ID:11 PMID:20935092 Borrelia burgdorferi str. 156a Borrelia burgdorferi strain 156a ncbi_taxonomy Borrelia burgdorferi 156a GC_ID:11 PMID:20935092 Borrelia burgdorferi str. ZS7 Borrelia burgdorferi strain ZS7 ncbi_taxonomy Borrelia burgdorferi ZS7 GC_ID:11 PMID:434652 ncbi_taxonomy Legionella pneumophila Dictyostelium discoideum GC_ID:1 slime mold ncbi_taxonomy NCBITaxon:44689 Dictyostelium discoideum slime mold GC_ID:1 PMID:15689432 PMID:16151185 PMID:17010206 PMID:17051209 PMID:17572334 ncbi_taxonomy Dikarya GC_ID:1 ncbi_taxonomy Eurotiomycetidae GC_ID:11 Francisella tularensis subsp. holarctica str. FTNF002-00 Francisella tularensis subsp. holarctica strain FTNF002-00 ncbi_taxonomy Francisella tularensis subsp. holarctica FTA Francisella tularensis subsp. holarctica FTNF002-00 GC_ID:11 ncbi_taxonomy Vibrio cholerae O139 strain Vibrio cholerae serogroup O139 Vibrio cholerae O139 NCBITaxon:10446 AcMNPV GC_ID:1 ncbi_taxonomy Autographa californica multicapsid nuclear polyhedrosis virus Autographa californica multicapsid nuclear polyhedrosis virus AcMNPV Autographa californica nuclear polyhedrosis virus Autographa californica nuclear polyhedrosis virus AcMNPV Autographa californica nuclear polyhedrosis virus AcNPV Autographa californica nuclear polyhedrosis virus, AcMNPV Autographa californica nucleopolyhedrovirus GC_ID:11 Staphylococcus aureus aureus ncbi_taxonomy Staphylococcus aureus subsp. aureus GC_ID:11 PMID:18820018 Streptococcus pyogenes str. NZ131 Streptococcus pyogenes strain NZ131 ncbi_taxonomy Streptococcus pyogenes NZ131 GC_ID:11 Enterococcus faecalis str. OG1RF Enterococcus faecalis strain OG1RF ncbi_taxonomy Enterococcus faecalis OG1RF ncbi_taxonomy fungal- NCBITaxon:4751 Fungi fungal- PRO:DAN GC_ID:11 Salmonella enterica subsp. enterica serovar Paratyphi C str. RKS4594 ncbi_taxonomy Salmonella paratyphi C str. RKS4594 Salmonella paratyphi C strain RKS4594 Salmonella enterica subsp. enterica serovar Paratyphi C strain RKS4594 GC_ID:11 ncbi_taxonomy Geobacillus sp. Y412MC10 Paenibacillus sp. Y412MC10 GC_ID:11 ncbi_taxonomy Diplokokkus intracellularis meningitidis Micrococcus intracellularis Micrococcus meningitidis Micrococcus meningitidis cerebrospinalis Neisseria meningitidis. Neisseria weichselbaumii Neisseria meningitidis GC_ID:11 Streptococcus pneumoniae str. Taiwan19F-14 Streptococcus pneumoniae strain Taiwan19F-14 ncbi_taxonomy Streptococcus pneumoniae Taiwan19F-14 GC_ID:11 Streptococcus pneumoniae str. Hungary19A-6 Streptococcus pneumoniae strain Hungary19A-6 ncbi_taxonomy Streptococcus pneumoniae Hungary19A-6 GC_ID:11 Streptococcus pneumoniae str. 70585 Streptococcus pneumoniae strain 70585 ncbi_taxonomy Streptococcus pneumoniae 70585 GC_ID:11 Streptococcus pneumoniae str. JJA Streptococcus pneumoniae strain JJA ncbi_taxonomy Streptococcus pneumoniae JJA GC_ID:11 Streptococcus pneumoniae str. P1031 Streptococcus pneumoniae strain P1031 ncbi_taxonomy Streptococcus pneumoniae P1031 Ascomycota ascomycetes sac fungi Ascomycota GC_ID:1 budding yeasts ncbi_taxonomy Endomycetales Saccharomycetales NCBITaxon:221665 NCBITaxon:44280 GC_ID:1 ncbi_taxonomy Saccharomycetaceae Saccharomyces cerevisiae baker's yeast brewer's yeast lager beer yeast yeast GC_ID:1 baker's yeast brewer's yeast lager beer yeast yeast ncbi_taxonomy Candida robusta Saccaromyces cerevisiae Saccharomyce cerevisiae Saccharomyces capensis Saccharomyces italicus Saccharomyces oviformis Saccharomyces uvarum var. melibiosus Saccharomyes cerevisiae Sccharomyces cerevisiae NCBITaxon:4932 Saccharomyces cerevisiae GC_ID:11 Clostridium botulinum B1 strain Okra ncbi_taxonomy Clostridium botulinum B1 str. Okra GC_ID:11 Clostridium botulinum A3 strain Loch Maree ncbi_taxonomy Clostridium botulinum A3 str. Loch Maree GC_ID:11 Edwardsiella tarda str. EIB202 Edwardsiella tarda strain EIB202 ncbi_taxonomy Edwardsiella tarda EIB202 GC_ID:11 Yersinia pseudotuberculosis str. YPIII Yersinia pseudotuberculosis strain YPIII ncbi_taxonomy Yersinia pseudotuberculosis YPIII GC_ID:11 Yersinia pseudotuberculosis str. PB1/+ Yersinia pseudotuberculosis strain PB1/+ ncbi_taxonomy Yersinia pseudotuberculosis PB1/+ NCBITaxon:61255 GC_ID:1 ncbi_taxonomy Ajellomyces capsulata Ajellomyces capsulatas Ajellomyces capsulatus Cryptococcus capsulatus Emmonsiella capsulata Histoplasma capsulatum Ajellomyces capsulatus Histoplasma capsulatum GC_ID:1 trouts, salmons & chars ncbi_taxonomy Salmoninae GC_ID:11 Clostridium botulinum E3 strain Alaska E43 ncbi_taxonomy Clostridium botulinum E3 str. Alaska E43 GC_ID:1 ncbi_taxonomy Toxoplasma gondii strain ME49 Toxoplasma gondii ME49 GC_ID:11 Escherichia coli str. K12 substr. MG1655 Escherichia coli str. MG1655 Escherichia coli strain MG1655 ncbi_taxonomy Escherichia coli MG1655 Escherichia coli str. K-12 substr. MG1655 GC_ID:11 Streptococcus pneumoniae str. G54 Streptococcus pneumoniae strain G54 ncbi_taxonomy Streptococcus pneumoniae G54 GC_ID:11 Streptococcus pneumoniae str. CGSP14 Streptococcus pneumoniae strain CGSP14 ncbi_taxonomy Streptococcus pneumoniae CGSP14 GC_ID:11 PMID:11491321 ncbi_taxonomy Bordetella Moreno-Lopez 1952 (Approved Lists 1980) emend. Von Wintzingerode et al. 2001 Bordetella NCBITaxon:514 GC_ID:11 PMID:8240949 PMID:8782670 PMID:9226899 ncbi_taxonomy Alcaligenes bronchicanis Alcaligenes bronchisepticus Bacillus bronchicanis Bacillus bronchisepticus Bacterium bronchisepticus Bordetella bronchiseptica@ Brucella bronchiseptica Brucella bronchispetica Haemophilus bronchisepticus Bordetella bronchiseptica GC_ID:11 PMID:8240949 ncbi_taxonomy Bacterium tussis-convulsivae Haemophilus pertussis Hemophilus pertussis Microbe de la coqueluche Bordetella pertussis NCBITaxon:107441 NCBITaxon:192653 NCBITaxon:5415 GC_ID:1 Cryptococcus ncbi_taxonomy Filobasidiella Cryptococcus <basidiomycete yeast> GC_ID:1 ncbi_taxonomy Blastomyces neoformans Debaryomyces neoformans Filobasidiella neoformans Filobasidiella neoformornans Filobaxidiella neoformans Lipomyces neoformans Saccharomyces neoformans Torula neoformans Torulopsis neoformans Cryptococcus neoformans GC_ID:11 PMID:4074238 ncbi_taxonomy Bordetella avium GC_ID:11 PMID:20935092 Borrelia burgdorferi str. N40 Borrelia burgdorferi strain N40 ncbi_taxonomy Borrelia burgdorferi N40 GC_ID:11 PMID:20935092 Borrelia burgdorferi str. 297 Borrelia burgdorferi strain 297 ncbi_taxonomy Borrelia burgdorferi 297 GC_ID:1 Hymenomycetes ncbi_taxonomy Agaricomycotina GC_ID:11 Burkholderia pseudomallei str. MSHR346 Burkholderia pseudomallei strain MSHR346 ncbi_taxonomy Burkholderia pseudomallei MSHR346 GC_ID:11 Actinobacillus pleuropneumoniae serovar 7 strain AP76 ncbi_taxonomy Actinobacillus pleuropneumoniae serovar 7 str. AP76 GC_ID:11 PMID:10555323 PMID:10555334 PMID:16166704 PMID:27620848 ncbi_taxonomy Enterobacteraceae Enterobacteraceae (ex Lapage 1979) Lapage 1982, fam. nov., nom. rev. Enterobacteriaceae (ex Rahn 1937) Ewing et al. 1980, fam. nov., nom. rev. Enterobacteriaceae Rahn 1937 gamma-3 proteobacteria Enterobacteriaceae GC_ID:11 Escherichia coli O157:H7 strain TW14359 ncbi_taxonomy Escherichia coli O157:H7 str. TW14359 GC_ID:1 ncbi_taxonomy Torulopsis Candida NCBITaxon:39399 GC_ID:12 ncbi_taxonomy Candida albican Candida stellatoidea Candida stellatoidea type I Candida albicans GC_ID:1 PMID:14654427 Candida glabrata ncbi_taxonomy Candidia glabrata Cryptococcus glabratus Torulopsis glabrata Candida glabrata [Candida] glabrata GC_ID:1 ncbi_taxonomy Coccidioides GC_ID:11 Salmonella enterica subsp. enterica serovar Enteritidis strain P125109 ncbi_taxonomy Salmonella enterica subsp. enterica serovar Enteritidis str. P125109 GC_ID:11 Salmonella enterica subsp. enterica serovar Gallinarum strain 287/91 ncbi_taxonomy Salmonella enterica subsp. enterica serovar Gallinarum str. 287/91 GC_ID:1 ncbi_taxonomy Filobasidiella/Cryptococcus neoformans species complex NCBITaxon:292817 NCBITaxon:37768 NCBITaxon:37769 NCBITaxon:413065 GC_ID:1 ncbi_taxonomy Cryptococcus bacillisporus Cryptococcus neoformans B Cryptococcus neoformans serotype B Cryptococcus neoformans serotype C Cryptococcus neoformans var. gatti Cryptococcus neoformans var. gattii Cryptococcus neoformans var. shanghaiensis Filobasidiella bacillispora Filobasidiella neoformans var. bacillispora Filobasidiella neoformans var. gattii anamorph of Filobasidiella bacillispora Cryptococcus gattii GC_ID:11 Streptococcus equi subsp. zooepidemicus str. MGCS10565 Streptococcus equi subsp. zooepidemicus strain MGCS10565 ncbi_taxonomy Streptococcus equi subsp. zooepidemicus MGCS10565 GC_ID:11 PMID:21602330 Listeria monocytogenes str. HCC23 Listeria monocytogenes strain HCC23 ncbi_taxonomy Listeria monocytogenes HCC23 GC_ID:1 PMID:23020233 ncbi_taxonomy Amoebozoa GC_ID:11 PMID:19047519 Pseudomonas aeruginosa str. LESB58 Pseudomonas aeruginosa strain LESB58 ncbi_taxonomy Pseudomonas aeruginosa LESB58 GC_ID:1 ncbi_taxonomy Nucleopolyhedrovirus Alphabaculovirus GC_ID:1 ncbi_taxonomy y yeast NCBITaxon:559292 Saccharomyces cerevisiae S288c y PRO:DAN yeast PRO:DAN GC_ID:11 Streptococcus pneumoniae str. ATCC 700669 Streptococcus pneumoniae strain ATCC 700669 ncbi_taxonomy Streptococcus pneumoniae ATCC 700669 NCBITaxon:662101 NCBITaxon:662104 GC_ID:11 PMID:10319482 ncbi_taxonomy Bacillus coli Bacterium coli Bacterium coli commune Enterococcus coli Escherchia coli Eschericia coli bacterium E3 NCBITaxon:562 Escherichia coli GC_ID:11 PMID:18952803 Helicobacter pylori str. G27 Helicobacter pylori strain G27 ncbi_taxonomy Helicobacter pylori G27 GC_ID:11 Listeria monocytogenes str. L99 Listeria monocytogenes strain L99 ncbi_taxonomy Listeria monocytogenes L99 GC_ID:11 Escherichia coli str. Vir68 Escherichia coli strain Vir68 ncbi_taxonomy Escherichia coli Vir68 GC_ID:1 ncbi_taxonomy Trypanosomatidae GC_ID:1 ncbi_taxonomy Leishmania (Leishmania) donovani Leishmania donovani GC_ID:1 ncbi_taxonomy Leishmania (Leishmania) major Leishmania tropica major NCBITaxon:5664 Leishmania major GC_ID:1 ncbi_taxonomy Leishmania (Leishmania) mexicana Leishmania mexicana NCBITaxon:5662 GC_ID:1 ncbi_taxonomy Leishmania (Leishmania) infantum Leishmania donovani infantum Leishmania infantum GC_ID:11 Bacillus anthracis CDC 684 Bacillus anthracis strain CDC 684 ncbi_taxonomy Bacillus anthracis CDC 684/NRRL 349S/NRS 234 NCBITaxon:568206 Bacillus anthracis str. CDC 684 NCBITaxon:634178 GC_ID:11 Listeria monocytogenes serotype 4b strain CLIP 80459 Listeria monocytogenes str. Clip80459 Listeria monocytogenes strain Clip80459 ncbi_taxonomy Listeria monocytogenes Clip80459 Listeria monocytogenes Clip81459 Listeria monocytogenes strain CLIP 80459 serovar 4b Listeria monocytogenes serotype 4b str. CLIP 80459 GC_ID:1 ncbi_taxonomy Trypanosoma GC_ID:1 ncbi_taxonomy Trypanosoma (Trypanozoon) brucei Trypanosoma brucei subgroup Trypanosoma brucei GC_ID:1 ncbi_taxonomy Trypanosoma cruzi GC_ID:11 Helicobacter pylori str. P12 Helicobacter pylori strain P12 ncbi_taxonomy Helicobacter pylori P12 GC_ID:11 PMID:19815525 Escherichia coli O26:H11 11368 Escherichia coli O26:H11 strain 11368 ncbi_taxonomy Escherichia coli O26:H11 str. 11368 GC_ID:11 PMID:18952797 Escherichia coli O127:H6 E2348/69 Escherichia coli O127:H6 strain E2348/69 ncbi_taxonomy Escherichia coli 0127:H6 str. E2348/69 Escherichia coli O127:H6 str. E2348/69 GC_ID:1 ncbi_taxonomy Entamoeba histolytica GC_ID:11 Vibrio cholerae str. M66-2 Vibrio cholerae strain M66-2 ncbi_taxonomy Vibrio cholerae M66-2 GC_ID:1 apicomplexans ncbi_taxonomy apicomplexans Apicomplexa GC_ID:1 ncbi_taxonomy Cryptosporidium parvum GC_ID:1 ncbi_taxonomy Toxoplasma gondii GC_ID:1 ncbi_taxonomy Plasmodium GC_ID:1 ncbi_taxonomy Plasmodium berghei (strain ANKA) Plasmodium berghei str. ANKA Plasmodium berghei strain ANKA Plasmodium berghei ANKA ncbi_taxonomy malaria parasite NCBITaxon:5833 Plasmodium falciparum malaria parasite PRO:DAN GC_ID:11 Escherichia coli str. IAI1 Escherichia coli strain IAI1 ncbi_taxonomy Escherichia coli IAI1 GC_ID:11 Escherichia coli str. S88 Escherichia coli strain S88 ncbi_taxonomy Escherichia coli S88 GC_ID:11 ncbi_taxonomy Escherichia coli 55989 GC_ID:11 ncbi_taxonomy NCBITaxon:585056 Escherichia coli UMN026 GC_ID:11 ncbi_taxonomy NCBITaxon:585057 Escherichia coli IAI39 GC_ID:11 PMID:19815525 Escherichia coli O103:H2 strain 12009 ncbi_taxonomy Escherichia coli O103:H2 str. 12009 GC_ID:11 PMID:19815525 Escherichia coli O111:H- strain 11128 ncbi_taxonomy Escherichia coli O111:H- str. 11128 GC_ID:11 Escherichia coli str. ED1a Escherichia coli strain ED1a ncbi_taxonomy Escherichia coli ED1a GC_ID:1 ncbi_taxonomy Plasmodium yoelli Plasmodium yoelii GC_ID:11 ncbi_taxonomy Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S GC_ID:11 PMID:10319519 PMID:10939679 PMID:12072558 PMID:15653929 PMID:15653930 PMID:3231714 PMID:9731304 ncbi_taxonomy Samonella Salmonella NCBITaxon:149049 GC_ID:11 PMID:15653929 PMID:15653930 PMID:7149525 ncbi_taxonomy Salmonella cholerae-suis subsp. cholerae-suis Salmonella choleraesuis subsp. choleraesuis Salmonella enterica I Salmonella enterica subsp. I Salmonella enterica subsp. enterica GC_ID:11 PMID:17283804 Bacillus anthracis A0248 Bacillus anthracis strain A0248 ncbi_taxonomy Bacillus anthracis str. A0248 GC_ID:11 Helicobacter pylori str. B38 Helicobacter pylori strain B38 ncbi_taxonomy Helicobacter pylori B38 GC_ID:11 Escherichia coli str. BW2952 Escherichia coli strain BW2952 ncbi_taxonomy Escherichia coli BW2952 GC_ID:1 ncbi_taxonomy Exophilia dermatitidis Wangiella dermatitidis Exophiala dermatitidis GC_ID:11 PMID:26834722 ncbi_taxonomy Shigella GC_ID:11 PMID:16561743 ncbi_taxonomy Shigella boydii GC_ID:11 ncbi_taxonomy Shigella paradysenteriae NCBITaxon:623 Shigella flexneri Caenorhabditis elegans roundworm GC_ID:1 roundworm ncbi_taxonomy Rhabditis elegans w worm NCBITaxon:6239 Caenorhabditis elegans w PRO:DAN worm PRO:DAN GC_ID:1 ncbi_taxonomy SARS coronavirus ExoN1 GC_ID:11 Yersinia ncbi_taxonomy Yersinia <bacteria> GC_ID:11 ncbi_taxonomy Bacterium enterocoliticum NCBITaxon:630 Yersinia enterocolitica GC_ID:11 PMID:15084509 ncbi_taxonomy Bacillus pestis Bacterium pestis Pasteurella pestis Pestisella pestis Yersinia pseudotuberculosis subsp. pestis Ypes- NCBITaxon:632 Yersinia pestis Ypes- PRO:DAN NCBITaxon:1161941 GC_ID:11 PMID:2223608 PMID:23919959 ncbi_taxonomy Bacillus pseudotuberkulosis Bacterium pseudotuberculosis Pasteurella lymphangitidis Pasteurella pseudotuberculosis Shigella pseudotuberculosis [Pasteurella] lymphangitidis Yersinia pseudotuberculosis NCBITaxon:1471792 NCBITaxon:1471793 GC_ID:11 PMID:27539016 ncbi_taxonomy Edwardsiella anguillimortifera Paracolobactrum anguillimortiferum Edwardsiella tarda GC_ID:11 Listeria monocytogenes str. 08-5923 Listeria monocytogenes strain 08-5923 ncbi_taxonomy Listeria monocytogenes 08-5923 GC_ID:11 PMID:11155981 PMID:12067377 PMID:12807216 PMID:1380286 PMID:1380289 PMID:15388703 PMID:16560691 PMID:17012583 PMID:17158971 PMID:19567585 PMID:7520733 PMID:8347521 PMID:8934910 ncbi_taxonomy Aeromonas NCBITaxon:1471787 NCBITaxon:1471788 NCBITaxon:582196 NCBITaxon:582198 NCBITaxon:582214 NCBITaxon:582215 NCBITaxon:582216 NCBITaxon:582217 NCBITaxon:582218 NCBITaxon:582219 NCBITaxon:582220 NCBITaxon:582221 NCBITaxon:582222 NCBITaxon:582223 NCBITaxon:582224 NCBITaxon:582225 NCBITaxon:582226 NCBITaxon:582228 NCBITaxon:582229 NCBITaxon:582231 NCBITaxon:582236 NCBITaxon:582237 NCBITaxon:582240 NCBITaxon:582250 NCBITaxon:582251 NCBITaxon:582253 NCBITaxon:582254 NCBITaxon:582265 NCBITaxon:582266 NCBITaxon:582267 NCBITaxon:582279 NCBITaxon:582282 NCBITaxon:582284 NCBITaxon:582286 NCBITaxon:582287 NCBITaxon:582289 NCBITaxon:582290 NCBITaxon:582291 NCBITaxon:582292 NCBITaxon:582295 NCBITaxon:582297 NCBITaxon:582299 NCBITaxon:582300 NCBITaxon:582302 NCBITaxon:582303 NCBITaxon:582304 NCBITaxon:582305 NCBITaxon:582306 NCBITaxon:582307 NCBITaxon:582308 NCBITaxon:582309 NCBITaxon:582310 NCBITaxon:582311 NCBITaxon:582312 NCBITaxon:582313 NCBITaxon:582314 NCBITaxon:582315 NCBITaxon:582316 NCBITaxon:582317 NCBITaxon:582318 NCBITaxon:582319 NCBITaxon:582320 NCBITaxon:582321 NCBITaxon:582322 NCBITaxon:582323 NCBITaxon:582324 NCBITaxon:98358 GC_ID:11 PMID:16560691 PMID:19965992 PMID:23485124 PMID:932684 ncbi_taxonomy Aeromonas dourgesi Aeromonas hydrophilia Aeromonas liquefaciens Bacillus hydrophilus Bacillus hydrophilus fuscus Bacterium hydrophilum Proteus hydrophilus Proteus ichthyosmius Pseudomonas hydrophila Aeromonas hydrophila NCBITaxon:697046 GC_ID:11 PMID:19965992 ncbi_taxonomy Bacillus salmonicida Bacterium salmonicida Proteus salmonicida Aeromonas salmonicida GC_ID:11 Listeria monocytogenes str. 08-5578 Listeria monocytogenes strain 08-5578 ncbi_taxonomy Listeria monocytogenes 08-5578 GC_ID:11 Neisseria meningitidis str. alpha14 Neisseria meningitidis strain alpha14 ncbi_taxonomy Neisseria meningitidis alpha14 GC_ID:11 PMID:9272984 ncbi_taxonomy Bacillo virgola del Koch Bacillus cholerae Bacillus cholerae-asiaticae Kommabacillus Liquidivibrio cholerae Microspira comma Pacinia cholerae-asiaticae Spirillum cholerae Spirillum cholerae-asiaticae Vibrio choleae Vibrio cholera Vibrio cholerae-asiaticae Vibrio comma Vibrio cholerae GC_ID:11 ncbi_taxonomy Legionella pneumophila serogroup 1 NCBITaxon:665030 GC_ID:11 Staphylococcus aureus subsp. aureus str. ED98 Staphylococcus aureus subsp. aureus strain ED98 ncbi_taxonomy Staphylococcus aureus ED98 Staphylococcus aureus subsp. aureus ED98 GC_ID:1 ncbi_taxonomy Murine cytomegalovirus (strain K181) GC_ID:1 ncbi_taxonomy Coronavirinae GC_ID:1 ncbi_taxonomy Alphacoronavirus-1 Alphacoronavirus 1 SARSr-CoV GC_ID:1 ncbi_taxonomy SARS-like coronavirus SARS-related coronavirus Severe acute respiratory syndrome-related coronavirus GC_ID:1 ncbi_taxonomy Human metapneumovirus CAN97-83 GC_ID:1 ncbi_taxonomy Mileewa branchiuma GC_ID:11 ncbi_taxonomy Staphylococcus aureus 04-02981 GC_ID:1 domestic silkworm silk moth silkworm ncbi_taxonomy Bombyx mori GC_ID:4 PMID:12949158 Mycoplasma gallisepticum R(low) Mycoplasma gallisepticum strain R(low) ncbi_taxonomy Mycoplasma gallisepticum str. R(low) GC_ID:11 PMID:10843050 PMID:15280320 PMID:15388716 PMID:17220461 PMID:2223605 PMID:29923825 ncbi_taxonomy Pasteurellaceae Pohl 1981 Pasteurellaceae NCBITaxon:185836 GC_ID:1 greater wax moth ncbi_taxonomy Galleria mellonela Galleria melonella Galleria mellonella GC_ID:11 Haemophilus influenzae KW20 Haemophilus influenzae Rd ncbi_taxonomy NCBITaxon:71421 Haemophilus influenzae Rd KW20 GC_ID:11 PMID:1847295 ncbi_taxonomy Actinobacillus pleuropneumonia Haemophilus pleuropneumoniae Actinobacillus pleuropneumoniae saccharomyceta GC_ID:1 ncbi_taxonomy saccharomyceta Drosophila melanogaster fruit fly GC_ID:1 fruit fly ncbi_taxonomy Drosophila melangaster Sophophora melanogaster NCBITaxon:7227 Drosophila melanogaster fruit fly GC_ID:11 ncbi_taxonomy Bacterium influenzae Coccobacillus pfeifferi Haemophilus meningitidis Influenza-bacillus Mycobacterium influenzae Haemophilus influenzae GC_ID:1 ncbi_taxonomy NCBITaxon:73239 Plasmodium yoelii yoelii GC_ID:11 PMID:15184562 ncbi_taxonomy Bacterium multocidum Micrococcus gallicidus Pasteurella cholerae-gallinarum Pasteurella gallicida Pateurella multocida Pasteurella multocida NCBITaxon:746 GC_ID:11 PMID:10028248 PMID:8782683 ncbi_taxonomy Pasteurella haemolytica Mannheimia haemolytica GC_ID:1 ncbi_taxonomy Nidovirales NCBITaxon:802 GC_ID:11 PMID:10425758 PMID:11837299 PMID:12508871 PMID:7857789 PMID:8240958 PMID:8863415 ncbi_taxonomy "Bartonia" Strong et al. 1913 "Grahamella" Brumpt 1911 "Grahmia" Tartakowsky 1910 "Rocha-Limae" (sic) Machiavello 1947 Bartonella Strong et al. 1915 (Approved Lists 1980) emend. Birtles et al. 1995 Bartonella Strong et al. 1915 (Approved Lists 1980) emend. Brenner et al. 1993 Grahamella Grahamella (ex Brumpt 1911) Ristic and Kreier 1984 Grahmia Rocha-Limae Rochalimaea Rochalimaea (Macchiavello 1947) Krieg 1961 Bartonella Vertebrata <Metazoa> Vertebrata vertebrates GC_ID:1 Vertebrata vertebrates ncbi_taxonomy vertebrates Vertebrata <Metazoa> GC_ID:11 PMID:9226923 ncbi_taxonomy Coxiella burnetii8 Rickettsia burneti Rickettsia diaporica Coxiella burnetii GC_ID:11 PMID:10939649 PMID:11491333 PMID:14662925 PMID:9103608 ncbi_taxonomy Rickettsia Danio rerio leopard danio zebra danio zebra fish zebrafish NCBITaxon:27702 NCBITaxon:37966 GC_ID:1 leopard danio zebra danio zebra fish zebrafish ncbi_taxonomy Brachidanio rerio Brachydanio rerio Brachydanio rerio frankei Cyprinus rerio Danio frankei Danio rerio frankei NCBITaxon:7955 Danio rerio zebrafish GC_ID:1 ncbi_taxonomy Lythrurus GC_ID:1 ncbi_taxonomy Bovine herpesvirus type 1.1 GC_ID:1 PMID:15062801 salmonids ncbi_taxonomy Salmonidae NCBITaxon:1311475 GC_ID:1 rainbow trout ncbi_taxonomy Onchorhynchus mykiss Oncorhynchus nerka mykiss Parasalmo mykiss Salmo mykiss Oncorhynchus mykiss GC_ID:1 ncbi_taxonomy Melanogaster GC_ID:11 PMID:16403855 ncbi_taxonomy 'Burkholderiales' Burkholderia/Oxalobacter/Ralstonia group Burkholderiales NCBITaxon:83553 GC_ID:11 PMID:10319462 PMID:11211265 PMID:21048221 PMID:21048222 PMID:23620152 PMID:25618261 PMID:9103632 PMID:9103637 ncbi_taxonomy Bedsonia Chlamydophila Miyagawanella Rakeia Rickettsiaformis Chlamydia GC_ID:11 PMID:10192388 PMID:10319462 PMID:8102247 PMID:8347519 ncbi_taxonomy Chlamydozoon trachomatis Rickettsia trachomae Rickettsia trachomatis Chlamydia trachomatis GC_ID:11 PMID:12218036 ncbi_taxonomy Mycobacterium tuberculosis CSU#93 Mycobacterium tuberculosis CDC1551 GC_ID:11 PMID:12218036 PMID:12368430 PMID:9634230 Mycobacterium tuberculosis str. H37Rv Mycobacterium tuberculosis strain H37Rv ncbi_taxonomy NCBITaxon:83332 Mycobacterium tuberculosis H37Rv GC_ID:11 Escherichia coli K12 ncbi_taxonomy Ec- NCBITaxon:83333 Escherichia coli K-12 Ec- PRO:DAN GC_ID:11 ncbi_taxonomy Escherichia coli 0157:H7 Escherichia coli O157:H7 NCBITaxon:811 GC_ID:11 PMID:10319462 PMID:8102247 PMID:8347519 ncbi_taxonomy Chlamydophila pneumoniae Chlamydia pneumoniae NCBITaxon:1761 GC_ID:11 PMID:11837321 PMID:1736962 PMID:19244447 ncbi_taxonomy Corynebacterineae Corynebacteriales Corynebacterineae GC_ID:1 ncbi_taxonomy charr Salvelinus alpinus alpinus GC_ID:1 ncbi_taxonomy Porcine circovirus Type II Porcine circovirus type 2 Porcine circovirus 2 GC_ID:11 PMID:9252185 Helicobacter pylori (strain 26695) Helicobacter pylori str. 26695 Helicobacter pylori strain 26695 ncbi_taxonomy Helicobacter pylori ATCC 700392 Helicobacter pylori KE26695 NCBITaxon:85962 Helicobacter pylori 26695 GC_ID:11 PMID:9923682 Helicobacter pylori str. J99 Helicobacter pylori strain J99 ncbi_taxonomy NCBITaxon:85963 Helicobacter pylori J99 GC_ID:11 Legionella pneumophila str. 130b Legionella pneumophila strain 130b ncbi_taxonomy Legionella pneumophila ATCC BAA-74 Legionella pneumophila serogroup 1 strain 130b Legionella pneumophila 130b NCBITaxon:9099 GC_ID:1 turkeys ncbi_taxonomy Phasianidae Gallus gallus bantam chicken chickens GC_ID:1 bantam chicken chickens ncbi_taxonomy Gallus domesticus Gallus gallus domesticus chick- chicken NCBITaxon:9031 Gallus gallus chick- PRO:DAN chicken NCBITaxon:41530 NCBITaxon:601 NCBITaxon:72667 GC_ID:11 PMID:10319519 PMID:10758910 PMID:15653930 PMID:16558776 PMID:9336938 ncbi_taxonomy Bacillus typhi Bacterium (subgen. Eberthella) typhi Salmonella choleraesuis serovar Typhi Salmonella choleraesuis typhi Salmonella enterica ser. typhi Salmonella enterica serotype Typhi Salmonella enterica serovar Typhi Salmonella typhi NCBITaxon:90370 Salmonella enterica subsp. enterica serovar Typhi NCBITaxon:41532 NCBITaxon:59210 NCBITaxon:602 GC_ID:11 PMID:10758910 PMID:15653930 PMID:9336938 ncbi_taxonomy Bacillus typhimurium Salmonella choleraesuis serotype typhimurium Salmonella enterica 1,4,[5],12,:i:1,2 Salmonella enterica ser. typhimurium Salmonella enterica serotype Typhimurium Salmonella enterica serovar Typhimurium Salmonella enterica subsp. enterica serovar 1,4,[5],12,:i:1,2 Salmonella typhi-murium Salmonella typhimurium Samonella typhimurium Styphi- NCBITaxon:90371 Salmonella enterica subsp. enterica serovar Typhimurium Styphi- PRO:DAN GC_ID:11 PMID:21478351 Salmonella enterica subsp. enterica serovar Typhimurium strain ST4/74 ncbi_taxonomy Salmonella enterica subsp. enterica serovar Typhimurium str. 4/74 Salmonella enterica subsp. enterica serovar Typhimurium str. 474 Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74 GC_ID:11 PMID:20212322 ncbi_taxonomy Bacillus/Lactobacillus/Streptococcus group Firmibacteria Bacilli GC_ID:11 PMID:27620848 ncbi_taxonomy Enterobacteriaceae and related endosymbionts Enterobacteriaceae group Enterobacteriales enterobacteria gamma-3 proteobacteria Enterobacterales GC_ID:1 whales, hippos, ruminants, pigs, camels etc. ncbi_taxonomy even-toed ungulates Cetartiodactyla GC_ID:11 Staphylococcus aureus subsp. aureus str. NCTC 8325 Staphylococcus aureus subsp. aureus strain NCTC 8325 ncbi_taxonomy Staphylococcus aureus NCTC 8325 NCBITaxon:93061 Staphylococcus aureus subsp. aureus NCTC 8325 NCBITaxon:95751 GC_ID:1 ncbi_taxonomy influenza A virus (A/goose/Guangdong/1/96/(H5N1)) NCBITaxon:93838 Influenza A virus (A/Goose/Guangdong/1/96(H5N1)) Influenza A virus (A/goose/Guangdong/1/1996(H5N1)) GC_ID:1 New World monkeys monkey monkeys ncbi_taxonomy Platyrrhini GC_ID:1 ncbi_taxonomy Catarrhini GC_ID:1 Old World monkeys monkey monkeys ncbi_taxonomy Cercopithecidae green monkey ncbi_taxonomy GrMonkey- NCBITaxon:9534 Chlorocebus aethiops Chlorocebus aethiops 绿猴属 green monkey GrMonkey- PRO:DAN Homo sapiens human human being man GC_ID:1 human man ncbi_taxonomy Home sapiens Homo sampiens Homo sapeins Homo sapian Homo sapians Homo sapien Homo sapience Homo sapiense Homo sapients Homo sapines Homo spaiens Homo spiens Humo sapiens h human NCBITaxon:9606 Homo sapiens Homo sapiens 人类 h PRO:DAN human PRO:DAN NCBITaxon:77150 GC_ID:1 black ferret domestic ferret ferret ncbi_taxonomy Mustela furo Mustela putoris furo Mustela putorius furo GC_ID:1 pig pigs swine wild boar ncbi_taxonomy Sus scrofus pig pig- NCBITaxon:9823 Sus scrofa pig pig- PRO:DAN GC_ID:1 ncbi_taxonomy Bovidae NCBITaxon:272461 GC_ID:1 bovine cattle cow dairy cow domestic cattle domestic cow ncbi_taxonomy Bos Tauurus Bos bovis Bos primigenius taurus cow cow- NCBITaxon:9913 Bos taurus cow cow- PRO:DAN NCBITaxon:57076 GC_ID:1 domestic goat goat goats ncbi_taxonomy Capra aegagrus hircus Carpa hircus South African angora goat Capra hircus NCBITaxon:870965 GC_ID:11 PMID:11677609 Salmonella enterica subsp. enterica serovar Typhimurium LT2 Salmonella enterica subsp. enterica serovar Typhimurium strain LT2 Salmonella enterica subsp. enterica serovar Typhimurium strain LT2-LTL2 ncbi_taxonomy Salmonella typhimurium LT2 SaltyLT2- NCBITaxon:99287 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 SaltyLT2- PRO:DAN NCBITaxon:9936 GC_ID:1 domestic sheep lambs sheep wild sheep ncbi_taxonomy Ovis ammon aries Ovis orientalis aries Ovis ovis NCBITaxon:9940 Ovis aries sheep GC_ID:1 ncbi_taxonomy Caprinae NCBITaxon:34833 NCBITaxon:9985 GC_ID:1 European rabbit Japanese white rabbit domestic rabbit rabbit rabbits ncbi_taxonomy Lepus cuniculus rabbit- NCBITaxon:9986 Oryctolagus cuniculus rabbit rabbit- PRO:DAN Rodentia rodent GC_ID:1 rodent ncbi_taxonomy rodents NCBITaxon:9989 Rodentia rodent planned process planned process Injecting mice with a vaccine in order to test its efficacy A processual entity that realizes a plan which is the concretization of a plan specification. 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process. Bjoern Peters branch derived 6/11/9: Edited at workshop. Used to include: is initiated by an agent This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) planned process regulator role Fact sheet - Regulating the companies The role of the regulator. Ofwat is the economic regulator of the water and sewerage industry in England and Wales. http://www.ofwat.gov.uk/aptrix/ofwat/publish.nsf/Content/roleofregulator_factsheet170805 a regulatory role involved with making and/or enforcing relevant legislation and governmental orders Person:Jennifer Fostel regulator OBI regulator role regulatory role Regulatory agency, Ethics committee, Approval letter; example: Browse these EPA Regulatory Role subtopics http://www.epa.gov/ebtpages/enviregulatoryrole.html Feb 29, 2008 a role which inheres in material entities and is realized in the processes of making, enforcing or being defined by legislation or orders issued by a governmental body. GROUP: Role branch OBI, CDISC govt agents responsible for creating regulations; proxies for enforcing regulations. CDISC definition: regulatory authorities. Bodies having the power to regulate. NOTE: In the ICH GCP guideline the term includes the authorities that review submitted clinical data and those that conduct inspections. These bodies are sometimes referred to as competent regulatory role material supplier role Jackson Labs is an organization which provide mice as experimental material a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation. Supplier role is a special kind of service, e.g. biobank PERSON:Jennifer Fostel material provider role supplier material supplier role classified data set A data set that is produced as the output of a class prediction data transformation and consists of a data set with assigned class labels. PERSON: James Malone PERSON: Monnie McGee data set with assigned class labels classified data set processed material Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples Is a material entity that is created or changed during material processing. PERSON: Alan Ruttenberg processed material culture medium A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008 a processed material that provides the needed nourishment for microorganisms or cells grown in vitro. changed from a role to a processed material based on on Aug 22, 2011 dev call. Details see the tracker item: http://sourceforge.net/tracker/?func=detail&aid=3325270&group_id=177891&atid=886178 Modification made by JZ. Person: Jennifer Fostel, Jie Zheng OBI culture medium material processing A cell lysis, production of a cloning vector, creating a buffer. A planned process which results in physical changes in a specified input material PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca Serra material transformation OBI branch derived material processing specimen role liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient. a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation 22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. blood taken from animal: animal continues in study, whereas blood has role specimen. something taken from study subject, leaves the study and becomes the specimen. parasite example - when parasite in people we study people, people are subjects and parasites are specimen - when parasite extracted, they become subject in the following study specimen can later be subject. GROUP: Role Branch OBI specimen role antigen role Antigen is a role played by material which when introduced into an immune-competent organism causes an immune response a role that inheres in a vaccine component and plays an antigen role, i.e., it is introducd into an immune-competent organism to cause an immune response An antigen is a substance that prompts the generation of antibodies and can cause an immune response. Wikipedia http://en.wikipedia.org/wiki/Antigen. In the strict sense, immunogens are those substances that elicit a response from the immune system, whereas antigens are defined as substances that bind to specific antibodies. Not all antigens produce an immunogenic response, but all immunogens are antigens Role Branch OBI 9Mar09 waiting for discussion with immunology terms antigen role organization PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods. An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: 1) there are organization_member_roles (president, treasurer, branch editor), with individual persons as bearers 2) there are organization_roles (employer, owner, vendor, patent holder) 3) an organization has a charter / rules / bylaws, which specify what roles there are, how they should be realized, and how to modify the charter/rules/bylaws themselves. It is debatable what the organization itself is (some kind of dependent continuant or an aggregate of people). This also determines who/what the bearer of organization_roles' are. My personal favorite is still to define organization as a kind of 'legal entity', but thinking it through leads to all kinds of questions that are clearly outside the scope of OBI. Interestingly enough, it does not seem to matter much where we place organization itself, as long as we can subclass it (University, Corporation, Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, W3C, University of Oklahoma), and have it play roles. This leads to my proposal: We define organization through the statements 1 - 3 above, but without an 'is a' statement for now. We can leave it in its current place in the is_a hierarchy (material entity) or move it up to 'continuant'. We leave further clarifications to BFO, and close this issue for now. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Philippe Rocca-Serra PERSON: Susanna Sansone GROUP: OBI organization organization 组织 regulatory agency The US Environmental Protection Agency A regulatory agency is a organization that has responsibility over or for the legislation (acts and regulations) for a given sector of the government. GROUP: OBI Biomaterial Branch WEB: en.wikipedia.org/wiki/Regulator regulatory agency material transformation objective The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS. an objective specifiction that creates an specific output object from input materials. PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra artifact creation objective GROUP: OBI PlanAndPlannedProcess Branch material transformation objective manufacturing Manufacturing is a process with the intent to produce a processed material which will have a function for future use. A person or organization (having manufacturer role) is a participant in this process Manufacturing implies reproducibility and responsibility AR This includes a single scientist making a processed material for personal use. PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra GROUP: OBI PlanAndPlannedProcess Branch manufacturing manufacturing objective is the objective to manufacture a material of a certain function (device) PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra GROUP: OBI PlanAndPlannedProcess Branch manufacturing objective manufacturer role With respect to The Accuri C6 Flow Cytometer System, the organization Accuri bears the role manufacturer role. With respect to a transformed line of tissue culture cells derived by a specific lab, the lab whose personnel isolated the cll line bears the role manufacturer role. With respect to a specific antibody produced by an individual scientist, the scientist who purifies, characterizes and distributes the anitbody bears the role manufacturer role. Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process. GROUP: Role Branch OBI manufacturer role material separation objective The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood. is an objective to transform a material entity into spatially separated components. PPPB branch PPPB branch material separation objective clustered data set A clustered data set is the output of a K means clustering data transformation A data set that is produced as the output of a class discovery data transformation and consists of a data set with assigned discovered class labels. PERSON: James Malone PERSON: Monnie McGee data set with assigned discovered class labels AR thinks could be a data item instead clustered data set specimen collection process drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation A planned process with the objective of collecting a specimen. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role. Philly2013: The specimen_role for the specimen is created during the specimen collection process. label changed to 'specimen collection process' on 10/27/2014, details see tracker: http://sourceforge.net/p/obi/obi-terms/716/ Bjoern Peters specimen collection 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession 6/9/09: used at workshop specimen collection process class prediction data transformation A class prediction data transformation (sometimes called supervised classification) is a data transformation that has objective class prediction. James Malone supervised classification data transformation PERSON: James Malone class prediction data transformation portioning objective The objective to obtain multiple aliquots of an enzyme preparation. A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material. portioning objective separation into different composition objective The objective to obtain cells contained in a sample of blood. A material separation objective aiming to separate a material entity that has parts of different types, and end with at least one output that is a material with parts of fewer types (modulo impurities). We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives separation into different composition objective specimen collection objective The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient. A objective specification to obtain a material entity for potential use as an input during an investigation. Bjoern Peters Bjoern Peters specimen collection objective support vector machine A support vector machine is a data transformation with a class prediction objective based on the construction of a separating hyperplane that maximizes the margin between two data sets of vectors in n-dimensional space. James Malone Ryan Brinkman SVM PERSON: Ryan Brinkman support vector machine decision tree induction objective A decision tree induction objective is a data transformation objective in which a tree-like graph of edges and nodes is created and from which the selection of each branch requires that some type of logical decision is made. James Malone decision tree induction objective decision tree building data transformation A decision tree building data transformation is a data transformation that has objective decision tree induction. James Malone PERSON: James Malone decision tree building data transformation GenePattern software a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks. James Malone Person:Helen Parkinson WEB: http://www.broadinstitute.org/cancer/software/genepattern/ GenePattern software host role In biology, a host is an organism that harbors a virus or parasite, or a mutual or commensal symbiont, typically providing nourishment and shelter. http://en.wikipedia.org/wiki/Host_(biology) 30 March 09 host role is a role played by an organism and realized by providing nourishment, shelter or a means of reproduction to another organism within the organism playing the host role 30Mar09 virus reproducing inside a cell; bacteria causing a disease, host can be harmed or not. we want to avoid a cat sitting on my lap and an animal care technician; these are not examples or hosts; dental cares = on tooth, but part of outer layer of tooth, so covered by "within" in the definition GROUP: Role Branch 30 Mar09 submitted by vaccine community OBI http://en.wikipedia.org/wiki/Host_(biology) host role peak matching Peak matching is a data transformation performed on a dataset of a graph of ordered data points (e.g. a spectrum) with the objective of pattern matching local maxima above a noise threshold James Malone Ryan Brinkman PERSON: Ryan Brinkman peak matching k-nearest neighbors A k-nearest neighbors is a data transformation which achieves a class discovery or partitioning objective, in which an input data object with vector y is assigned to a class label based upon the k closest training data set points to y; where k is the largest value that class label is assigned. James Malone k-NN PERSON: James Malone k-nearest neighbors CART A CART (classification and regression trees) is a data transformation method for producing a classification or regression model with a tree-based structure. James Malone classification and regression trees BOOK: David J. Hand, Heikki Mannila and Padhraic Smyth (2001) Principles of Data Mining. CART statistical model validation Using the expression levels of 20 proteins to predict whether a cancer patient will respond to a drug. A practical goal would be to determine which subset of the 20 features should be used to produce the best predictive model. - wikipedia A data transformation which assesses how the results of a statistical analysis will generalize to an independent data set. Helen Parkinson http://en.wikipedia.org/wiki/Cross-validation_%28statistics%29 statistical model validation material maintenance objective An objective specification maintains some or all of the qualities of a material over time. PERSON: Bjoern Peters PERSON: Bjoern Peters material maintenance objective manufacturer A person or organization that has a manufacturer role manufacturer material maintenance a process with that achieves the objective to maintain some or all of the characteristics of an input material over time material maintenance service provider role Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer. is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person PERSON:Helen Parkinson service provider role processed specimen A tissue sample that has been sliced and stained for a histology study. A blood specimen that has been centrifuged to obtain the white blood cells. A specimen that has been intentionally physically modified. Bjoern Peters Bjoern Peters A tissue sample that has been sliced and stained for a histology study. processed specimen categorical label The labels 'positive' vs. 'negative', or 'left handed', 'right handed', 'ambidexterous', or 'strongly binding', 'weakly binding' , 'not binding', or '+++', '++', '+', '-' etc. form scales of categorical labels. A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale. Bjoern Peters Bjoern Peters categorical label questionnaire A document with a set of printed or written questions with a choice of answers, devised for the purposes of a survey or statistical study. JT: It plays a role in collecting data that could be fleshed out more; but I'm thinking it is, in itself, an edited document. JZ: based on textual definition of edited document, it can be defined as N&S. I prefer to leave questionnaire as a document now. We can add more restrictions in the future and use that to determine it is an edited document or not. Need to clarify if this is a document or a directive information entity (or what their connection is)) PERSON: Jessica Turner Merriam-Webster questionnaire specimen from organism A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm). PERSON: Chris Stoeckert, Jie Zheng tissue specimen MO_954 organism_part specimen from organism secondary cultured cell A cultured cell that has been passaged or derives from a cell that has been passaged in culture. The term 'secondary cell culture' is generally used in biological texts/protocols to refer to any culture following an initial passage. We include it here because there are often a number of passages between a primary culture and the establishment of a stable, homogenous cell line. Such cultures are considered to be 'secondary cultures' but not 'cell lines' during this intermediate passaging/selection period between their derivation from a 'primary cell culture' and derivation into a 'cell line', which is a more specific type of secondary culture. Person: Matthew Brush PERSON: Matthew Brush A secondary cultured cell has been passaged in culture or is a descendant of such a cell that is derived through propagation in culture. secondary cultured cell establishing cell line a process whereby a new type of cell line is created, either through passaging of a primary cell culture to relative genetic stability and compositional homogeneity, or through some experimental modification of an existing cell line to produce a new line with novel characteristics (e.g. immortalization or some other stable genetic modification, or selection of some defined subset). 2013-4-20 MHB: For cases of initial establilshment of a line from a primary culture, successive passaging and/or selection processes can confer increasing degrees of genetic stability and compositional homogeneity as compared to the input primary culture. Historically, many texts consider the first passage as the clearest point to define the beginning of a line. However, in practice it is more often that case that more than one passage, and possibly additional selective techniques, may be required before a culture is deemed to have sufficient stability and homogeneity to be considered cell line. This is the view taken in OBI. Regardless, what is important is that some intentional, experimental step has been taken to establish a more homogenous and stable culture that can be characterized and progatated over time. Person: Matthew Brush PERSON:Matthew Brush establishing cell line establishing cell line 建立细胞系 secondary cultured cell population A cultured cell population that is derived through one or more passages in culture. The term 'secondary cell culture' is generally used in biological texts/protocols to refer to any culture of cells following an initial passage. We include it here because there are often a number of passages between a primary culture and the establishment of a stable, homogenous cell line. Such cultures are considered to be 'secondary cultures' but not 'cell lines' during this intermediate passaging/selection period between their derivation from a 'primary cell culture' and derivation into a 'cell line', which is a more specific type of secondary culture. PERSON:Matthew Brush secondary cell culture sample PERSON:Matthew Brush The concept of a 'secondary cultured cell population' covers cell lines as well as cultured cell populations more immediately derived from a primary culture which have yet to achieve adequate genetic stability and compositional homogeneity to be considered a cell line. The extent of the collection of cells in a 'secondary cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). Secondary cultured cell populations can be under active culture, stored in a quiescent state for future use, or applied experimentally. secondary cultured cell population cell freezing medium A processed material that serves as a liquid vehicle for freezing cells for long term quiescent stroage, which contains chemicls needed to sustain cell viability across freeze-thaw cycles. PERSON: Matthew Brush cell freezing medium categorical value specification A value specification that is specifies one category out of a fixed number of nominal categories PERSON:Bjoern Peters categorical value specification value specification The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass. An information content entity that specifies a value within a classification scheme or on a quantitative scale. This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement. PERSON:Bjoern Peters value specification collection of specimens Blood cells collected from multiple donors over the course of a study. A material entity that has two or more specimens as its parts. Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/ Person: Chris Stoeckert, Jie Zheng OBIB, OBI Biobank collection of specimens histologic grade according to AJCC 7th edition G4: Undifferentiated G1:Well differentiated A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the American Joint Committee on Cancer (AJCC) 7th Edition grading system. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB histologic grade according to AJCC 7th edition histologic grade according to the Fuhrman Nuclear Grading System A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the Fuhrman Nuclear Grading System. Chris Stoeckert, Helena Ellis Histologic Grade (Fuhrman Nuclear Grading System) NCI BBRB, OBI NCI BBRB histologic grade according to the Fuhrman Nuclear Grading System histologic grade for ovarian tumor A categorical value specification that is a histologic grade assigned to a ovarian tumor. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB histologic grade for ovarian tumor histologic grade for ovarian tumor according to a two-tier grading system A histologic grade for ovarian tumor that is from a two-tier histological classification of tumors. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB histologic grade for ovarian tumor according to a two-tier grading system histologic grade for ovarian tumor according to the World Health Organization A histologic grade for ovarian tumor that is from a histological classification by the World Health Organization (WHO). Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB histologic grade for ovarian tumor according to the World Health Organization pathologic primary tumor stage for colon and rectum according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis pT: Pathologic spread colorectal primary tumor (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic primary tumor stage for colon and rectum according to AJCC 7th edition pathologic primary tumor stage for lung according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis pT: Pathologic spread lung primary tumor (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic primary tumor stage for lung according to AJCC 7th edition pathologic primary tumor stage for kidney according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis pT: Pathologic spread kidney primary tumor (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic primary tumor stage for kidney according to AJCC 7th edition pathologic primary tumor stage for ovary according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis pT: Pathologic spread ovarian primary tumor (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic primary tumor stage for ovary according to AJCC 7th edition pathologic lymph node stage for colon and rectum according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. Chris Stoeckert, Helena Ellis pN: Pathologic spread colon lymph nodes (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic lymph node stage for colon and rectum according to AJCC 7th edition pathologic lymph node stage for lung according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. Chris Stoeckert, Helena Ellis pN: Pathologic spread colon lymph nodes (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic lymph node stage for lung according to AJCC 7th edition pathologic lymph node stage for kidney according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. Chris Stoeckert, Helena Ellis pN: Pathologic spread kidney lymph nodes (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic lymph node stage for kidney according to AJCC 7th edition pathologic lymph node stage for ovary according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. Chris Stoeckert, Helena Ellis pN: Pathologic spread ovarian lymph nodes (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic lymph node stage for ovary according to AJCC 7th edition pathologic distant metastases stage for colon according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of colon cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis M: colon distant metastases (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic distant metastases stage for colon according to AJCC 7th edition pathologic distant metastases stage for lung according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis M: lung distant metastases (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic distant metastases stage for lung according to AJCC 7th edition pathologic distant metastases stage for kidney according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis M: kidney distant Metastases (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic distant metastases stage for kidney according to AJCC 7th edition pathologic distant metastases stage for ovary according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis M: ovarian distant metastases (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic distant metastases stage for ovary according to AJCC 7th edition clinical tumor stage group according to AJCC 7th edition A categorical value specification that is an assessment of the stage of a cancer according to the American Joint Committee on Cancer (AJCC) v7 staging systems. Chris Stoeckert, Helena Ellis Clinical tumor stage group (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB clinical tumor stage group according to AJCC 7th edition International Federation of Gynecology and Obstetrics cervical cancer stage value specification A categorical value specification that is an assessment of the stage of a gynecologic cancer according to the International Federation of Gynecology and Obstetrics (FIGO) staging systems. Chris Stoeckert, Helena Ellis Clinical FIGO stage NCI BBRB, OBI NCI BBRB International Federation of Gynecology and Obstetrics cervical cancer stage value specification International Federation of Gynecology and Obstetrics ovarian cancer stage value specification A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the FIGO classification system. Chris Stoeckert, Helena Ellis Pathologic Tumor Stage Grouping for ovarian cancer (FIGO) NCI BBRB, OBI NCI BBRB International Federation of Gynecology and Obstetrics ovarian cancer stage value specification performance status value specification A categorical value specification that is an assessment of a participant's performance status (general well-being and activities of daily life). Chris Stoeckert, Helena Ellis Performance Status Scale https://en.wikipedia.org/wiki/Performance_status NCI BBRB performance status value specification Eastern Cooperative Oncology Group score value specification A performance status value specification designed by the Eastern Cooperative Oncology Group to assess disease progression and its affect on the daily living abilities of the patient. Chris Stoeckert, Helena Ellis ECOG score NCI BBRB, OBI NCI BBRB Eastern Cooperative Oncology Group score value specification Karnofsky score vaue specification A performance status value specification designed for classifying patients 16 years of age or older by their functional impairment. Chris Stoeckert, Helena Ellis Karnofsky Score NCI BBRB, OBI NCI BBRB Karnofsky score vaue specification Epstein Barr virus transformed B cell PMID: 8777380. Expression of thyroid peroxidase in EBV-transformed B cell lines using adenovirus.Thyroid. 1996 Feb;6(1):23-8. A material entity which results from viral transformation process using EBV as transformation agent when applied to B-cell entity PERSON: Susanna Sansone GROUP: OBI Biomaterial Branch Epstein Barr virus transformed B cell organism animal fungus plant virus A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') 13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI. GROUP: OBI Biomaterial Branch WEB: http://en.wikipedia.org/wiki/Organism obi OBI:0100026 organism organism specimen Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen. A material entity that has the specimen role. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. PERSON: James Malone PERSON: Philippe Rocca-Serra GROUP: OBI Biomaterial Branch specimen cultured cell population A cultured cell population applied in an experiment: "293 cells expressing TrkA were serum-starved for 18 hours and then neurotrophins were added for 10 min before cell harvest." (Lee, Ramee, et al. "Regulation of cell survival by secreted proneurotrophins." Science 294.5548 (2001): 1945-1948). A cultured cell population maintained in vitro: "Rat cortical neurons from 15 day embryos are grown in dissociated cell culture and maintained in vitro for 8–12 weeks" (Dichter, Marc A. "Rat cortical neurons in cell culture: culture methods, cell morphology, electrophysiology, and synapse formation." Brain Research 149.2 (1978): 279-293). A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history. 2013-6-5 MHB: This OBI class was formerly called 'cell culture', but label changed and definition updated following CLO alignment efforts in spring 2013, during which the intent of this class was clarified to refer to portions of a culture or line rather than a complete cell culture or line. PERSON:Matthew Brush cell culture sample PERSON:Matthew Brush The extent of a 'cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). In being defined in this way, this class can be used to refer to the populations that researchers actually use in the practice of science - ie are the inputs to culturing, experimentation, and sharing. The cells in such populations will be a relatively uniform population as they have experienced similar selective pressures due to their continuous co-propagation. And this population will also have a single passage number, again owing to their common passaging history. Cultured cell populations represent only a collection of cells (ie do not include media, culture dishes, etc), and include populations of cultured unicellular organisms or cultured multicellular organism cells. They can exist under active culture, stored in a quiescent state for future use, or applied experimentally. cultured cell population data transformation The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value. A planned process that produces output data from input data. Elisabetta Manduchi Helen Parkinson James Malone Melanie Courtot Philippe Rocca-Serra Richard Scheuermann Ryan Brinkman Tina Hernandez-Boussard data analysis data processing Branch editors data transformation leave one out cross validation method The authors conducted leave-one-out cross validation to estimate the strength and accuracy of the differentially expressed filtered genes. http://bioinformatics.oxfordjournals.org/cgi/content/abstract/19/3/368 is a data transformation : leave-one-out cross-validation (LOOCV) involves using a single observation from the original sample as the validation data, and the remaining observations as the training data. This is repeated such that each observation in the sample is used once as the validation data 2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893049&group_id=177891&atid=886178 Person:Helen Parkinson leave one out cross validation method k-means clustering A k-means clustering is a data transformation which achieves a class discovery or partitioning objective, which takes as input a collection of objects (represented as points in multidimensional space) and which partitions them into a specified number k of clusters. The algorithm attempts to find the centers of natural clusters in the data. The most common form of the algorithm starts by partitioning the input points into k initial sets, either at random or using some heuristic data. It then calculates the mean point, or centroid, of each set. It constructs a new partition by associating each point with the closest centroid. Then the centroids are recalculated for the new clusters, and the algorithm repeated by alternate applications of these two steps until convergence, which is obtained when the points no longer switch clusters (or alternatively centroids are no longer changed). Elisabetta Manduchi James Malone Philippe Rocca-Serra WEB: http://en.wikipedia.org/wiki/K-means k-means clustering hierarchical clustering A hierarchical clustering is a data transformation which achieves a class discovery objective, which takes as input data item and builds a hierarchy of clusters. The traditional representation of this hierarchy is a tree (visualized by a dendrogram), with the individual input objects at one end (leaves) and a single cluster containing every object at the other (root). James Malone WEB: http://en.wikipedia.org/wiki/Data_clustering#Hierarchical_clustering hierarchical clustering dimensionality reduction A dimensionality reduction is data partitioning which transforms each input m-dimensional vector (x_1, x_2, ..., x_m) into an output n-dimensional vector (y_1, y_2, ..., y_n), where n is smaller than m. Elisabetta Manduchi James Malone Melanie Courtot Philippe Rocca-Serra data projection PERSON: Elisabetta Manduchi PERSON: James Malone PERSON: Melanie Courtot dimensionality reduction principal components analysis dimensionality reduction A principal components analysis dimensionality reduction is a dimensionality reduction achieved by applying principal components analysis and by keeping low-order principal components and excluding higher-order ones. Elisabetta Manduchi James Malone Melanie Courtot Philippe Rocca-Serra pca data reduction PERSON: Elisabetta Manduchi PERSON: James Malone PERSON: Melanie Courtot principal components analysis dimensionality reduction data visualization Generation of a heatmap from a microarray dataset An planned process that creates images, diagrams or animations from the input data. Elisabetta Manduchi James Malone Melanie Courtot Tina Boussard data encoding as image visualization PERSON: Elisabetta Manduchi PERSON: James Malone PERSON: Melanie Courtot PERSON: Tina Boussard Possible future hierarchy might include this: information_encoding >data_encoding >>image_encoding data visualization data transformation objective normalize objective An objective specification to transformation input data into output data Modified definition in 2013 Philly OBI workshop James Malone PERSON: James Malone data transformation objective partitioning data transformation A partitioning data transformation is a data transformation that has objective partitioning. James Malone PERSON: James Malone partitioning data transformation partitioning objective A k-means clustering which has partitioning objective is a data transformation in which the input data is partitioned into k output sets. A partitioning objective is a data transformation objective where the aim is to generate a collection of disjoint non-empty subsets whose union equals a non-empty input set. Elisabetta Manduchi James Malone PERSON: Elisabetta Manduchi partitioning objective class discovery data transformation A class discovery data transformation (sometimes called unsupervised classification) is a data transformation that has objective class discovery. James Malone clustering data transformation unsupervised classification data transformation PERSON: James Malone class discovery data transformation class discovery objective A class discovery objective (sometimes called unsupervised classification) is a data transformation objective where the aim is to organize input data (typically vectors of attributes) into classes, where the number of classes and their specifications are not known a priori. Depending on usage, the class assignment can be definite or probabilistic. James Malone clustering objective discriminant analysis objective unsupervised classification objective PERSON: Elisabetta Manduchi PERSON: James Malone class discovery objective class prediction objective A class prediction objective (sometimes called supervised classification) is a data transformation objective where the aim is to create a predictor from training data through a machine learning technique. The training data consist of pairs of objects (typically vectors of attributes) and class labels for these objects. The resulting predictor can be used to attach class labels to any valid novel input object. Depending on usage, the prediction can be definite or probabilistic. A classification is learned from the training data and can then be tested on test data. James Malone classification objective supervised classification objective PERSON: Elisabetta Manduchi PERSON: James Malone class prediction objective cross validation objective A cross validation objective is a data transformation objective in which the aim is to partition a sample of data into subsets such that the analysis is initially performed on a single subset, while the other subset(s) are retained for subsequent use in confirming and validating the initial analysis. James Malone rotation estimation objective WEB: http://en.wikipedia.org/wiki/Cross_validation cross validation objective clustered data visualization A data visualization which has input of a clustered data set and produces an output of a report graph which is capable of rendering data of this type. James Malone clustered data visualization material component separation Using a cell sorter to separate a mixture of T cells into two fractions; one with surface receptor CD8 and the other lacking the receptor, or purification a material processing in which components of an input material become segregated in space Bjoern Peters IEDB material component separation maintaining cell culture When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the maintaining_cell_culture step comprises all steps after the initial dilution and plating of the cells into culture, e.g. placing the culture into an incubator, changing or adding media, and splitting a cell culture a protocol application in which cells are kept alive in a defined environment outside of an organism. part of cell_culturing PlanAndPlannedProcess Branch OBI branch derived maintaining cell culture 'establishing cell culture' a process through which a new type of cell culture or cell line is created, either through the isolation and culture of one or more cells from a fresh source, or the deliberate experimental modification of an existing cell culture (e.g passaging a primary culture to become a secondary culture or line, or the immortalization or stable genetic modification of an existing culture or line). PERSON:Matthew Brush PERSON:Matthew Brush A 'cell culture' as used here referes to a new lineage of cells in culture deriving from a single biological source.. New cultures are established through the initial isolation and culturing of cells from an organismal source, or through changes in an existing cell culture or line that result in a new culture with unique characteristics. This can occur through the passaging/selection of a primary culture into a secondary culture or line, or experimental modifications of an existing cell culture or line such as an immortalization process or other stable genetic modification. This class covers establishment of cultures of either multicellular organism cells or unicellular organisms. establishing cell culture cell culture splitting The act of taking a cell culture of high density, counting the cells, removing part of the cells, and re-seeding a select number of the cells into new flasks with fresh tissue culture media. The act of taking part of a homogeneous cell culture and creating one or more additional separate cultures of similar qualities. input: cell_culture, output cell_culture min cardinality 2. part of cell culturing PlanAndPlannedProcess Branch cell culture passaging OBI branch derived An active cell culture is typically split when it has grown to confluence in its culture dish. Cell culture splitting of a cell culture sample results in an increase in its passage number, which measures how long a sample has been propagated in vitro, and therefore how many selective or genetic changes it is likely to have undergone. cell culture splitting A genome is a material entity that represents the entirety of an organism's hereditary information. The genome includes both the genes and the non-coding sequences of the DNA and RNA. Oliver He Book: Eugene Nester, Denise Anderson, C. Evans Roberts, Jr., Microbiology (Companion Site): A Human Perspective, 7th Edition. Mcgraw Hill, October 18, 2011. ISBN-13: 978-0073375311 WEB: http://en.wikipedia.org/wiki/Genome genome A gene is a material entity that represents the entire DNA sequence required for synthesis of a functional protein or RNA molecule. Oliver He WEB: http://www.ncbi.nlm.nih.gov/books/NBK21640/ In addition to the coding regions (exons), a gene includes transcription-control regions and sometimes introns. Although the majority of genes encode proteins, some encode tRNAs, rRNAs, and other types of RNA. gene a disposition that a gene can be used as a blueprint for generating a new form of product such as protein. Yongqun He, Bin Zhao WEB: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/entrezgene/entrezgene.asn According to NCBI Gene project, there are two gene types: unknown (0) , tRNA (1) , rRNA (2) , snRNA (3) , scRNA (4) , snoRNA (5) , protein-coding (6) , pseudo (7) , transposon (8) , miscRNA (9) , ncRNA (10) , other (255). gene type a gene type that is protein-coding, i.e., the gene encodes for a protein. . Yongqun He, Bin Zhao WEB: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/entrezgene/entrezgene.asn protein-coding gene type a gene type that is tRNA, i.e., this gene encodes for a RNA. Yongqun He, Bin Zhao WEB: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/entrezgene/entrezgene.asn RNA gene type a RNA gene type that is tRNA, i.e., this gene encodes for a rRNA. Yongqun He, Bin Zhao WEB: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/entrezgene/entrezgene.asn rRNA gene type a RNA gene type that is tRNA, i.e., this gene encodes for a rRNA. Yongqun He, Bin Zhao WEB: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/entrezgene/entrezgene.asn snRNA gene type a RNA gene type that is tRNA, i.e., this gene encodes for a tRNA. Yongqun He, Bin Zhao WEB: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/entrezgene/entrezgene.asn tRNA gene type a RNA gene type that is scRNA, i.e., this gene encodes for a scRNA. Yongqun He, Bin Zhao WEB: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/entrezgene/entrezgene.asn scRNA gene type a RNA gene type that is snoRNA, i.e., this gene encodes for a snoRNA. Yongqun He, Bin Zhao WEB: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/entrezgene/entrezgene.asn snoRNA gene type a RNA gene type that is miscRNA, i.e., this gene encodes for a miscRNA. Yongqun He, Bin Zhao WEB: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/entrezgene/entrezgene.asn miscRNA gene type a RNA gene type that is ncRNA, i.e., this gene encodes for a ncRNA. Yongqun He, Bin Zhao WEB: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/entrezgene/entrezgene.asn ncRNA gene type a gene type that is pseudo, i.e., the gene is a pseudogene. Yongqun He, Bin Zhao WEB: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/entrezgene/entrezgene.asn pseudo gene type a gene type that is transposon, i.e., the gene encodes for a transposon. Yongqun He, Bin Zhao WEB: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/entrezgene/entrezgene.asn transposon gene type a gene type that is "other", i.e., the gene is for a gene product that is not listed for another other gene type. Yongqun He, Bin Zhao WEB: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/entrezgene/entrezgene.asn other gene type a gene type that is "unknown", i.e., the gene product is unknown. Yongqun He, Bin Zhao WEB: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/entrezgene/entrezgene.asn unknown gene type The genome of an organism of Bacteria Bin Zhao, Oliver He 2 genome of Bacteria The genome of an organism of Spirochaetales Bin Zhao, Oliver He 136 genome of Spirochaetales The genome of an organism of Borrelia burgdorferi Bin Zhao, Oliver He 139 genome of Borrelia burgdorferi The genome of an organism of Campylobacter jejuni Bin Zhao, Oliver He 197 genome of Campylobacter jejuni The genome of an organism of Helicobacter pylori Bin Zhao, Oliver He 210 genome of Helicobacter pylori The genome of an organism of Brucella Bin Zhao, Oliver He 234 genome of Brucella The genome of an organism of Brucella abortus Bin Zhao, Oliver He 235 genome of Brucella abortus The genome of an organism of Francisella tularensis Bin Zhao, Oliver He 263 genome of Francisella tularensis The genome of an organism of Pseudomonas aeruginosa Bin Zhao, Oliver He 287 genome of Pseudomonas aeruginosa The genome of an organism of Rhizobiales Bin Zhao, Oliver He 356 genome of Rhizobiales The genome of an organism of Legionella pneumophila Bin Zhao, Oliver He 446 genome of Legionella pneumophila The genome of an organism of Neisseria meningitidis Bin Zhao, Oliver He 487 genome of Neisseria meningitidis The genome of an organism of Bordetella Bin Zhao, Oliver He 517 genome of Bordetella The genome of an organism of Bordetella pertussis Bin Zhao, Oliver He 520 genome of Bordetella pertussis The genome of an organism of Enterobacteriaceae Bin Zhao, Oliver He 543 genome of Enterobacteriaceae The genome of an organism of Escherichia coli Bin Zhao, Oliver He 562 genome of Escherichia coli The genome of an organism of Shigella Bin Zhao, Oliver He 620 genome of Shigella The genome of an organism of Shigella boydii Bin Zhao, Oliver He 621 genome of Shigella boydii The genome of an organism of Shigella flexneri Bin Zhao, Oliver He 623 genome of Shigella flexneri The genome of an organism of Yersinia <bacteria> Bin Zhao, Oliver He 629 genome of Yersinia <bacteria> The genome of an organism of Yersinia enterocolitica Bin Zhao, Oliver He 630 genome of Yersinia enterocolitica The genome of an organism of Yersinia pestis Bin Zhao, Oliver He 632 genome of Yersinia pestis The genome of an organism of Yersinia pseudotuberculosis Bin Zhao, Oliver He 633 genome of Yersinia pseudotuberculosis The genome of an organism of Vibrio cholerae Bin Zhao, Oliver He 666 genome of Vibrio cholerae The genome of an organism of Pasteurellaceae Bin Zhao, Oliver He 712 genome of Pasteurellaceae The genome of an organism of Actinobacillus pleuropneumoniae Bin Zhao, Oliver He 715 genome of Actinobacillus pleuropneumoniae The genome of an organism of Haemophilus influenzae Bin Zhao, Oliver He 727 genome of Haemophilus influenzae The genome of an organism of Pasteurella multocida Bin Zhao, Oliver He 747 genome of Pasteurella multocida The genome of an organism of Bartonella Bin Zhao, Oliver He 773 genome of Bartonella The genome of an organism of Chlamydia Bin Zhao, Oliver He 810 genome of Chlamydia The genome of an organism of Proteobacteria Bin Zhao, Oliver He 1224 genome of Proteobacteria The genome of an organism of Gammaproteobacteria Bin Zhao, Oliver He 1236 genome of Gammaproteobacteria The genome of an organism of Firmicutes Bin Zhao, Oliver He 1239 genome of Firmicutes The genome of an organism of Staphylococcus aureus Bin Zhao, Oliver He 1280 genome of Staphylococcus aureus The genome of an organism of Streptococcus Bin Zhao, Oliver He 1301 genome of Streptococcus The genome of an organism of Streptococcus agalactiae Bin Zhao, Oliver He 1311 genome of Streptococcus agalactiae The genome of an organism of Streptococcus pneumoniae Bin Zhao, Oliver He 1313 genome of Streptococcus pneumoniae The genome of an organism of Streptococcus pyogenes Bin Zhao, Oliver He 1314 genome of Streptococcus pyogenes The genome of an organism of Enterococcus Bin Zhao, Oliver He 1350 genome of Enterococcus The genome of an organism of Enterococcus faecalis Bin Zhao, Oliver He 1351 genome of Enterococcus faecalis The genome of an organism of Enterococcus faecium Bin Zhao, Oliver He 1352 genome of Enterococcus faecium The genome of an organism of Bacillales Bin Zhao, Oliver He 1385 genome of Bacillales The genome of an organism of Bacillus anthracis Bin Zhao, Oliver He 1392 genome of Bacillus anthracis The genome of an organism of Clostridium Bin Zhao, Oliver He 1485 genome of Clostridium The genome of an organism of Clostridium botulinum Bin Zhao, Oliver He 1491 genome of Clostridium botulinum The genome of an organism of [Clostridium] difficile Bin Zhao, Oliver He 1496 genome of [Clostridium] difficile The genome of an organism of Clostridium perfringens Bin Zhao, Oliver He 1502 genome of Clostridium perfringens The genome of an organism of Listeria monocytogenes Bin Zhao, Oliver He 1639 genome of Listeria monocytogenes The genome of an organism of Mycobacterium Bin Zhao, Oliver He 1763 genome of Mycobacterium The genome of an organism of Mycobacterium tuberculosis Bin Zhao, Oliver He 1773 genome of Mycobacterium tuberculosis The genome of an organism of Eukaryota Bin Zhao, Oliver He 2759 genome of Eukaryota The genome of an organism of Saccharomycetales Bin Zhao, Oliver He 4892 genome of Saccharomycetales The genome of an organism of Saccharomycetaceae Bin Zhao, Oliver He 4893 genome of Saccharomycetaceae The genome of an organism of Saccharomyces cerevisiae Bin Zhao, Oliver He 4932 genome of Saccharomyces cerevisiae The genome of an organism of Ajellomyces capsulatus Bin Zhao, Oliver He 5037 genome of Ajellomyces capsulatus The genome of an organism of Cryptococcus neoformans Bin Zhao, Oliver He 5207 genome of Cryptococcus neoformans The genome of an organism of Candida Bin Zhao, Oliver He 5475 genome of Candida The genome of an organism of Candida albicans Bin Zhao, Oliver He 5476 genome of Candida albicans The genome of an organism of Candida glabrata Bin Zhao, Oliver He 5478 genome of Candida glabrata The genome of an organism of Trypanosomatidae Bin Zhao, Oliver He 5654 genome of Trypanosomatidae The genome of an organism of Leishmania donovani Bin Zhao, Oliver He 5661 genome of Leishmania donovani The genome of an organism of Leishmania major Bin Zhao, Oliver He 5664 genome of Leishmania major The genome of an organism of Leishmania mexicana Bin Zhao, Oliver He 5665 genome of Leishmania mexicana The genome of an organism of Leishmania infantum Bin Zhao, Oliver He 5671 genome of Leishmania infantum The genome of an organism of Trypanosoma Bin Zhao, Oliver He 5690 genome of Trypanosoma The genome of an organism of Trypanosoma cruzi Bin Zhao, Oliver He 5693 genome of Trypanosoma cruzi The genome of an organism of Entamoeba histolytica Bin Zhao, Oliver He 5759 genome of Entamoeba histolytica The genome of an organism of Apicomplexa Bin Zhao, Oliver He 5794 genome of Apicomplexa The genome of an organism of Toxoplasma gondii Bin Zhao, Oliver He 5811 genome of Toxoplasma gondii The genome of an organism of Plasmodium Bin Zhao, Oliver He 5820 genome of Plasmodium The genome of an organism of Plasmodium berghei ANKA Bin Zhao, Oliver He 5823 genome of Plasmodium berghei ANKA The genome of an organism of Plasmodium yoelii Bin Zhao, Oliver He 5861 genome of Plasmodium yoelii The genome of an organism of Exophiala dermatitidis Bin Zhao, Oliver He 5970 genome of Exophiala dermatitidis The genome of an organism of Lythrurus Bin Zhao, Oliver He 7966 genome of Lythrurus The genome of an organism of Viruses Bin Zhao, Oliver He 10239 genome of Viruses The genome of an organism of Chordopoxvirinae Bin Zhao, Oliver He 10241 genome of Chordopoxvirinae The genome of an organism of Orthopoxvirus Bin Zhao, Oliver He 10242 genome of Orthopoxvirus The genome of an organism of Cowpox virus Bin Zhao, Oliver He 10243 genome of Cowpox virus The genome of an organism of Vaccinia virus Bin Zhao, Oliver He 10245 genome of Vaccinia virus The genome of an organism of Vaccinia virus Tian Tan Bin Zhao, Oliver He 10253 genome of Vaccinia virus Tian Tan The genome of an organism of Vaccinia virus WR Bin Zhao, Oliver He 10254 genome of Vaccinia virus WR The genome of an organism of Orf virus Bin Zhao, Oliver He 10258 genome of Orf virus The genome of an organism of Sheeppox virus Bin Zhao, Oliver He 10266 genome of Sheeppox virus The genome of an organism of Leporipoxvirus Bin Zhao, Oliver He 10270 genome of Leporipoxvirus The genome of an organism of Rabbit fibroma virus Bin Zhao, Oliver He 10271 genome of Rabbit fibroma virus The genome of an organism of Myxoma virus Bin Zhao, Oliver He 10273 genome of Myxoma virus The genome of an organism of Herpesviridae Bin Zhao, Oliver He 10292 genome of Herpesviridae The genome of an organism of Alphaherpesvirinae Bin Zhao, Oliver He 10293 genome of Alphaherpesvirinae The genome of an organism of Simplexvirus Bin Zhao, Oliver He 10294 genome of Simplexvirus The genome of an organism of Human herpesvirus 1 Bin Zhao, Oliver He 10298 genome of Human herpesvirus 1 The genome of an organism of Herpes simplex virus (type 1 / strain 17) Bin Zhao, Oliver He 10299 genome of Herpes simplex virus (type 1 / strain 17) The genome of an organism of Human herpesvirus 2 Bin Zhao, Oliver He 10310 genome of Human herpesvirus 2 The genome of an organism of Varicellovirus Bin Zhao, Oliver He 10319 genome of Varicellovirus The genome of an organism of Bovine herpesvirus 1 Bin Zhao, Oliver He 10320 genome of Bovine herpesvirus 1 The genome of an organism of Equid herpesvirus 1 Bin Zhao, Oliver He 10326 genome of Equid herpesvirus 1 The genome of an organism of Felid herpesvirus 1 Bin Zhao, Oliver He 10334 genome of Felid herpesvirus 1 The genome of an organism of Human herpesvirus 3 Bin Zhao, Oliver He 10335 genome of Human herpesvirus 3 The genome of an organism of Suid herpesvirus 1 Bin Zhao, Oliver He 10345 genome of Suid herpesvirus 1 The genome of an organism of Gallid herpesvirus 1 Bin Zhao, Oliver He 10386 genome of Gallid herpesvirus 1 The genome of an organism of Gallid herpesvirus 2 Bin Zhao, Oliver He 10390 genome of Gallid herpesvirus 2 The genome of an organism of African swine fever virus Bin Zhao, Oliver He 10497 genome of African swine fever virus The genome of an organism of Rotavirus Bin Zhao, Oliver He 10912 genome of Rotavirus The genome of an organism of Alphavirus Bin Zhao, Oliver He 11019 genome of Alphavirus The genome of an organism of Ross River virus Bin Zhao, Oliver He 11029 genome of Ross River virus The genome of an organism of Sindbis virus Bin Zhao, Oliver He 11034 genome of Sindbis virus The genome of an organism of Venezuelan equine encephalitis virus Bin Zhao, Oliver He 11036 genome of Venezuelan equine encephalitis virus The genome of an organism of Western equine encephalomyelitis virus Bin Zhao, Oliver He 11039 genome of Western equine encephalomyelitis virus The genome of an organism of Flaviviridae Bin Zhao, Oliver He 11050 genome of Flaviviridae The genome of an organism of Flavivirus Bin Zhao, Oliver He 11051 genome of Flavivirus The genome of an organism of West Nile virus Bin Zhao, Oliver He 11082 genome of West Nile virus The genome of an organism of Tick-borne encephalitis virus Bin Zhao, Oliver He 11084 genome of Tick-borne encephalitis virus The genome of an organism of Yellow fever virus Bin Zhao, Oliver He 11089 genome of Yellow fever virus The genome of an organism of Classical swine fever virus Bin Zhao, Oliver He 11096 genome of Classical swine fever virus The genome of an organism of Classical swine fever virus - Brescia Bin Zhao, Oliver He 11098 genome of Classical swine fever virus - Brescia The genome of an organism of Feline infectious peritonitis virus Bin Zhao, Oliver He 11135 genome of Feline infectious peritonitis virus The genome of an organism of Porcine respiratory coronavirus Bin Zhao, Oliver He 11146 genome of Porcine respiratory coronavirus The genome of an organism of Mononegavirales Bin Zhao, Oliver He 11157 genome of Mononegavirales The genome of an organism of Paramyxoviridae Bin Zhao, Oliver He 11158 genome of Paramyxoviridae The genome of an organism of Paramyxovirinae Bin Zhao, Oliver He 11159 genome of Paramyxovirinae The genome of an organism of Newcastle disease virus Bin Zhao, Oliver He 11176 genome of Newcastle disease virus The genome of an organism of Human parainfluenza virus 3 Bin Zhao, Oliver He 11216 genome of Human parainfluenza virus 3 The genome of an organism of Measles virus Bin Zhao, Oliver He 11234 genome of Measles virus The genome of an organism of Pneumovirinae Bin Zhao, Oliver He 11244 genome of Pneumovirinae The genome of an organism of Pneumovirus Bin Zhao, Oliver He 11245 genome of Pneumovirus The genome of an organism of Bovine respiratory syncytial virus Bin Zhao, Oliver He 11246 genome of Bovine respiratory syncytial virus The genome of an organism of Human respiratory syncytial virus A2 Bin Zhao, Oliver He 11259 genome of Human respiratory syncytial virus A2 The genome of an organism of Rhabdoviridae Bin Zhao, Oliver He 11270 genome of Rhabdoviridae The genome of an organism of Infectious hematopoietic necrosis virus Bin Zhao, Oliver He 11290 genome of Infectious hematopoietic necrosis virus The genome of an organism of Rabies virus Bin Zhao, Oliver He 11292 genome of Rabies virus The genome of an organism of Influenza A virus Bin Zhao, Oliver He 11320 genome of Influenza A virus The genome of an organism of Bunyaviridae Bin Zhao, Oliver He 11571 genome of Bunyaviridae The genome of an organism of La Crosse virus Bin Zhao, Oliver He 11577 genome of La Crosse virus The genome of an organism of Rift Valley fever virus Bin Zhao, Oliver He 11588 genome of Rift Valley fever virus The genome of an organism of Hantaan virus Bin Zhao, Oliver He 11599 genome of Hantaan virus The genome of an organism of Lentivirus Bin Zhao, Oliver He 11646 genome of Lentivirus The genome of an organism of Primate lentivirus group Bin Zhao, Oliver He 11652 genome of Primate lentivirus group The genome of an organism of Feline immunodeficiency virus Bin Zhao, Oliver He 11673 genome of Feline immunodeficiency virus The genome of an organism of Human immunodeficiency virus 1 Bin Zhao, Oliver He 11676 genome of Human immunodeficiency virus 1 The genome of an organism of Simian immunodeficiency virus Bin Zhao, Oliver He 11723 genome of Simian immunodeficiency virus The genome of an organism of Encephalomyocarditis virus Bin Zhao, Oliver He 12104 genome of Encephalomyocarditis virus The genome of an organism of Chicken anemia virus Bin Zhao, Oliver He 12618 genome of Chicken anemia virus The genome of an organism of Ectromelia virus Bin Zhao, Oliver He 12643 genome of Ectromelia virus The genome of an organism of Burkholderia mallei Bin Zhao, Oliver He 13373 genome of Burkholderia mallei The genome of an organism of Alphaproteobacteria Bin Zhao, Oliver He 28211 genome of Alphaproteobacteria The genome of an organism of Betaproteobacteria Bin Zhao, Oliver He 28216 genome of Betaproteobacteria The genome of an organism of Porcine reproductive and respiratory syndrome virus Bin Zhao, Oliver He 28344 genome of Porcine reproductive and respiratory syndrome virus The genome of an organism of Burkholderia pseudomallei Bin Zhao, Oliver He 28450 genome of Burkholderia pseudomallei The genome of an organism of Trichocomaceae Bin Zhao, Oliver He 28568 genome of Trichocomaceae The genome of an organism of Rotavirus A Bin Zhao, Oliver He 28875 genome of Rotavirus A The genome of an organism of Brucella melitensis Bin Zhao, Oliver He 29459 genome of Brucella melitensis The genome of an organism of Yersinia ruckeri Bin Zhao, Oliver He 29486 genome of Yersinia ruckeri The genome of an organism of Campylobacter jejuni subsp. jejuni Bin Zhao, Oliver He 32022 genome of Campylobacter jejuni subsp. jejuni The genome of an organism of Opisthokonta Bin Zhao, Oliver He 33154 genome of Opisthokonta The genome of an organism of Onygenales Bin Zhao, Oliver He 33183 genome of Onygenales The genome of an organism of Bilateria Bin Zhao, Oliver He 33213 genome of Bilateria The genome of an organism of Suid herpesvirus 1 strain Kaplan Bin Zhao, Oliver He 33703 genome of Suid herpesvirus 1 strain Kaplan The genome of an organism of Actinobacillus pleuropneumoniae serovar 2 Bin Zhao, Oliver He 34063 genome of Actinobacillus pleuropneumoniae serovar 2 The genome of an organism of dsDNA viruses, no RNA stage Bin Zhao, Oliver He 35237 genome of dsDNA viruses, no RNA stage The genome of an organism of Bovine herpesvirus 5 Bin Zhao, Oliver He 35244 genome of Bovine herpesvirus 5 The genome of an organism of ssRNA positive-strand viruses, no DNA stage Bin Zhao, Oliver He 35278 genome of ssRNA positive-strand viruses, no DNA stage The genome of an organism of ssRNA negative-strand viruses Bin Zhao, Oliver He 35301 genome of ssRNA negative-strand viruses The genome of an organism of Dictyochales Bin Zhao, Oliver He 35685 genome of Dictyochales The genome of an organism of Plasmodium falciparum 3D7 Bin Zhao, Oliver He 36329 genome of Plasmodium falciparum 3D7 The genome of an organism of Rotavirus C Bin Zhao, Oliver He 36427 genome of Rotavirus C The genome of an organism of Clostridium botulinum A Bin Zhao, Oliver He 36826 genome of Clostridium botulinum A The genome of an organism of Bartonella henselae Bin Zhao, Oliver He 38323 genome of Bartonella henselae The genome of an organism of Leishmania <subgenus> Bin Zhao, Oliver He 38568 genome of Leishmania <subgenus> The genome of an organism of Leishmania donovani species complex Bin Zhao, Oliver He 38574 genome of Leishmania donovani species complex The genome of an organism of Circoviridae Bin Zhao, Oliver He 39724 genome of Circoviridae The genome of an organism of Cryptococcus neoformans var. neoformans Bin Zhao, Oliver He 40410 genome of Cryptococcus neoformans var. neoformans The genome of an organism of Candida dubliniensis Bin Zhao, Oliver He 42374 genome of Candida dubliniensis The genome of an organism of Shigella flexneri 2a Bin Zhao, Oliver He 42897 genome of Shigella flexneri 2a The genome of an organism of Vibrio cholerae O139 Bin Zhao, Oliver He 45888 genome of Vibrio cholerae O139 The genome of an organism of Autographa californica nucleopolyhedrovirus Bin Zhao, Oliver He 46015 genome of Autographa californica nucleopolyhedrovirus The genome of an organism of Staphylococcus aureus subsp. aureus Bin Zhao, Oliver He 46170 genome of Staphylococcus aureus subsp. aureus The genome of an organism of Salmonella enterica subsp. enterica Bin Zhao, Oliver He 59201 genome of Salmonella enterica subsp. enterica The genome of an organism of Legionella pneumophila serogroup 1 Bin Zhao, Oliver He 66976 genome of Legionella pneumophila serogroup 1 The genome of an organism of Murine cytomegalovirus (strain K181) Bin Zhao, Oliver He 69156 genome of Murine cytomegalovirus (strain K181) The genome of an organism of Haemophilus influenzae Rd KW20 Bin Zhao, Oliver He 71421 genome of Haemophilus influenzae Rd KW20 The genome of an organism of Plasmodium yoelii yoelii Bin Zhao, Oliver He 73239 genome of Plasmodium yoelii yoelii The genome of an organism of Mannheimia haemolytica Bin Zhao, Oliver He 75985 genome of Mannheimia haemolytica The genome of an organism of Nidovirales Bin Zhao, Oliver He 76804 genome of Nidovirales The genome of an organism of Bovine herpesvirus type 1.1 Bin Zhao, Oliver He 79889 genome of Bovine herpesvirus type 1.1 The genome of an organism of Burkholderiales Bin Zhao, Oliver He 80840 genome of Burkholderiales The genome of an organism of Mycobacterium tuberculosis CDC1551 Bin Zhao, Oliver He 83331 genome of Mycobacterium tuberculosis CDC1551 The genome of an organism of Mycobacterium tuberculosis H37Rv Bin Zhao, Oliver He 83332 genome of Mycobacterium tuberculosis H37Rv The genome of an organism of Escherichia coli K-12 Bin Zhao, Oliver He 83333 genome of Escherichia coli K-12 The genome of an organism of Escherichia coli O157:H7 Bin Zhao, Oliver He 83334 genome of Escherichia coli O157:H7 The genome of an organism of Chlamydia pneumoniae Bin Zhao, Oliver He 83558 genome of Chlamydia pneumoniae The genome of an organism of Corynebacterineae Bin Zhao, Oliver He 85007 genome of Corynebacterineae The genome of an organism of Porcine circovirus 2 Bin Zhao, Oliver He 85708 genome of Porcine circovirus 2 The genome of an organism of Helicobacter pylori 26695 Bin Zhao, Oliver He 85962 genome of Helicobacter pylori 26695 The genome of an organism of Helicobacter pylori J99 Bin Zhao, Oliver He 85963 genome of Helicobacter pylori J99 The genome of an organism of Salmonella enterica subsp. enterica serovar Typhi Bin Zhao, Oliver He 90370 genome of Salmonella enterica subsp. enterica serovar Typhi The genome of an organism of Salmonella enterica subsp. enterica serovar Typhimurium Bin Zhao, Oliver He 90371 genome of Salmonella enterica subsp. enterica serovar Typhimurium The genome of an organism of Bacilli Bin Zhao, Oliver He 91061 genome of Bacilli The genome of an organism of Staphylococcus aureus subsp. aureus NCTC 8325 Bin Zhao, Oliver He 93061 genome of Staphylococcus aureus subsp. aureus NCTC 8325 The genome of an organism of Influenza A virus (A/Goose/Guangdong/1/96(H5N1)) Bin Zhao, Oliver He 93838 genome of Influenza A virus (A/Goose/Guangdong/1/96(H5N1)) The genome of an organism of Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 Bin Zhao, Oliver He 99287 genome of Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 The genome of an organism of H5N1 subtype Bin Zhao, Oliver He 102793 genome of H5N1 subtype The genome of an organism of Bartonella birtlesii Bin Zhao, Oliver He 111504 genome of Bartonella birtlesii The genome of an organism of pseudomallei group Bin Zhao, Oliver He 111527 genome of pseudomallei group The genome of an organism of Chlamydophila pneumoniae CWL029 Bin Zhao, Oliver He 115713 genome of Chlamydophila pneumoniae CWL029 The genome of an organism of Legionellales Bin Zhao, Oliver He 118969 genome of Legionellales The genome of an organism of Francisella tularensis subsp. holarctica Bin Zhao, Oliver He 119857 genome of Francisella tularensis subsp. holarctica The genome of an organism of Nipah virus Bin Zhao, Oliver He 121791 genome of Nipah virus The genome of an organism of Neisseria meningitidis MC58 Bin Zhao, Oliver He 122586 genome of Neisseria meningitidis MC58 The genome of an organism of Neisseria meningitidis Z2491 Bin Zhao, Oliver He 122587 genome of Neisseria meningitidis Z2491 The genome of an organism of Neisseria meningitidis serogroup C Bin Zhao, Oliver He 135720 genome of Neisseria meningitidis serogroup C The genome of an organism of Chlamydophila pneumoniae J138 Bin Zhao, Oliver He 138677 genome of Chlamydophila pneumoniae J138 The genome of an organism of Eurotiomycetes Bin Zhao, Oliver He 147545 genome of Eurotiomycetes The genome of an organism of Escherichia coli O157:H7 str. EDL933 Bin Zhao, Oliver He 155864 genome of Escherichia coli O157:H7 str. EDL933 The genome of an organism of Staphylococcus aureus subsp. aureus Mu50 Bin Zhao, Oliver He 158878 genome of Staphylococcus aureus subsp. aureus Mu50 The genome of an organism of Staphylococcus aureus subsp. aureus N315 Bin Zhao, Oliver He 158879 genome of Staphylococcus aureus subsp. aureus N315 The genome of an organism of Streptococcus pyogenes M1 GAS Bin Zhao, Oliver He 160490 genome of Streptococcus pyogenes M1 GAS The genome of an organism of Streptococcus pyogenes str. Manfredo Bin Zhao, Oliver He 160491 genome of Streptococcus pyogenes str. Manfredo The genome of an organism of Emericella nidulans Bin Zhao, Oliver He 162425 genome of Emericella nidulans The genome of an organism of Listeria monocytogenes EGD-e Bin Zhao, Oliver He 169963 genome of Listeria monocytogenes EGD-e The genome of an organism of Streptococcus pneumoniae TIGR4 Bin Zhao, Oliver He 170187 genome of Streptococcus pneumoniae TIGR4 The genome of an organism of Streptococcus pneumoniae R6 Bin Zhao, Oliver He 171101 genome of Streptococcus pneumoniae R6 The genome of an organism of Francisella tularensis subsp. tularensis SCHU S4 Bin Zhao, Oliver He 177416 genome of Francisella tularensis subsp. tularensis SCHU S4 The genome of an organism of WEEV complex Bin Zhao, Oliver He 177874 genome of WEEV complex The genome of an organism of Cryptococcus neoformans var. grubii Bin Zhao, Oliver He 178876 genome of Cryptococcus neoformans var. grubii The genome of an organism of Chlamydophila pneumoniae TW-183 Bin Zhao, Oliver He 182082 genome of Chlamydophila pneumoniae TW-183 The genome of an organism of Trypanosoma brucei TREU927 Bin Zhao, Oliver He 185431 genome of Trypanosoma brucei TREU927 The genome of an organism of Streptococcus pyogenes MGAS8232 Bin Zhao, Oliver He 186103 genome of Streptococcus pyogenes MGAS8232 The genome of an organism of Zaire ebolavirus Bin Zhao, Oliver He 186538 genome of Zaire ebolavirus The genome of an organism of Clostridiales Bin Zhao, Oliver He 186802 genome of Clostridiales The genome of an organism of Lactobacillales Bin Zhao, Oliver He 186826 genome of Lactobacillales The genome of an organism of Yersinia pestis KIM10+ Bin Zhao, Oliver He 187410 genome of Yersinia pestis KIM10+ The genome of an organism of Leptospira interrogans serovar Lai str. 56601 Bin Zhao, Oliver He 189518 genome of Leptospira interrogans serovar Lai str. 56601 The genome of an organism of Bacillus anthracis str. A2012 Bin Zhao, Oliver He 191218 genome of Bacillus anthracis str. A2012 The genome of an organism of Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 Bin Zhao, Oliver He 192222 genome of Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 The genome of an organism of Streptococcus pyogenes SSI-1 Bin Zhao, Oliver He 193567 genome of Streptococcus pyogenes SSI-1 The genome of an organism of Campylobacter jejuni RM1221 Bin Zhao, Oliver He 195099 genome of Campylobacter jejuni RM1221 The genome of an organism of Clostridium perfringens str. 13 Bin Zhao, Oliver He 195102 genome of Clostridium perfringens str. 13 The genome of an organism of Clostridium perfringens ATCC 13124 Bin Zhao, Oliver He 195103 genome of Clostridium perfringens ATCC 13124 The genome of an organism of Staphylococcus aureus subsp. aureus MW2 Bin Zhao, Oliver He 196620 genome of Staphylococcus aureus subsp. aureus MW2 The genome of an organism of Bacillus anthracis str. Ames Bin Zhao, Oliver He 198094 genome of Bacillus anthracis str. Ames The genome of an organism of Shigella flexneri 2a str. 301 Bin Zhao, Oliver He 198214 genome of Shigella flexneri 2a str. 301 The genome of an organism of Shigella flexneri 2a str. 2457T Bin Zhao, Oliver He 198215 genome of Shigella flexneri 2a str. 2457T The genome of an organism of Streptococcus pyogenes MGAS315 Bin Zhao, Oliver He 198466 genome of Streptococcus pyogenes MGAS315 The genome of an organism of Coccidioides posadasii Bin Zhao, Oliver He 199306 genome of Coccidioides posadasii The genome of an organism of Escherichia coli CFT073 Bin Zhao, Oliver He 199310 genome of Escherichia coli CFT073 The genome of an organism of Brucella suis 1330 Bin Zhao, Oliver He 204722 genome of Brucella suis 1330 The genome of an organism of Streptococcus agalactiae A909 Bin Zhao, Oliver He 205921 genome of Streptococcus agalactiae A909 The genome of an organism of Streptococcus agalactiae 2603V/R Bin Zhao, Oliver He 208435 genome of Streptococcus agalactiae 2603V/R The genome of an organism of Pseudomonas aeruginosa UCBPP-PA14 Bin Zhao, Oliver He 208963 genome of Pseudomonas aeruginosa UCBPP-PA14 The genome of an organism of Pseudomonas aeruginosa PAO1 Bin Zhao, Oliver He 208964 genome of Pseudomonas aeruginosa PAO1 The genome of an organism of Salmonella enterica subsp. enterica serovar Typhi str. Ty2 Bin Zhao, Oliver He 209261 genome of Salmonella enterica subsp. enterica serovar Typhi str. Ty2 The genome of an organism of Influenza A virus (A/Puerto Rico/8/1934(H1N1)) Bin Zhao, Oliver He 211044 genome of Influenza A virus (A/Puerto Rico/8/1934(H1N1)) The genome of an organism of Streptococcus agalactiae NEM316 Bin Zhao, Oliver He 211110 genome of Streptococcus agalactiae NEM316 The genome of an organism of Clostridium tetani E88 Bin Zhao, Oliver He 212717 genome of Clostridium tetani E88 The genome of an organism of Campylobacterales Bin Zhao, Oliver He 213849 genome of Campylobacterales The genome of an organism of Yersinia pestis CO92 Bin Zhao, Oliver He 214092 genome of Yersinia pestis CO92 The genome of an organism of Cryptococcus neoformans var. neoformans JEC21 Bin Zhao, Oliver He 214684 genome of Cryptococcus neoformans var. neoformans JEC21 The genome of an organism of Salmonella enterica subsp. enterica serovar Typhi str. CT18 Bin Zhao, Oliver He 220341 genome of Salmonella enterica subsp. enterica serovar Typhi str. CT18 The genome of an organism of Borrelia burgdorferi B31 Bin Zhao, Oliver He 224326 genome of Borrelia burgdorferi B31 The genome of an organism of Brucella melitensis bv. 1 str. 16M Bin Zhao, Oliver He 224914 genome of Brucella melitensis bv. 1 str. 16M The genome of an organism of Enterococcus faecalis V583 Bin Zhao, Oliver He 226185 genome of Enterococcus faecalis V583 The genome of an organism of Aspergillus nidulans FGSC A4 Bin Zhao, Oliver He 227321 genome of Aspergillus nidulans FGSC A4 The genome of an organism of Coxiella burnetii RSA 493 Bin Zhao, Oliver He 227377 genome of Coxiella burnetii RSA 493 The genome of an organism of Yersinia pestis biovar Microtus str. 91001 Bin Zhao, Oliver He 229193 genome of Yersinia pestis biovar Microtus str. 91001 The genome of an organism of Candida albicans SC5314 Bin Zhao, Oliver He 237561 genome of Candida albicans SC5314 The genome of an organism of Burkholderia mallei ATCC 23344 Bin Zhao, Oliver He 243160 genome of Burkholderia mallei ATCC 23344 The genome of an organism of Vibrio cholerae O1 biovar El Tor str. N16961 Bin Zhao, Oliver He 243277 genome of Vibrio cholerae O1 biovar El Tor str. N16961 The genome of an organism of Corynebacterium diphtheriae NCTC 13129 Bin Zhao, Oliver He 257309 genome of Corynebacterium diphtheriae NCTC 13129 The genome of an organism of Bordetella bronchiseptica RB50 Bin Zhao, Oliver He 257310 genome of Bordetella bronchiseptica RB50 The genome of an organism of Bordetella pertussis Tohama I Bin Zhao, Oliver He 257313 genome of Bordetella pertussis Tohama I The genome of an organism of Bacillus anthracis str. Sterne Bin Zhao, Oliver He 260799 genome of Bacillus anthracis str. Sterne The genome of an organism of Bacillus anthracis str. 'Ames Ancestor' Bin Zhao, Oliver He 261594 genome of Bacillus anthracis str. 'Ames Ancestor' The genome of an organism of Orgyia pseudotsugata MNPV Bin Zhao, Oliver He 262177 genome of Orgyia pseudotsugata MNPV The genome of an organism of Mycobacterium avium subsp. paratuberculosis K-10 Bin Zhao, Oliver He 262316 genome of Mycobacterium avium subsp. paratuberculosis K-10 The genome of an organism of Listeria monocytogenes serotype 4b str. F2365 Bin Zhao, Oliver He 265669 genome of Listeria monocytogenes serotype 4b str. F2365 The genome of an organism of Pneumonia virus of mice J3666 Bin Zhao, Oliver He 270473 genome of Pneumonia virus of mice J3666 The genome of an organism of Bombyx mori NPV Bin Zhao, Oliver He 271108 genome of Bombyx mori NPV The genome of an organism of Burkholderia pseudomallei K96243 Bin Zhao, Oliver He 272560 genome of Burkholderia pseudomallei K96243 The genome of an organism of Chlamydia trachomatis D/UW-3/CX Bin Zhao, Oliver He 272561 genome of Chlamydia trachomatis D/UW-3/CX The genome of an organism of Clostridium difficile 630 Bin Zhao, Oliver He 272563 genome of Clostridium difficile 630 The genome of an organism of Legionella pneumophila subsp. pneumophila str. Philadelphia 1 Bin Zhao, Oliver He 272624 genome of Legionella pneumophila subsp. pneumophila str. Philadelphia 1 The genome of an organism of Neisseria meningitidis FAM18 Bin Zhao, Oliver He 272831 genome of Neisseria meningitidis FAM18 The genome of an organism of Pasteurella multocida subsp. multocida str. Pm70 Bin Zhao, Oliver He 272843 genome of Pasteurella multocida subsp. multocida str. Pm70 The genome of an organism of Rickettsia prowazekii str. Madrid E Bin Zhao, Oliver He 272947 genome of Rickettsia prowazekii str. Madrid E The genome of an organism of Staphylococcus aureus RF122 Bin Zhao, Oliver He 273036 genome of Staphylococcus aureus RF122 The genome of an organism of Yersinia pseudotuberculosis IP 32953 Bin Zhao, Oliver He 273123 genome of Yersinia pseudotuberculosis IP 32953 The genome of an organism of Haemophilus influenzae 86-028NP Bin Zhao, Oliver He 281310 genome of Haemophilus influenzae 86-028NP The genome of an organism of Staphylococcus aureus subsp. aureus MRSA252 Bin Zhao, Oliver He 282458 genome of Staphylococcus aureus subsp. aureus MRSA252 The genome of an organism of Bartonella henselae str. Houston-1 Bin Zhao, Oliver He 283166 genome of Bartonella henselae str. Houston-1 The genome of an organism of Cryptococcus neoformans var. neoformans B-3501A Bin Zhao, Oliver He 283643 genome of Cryptococcus neoformans var. neoformans B-3501A The genome of an organism of Influenza A virus (A/Viet Nam/1203/2004(H5N1)) Bin Zhao, Oliver He 284218 genome of Influenza A virus (A/Viet Nam/1203/2004(H5N1)) The genome of an organism of Candida glabrata CBS 138 Bin Zhao, Oliver He 284593 genome of Candida glabrata CBS 138 The genome of an organism of Streptococcus pyogenes MGAS10394 Bin Zhao, Oliver He 286636 genome of Streptococcus pyogenes MGAS10394 The genome of an organism of Clostridium perfringens SM101 Bin Zhao, Oliver He 289380 genome of Clostridium perfringens SM101 The genome of an organism of Streptococcus pyogenes MGAS5005 Bin Zhao, Oliver He 293653 genome of Streptococcus pyogenes MGAS5005 The genome of an organism of Entamoeba histolytica HM-1:IMSS Bin Zhao, Oliver He 294381 genome of Entamoeba histolytica HM-1:IMSS The genome of an organism of Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150 Bin Zhao, Oliver He 295319 genome of Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150 The genome of an organism of Legionella pneumophila str. Lens Bin Zhao, Oliver He 297245 genome of Legionella pneumophila str. Lens The genome of an organism of Legionella pneumophila str. Paris Bin Zhao, Oliver He 297246 genome of Legionella pneumophila str. Paris The genome of an organism of Shigella dysenteriae Sd197 Bin Zhao, Oliver He 300267 genome of Shigella dysenteriae Sd197 The genome of an organism of Shigella boydii Sb227 Bin Zhao, Oliver He 300268 genome of Shigella boydii Sb227 The genome of an organism of Shigella sonnei Ss046 Bin Zhao, Oliver He 300269 genome of Shigella sonnei Ss046 The genome of an organism of Streptococcus pyogenes serotype M1 Bin Zhao, Oliver He 301447 genome of Streptococcus pyogenes serotype M1 The genome of an organism of Streptococcus pyogenes serotype M3 Bin Zhao, Oliver He 301448 genome of Streptococcus pyogenes serotype M3 The genome of an organism of Escherichia coli str. K-12 substr. DH10B Bin Zhao, Oliver He 316385 genome of Escherichia coli str. K-12 substr. DH10B The genome of an organism of Escherichia coli ETEC H10407 Bin Zhao, Oliver He 316401 genome of Escherichia coli ETEC H10407 The genome of an organism of Streptococcus pyogenes MGAS6180 Bin Zhao, Oliver He 319701 genome of Streptococcus pyogenes MGAS6180 The genome of an organism of Burkholderia pseudomallei 1710b Bin Zhao, Oliver He 320372 genome of Burkholderia pseudomallei 1710b The genome of an organism of Burkholderia pseudomallei 668 Bin Zhao, Oliver He 320373 genome of Burkholderia pseudomallei 668 The genome of an organism of Burkholderia mallei SAVP1 Bin Zhao, Oliver He 320388 genome of Burkholderia mallei SAVP1 The genome of an organism of Burkholderia mallei NCTC 10247 Bin Zhao, Oliver He 320389 genome of Burkholderia mallei NCTC 10247 The genome of an organism of Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67 Bin Zhao, Oliver He 321314 genome of Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67 The genome of an organism of Aspergillus fumigatus Af293 Bin Zhao, Oliver He 330879 genome of Aspergillus fumigatus Af293 The genome of an organism of Escherichia coli E24377A Bin Zhao, Oliver He 331111 genome of Escherichia coli E24377A The genome of an organism of Escherichia coli HS Bin Zhao, Oliver He 331112 genome of Escherichia coli HS The genome of an organism of Mycobacterium tuberculosis F11 Bin Zhao, Oliver He 336982 genome of Mycobacterium tuberculosis F11 The genome of an organism of Streptococcus pyogenes serotype M12 Bin Zhao, Oliver He 342023 genome of Streptococcus pyogenes serotype M12 The genome of an organism of Shigella boydii CDC 3083-94 Bin Zhao, Oliver He 344609 genome of Shigella boydii CDC 3083-94 The genome of an organism of SARS coronavirus ZJ0301 Bin Zhao, Oliver He 344702 genome of SARS coronavirus ZJ0301 The genome of an organism of Vibrio cholerae O395 Bin Zhao, Oliver He 345073 genome of Vibrio cholerae O395 The genome of an organism of Leishmania major strain Friedlin Bin Zhao, Oliver He 347515 genome of Leishmania major strain Friedlin The genome of an organism of Yersinia pestis Angola Bin Zhao, Oliver He 349746 genome of Yersinia pestis Angola The genome of an organism of Yersinia pseudotuberculosis IP 31758 Bin Zhao, Oliver He 349747 genome of Yersinia pseudotuberculosis IP 31758 The genome of an organism of Plasmodium yoelii yoelii 17XNL Bin Zhao, Oliver He 352914 genome of Plasmodium yoelii yoelii 17XNL The genome of an organism of Cryptosporidium parvum Iowa II Bin Zhao, Oliver He 353152 genome of Cryptosporidium parvum Iowa II The genome of an organism of Trypanosoma cruzi strain CL Brener Bin Zhao, Oliver He 353153 genome of Trypanosoma cruzi strain CL Brener The genome of an organism of Campylobacter jejuni subsp. jejuni 81-176 Bin Zhao, Oliver He 354242 genome of Campylobacter jejuni subsp. jejuni 81-176 The genome of an organism of Burkholderia pseudomallei 1106a Bin Zhao, Oliver He 357348 genome of Burkholderia pseudomallei 1106a The genome of an organism of Brucella melitensis biovar Abortus 2308 Bin Zhao, Oliver He 359391 genome of Brucella melitensis biovar Abortus 2308 The genome of an organism of Bartonella bacilliformis KC583 Bin Zhao, Oliver He 360095 genome of Bartonella bacilliformis KC583 The genome of an organism of Yersinia pestis Antiqua Bin Zhao, Oliver He 360102 genome of Yersinia pestis Antiqua The genome of an organism of Campylobacter jejuni subsp. doylei 269.97 Bin Zhao, Oliver He 360109 genome of Campylobacter jejuni subsp. doylei 269.97 The genome of an organism of Bordetella avium 197N Bin Zhao, Oliver He 360910 genome of Bordetella avium 197N The genome of an organism of Escherichia coli 536 Bin Zhao, Oliver He 362663 genome of Escherichia coli 536 The genome of an organism of Escherichia coli UTI89 Bin Zhao, Oliver He 364106 genome of Escherichia coli UTI89 The genome of an organism of Streptococcus pyogenes MGAS9429 Bin Zhao, Oliver He 370551 genome of Streptococcus pyogenes MGAS9429 The genome of an organism of Streptococcus pyogenes MGAS10270 Bin Zhao, Oliver He 370552 genome of Streptococcus pyogenes MGAS10270 The genome of an organism of Streptococcus pyogenes MGAS2096 Bin Zhao, Oliver He 370553 genome of Streptococcus pyogenes MGAS2096 The genome of an organism of Streptococcus pyogenes MGAS10750 Bin Zhao, Oliver He 370554 genome of Streptococcus pyogenes MGAS10750 The genome of an organism of Streptococcus pneumoniae D39 Bin Zhao, Oliver He 373153 genome of Streptococcus pneumoniae D39 The genome of an organism of Shigella flexneri 5 str. 8401 Bin Zhao, Oliver He 373384 genome of Shigella flexneri 5 str. 8401 The genome of an organism of Neisseria meningitidis 053442 Bin Zhao, Oliver He 374833 genome of Neisseria meningitidis 053442 The genome of an organism of Francisella tularensis subsp. holarctica LVS Bin Zhao, Oliver He 376619 genome of Francisella tularensis subsp. holarctica LVS The genome of an organism of Escherichia coli O26:H- Bin Zhao, Oliver He 376724 genome of Escherichia coli O26:H- The genome of an organism of Yersinia pestis Nepal516 Bin Zhao, Oliver He 377628 genome of Yersinia pestis Nepal516 The genome of an organism of Aeromonas salmonicida subsp. salmonicida A449 Bin Zhao, Oliver He 382245 genome of Aeromonas salmonicida subsp. salmonicida A449 The genome of an organism of Bartonella tribocorum CIP 105476 Bin Zhao, Oliver He 382640 genome of Bartonella tribocorum CIP 105476 The genome of an organism of Escherichia coli O157:H7 str. Sakai Bin Zhao, Oliver He 386585 genome of Escherichia coli O157:H7 str. Sakai The genome of an organism of Yersinia pestis Pestoides F Bin Zhao, Oliver He 386656 genome of Yersinia pestis Pestoides F The genome of an organism of Yersinia enterocolitica subsp. enterocolitica 8081 Bin Zhao, Oliver He 393305 genome of Yersinia enterocolitica subsp. enterocolitica 8081 The genome of an organism of Legionella pneumophila str. Corby Bin Zhao, Oliver He 400673 genome of Legionella pneumophila str. Corby The genome of an organism of Escherichia coli APEC O1 Bin Zhao, Oliver He 405955 genome of Escherichia coli APEC O1 The genome of an organism of Campylobacter jejuni subsp. jejuni 81116 Bin Zhao, Oliver He 407148 genome of Campylobacter jejuni subsp. jejuni 81116 The genome of an organism of Escherichia coli SE11 Bin Zhao, Oliver He 409438 genome of Escherichia coli SE11 The genome of an organism of Burkholderia mallei NCTC 10229 Bin Zhao, Oliver He 412022 genome of Burkholderia mallei NCTC 10229 The genome of an organism of Yersinia pestis CA88-4125 Bin Zhao, Oliver He 412420 genome of Yersinia pestis CA88-4125 The genome of an organism of Escherichia coli B str. REL606 Bin Zhao, Oliver He 413997 genome of Escherichia coli B str. REL606 The genome of an organism of Actinobacillus pleuropneumoniae serovar 5b str. L20 Bin Zhao, Oliver He 416269 genome of Actinobacillus pleuropneumoniae serovar 5b str. L20 The genome of an organism of Plasmodium (Vinckeia) Bin Zhao, Oliver He 418101 genome of Plasmodium (Vinckeia) The genome of an organism of Staphylococcus aureus subsp. aureus Mu3 Bin Zhao, Oliver He 418127 genome of Staphylococcus aureus subsp. aureus Mu3 The genome of an organism of Mycobacterium tuberculosis H37Ra Bin Zhao, Oliver He 419947 genome of Mycobacterium tuberculosis H37Ra The genome of an organism of Eimeriorina Bin Zhao, Oliver He 423054 genome of Eimeriorina The genome of an organism of Legionella pneumophila 2300/99 Alcoy Bin Zhao, Oliver He 423212 genome of Legionella pneumophila 2300/99 Alcoy The genome of an organism of Staphylococcus aureus subsp. aureus str. Newman Bin Zhao, Oliver He 426430 genome of Staphylococcus aureus subsp. aureus str. Newman The genome of an organism of Actinobacillus pleuropneumoniae serovar 3 str. JL03 Bin Zhao, Oliver He 434271 genome of Actinobacillus pleuropneumoniae serovar 3 str. JL03 The genome of an organism of ssRNA viruses Bin Zhao, Oliver He 439488 genome of ssRNA viruses The genome of an organism of Escherichia coli SMS-3-5 Bin Zhao, Oliver He 439855 genome of Escherichia coli SMS-3-5 The genome of an organism of Clostridium botulinum A str. ATCC 19397 Bin Zhao, Oliver He 441770 genome of Clostridium botulinum A str. ATCC 19397 The genome of an organism of Clostridium botulinum A str. Hall Bin Zhao, Oliver He 441771 genome of Clostridium botulinum A str. Hall The genome of an organism of Escherichia coli O157:H7 str. EC4115 Bin Zhao, Oliver He 444450 genome of Escherichia coli O157:H7 str. EC4115 The genome of an organism of Borrelia burgdorferi 156a Bin Zhao, Oliver He 445983 genome of Borrelia burgdorferi 156a The genome of an organism of Borrelia burgdorferi ZS7 Bin Zhao, Oliver He 445985 genome of Borrelia burgdorferi ZS7 The genome of an organism of Dikarya Bin Zhao, Oliver He 451864 genome of Dikarya The genome of an organism of Eurotiomycetidae Bin Zhao, Oliver He 451871 genome of Eurotiomycetidae The genome of an organism of Francisella tularensis subsp. holarctica FTNF002-00 Bin Zhao, Oliver He 458234 genome of Francisella tularensis subsp. holarctica FTNF002-00 The genome of an organism of Streptococcus pyogenes NZ131 Bin Zhao, Oliver He 471876 genome of Streptococcus pyogenes NZ131 The genome of an organism of Enterococcus faecalis OG1RF Bin Zhao, Oliver He 474186 genome of Enterococcus faecalis OG1RF The genome of an organism of Salmonella enterica subsp. enterica serovar Paratyphi C strain RKS4594 Bin Zhao, Oliver He 476213 genome of Salmonella enterica subsp. enterica serovar Paratyphi C strain RKS4594 The genome of an organism of Paenibacillus sp. Y412MC10 Bin Zhao, Oliver He 481743 genome of Paenibacillus sp. Y412MC10 The genome of an organism of Streptococcus pneumoniae Taiwan19F-14 Bin Zhao, Oliver He 487213 genome of Streptococcus pneumoniae Taiwan19F-14 The genome of an organism of Streptococcus pneumoniae Hungary19A-6 Bin Zhao, Oliver He 487214 genome of Streptococcus pneumoniae Hungary19A-6 The genome of an organism of Streptococcus pneumoniae 70585 Bin Zhao, Oliver He 488221 genome of Streptococcus pneumoniae 70585 The genome of an organism of Streptococcus pneumoniae JJA Bin Zhao, Oliver He 488222 genome of Streptococcus pneumoniae JJA The genome of an organism of Streptococcus pneumoniae P1031 Bin Zhao, Oliver He 488223 genome of Streptococcus pneumoniae P1031 The genome of an organism of Clostridium botulinum B1 str. Okra Bin Zhao, Oliver He 498213 genome of Clostridium botulinum B1 str. Okra The genome of an organism of Clostridium botulinum A3 str. Loch Maree Bin Zhao, Oliver He 498214 genome of Clostridium botulinum A3 str. Loch Maree The genome of an organism of Edwardsiella tarda EIB202 Bin Zhao, Oliver He 498217 genome of Edwardsiella tarda EIB202 The genome of an organism of Yersinia pseudotuberculosis YPIII Bin Zhao, Oliver He 502800 genome of Yersinia pseudotuberculosis YPIII The genome of an organism of Yersinia pseudotuberculosis PB1/+ Bin Zhao, Oliver He 502801 genome of Yersinia pseudotuberculosis PB1/+ The genome of an organism of Clostridium botulinum E3 str. Alaska E43 Bin Zhao, Oliver He 508767 genome of Clostridium botulinum E3 str. Alaska E43 The genome of an organism of Toxoplasma gondii ME49 Bin Zhao, Oliver He 508771 genome of Toxoplasma gondii ME49 The genome of an organism of Escherichia coli str. K-12 substr. MG1655 Bin Zhao, Oliver He 511145 genome of Escherichia coli str. K-12 substr. MG1655 The genome of an organism of Streptococcus pneumoniae G54 Bin Zhao, Oliver He 512566 genome of Streptococcus pneumoniae G54 The genome of an organism of Streptococcus pneumoniae CGSP14 Bin Zhao, Oliver He 516950 genome of Streptococcus pneumoniae CGSP14 The genome of an organism of Borrelia burgdorferi N40 Bin Zhao, Oliver He 521007 genome of Borrelia burgdorferi N40 The genome of an organism of Borrelia burgdorferi 297 Bin Zhao, Oliver He 521009 genome of Borrelia burgdorferi 297 The genome of an organism of Burkholderia pseudomallei MSHR346 Bin Zhao, Oliver He 536230 genome of Burkholderia pseudomallei MSHR346 The genome of an organism of Actinobacillus pleuropneumoniae serovar 7 str. AP76 Bin Zhao, Oliver He 537457 genome of Actinobacillus pleuropneumoniae serovar 7 str. AP76 The genome of an organism of Escherichia coli O157:H7 str. TW14359 Bin Zhao, Oliver He 544404 genome of Escherichia coli O157:H7 str. TW14359 The genome of an organism of Salmonella enterica subsp. enterica serovar Enteritidis str. P125109 Bin Zhao, Oliver He 550537 genome of Salmonella enterica subsp. enterica serovar Enteritidis str. P125109 The genome of an organism of Salmonella enterica subsp. enterica serovar Gallinarum str. 287/91 Bin Zhao, Oliver He 550538 genome of Salmonella enterica subsp. enterica serovar Gallinarum str. 287/91 The genome of an organism of Filobasidiella/Cryptococcus neoformans species complex Bin Zhao, Oliver He 552466 genome of Filobasidiella/Cryptococcus neoformans species complex The genome of an organism of Cryptococcus gattii Bin Zhao, Oliver He 552467 genome of Cryptococcus gattii The genome of an organism of Streptococcus equi subsp. zooepidemicus MGCS10565 Bin Zhao, Oliver He 552526 genome of Streptococcus equi subsp. zooepidemicus MGCS10565 The genome of an organism of Listeria monocytogenes HCC23 Bin Zhao, Oliver He 552536 genome of Listeria monocytogenes HCC23 The genome of an organism of Pseudomonas aeruginosa LESB58 Bin Zhao, Oliver He 557722 genome of Pseudomonas aeruginosa LESB58 The genome of an organism of Alphabaculovirus Bin Zhao, Oliver He 558016 genome of Alphabaculovirus The genome of an organism of Saccharomyces cerevisiae S288c Bin Zhao, Oliver He 559292 genome of Saccharomyces cerevisiae S288c The genome of an organism of Streptococcus pneumoniae ATCC 700669 Bin Zhao, Oliver He 561276 genome of Streptococcus pneumoniae ATCC 700669 The genome of an organism of Helicobacter pylori G27 Bin Zhao, Oliver He 563041 genome of Helicobacter pylori G27 The genome of an organism of Listeria monocytogenes L99 Bin Zhao, Oliver He 563174 genome of Listeria monocytogenes L99 The genome of an organism of Escherichia coli Vir68 Bin Zhao, Oliver He 563770 genome of Escherichia coli Vir68 The genome of an organism of Bacillus anthracis str. CDC 684 Bin Zhao, Oliver He 568206 genome of Bacillus anthracis str. CDC 684 The genome of an organism of Listeria monocytogenes serotype 4b str. CLIP 80459 Bin Zhao, Oliver He 568819 genome of Listeria monocytogenes serotype 4b str. CLIP 80459 The genome of an organism of Helicobacter pylori P12 Bin Zhao, Oliver He 570508 genome of Helicobacter pylori P12 The genome of an organism of Escherichia coli O26:H11 str. 11368 Bin Zhao, Oliver He 573235 genome of Escherichia coli O26:H11 str. 11368 The genome of an organism of Escherichia coli O127:H6 str. E2348/69 Bin Zhao, Oliver He 574521 genome of Escherichia coli O127:H6 str. E2348/69 The genome of an organism of Vibrio cholerae M66-2 Bin Zhao, Oliver He 579112 genome of Vibrio cholerae M66-2 The genome of an organism of Escherichia coli IAI1 Bin Zhao, Oliver He 585034 genome of Escherichia coli IAI1 The genome of an organism of Escherichia coli S88 Bin Zhao, Oliver He 585035 genome of Escherichia coli S88 The genome of an organism of Escherichia coli 55989 Bin Zhao, Oliver He 585055 genome of Escherichia coli 55989 The genome of an organism of Escherichia coli UMN026 Bin Zhao, Oliver He 585056 genome of Escherichia coli UMN026 The genome of an organism of Escherichia coli IAI39 Bin Zhao, Oliver He 585057 genome of Escherichia coli IAI39 The genome of an organism of Escherichia coli O103:H2 str. 12009 Bin Zhao, Oliver He 585395 genome of Escherichia coli O103:H2 str. 12009 The genome of an organism of Escherichia coli O111:H- str. 11128 Bin Zhao, Oliver He 585396 genome of Escherichia coli O111:H- str. 11128 The genome of an organism of Escherichia coli ED1a Bin Zhao, Oliver He 585397 genome of Escherichia coli ED1a The genome of an organism of Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S Bin Zhao, Oliver He 588858 genome of Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S The genome of an organism of Bacillus anthracis str. A0248 Bin Zhao, Oliver He 592021 genome of Bacillus anthracis str. A0248 The genome of an organism of Helicobacter pylori B38 Bin Zhao, Oliver He 592205 genome of Helicobacter pylori B38 The genome of an organism of Escherichia coli BW2952 Bin Zhao, Oliver He 595496 genome of Escherichia coli BW2952 The genome of an organism of SARS coronavirus ExoN1 Bin Zhao, Oliver He 627440 genome of SARS coronavirus ExoN1 The genome of an organism of Listeria monocytogenes 08-5923 Bin Zhao, Oliver He 637381 genome of Listeria monocytogenes 08-5923 The genome of an organism of Listeria monocytogenes 08-5578 Bin Zhao, Oliver He 653938 genome of Listeria monocytogenes 08-5578 The genome of an organism of Neisseria meningitidis alpha14 Bin Zhao, Oliver He 662598 genome of Neisseria meningitidis alpha14 The genome of an organism of Staphylococcus aureus subsp. aureus ED98 Bin Zhao, Oliver He 681288 genome of Staphylococcus aureus subsp. aureus ED98 The genome of an organism of Coronavirinae Bin Zhao, Oliver He 693995 genome of Coronavirinae The genome of an organism of Alphacoronavirus 1 Bin Zhao, Oliver He 693997 genome of Alphacoronavirus 1 The genome of an organism of Severe acute respiratory syndrome-related coronavirus Bin Zhao, Oliver He 694009 genome of Severe acute respiratory syndrome-related coronavirus The genome of an organism of Human metapneumovirus CAN97-83 Bin Zhao, Oliver He 694067 genome of Human metapneumovirus CAN97-83 The genome of an organism of Mileewa branchiuma Bin Zhao, Oliver He 700720 genome of Mileewa branchiuma The genome of an organism of Staphylococcus aureus 04-02981 Bin Zhao, Oliver He 703339 genome of Staphylococcus aureus 04-02981 The genome of an organism of Mycoplasma gallisepticum str. R(low) Bin Zhao, Oliver He 710127 genome of Mycoplasma gallisepticum str. R(low) The genome of an organism of saccharomyceta Bin Zhao, Oliver He 716545 genome of saccharomyceta The genome of an organism of Legionella pneumophila 130b Bin Zhao, Oliver He 866628 genome of Legionella pneumophila 130b The genome of an organism of Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74 Bin Zhao, Oliver He 909946 genome of Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74 A gene of an organism of Bacteria Bin Zhao, Oliver He 2 gene of Bacteria A gene of an organism of Spirochaetales Bin Zhao, Oliver He 136 gene of Spirochaetales A gene of an organism of Borrelia burgdorferi Bin Zhao, Oliver He 139 gene of Borrelia burgdorferi A gene of an organism of Campylobacter jejuni Bin Zhao, Oliver He 197 gene of Campylobacter jejuni A gene of an organism of Helicobacter pylori Bin Zhao, Oliver He 210 gene of Helicobacter pylori A gene of an organism of Brucella Bin Zhao, Oliver He 234 gene of Brucella A gene of an organism of Brucella abortus Bin Zhao, Oliver He 235 gene of Brucella abortus A gene of an organism of Francisella tularensis Bin Zhao, Oliver He 263 gene of Francisella tularensis A gene of an organism of Pseudomonas aeruginosa Bin Zhao, Oliver He 287 gene of Pseudomonas aeruginosa A gene of an organism of Rhizobiales Bin Zhao, Oliver He 356 gene of Rhizobiales A gene of an organism of Legionella pneumophila Bin Zhao, Oliver He 446 gene of Legionella pneumophila A gene of an organism of Neisseria meningitidis Bin Zhao, Oliver He 487 gene of Neisseria meningitidis A gene of an organism of Bordetella Bin Zhao, Oliver He 517 gene of Bordetella A gene of an organism of Bordetella pertussis Bin Zhao, Oliver He 520 gene of Bordetella pertussis A gene of an organism of Enterobacteriaceae Bin Zhao, Oliver He 543 gene of Enterobacteriaceae A gene of an organism of Escherichia coli Bin Zhao, Oliver He 562 gene of Escherichia coli A gene of an organism of Shigella Bin Zhao, Oliver He 620 gene of Shigella A gene of an organism of Shigella boydii Bin Zhao, Oliver He 621 gene of Shigella boydii A gene of an organism of Shigella flexneri Bin Zhao, Oliver He 623 gene of Shigella flexneri A gene of an organism of Yersinia <bacteria> Bin Zhao, Oliver He 629 gene of Yersinia <bacteria> A gene of an organism of Yersinia enterocolitica Bin Zhao, Oliver He 630 gene of Yersinia enterocolitica A gene of an organism of Yersinia pestis Bin Zhao, Oliver He 632 gene of Yersinia pestis A gene of an organism of Yersinia pseudotuberculosis Bin Zhao, Oliver He 633 gene of Yersinia pseudotuberculosis A gene of an organism of Vibrio cholerae Bin Zhao, Oliver He 666 gene of Vibrio cholerae A gene of an organism of Pasteurellaceae Bin Zhao, Oliver He 712 gene of Pasteurellaceae A gene of an organism of Actinobacillus pleuropneumoniae Bin Zhao, Oliver He 715 gene of Actinobacillus pleuropneumoniae A gene of an organism of Haemophilus influenzae Bin Zhao, Oliver He 727 gene of Haemophilus influenzae A gene of an organism of Pasteurella multocida Bin Zhao, Oliver He 747 gene of Pasteurella multocida A gene of an organism of Bartonella Bin Zhao, Oliver He 773 gene of Bartonella A gene of an organism of Chlamydia Bin Zhao, Oliver He 810 gene of Chlamydia A gene of an organism of Proteobacteria Bin Zhao, Oliver He 1224 gene of Proteobacteria A gene of an organism of Gammaproteobacteria Bin Zhao, Oliver He 1236 gene of Gammaproteobacteria A gene of an organism of Firmicutes Bin Zhao, Oliver He 1239 gene of Firmicutes A gene of an organism of Staphylococcus aureus Bin Zhao, Oliver He 1280 gene of Staphylococcus aureus A gene of an organism of Streptococcus Bin Zhao, Oliver He 1301 gene of Streptococcus A gene of an organism of Streptococcus agalactiae Bin Zhao, Oliver He 1311 gene of Streptococcus agalactiae A gene of an organism of Streptococcus pneumoniae Bin Zhao, Oliver He 1313 gene of Streptococcus pneumoniae A gene of an organism of Streptococcus pyogenes Bin Zhao, Oliver He 1314 gene of Streptococcus pyogenes A gene of an organism of Enterococcus Bin Zhao, Oliver He 1350 gene of Enterococcus A gene of an organism of Enterococcus faecalis Bin Zhao, Oliver He 1351 gene of Enterococcus faecalis A gene of an organism of Enterococcus faecium Bin Zhao, Oliver He 1352 gene of Enterococcus faecium A gene of an organism of Bacillales Bin Zhao, Oliver He 1385 gene of Bacillales A gene of an organism of Bacillus anthracis Bin Zhao, Oliver He 1392 gene of Bacillus anthracis A gene of an organism of Clostridium Bin Zhao, Oliver He 1485 gene of Clostridium A gene of an organism of Clostridium botulinum Bin Zhao, Oliver He 1491 gene of Clostridium botulinum A gene of an organism of [Clostridium] difficile Bin Zhao, Oliver He 1496 gene of [Clostridium] difficile A gene of an organism of Clostridium perfringens Bin Zhao, Oliver He 1502 gene of Clostridium perfringens A gene of an organism of Listeria monocytogenes Bin Zhao, Oliver He 1639 gene of Listeria monocytogenes A gene of an organism of Mycobacterium Bin Zhao, Oliver He 1763 gene of Mycobacterium A gene of an organism of Mycobacterium tuberculosis Bin Zhao, Oliver He 1773 gene of Mycobacterium tuberculosis A gene of an organism of Eukaryota Bin Zhao, Oliver He 2759 gene of Eukaryota A gene of an organism of Saccharomycetales Bin Zhao, Oliver He 4892 gene of Saccharomycetales A gene of an organism of Saccharomycetaceae Bin Zhao, Oliver He 4893 gene of Saccharomycetaceae A gene of an organism of Saccharomyces cerevisiae Bin Zhao, Oliver He 4932 gene of Saccharomyces cerevisiae A gene of an organism of Ajellomyces capsulatus Bin Zhao, Oliver He 5037 gene of Ajellomyces capsulatus A gene of an organism of Cryptococcus neoformans Bin Zhao, Oliver He 5207 gene of Cryptococcus neoformans A gene of an organism of Candida Bin Zhao, Oliver He 5475 gene of Candida A gene of an organism of Candida albicans Bin Zhao, Oliver He 5476 gene of Candida albicans A gene of an organism of Candida glabrata Bin Zhao, Oliver He 5478 gene of Candida glabrata A gene of an organism of Trypanosomatidae Bin Zhao, Oliver He 5654 gene of Trypanosomatidae A gene of an organism of Leishmania donovani Bin Zhao, Oliver He 5661 gene of Leishmania donovani A gene of an organism of Leishmania major Bin Zhao, Oliver He 5664 gene of Leishmania major A gene of an organism of Leishmania mexicana Bin Zhao, Oliver He 5665 gene of Leishmania mexicana A gene of an organism of Leishmania infantum Bin Zhao, Oliver He 5671 gene of Leishmania infantum A gene of an organism of Trypanosoma Bin Zhao, Oliver He 5690 gene of Trypanosoma A gene of an organism of Trypanosoma cruzi Bin Zhao, Oliver He 5693 gene of Trypanosoma cruzi A gene of an organism of Entamoeba histolytica Bin Zhao, Oliver He 5759 gene of Entamoeba histolytica A gene of an organism of Apicomplexa Bin Zhao, Oliver He 5794 gene of Apicomplexa A gene of an organism of Toxoplasma gondii Bin Zhao, Oliver He 5811 gene of Toxoplasma gondii A gene of an organism of Plasmodium Bin Zhao, Oliver He 5820 gene of Plasmodium A gene of an organism of Plasmodium berghei ANKA Bin Zhao, Oliver He 5823 gene of Plasmodium berghei ANKA A gene of an organism of Plasmodium yoelii Bin Zhao, Oliver He 5861 gene of Plasmodium yoelii A gene of an organism of Exophiala dermatitidis Bin Zhao, Oliver He 5970 gene of Exophiala dermatitidis A gene of an organism of Lythrurus Bin Zhao, Oliver He 7966 gene of Lythrurus A gene of an organism of Viruses Bin Zhao, Oliver He 10239 gene of Viruses A gene of an organism of Chordopoxvirinae Bin Zhao, Oliver He 10241 gene of Chordopoxvirinae A gene of an organism of Orthopoxvirus Bin Zhao, Oliver He 10242 gene of Orthopoxvirus A gene of an organism of Cowpox virus Bin Zhao, Oliver He 10243 gene of Cowpox virus A gene of an organism of Vaccinia virus Bin Zhao, Oliver He 10245 gene of Vaccinia virus A gene of an organism of Vaccinia virus Tian Tan Bin Zhao, Oliver He 10253 gene of Vaccinia virus Tian Tan A gene of an organism of Vaccinia virus WR Bin Zhao, Oliver He 10254 gene of Vaccinia virus WR A gene of an organism of Orf virus Bin Zhao, Oliver He 10258 gene of Orf virus A gene of an organism of Sheeppox virus Bin Zhao, Oliver He 10266 gene of Sheeppox virus A gene of an organism of Leporipoxvirus Bin Zhao, Oliver He 10270 gene of Leporipoxvirus A gene of an organism of Rabbit fibroma virus Bin Zhao, Oliver He 10271 gene of Rabbit fibroma virus A gene of an organism of Myxoma virus Bin Zhao, Oliver He 10273 gene of Myxoma virus A gene of an organism of Herpesviridae Bin Zhao, Oliver He 10292 gene of Herpesviridae A gene of an organism of Alphaherpesvirinae Bin Zhao, Oliver He 10293 gene of Alphaherpesvirinae A gene of an organism of Simplexvirus Bin Zhao, Oliver He 10294 gene of Simplexvirus A gene of an organism of Human herpesvirus 1 Bin Zhao, Oliver He 10298 gene of Human herpesvirus 1 A gene of an organism of Herpes simplex virus (type 1 / strain 17) Bin Zhao, Oliver He 10299 gene of Herpes simplex virus (type 1 / strain 17) A gene of an organism of Human herpesvirus 2 Bin Zhao, Oliver He 10310 gene of Human herpesvirus 2 A gene of an organism of Varicellovirus Bin Zhao, Oliver He 10319 gene of Varicellovirus A gene of an organism of Bovine herpesvirus 1 Bin Zhao, Oliver He 10320 gene of Bovine herpesvirus 1 A gene of an organism of Equid herpesvirus 1 Bin Zhao, Oliver He 10326 gene of Equid herpesvirus 1 A gene of an organism of Felid herpesvirus 1 Bin Zhao, Oliver He 10334 gene of Felid herpesvirus 1 A gene of an organism of Human herpesvirus 3 Bin Zhao, Oliver He 10335 gene of Human herpesvirus 3 A gene of an organism of Suid herpesvirus 1 Bin Zhao, Oliver He 10345 gene of Suid herpesvirus 1 A gene of an organism of Gallid herpesvirus 1 Bin Zhao, Oliver He 10386 gene of Gallid herpesvirus 1 A gene of an organism of Gallid herpesvirus 2 Bin Zhao, Oliver He 10390 gene of Gallid herpesvirus 2 A gene of an organism of African swine fever virus Bin Zhao, Oliver He 10497 gene of African swine fever virus A gene of an organism of Rotavirus Bin Zhao, Oliver He 10912 gene of Rotavirus A gene of an organism of Alphavirus Bin Zhao, Oliver He 11019 gene of Alphavirus A gene of an organism of Ross River virus Bin Zhao, Oliver He 11029 gene of Ross River virus A gene of an organism of Sindbis virus Bin Zhao, Oliver He 11034 gene of Sindbis virus A gene of an organism of Venezuelan equine encephalitis virus Bin Zhao, Oliver He 11036 gene of Venezuelan equine encephalitis virus A gene of an organism of Western equine encephalomyelitis virus Bin Zhao, Oliver He 11039 gene of Western equine encephalomyelitis virus A gene of an organism of Flaviviridae Bin Zhao, Oliver He 11050 gene of Flaviviridae A gene of an organism of Flavivirus Bin Zhao, Oliver He 11051 gene of Flavivirus A gene of an organism of West Nile virus Bin Zhao, Oliver He 11082 gene of West Nile virus A gene of an organism of Tick-borne encephalitis virus Bin Zhao, Oliver He 11084 gene of Tick-borne encephalitis virus A gene of an organism of Yellow fever virus Bin Zhao, Oliver He 11089 gene of Yellow fever virus A gene of an organism of Classical swine fever virus Bin Zhao, Oliver He 11096 gene of Classical swine fever virus A gene of an organism of Classical swine fever virus - Brescia Bin Zhao, Oliver He 11098 gene of Classical swine fever virus - Brescia A gene of an organism of Feline infectious peritonitis virus Bin Zhao, Oliver He 11135 gene of Feline infectious peritonitis virus A gene of an organism of Porcine respiratory coronavirus Bin Zhao, Oliver He 11146 gene of Porcine respiratory coronavirus A gene of an organism of Mononegavirales Bin Zhao, Oliver He 11157 gene of Mononegavirales A gene of an organism of Paramyxoviridae Bin Zhao, Oliver He 11158 gene of Paramyxoviridae A gene of an organism of Paramyxovirinae Bin Zhao, Oliver He 11159 gene of Paramyxovirinae A gene of an organism of Newcastle disease virus Bin Zhao, Oliver He 11176 gene of Newcastle disease virus A gene of an organism of Human parainfluenza virus 3 Bin Zhao, Oliver He 11216 gene of Human parainfluenza virus 3 A gene of an organism of Measles virus Bin Zhao, Oliver He 11234 gene of Measles virus A gene of an organism of Pneumovirinae Bin Zhao, Oliver He 11244 gene of Pneumovirinae A gene of an organism of Pneumovirus Bin Zhao, Oliver He 11245 gene of Pneumovirus A gene of an organism of Bovine respiratory syncytial virus Bin Zhao, Oliver He 11246 gene of Bovine respiratory syncytial virus A gene of an organism of Human respiratory syncytial virus A2 Bin Zhao, Oliver He 11259 gene of Human respiratory syncytial virus A2 A gene of an organism of Rhabdoviridae Bin Zhao, Oliver He 11270 gene of Rhabdoviridae A gene of an organism of Infectious hematopoietic necrosis virus Bin Zhao, Oliver He 11290 gene of Infectious hematopoietic necrosis virus A gene of an organism of Rabies virus Bin Zhao, Oliver He 11292 gene of Rabies virus A gene of an organism of Influenza A virus Bin Zhao, Oliver He 11320 gene of Influenza A virus A gene of an organism of Bunyaviridae Bin Zhao, Oliver He 11571 gene of Bunyaviridae A gene of an organism of La Crosse virus Bin Zhao, Oliver He 11577 gene of La Crosse virus A gene of an organism of Rift Valley fever virus Bin Zhao, Oliver He 11588 gene of Rift Valley fever virus A gene of an organism of Hantaan virus Bin Zhao, Oliver He 11599 gene of Hantaan virus A gene of an organism of Lentivirus Bin Zhao, Oliver He 11646 gene of Lentivirus A gene of an organism of Primate lentivirus group Bin Zhao, Oliver He 11652 gene of Primate lentivirus group A gene of an organism of Feline immunodeficiency virus Bin Zhao, Oliver He 11673 gene of Feline immunodeficiency virus A gene of an organism of Human immunodeficiency virus 1 Bin Zhao, Oliver He 11676 gene of Human immunodeficiency virus 1 A gene of an organism of Simian immunodeficiency virus Bin Zhao, Oliver He 11723 gene of Simian immunodeficiency virus A gene of an organism of Encephalomyocarditis virus Bin Zhao, Oliver He 12104 gene of Encephalomyocarditis virus A gene of an organism of Chicken anemia virus Bin Zhao, Oliver He 12618 gene of Chicken anemia virus A gene of an organism of Ectromelia virus Bin Zhao, Oliver He 12643 gene of Ectromelia virus A gene of an organism of Burkholderia mallei Bin Zhao, Oliver He 13373 gene of Burkholderia mallei A gene of an organism of Alphaproteobacteria Bin Zhao, Oliver He 28211 gene of Alphaproteobacteria A gene of an organism of Betaproteobacteria Bin Zhao, Oliver He 28216 gene of Betaproteobacteria A gene of an organism of Porcine reproductive and respiratory syndrome virus Bin Zhao, Oliver He 28344 gene of Porcine reproductive and respiratory syndrome virus A gene of an organism of Burkholderia pseudomallei Bin Zhao, Oliver He 28450 gene of Burkholderia pseudomallei A gene of an organism of Trichocomaceae Bin Zhao, Oliver He 28568 gene of Trichocomaceae A gene of an organism of Rotavirus A Bin Zhao, Oliver He 28875 gene of Rotavirus A A gene of an organism of Brucella melitensis Bin Zhao, Oliver He 29459 gene of Brucella melitensis A gene of an organism of Yersinia ruckeri Bin Zhao, Oliver He 29486 gene of Yersinia ruckeri A gene of an organism of Campylobacter jejuni subsp. jejuni Bin Zhao, Oliver He 32022 gene of Campylobacter jejuni subsp. jejuni A gene of an organism of Opisthokonta Bin Zhao, Oliver He 33154 gene of Opisthokonta A gene of an organism of Onygenales Bin Zhao, Oliver He 33183 gene of Onygenales A gene of an organism of Bilateria Bin Zhao, Oliver He 33213 gene of Bilateria A gene of an organism of Suid herpesvirus 1 strain Kaplan Bin Zhao, Oliver He 33703 gene of Suid herpesvirus 1 strain Kaplan A gene of an organism of Actinobacillus pleuropneumoniae serovar 2 Bin Zhao, Oliver He 34063 gene of Actinobacillus pleuropneumoniae serovar 2 A gene of an organism of dsDNA viruses, no RNA stage Bin Zhao, Oliver He 35237 gene of dsDNA viruses, no RNA stage A gene of an organism of Bovine herpesvirus 5 Bin Zhao, Oliver He 35244 gene of Bovine herpesvirus 5 A gene of an organism of ssRNA positive-strand viruses, no DNA stage Bin Zhao, Oliver He 35278 gene of ssRNA positive-strand viruses, no DNA stage A gene of an organism of ssRNA negative-strand viruses Bin Zhao, Oliver He 35301 gene of ssRNA negative-strand viruses A gene of an organism of Dictyochales Bin Zhao, Oliver He 35685 gene of Dictyochales A gene of an organism of Plasmodium falciparum 3D7 Bin Zhao, Oliver He 36329 gene of Plasmodium falciparum 3D7 A gene of an organism of Rotavirus C Bin Zhao, Oliver He 36427 gene of Rotavirus C A gene of an organism of Clostridium botulinum A Bin Zhao, Oliver He 36826 gene of Clostridium botulinum A A gene of an organism of Bartonella henselae Bin Zhao, Oliver He 38323 gene of Bartonella henselae A gene of an organism of Leishmania <subgenus> Bin Zhao, Oliver He 38568 gene of Leishmania <subgenus> A gene of an organism of Leishmania donovani species complex Bin Zhao, Oliver He 38574 gene of Leishmania donovani species complex A gene of an organism of Circoviridae Bin Zhao, Oliver He 39724 gene of Circoviridae A gene of an organism of Cryptococcus neoformans var. neoformans Bin Zhao, Oliver He 40410 gene of Cryptococcus neoformans var. neoformans A gene of an organism of Candida dubliniensis Bin Zhao, Oliver He 42374 gene of Candida dubliniensis A gene of an organism of Shigella flexneri 2a Bin Zhao, Oliver He 42897 gene of Shigella flexneri 2a A gene of an organism of Vibrio cholerae O139 Bin Zhao, Oliver He 45888 gene of Vibrio cholerae O139 A gene of an organism of Autographa californica nucleopolyhedrovirus Bin Zhao, Oliver He 46015 gene of Autographa californica nucleopolyhedrovirus A gene of an organism of Staphylococcus aureus subsp. aureus Bin Zhao, Oliver He 46170 gene of Staphylococcus aureus subsp. aureus A gene of an organism of Salmonella enterica subsp. enterica Bin Zhao, Oliver He 59201 gene of Salmonella enterica subsp. enterica A gene of an organism of Legionella pneumophila serogroup 1 Bin Zhao, Oliver He 66976 gene of Legionella pneumophila serogroup 1 A gene of an organism of Murine cytomegalovirus (strain K181) Bin Zhao, Oliver He 69156 gene of Murine cytomegalovirus (strain K181) A gene of an organism of Haemophilus influenzae Rd KW20 Bin Zhao, Oliver He 71421 gene of Haemophilus influenzae Rd KW20 A gene of an organism of Plasmodium yoelii yoelii Bin Zhao, Oliver He 73239 gene of Plasmodium yoelii yoelii A gene of an organism of Mannheimia haemolytica Bin Zhao, Oliver He 75985 gene of Mannheimia haemolytica A gene of an organism of Nidovirales Bin Zhao, Oliver He 76804 gene of Nidovirales A gene of an organism of Bovine herpesvirus type 1.1 Bin Zhao, Oliver He 79889 gene of Bovine herpesvirus type 1.1 A gene of an organism of Burkholderiales Bin Zhao, Oliver He 80840 gene of Burkholderiales A gene of an organism of Mycobacterium tuberculosis CDC1551 Bin Zhao, Oliver He 83331 gene of Mycobacterium tuberculosis CDC1551 A gene of an organism of Mycobacterium tuberculosis H37Rv Bin Zhao, Oliver He 83332 gene of Mycobacterium tuberculosis H37Rv A gene of an organism of Escherichia coli K-12 Bin Zhao, Oliver He 83333 gene of Escherichia coli K-12 A gene of an organism of Escherichia coli O157:H7 Bin Zhao, Oliver He 83334 gene of Escherichia coli O157:H7 A gene of an organism of Chlamydia pneumoniae Bin Zhao, Oliver He 83558 gene of Chlamydia pneumoniae A gene of an organism of Corynebacterineae Bin Zhao, Oliver He 85007 gene of Corynebacterineae A gene of an organism of Porcine circovirus 2 Bin Zhao, Oliver He 85708 gene of Porcine circovirus 2 A gene of an organism of Helicobacter pylori 26695 Bin Zhao, Oliver He 85962 gene of Helicobacter pylori 26695 A gene of an organism of Helicobacter pylori J99 Bin Zhao, Oliver He 85963 gene of Helicobacter pylori J99 A gene of an organism of Salmonella enterica subsp. enterica serovar Typhi Bin Zhao, Oliver He 90370 gene of Salmonella enterica subsp. enterica serovar Typhi A gene of an organism of Salmonella enterica subsp. enterica serovar Typhimurium Bin Zhao, Oliver He 90371 gene of Salmonella enterica subsp. enterica serovar Typhimurium A gene of an organism of Bacilli Bin Zhao, Oliver He 91061 gene of Bacilli A gene of an organism of Staphylococcus aureus subsp. aureus NCTC 8325 Bin Zhao, Oliver He 93061 gene of Staphylococcus aureus subsp. aureus NCTC 8325 A gene of an organism of Influenza A virus (A/Goose/Guangdong/1/96(H5N1)) Bin Zhao, Oliver He 93838 gene of Influenza A virus (A/Goose/Guangdong/1/96(H5N1)) A gene of an organism of Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 Bin Zhao, Oliver He 99287 gene of Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 A gene of an organism of H5N1 subtype Bin Zhao, Oliver He 102793 gene of H5N1 subtype A gene of an organism of Bartonella birtlesii Bin Zhao, Oliver He 111504 gene of Bartonella birtlesii A gene of an organism of pseudomallei group Bin Zhao, Oliver He 111527 gene of pseudomallei group A gene of an organism of Chlamydophila pneumoniae CWL029 Bin Zhao, Oliver He 115713 gene of Chlamydophila pneumoniae CWL029 A gene of an organism of Legionellales Bin Zhao, Oliver He 118969 gene of Legionellales A gene of an organism of Francisella tularensis subsp. holarctica Bin Zhao, Oliver He 119857 gene of Francisella tularensis subsp. holarctica A gene of an organism of Nipah virus Bin Zhao, Oliver He 121791 gene of Nipah virus A gene of an organism of Neisseria meningitidis MC58 Bin Zhao, Oliver He 122586 gene of Neisseria meningitidis MC58 A gene of an organism of Neisseria meningitidis Z2491 Bin Zhao, Oliver He 122587 gene of Neisseria meningitidis Z2491 A gene of an organism of Neisseria meningitidis serogroup C Bin Zhao, Oliver He 135720 gene of Neisseria meningitidis serogroup C A gene of an organism of Chlamydophila pneumoniae J138 Bin Zhao, Oliver He 138677 gene of Chlamydophila pneumoniae J138 A gene of an organism of Eurotiomycetes Bin Zhao, Oliver He 147545 gene of Eurotiomycetes A gene of an organism of Escherichia coli O157:H7 str. EDL933 Bin Zhao, Oliver He 155864 gene of Escherichia coli O157:H7 str. EDL933 A gene of an organism of Staphylococcus aureus subsp. aureus Mu50 Bin Zhao, Oliver He 158878 gene of Staphylococcus aureus subsp. aureus Mu50 A gene of an organism of Staphylococcus aureus subsp. aureus N315 Bin Zhao, Oliver He 158879 gene of Staphylococcus aureus subsp. aureus N315 A gene of an organism of Streptococcus pyogenes M1 GAS Bin Zhao, Oliver He 160490 gene of Streptococcus pyogenes M1 GAS A gene of an organism of Streptococcus pyogenes str. Manfredo Bin Zhao, Oliver He 160491 gene of Streptococcus pyogenes str. Manfredo A gene of an organism of Emericella nidulans Bin Zhao, Oliver He 162425 gene of Emericella nidulans A gene of an organism of Listeria monocytogenes EGD-e Bin Zhao, Oliver He 169963 gene of Listeria monocytogenes EGD-e A gene of an organism of Streptococcus pneumoniae TIGR4 Bin Zhao, Oliver He 170187 gene of Streptococcus pneumoniae TIGR4 A gene of an organism of Streptococcus pneumoniae R6 Bin Zhao, Oliver He 171101 gene of Streptococcus pneumoniae R6 A gene of an organism of Francisella tularensis subsp. tularensis SCHU S4 Bin Zhao, Oliver He 177416 gene of Francisella tularensis subsp. tularensis SCHU S4 A gene of an organism of WEEV complex Bin Zhao, Oliver He 177874 gene of WEEV complex A gene of an organism of Cryptococcus neoformans var. grubii Bin Zhao, Oliver He 178876 gene of Cryptococcus neoformans var. grubii A gene of an organism of Chlamydophila pneumoniae TW-183 Bin Zhao, Oliver He 182082 gene of Chlamydophila pneumoniae TW-183 A gene of an organism of Trypanosoma brucei TREU927 Bin Zhao, Oliver He 185431 gene of Trypanosoma brucei TREU927 A gene of an organism of Streptococcus pyogenes MGAS8232 Bin Zhao, Oliver He 186103 gene of Streptococcus pyogenes MGAS8232 A gene of an organism of Zaire ebolavirus Bin Zhao, Oliver He 186538 gene of Zaire ebolavirus A gene of an organism of Clostridiales Bin Zhao, Oliver He 186802 gene of Clostridiales A gene of an organism of Lactobacillales Bin Zhao, Oliver He 186826 gene of Lactobacillales A gene of an organism of Yersinia pestis KIM10+ Bin Zhao, Oliver He 187410 gene of Yersinia pestis KIM10+ A gene of an organism of Leptospira interrogans serovar Lai str. 56601 Bin Zhao, Oliver He 189518 gene of Leptospira interrogans serovar Lai str. 56601 A gene of an organism of Bacillus anthracis str. A2012 Bin Zhao, Oliver He 191218 gene of Bacillus anthracis str. A2012 A gene of an organism of Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 Bin Zhao, Oliver He 192222 gene of Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 A gene of an organism of Streptococcus pyogenes SSI-1 Bin Zhao, Oliver He 193567 gene of Streptococcus pyogenes SSI-1 A gene of an organism of Campylobacter jejuni RM1221 Bin Zhao, Oliver He 195099 gene of Campylobacter jejuni RM1221 A gene of an organism of Clostridium perfringens str. 13 Bin Zhao, Oliver He 195102 gene of Clostridium perfringens str. 13 A gene of an organism of Clostridium perfringens ATCC 13124 Bin Zhao, Oliver He 195103 gene of Clostridium perfringens ATCC 13124 A gene of an organism of Staphylococcus aureus subsp. aureus MW2 Bin Zhao, Oliver He 196620 gene of Staphylococcus aureus subsp. aureus MW2 A gene of an organism of Bacillus anthracis str. Ames Bin Zhao, Oliver He 198094 gene of Bacillus anthracis str. Ames A gene of an organism of Shigella flexneri 2a str. 301 Bin Zhao, Oliver He 198214 gene of Shigella flexneri 2a str. 301 A gene of an organism of Shigella flexneri 2a str. 2457T Bin Zhao, Oliver He 198215 gene of Shigella flexneri 2a str. 2457T A gene of an organism of Streptococcus pyogenes MGAS315 Bin Zhao, Oliver He 198466 gene of Streptococcus pyogenes MGAS315 A gene of an organism of Coccidioides posadasii Bin Zhao, Oliver He 199306 gene of Coccidioides posadasii A gene of an organism of Escherichia coli CFT073 Bin Zhao, Oliver He 199310 gene of Escherichia coli CFT073 A gene of an organism of Brucella suis 1330 Bin Zhao, Oliver He 204722 gene of Brucella suis 1330 A gene of an organism of Streptococcus agalactiae A909 Bin Zhao, Oliver He 205921 gene of Streptococcus agalactiae A909 A gene of an organism of Streptococcus agalactiae 2603V/R Bin Zhao, Oliver He 208435 gene of Streptococcus agalactiae 2603V/R A gene of an organism of Pseudomonas aeruginosa UCBPP-PA14 Bin Zhao, Oliver He 208963 gene of Pseudomonas aeruginosa UCBPP-PA14 A gene of an organism of Pseudomonas aeruginosa PAO1 Bin Zhao, Oliver He 208964 gene of Pseudomonas aeruginosa PAO1 A gene of an organism of Salmonella enterica subsp. enterica serovar Typhi str. Ty2 Bin Zhao, Oliver He 209261 gene of Salmonella enterica subsp. enterica serovar Typhi str. Ty2 A gene of an organism of Influenza A virus (A/Puerto Rico/8/1934(H1N1)) Bin Zhao, Oliver He 211044 gene of Influenza A virus (A/Puerto Rico/8/1934(H1N1)) A gene of an organism of Streptococcus agalactiae NEM316 Bin Zhao, Oliver He 211110 gene of Streptococcus agalactiae NEM316 A gene of an organism of Clostridium tetani E88 Bin Zhao, Oliver He 212717 gene of Clostridium tetani E88 A gene of an organism of Campylobacterales Bin Zhao, Oliver He 213849 gene of Campylobacterales A gene of an organism of Yersinia pestis CO92 Bin Zhao, Oliver He 214092 gene of Yersinia pestis CO92 A gene of an organism of Cryptococcus neoformans var. neoformans JEC21 Bin Zhao, Oliver He 214684 gene of Cryptococcus neoformans var. neoformans JEC21 A gene of an organism of Salmonella enterica subsp. enterica serovar Typhi str. CT18 Bin Zhao, Oliver He 220341 gene of Salmonella enterica subsp. enterica serovar Typhi str. CT18 A gene of an organism of Borrelia burgdorferi B31 Bin Zhao, Oliver He 224326 gene of Borrelia burgdorferi B31 A gene of an organism of Brucella melitensis bv. 1 str. 16M Bin Zhao, Oliver He 224914 gene of Brucella melitensis bv. 1 str. 16M A gene of an organism of Enterococcus faecalis V583 Bin Zhao, Oliver He 226185 gene of Enterococcus faecalis V583 A gene of an organism of Aspergillus nidulans FGSC A4 Bin Zhao, Oliver He 227321 gene of Aspergillus nidulans FGSC A4 A gene of an organism of Coxiella burnetii RSA 493 Bin Zhao, Oliver He 227377 gene of Coxiella burnetii RSA 493 A gene of an organism of Yersinia pestis biovar Microtus str. 91001 Bin Zhao, Oliver He 229193 gene of Yersinia pestis biovar Microtus str. 91001 A gene of an organism of Candida albicans SC5314 Bin Zhao, Oliver He 237561 gene of Candida albicans SC5314 A gene of an organism of Burkholderia mallei ATCC 23344 Bin Zhao, Oliver He 243160 gene of Burkholderia mallei ATCC 23344 A gene of an organism of Vibrio cholerae O1 biovar El Tor str. N16961 Bin Zhao, Oliver He 243277 gene of Vibrio cholerae O1 biovar El Tor str. N16961 A gene of an organism of Corynebacterium diphtheriae NCTC 13129 Bin Zhao, Oliver He 257309 gene of Corynebacterium diphtheriae NCTC 13129 A gene of an organism of Bordetella bronchiseptica RB50 Bin Zhao, Oliver He 257310 gene of Bordetella bronchiseptica RB50 A gene of an organism of Bordetella pertussis Tohama I Bin Zhao, Oliver He 257313 gene of Bordetella pertussis Tohama I A gene of an organism of Bacillus anthracis str. Sterne Bin Zhao, Oliver He 260799 gene of Bacillus anthracis str. Sterne A gene of an organism of Bacillus anthracis str. 'Ames Ancestor' Bin Zhao, Oliver He 261594 gene of Bacillus anthracis str. 'Ames Ancestor' A gene of an organism of Orgyia pseudotsugata MNPV Bin Zhao, Oliver He 262177 gene of Orgyia pseudotsugata MNPV A gene of an organism of Mycobacterium avium subsp. paratuberculosis K-10 Bin Zhao, Oliver He 262316 gene of Mycobacterium avium subsp. paratuberculosis K-10 A gene of an organism of Listeria monocytogenes serotype 4b str. F2365 Bin Zhao, Oliver He 265669 gene of Listeria monocytogenes serotype 4b str. F2365 A gene of an organism of Pneumonia virus of mice J3666 Bin Zhao, Oliver He 270473 gene of Pneumonia virus of mice J3666 A gene of an organism of Bombyx mori NPV Bin Zhao, Oliver He 271108 gene of Bombyx mori NPV A gene of an organism of Burkholderia pseudomallei K96243 Bin Zhao, Oliver He 272560 gene of Burkholderia pseudomallei K96243 A gene of an organism of Chlamydia trachomatis D/UW-3/CX Bin Zhao, Oliver He 272561 gene of Chlamydia trachomatis D/UW-3/CX A gene of an organism of Clostridium difficile 630 Bin Zhao, Oliver He 272563 gene of Clostridium difficile 630 A gene of an organism of Legionella pneumophila subsp. pneumophila str. Philadelphia 1 Bin Zhao, Oliver He 272624 gene of Legionella pneumophila subsp. pneumophila str. Philadelphia 1 A gene of an organism of Neisseria meningitidis FAM18 Bin Zhao, Oliver He 272831 gene of Neisseria meningitidis FAM18 A gene of an organism of Pasteurella multocida subsp. multocida str. Pm70 Bin Zhao, Oliver He 272843 gene of Pasteurella multocida subsp. multocida str. Pm70 A gene of an organism of Rickettsia prowazekii str. Madrid E Bin Zhao, Oliver He 272947 gene of Rickettsia prowazekii str. Madrid E A gene of an organism of Staphylococcus aureus RF122 Bin Zhao, Oliver He 273036 gene of Staphylococcus aureus RF122 A gene of an organism of Yersinia pseudotuberculosis IP 32953 Bin Zhao, Oliver He 273123 gene of Yersinia pseudotuberculosis IP 32953 A gene of an organism of Haemophilus influenzae 86-028NP Bin Zhao, Oliver He 281310 gene of Haemophilus influenzae 86-028NP A gene of an organism of Staphylococcus aureus subsp. aureus MRSA252 Bin Zhao, Oliver He 282458 gene of Staphylococcus aureus subsp. aureus MRSA252 A gene of an organism of Bartonella henselae str. Houston-1 Bin Zhao, Oliver He 283166 gene of Bartonella henselae str. Houston-1 A gene of an organism of Cryptococcus neoformans var. neoformans B-3501A Bin Zhao, Oliver He 283643 gene of Cryptococcus neoformans var. neoformans B-3501A A gene of an organism of Influenza A virus (A/Viet Nam/1203/2004(H5N1)) Bin Zhao, Oliver He 284218 gene of Influenza A virus (A/Viet Nam/1203/2004(H5N1)) A gene of an organism of Candida glabrata CBS 138 Bin Zhao, Oliver He 284593 gene of Candida glabrata CBS 138 A gene of an organism of Streptococcus pyogenes MGAS10394 Bin Zhao, Oliver He 286636 gene of Streptococcus pyogenes MGAS10394 A gene of an organism of Clostridium perfringens SM101 Bin Zhao, Oliver He 289380 gene of Clostridium perfringens SM101 A gene of an organism of Streptococcus pyogenes MGAS5005 Bin Zhao, Oliver He 293653 gene of Streptococcus pyogenes MGAS5005 A gene of an organism of Entamoeba histolytica HM-1:IMSS Bin Zhao, Oliver He 294381 gene of Entamoeba histolytica HM-1:IMSS A gene of an organism of Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150 Bin Zhao, Oliver He 295319 gene of Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150 A gene of an organism of Legionella pneumophila str. Lens Bin Zhao, Oliver He 297245 gene of Legionella pneumophila str. Lens A gene of an organism of Legionella pneumophila str. Paris Bin Zhao, Oliver He 297246 gene of Legionella pneumophila str. Paris A gene of an organism of Shigella dysenteriae Sd197 Bin Zhao, Oliver He 300267 gene of Shigella dysenteriae Sd197 A gene of an organism of Shigella boydii Sb227 Bin Zhao, Oliver He 300268 gene of Shigella boydii Sb227 A gene of an organism of Shigella sonnei Ss046 Bin Zhao, Oliver He 300269 gene of Shigella sonnei Ss046 A gene of an organism of Streptococcus pyogenes serotype M1 Bin Zhao, Oliver He 301447 gene of Streptococcus pyogenes serotype M1 A gene of an organism of Streptococcus pyogenes serotype M3 Bin Zhao, Oliver He 301448 gene of Streptococcus pyogenes serotype M3 A gene of an organism of Escherichia coli str. K-12 substr. DH10B Bin Zhao, Oliver He 316385 gene of Escherichia coli str. K-12 substr. DH10B A gene of an organism of Escherichia coli ETEC H10407 Bin Zhao, Oliver He 316401 gene of Escherichia coli ETEC H10407 A gene of an organism of Streptococcus pyogenes MGAS6180 Bin Zhao, Oliver He 319701 gene of Streptococcus pyogenes MGAS6180 A gene of an organism of Burkholderia pseudomallei 1710b Bin Zhao, Oliver He 320372 gene of Burkholderia pseudomallei 1710b A gene of an organism of Burkholderia pseudomallei 668 Bin Zhao, Oliver He 320373 gene of Burkholderia pseudomallei 668 A gene of an organism of Burkholderia mallei SAVP1 Bin Zhao, Oliver He 320388 gene of Burkholderia mallei SAVP1 A gene of an organism of Burkholderia mallei NCTC 10247 Bin Zhao, Oliver He 320389 gene of Burkholderia mallei NCTC 10247 A gene of an organism of Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67 Bin Zhao, Oliver He 321314 gene of Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67 A gene of an organism of Aspergillus fumigatus Af293 Bin Zhao, Oliver He 330879 gene of Aspergillus fumigatus Af293 A gene of an organism of Escherichia coli E24377A Bin Zhao, Oliver He 331111 gene of Escherichia coli E24377A A gene of an organism of Escherichia coli HS Bin Zhao, Oliver He 331112 gene of Escherichia coli HS A gene of an organism of Mycobacterium tuberculosis F11 Bin Zhao, Oliver He 336982 gene of Mycobacterium tuberculosis F11 A gene of an organism of Streptococcus pyogenes serotype M12 Bin Zhao, Oliver He 342023 gene of Streptococcus pyogenes serotype M12 A gene of an organism of Shigella boydii CDC 3083-94 Bin Zhao, Oliver He 344609 gene of Shigella boydii CDC 3083-94 A gene of an organism of SARS coronavirus ZJ0301 Bin Zhao, Oliver He 344702 gene of SARS coronavirus ZJ0301 A gene of an organism of Vibrio cholerae O395 Bin Zhao, Oliver He 345073 gene of Vibrio cholerae O395 A gene of an organism of Leishmania major strain Friedlin Bin Zhao, Oliver He 347515 gene of Leishmania major strain Friedlin A gene of an organism of Yersinia pestis Angola Bin Zhao, Oliver He 349746 gene of Yersinia pestis Angola A gene of an organism of Yersinia pseudotuberculosis IP 31758 Bin Zhao, Oliver He 349747 gene of Yersinia pseudotuberculosis IP 31758 A gene of an organism of Plasmodium yoelii yoelii 17XNL Bin Zhao, Oliver He 352914 gene of Plasmodium yoelii yoelii 17XNL A gene of an organism of Cryptosporidium parvum Iowa II Bin Zhao, Oliver He 353152 gene of Cryptosporidium parvum Iowa II A gene of an organism of Trypanosoma cruzi strain CL Brener Bin Zhao, Oliver He 353153 gene of Trypanosoma cruzi strain CL Brener A gene of an organism of Campylobacter jejuni subsp. jejuni 81-176 Bin Zhao, Oliver He 354242 gene of Campylobacter jejuni subsp. jejuni 81-176 A gene of an organism of Burkholderia pseudomallei 1106a Bin Zhao, Oliver He 357348 gene of Burkholderia pseudomallei 1106a A gene of an organism of Brucella melitensis biovar Abortus 2308 Bin Zhao, Oliver He 359391 gene of Brucella melitensis biovar Abortus 2308 A gene of an organism of Bartonella bacilliformis KC583 Bin Zhao, Oliver He 360095 gene of Bartonella bacilliformis KC583 A gene of an organism of Yersinia pestis Antiqua Bin Zhao, Oliver He 360102 gene of Yersinia pestis Antiqua A gene of an organism of Campylobacter jejuni subsp. doylei 269.97 Bin Zhao, Oliver He 360109 gene of Campylobacter jejuni subsp. doylei 269.97 A gene of an organism of Bordetella avium 197N Bin Zhao, Oliver He 360910 gene of Bordetella avium 197N A gene of an organism of Escherichia coli 536 Bin Zhao, Oliver He 362663 gene of Escherichia coli 536 A gene of an organism of Escherichia coli UTI89 Bin Zhao, Oliver He 364106 gene of Escherichia coli UTI89 A gene of an organism of Streptococcus pyogenes MGAS9429 Bin Zhao, Oliver He 370551 gene of Streptococcus pyogenes MGAS9429 A gene of an organism of Streptococcus pyogenes MGAS10270 Bin Zhao, Oliver He 370552 gene of Streptococcus pyogenes MGAS10270 A gene of an organism of Streptococcus pyogenes MGAS2096 Bin Zhao, Oliver He 370553 gene of Streptococcus pyogenes MGAS2096 A gene of an organism of Streptococcus pyogenes MGAS10750 Bin Zhao, Oliver He 370554 gene of Streptococcus pyogenes MGAS10750 A gene of an organism of Streptococcus pneumoniae D39 Bin Zhao, Oliver He 373153 gene of Streptococcus pneumoniae D39 A gene of an organism of Shigella flexneri 5 str. 8401 Bin Zhao, Oliver He 373384 gene of Shigella flexneri 5 str. 8401 A gene of an organism of Neisseria meningitidis 053442 Bin Zhao, Oliver He 374833 gene of Neisseria meningitidis 053442 A gene of an organism of Francisella tularensis subsp. holarctica LVS Bin Zhao, Oliver He 376619 gene of Francisella tularensis subsp. holarctica LVS A gene of an organism of Escherichia coli O26:H- Bin Zhao, Oliver He 376724 gene of Escherichia coli O26:H- A gene of an organism of Yersinia pestis Nepal516 Bin Zhao, Oliver He 377628 gene of Yersinia pestis Nepal516 A gene of an organism of Aeromonas salmonicida subsp. salmonicida A449 Bin Zhao, Oliver He 382245 gene of Aeromonas salmonicida subsp. salmonicida A449 A gene of an organism of Bartonella tribocorum CIP 105476 Bin Zhao, Oliver He 382640 gene of Bartonella tribocorum CIP 105476 A gene of an organism of Escherichia coli O157:H7 str. Sakai Bin Zhao, Oliver He 386585 gene of Escherichia coli O157:H7 str. Sakai A gene of an organism of Yersinia pestis Pestoides F Bin Zhao, Oliver He 386656 gene of Yersinia pestis Pestoides F A gene of an organism of Yersinia enterocolitica subsp. enterocolitica 8081 Bin Zhao, Oliver He 393305 gene of Yersinia enterocolitica subsp. enterocolitica 8081 A gene of an organism of Legionella pneumophila str. Corby Bin Zhao, Oliver He 400673 gene of Legionella pneumophila str. Corby A gene of an organism of Escherichia coli APEC O1 Bin Zhao, Oliver He 405955 gene of Escherichia coli APEC O1 A gene of an organism of Campylobacter jejuni subsp. jejuni 81116 Bin Zhao, Oliver He 407148 gene of Campylobacter jejuni subsp. jejuni 81116 A gene of an organism of Escherichia coli SE11 Bin Zhao, Oliver He 409438 gene of Escherichia coli SE11 A gene of an organism of Burkholderia mallei NCTC 10229 Bin Zhao, Oliver He 412022 gene of Burkholderia mallei NCTC 10229 A gene of an organism of Yersinia pestis CA88-4125 Bin Zhao, Oliver He 412420 gene of Yersinia pestis CA88-4125 A gene of an organism of Escherichia coli B str. REL606 Bin Zhao, Oliver He 413997 gene of Escherichia coli B str. REL606 A gene of an organism of Actinobacillus pleuropneumoniae serovar 5b str. L20 Bin Zhao, Oliver He 416269 gene of Actinobacillus pleuropneumoniae serovar 5b str. L20 A gene of an organism of Plasmodium (Vinckeia) Bin Zhao, Oliver He 418101 gene of Plasmodium (Vinckeia) A gene of an organism of Staphylococcus aureus subsp. aureus Mu3 Bin Zhao, Oliver He 418127 gene of Staphylococcus aureus subsp. aureus Mu3 A gene of an organism of Mycobacterium tuberculosis H37Ra Bin Zhao, Oliver He 419947 gene of Mycobacterium tuberculosis H37Ra A gene of an organism of Eimeriorina Bin Zhao, Oliver He 423054 gene of Eimeriorina A gene of an organism of Legionella pneumophila 2300/99 Alcoy Bin Zhao, Oliver He 423212 gene of Legionella pneumophila 2300/99 Alcoy A gene of an organism of Staphylococcus aureus subsp. aureus str. Newman Bin Zhao, Oliver He 426430 gene of Staphylococcus aureus subsp. aureus str. Newman A gene of an organism of Actinobacillus pleuropneumoniae serovar 3 str. JL03 Bin Zhao, Oliver He 434271 gene of Actinobacillus pleuropneumoniae serovar 3 str. JL03 A gene of an organism of ssRNA viruses Bin Zhao, Oliver He 439488 gene of ssRNA viruses A gene of an organism of Escherichia coli SMS-3-5 Bin Zhao, Oliver He 439855 gene of Escherichia coli SMS-3-5 A gene of an organism of Clostridium botulinum A str. ATCC 19397 Bin Zhao, Oliver He 441770 gene of Clostridium botulinum A str. ATCC 19397 A gene of an organism of Clostridium botulinum A str. Hall Bin Zhao, Oliver He 441771 gene of Clostridium botulinum A str. Hall A gene of an organism of Escherichia coli O157:H7 str. EC4115 Bin Zhao, Oliver He 444450 gene of Escherichia coli O157:H7 str. EC4115 A gene of an organism of Borrelia burgdorferi 156a Bin Zhao, Oliver He 445983 gene of Borrelia burgdorferi 156a A gene of an organism of Borrelia burgdorferi ZS7 Bin Zhao, Oliver He 445985 gene of Borrelia burgdorferi ZS7 A gene of an organism of Dikarya Bin Zhao, Oliver He 451864 gene of Dikarya A gene of an organism of Eurotiomycetidae Bin Zhao, Oliver He 451871 gene of Eurotiomycetidae A gene of an organism of Francisella tularensis subsp. holarctica FTNF002-00 Bin Zhao, Oliver He 458234 gene of Francisella tularensis subsp. holarctica FTNF002-00 A gene of an organism of Streptococcus pyogenes NZ131 Bin Zhao, Oliver He 471876 gene of Streptococcus pyogenes NZ131 A gene of an organism of Enterococcus faecalis OG1RF Bin Zhao, Oliver He 474186 gene of Enterococcus faecalis OG1RF A gene of an organism of Salmonella enterica subsp. enterica serovar Paratyphi C strain RKS4594 Bin Zhao, Oliver He 476213 gene of Salmonella enterica subsp. enterica serovar Paratyphi C strain RKS4594 A gene of an organism of Paenibacillus sp. Y412MC10 Bin Zhao, Oliver He 481743 gene of Paenibacillus sp. Y412MC10 A gene of an organism of Streptococcus pneumoniae Taiwan19F-14 Bin Zhao, Oliver He 487213 gene of Streptococcus pneumoniae Taiwan19F-14 A gene of an organism of Streptococcus pneumoniae Hungary19A-6 Bin Zhao, Oliver He 487214 gene of Streptococcus pneumoniae Hungary19A-6 A gene of an organism of Streptococcus pneumoniae 70585 Bin Zhao, Oliver He 488221 gene of Streptococcus pneumoniae 70585 A gene of an organism of Streptococcus pneumoniae JJA Bin Zhao, Oliver He 488222 gene of Streptococcus pneumoniae JJA A gene of an organism of Streptococcus pneumoniae P1031 Bin Zhao, Oliver He 488223 gene of Streptococcus pneumoniae P1031 A gene of an organism of Clostridium botulinum B1 str. Okra Bin Zhao, Oliver He 498213 gene of Clostridium botulinum B1 str. Okra A gene of an organism of Clostridium botulinum A3 str. Loch Maree Bin Zhao, Oliver He 498214 gene of Clostridium botulinum A3 str. Loch Maree A gene of an organism of Edwardsiella tarda EIB202 Bin Zhao, Oliver He 498217 gene of Edwardsiella tarda EIB202 A gene of an organism of Yersinia pseudotuberculosis YPIII Bin Zhao, Oliver He 502800 gene of Yersinia pseudotuberculosis YPIII A gene of an organism of Yersinia pseudotuberculosis PB1/+ Bin Zhao, Oliver He 502801 gene of Yersinia pseudotuberculosis PB1/+ A gene of an organism of Clostridium botulinum E3 str. Alaska E43 Bin Zhao, Oliver He 508767 gene of Clostridium botulinum E3 str. Alaska E43 A gene of an organism of Toxoplasma gondii ME49 Bin Zhao, Oliver He 508771 gene of Toxoplasma gondii ME49 A gene of an organism of Escherichia coli str. K-12 substr. MG1655 Bin Zhao, Oliver He 511145 gene of Escherichia coli str. K-12 substr. MG1655 A gene of an organism of Streptococcus pneumoniae G54 Bin Zhao, Oliver He 512566 gene of Streptococcus pneumoniae G54 A gene of an organism of Streptococcus pneumoniae CGSP14 Bin Zhao, Oliver He 516950 gene of Streptococcus pneumoniae CGSP14 A gene of an organism of Borrelia burgdorferi N40 Bin Zhao, Oliver He 521007 gene of Borrelia burgdorferi N40 A gene of an organism of Borrelia burgdorferi 297 Bin Zhao, Oliver He 521009 gene of Borrelia burgdorferi 297 A gene of an organism of Burkholderia pseudomallei MSHR346 Bin Zhao, Oliver He 536230 gene of Burkholderia pseudomallei MSHR346 A gene of an organism of Actinobacillus pleuropneumoniae serovar 7 str. AP76 Bin Zhao, Oliver He 537457 gene of Actinobacillus pleuropneumoniae serovar 7 str. AP76 A gene of an organism of Escherichia coli O157:H7 str. TW14359 Bin Zhao, Oliver He 544404 gene of Escherichia coli O157:H7 str. TW14359 A gene of an organism of Salmonella enterica subsp. enterica serovar Enteritidis str. P125109 Bin Zhao, Oliver He 550537 gene of Salmonella enterica subsp. enterica serovar Enteritidis str. P125109 A gene of an organism of Salmonella enterica subsp. enterica serovar Gallinarum str. 287/91 Bin Zhao, Oliver He 550538 gene of Salmonella enterica subsp. enterica serovar Gallinarum str. 287/91 A gene of an organism of Filobasidiella/Cryptococcus neoformans species complex Bin Zhao, Oliver He 552466 gene of Filobasidiella/Cryptococcus neoformans species complex A gene of an organism of Cryptococcus gattii Bin Zhao, Oliver He 552467 gene of Cryptococcus gattii A gene of an organism of Streptococcus equi subsp. zooepidemicus MGCS10565 Bin Zhao, Oliver He 552526 gene of Streptococcus equi subsp. zooepidemicus MGCS10565 A gene of an organism of Listeria monocytogenes HCC23 Bin Zhao, Oliver He 552536 gene of Listeria monocytogenes HCC23 A gene of an organism of Pseudomonas aeruginosa LESB58 Bin Zhao, Oliver He 557722 gene of Pseudomonas aeruginosa LESB58 A gene of an organism of Alphabaculovirus Bin Zhao, Oliver He 558016 gene of Alphabaculovirus A gene of an organism of Saccharomyces cerevisiae S288c Bin Zhao, Oliver He 559292 gene of Saccharomyces cerevisiae S288c A gene of an organism of Streptococcus pneumoniae ATCC 700669 Bin Zhao, Oliver He 561276 gene of Streptococcus pneumoniae ATCC 700669 A gene of an organism of Helicobacter pylori G27 Bin Zhao, Oliver He 563041 gene of Helicobacter pylori G27 A gene of an organism of Listeria monocytogenes L99 Bin Zhao, Oliver He 563174 gene of Listeria monocytogenes L99 A gene of an organism of Escherichia coli Vir68 Bin Zhao, Oliver He 563770 gene of Escherichia coli Vir68 A gene of an organism of Bacillus anthracis str. CDC 684 Bin Zhao, Oliver He 568206 gene of Bacillus anthracis str. CDC 684 A gene of an organism of Listeria monocytogenes serotype 4b str. CLIP 80459 Bin Zhao, Oliver He 568819 gene of Listeria monocytogenes serotype 4b str. CLIP 80459 A gene of an organism of Helicobacter pylori P12 Bin Zhao, Oliver He 570508 gene of Helicobacter pylori P12 A gene of an organism of Escherichia coli O26:H11 str. 11368 Bin Zhao, Oliver He 573235 gene of Escherichia coli O26:H11 str. 11368 A gene of an organism of Escherichia coli O127:H6 str. E2348/69 Bin Zhao, Oliver He 574521 gene of Escherichia coli O127:H6 str. E2348/69 A gene of an organism of Vibrio cholerae M66-2 Bin Zhao, Oliver He 579112 gene of Vibrio cholerae M66-2 A gene of an organism of Escherichia coli IAI1 Bin Zhao, Oliver He 585034 gene of Escherichia coli IAI1 A gene of an organism of Escherichia coli S88 Bin Zhao, Oliver He 585035 gene of Escherichia coli S88 A gene of an organism of Escherichia coli 55989 Bin Zhao, Oliver He 585055 gene of Escherichia coli 55989 A gene of an organism of Escherichia coli UMN026 Bin Zhao, Oliver He 585056 gene of Escherichia coli UMN026 A gene of an organism of Escherichia coli IAI39 Bin Zhao, Oliver He 585057 gene of Escherichia coli IAI39 A gene of an organism of Escherichia coli O103:H2 str. 12009 Bin Zhao, Oliver He 585395 gene of Escherichia coli O103:H2 str. 12009 A gene of an organism of Escherichia coli O111:H- str. 11128 Bin Zhao, Oliver He 585396 gene of Escherichia coli O111:H- str. 11128 A gene of an organism of Escherichia coli ED1a Bin Zhao, Oliver He 585397 gene of Escherichia coli ED1a A gene of an organism of Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S Bin Zhao, Oliver He 588858 gene of Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S A gene of an organism of Bacillus anthracis str. A0248 Bin Zhao, Oliver He 592021 gene of Bacillus anthracis str. A0248 A gene of an organism of Helicobacter pylori B38 Bin Zhao, Oliver He 592205 gene of Helicobacter pylori B38 A gene of an organism of Escherichia coli BW2952 Bin Zhao, Oliver He 595496 gene of Escherichia coli BW2952 A gene of an organism of SARS coronavirus ExoN1 Bin Zhao, Oliver He 627440 gene of SARS coronavirus ExoN1 A gene of an organism of Listeria monocytogenes 08-5923 Bin Zhao, Oliver He 637381 gene of Listeria monocytogenes 08-5923 A gene of an organism of Listeria monocytogenes 08-5578 Bin Zhao, Oliver He 653938 gene of Listeria monocytogenes 08-5578 A gene of an organism of Neisseria meningitidis alpha14 Bin Zhao, Oliver He 662598 gene of Neisseria meningitidis alpha14 A gene of an organism of Staphylococcus aureus subsp. aureus ED98 Bin Zhao, Oliver He 681288 gene of Staphylococcus aureus subsp. aureus ED98 A gene of an organism of Coronavirinae Bin Zhao, Oliver He 693995 gene of Coronavirinae A gene of an organism of Alphacoronavirus 1 Bin Zhao, Oliver He 693997 gene of Alphacoronavirus 1 A gene of an organism of Severe acute respiratory syndrome-related coronavirus Bin Zhao, Oliver He 694009 gene of Severe acute respiratory syndrome-related coronavirus A gene of an organism of Human metapneumovirus CAN97-83 Bin Zhao, Oliver He 694067 gene of Human metapneumovirus CAN97-83 A gene of an organism of Mileewa branchiuma Bin Zhao, Oliver He 700720 gene of Mileewa branchiuma A gene of an organism of Staphylococcus aureus 04-02981 Bin Zhao, Oliver He 703339 gene of Staphylococcus aureus 04-02981 A gene of an organism of Mycoplasma gallisepticum str. R(low) Bin Zhao, Oliver He 710127 gene of Mycoplasma gallisepticum str. R(low) A gene of an organism of saccharomyceta Bin Zhao, Oliver He 716545 gene of saccharomyceta A gene of an organism of Legionella pneumophila 130b Bin Zhao, Oliver He 866628 gene of Legionella pneumophila 130b A gene of an organism of Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74 Bin Zhao, Oliver He 909946 gene of Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74 A gene of Francisella tularensis subsp. holarctica LVS that has a tRNA gene type Bin Zhao, Oliver He 376619 tRNA gene of Francisella tularensis subsp. holarctica LVS A gene of Francisella tularensis subsp. tularensis SCHU S4 that has a rRNA gene type Bin Zhao, Oliver He 177416 rRNA gene of Francisella tularensis subsp. tularensis SCHU S4 A gene of Francisella tularensis subsp. holarctica LVS that has a rRNA gene type Bin Zhao, Oliver He 376619 rRNA gene of Francisella tularensis subsp. holarctica LVS A gene of Campylobacter jejuni that has a protein-coding gene type Bin Zhao, Oliver He 197 protein-coding gene of Campylobacter jejuni A gene of Escherichia coli that has a protein-coding gene type Bin Zhao, Oliver He 562 protein-coding gene of Escherichia coli A gene of Yersinia enterocolitica that has a protein-coding gene type Bin Zhao, Oliver He 630 protein-coding gene of Yersinia enterocolitica A gene of Yersinia pestis that has a protein-coding gene type Bin Zhao, Oliver He 632 protein-coding gene of Yersinia pestis A gene of Enterococcus faecalis that has a protein-coding gene type Bin Zhao, Oliver He 1351 protein-coding gene of Enterococcus faecalis A gene of Clostridium botulinum that has a protein-coding gene type Bin Zhao, Oliver He 1491 protein-coding gene of Clostridium botulinum A gene of Clostridium perfringens that has a protein-coding gene type Bin Zhao, Oliver He 1502 protein-coding gene of Clostridium perfringens A gene of Listeria monocytogenes that has a protein-coding gene type Bin Zhao, Oliver He 1639 protein-coding gene of Listeria monocytogenes A gene of Plasmodium berghei ANKA that has a protein-coding gene type Bin Zhao, Oliver He 5823 protein-coding gene of Plasmodium berghei ANKA A gene of Cowpox virus that has a protein-coding gene type Bin Zhao, Oliver He 10243 protein-coding gene of Cowpox virus A gene of Vaccinia virus that has a protein-coding gene type Bin Zhao, Oliver He 10245 protein-coding gene of Vaccinia virus A gene of Sheeppox virus that has a protein-coding gene type Bin Zhao, Oliver He 10266 protein-coding gene of Sheeppox virus A gene of Rabbit fibroma virus that has a protein-coding gene type Bin Zhao, Oliver He 10271 protein-coding gene of Rabbit fibroma virus A gene of Myxoma virus that has a protein-coding gene type Bin Zhao, Oliver He 10273 protein-coding gene of Myxoma virus A gene of Human herpesvirus 1 that has a protein-coding gene type Bin Zhao, Oliver He 10298 protein-coding gene of Human herpesvirus 1 A gene of Human herpesvirus 2 that has a protein-coding gene type Bin Zhao, Oliver He 10310 protein-coding gene of Human herpesvirus 2 A gene of Bovine herpesvirus 1 that has a protein-coding gene type Bin Zhao, Oliver He 10320 protein-coding gene of Bovine herpesvirus 1 A gene of Felid herpesvirus 1 that has a protein-coding gene type Bin Zhao, Oliver He 10334 protein-coding gene of Felid herpesvirus 1 A gene of Human herpesvirus 3 that has a protein-coding gene type Bin Zhao, Oliver He 10335 protein-coding gene of Human herpesvirus 3 A gene of Suid herpesvirus 1 that has a protein-coding gene type Bin Zhao, Oliver He 10345 protein-coding gene of Suid herpesvirus 1 A gene of Gallid herpesvirus 1 that has a protein-coding gene type Bin Zhao, Oliver He 10386 protein-coding gene of Gallid herpesvirus 1 A gene of Gallid herpesvirus 2 that has a protein-coding gene type Bin Zhao, Oliver He 10390 protein-coding gene of Gallid herpesvirus 2 A gene of African swine fever virus that has a protein-coding gene type Bin Zhao, Oliver He 10497 protein-coding gene of African swine fever virus A gene of Ross River virus that has a protein-coding gene type Bin Zhao, Oliver He 11029 protein-coding gene of Ross River virus A gene of Classical swine fever virus that has a protein-coding gene type Bin Zhao, Oliver He 11096 protein-coding gene of Classical swine fever virus A gene of Feline infectious peritonitis virus that has a protein-coding gene type Bin Zhao, Oliver He 11135 protein-coding gene of Feline infectious peritonitis virus A gene of Measles virus that has a protein-coding gene type Bin Zhao, Oliver He 11234 protein-coding gene of Measles virus A gene of Bovine respiratory syncytial virus that has a protein-coding gene type Bin Zhao, Oliver He 11246 protein-coding gene of Bovine respiratory syncytial virus A gene of Infectious hematopoietic necrosis virus that has a protein-coding gene type Bin Zhao, Oliver He 11290 protein-coding gene of Infectious hematopoietic necrosis virus A gene of Rabies virus that has a protein-coding gene type Bin Zhao, Oliver He 11292 protein-coding gene of Rabies virus A gene of La Crosse virus that has a protein-coding gene type Bin Zhao, Oliver He 11577 protein-coding gene of La Crosse virus A gene of Hantaan virus that has a protein-coding gene type Bin Zhao, Oliver He 11599 protein-coding gene of Hantaan virus A gene of Feline immunodeficiency virus that has a protein-coding gene type Bin Zhao, Oliver He 11673 protein-coding gene of Feline immunodeficiency virus A gene of Human immunodeficiency virus 1 that has a protein-coding gene type Bin Zhao, Oliver He 11676 protein-coding gene of Human immunodeficiency virus 1 A gene of Simian immunodeficiency virus that has a protein-coding gene type Bin Zhao, Oliver He 11723 protein-coding gene of Simian immunodeficiency virus A gene of Ectromelia virus that has a protein-coding gene type Bin Zhao, Oliver He 12643 protein-coding gene of Ectromelia virus A gene of Rotavirus A that has a protein-coding gene type Bin Zhao, Oliver He 28875 protein-coding gene of Rotavirus A A gene of Bovine herpesvirus 5 that has a protein-coding gene type Bin Zhao, Oliver He 35244 protein-coding gene of Bovine herpesvirus 5 A gene of Plasmodium falciparum 3D7 that has a protein-coding gene type Bin Zhao, Oliver He 36329 protein-coding gene of Plasmodium falciparum 3D7 A gene of Rotavirus C that has a protein-coding gene type Bin Zhao, Oliver He 36427 protein-coding gene of Rotavirus C A gene of Autographa californica nucleopolyhedrovirus that has a protein-coding gene type Bin Zhao, Oliver He 46015 protein-coding gene of Autographa californica nucleopolyhedrovirus A gene of Haemophilus influenzae Rd KW20 that has a protein-coding gene type Bin Zhao, Oliver He 71421 protein-coding gene of Haemophilus influenzae Rd KW20 A gene of Mycobacterium tuberculosis CDC1551 that has a protein-coding gene type Bin Zhao, Oliver He 83331 protein-coding gene of Mycobacterium tuberculosis CDC1551 A gene of Mycobacterium tuberculosis H37Rv that has a protein-coding gene type Bin Zhao, Oliver He 83332 protein-coding gene of Mycobacterium tuberculosis H37Rv A gene of Porcine circovirus 2 that has a protein-coding gene type Bin Zhao, Oliver He 85708 protein-coding gene of Porcine circovirus 2 A gene of Helicobacter pylori 26695 that has a protein-coding gene type Bin Zhao, Oliver He 85962 protein-coding gene of Helicobacter pylori 26695 A gene of Helicobacter pylori J99 that has a protein-coding gene type Bin Zhao, Oliver He 85963 protein-coding gene of Helicobacter pylori J99 A gene of Staphylococcus aureus subsp. aureus NCTC 8325 that has a protein-coding gene type Bin Zhao, Oliver He 93061 protein-coding gene of Staphylococcus aureus subsp. aureus NCTC 8325 A gene of Influenza A virus (A/Goose/Guangdong/1/96(H5N1)) that has a protein-coding gene type Bin Zhao, Oliver He 93838 protein-coding gene of Influenza A virus (A/Goose/Guangdong/1/96(H5N1)) A gene of Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 that has a protein-coding gene type Bin Zhao, Oliver He 99287 protein-coding gene of Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 A gene of Chlamydophila pneumoniae CWL029 that has a protein-coding gene type Bin Zhao, Oliver He 115713 protein-coding gene of Chlamydophila pneumoniae CWL029 A gene of Neisseria meningitidis MC58 that has a protein-coding gene type Bin Zhao, Oliver He 122586 protein-coding gene of Neisseria meningitidis MC58 A gene of Neisseria meningitidis Z2491 that has a protein-coding gene type Bin Zhao, Oliver He 122587 protein-coding gene of Neisseria meningitidis Z2491 A gene of Chlamydophila pneumoniae J138 that has a protein-coding gene type Bin Zhao, Oliver He 138677 protein-coding gene of Chlamydophila pneumoniae J138 A gene of Escherichia coli O157:H7 str. EDL933 that has a protein-coding gene type Bin Zhao, Oliver He 155864 protein-coding gene of Escherichia coli O157:H7 str. EDL933 A gene of Staphylococcus aureus subsp. aureus Mu50 that has a protein-coding gene type Bin Zhao, Oliver He 158878 protein-coding gene of Staphylococcus aureus subsp. aureus Mu50 A gene of Staphylococcus aureus subsp. aureus N315 that has a protein-coding gene type Bin Zhao, Oliver He 158879 protein-coding gene of Staphylococcus aureus subsp. aureus N315 A gene of Streptococcus pyogenes M1 GAS that has a protein-coding gene type Bin Zhao, Oliver He 160490 protein-coding gene of Streptococcus pyogenes M1 GAS A gene of Streptococcus pyogenes str. Manfredo that has a protein-coding gene type Bin Zhao, Oliver He 160491 protein-coding gene of Streptococcus pyogenes str. Manfredo A gene of Listeria monocytogenes EGD-e that has a protein-coding gene type Bin Zhao, Oliver He 169963 protein-coding gene of Listeria monocytogenes EGD-e A gene of Streptococcus pneumoniae TIGR4 that has a protein-coding gene type Bin Zhao, Oliver He 170187 protein-coding gene of Streptococcus pneumoniae TIGR4 A gene of Streptococcus pneumoniae R6 that has a protein-coding gene type Bin Zhao, Oliver He 171101 protein-coding gene of Streptococcus pneumoniae R6 A gene of Francisella tularensis subsp. tularensis SCHU S4 that has a protein-coding gene type Bin Zhao, Oliver He 177416 protein-coding gene of Francisella tularensis subsp. tularensis SCHU S4 A gene of Chlamydophila pneumoniae TW-183 that has a protein-coding gene type Bin Zhao, Oliver He 182082 protein-coding gene of Chlamydophila pneumoniae TW-183 A gene of Streptococcus pyogenes MGAS8232 that has a protein-coding gene type Bin Zhao, Oliver He 186103 protein-coding gene of Streptococcus pyogenes MGAS8232 A gene of Yersinia pestis KIM10+ that has a protein-coding gene type Bin Zhao, Oliver He 187410 protein-coding gene of Yersinia pestis KIM10+ A gene of Leptospira interrogans serovar Lai str. 56601 that has a protein-coding gene type Bin Zhao, Oliver He 189518 protein-coding gene of Leptospira interrogans serovar Lai str. 56601 A gene of Bacillus anthracis str. A2012 that has a protein-coding gene type Bin Zhao, Oliver He 191218 protein-coding gene of Bacillus anthracis str. A2012 A gene of Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 that has a protein-coding gene type Bin Zhao, Oliver He 192222 protein-coding gene of Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 A gene of Streptococcus pyogenes SSI-1 that has a protein-coding gene type Bin Zhao, Oliver He 193567 protein-coding gene of Streptococcus pyogenes SSI-1 A gene of Campylobacter jejuni RM1221 that has a protein-coding gene type Bin Zhao, Oliver He 195099 protein-coding gene of Campylobacter jejuni RM1221 A gene of Clostridium perfringens str. 13 that has a protein-coding gene type Bin Zhao, Oliver He 195102 protein-coding gene of Clostridium perfringens str. 13 A gene of Clostridium perfringens ATCC 13124 that has a protein-coding gene type Bin Zhao, Oliver He 195103 protein-coding gene of Clostridium perfringens ATCC 13124 A gene of Staphylococcus aureus subsp. aureus MW2 that has a protein-coding gene type Bin Zhao, Oliver He 196620 protein-coding gene of Staphylococcus aureus subsp. aureus MW2 A gene of Bacillus anthracis str. Ames that has a protein-coding gene type Bin Zhao, Oliver He 198094 protein-coding gene of Bacillus anthracis str. Ames A gene of Shigella flexneri 2a str. 301 that has a protein-coding gene type Bin Zhao, Oliver He 198214 protein-coding gene of Shigella flexneri 2a str. 301 A gene of Shigella flexneri 2a str. 2457T that has a protein-coding gene type Bin Zhao, Oliver He 198215 protein-coding gene of Shigella flexneri 2a str. 2457T A gene of Streptococcus pyogenes MGAS315 that has a protein-coding gene type Bin Zhao, Oliver He 198466 protein-coding gene of Streptococcus pyogenes MGAS315 A gene of Escherichia coli CFT073 that has a protein-coding gene type Bin Zhao, Oliver He 199310 protein-coding gene of Escherichia coli CFT073 A gene of Brucella suis 1330 that has a protein-coding gene type Bin Zhao, Oliver He 204722 protein-coding gene of Brucella suis 1330 A gene of Streptococcus agalactiae A909 that has a protein-coding gene type Bin Zhao, Oliver He 205921 protein-coding gene of Streptococcus agalactiae A909 A gene of Streptococcus agalactiae 2603V/R that has a protein-coding gene type Bin Zhao, Oliver He 208435 protein-coding gene of Streptococcus agalactiae 2603V/R A gene of Pseudomonas aeruginosa UCBPP-PA14 that has a protein-coding gene type Bin Zhao, Oliver He 208963 protein-coding gene of Pseudomonas aeruginosa UCBPP-PA14 A gene of Pseudomonas aeruginosa PAO1 that has a protein-coding gene type Bin Zhao, Oliver He 208964 protein-coding gene of Pseudomonas aeruginosa PAO1 A gene of Influenza A virus (A/Puerto Rico/8/1934(H1N1)) that has a protein-coding gene type Bin Zhao, Oliver He 211044 protein-coding gene of Influenza A virus (A/Puerto Rico/8/1934(H1N1)) A gene of Streptococcus agalactiae NEM316 that has a protein-coding gene type Bin Zhao, Oliver He 211110 protein-coding gene of Streptococcus agalactiae NEM316 A gene of Clostridium tetani E88 that has a protein-coding gene type Bin Zhao, Oliver He 212717 protein-coding gene of Clostridium tetani E88 A gene of Yersinia pestis CO92 that has a protein-coding gene type Bin Zhao, Oliver He 214092 protein-coding gene of Yersinia pestis CO92 A gene of Cryptococcus neoformans var. neoformans JEC21 that has a protein-coding gene type Bin Zhao, Oliver He 214684 protein-coding gene of Cryptococcus neoformans var. neoformans JEC21 A gene of Salmonella enterica subsp. enterica serovar Typhi str. CT18 that has a protein-coding gene type Bin Zhao, Oliver He 220341 protein-coding gene of Salmonella enterica subsp. enterica serovar Typhi str. CT18 A gene of Borrelia burgdorferi B31 that has a protein-coding gene type Bin Zhao, Oliver He 224326 protein-coding gene of Borrelia burgdorferi B31 A gene of Brucella melitensis bv. 1 str. 16M that has a protein-coding gene type Bin Zhao, Oliver He 224914 protein-coding gene of Brucella melitensis bv. 1 str. 16M A gene of Enterococcus faecalis V583 that has a protein-coding gene type Bin Zhao, Oliver He 226185 protein-coding gene of Enterococcus faecalis V583 A gene of Aspergillus nidulans FGSC A4 that has a protein-coding gene type Bin Zhao, Oliver He 227321 protein-coding gene of Aspergillus nidulans FGSC A4 A gene of Coxiella burnetii RSA 493 that has a protein-coding gene type Bin Zhao, Oliver He 227377 protein-coding gene of Coxiella burnetii RSA 493 A gene of Yersinia pestis biovar Microtus str. 91001 that has a protein-coding gene type Bin Zhao, Oliver He 229193 protein-coding gene of Yersinia pestis biovar Microtus str. 91001 A gene of Candida albicans SC5314 that has a protein-coding gene type Bin Zhao, Oliver He 237561 protein-coding gene of Candida albicans SC5314 A gene of Burkholderia mallei ATCC 23344 that has a protein-coding gene type Bin Zhao, Oliver He 243160 protein-coding gene of Burkholderia mallei ATCC 23344 A gene of Vibrio cholerae O1 biovar El Tor str. N16961 that has a protein-coding gene type Bin Zhao, Oliver He 243277 protein-coding gene of Vibrio cholerae O1 biovar El Tor str. N16961 A gene of Corynebacterium diphtheriae NCTC 13129 that has a protein-coding gene type Bin Zhao, Oliver He 257309 protein-coding gene of Corynebacterium diphtheriae NCTC 13129 A gene of Bordetella bronchiseptica RB50 that has a protein-coding gene type Bin Zhao, Oliver He 257310 protein-coding gene of Bordetella bronchiseptica RB50 A gene of Bordetella pertussis Tohama I that has a protein-coding gene type Bin Zhao, Oliver He 257313 protein-coding gene of Bordetella pertussis Tohama I A gene of Bacillus anthracis str. Sterne that has a protein-coding gene type Bin Zhao, Oliver He 260799 protein-coding gene of Bacillus anthracis str. Sterne A gene of Bacillus anthracis str. 'Ames Ancestor' that has a protein-coding gene type Bin Zhao, Oliver He 261594 protein-coding gene of Bacillus anthracis str. 'Ames Ancestor' A gene of Orgyia pseudotsugata MNPV that has a protein-coding gene type Bin Zhao, Oliver He 262177 protein-coding gene of Orgyia pseudotsugata MNPV A gene of Mycobacterium avium subsp. paratuberculosis K-10 that has a protein-coding gene type Bin Zhao, Oliver He 262316 protein-coding gene of Mycobacterium avium subsp. paratuberculosis K-10 A gene of Listeria monocytogenes serotype 4b str. F2365 that has a protein-coding gene type Bin Zhao, Oliver He 265669 protein-coding gene of Listeria monocytogenes serotype 4b str. F2365 A gene of Bombyx mori NPV that has a protein-coding gene type Bin Zhao, Oliver He 271108 protein-coding gene of Bombyx mori NPV A gene of Burkholderia pseudomallei K96243 that has a protein-coding gene type Bin Zhao, Oliver He 272560 protein-coding gene of Burkholderia pseudomallei K96243 A gene of Chlamydia trachomatis D/UW-3/CX that has a protein-coding gene type Bin Zhao, Oliver He 272561 protein-coding gene of Chlamydia trachomatis D/UW-3/CX A gene of Clostridium difficile 630 that has a protein-coding gene type Bin Zhao, Oliver He 272563 protein-coding gene of Clostridium difficile 630 A gene of Legionella pneumophila subsp. pneumophila str. Philadelphia 1 that has a protein-coding gene type Bin Zhao, Oliver He 272624 protein-coding gene of Legionella pneumophila subsp. pneumophila str. Philadelphia 1 A gene of Neisseria meningitidis FAM18 that has a protein-coding gene type Bin Zhao, Oliver He 272831 protein-coding gene of Neisseria meningitidis FAM18 A gene of Pasteurella multocida subsp. multocida str. Pm70 that has a protein-coding gene type Bin Zhao, Oliver He 272843 protein-coding gene of Pasteurella multocida subsp. multocida str. Pm70 A gene of Rickettsia prowazekii str. Madrid E that has a protein-coding gene type Bin Zhao, Oliver He 272947 protein-coding gene of Rickettsia prowazekii str. Madrid E A gene of Staphylococcus aureus RF122 that has a protein-coding gene type Bin Zhao, Oliver He 273036 protein-coding gene of Staphylococcus aureus RF122 A gene of Yersinia pseudotuberculosis IP 32953 that has a protein-coding gene type Bin Zhao, Oliver He 273123 protein-coding gene of Yersinia pseudotuberculosis IP 32953 A gene of Haemophilus influenzae 86-028NP that has a protein-coding gene type Bin Zhao, Oliver He 281310 protein-coding gene of Haemophilus influenzae 86-028NP A gene of Staphylococcus aureus subsp. aureus MRSA252 that has a protein-coding gene type Bin Zhao, Oliver He 282458 protein-coding gene of Staphylococcus aureus subsp. aureus MRSA252 A gene of Bartonella henselae str. Houston-1 that has a protein-coding gene type Bin Zhao, Oliver He 283166 protein-coding gene of Bartonella henselae str. Houston-1 A gene of Cryptococcus neoformans var. neoformans B-3501A that has a protein-coding gene type Bin Zhao, Oliver He 283643 protein-coding gene of Cryptococcus neoformans var. neoformans B-3501A A gene of Candida glabrata CBS 138 that has a protein-coding gene type Bin Zhao, Oliver He 284593 protein-coding gene of Candida glabrata CBS 138 A gene of Streptococcus pyogenes MGAS10394 that has a protein-coding gene type Bin Zhao, Oliver He 286636 protein-coding gene of Streptococcus pyogenes MGAS10394 A gene of Clostridium perfringens SM101 that has a protein-coding gene type Bin Zhao, Oliver He 289380 protein-coding gene of Clostridium perfringens SM101 A gene of Streptococcus pyogenes MGAS5005 that has a protein-coding gene type Bin Zhao, Oliver He 293653 protein-coding gene of Streptococcus pyogenes MGAS5005 A gene of Entamoeba histolytica HM-1:IMSS that has a protein-coding gene type Bin Zhao, Oliver He 294381 protein-coding gene of Entamoeba histolytica HM-1:IMSS A gene of Legionella pneumophila str. Lens that has a protein-coding gene type Bin Zhao, Oliver He 297245 protein-coding gene of Legionella pneumophila str. Lens A gene of Legionella pneumophila str. Paris that has a protein-coding gene type Bin Zhao, Oliver He 297246 protein-coding gene of Legionella pneumophila str. Paris A gene of Shigella dysenteriae Sd197 that has a protein-coding gene type Bin Zhao, Oliver He 300267 protein-coding gene of Shigella dysenteriae Sd197 A gene of Shigella boydii Sb227 that has a protein-coding gene type Bin Zhao, Oliver He 300268 protein-coding gene of Shigella boydii Sb227 A gene of Shigella sonnei Ss046 that has a protein-coding gene type Bin Zhao, Oliver He 300269 protein-coding gene of Shigella sonnei Ss046 A gene of Escherichia coli str. K-12 substr. DH10B that has a protein-coding gene type Bin Zhao, Oliver He 316385 protein-coding gene of Escherichia coli str. K-12 substr. DH10B A gene of Escherichia coli ETEC H10407 that has a protein-coding gene type Bin Zhao, Oliver He 316401 protein-coding gene of Escherichia coli ETEC H10407 A gene of Streptococcus pyogenes MGAS6180 that has a protein-coding gene type Bin Zhao, Oliver He 319701 protein-coding gene of Streptococcus pyogenes MGAS6180 A gene of Burkholderia pseudomallei 1710b that has a protein-coding gene type Bin Zhao, Oliver He 320372 protein-coding gene of Burkholderia pseudomallei 1710b A gene of Burkholderia pseudomallei 668 that has a protein-coding gene type Bin Zhao, Oliver He 320373 protein-coding gene of Burkholderia pseudomallei 668 A gene of Burkholderia mallei SAVP1 that has a protein-coding gene type Bin Zhao, Oliver He 320388 protein-coding gene of Burkholderia mallei SAVP1 A gene of Burkholderia mallei NCTC 10247 that has a protein-coding gene type Bin Zhao, Oliver He 320389 protein-coding gene of Burkholderia mallei NCTC 10247 A gene of Aspergillus fumigatus Af293 that has a protein-coding gene type Bin Zhao, Oliver He 330879 protein-coding gene of Aspergillus fumigatus Af293 A gene of Escherichia coli E24377A that has a protein-coding gene type Bin Zhao, Oliver He 331111 protein-coding gene of Escherichia coli E24377A A gene of Escherichia coli HS that has a protein-coding gene type Bin Zhao, Oliver He 331112 protein-coding gene of Escherichia coli HS A gene of Mycobacterium tuberculosis F11 that has a protein-coding gene type Bin Zhao, Oliver He 336982 protein-coding gene of Mycobacterium tuberculosis F11 A gene of Shigella boydii CDC 3083-94 that has a protein-coding gene type Bin Zhao, Oliver He 344609 protein-coding gene of Shigella boydii CDC 3083-94 A gene of Vibrio cholerae O395 that has a protein-coding gene type Bin Zhao, Oliver He 345073 protein-coding gene of Vibrio cholerae O395 A gene of Leishmania major strain Friedlin that has a protein-coding gene type Bin Zhao, Oliver He 347515 protein-coding gene of Leishmania major strain Friedlin A gene of Yersinia pestis Angola that has a protein-coding gene type Bin Zhao, Oliver He 349746 protein-coding gene of Yersinia pestis Angola A gene of Yersinia pseudotuberculosis IP 31758 that has a protein-coding gene type Bin Zhao, Oliver He 349747 protein-coding gene of Yersinia pseudotuberculosis IP 31758 A gene of Plasmodium yoelii yoelii 17XNL that has a protein-coding gene type Bin Zhao, Oliver He 352914 protein-coding gene of Plasmodium yoelii yoelii 17XNL A gene of Cryptosporidium parvum Iowa II that has a protein-coding gene type Bin Zhao, Oliver He 353152 protein-coding gene of Cryptosporidium parvum Iowa II A gene of Trypanosoma cruzi strain CL Brener that has a protein-coding gene type Bin Zhao, Oliver He 353153 protein-coding gene of Trypanosoma cruzi strain CL Brener A gene of Campylobacter jejuni subsp. jejuni 81-176 that has a protein-coding gene type Bin Zhao, Oliver He 354242 protein-coding gene of Campylobacter jejuni subsp. jejuni 81-176 A gene of Burkholderia pseudomallei 1106a that has a protein-coding gene type Bin Zhao, Oliver He 357348 protein-coding gene of Burkholderia pseudomallei 1106a A gene of Brucella melitensis biovar Abortus 2308 that has a protein-coding gene type Bin Zhao, Oliver He 359391 protein-coding gene of Brucella melitensis biovar Abortus 2308 A gene of Bartonella bacilliformis KC583 that has a protein-coding gene type Bin Zhao, Oliver He 360095 protein-coding gene of Bartonella bacilliformis KC583 A gene of Yersinia pestis Antiqua that has a protein-coding gene type Bin Zhao, Oliver He 360102 protein-coding gene of Yersinia pestis Antiqua A gene of Campylobacter jejuni subsp. doylei 269.97 that has a protein-coding gene type Bin Zhao, Oliver He 360109 protein-coding gene of Campylobacter jejuni subsp. doylei 269.97 A gene of Bordetella avium 197N that has a protein-coding gene type Bin Zhao, Oliver He 360910 protein-coding gene of Bordetella avium 197N A gene of Escherichia coli 536 that has a protein-coding gene type Bin Zhao, Oliver He 362663 protein-coding gene of Escherichia coli 536 A gene of Escherichia coli UTI89 that has a protein-coding gene type Bin Zhao, Oliver He 364106 protein-coding gene of Escherichia coli UTI89 A gene of Streptococcus pyogenes MGAS9429 that has a protein-coding gene type Bin Zhao, Oliver He 370551 protein-coding gene of Streptococcus pyogenes MGAS9429 A gene of Streptococcus pyogenes MGAS10270 that has a protein-coding gene type Bin Zhao, Oliver He 370552 protein-coding gene of Streptococcus pyogenes MGAS10270 A gene of Streptococcus pyogenes MGAS2096 that has a protein-coding gene type Bin Zhao, Oliver He 370553 protein-coding gene of Streptococcus pyogenes MGAS2096 A gene of Streptococcus pyogenes MGAS10750 that has a protein-coding gene type Bin Zhao, Oliver He 370554 protein-coding gene of Streptococcus pyogenes MGAS10750 A gene of Streptococcus pneumoniae D39 that has a protein-coding gene type Bin Zhao, Oliver He 373153 protein-coding gene of Streptococcus pneumoniae D39 A gene of Shigella flexneri 5 str. 8401 that has a protein-coding gene type Bin Zhao, Oliver He 373384 protein-coding gene of Shigella flexneri 5 str. 8401 A gene of Neisseria meningitidis 053442 that has a protein-coding gene type Bin Zhao, Oliver He 374833 protein-coding gene of Neisseria meningitidis 053442 A gene of Francisella tularensis subsp. holarctica LVS that has a protein-coding gene type Bin Zhao, Oliver He 376619 protein-coding gene of Francisella tularensis subsp. holarctica LVS A gene of Escherichia coli O26:H- that has a protein-coding gene type Bin Zhao, Oliver He 376724 protein-coding gene of Escherichia coli O26:H- A gene of Yersinia pestis Nepal516 that has a protein-coding gene type Bin Zhao, Oliver He 377628 protein-coding gene of Yersinia pestis Nepal516 A gene of Aeromonas salmonicida subsp. salmonicida A449 that has a protein-coding gene type Bin Zhao, Oliver He 382245 protein-coding gene of Aeromonas salmonicida subsp. salmonicida A449 A gene of Bartonella tribocorum CIP 105476 that has a protein-coding gene type Bin Zhao, Oliver He 382640 protein-coding gene of Bartonella tribocorum CIP 105476 A gene of Escherichia coli O157:H7 str. Sakai that has a protein-coding gene type Bin Zhao, Oliver He 386585 protein-coding gene of Escherichia coli O157:H7 str. Sakai A gene of Yersinia pestis Pestoides F that has a protein-coding gene type Bin Zhao, Oliver He 386656 protein-coding gene of Yersinia pestis Pestoides F A gene of Yersinia enterocolitica subsp. enterocolitica 8081 that has a protein-coding gene type Bin Zhao, Oliver He 393305 protein-coding gene of Yersinia enterocolitica subsp. enterocolitica 8081 A gene of Legionella pneumophila str. Corby that has a protein-coding gene type Bin Zhao, Oliver He 400673 protein-coding gene of Legionella pneumophila str. Corby A gene of Escherichia coli APEC O1 that has a protein-coding gene type Bin Zhao, Oliver He 405955 protein-coding gene of Escherichia coli APEC O1 A gene of Campylobacter jejuni subsp. jejuni 81116 that has a protein-coding gene type Bin Zhao, Oliver He 407148 protein-coding gene of Campylobacter jejuni subsp. jejuni 81116 A gene of Escherichia coli SE11 that has a protein-coding gene type Bin Zhao, Oliver He 409438 protein-coding gene of Escherichia coli SE11 A gene of Burkholderia mallei NCTC 10229 that has a protein-coding gene type Bin Zhao, Oliver He 412022 protein-coding gene of Burkholderia mallei NCTC 10229 A gene of Yersinia pestis CA88-4125 that has a protein-coding gene type Bin Zhao, Oliver He 412420 protein-coding gene of Yersinia pestis CA88-4125 A gene of Escherichia coli B str. REL606 that has a protein-coding gene type Bin Zhao, Oliver He 413997 protein-coding gene of Escherichia coli B str. REL606 A gene of Actinobacillus pleuropneumoniae serovar 5b str. L20 that has a protein-coding gene type Bin Zhao, Oliver He 416269 protein-coding gene of Actinobacillus pleuropneumoniae serovar 5b str. L20 A gene of Staphylococcus aureus subsp. aureus Mu3 that has a protein-coding gene type Bin Zhao, Oliver He 418127 protein-coding gene of Staphylococcus aureus subsp. aureus Mu3 A gene of Mycobacterium tuberculosis H37Ra that has a protein-coding gene type Bin Zhao, Oliver He 419947 protein-coding gene of Mycobacterium tuberculosis H37Ra A gene of Legionella pneumophila 2300/99 Alcoy that has a protein-coding gene type Bin Zhao, Oliver He 423212 protein-coding gene of Legionella pneumophila 2300/99 Alcoy A gene of Staphylococcus aureus subsp. aureus str. Newman that has a protein-coding gene type Bin Zhao, Oliver He 426430 protein-coding gene of Staphylococcus aureus subsp. aureus str. Newman A gene of Actinobacillus pleuropneumoniae serovar 3 str. JL03 that has a protein-coding gene type Bin Zhao, Oliver He 434271 protein-coding gene of Actinobacillus pleuropneumoniae serovar 3 str. JL03 A gene of Escherichia coli SMS-3-5 that has a protein-coding gene type Bin Zhao, Oliver He 439855 protein-coding gene of Escherichia coli SMS-3-5 A gene of Clostridium botulinum A str. ATCC 19397 that has a protein-coding gene type Bin Zhao, Oliver He 441770 protein-coding gene of Clostridium botulinum A str. ATCC 19397 A gene of Clostridium botulinum A str. Hall that has a protein-coding gene type Bin Zhao, Oliver He 441771 protein-coding gene of Clostridium botulinum A str. Hall A gene of Escherichia coli O157:H7 str. EC4115 that has a protein-coding gene type Bin Zhao, Oliver He 444450 protein-coding gene of Escherichia coli O157:H7 str. EC4115 A gene of Borrelia burgdorferi 156a that has a protein-coding gene type Bin Zhao, Oliver He 445983 protein-coding gene of Borrelia burgdorferi 156a A gene of Borrelia burgdorferi ZS7 that has a protein-coding gene type Bin Zhao, Oliver He 445985 protein-coding gene of Borrelia burgdorferi ZS7 A gene of Francisella tularensis subsp. holarctica FTNF002-00 that has a protein-coding gene type Bin Zhao, Oliver He 458234 protein-coding gene of Francisella tularensis subsp. holarctica FTNF002-00 A gene of Streptococcus pyogenes NZ131 that has a protein-coding gene type Bin Zhao, Oliver He 471876 protein-coding gene of Streptococcus pyogenes NZ131 A gene of Paenibacillus sp. Y412MC10 that has a protein-coding gene type Bin Zhao, Oliver He 481743 protein-coding gene of Paenibacillus sp. Y412MC10 A gene of Streptococcus pneumoniae Taiwan19F-14 that has a protein-coding gene type Bin Zhao, Oliver He 487213 protein-coding gene of Streptococcus pneumoniae Taiwan19F-14 A gene of Streptococcus pneumoniae Hungary19A-6 that has a protein-coding gene type Bin Zhao, Oliver He 487214 protein-coding gene of Streptococcus pneumoniae Hungary19A-6 A gene of Streptococcus pneumoniae 70585 that has a protein-coding gene type Bin Zhao, Oliver He 488221 protein-coding gene of Streptococcus pneumoniae 70585 A gene of Streptococcus pneumoniae JJA that has a protein-coding gene type Bin Zhao, Oliver He 488222 protein-coding gene of Streptococcus pneumoniae JJA A gene of Streptococcus pneumoniae P1031 that has a protein-coding gene type Bin Zhao, Oliver He 488223 protein-coding gene of Streptococcus pneumoniae P1031 A gene of Clostridium botulinum B1 str. Okra that has a protein-coding gene type Bin Zhao, Oliver He 498213 protein-coding gene of Clostridium botulinum B1 str. Okra A gene of Clostridium botulinum A3 str. Loch Maree that has a protein-coding gene type Bin Zhao, Oliver He 498214 protein-coding gene of Clostridium botulinum A3 str. Loch Maree A gene of Edwardsiella tarda EIB202 that has a protein-coding gene type Bin Zhao, Oliver He 498217 protein-coding gene of Edwardsiella tarda EIB202 A gene of Yersinia pseudotuberculosis YPIII that has a protein-coding gene type Bin Zhao, Oliver He 502800 protein-coding gene of Yersinia pseudotuberculosis YPIII A gene of Yersinia pseudotuberculosis PB1/+ that has a protein-coding gene type Bin Zhao, Oliver He 502801 protein-coding gene of Yersinia pseudotuberculosis PB1/+ A gene of Clostridium botulinum E3 str. Alaska E43 that has a protein-coding gene type Bin Zhao, Oliver He 508767 protein-coding gene of Clostridium botulinum E3 str. Alaska E43 A gene of Toxoplasma gondii ME49 that has a protein-coding gene type Bin Zhao, Oliver He 508771 protein-coding gene of Toxoplasma gondii ME49 A gene of Escherichia coli str. K-12 substr. MG1655 that has a protein-coding gene type Bin Zhao, Oliver He 511145 protein-coding gene of Escherichia coli str. K-12 substr. MG1655 A gene of Streptococcus pneumoniae G54 that has a protein-coding gene type Bin Zhao, Oliver He 512566 protein-coding gene of Streptococcus pneumoniae G54 A gene of Streptococcus pneumoniae CGSP14 that has a protein-coding gene type Bin Zhao, Oliver He 516950 protein-coding gene of Streptococcus pneumoniae CGSP14 A gene of Borrelia burgdorferi N40 that has a protein-coding gene type Bin Zhao, Oliver He 521007 protein-coding gene of Borrelia burgdorferi N40 A gene of Borrelia burgdorferi 297 that has a protein-coding gene type Bin Zhao, Oliver He 521009 protein-coding gene of Borrelia burgdorferi 297 A gene of Burkholderia pseudomallei MSHR346 that has a protein-coding gene type Bin Zhao, Oliver He 536230 protein-coding gene of Burkholderia pseudomallei MSHR346 A gene of Actinobacillus pleuropneumoniae serovar 7 str. AP76 that has a protein-coding gene type Bin Zhao, Oliver He 537457 protein-coding gene of Actinobacillus pleuropneumoniae serovar 7 str. AP76 A gene of Escherichia coli O157:H7 str. TW14359 that has a protein-coding gene type Bin Zhao, Oliver He 544404 protein-coding gene of Escherichia coli O157:H7 str. TW14359 A gene of Streptococcus equi subsp. zooepidemicus MGCS10565 that has a protein-coding gene type Bin Zhao, Oliver He 552526 protein-coding gene of Streptococcus equi subsp. zooepidemicus MGCS10565 A gene of Listeria monocytogenes HCC23 that has a protein-coding gene type Bin Zhao, Oliver He 552536 protein-coding gene of Listeria monocytogenes HCC23 A gene of Pseudomonas aeruginosa LESB58 that has a protein-coding gene type Bin Zhao, Oliver He 557722 protein-coding gene of Pseudomonas aeruginosa LESB58 A gene of Saccharomyces cerevisiae S288c that has a protein-coding gene type Bin Zhao, Oliver He 559292 protein-coding gene of Saccharomyces cerevisiae S288c A gene of Streptococcus pneumoniae ATCC 700669 that has a protein-coding gene type Bin Zhao, Oliver He 561276 protein-coding gene of Streptococcus pneumoniae ATCC 700669 A gene of Helicobacter pylori G27 that has a protein-coding gene type Bin Zhao, Oliver He 563041 protein-coding gene of Helicobacter pylori G27 A gene of Escherichia coli Vir68 that has a protein-coding gene type Bin Zhao, Oliver He 563770 protein-coding gene of Escherichia coli Vir68 A gene of Bacillus anthracis str. CDC 684 that has a protein-coding gene type Bin Zhao, Oliver He 568206 protein-coding gene of Bacillus anthracis str. CDC 684 A gene of Listeria monocytogenes serotype 4b str. CLIP 80459 that has a protein-coding gene type Bin Zhao, Oliver He 568819 protein-coding gene of Listeria monocytogenes serotype 4b str. CLIP 80459 A gene of Helicobacter pylori P12 that has a protein-coding gene type Bin Zhao, Oliver He 570508 protein-coding gene of Helicobacter pylori P12 A gene of Escherichia coli O26:H11 str. 11368 that has a protein-coding gene type Bin Zhao, Oliver He 573235 protein-coding gene of Escherichia coli O26:H11 str. 11368 A gene of Escherichia coli O127:H6 str. E2348/69 that has a protein-coding gene type Bin Zhao, Oliver He 574521 protein-coding gene of Escherichia coli O127:H6 str. E2348/69 A gene of Vibrio cholerae M66-2 that has a protein-coding gene type Bin Zhao, Oliver He 579112 protein-coding gene of Vibrio cholerae M66-2 A gene of Escherichia coli IAI1 that has a protein-coding gene type Bin Zhao, Oliver He 585034 protein-coding gene of Escherichia coli IAI1 A gene of Escherichia coli S88 that has a protein-coding gene type Bin Zhao, Oliver He 585035 protein-coding gene of Escherichia coli S88 A gene of Escherichia coli 55989 that has a protein-coding gene type Bin Zhao, Oliver He 585055 protein-coding gene of Escherichia coli 55989 A gene of Escherichia coli UMN026 that has a protein-coding gene type Bin Zhao, Oliver He 585056 protein-coding gene of Escherichia coli UMN026 A gene of Escherichia coli IAI39 that has a protein-coding gene type Bin Zhao, Oliver He 585057 protein-coding gene of Escherichia coli IAI39 A gene of Escherichia coli O103:H2 str. 12009 that has a protein-coding gene type Bin Zhao, Oliver He 585395 protein-coding gene of Escherichia coli O103:H2 str. 12009 A gene of Escherichia coli O111:H- str. 11128 that has a protein-coding gene type Bin Zhao, Oliver He 585396 protein-coding gene of Escherichia coli O111:H- str. 11128 A gene of Escherichia coli ED1a that has a protein-coding gene type Bin Zhao, Oliver He 585397 protein-coding gene of Escherichia coli ED1a A gene of Bacillus anthracis str. A0248 that has a protein-coding gene type Bin Zhao, Oliver He 592021 protein-coding gene of Bacillus anthracis str. A0248 A gene of Helicobacter pylori B38 that has a protein-coding gene type Bin Zhao, Oliver He 592205 protein-coding gene of Helicobacter pylori B38 A gene of Escherichia coli BW2952 that has a protein-coding gene type Bin Zhao, Oliver He 595496 protein-coding gene of Escherichia coli BW2952 A gene of Listeria monocytogenes 08-5923 that has a protein-coding gene type Bin Zhao, Oliver He 637381 protein-coding gene of Listeria monocytogenes 08-5923 A gene of Listeria monocytogenes 08-5578 that has a protein-coding gene type Bin Zhao, Oliver He 653938 protein-coding gene of Listeria monocytogenes 08-5578 A gene of Neisseria meningitidis alpha14 that has a protein-coding gene type Bin Zhao, Oliver He 662598 protein-coding gene of Neisseria meningitidis alpha14 A gene of Staphylococcus aureus subsp. aureus ED98 that has a protein-coding gene type Bin Zhao, Oliver He 681288 protein-coding gene of Staphylococcus aureus subsp. aureus ED98 A gene of Mycoplasma gallisepticum str. R(low) that has a protein-coding gene type Bin Zhao, Oliver He 710127 protein-coding gene of Mycoplasma gallisepticum str. R(low) A gene of Feline infectious peritonitis virus that has a pseudo gene type Bin Zhao, Oliver He 11135 pseudo gene of Feline infectious peritonitis virus A gene of Haemophilus influenzae Rd KW20 that has a pseudo gene type Bin Zhao, Oliver He 71421 pseudo gene of Haemophilus influenzae Rd KW20 A gene of Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 that has a pseudo gene type Bin Zhao, Oliver He 99287 pseudo gene of Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 A gene of Streptococcus pneumoniae TIGR4 that has a pseudo gene type Bin Zhao, Oliver He 170187 pseudo gene of Streptococcus pneumoniae TIGR4 A gene of Francisella tularensis subsp. tularensis SCHU S4 that has a pseudo gene type Bin Zhao, Oliver He 177416 pseudo gene of Francisella tularensis subsp. tularensis SCHU S4 A gene of Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 that has a pseudo gene type Bin Zhao, Oliver He 192222 pseudo gene of Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 A gene of Brucella suis 1330 that has a pseudo gene type Bin Zhao, Oliver He 204722 pseudo gene of Brucella suis 1330 A gene of Vibrio cholerae O1 biovar El Tor str. N16961 that has a pseudo gene type Bin Zhao, Oliver He 243277 pseudo gene of Vibrio cholerae O1 biovar El Tor str. N16961 A gene of Listeria monocytogenes serotype 4b str. F2365 that has a pseudo gene type Bin Zhao, Oliver He 265669 pseudo gene of Listeria monocytogenes serotype 4b str. F2365 A gene of Clostridium difficile 630 that has a pseudo gene type Bin Zhao, Oliver He 272563 pseudo gene of Clostridium difficile 630 A gene of Brucella melitensis biovar Abortus 2308 that has a pseudo gene type Bin Zhao, Oliver He 359391 pseudo gene of Brucella melitensis biovar Abortus 2308 A gene of Neisseria meningitidis 053442 that has a pseudo gene type Bin Zhao, Oliver He 374833 pseudo gene of Neisseria meningitidis 053442 A gene of Francisella tularensis subsp. holarctica LVS that has a pseudo gene type Bin Zhao, Oliver He 376619 pseudo gene of Francisella tularensis subsp. holarctica LVS A gene of Aeromonas salmonicida subsp. salmonicida A449 that has a pseudo gene type Bin Zhao, Oliver He 382245 pseudo gene of Aeromonas salmonicida subsp. salmonicida A449 A gene of Escherichia coli IAI39 that has a pseudo gene type Bin Zhao, Oliver He 585057 pseudo gene of Escherichia coli IAI39 A gene of Yersinia pestis CO92 that has a miscRNA gene type Bin Zhao, Oliver He 214092 miscRNA gene of Yersinia pestis CO92 A gene of Yersinia pestis biovar Microtus str. 91001 that has a miscRNA gene type Bin Zhao, Oliver He 229193 miscRNA gene of Yersinia pestis biovar Microtus str. 91001 A gene of Yersinia pestis Angola that has a miscRNA gene type Bin Zhao, Oliver He 349746 miscRNA gene of Yersinia pestis Angola A gene of Yersinia pestis Antiqua that has a miscRNA gene type Bin Zhao, Oliver He 360102 miscRNA gene of Yersinia pestis Antiqua A gene of Yersinia pestis Nepal516 that has a miscRNA gene type Bin Zhao, Oliver He 377628 miscRNA gene of Yersinia pestis Nepal516 A gene of Yersinia pestis Pestoides F that has a miscRNA gene type Bin Zhao, Oliver He 386656 miscRNA gene of Yersinia pestis Pestoides F A gene of Francisella tularensis subsp. tularensis SCHU S4 that has a RNA gene type Bin Zhao, Oliver He 177416 RNA gene of Francisella tularensis subsp. tularensis SCHU S4 A gene of Yersinia pestis CO92 that has a RNA gene type Bin Zhao, Oliver He 214092 RNA gene of Yersinia pestis CO92 A gene of Yersinia pestis biovar Microtus str. 91001 that has a RNA gene type Bin Zhao, Oliver He 229193 RNA gene of Yersinia pestis biovar Microtus str. 91001 A gene of Yersinia pestis Angola that has a RNA gene type Bin Zhao, Oliver He 349746 RNA gene of Yersinia pestis Angola A gene of Yersinia pestis Antiqua that has a RNA gene type Bin Zhao, Oliver He 360102 RNA gene of Yersinia pestis Antiqua A gene of Francisella tularensis subsp. holarctica LVS that has a RNA gene type Bin Zhao, Oliver He 376619 RNA gene of Francisella tularensis subsp. holarctica LVS A gene of Yersinia pestis Nepal516 that has a RNA gene type Bin Zhao, Oliver He 377628 RNA gene of Yersinia pestis Nepal516 A gene of Yersinia pestis Pestoides F that has a RNA gene type Bin Zhao, Oliver He 386656 RNA gene of Yersinia pestis Pestoides F A gene of Haemophilus influenzae Rd KW20 that has a other gene type Bin Zhao, Oliver He 71421 gene of Haemophilus influenzae Rd KW20 with other gene type A gene of Brucella suis 1330 that has a other gene type Bin Zhao, Oliver He 204722 gene of Brucella suis 1330 with other gene type A gene of Plasmodium yoelii yoelii 17XNL that has a other gene type Bin Zhao, Oliver He 352914 gene of Plasmodium yoelii yoelii 17XNL with other gene type Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 155459 HIV1gp3 20140406 11676 protein-coding NCBI-supplied PMID: 2059206; 7884893; 8523563; 8626571; 8924209; 9188594; 9362478; 9792705; 9811770; 9846577; 10074203; 10613270; 11158303; 11172097; 11278465; 11406603; 11780123; 12167863; 12368356; 12600646; 12719574; 12750511; 12808465; 12808466; 12809610; 12830140; 12840737; 12859895; 12914693; 12920286; 12970355; 14527406; 14528300; 14528301; 14557625; 14564014; 14614829; 14672928; 14722068; 14747572; 14966139; 14978281; 14999100; 15013426; 15054139; 15080177; 15116720; 15139295; 15141007; 15152192; 15156567; 15168739; 15177194; 15183343; 15245742; 15296757; 15296758; 15353294; 15367624; 15373943; 15383144; 15537645; 15574592; 15574593; 15578976; 15602725; 15611076; 15638724; 15781449; 15809227; 15989462; 16014920; 16035254; 16046164; 16146763; 16250885; 16303161; 16354571; 16414984; 16418394; 16460778; 16492778; 16501124; 16530799; 16580072; 16631224; 16636053; 16641889; 16678488; 16699599; 16731937; 16822376; 16920826; 16940537; 17020885; 17023652; 17038330; 17049578; 17067930; 17083721; 17121840; 17126871; 17135358; 17267497; 17272283; 17285170; 17303427; 17331040; 17338854; 17522211; 17522216; 17586316; 17598142; 17609216; 17660191; 17727729; 17824250; 17825339; 17869271; 17898068; 17916373; 17928335; 17967058; 17977970; 18023836; 18036235; 18082865; 18184715; 18187620; 18262674; 18272582; 18272764; 18299330; 18304004; 18326044; 18338854; 18366335; 18391217; 18414671; 18414697; 18419775; 18448538; 18495196; 18499212; 18501607; 18541215; 18562529; 18577210; 18596088; 18603011; 18604271; 18619467; 18639915; 18675436; 18680593; 18789977; 18806783; 18809921; 18819469; 18827027; 18836454; 18842592; 18846074; 18945781; 18971252; 18976462; 18976920; 18987139; 19004939; 19004943; 19008196; 19020832; 19036809; 19038776; 19050398; 19056509; 19057663; 19088851; 19105849; 19109396; 19128510; 19149577; 19149995; 19211937; 19216784; 19218568; 19297501; 19304304; 19324886; 19344514; 19357165; 19401538; 19487726; 19535447; 19535450; 19581596; 19588889; 19649317; 19669862; 19694548; 19717177; 19776130; 19826902; 19828612; 19837465; 19841153; 19887642; 19910370; 19923175; 19939923; 19944180; 20012521; 20015971; 20018238; 20096141; 20126615; 20147392; 20174454; 20219919; 20220118; 20299747; 20335268; 20363737; 20450485; 20463065; 20463080; 20519393; 20519396; 20532212; 20538015; 20571604; 20592083; 20610708; 20624919; 20638642; 20642434; 20686027; 20728451; 20809132; 20833716; 20844042; 20926562; 20939174; 20943965; 20971849; 21071676; 21084468; 21147461; 21147467; 21149631; 21152581; 21167246; 21182427; 21228271; 21239176; 21270145; 21279453; 21345952; 21370050; 21393191; 21480314; 21489586; 21569376; 21571098; 21734563; 21741003; 21752914; 21763503; 21763507; 21835787; 21874023; 21934670; 21994560; 22013041; 22017399; 22023594; 22190034; 22190036; 22190037; 22203821; 22205746; 22218868; 22286874; 22346743; 22347227; 22369580; 22379088; 22451677; 22479405; 22509177; 22553496; 22555953; 22590503; 22720156; 22725134; 22728817; 22767258; 22787460; 22807680; 22855686; 22894923; 22970171; 23001005; 23080486; 23098073; 23175372; 23316055; 23417613; 23469063; 23576497; 23689841; 23707381; 23988114; 24225024; 24402281; 24422669 MUTATION: A mutation in the vif gene reduces viral replication and infectivity in nonpermissive cells [PMID:15989462]. 1918 p23 Other designations: Vif vif Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 155807 HIV1gp4 20140406 11676 protein-coding NCBI-supplied PMID: 7474080; 7474100; 7494303; 7592727; 7666531; 7724608; 8195203; 8551605; 8800208; 9013886; 9094673; 9151883; 9188632; 9199338; 9261351; 9334723; 9362478; 9371639; 9436978; 9449720; 9463369; 9520381; 9525626; 9525900; 9560267; 9582382; 9621063; 9636371; 9685344; 9817747; 9846873; 9874563; 9882380; 10359081; 10438581; 10561576; 10620603; 10708425; 10713718; 10772949; 10775602; 10888643; 10888660; 10931842; 10933727; 10958988; 10964507; 10985253; 11000244; 11024150; 11087358; 11152524; 11175251; 11181702; 11193032; 11196199; 11223251; 11259200; 11426943; 11437653; 11531413; 11689055; 11691994; 11878934; 11935461; 12079361; 12084067; 12095993; 12096338; 12208951; 12228227; 12237292; 12359436; 12379213; 12404120; 12444143; 12457980; 12504543; 12510154; 12525641; 12525642; 12573582; 12634356; 12639957; 12642036; 12738771; 12750393; 12750404; 12788643; 12805458; 12853482; 12881522; 12881523; 14506268; 14751250; 14767062; 14972559; 15063744; 15096517; 15142377; 15142379; 15142380; 15142381; 15142382; 15166037; 15254189; 15265780; 15294897; 15302882; 15331702; 15353294; 15380361; 15449141; 15485898; 15578586; 15578977; 15611322; 15616007; 15638722; 15650754; 15659641; 15708996; 15725353; 15731250; 15780175; 15817944; 15832179; 15956545; 16103149; 16103171; 16103188; 16120388; 16243842; 16305395; 16306615; 16337983; 16338743; 16354571; 16429131; 16480911; 16492162; 16492778; 16511342; 16520893; 16571786; 16877301; 16923959; 16950655; 16956949; 16968670; 16969134; 16983346; 17020411; 17023015; 17090531; 17140287; 17172832; 17176760; 17210576; 17254575; 17304248; 17314515; 17328670; 17331040; 17344301; 17347016; 17349711; 17360488; 17409234; 17433108; 17475642; 17553868; 17553871; 17559673; 17560997; 17586316; 17586317; 17609381; 17620334; 17622316; 17626091; 17630831; 17652391; 17824250; 17855541; 17932108; 17967742; 18039376; 18060429; 18061232; 18082865; 18094160; 18160429; 18187620; 18220834; 18275585; 18295813; 18385244; 18414671; 18414697; 18417583; 18434400; 18445273; 18514189; 18524771; 18541215; 18577246; 18606781; 18614999; 18638397; 18829761; 18987145; 19013323; 19020832; 19149577; 19160543; 19204000; 19254034; 19275579; 19275580; 19275582; 19275583; 19275584; 19275585; 19275586; 19275587; 19275588; 19328187; 19338763; 19344781; 19458171; 19516896; 19559726; 19581932; 19625402; 19629466; 19655254; 19657269; 19667756; 19674438; 19692467; 19696076; 19726511; 19798433; 19803398; 19838296; 19883084; 19895210; 19925402; 20008788; 20012529; 20015032; 20018238; 20069611; 20089662; 20097875; 20145198; 20347598; 20380698; 20380700; 20392842; 20404718; 20446002; 20529298; 20558198; 20609246; 20614012; 20628092; 20628645; 20685659; 20719241; 20801175; 20824083; 20870715; 20877724; 20920334; 21072166; 21084468; 21318276; 21411754; 21489275; 21519849; 21526938; 21566118; 21645334; 21651489; 21704113; 21763498; 21816823; 21827382; 21874023; 21875947; 21918813; 21934670; 21957298; 21994772; 22023789; 22077140; 22094081; 22110766; 22171270; 22185200; 22190034; 22190037; 22274659; 22292079; 22403404; 22422068; 22438978; 22457629; 22509482; 22552851; 22590503; 22720156; 22727020; 22776683; 22832123; 23001849; 23017337; 23255807; 23453579; 23467037; 23612978; 23726848; 23842279; 23849790; 23874603; 24045107; 24116224; 24178031 MUTATION: T cell infections using vesicular stomatitis virus G (VSV-G) pseudotyped HIV-1 Vpr R77Q result in less (P = 0.01) T cell death than infections using wild-type Vpr, despite similar levels of viral replication. Wild-type Vpr-associated events, including procaspase-8 and -3 cleavage, loss of mitochondrial transmembrane potential (deltapsi(m)), and DNA fragmentation factor activation are attenuated by R77Q Vpr. There is also a higher frequency of R77Q Vpr mutations in patients with LTNP than in patients with progressive disease [PMID:12750404]. 1919 p15 Other designations: Vpr vpr Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 156110 HIV1gp9 20140406 11676 protein-coding NCBI-supplied PMID: 1527859; 1565858; 2014052; 2052609; 3118220; 7540194; 7588629; 7769669; 7797518; 7831289; 7853525; 7859737; 7871751; 7884893; 7902127; 7903128; 7912927; 7975260; 7982906; 7983750; 8035515; 8057354; 8086129; 8102828; 8108442; 8124721; 8151774; 8151786; 8178481; 8262036; 8331733; 8437228; 8480425; 8516299; 8598486; 8599214; 8599229; 8599760; 8612235; 8626429; 8636073; 8663223; 8681387; 8709227; 8709241; 8709288; 8765022; 8769094; 8794306; 8862424; 8871625; 8939608; 8994833; 9017839; 9032396; 9049297; 9049329; 9052838; 9070423; 9075929; 9096366; 9108086; 9110068; 9123874; 9139671; 9153233; 9168885; 9218412; 9247029; 9288906; 9299485; 9314527; 9344905; 9351809; 9362478; 9371615; 9384576; 9453574; 9473011; 9490697; 9564030; 9582271; 9586638; 9617893; 9620685; 9624170; 9656992; 9705913; 9736718; 9778343; 9792838; 9811606; 9811611; 9920849; 9923610; 9971776; 10074203; 10196292; 10199403; 10208934; 10224289; 10339411; 10364375; 10366557; 10366564; 10375525; 10375528; 10388525; 10388555; 10393966; 10394361; 10403641; 10415019; 10417813; 10451539; 10470075; 10544125; 10547288; 10559302; 10574946; 10597774; 10607567; 10618429; 10636480; 10642173; 10684310; 10707087; 10713183; 10748182; 10753665; 10799608; 10807905; 10814565; 10906142; 10982373; 10985305; 11000208; 11006130; 11023665; 11070003; 11122241; 11123279; 11137132; 11153078; 11160719; 11177389; 11180285; 11208076; 11222731; 11251883; 11264384; 11264386; 11285224; 11289809; 11298321; 11298454; 11312657; 11323689; 11328823; 11331585; 11396948; 11420046; 11438519; 11448168; 11463741; 11500821; 11519482; 11525746; 11533201; 11578695; 11581379; 11593029; 11602047; 11602785; 11675348; 11689886; 11726657; 11810028; 11825573; 11847276; 11861836; 11884542; 11922627; 11932428; 11956293; 11958689; 11969293; 11976726; 12009866; 12032142; 12033791; 12058068; 12076760; 12097566; 12241561; 12270545; 12354773; 12359436; 12370346; 12396456; 12414752; 12414957; 12419805; 12482663; 12486136; 12502873; 12504564; 12525647; 12526811; 12574335; 12584329; 12682255; 12734410; 12746459; 12767938; 12788643; 12810958; 12816953; 12824470; 12836198; 12842621; 12853962; 12855553; 12884192; 12884293; 12960275; 12970439; 13679604; 14531802; 14557639; 14597672; 14617802; 14670336; 14691137; 14694087; 14737186; 14747534; 14759364; 14965316; 14990729; 15033985; 15047825; 15075535; 15078178; 15137387; 15140972; 15163745; 15166428; 15166429; 15186530; 15194762; 15202998; 15258149; 15262497; 15343382; 15371598; 15452229; 15459189; 15491611; 15494497; 15518810; 15556689; 15569681; 15569716; 15576488; 15595833; 15596859; 15611114; 15611225; 15613341; 15626739; 15629779; 15632291; 15637102; 15638726; 15653685; 15681409; 15722538; 15767427; 15827086; 15847608; 15854903; 15858021; 15878340; 15892963; 15916790; 15928037; 15942894; 15956605; 15976924; 16000390; 16014965; 16021629; 16043695; 16091223; 16103193; 16116206; 16177101; 16177107; 16179353; 16237100; 16253302; 16260903; 16272310; 16282498; 16310238; 16354571; 16356860; 16365153; 16374509; 16385629; 16429138; 16439540; 16445909; 16454711; 16475823; 16476977; 16501114; 16515720; 16684552; 16687395; 16730880; 16764724; 16775006; 16777597; 16847125; 16849330; 16857988; 16873261; 16877303; 16912329; 16916529; 16921384; 16928758; 16978607; 16979207; 16987968; 16988698; 17042973; 17046994; 17076584; 17077296; 17083721; 17086054; 17116886; 17140399; 17170457; 17182689; 17209762; 17261081; 17266559; 17267500; 17314161; 17329339; 17331028; 17346169; 17411376; 17411382; 17412836; 17431094; 17443671; 17547741; 17581864; 17586321; 17600593; 17630924; 17632197; 17632570; 17634131; 17652391; 17670831; 17707624; 17824250; 17878955; 17881449; 17893228; 17904606; 17920628; 17928336; 17947540; 17967742; 18003888; 18005680; 18005690; 18030346; 18032517; 18042718; 18057255; 18073204; 18089753; 18094167; 18155264; 18178851; 18187620; 18220834; 18234668; 18296443; 18322217; 18336259; 18337699; 18438604; 18443354; 18462992; 18473783; 18489774; 18523251; 18524831; 18539368; 18541215; 18555888; 18596106; 18621011; 18653452; 18707241; 18715908; 18725938; 18799583; 18808677; 18826950; 18854243; 18987145; 18991615; 19013323; 19050260; 19081837; 19091857; 19102781; 19129443; 19130504; 19146681; 19149577; 19150430; 19254361; 19263804; 19269660; 19324886; 19327048; 19403684; 19439470; 19449444; 19455469; 19540523; 19555986; 19585521; 19605470; 19615357; 19620308; 19635843; 19641037; 19643141; 19651874; 19683683; 19726522; 19748111; 19759518; 19770068; 19781555; 19807124; 19847956; 19859083; 19878567; 19895210; 19912576; 19917496; 19935658; 20012528; 20015995; 20020046; 20056088; 20068037; 20126615; 20147394; 20156100; 20179761; 20299515; 20367240; 20377428; 20380698; 20392440; 20444900; 20463068; 20465832; 20479131; 20488787; 20504918; 20530791; 20535218; 20566577; 20594957; 20598119; 20622010; 20638642; 20659345; 20667578; 20702582; 20731376; 20739067; 20810664; 20826747; 20881088; 20942936; 21044805; 21068258; 21093412; 21165790; 21176845; 21179446; 21209113; 21255447; 21292773; 21336563; 21347424; 21365684; 21394196; 21449607; 21459854; 21464919; 21477083; 21482738; 21504576; 21543478; 21555514; 21567396; 21606541; 21625496; 21642447; 21653836; 21668366; 21696586; 21738584; 21762823; 21763498; 21814282; 21819585; 21824805; 21845735; 21849975; 21858117; 21861776; 21886773; 21892329; 21896007; 21917951; 21922073; 21923909; 21970979; 21994772; 22013042; 22013062; 22066947; 22103831; 22103832; 22103833; 22103834; 22103836; 22103837; 22103838; 22110726; 22123847; 22171785; 22174682; 22175768; 22190034; 22190037; 22262807; 22291690; 22301137; 22301152; 22323535; 22345473; 22345475; 22393415; 22395607; 22407921; 22422068; 22479639; 22496420; 22534017; 22537596; 22553319; 22583022; 22613796; 22640559; 22643973; 22651890; 22655069; 22672539; 22705789; 22721673; 22767237; 22802418; 22808111; 22826228; 22844345; 22980332; 22980333; 23067370; 23071112; 23093676; 23151229; 23170180; 23185362; 23284715; 23417613; 23490051; 23678182; 23746211; 23799149; 23855121; 23899341; 24051604; 24489825 MUTATION: HIV-1 replication in vivo can be separated from its pathogenic activity, in that the HXB/LW virus replicated to high levels in SCID-hu Thy/Liv mice, with no significant thymocyte depletion. Restoration of the nef gene in the recombinant HXB/LW genome restored its pathogenic activity, with no significant effect on HIV-1 replication in the thymus. Implicating nef as a determinant of pathogenicity [PMID:11264380]. 1920 p27 Other designations: Nef nef Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 811213 PFL0800c 20120919 36329 12 protein-coding NCBI-supplied PMID: 12368864 MUTATION: CelTOS mutant has reduced infectivity in rat liver and almost abolished its cell-passage ability [PMID:16468982]. 1979 CelTOS, putative CelTOS Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 812450 PFD0210c 20140406 36329 4 protein-coding NCBI-supplied PMID: 12368867; 16267556 MUTATION: pbs36 had arrested intracellular growth in liver HC-04 cells [PMID:19625622]. 1978 pbs36 homologue PFD0210c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 812616 PFB0100c 20140406 36329 2 protein-coding NCBI-supplied PMID: 9804551; 12368864; 16006556; 16267556; 16507777; 21594767; 21696460; 24090929 MUTATION: KAHRP mutant has reduced adherence to CD36 when tested under flow conditions that mimic those of postcapillary venules [PMID:9108483]. 1977 knob-associated histidine-rich protein PFB0100c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 814166 PF13_0197 20140406 36329 13 protein-coding NCBI-supplied GO_0016020 (EC: TAS, PMID: 11551634); GO_0030260 (EC: TAS, PMID: 11551634) PMID: 11551634; 16267556; 16940297; 17944453; 20472690; 23049905 MUTATION: msp7 mutant is attenuated for invasion of erythrocytes compared to the wild type [PMID:18820076]. 2018 Merozoite Surface Protein 7 precursor, MSP7 MSP7 Bin Zhao, Oliver He SSP-2 SSP2 WEB: http://www.ncbi.nlm.nih.gov/gene 814170 PF13_0201 20140222 36329 13 protein-coding NCBI-supplied MUTATION: TRAP mutant is attenuated for sporozoite infection of rat liver [PMID:9267031]. 2017 Thrombospondin-related anonymous protein, TRAP - TRAP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 850342 YCL018W 20140406 559292 III protein-coding NCBI-supplied GO_0000287 (EC: IEA); GO_0003862 (EC: IDA, PMID: 3071718); GO_0003862 (EC: IEA); GO_0003862 (EC: IMP, PMID: 6297759); GO_0005737 (EC: IEA); GO_0005829 (EC: IDA, PMID: 4355481); GO_0006097 (EC: IMP); GO_0008652 (EC: IEA); GO_0009082 (EC: IEA); GO_0009098 (EC: IEA); GO_0009098 (EC: IMP, PMID: 6297759); GO_0016491 (EC: IEA); GO_0016616 (EC: IEA); GO_0046872 (EC: IEA); GO_0051287 (EC: IEA); GO_0055114 (EC: IEA) PMID: 1574125; 3071718; 4355481; 6297759; 8849441; 10409731; 11788966; 15292183; 16319894; 18071269; 18087042; 19270382; 21427232; 21441928; 21526172; 21825077; 21919885; 21926174; 23050233 MUTATION: leu2 mutant is attenuated in mice [PMID:11606528]. 4821 3-isopropylmalate dehydrogenase LEU2 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 854295 YOR128C 20140406 559292 XV protein-coding NCBI-supplied GO_0000166 (EC: IEA); GO_0003824 (EC: IEA); GO_0004638 (EC: IEA); GO_0004638 (EC: IMP, PMID: 5767024); GO_0005524 (EC: IEA); GO_0005737 (EC: IDA, PMID: 14562095); GO_0006144 (EC: IMP, PMID: 8939809); GO_0006164 (EC: IC, PMID: 5767024); GO_0006164 (EC: IEA); GO_0006189 (EC: IC, PMID: 5767024); GO_0006189 (EC: IEA); GO_0016829 (EC: IEA); GO_0016831 (EC: IEA); GO_0034023 (EC: IEA); GO_0046872 (EC: IEA) PMID: 5767024; 8849441; 8939809; 9169874; 9589850; 10688190; 10822807; 11283351; 14562095; 16554755; 16630557; 17720931; 17923092; 18087042; 18245832; 18762987; 19160453; 19840948; 20093466; 20170199; 21552543; 21623372; 22140548; 23209445; 23222640; 23793018; 23831759 MUTATION: ade2 mutant is attenuated in mice [PMID:11606528]. 4818 phosphoribosylaminoimidazole carboxylase ADE2 ADE2 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 854508 YOR330C 20140406 559292 XV protein-coding NCBI-supplied GO_0003676 (EC: IEA); GO_0003677 (EC: IEA); GO_0003887 (EC: IDA); GO_0003887 (EC: IEA); GO_0005739 (EC: IDA, PMID: 14576278); GO_0005739 (EC: IEA); GO_0005760 (EC: IEA); GO_0006260 (EC: IEA); GO_0006261 (EC: IEA); GO_0006264 (EC: IDA, PMID: 12023279); GO_0006264 (EC: IMP, PMID: 2684980); GO_0008408 (EC: IDA); GO_0016740 (EC: IEA); GO_0016779 (EC: IEA) PMID: 2684980; 8552025; 8849441; 9169874; 9774971; 12023279; 14576278; 15351639; 16487579; 16940310; 17314980; 17720904; 17980715; 18676811; 19547744; 20185557; 20601675; 21987634; 22114710; 22199229; 22470557; 23589460 MUTATION: mip1 mutant is attenuated in mice [PMID:11606528]. 4822 Mip1p MIP1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 856692 YEL021W 20140406 559292 V protein-coding NCBI-supplied GO_0003824 (EC: IEA); GO_0004590 (EC: IDA, PMID: 2061334); GO_0004590 (EC: IEA); GO_0004590 (EC: IMP, PMID: 4550660); GO_0005829 (EC: IDA, PMID: 18812321); GO_0006207 (EC: IEA); GO_0006207 (EC: IMP, PMID: 4550660); GO_0006221 (EC: IEA); GO_0006222 (EC: IDA, PMID: 2061334); GO_0006222 (EC: IMP, PMID: 5651325); GO_0008152 (EC: IEA); GO_0016829 (EC: IEA); GO_0016831 (EC: IEA); GO_0044205 (EC: IEA) PMID: 2061334; 4550660; 5651325; 8849441; 9169868; 9829833; 10207060; 10688190; 11805837; 12684846; 12872131; 15455074; 16554755; 18186026; 18812321; 19435314; 19618917; 19840948; 23276261; 23749301; 23793018 MUTATION: ura3 mutant is attenuated in mice [PMID:11606528]. 4823 orotidine-5'-phosphate decarboxylase URA3 MUTATION: mxiC mutant has a 10-fold decrease in efficiency in invading epithelial cells [PMID:19017268]. 24 MUTATION: virF knockouts are non-invasive to host cells [PMID:20237205]. 25 MUTATION: spa47 mutants form needle-less type III structure which is defective, and thus incapable of invasion of host cells [PMID:10921870]. 26 MUTATION: spa15 mutant was attenuated in entry into epithelial cells compared to the wild-type [PMID:11952903]. 27 MUTATION: transposon mutants of ipgA cannot invade epithelial cells and cannot induce keratoconjunctivitis in mice [PMID:8376337]. 28 MUTATION: ipaD mutants are completely unable to invade cultured cells or lyse RBCs [PMID:15731041] . 29 MUTATION: ipgC mutant attenuated in infecting Caco-2 cells monolayer [PMID:11207551]. 30 MUTATION: ipaC mutants cannot invade cultured cells or lyse red blood cells [PMID:18656530]. 31 MUTATION: ipaB mutant is unable to infect HeLa cells [PMID:20086081]. 32 MUTATION: spa33 mutants are unable to secrete effectors necessary to cell invasion [PMID:16246841]. 33 MUTATION: virA mutants did not move within the host cytoplasm and failed to move into adjacent cells [PMID:17095701]. 34 MUTATION: virG mutants are able to replicate in cells, but cell to cell spread is attenuated in monkey kidney epithelial cells [PMID:2644195]. 35 MUTATION: transposon mutants of ipgB cannot invade epithelial cells and cannot induce keratoconjunctivitis in mice [PMID:8376337]. 36 MUTATION: ipgD mutant is unable to dephosphorylate phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P2] and induces shorter filapodia in host cells [PMID:12356723]. 37 MUTATION: mxiG mutant was unable to enter HeLa cells and to provoke keratoconjunctivitis in guinea-pigs [PMID:8559065]. 38 MUTATION: spa32 mutants are unable to invade HeLa cells and do not secrete type III effectors [PMID:11844752]. 39 MUTATION: mxiI mutant is unable to invade HeLa cells [PMID:11169106]. 40 MUTATION: mxiM mutants are phenotypically avirulent, and also unable to invade semiconfluent L2 cell monolayers [PMID:10085046]. 41 MUTATION: mxiJ mutant was unable to invade HeLa cells, to induce the formation of plaques on confluent monolayers of HeLa cells, and to provoke keratoconjunctivitis in guinea pigs [PMID:1332940]. 42 MUTATION: mxiD mutant is unable to invade HeLa cells or to provoke keratoconjunctivitis in guinea-pigs [PMID:8437520]. 43 MUTATION: mxiE deletion mutants are unable to block apoptosis of host epithelial cells [PMID:17339354]. 44 MUTATION: mxiK mutants are unable to invade HeLa cells [PMID:12864857]. 45 MUTATION: virB mutants have an avirulent phenotype and do not invade host cells [PMID:8385666]. 46 MUTATION: mxiA mutants were attenuated in invasion of HeLa cells [PMID:2037361]. 47 MUTATION: mxiD mutant is unable to invade HeLa cells or to provoke keratoconjunctivitis in guinea-pigs [PMID:8437520]. 48 MUTATION: icsB mutants are attenuated in guinea pig eyes [PMID:12753186]. 49 MUTATION: virK mutants have attenuated ability for intracellular spreading in host cells [PMID:15664968]. 50 MUTATION: mxiH mutants are unable to invade HeLa cells [PMID:11169106]. 51 MUTATION: ipaA mutants are attenuated in invasion of HeLa cells [PMID:9184218]. 52 MUTATION: ipaH9.8 deletion mutant caused more severe inflammatory responses with increased pro-inflammatory cytokine production levels than did wild-type Shigella, which resulted in a 30-fold decrease in bacterial colonization in murine lungs [PMID:15950937]. 53 MUTATION: sopA mutant was able to infect HeLa cells, but was attenuated in its ability to spread to other cells compared to the wild type [PMID:9076742]. 54 MUTATION: sepA mutant has attenuated virulence in ligated rabbit ileal loop model [PMID:7476198]. 55 MUTATION: ipaH7.8 mutants had a lower rate of exit from the endocytic vacuoles into the cytoplasm in mouse macrophages than the wild-type strain [PMID:10816519]. 56 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 877618 PA0584 20140322 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025 MUTATION: cca mutant is attenuated in rats [PMID:14641575]. 4201 multifunctional tRNA nucleotidyl transferase/2'3'-cyclic phosphodiesterase/2'nucleotidase/phosphatase cca Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 877661 PA1863 20140322 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025 MUTATION: modA mutant is attenuated in rats [PMID:14641575]. 4202 molybdate-binding periplasmic protein ModA modA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 877662 PA1927 20140405 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025 MUTATION: metE mutant is attenuated in rats [PMID:14641575]. 4203 5-methyltetrahydropteroyltriglutamate/homocysteine S-methyltransferase metE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 877674 PA5261 20140405 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 17766417; 18178737; 18978025; 19270096; 24097945 MUTATION: algR mutant is attenuated in mice [PMID:12379685]. 4204 alginate biosynthesis regulatory protein AlgR algR Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 877847 PA5441 20120929 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18083816; 18978025 MUTATION: PA5441 mutant is attenuated in rats [PMID:14641575]. 4205 hypothetical protein PA5441 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 877850 PA1148 20140406 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025; 19686346; 21945328; 22013118; 22520464; 22844393; 24605680 exotoxin A toxA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 877859 PA4554 20140406 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025 MUTATION: pilY1 mutant is attenuated in rats [PMID:14641575]. 4207 type 4 fimbrial biogenesis protein PilY1 pilY1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 877861 PA4528 20140322 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025 MUTATION: pilD mutant is attenuated in rats [PMID:14641575]. 4208 type 4 prepilin peptidase PilD pilD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 877878 PA5437 20140222 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18599838; 18978025 MUTATION: PA5437 mutant is attenuated in rats [PMID:14641575]. 4209 transcriptional regulator PA5437 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 877893 PA0151 20130511 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025 MUTATION: PA0151 mutant is attenuated in rats [PMID:14641575]. 4210 TonB-dependent receptor PA0151 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 877954 PA0765 20140322 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025 MUTATION: mucC mutant is attenuated in rats [PMID:14641575]. 4211 positive regulator for alginate biosynthesis MucC mucC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 877979 PA5312 20140315 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025 MUTATION: PA5312 mutant is attenuated in rats [PMID:14641575]. 4212 aldehyde dehydrogenase PA5312 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 878014 PA5449 20131030 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025 MUTATION: wbpX mutant is attenuated in rats [PMID:14641575]. 4213 glycosyltransferase WbpX wbpX Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 878015 PA4944 20140322 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 16468994; 17015649; 18978025; 21169425; 23897473 MUTATION: When compared to PAO1 wild-type and the rpoS- mutant, the hfq- mutant decreased virulence in Galleria mellonella by a factor of 1 x 10(4) and 5 x 10(3), respectively. Likewise, when compared to wild-type, the PAO1hfq- mutant was significantly attenuated in virulence when administered intraperitoneally in mice [PMID:14521880]. 4214 RNA-binding protein Hfq hfq Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 878134 PA5131 20140405 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025 MUTATION: pgm mutant is attenuated in rats [PMID:14641575]. 4215 phosphoglyceromutase pgm Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 878186 PA0410 20140322 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025 MUTATION: pilI mutant is attenuated in rats [PMID:14641575]. 4216 twitching motility protein PilI pilI Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 878236 PA4855 20140405 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025 MUTATION: purD mutant is attenuated in rats [PMID:14641575]. 4217 phosphoribosylamine--glycine ligase purD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 878250 PA5327 20130511 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025 MUTATION: PA5327 mutant is attenuated in rats [PMID:14641575]. 4218 oxidoreductase PA5327 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 878350 PA0044 20140222 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15731071; 15908409; 15995206; 16030221; 17015649; 18053004; 18978025; 22250085 exoenzyme T exoT Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 878396 PA0073 20140215 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025 MUTATION: PA0073 mutant is attenuated in rats [PMID:14641575]. 4220 ABC transporter ATP-binding protein PA0073 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 878601 PA0041 20140215 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025 MUTATION: PA0041 mutant is attenuated in rats [PMID:14641575]. 4221 hemagglutinin PA0041 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 878826 PA5112 20140322 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 17631636; 18978025 MUTATION: estA mutant is attenuated in rats [PMID:14641575]. 4222 esterase estA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 878954 PA3478 20140215 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025 MUTATION: rhlB mutant is attenuated in rats [PMID:14641575]. 4223 rhamnosyltransferase subunit B rhlB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 879028 PA1157 20140406 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025 MUTATION: PA1157 mutant is attenuated in rats [PMID:14641575]. 4224 two-component response regulator PA1157 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 879198 PA0552 20140405 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025 MUTATION: pgk mutant is attenuated in rats [PMID:14641575]. 4225 phosphoglycerate kinase pgk Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 879264 PA1009 20140222 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025 MUTATION: PA1009 mutant is attenuated in rats [PMID:14641575]. 4226 hypothetical protein PA1009 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 879357 PA0763 20140215 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025; 19168621; 19298369; 20045914; 20174684; 21194804; 21631603; 22842599; 23068105 MUTATION: mucA mutant is attenuated in wounded alfalfa seedling infection model [PMID:12426404]. 4227 anti-sigma factor MucA mucA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 879402 PA0082 20140222 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025 MUTATION: PA0082 mutant is attenuated in rats [PMID:12023080]. 4228 hypothetical protein PA0082 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 879406 PA5322 20140406 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 16880541; 17015649; 18978025; 19253818 MUTATION: algC mutant is attenuated in neonatal mouse model of infection [PMID:8557368]. 4229 phosphomannomutase algC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 879421 PA2191 20140222 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15192021; 15608211; 15716452; 15731071; 15908409; 15995206; 16030221; 16039071; 17015649; 18978025; 21843628 adenylate cyclase exoY Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 879553 PA0090 20140322 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025 MUTATION: clpV1 mutant is attenuated in rats [PMID:14641575]. 4231 ClpV1 protein clpV1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 879629 PA5078 20140215 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025 MUTATION: mdoG mutant is attenuated in rats [PMID:14641575]. 4232 glucan biosynthesis protein G PA5078 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 879752 PA3763 20140405 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025 MUTATION: purL mutant is attenuated in rats [PMID:14641575]. 4233 phosphoribosylformylglycinamidine synthase purL Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 879777 PA4115 20140215 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025; 20855735 MUTATION: PA4115 mutant is attenuated in rats [PMID:14641575]. 4234 hypothetical protein PA4115 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 879781 PA3876 20140222 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 16391109; 17015649; 18978025 MUTATION: narK2 mutant is attenuated in rats [PMID:14641575]. 4235 nitrite extrusion protein 2 narK2 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 879799 PA2972 20140322 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025 MUTATION: PA2972 mutant is attenuated in rats [PMID:14641575]. 4236 Maf-like protein PA2972 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 879837 PA3841 20140406 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15668029; 15716452; 15731071; 15901720; 15908409; 15995206; 16030221; 17015649; 17490406; 18039770; 18978025; 20144150; 20732998; 20805335; 22080193; 22250085; 23428533 MUTATION: exoS mutant is attenuated in a silk worm oral infection model [PMID:20805335]. 4237 exoenzyme S exoS Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 879865 PA3831 20140406 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025 MUTATION: pepA mutant is attenuated in rats [PMID:14641575]. 4238 leucyl aminopeptidase pepA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 879871 PA3826 20140215 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025 MUTATION: PA3826 mutant is attenuated in rats [PMID:14641575]. 4239 hypothetical protein PA3826 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 879922 PA3160 20140222 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025 MUTATION: wzz (wzz1) mutant is attenuated in mouse pneumonia model of infection [PMID:18065548]. 4240 O-antigen chain length regulator wzz Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 879968 PA2023 20140405 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025 MUTATION: galU mutant is attenuated in corneal mouse model of infection [PMID:15213167]. 4241 UTP-glucose-1-phosphate uridylyltransferase galU Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 880024 PA3498 20140222 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025 MUTATION: PA3498 mutant is attenuated in rats [PMID:14641575]. 4242 oxidoreductase PA3498 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 880046 PA4854 20140329 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025 MUTATION: purH mutant is attenuated in rats [PMID:14641575]. 4243 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase purH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 880205 PA2998 20140322 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025 MUTATION: ngrB mutant is attenuated in rats [PMID:14641575]. 4244 Na(+)-translocating NADH-quinone reductase subunit B nqrB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 880314 PA3756 20130420 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025 MUTATION: PA3756 mutant is attenuated in rats [PMID:14641575]. 4245 hypothetical protein PA3756 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 880336 PA3735 20140406 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025 MUTATION: thrC mutant is attenuated in rats [PMID:14641575]. 4246 threonine synthase thrC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 880414 PA3001 20140405 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025 MUTATION: PA3001 mutant is attenuated in rats [PMID:14641575]. 4247 glyceraldehyde-3-phosphate dehydrogenase PA3001 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 880514 PA4209 20140322 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 16946471; 17015649; 18292577; 18978025; 22562990 MUTATION: phzM mutant is attenuated in mice [PMID:15213173]. 4248 phenazine-specific methyltransferase phzM Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 880908 PA4564 20140222 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025 MUTATION: PA4564 mutant is attenuated in rats [PMID:14641575]. 4249 hypothetical protein PA4564 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 880976 PA4446 20140322 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025; 19168621; 19298369 MUTATION: algW mutant is attenuated in rats [PMID:14641575]. 4250 AlgW protein algW Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 881054 PA4491 20140406 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025 MUTATION: PA4491 mutant is attenuated in rats [PMID:14641575]. 4251 hypothetical protein PA4491 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 881072 PA4489 20140217 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025; 23919994 MUTATION: PA4489 mutant is attenuated in rats [PMID:14641575]. 4252 hypothetical protein PA4489 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 881219 PA4488 20140322 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025 MUTATION: PA4488 mutant is attenuated in rats [PMID:14641575]. 4253 hypothetical protein PA4488 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 881227 PA1248 20140322 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025 MUTATION: aprF mutant is attenuated in rats [PMID:14641575]. 4254 alkaline protease secretion outer membrane protein AprF aprF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 881299 PA0934 20140406 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025; 22982211 MUTATION: relA mutant is attenuated in D. melanogaster [PMID:15385461]. 4255 GTP pyrophosphokinase relA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 881475 PA4692 20140215 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025 MUTATION: PA4692 mutant is attenuated in rats [PMID:14641575]. 4256 sulfite oxidase subunit YedY PA4692 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 881780 PA4764 20140322 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025; 23180123 MUTATION: fur mutant is attenuated in mouse corneal scratch model [PMID:7642283]. 4257 ferric uptake regulation protein fur Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 881789 PA1430 20140322 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15505212; 15608211; 15686549; 15716452; 15817780; 15908409; 15995202; 15995206; 16030221; 17015649; 17367209; 17449616; 17493132; 17559399; 18408026; 18978025; 19246742; 19682264; 21325039; 21415115; 21614486 MUTATION: lasR mutant is attenuated in neonatal mouse model of infection [PMID:8557368]. 4258 transcriptional regulator LasR lasR Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 881836 PA4217 20140215 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025 MUTATION: phzS mutant is attenuated in mice [PMID:15213173]. 4259 hypothetical protein phzS Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 881933 PA1596 20140222 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025 MUTATION: htpG mutant is attenuated in rats [PMID:12023080]. 4260 heat shock protein 90 htpG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 882052 PA1092 20140329 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15494517; 15608211; 15716452; 15908409; 15995206; 16030221; 16410345; 17015649; 18978025; 21205009 MUTATION: fliC mutant is attenuated in mice [PMID:9423837]. 4261 flagellin type B fliC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 882125 PA0762 20140322 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025; 19226327; 20236169; 20348252; 22088575; 22842599 MUTATION: algU mutant is attenuated in rats [PMID:14641575]. 4262 RNA polymerase sigma factor AlgU algU Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 882140 PA0158 20140222 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025 MUTATION: PA0158 mutant is attenuated in rats [PMID:12023080]. 4263 resistance-nodulation-cell division (RND) efflux transporter PA0158 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 882278 PA4887 20140406 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025 MUTATION: PA4887 mutant is attenuated in rats [PMID:14641575]. 4264 major facilitator superfamily (MFS) transporter PA4887 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 882346 PA2639 20140405 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025 MUTATION: nuoD mutant is attenuated in rats [PMID:14641575]. 4265 bifunctional NADH:ubiquinone oxidoreductase subunit C/D nuoD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 882449 PA3286 20140222 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025 MUTATION: PA3286 mutant is attenuated in rats [PMID:14641575]. 4266 3-oxoacyl-ACP synthase PA3286 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 882585 PA2876 20140329 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025 MUTATION: pyrF mutant is attenuated in rats [PMID:14641575]. 4267 orotidine 5'-phosphate decarboxylase pyrF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 882601 PA2895 20120929 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025 MUTATION: PA2895 mutant is attenuated in rats [PMID:14641575]. 4268 hypothetical protein PA2895 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 882633 PA3173 20140215 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025 MUTATION: PA3173 mutant is attenuated in rats [PMID:14641575]. 4269 short-chain dehydrogenase PA3173 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 882839 PA2426 20140322 208964 protein-coding NCBI-supplied PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18047579; 18048935; 18502853; 18978025; 20370820; 21840975 MUTATION: pvdS mutant is attenuated in rabbit aortic endocarditis model [PMID:10720526]. 4270 extracytoplasmic-function sigma-70 factor pvdS Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 883600 RP819 20140301 272947 protein-coding NCBI-supplied PMID: 9823893; 19506016 MUTATION: pld mutant is attenuated in guinea pigs [PMID:19506016]. 1451 hypothetical protein RP819 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 884125 CT_135 20140322 272561 protein-coding NCBI-supplied PMID: 9784136 MUTATION: mutations in CT135 were found responsible for different phenotypes of early clearance (less virulent) and late clearance (more virulent) in mouse urogenital tract [PMID:20547745]. 4456 hypothetical protein CT_135 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 884147 CT_119 20140322 272561 protein-coding NCBI-supplied PMID: 9784136; 15316015 MUTATION: IncA mutant showed decreased growth rate and infection in mice [PMID:18852248]. 4457 Inclusion Membrane Protein A incA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 885038 Rv0981 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 16513743; 17379732; 17601788; 20980199; 21821774; 22689819; 24187094 MUTATION: mprA mutant is attenuated in mice [PMID:11675502]. 82 Mycobacterial persistence regulator MRPA (two component response transcriptional regulatory protein) mprA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 885039 Rv3663c 20140222 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 83 Probable dipeptide-transport ATP-binding protein ABC transporter DppD dppD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 885072 Rv1807 20140301 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 84 PPE family protein PPE31 PPE31 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 885108 Rv1661 20131207 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: pks7 mutant is attenuated in mice [PMID:12855735]. 85 Probable polyketide synthase Pks7 pks7 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 885112 Rv1660 20140215 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: pks10 mutant is attenuated in mice [PMID:12730158]. 86 Chalcone synthase Pks10 pks10 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 885116 Rv1710 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 18084093; 18300244; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 87 Possible segregation and condensation protein ScpB scpB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 885120 Rv1092c 20140405 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 16508093; 16699190; 19307712; 20451532; 20576686; 20980199; 23661699 MUTATION: attenuated in mice [PMID:14569030]. 88 Probable pantothenate kinase CoaA (pantothenic acid kinase) coaA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 885125 Rv1653 20140405 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20184895; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 89 Probable glutamate N-acetyltransferase ArgJ argJ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 885209 Rv0903c 20140215 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 16434396; 20980199; 22081401 MUTATION: prrA mutant is attenuated in murine macrophages [PMID:11953357]. 90 Two component response transcriptional regulatory protein PrrA prrA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 885250 Rv2392 20140405 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 16553880; 20980199 MUTATION: cysH mutants are attenuated in mice [PMID:16553880]. 91 Probable 3'-phosphoadenosine 5'-phosphosulfate reductase CysH (PAPS reductase, thioredoxin DEP.) (padops reductase) (3'-phosphoadenylylsulfate reductase) (PAPS sulfotransferase) cysH Bin Zhao, Oliver He ompATb WEB: http://www.ncbi.nlm.nih.gov/gene 885286 Rv0899 20140215 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 17573469; 20199110; 20980199; 21117233; 21410778; 21802366; 22108166 MUTATION: ompA mutant is impaired in its ability to grow in macrophages and in normal mice, although it was as virulent as the wild type in mice that lack T cells [PMID:12366842]. 92 Outer membrane protein A OmpA - ompA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 885296 Rv3651 20131207 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 93 hypothetical protein Rv3651 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 885300 Rv2388c 20140405 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 94 Probable oxygen-independent coproporphyrinogen III oxidase HemN (coproporphyrinogenase) (coprogen oxidase) hemN Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 885302 Rv2387 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 95 hypothetical protein Rv2387 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 885311 Rv1747 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199; 21622570 MUTATION: Rv1747 mutant is attenuated in mice [PMID:16040957]. 96 Probable conserved transmembrane ATP-binding protein ABC transporter Rv1747 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 885314 Rv3631 20140406 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 97 Possible transferase (possibly glycosyltransferase) Rv3631 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 885344 Rv1930c 20131130 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 98 hypothetical protein Rv1930c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 885364 Rv0986 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: Rv0986 mutant is attenuated in survival within macrophages [PMID:15340136]. 99 Probable adhesion component transport ATP-binding protein ABC transporter Rv0986 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 885377 Rv3616c 20140125 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199; 24078612 MUTATION: Rv3616c mutant is attenuated in mice [PMID:16030141]. 100 ESX-1 secretion-associated protein A, EspA espA Bin Zhao, Oliver He mtb32b WEB: http://www.ncbi.nlm.nih.gov/gene 885382 Rv0983 20140215 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199; 21445360 MUTATION: pepD mutant has altered virulence in mouse model of infection [PMID:20061478]. 101 Probable serine protease PepD (serine proteinase) (MTB32B) - pepD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 885428 Rv1640c 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 102 Lysyl-tRNA synthetase 2 LysX lysX Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 885437 Rv1931c 20140406 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 103 Probable transcriptional regulatory protein Rv1931c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 885438 Rv0950c 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 104 hypothetical protein Rv0950c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 885439 Rv1811 20140406 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: mgtC mutant is attenuated in human macrophages and mice [PMID:10760138]. 105 Possible Mg2+ transport P-type ATPase C MgtC mgtC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 885447 Rv1111c 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 106 hypothetical protein Rv1111c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 885459 Rv3602c 20140405 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: panCD mutant is attenuated in mice [PMID:12219086]. 107 Pantoate--beta-alanine ligase PanC (pantothenate synthetase) (pantoate activating enzyme) panC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 885472 Rv2391 20140329 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 15917234; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 108 Ferredoxin-dependent sulfite reductase SirA sirA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 885488 Rv1939 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 109 Probable oxidoreductase Rv1939 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 885502 Rv3676 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 15882420; 16267303; 16946467; 17702648; 19193643; 19740754; 20028978; 20980199; 21902733 MUTATION: Rv3676 mutant is attenuated in human macrophages and mice [PMID:15882420]. 110 Transcriptional regulatory protein Crp (Crp/Fnr-family) crp Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 885521 Rv3701c 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 111 hypothetical protein Rv3701c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 885594 Rv1821 20140329 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 17030572; 18487341; 19240020; 20980199; 24297168 MUTATION: secA2 mutant is attenuated in mice [PMID:12675804]. 112 Possible preprotein translocase ATPase SecA2 secA2 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 885596 Rv3601c 20140405 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: panCD mutant is attenuated in mice [PMID:12219086]. 113 Probable aspartate 1-decarboxylase precursor PanD (aspartate alpha-decarboxylase) panD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 885602 Rv3717 20140406 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199; 24019530 MUTATION: attenuated in mice [PMID:14569030]. 114 hypothetical protein Rv3717 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 885638 Rv1908c 20140405 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 15498158; 15628865; 15840564; 16285713; 16566587; 17204474; 17260948; 17309235; 17539290; 17978919; 18394163; 19050300; 19139098; 19139099; 19334480; 19741059; 19750330; 20054829; 20211896; 20980199; 21244531; 21388297; 21554227; 22272299; 22358357; 22381358; 22610803; 22808802; 22918833; 23325741; 23412028; 23453008 MUTATION: katG mutant is attenuated in mice and guinea pigs [PMID:9534978]. 115 Catalase-peroxidase-peroxynitritase T KatG katG from M. tuberculosis H37Rv Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 885717 Rv2428 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 15498158; 15886207; 20980199 MUTATION: ahpC mutant has decreased survival in unstimulated macrophages compared to the wild type [PMID:12368447]. 116 Alkyl hydroperoxide reductase C protein AhpC (alkyl hydroperoxidase C) ahpC Bin Zhao, Oliver He snm9 WEB: http://www.ncbi.nlm.nih.gov/gene 885770 Rv3615c 20140217 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 16135231; 20980199 MUTATION: Rv3615c mutant is attenuated in mice and has growth defects in macrophages [PMID:16135231]. 117 ESX-1 secretion-associated protein EspC - espC Bin Zhao, Oliver He snm10 WEB: http://www.ncbi.nlm.nih.gov/gene 885777 Rv3614c 20131207 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 16135231; 20980199 MUTATION: Rv3614c mutant is attenuated in mice and has growth defects in macrophages [PMID:16135231]. 118 ESX-1 secretion-associated protein EspD - espD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 885780 Rv3683 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 119 hypothetical protein Rv3683 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 885791 Rv3723 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 120 Probable conserved transmembrane protein Rv3723 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 885805 Rv1696 20140406 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 121 Probable DNA repair protein RecN (recombination protein N) recN Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 885814 Rv1524 20140222 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 122 Probable glycosyltransferase Rv1524 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 885828 Rv1109c 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 123 hypothetical protein Rv1109c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 885838 Rv2383c 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199; 22447909 MUTATION: mbtB mutant is attenuated in macrophage like THP-1 cells [PMID:10655517]. 124 Phenyloxazoline synthase MbtB (phenyloxazoline synthetase) mbtB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 885841 Rv3649 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 125 Probable helicase Rv3649 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 885849 Rv1128c 20140406 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 126 hypothetical protein Rv1128c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 885861 Rv1099c 20140405 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199; 21636919 MUTATION: attenuated in mice [PMID:14569030]. 127 Fructose 1,6-bisphosphatase GlpX glpX Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 885906 Rv2437 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 128 Conserved transmembrane protein Rv2437 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 885924 Rv2374c 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 129 Probable heat shock protein transcriptional repressor HrcA hrcA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 885929 Rv0353 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 18227252; 20980199; 22753065 MUTATION: hspR is attenuated in mice [PMID:11385512]. 130 Probable heat shock protein transcriptional repressor HspR (MerR family) hspR Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 885932 Rv1144 20140222 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 131 Probable short-chain type dehydrogenase/reductase Rv1144 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 885935 Rv1974 20140222 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 132 Probable conserved membrane protein Rv1974 Bin Zhao, Oliver He mce3 WEB: http://www.ncbi.nlm.nih.gov/gene 885944 Rv1966 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 15804490; 18201981; 20980199 MUTATION: mce3A mutant is attenuated in mice [PMID:15804490]. 133 Mce-family protein Mce3A - mce3A Bin Zhao, Oliver He mpcA WEB: http://www.ncbi.nlm.nih.gov/gene 885995 Rv2351c 20140405 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: plcABC triple mutants are attenuated in mice [PMID:12100560]. 134 Membrane-associated phospholipase C 1 PlcA (MTP40 antigen) - plcA Bin Zhao, Oliver He mpcB WEB: http://www.ncbi.nlm.nih.gov/gene 885999 Rv2350c 20140406 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: plcABC triple mutants are attenuated in mice [PMID:12100560]. 135 Membrane-associated phospholipase C 2 PlcB - plcB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886000 Rv2349c 20140329 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: plcABC triple mutants are attenuated in mice [PMID:12100560]. 136 Probable phospholipase C 3 PlcC plcC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886007 Rv1192 20140406 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 137 hypothetical protein Rv1192 Bin Zhao, Oliver He furB WEB: http://www.ncbi.nlm.nih.gov/gene 886009 Rv2359 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 17098899; 17213192; 18452427; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 138 Probable zinc uptake regulation protein Zur - zur Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886012 Rv2335 20140405 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199; 23483228 MUTATION: attenuated in mice [PMID:14569030]. 139 Probable serine acetyltransferase CysE (sat) cysE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886030 Rv0386 20140222 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 15955067; 20980199 MUTATION: Rv0386 mutant is attenuated in mice [PMID:20039878]. 140 Probable transcriptional regulatory protein (probably LuxR/UhpA-family) Rv0386 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886035 Rv1013 20140222 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 141 Putative polyketide synthase Pks16 pks16 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886052 Rv1021 20140405 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20529853; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 142 hypothetical protein Rv1021 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886063 Rv1184c 20140222 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 143 Possible exported protein Rv1184c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886065 Rv1185c 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 144 Probable fatty-acid-AMP ligase FadD21 (fatty-acid-AMP synthetase) (fatty-acid-AMP synthase) fadD21 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886066 Rv1016c 20140406 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 145 Probable conserved lipoprotein LpqT lpqT Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886068 Rv1183 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 146 Probable conserved transmembrane transport protein MmpL10 mmpL10 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886084 Rv1028c 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 12581360; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 147 Probable sensor protein KdpD kdpD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886113 Rv3781 20140222 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 148 Probable O-antigen/lipopolysaccharide transport ATP-binding protein ABC transporter RfbE rfbE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886123 Rv3794 20131207 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 16585755; 18174142; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 149 Integral membrane indolylacetylinositol arabinosyltransferase EmbA (arabinosylindolylacetylinositol synthase) embA Bin Zhao, Oliver He 85A mpt44 WEB: http://www.ncbi.nlm.nih.gov/gene 886132 Rv3804c 20140406 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 17357846; 19959397; 20375425; 20980199; 21819455 MUTATION: fbpA mutant is attenuated in mice [PMID:15557632]. 150 Secreted antigen 85-a FbpA (mycolyl transferase 85A) (fibronectin-binding protein A) (antigen 85 complex A) - fbpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886138 Rv3805c 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 151 Possible arabinofuranosyltransferase AftB aftB Bin Zhao, Oliver He P36 erp WEB: http://www.ncbi.nlm.nih.gov/gene 886139 Rv3810 20131130 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 152 Exported repetitive protein precursor PirG (cell surface protein) (EXP53) - pirG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886145 Rv3823c 20140217 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: mmpL8 mutant is attenuated in mice [PMID:12724526]. 153 Conserved integral membrane transport protein MmpL8 mmpL8 Bin Zhao, Oliver He snm6 WEB: http://www.ncbi.nlm.nih.gov/gene 886166 Rv3869 20140222 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 154 ESX conserved component EccB1 ESX-1 type VII secretion system protein Possible membrane protein - eccB1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886172 Rv3865 20140406 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: Rv3865 mutant is attenuated in mice [PMID:16368961]. 155 ESX-1 secretion-associated protein EspF espF Bin Zhao, Oliver He sod sodB WEB: http://www.ncbi.nlm.nih.gov/gene 886174 Rv3846 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: sodA mutant is attenuated in mice [PMID:11751190]. 156 Superoxide dismutase [FE] SodA - sodA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886185 Rv3864 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 157 ESX-1 secretion-associated protein EspE espE Bin Zhao, Oliver He aka etaR WEB: http://www.ncbi.nlm.nih.gov/gene 886189 Rv3855 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199; 22156370 MUTATION: attenuated in mice [PMID:14569030]. 158 Transcriptional regulatory repressor protein (TetR-family) EthR - ethR Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886191 Rv3872 20140406 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 159 PE family-related protein PE35 PE35 Bin Zhao, Oliver He cfp10 lhp WEB: http://www.ncbi.nlm.nih.gov/gene 886194 Rv3874 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 15378760; 15973432; 16689931; 16785544; 16973880; 17676952; 19682254; 19854905; 20980199; 22723257; 23308124; 24078612 MUTATION: esxB (CFP-10) mutant is attenuated in mice [PMID:16030141]. 160 10 kDa culture filtrate antigen EsxB (LHP) (CFP10) - esxB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886199 Rv3868 20140222 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 17676952; 19682254; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 161 ESX conserved component EccA1 ESX-1 type VII secretion system protein eccA1 Bin Zhao, Oliver He snm5 WEB: http://www.ncbi.nlm.nih.gov/gene 886200 Rv3866 20140405 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 17676952; 20980199 MUTATION: Rv3866 mutant is attenuated in mice [PMID:16368961]. 162 ESX-1 secretion-associated protein EspG1 - espG1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886201 Rv3873 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 18686610; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 163 PPE family protein PPE68 PPE68 Bin Zhao, Oliver He snm2 WEB: http://www.ncbi.nlm.nih.gov/gene 886202 Rv3871 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 17676952; 20034878; 20980199; 22723257 MUTATION: Rv3871 mutant is attenuated in mice [PMID:14557536]. 164 ESX conserved component EccCb1 ESX-1 type VII secretion system protein - eccCb1 Bin Zhao, Oliver He snm1 WEB: http://www.ncbi.nlm.nih.gov/gene 886204 Rv3870 20140405 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 17676952; 20980199 MUTATION: Rv3870 mutant is attenuated in mice [PMID:14557536]. 165 ESX conserved component EccCa1 ESX-1 type VII secretion system protein Possible transmembrane protein - eccCa1 Bin Zhao, Oliver He snm3 WEB: http://www.ncbi.nlm.nih.gov/gene 886206 Rv3876 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 17676952; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 166 ESX-1 secretion-associated protein EspI Conserved proline and alanine rich protein - espI Bin Zhao, Oliver He snm4 WEB: http://www.ncbi.nlm.nih.gov/gene 886207 Rv3877 20140222 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 17676952; 20980199 MUTATION: Rv3877 (snm4) mutant is attenuated in mice [PMID:14557536]. 167 ESX conserved component EccD1 ESX-1 type VII secretion system protein Probable transmembrane protein - eccD1 Bin Zhao, Oliver He snm7 WEB: http://www.ncbi.nlm.nih.gov/gene 886208 Rv3882c 20140406 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 168 ESX conserved component EccE1 ESX-1 type VII secretion system protein Possible membrane protein - eccE1 Bin Zhao, Oliver He esat-6 WEB: http://www.ncbi.nlm.nih.gov/gene 886209 Rv3875 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 15488391; 15860216; 15973432; 16368961; 17298391; 17486091; 17676952; 17915024; 18779346; 19265145; 19340290; 19854905; 19901982; 19906174; 20006311; 20007864; 20148899; 20617139; 20980199; 21039742; 21586573; 21637850; 21689705; 22712528; 22808273; 23150662; 23308124; 24078612 MUTATION: esxA (ESAT-6) mutant is attenuated in mice [PMID:16030141]. 169 6 kDa early secretory antigenic target EsxA (ESAT-6) - esxA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886211 Rv3887c 20140406 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: Rv3887c mutant is attenuated in mice [PMID:17353284]. 170 ESX conserved component EccD2 ESX-2 type VII secretion system protein Probable transmembrane protein eccD2 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886214 Rv3881c 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 17676952; 20980199 MUTATION: Rv3881c (espB) mutant is attenuated in macrophages [PMID:17676952]. 171 Secreted ESX-1 substrate protein B, EspB. Conserved alanine and glycine rich protein espB Bin Zhao, Oliver He snm8 WEB: http://www.ncbi.nlm.nih.gov/gene 886217 Rv3883c 20140222 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20227664; 20980199 MUTATION: mycP1 mutant is attenuated in chronic infection of mice [PMID:20227664]. 172 Membrane-anchored mycosin MycP1 (serine protease) (subtilisin-like protease) (subtilase-like) (mycosin-1) - mycP1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886247 Rv3910 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 173 Probable conserved transmembrane protein Rv3910 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886272 Rv0475 20131207 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 15973422; 16893986; 17933894; 18441065; 20178790; 20980199; 21398546; 21672524; 22174691; 22306117; 22403657 MUTATION: hbhA mutant is attenuated in attachment and invasion of pneumocytes [PMID:11449276]. 174 Iron-regulated heparin binding hemagglutinin HbhA (adhesin) hbhA Bin Zhao, Oliver He umaA2 WEB: http://www.ncbi.nlm.nih.gov/gene 886284 Rv0470c 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199; 22621931 MUTATION: pcaA mutant is attenuated in mice [PMID:10882107]. 175 Mycolic acid synthase PcaA (cyclopropane synthase) - pcaA Bin Zhao, Oliver He aceA icl WEB: http://www.ncbi.nlm.nih.gov/gene 886291 Rv0467 20140405 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 16879647; 18275086; 19767422; 20980199; 21814509 MUTATION: icl mutant is attenuated in activated macrophages [PMID:10963599]. 176 Isocitrate lyase Icl (isocitrase) (isocitratase) - icl1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886292 Rv1590 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 177 hypothetical protein Rv1590 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886293 Rv3758c 20131207 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 18390665; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 178 Possible osmoprotectant (glycine betaine/carnitine/choline/L-proline) transport ATP-binding protein ABC transporter ProV proV Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886301 Rv1589 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 179 Probable biotin synthetase BioB bioB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886343 Rv1568 20140406 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 16754301; 20565114; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 180 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase BioA bioA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886345 Rv1569 20140406 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 181 Probable 8-amino-7-oxononanoate synthase BioF1 (AONS) (8-amino-7-ketopelargonate synthase) (7-keto-8-amino-pelargonic acid synthetase) (7-KAP synthetase) (L-alanine--pimelyl CoA ligase) bioF1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886358 Rv0432 20140406 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: sodC mutant is more susceptible to killing by activated murine macrophages than the wild type [PMID:11447176]. 182 Periplasmic superoxide dismutase [Cu-Zn] SodC sodC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886359 Rv1560 20140222 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 183 Possible antitoxin VapB11 vapB11 Bin Zhao, Oliver He xth WEB: http://www.ncbi.nlm.nih.gov/gene 886370 Rv0427c 20140215 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 184 Probable exodeoxyribonuclease III protein XthA (exonuclease III) (EXO III) (AP endonuclease VI) - xthA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886391 Rv0414c 20140406 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 185 Thiamine-phosphate pyrophosphorylase ThiE (TMP pyrophosphorylase) (TMP-PPASE) (thiamine-phosphate synthase) thiE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886397 Rv0410c 20140222 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 15155913; 17616581; 17641049; 19447903; 20030858; 20980199 MUTATION: pknG mutant is attenuated in mice [PMID:15186418]. 186 Serine/threonine-protein kinase PknG (protein kinase G) (STPK G) pknG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886408 Rv1539 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 18832305; 20980199 MUTATION: lspA mutant is attenuated in mice [PMID:18832305]. 187 Probable lipoprotein signal peptidase LspA lspA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886442 Rv1527c 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: pks5 mutant is attenuated in mice [PMID:12855735]. 188 Probable polyketide synthase Pks5 pks5 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886457 Rv1514c 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 189 hypothetical protein Rv1514c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886544 Rv0326 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 190 Hypothetical protein Rv0326 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886569 Rv1465 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 191 Possible nitrogen fixation related protein Rv1465 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886573 Rv1460 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 192 Probable transcriptional regulatory protein Rv1460 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886578 Rv1469 20131207 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 193 Probable cation transporter P-type ATPase D CtpD ctpD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886670 Rv1422 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 194 hypothetical protein Rv1422 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886671 Rv0249c 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 195 Probable succinate dehydrogenase [membrane anchor subunit] (succinic dehydrogenase) Rv0249c Bin Zhao, Oliver He P27 WEB: http://www.ncbi.nlm.nih.gov/gene 886700 Rv1411c 20140406 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 16815070; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 196 Conserved lipoprotein LprG - lprG Bin Zhao, Oliver He P55 WEB: http://www.ncbi.nlm.nih.gov/gene 886709 Rv1410c 20140215 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 19564371; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 197 Aminoglycosides/tetracycline-transport integral membrane protein - Rv1410c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886714 Rv1405c 20140405 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 198 Putative methyltransferase Rv1405c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886727 Rv0218 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 199 Probable conserved transmembrane protein Rv0218 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886729 Rv0216 20140222 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 200 Double hotdog hydratase Rv0216 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886747 Rv0204c 20140215 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 201 Probable conserved transmembrane protein Rv0204c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886750 Rv0202c 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199; 23760277 MUTATION: mmpL11 mutant is attenuated in mice [PMID:15908378]. 202 Probable conserved transmembrane transport protein MmpL11 mmpL11 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886753 Rv0199 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 203 Probable conserved membrane protein Rv0199 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886799 Rv0176 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 204 Probable conserved Mce associated transmembrane protein Rv0176 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886800 Rv1371 20140222 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 205 Probable conserved membrane protein Rv1371 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886801 Rv0175 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 206 Probable conserved Mce associated membrane protein Rv0175 Bin Zhao, Oliver He mce1E WEB: http://www.ncbi.nlm.nih.gov/gene 886804 Rv0173 20131207 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 207 Possible Mce-family lipoprotein LprK (Mce-family lipoprotein Mce1E) - lprK Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886808 Rv0171 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 208 Mce-family protein Mce1C mce1C Bin Zhao, Oliver He mceD WEB: http://www.ncbi.nlm.nih.gov/gene 886810 Rv0170 20140215 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 209 Mce-family protein Mce1B - mce1B Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886812 Rv0168 20140406 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: yrbE1B mutant is attenuated in mice [PMID:15804490]. 210 Conserved integral membrane protein YrbE1B yrbE1B Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886822 Rv0166 20140406 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20214478; 20980199 MUTATION: fadD5 mutant is attenuated in mice [PMID:20214478]. 211 Probable fatty-acid-CoA ligase FadD5 (fatty-acid-CoA synthetase) (fatty-acid-CoA synthase) fadD5 Bin Zhao, Oliver He mce1 WEB: http://www.ncbi.nlm.nih.gov/gene 886823 Rv0169 20140406 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 15804490; 16620748; 17046327; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 212 Mce-family protein Mce1A - mce1A Bin Zhao, Oliver He fadD33 WEB: http://www.ncbi.nlm.nih.gov/gene 886855 Rv1345 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: fadD33 mutant is attenuated in mice [PMID:12480891]. 213 Probable fatty acyl-AMP ligase MbtM - mbtM Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886866 Rv1338 20140405 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 18757813; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 214 Probable glutamate racemase MurI murI Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886882 Rv1333 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 215 Probable hydrolase Rv1333 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886901 Rv1332 20140406 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 216 Probable transcriptional regulatory protein Rv1332 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886904 Rv1323 20140405 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 217 Probable acetyl-CoA acetyltransferase FadA4 (acetoacetyl-CoA thiolase) fadA4 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886931 Rv0100 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 218 hypothetical protein Rv0100 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886933 Rv0099 20140406 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199; 23625916 MUTATION: attenuated in mice [PMID:14569030]. 219 Possible fatty-acid-CoA ligase FadD10 (fatty-acid-CoA synthetase) (fatty-acid-CoA synthase) fadD10 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886935 Rv0098 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199; 22292955 MUTATION: attenuated in mice [PMID:14569030]. 220 Probable fatty acyl CoA thioesterase type III FcoT fcoT Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886941 Rv1304 20140406 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 221 Probable ATP synthase a chain AtpB (protein 6) atpB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886951 Rv0101 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION attenuated in mice [PMID:14569030]. 222 Probable peptide synthetase Nrp (peptide synthase) nrp Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886960 Rv1293 20140405 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 16511157; 19543810; 20980199 MUTATION: lysA mutant is markedly attenuated in SCID mice, and is strongly attenuated in mice when in combination with a secA2 mutation [PMID:21264335]. 4915 Diaminopimelate decarboxylase LysA (DAP decarboxylase) lysA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 886987 Rv1284 20131130 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 15753099; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 223 Beta-carbonic anhydrase canA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 887021 Rv1272c 20140406 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 224 Probable drugs-transport transmembrane ATP-binding protein ABC transporter Rv1272c Bin Zhao, Oliver He tbINO WEB: http://www.ncbi.nlm.nih.gov/gene 887028 Rv0046c 20140405 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: ino1 mutant is attenuated in resting macrophages and guinea pigs [PMID:14763976]. 225 myo-inositol-1-phosphate synthase Ino1 (inositol 1-phosphate synthetase) (D-glucose 6-phosphate cycloaldolase) (glucose 6-phosphate cyclase) (glucocycloaldolase) - ino1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 887093 Rv1244 20140222 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 226 Probable lipoprotein LpqZ lpqZ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 887104 Rv1238 20140406 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199; 21118978 MUTATION: attenuated in mice [PMID:14569030] 227 Probable sugar-transport ATP-binding protein ABC transporter SugC sugC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 887121 Rv1237 20131130 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199; 21118978 MUTATION: attenuated in mice [PMID:14569030]. 228 Probable sugar-transport integral membrane protein ABC transporter SugB sugB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 887124 Rv1236 20140222 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199; 21118978 MUTATION: attenuated in mice [PMID:14569030]. 229 Probable sugar-transport integral membrane protein ABC transporter SugA sugA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 887143 Rv1224 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 230 Probable protein TatB tatB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 887145 Rv1235 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199; 21118978 MUTATION: attenuated in mice [PMID:14569030]. 231 Probable sugar-binding lipoprotein LpqY lpqY Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 887168 Rv2502c 20140329 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 232 Probable acetyl-/propionyl-CoA carboxylase (beta subunit) AccD1 accD1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 887170 Rv0485 20140405 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 19651861; 20980199 MUTATION: Rv0485 mutant is attenuated in mice [PMID:19651861]. 233 Possible transcriptional regulatory protein Rv0485 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 887173 Rv2885c 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 234 Probable transposase Rv2885c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 887185 Rv0490 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: senX3-regX3 deletion mutant is attenuated in mice [PMID:12777483]. 235 Putative two component sensor histidine kinase SenX3 senX3 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 887195 Rv0491 20140222 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 17942407; 20980199 MUTATION: senX3-regX3 deletion mutant is attenuated in mice [PMID:12777483]. 236 Two component sensory transduction protein RegX3 (transcriptional regulatory protein) (probably LuxR-family) regX3 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 887204 Rv3574 20140217 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 237 Transcriptional regulatory protein KstR (probably TetR-family) kstR Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 887205 Rv2921c 20140405 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 238 Probable cell division protein FtsY (SRP receptor) (signal recognition particle receptor) ftsY Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 887233 Rv2211c 20140406 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 239 Probable aminomethyltransferase GcvT (glycine cleavage system T protein) gcvT Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 887235 Rv3551 20140405 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 240 Possible CoA-transferase (alpha subunit) Rv3551 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 887246 Rv2241 20140405 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 16045627; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 241 Pyruvate dehydrogenase E1 component AceE (pyruvate decarboxylase) (pyruvate dehydrogenase) (pyruvic dehydrogenase) aceE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 887247 Rv3519 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 242 hypothetical protein Rv3519 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 887255 Rv2472 20131130 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 243 hypothetical protein Rv2472 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 887256 Rv0500 20140405 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: proC mutant is attenuated in mice [PMID:11160012]. 244 Probable pyrroline-5-carboxylate reductase ProC (P5CR) (P5C reductase) proC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 887285 Rv3556c 20140405 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 245 Probable acetyl-CoA acetyltransferase FadA6 (acetoacetyl-CoA thiolase) fadA6 Bin Zhao, Oliver He ilvB WEB: http://www.ncbi.nlm.nih.gov/gene 887286 Rv3003c 20140405 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 19542000; 20884690; 20980199 MUTATION: ilvB1 mutant is attenuated in mice [PMID:19542000]. 246 Acetolactate synthase (large subunit) IlvB1 (acetohydroxy-acid synthase) - ilvB1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 887291 Rv2947c 20140217 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: pks15 mutant is attenuated in mice [PMID:12730158]. 247 Probable polyketide synthase Pks15 pks15 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 887313 Rv2702 20140405 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 248 Polyphosphate glucokinase PpgK (polyphosphate-glucose phosphotransferase) ppgK Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 887410 Rv2976c 20131207 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 17142904; 20693660; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 249 Probable uracil-DNA glycosylase Ung (UDG) ung Bin Zhao, Oliver He acoas WEB: http://www.ncbi.nlm.nih.gov/gene 887454 Rv2941 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: fadD28 mutant is attenuated in mice [PMID:10573420]. 250 Fatty-acid-AMP ligase FadD28 (fatty-acid-AMP synthetase) (fatty-acid-AMP synthase) - fadD28 Bin Zhao, Oliver He trkA trkB WEB: http://www.ncbi.nlm.nih.gov/gene 887493 Rv2692 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 251 TRK system potassium uptake protein CeoC - ceoC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 887548 Rv2942 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 16879801; 20980199 MUTATION: mmpL7 mutant is attenuated in mice [PMID:10573420]. 252 Conserved transmembrane transport protein MmpL7 mmpL7 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 887552 Rv1204c 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 253 hypothetical protein Rv1204c Bin Zhao, Oliver He acr WEB: http://www.ncbi.nlm.nih.gov/gene 887579 Rv2031c 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 15545279; 15860225; 16428728; 16784488; 16930542; 17194806; 19874551; 20980199; 22504645; 22984534; 23133523 MUTATION: hspX mutant is attenuated in murine macrophages and THP-1 cells [PMID:9689123]. 254 Heat shock protein HspX (alpha-crystallin homolog) (14 kDa antigen) (HSP16.3) - hspX Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 887594 Rv3414c 20140215 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199; 23314154 MUTATION: sigD mutant is attenuated in human macrophages and mice [PMID:15659067]. 255 Probable alternative RNA polymerase sigma-D factor SigD sigD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 887595 Rv3419c 20131130 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 256 Probable O-sialoglycoprotein endopeptidase Gcp (glycoprotease) gcp Bin Zhao, Oliver He whmB WEB: http://www.ncbi.nlm.nih.gov/gene 887598 Rv3416 20140215 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 16923787; 17609386; 20980199 MUTATION: whiB3 mutant is attenuated in mice [PMID:11880648]. 257 Transcriptional regulatory protein WhiB-like WhiB3 Contains [4FE-4S] cluster - whiB3 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 887603 Rv2930 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 15749014; 20553505; 20980199 MUTATION: fadD26 mutant is attenuated in mice [PMID:15958066]. 258 Fatty-acid-AMP ligase FadD26 (fatty-acid-AMP synthetase) (fatty-acid-AMP synthase) fadD26 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 887617 Rv3061c 20140217 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 259 Probable acyl-CoA dehydrogenase FadE22 fadE22 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 887633 Rv0566c 20140405 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 260 hypothetical protein Rv0566c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 887681 Rv2192c 20140405 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 16337227; 20980199; 23363292 MUTATION: trpD mutant is attenuated in mice [PMID:11160012]. 261 Probable anthranilate phosphoribosyltransferase TrpD trpD Bin Zhao, Oliver He hsd4A WEB: http://www.ncbi.nlm.nih.gov/gene 887697 Rv3502c 20140406 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 262 Probable short-chain type dehydrogenase/reductase Possible 17-beta-hydroxysteroid dehydrogenase - Rv3502c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 887744 Rv2483c 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199; 24359335 MUTATION: attenuated in mice [PMID:14569030]. 263 Possible transmembrane phospholipid biosynthesis bifunctional enzyme PlsC: putative L-3-phosphoserine phosphatase (O-phosphoserine phosphohydrolase) (PSP) (pspase) + 1-acyl-SN-glycerol-3-phosphate acyltransferase (1-AGP acyltransferase) (1-AGPAT) (lysophosphatidic acid acyltransferase) (LPAAT) plsC Bin Zhao, Oliver He mce2 WEB: http://www.ncbi.nlm.nih.gov/gene 887745 Rv0589 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 15804490; 20980199 MUTATION: mce2A mutant is attenuated in mice [PMID:15804490]. 264 Mce-family protein Mce2A - mce2A Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 887750 Rv2707 20140222 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 18096644; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 265 Probable conserved transmembrane alanine and leucine rich protein Rv2707 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 887782 Rv3545c 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 19146393; 19846551; 19846552; 20545858; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 266 Probable cytochrome P450 125 Cyp125 cyp125 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 887815 Rv3042c 20140406 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 267 Probable phosphoserine phosphatase SerB2 (PSP) (O-phosphoserine phosphohydrolase) (pspase) serB2 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 887818 Rv3563 20140405 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 268 Probable acyl-CoA dehydrogenase FadE32 fadE32 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 887836 Rv3588c 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 15753099; 16321983; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 269 Beta-carbonic anhydrase CanB canB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 887838 Rv3560c 20140329 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 270 Probable acyl-CoA dehydrogenase FadE30 fadE30 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 887857 Rv2224c 20140405 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 271 Probable carboxylesterase CaeA caeA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 887888 Rv2583c 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 16026164; 20980199 MUTATION: Long-term survival of the relA mutant during in vitro starvation or nutrient run out in normal media was significantly impaired compared to that in the wild type. In addition, the mutant was significantly less able to survive extended anaerobic incubation than the wild-type virulent organism [PMID:10940033]. 272 Probable GTP pyrophosphokinase RelA (ATP:GTP 3'-pyrophosphotransferase) (PPGPP synthetase I) ((P)PPGPP synthetase) (GTP diphosphokinase) relA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 887893 Rv2040c 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 273 Probable sugar-transport integral membrane protein ABC transporter Rv2040c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 887917 Rv2693c 20131207 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: Rv2693c mutant is attenuated in mice [PMID:17353284]. 274 Probable conserved integral membrane alanine and leucine rich protein Rv2693c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 887918 Rv3400 20140406 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 275 Probable hydrolase Rv3400 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 887956 Rv2945c 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 276 Probable conserved lipoprotein LppX lppX Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 887968 Rv2937 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 277 Daunorubicin-dim-transport integral membrane protein ABC transporter DrrB drrB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 887990 Rv1211 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 278 hypothetical protein Rv1211 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 887998 Rv2038c 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 279 Probable sugar-transport ATP-binding protein ABC transporter Rv2038c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888006 Rv3472 20140222 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 280 hypothetical protein Rv3472 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888017 Rv2912c 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 281 Probable transcriptional regulatory protein (probably TetR-family) Rv2912c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888029 Rv3335c 20131207 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 282 Probable conserved integral membrane protein Rv3335c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888031 Rv0636 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 17906131; 18048930; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 283 (3R)-hydroxyacyl-ACP dehydratase subunit HadB hadB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888053 Rv3371 20131130 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 284 Possible triacylglycerol synthase (diacylglycerol acyltransferase) Rv3371 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888058 Rv0643c 20140406 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 285 Methoxy mycolic acid synthase 3 MmaA3 (methyl mycolic acid synthase 3) (MMA3) (hydroxy mycolic acid synthase) mmaA3 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888064 Rv3375 20140406 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 286 Probable amidase AmiD (acylamidase) (acylase) amiD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888073 Rv3377c 20140215 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 15719101; 19574210; 20980199 MUTATION: Rv3377c mutant is attenuated in survival inside of macrophages [PMID:15340136]. 287 Halimadienyl diphosphate synthase Rv3377c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888075 Rv3378c 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199; 21228491 MUTATION: Rv3378c mutant is attenuated in survival within macrophages [PMID:15340136]. 288 Diterpene synthase Rv3378c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888081 Rv0655 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 289 Possible ribonucleotide-transport ATP-binding protein ABC transporter Mkl mkl Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888091 Rv3544c 20140405 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 18486437; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 290 Probable acyl-CoA dehydrogenase FadE28 fadE28 Bin Zhao, Oliver He rpoE WEB: http://www.ncbi.nlm.nih.gov/gene 888094 Rv3223c 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 18192397; 19376862; 20980199 MUTATION: sigH mutant has diminished immunopathology and is nonlethal in mice [PMID:12060776]. 291 Alternative RNA polymerase sigma-E factor (sigma-24) SigH (RPOE) - sigH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888107 Rv2206 20140222 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: Rv2206 mutant is attenuated in mice [PMID:17353284]. 292 Probable conserved transmembrane protein Rv2206 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888122 Rv2946c 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 15308633; 20980199 MUTATION: pks1 mutant is attenuated in mice [PMID:12730158]. 293 Probable polyketide synthase Pks1 pks1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888168 Rv2936 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 294 Daunorubicin-dim-transport ATP-binding protein ABC transporter DrrA drrA Bin Zhao, Oliver He nfo WEB: http://www.ncbi.nlm.nih.gov/gene 888190 Rv0670 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 295 Probable endonuclease IV End (endodeoxyribonuclease IV) (apurinase) - end Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888225 Rv2987c 20140405 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 19194004; 20980199 MUTATION: leuD mutant is attenuated in mice [PMID:10768986]. 296 Probable 3-isopropylmalate dehydratase (small subunit) LeuD (isopropylmalate isomerase) (alpha-IPM isomerase) (IPMI) leuD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888228 Rv2553c 20140406 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 297 Probable conserved membrane protein Rv2553c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888247 Rv3523 20140405 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 298 Probable lipid carrier protein or keto acyl-CoA thiolase Ltp3 ltp3 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888279 Rv0687 20140222 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 299 Probable short-chain type dehydrogenase/reductase Rv0687 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888295 Rv3527 20131130 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: Rv3527 mutant is attenuated for intramacrophage survival [PMID:15340136]. 300 Hypothetical protein Rv3527 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888303 Rv2734 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 301 hypothetical protein Rv2734 Bin Zhao, Oliver He supA WEB: http://www.ncbi.nlm.nih.gov/gene 888320 Rv3501c 20140406 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 302 Conserved integral membrane protein YrbE4A Possible ABC transporter - yrbE4A Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888321 Rv2072c 20140329 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 303 Precorrin-6Y C(5,15)-methyltransferase (decarboxylating) CobL cobL Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888337 Rv2231c 20140222 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 304 Possible aminotransferase CobC cobC Bin Zhao, Oliver He mce4 WEB: http://www.ncbi.nlm.nih.gov/gene 888344 Rv3499c 20140222 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 18201981; 19019220; 20980199; 23622789 MUTATION: attenuated in mice [PMID:14569030]. 305 Mce-family protein Mce4A - mce4A Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888350 Rv2048c 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 15611286; 20980199 MUTATION: pks12 mutant is attenuated in mice [PMID:12819062]. 306 Polyketide synthase Pks12 pks12 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888354 Rv3497c 20140222 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 307 Mce-family protein Mce4C mce4C Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888355 Rv2275 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 308 hypothetical protein Rv2275 Bin Zhao, Oliver He mce4E WEB: http://www.ncbi.nlm.nih.gov/gene 888364 Rv3495c 20131130 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 309 Possible Mce-family lipoprotein LprN (Mce-family lipoprotein Mce4E) - lprN Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888387 Rv3534c 20140405 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 310 Probable 4-hydroxy-2-oxovalerate aldolase (HOA) hsaF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888410 Rv3489 20131207 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 311 hypothetical protein Rv3489 Bin Zhao, Oliver He ddl WEB: http://www.ncbi.nlm.nih.gov/gene 888415 Rv2981c 20140405 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199; 23286234 MUTATION: attenuated in mice [PMID:14569030]. 312 Probable D-alanine--D-alanine ligase DdlA (D-alanylalanine synthetase) (D-ala-D-ala ligase) - ddlA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888430 Rv3487c 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 15939293; 17434691; 17869077; 18535356; 18649013; 20980199 MUTATION: lipF mutant is attenuated in mice lungs [PMID:10564470]. 313 Probable esterase/lipase LipF lipF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888445 Rv3484 20140215 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 314 Possible conserved protein CpsA cpsA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888450 Rv3540c 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 315 Probable lipid transfer protein or keto acyl-CoA thiolase Ltp2 ltp2 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888475 Rv3541c 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 316 hypothetical protein Rv3541c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888482 Rv2696c 20140406 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 317 Conserved alanine and glycine and valine rich protein Rv2696c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888486 Rv3542c 20140222 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 318 hypothetical protein Rv3542c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888491 Rv2938 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: drrC mutant is attenuated in mice [PMID:10564470]. 319 Probable daunorubicin-dim-transport integral membrane protein ABC transporter DrrC drrC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888498 Rv2277c 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 320 Possible glycerolphosphodiesterase Rv2277c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888539 Rv2845c 20140406 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 321 Probable prolyl-tRNA synthetase ProS (proline--tRNA ligase) (PRORS) (global RNA synthesis factor) (proline translase) proS Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888560 Rv2857c 20131207 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 322 Probable short-chain type dehydrogenase/reductase Rv2857c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888570 Rv2813 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 323 hypothetical protein Rv2813 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888609 Rv0735 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 16199577; 20980199 MUTATION: sigL mutant is attenuated in mice [PMID:16199577]. 324 Probable alternative RNA polymerase sigma factor SigL sigL Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888646 Rv2998 20131130 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 325 Hypothetical protein Rv2998 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888653 Rv3087 20140406 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 326 Possible triacylglycerol synthase (diacylglycerol acyltransferase) Rv3087 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888694 Rv3258c 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 327 hypothetical protein Rv3258c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888705 Rv3270 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199; 21925112; 23482562 MUTATION: attenuated in mice [PMID:14569030]. 328 Probable metal cation-transporting P-type ATPase C CtpC ctpC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888723 Rv2069 20140222 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 16735723; 20980199; 22015173 MUTATION: sigC mutant is attenuated in mice [PMID:15049808]. 329 RNA polymerase sigma factor, ECF subfamily, SigC sigC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888727 Rv3286c 20140222 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 16735723; 20980199 MUTATION: sigF mutant is attenuated in mice [PMID:14977982]. 330 Alternative RNA polymerase sigma factor SigF sigF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888729 Rv3277 20140406 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 331 Probable conserved transmembrane protein Rv3277 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888743 Rv3246c 20140222 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 16629667; 17511470; 20223818; 20843371; 20980199; 22610443 MUTATION: attenuated in mice [PMID:14569030]. 332 Two component sensory transduction transcriptional regulatory protein MtrA mtrA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888751 Rv1221 20140406 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 16513743; 18192397; 18606740; 18657035; 20980199 MUTATION: sigE mutant is unable to grow in unactivated human and murine macrophages and is more susceptible to killing by activated macrophages than the wild type [PMID:11489128]. 333 Alternative RNA polymerase sigma factor SigE sigE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888772 Rv0757 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 16573683; 18052041; 18065542; 18065544; 18282096; 18757548; 18946503; 19820095; 20363229; 20814030; 20980199; 21634789; 22072719; 22880126 MUTATION: phoP mutant is attenuated in mice [PMID:11454210]. 334 Possible two component system response transcriptional positive regulator PhoP phoP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888778 Rv3168 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199; 21543877 MUTATION: attenuated in mice [PMID:14569030]. 335 Putative aminoglycoside phosphotransferase Rv3168 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888779 Rv3114 20140222 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 336 hypothetical protein Rv3114 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888786 Rv3178 20140215 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 337 hypothetical protein Rv3178 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888798 Rv3103c 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 338 Hypothetical proline-rich protein Rv3103c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888817 Rv2004c 20140406 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 16199660; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 339 hypothetical protein Rv2004c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888821 Rv3229c 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 18723625; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 340 Possible linoleoyl-CoA desaturase (delta(6)-desaturase) desA3 Bin Zhao, Oliver He dosR WEB: http://www.ncbi.nlm.nih.gov/gene 888842 Rv3133c 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 17059468; 18353359; 18359816; 18502855; 19103767; 19487478; 19648251; 20154135; 20195478; 20630871; 20980199; 21304599; 21518251; 21821774; 22142262; 22372912; 22563409; 22984534; 24317401 MUTATION: devR mutant is attenuated in guinea pigs [PMID:14987770]. 341 Two component transcriptional regulatory protein DevR (probably LuxR/UhpA-family) - devR Bin Zhao, Oliver He kefB WEB: http://www.ncbi.nlm.nih.gov/gene 888861 Rv3236c 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 342 Probable conserved integral membrane transport protein - Rv3236c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888866 Rv3050c 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 343 Probable transcriptional regulatory protein (probably AsnC-family) Rv3050c Bin Zhao, Oliver He moeZ WEB: http://www.ncbi.nlm.nih.gov/gene 888871 Rv3206c 20140222 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: moeB1 mutant is attenuated in mice [PMID:17353284]. 344 Probable molybdenum cofactor biosynthesis protein MoeB1 (MPT-synthase sulfurylase) (molybdopterin synthase sulphurylase) - moeB1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888876 Rv3210c 20140322 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 345 hypothetical protein Rv3210c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 888944 Rv2808 20131130 83332 protein-coding NCBI-supplied PMID: 9634230; 12368430; 20980199 MUTATION: attenuated in mice [PMID:14569030]. 346 Hypothetical protein Rv2808 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 889160 jhp0548 20140322 85963 protein-coding NCBI-supplied PMID: 9923682; 14573673; 15962368 MUTATION: mutant strains showed reduced colonization in piglets [PMID:8698465]. 395 flagellin A flaA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 889201 jhp0495 20140406 85963 protein-coding NCBI-supplied PMID: 9923682; 14573673; 15287151; 15377424; 15378755; 15484301; 15526375; 15563842; 15606640; 15628715; 15831497; 15856031; 15972330; 15980153; 16275761; 16367902; 16368981; 16469000; 16618412; 16909137; 17160020; 17194805; 17352012; 17454874; 17520364; 17539287; 17541440; 17728213; 18019737; 18227572; 18300359; 18324914; 18356158; 18483552; 18587223; 18822081; 19029944; 19030199; 19069914; 19147578; 19261108; 19344006; 19364040; 19546211; 19621632; 19798427; 19893742; 19930551; 20107966; 20136573; 20587874; 20676134; 21029692; 21406172; 21509655; 21518972; 21562218; 21859954; 21876621; 22189161; 22348604; 22383989; 22870595; 23163894; 23190390; 23432983; 23652164; 23888551; 24072713 MUTATION: attenuated in monkeys [PMID:18395086]. 396 cag island protein, cytotoxicity associated immunodominant antigen cagA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 889236 jhp0484 20130612 85963 protein-coding NCBI-supplied PMID: 9923682; 14573673 MUTATION: mutant strain adhered less to AGS cells than wild-type strain [PMID:12018657]. 397 cag island protein cagP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 889403 jhp0228 20140405 85963 protein-coding NCBI-supplied PMID: 9923682; 14573673; 16543949; 17237377; 19452583; 19965522; 22750540; 23352965; 24015282 MUTATION: deletion impaired adherence to host cells [PMID:16758245]. 398 neutrophil-activating protein A napA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 889505 jhp0107 20140329 85963 protein-coding NCBI-supplied PMID: 9923682; 14573673 MUTATION: mutant strains showed reduced motility and colonization in piglets [PMID:8698465]. 399 flagellin B flaB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 890058 jhp0833 20130612 85963 protein-coding NCBI-supplied PMID: 9923682; 14573673; 15273394; 16790815; 17202133; 19253298; 19706747; 22822069 MUTATION: modified strain eliminated binding to LEB and gastric tissue [PMID:20123715]. 400 hypothetical protein babA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 890075 jhp0819 20140329 85963 protein-coding NCBI-supplied PMID: 9923682; 14573673; 15606640; 15609407; 15628715; 15817461; 15980153; 16436379; 16552038; 16954403; 17352012; 17520364; 17539287; 17541440; 17591797; 18041306; 18227572; 18395110; 19069914; 19261108; 19798427; 19930551; 20107966; 20136573; 20178613; 20442789; 20615415; 20711119; 21903925; 22320038; 23163894; 23382221 MUTATION: knockout did not result in gastric ulcers in mice compared to wild type [PMID:20046046]. 401 vacuolating cytotoxin vacA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 890411 jhp0063 20140222 85963 protein-coding NCBI-supplied PMID: 9923682; 14573673 MUTATION: urease-negative strain showed reduced colonization in gnotobiotic piglets [PMID:8063376]. 402 urease accessory protein ureG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 895677 CPn0898 20140222 115713 protein-coding NCBI-supplied PMID: 10192388 MUTATION: mutant showed attenuated virulence in lungs of mice [PMID:10736106]. 3937 heat shock protein-60 groEL_3 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 898800 HP1206 20140322 85962 protein-coding NCBI-supplied PMID: 9252185; 10477311; 14500513; 18493595 MUTATION: a HP1206 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646] 347 multidrug resistance protein HetA HP1206 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 898810 HP0295 20140322 85962 protein-coding NCBI-supplied PMID: 9252185; 10477311; 14500513; 18493595 MUTATION: a flgL mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646] 348 flagellar hook-associated protein FlgL flgL Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 898835 HP0350 20140222 85962 protein-coding NCBI-supplied PMID: 9252185; 10477311; 14500513; 18493595 MUTATION: a HP0350 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646] 349 hypothetical protein HP0350 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 898859 HP0758 20140322 85962 protein-coding NCBI-supplied PMID: 9252185; 10477311; 14500513; 18493595 MUTATION: a HP0758 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646] 350 hypothetical protein HP0758 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 898900 HP0392 20140406 85962 protein-coding NCBI-supplied PMID: 9252185; 10477311; 14500513; 18493595 MUTATION: a HP03292 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646] 351 histidine kinase CheA HP0392 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 898975 HP0797 20131024 85962 protein-coding NCBI-supplied PMID: 9252185; 10477311; 14500513; 18493595 MUTATION: a HP0797 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646] 352 flagellar sheath adhesin hpaA HP0797 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 899006 HP0169 20140322 85962 protein-coding NCBI-supplied PMID: 9252185; 10477311; 14500513; 18493595 MUTATION: a HP0169 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646] 353 collagenase PrtC HP0169 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 899058 HP0254 20140215 85962 protein-coding NCBI-supplied PMID: 9252185; 10477311; 14500513; 18493595 MUTATION: a HP0254 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646] 354 hypothetical protein HP0254 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 899097 HP0017 20140222 85962 protein-coding NCBI-supplied PMID: 9252185; 10477311; 14500513; 18493595 MUTATION: a HP0017 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646] 355 protein VirB4 HP0017 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 899104 HP0072 20140405 85962 protein-coding NCBI-supplied PMID: 9252185; 10477311; 14500513; 18493595 MUTATION: a ureC mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646] 356 urease subunit beta ureB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 899174 HP0237 20140406 85962 protein-coding NCBI-supplied PMID: 9252185; 10477311; 14500513; 18493595 MUTATION: a hemC mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646] 357 porphobilinogen deaminase hemC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 899191 HP0055 20140222 85962 protein-coding NCBI-supplied PMID: 9252185; 10477311; 14500513; 18493595 MUTATION: a HP0055 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646] 358 sodium/proline symporter HP0055 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 899197 HP0289 20140322 85962 protein-coding NCBI-supplied PMID: 9252185; 10477311; 14500513; 18493595; 22566509 MUTATION: a HP0289 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646] 359 toxin-like outer membrane protein HP0289 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 899217 HP0360 20140405 85962 protein-coding NCBI-supplied PMID: 9252185; 10477311; 14500513; 18493595 MUTATION: a HP0360 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646] 360 UDP-glucose 4-epimerase HP0360 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 899219 HP0366 20140322 85962 protein-coding NCBI-supplied PMID: 9252185; 10477311; 14500513; 18493595 MUTATION: a HP0366 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646] 361 spore coat polysaccharide biosynthesis protein C HP0366 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 899333 HP0753 20140222 85962 protein-coding NCBI-supplied PMID: 9252185; 10477311; 14500513; 18493595 MUTATION: mutated strain showed a reduction in adherence ability [PMID:12018657]. 362 flagellar protein FliS fliS Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 899346 HP0788 20140322 85962 protein-coding NCBI-supplied PMID: 9252185; 10477311; 14500513; 18493595 MUTATION: a HP0788 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646] 363 hypothetical protein HP0788 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 899388 HP0859 20140405 85962 protein-coding NCBI-supplied PMID: 9252185; 10477311; 14500513; 18493595; 21256827; 21979583 MUTATION: HP0859 knockout mutant exhibited a severe truncation of LPS, a decreased growth rate, and a higher susceptibility to novobiocin. Disruption of HP0859 also reduced the adhesive capacity of H. pylori to AGS cells [PMID:21256827]. 4864 ADP-L-glycero-D-manno-heptose-6-epimerase HP0859 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 899399 HP0870 20140322 85962 protein-coding NCBI-supplied PMID: 9252185; 10477311; 14500513; 18493595 MUTATION: a flgE mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646] 364 flagellar hook protein FlgE flgE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 899436 HP0907 20140322 85962 protein-coding NCBI-supplied PMID: 9252185; 10477311; 14500513; 18493595 MUTATION: a flgD mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646] 365 flagellar basal body rod modification protein flgD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 899459 HP0930 20140405 85962 protein-coding NCBI-supplied PMID: 9252185; 10477311; 14500513; 18493595 MUTATION: a surE mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646] 366 stationary phase survival protein SurE surE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 899505 HP0973 20130612 85962 protein-coding NCBI-supplied PMID: 9252185; 10477311; 14500513; 18493595 MUTATION: a HP0973 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646] 367 hypothetical protein HP0973 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 899566 HP1031 20140406 85962 protein-coding NCBI-supplied PMID: 9252185; 10477311; 14500513; 18493595; 23614777 MUTATION: mutated strain showed a reduction in adherence ability [PMID:12018657]. 368 flagellar motor switch protein FliM fliM Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 899618 HP1082 20140322 85962 protein-coding NCBI-supplied PMID: 9252185; 10477311; 14500513; 18493595 MUTATION: a HP1082 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646] 369 multidrug resistance protein MsbA HP1082 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 899627 HP1091 20140222 85962 protein-coding NCBI-supplied PMID: 9252185; 10477311; 14500513; 18493595 MUTATION: a HP1091 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646] 370 alpha-ketoglutarate permease HP1091 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 899628 HP1092 20140406 85962 protein-coding NCBI-supplied PMID: 9252185; 10477311; 14500513; 18493595 MUTATION: a HP1092 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646] 371 flagellar basal-body rod protein FlgG HP1092 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 899733 HP1558 20140322 85962 protein-coding NCBI-supplied PMID: 9252185; 10477311; 14500513; 18493595 MUTATION: a flgC mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646] 372 flagellar basal body rod protein FlgC flgC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 899766 HP1525 20140322 85962 protein-coding NCBI-supplied PMID: 9252185; 10477311; 14500513; 18493595 MUTATION: a HP1525 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646] 373 hypothetical protein HP1525 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 899785 HP1506 20140222 85962 protein-coding NCBI-supplied PMID: 9252185; 10477311; 14500513; 18493595 MUTATION: a HP1506 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646] 374 glutamate permease GltS HP1506 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 899806 HP1486 20140322 85962 protein-coding NCBI-supplied PMID: 9252185; 10477311; 14500513; 18493595 MUTATION: a HP1486 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646] 375 hypothetical protein HP1486 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 899874 HP1421 20140315 85962 protein-coding NCBI-supplied PMID: 9252185; 10477311; 14500513; 18493595 MUTATION: a HP1421 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646] 376 conjugative transfer regulon protein TrbB HP1421 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 899875 HP1420 20140322 85962 protein-coding NCBI-supplied PMID: 9252185; 10477311; 14500513; 16260786; 18493595 MUTATION: a fliI mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646] 377 flagellum-specific ATP synthase fliI Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 899876 HP1419 20140322 85962 protein-coding NCBI-supplied PMID: 9252185; 10477311; 14500513; 18493595 MUTATION: mutated strain showed a reduction in adherence ability [PMID:12018657]. 378 flagellar biosynthesis protein FliQ fliQ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 899977 HP0601 20140329 85962 protein-coding NCBI-supplied PMID: 9252185; 10477311; 14500513; 18493595 MUTATION: a HP0601 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646] 379 flagellin A HP0601 MUTATION: a fliP mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646] 380 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 899986 HP0067 20140406 85962 protein-coding NCBI-supplied PMID: 9252185; 10477311; 14500513; 18493595; 22013070 MUTATION: a HP0067 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646] 381 urease accessory protein UreH HP0067 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 899995 HP0071 20140406 85962 protein-coding NCBI-supplied PMID: 9252185; 10477311; 14500513; 18493595; 19854893; 21877689 MUTATION: a HP0071 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646] 382 urease accessory protein UreI HP0071 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 899996 HP0393 20140405 85962 protein-coding NCBI-supplied PMID: 9252185; 10477311; 14500513; 18493595 MUTATION: a HP0393 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646] 383 chemotaxis protein CheV HP0393 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 900004 HP0752 20140322 85962 protein-coding NCBI-supplied PMID: 9252185; 10477311; 14500513; 18493595 MUTATION: a fliD mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646] 384 flagellar capping protein fliD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 900059 HP0486 20140406 85962 protein-coding NCBI-supplied PMID: 9252185; 10477311; 14500513; 18493595 MUTATION: a HP0486 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646] 385 hypothetical protein HP0486 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 900108 HP0288 20140222 85962 protein-coding NCBI-supplied PMID: 9252185; 10477311; 14500513; 18493595 MUTATION: a HP0288 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646] 386 hypothetical protein HP0288 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 900123 HP0245 20140322 85962 protein-coding NCBI-supplied PMID: 9252185; 10477311; 14500513; 18493595 MUTATION: a HP0245 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646] 387 hypothetical protein HP0245 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 900171 HP0073 20140405 85962 protein-coding NCBI-supplied PMID: 9252185; 10477311; 14500513; 18493595 MUTATION: a HP0073 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646] 388 urease subunit alpha HP0073 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 900177 HP0232 20140322 85962 protein-coding NCBI-supplied PMID: 9252185; 10477311; 14500513; 18493595 MUTATION: a HP0232 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646] 389 hypothetical protein HP0232 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 900194 HP0302 20140222 85962 protein-coding NCBI-supplied PMID: 9252185; 10477311; 14500513; 18493595 MUTATION: a HP0302 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646] 390 dipeptide ABC transporter ATP-binding protein DppF HP0302 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 900196 HP0325 20140406 85962 protein-coding NCBI-supplied PMID: 9252185; 10477311; 14500513; 18493595 MUTATION: a flgH mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646] 391 flagellar basal body L-ring protein flgH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 900244 HP0397 20140405 85962 protein-coding NCBI-supplied PMID: 9252185; 10477311; 14500513; 18493595 MUTATION: a HP0397 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646] 392 D-3-phosphoglycerate dehydrogenase HP0397 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 900248 HP0714 20140322 85962 protein-coding NCBI-supplied PMID: 9252185; 10477311; 14500513; 16684097; 18493595; 19383688 MUTATION: a HP0714 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646] 393 RNA polymerase factor sigma-54 HP0714 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 900354 HP0351 20130612 85962 protein-coding NCBI-supplied PMID: 9252185; 10477311; 14500513; 18493595 MUTATION: a fliF mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646] 394 flagellar MS-ring protein fliF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 900379 SPy_0019 20140406 160490 protein-coding NCBI-supplied PMID: 11296296 MUTATION: SPy_0019 (cdhA) mutant has severe cell division, growth defects and is attenuated in mice [PMID:20643653]. 4271 hypothetical protein SPy_0019 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 900488 SPy_0165 20140222 160490 protein-coding NCBI-supplied PMID: 11296296; 21300288; 23762025 MUTATION: nga mutant is attenuated in mice [PMID:20470439]. 4272 NAD glycohydrolase nga Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 900684 SPy_0436 20130628 160490 protein-coding NCBI-supplied PMID: 11296296 exotoxin speJ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 900920 SPy_0738 20130628 160490 protein-coding NCBI-supplied PMID: 11296296; 17635862; 19016875 MUTATION: sagA mutant is attenuated in mice [PMID:9529097]. 4274 streptolysin S associated protein sagA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 900995 SPy_0826 20140222 160490 protein-coding NCBI-supplied PMID: 11296296 MUTATION: lsp mutant is attenuated in a murine model of soft tissue infection [PMID:19398546]. 4275 lipoprotein signal peptidase lsp Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 901401 SPy_1312 20130628 160490 protein-coding NCBI-supplied PMID: 11296296 MUTATION: dltA mutant was diminished in its ability to adhere to and invade cultured human pharyngeal epithelial cells [PMID:16166534]. 4276 D-alanine--poly(phosphoribitol) ligase subunit 1 dltA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 901674 SPy_2010 20130628 160490 protein-coding NCBI-supplied PMID: 11296296 MUTATION: scpA mutant is attenuated in mouse pneumonia model [PMID:9119483]. 4277 C5A peptidase scpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 901676 SPy_2016 20140222 160490 protein-coding NCBI-supplied PMID: 11296296; 15769742; 16508336; 20705662; 20814187 MUTATION: sic mutant was phagocytosed and killed by human polymorphonuclear leukocytes significantly better than the wild-type strain [PMID:12032337]. 4278 inhibitor of complement-mediated lysis sic Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 901677 SPy_2018 20130628 160490 protein-coding NCBI-supplied PMID: 11296296; 18323455 MUTATION: emm1 mutant had greatly reduced invasion of HeLa cells [PMID:10048029]. 4279 M protein type 1 emm1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 901678 SPy_2019 20140215 160490 protein-coding NCBI-supplied PMID: 11296296; 15547255; 16513733; 22468267; 23651410 MUTATION: mga mutant is attenuated in a humanized mouse model for superficial skin infection [PMID:18588968]. 4280 M protein trans-acting positive regulator mga Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 901690 SPy_2039 20140406 160490 protein-coding NCBI-supplied PMID: 11296296; 15520011; 16790522; 16950917; 16980693; 18182097; 19116661; 19274094; 22163320; 23532847 MUTATION: Mice infected by M1, M3 and M49 speB mutants, through air pouch or intraperitoneal challenge, showed less mortality compared with that of the wild-type strains [PMID:18796357]. 4281 pyrogenic exotoxin B speB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 901831 SPy_2185 20130628 160490 protein-coding NCBI-supplied PMID: 11296296 MUTATION: gidA mutant is highly attenuated in the murine ulcer model of soft tissue infection [PMID:18426891]. 4282 tRNA uridine 5-carboxymethylaminomethyl modification protein GidA gidA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 901885 SPy_1633 20140406 160490 protein-coding NCBI-supplied PMID: 11296296 MUTATION: SPy_1633 (cvfA) mutant is attenuated in mice [PMID:20385762]. 4283 hypothetical protein SPy_1633 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 901955 SPy_1718 20130628 160490 protein-coding NCBI-supplied PMID: 11296296 MUTATION: SPy_1718 (sse) mutant is attenuated in mice [PMID:19805529]. 4284 esterase SPy_1718 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 902096 SPy_1889 20140405 160490 protein-coding NCBI-supplied PMID: 11296296 MUTATION: fba mutant showed diminished invasive capabilities to HEp-2 cells and low mortality in mice following skin infection [PMID:11679068]. 4285 fructose-bisphosphate aldolase fba Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 902133 NMB0030 20140329 122586 protein-coding NCBI-supplied PMID: 10710307 MUTATION: metG mutant is attenuated in rats [PMID:11062540]. 2980 methionyl-tRNA synthetase metG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 902187 NMB0083 20140406 122586 protein-coding NCBI-supplied PMID: 10710307 MUTATION: lipB mutant is attenuated in rats [PMID:11062540]. 2981 capsule polysaccharide modification protein lipB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 902207 NMB0103 20140222 122586 protein-coding NCBI-supplied PMID: 10710307 MUTATION: NMB0103 mutant was unable to colonize human nasopharyngeal tissue in an organ culture model [PMID:18936183]. 2982 bacteriocin resistance protein NMB0103 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 902216 NMB0112 20130709 122586 protein-coding NCBI-supplied PMID: 10710307 MUTATION: rsmB mutant is attenuated in rats [PMID:11062540]. 2983 16S RNA methyltransferase rsmB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 902220 NMB0116 20140222 122586 protein-coding NCBI-supplied PMID: 10710307 MUTATION: dprA mutant is attenuated in rats [PMID:11062540]. 2984 DNA processing protein DprA dprA Bin Zhao, Oliver He tuf WEB: http://www.ncbi.nlm.nih.gov/gene 902247 NMB0139 20140215 122586 protein-coding NCBI-supplied PMID: 10710307 MUTATION: tufA mutant is attenuated in rats [PMID:11062540]. 2985 elongation factor Tu - tufA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 902285 NMB0178 20140406 122586 protein-coding NCBI-supplied PMID: 10710307 MUTATION: lpxA mutant is attenuated in mice [PMID:16988225]. 2986 UDP-N-acetylglucosamine acyltransferase lpxA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 902423 NMB0307 20140329 122586 protein-coding NCBI-supplied PMID: 10710307 MUTATION: aroG mutant is attenuated in rats [PMID:11062540]. 2987 phospho-2-dehydro-3-deoxyheptonate aldolase aroG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 902429 NMB0313 20140322 122586 protein-coding NCBI-supplied PMID: 10710307 MUTATION: NMB0313 mutant was unable to colonize human nasopharyngeal tissue in an organ culture model [PMID:18936183]. 2988 hypothetical protein NMB0313 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 902445 NMB0329 20140222 122586 protein-coding NCBI-supplied PMID: 10710307 MUTATION: pilF mutant were unable to colonize human nasopharyngeal tissue in an organ culture model [PMID:18936183]. 2989 type IV pilus assembly protein pilF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 902474 NMB0358 20140405 122586 protein-coding NCBI-supplied PMID: 10710307 MUTATION: aroE mutant is attenuated in rats [PMID:11062540]. 2990 shikimate dehydrogenase aroE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 902509 NMB0394 20140329 122586 protein-coding NCBI-supplied PMID: 10710307; 19400792; 20041170; 21292554; 23290624 MUTATION: NadA mutation decreases epithelial adhesion of capsulate N. meningitidis and invasion by acapsulate N. meningitidis [PMID:19481311]. 2991 quinolinate synthetase nadA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 902656 NMB0541 20140406 122586 protein-coding NCBI-supplied PMID: 10710307; 22373915 MUTATION: NMB0541 mutant was unable to colonize human nasopharyngeal tissue in an organ culture model [PMID:18936183]. 2992 hypothetical protein NMB0541 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 902749 NMB0638 20140405 122586 protein-coding NCBI-supplied PMID: 10710307 MUTATION: galU mutant is attenuated in rats [PMID:11062540]. 2993 UTP-glucose-1-phosphate uridylyltransferase galU Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 902779 NMB0668 20140217 122586 protein-coding NCBI-supplied PMID: 10710307 MUTATION: ampD mutant is attenuated in rats [PMID:11062540]. 2994 N-acetyl-anhydromuranmyl-L-alanine amidase ampD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 902798 NMB0686 20140322 122586 protein-coding NCBI-supplied PMID: 10710307 MUTATION: rnc mutant is attenuated in rats [PMID:11062540]. 2995 ribonuclease III rnc Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 902863 NMB0748 20140217 122586 protein-coding NCBI-supplied PMID: 10710307; 19223479; 19374669; 20430815; 21338417 MUTATION: hfq mutant is attenuated in rats [PMID:19223479]. 2996 host factor-I hfq Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 902905 NMB0790 20140405 122586 protein-coding NCBI-supplied PMID: 10710307 MUTATION: pgm mutant is attenuated in mice [PMID:16428785]. 2997 phosphoglucomutase pgm Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 902942 NMB0828 20140406 122586 protein-coding NCBI-supplied PMID: 10710307 MUTATION: rfaD mutant is attenuated in mice [PMID:16988225]. 2998 ADP-L-glycero-D-manno-heptose-6-epimerase rfaD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 903063 NMB0943 20140406 122586 protein-coding NCBI-supplied PMID: 10710307 MUTATION: metF mutant is attenuated in rats [PMID:11062540]. 2999 5,10-methylenetetrahydrofolate reductase metF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 903064 NMB0944 20140405 122586 protein-coding NCBI-supplied PMID: 10710307 MUTATION: metF mutant is attenuated in rats [PMID:11062540]. 3000 5-methyltetrahydropteroyltriglutamate/homocysteine S-methyltransferase metH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 903122 NMB1812 20140322 122586 protein-coding NCBI-supplied PMID: 10710307; 18174140 MUTATION: pilQ mutant were unable to colonize human nasopharyngeal tissue in an organ culture model [PMID:18936183]. 3001 pilQ protein pilQ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 903150 NMB1012 20140215 122586 protein-coding NCBI-supplied PMID: 10710307 MUTATION: NMB1012 mutant was unable to colonize human nasopharyngeal tissue in an organ culture model [PMID:18936183]. 3002 hypothetical protein NMB1012 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 903189 NMB1052 20130709 122586 protein-coding NCBI-supplied PMID: 10710307 MUTATION: dedA mutant is attenuated in rats [PMID:11062540]. 3003 dedA protein dedA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 903235 NMB1053 20140222 122586 protein-coding NCBI-supplied PMID: 10710307; 19016781; 20502634 class 5 outer membrane protein opc Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 903260 NMB1839 20140405 122586 protein-coding NCBI-supplied PMID: 10710307 MUTATION: fhs mutant is attenuated in rats [PMID:11062540]. 3005 formate--tetrahydrofolate ligase fhs Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 903271 NMB1829 20140215 122586 protein-coding NCBI-supplied PMID: 10710307 MUTATION: NMB1829 mutant was unable to colonize human nasopharyngeal tissue in an organ culture model [PMID:18936183]. 3006 TonB-dependent receptor NMB1829 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 903286 NMB1814 20140405 122586 protein-coding NCBI-supplied PMID: 10710307 MUTATION: aroB mutant is attenuated in rats [PMID:11062540]. 3007 3-dehydroquinate synthase aroB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 903309 NMB1790 20140322 122586 protein-coding NCBI-supplied PMID: 10710307 MUTATION: grxC mutant is attenuated in rats [PMID:11062540]. 3008 glutaredoxin 3 grxC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 903369 NMB1730 20140222 122586 protein-coding NCBI-supplied PMID: 10710307 MUTATION: tonB mutant is unable to replicate within human epithelial cells [PMID:11854233]. 3009 TonB protein tonB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 903370 NMB1729 20130724 122586 protein-coding NCBI-supplied PMID: 10710307 MUTATION: exbB mutant is attenuated in rats [PMID:11062540]. 3010 biopolymer transport protein exbB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 903371 NMB1728 20140322 122586 protein-coding NCBI-supplied PMID: 10710307 MUTATION: exbD mutant is attenuated in rats [PMID:11062540]. 3011 biopolymer transport protein exbD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 903375 NMB1726 20130709 122586 protein-coding NCBI-supplied PMID: 10710307 MUTATION: NMB1726 mutant was unable to colonize human nasopharyngeal tissue in an organ culture model [PMID:18936183]. 3012 hypothetical protein NMB1726 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 903392 NMB1710 20140405 122586 protein-coding NCBI-supplied PMID: 10710307 MUTATION: gdhA mutant is attenuated in rats [PMID:11062540]. 3013 glutamate dehydrogenase gdhA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 903397 NMB1705 20140222 122586 protein-coding NCBI-supplied PMID: 10710307 MUTATION: rfaK mutant is attenuated in rats [PMID:11062540]. 3014 alpha 1,2 N-acetylglucosamine transferase rfaK Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 903428 NMB1680 20140405 122586 protein-coding NCBI-supplied PMID: 10710307 MUTATION: aroC mutant is attenuated in rats [PMID:11062540]. 3015 chorismate synthase aroC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 903442 NMB1668 20140406 122586 protein-coding NCBI-supplied PMID: 10710307 MUTATION: hmbR mutant was attenuated in an infant rat model [PMID:7783623]. 3016 hemoglobin receptor hmbR Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 903566 NMB1145 20140322 122586 protein-coding NCBI-supplied PMID: 10710307 MUTATION: mpl-1 mutant is attenuated in rats [PMID:11062540]. 3017 UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-diaminopimelate ligase mpl-1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 903866 NMB1446 20140405 122586 protein-coding NCBI-supplied PMID: 10710307 MUTATION: aroD mutant is attenuated in rats [PMID:11062540]. 3018 3-dehydroquinate dehydratase aroD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 903951 NMB1638 20140222 122586 protein-coding NCBI-supplied PMID: 10710307 MUTATION: MNB1638 (lptA) mutant had an approximately 10-fold decrease in N. meningitidis adhesion to four kinds of human endothelial and epithelial cell lines at an multiplicity of infection of 5,000 [PMID:18824535]. 3019 hypothetical protein NMB1638 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 904029 NMB1527 20140329 122586 protein-coding NCBI-supplied PMID: 10710307 MUTATION: rfaF mutant is attenuated in rats [PMID:11062540]. 3020 ADP-heptose--LPS heptosyltransferase rfaF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 904045 NMB2045 20140322 122586 protein-coding NCBI-supplied PMID: 10710307 MUTATION: ptsH mutant is attenuated in rats [PMID:11062540]. 3021 sugar transport PTS system phosphocarrier protein HPr ptsH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 904047 NMB2044 20140222 122586 protein-coding NCBI-supplied PMID: 10710307 MUTATION: ptsI mutant is attenuated in rats [PMID:11062540]. 3022 phosphoenolpyruvate-protein phosphotransferase ptsI Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 904121 NMB1558 20140405 122586 protein-coding NCBI-supplied PMID: 10710307 MUTATION: dgkA mutant is attenuated in rats [PMID:11062540]. 3023 diacylglycerol kinase dgkA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 904131 NMB1996 20140405 122586 protein-coding NCBI-supplied PMID: 10710307 MUTATION: purL mutant is attenuated in rats [PMID:11062540]. 3024 phosphoribosylformylglycinamidine synthase purL Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 904178 NMB1966 20140215 122586 protein-coding NCBI-supplied PMID: 10710307; 19050914 MUTATION: NMB1966 mutant was less adhesive and invasive for human bronchial epithelial cells, had reduced survival in human blood and was attenuated in a systemic mouse model of infection [PMID:19050914]. 3025 ABC transporter ATP-binding protein NMB1966 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 904184 NMB1577 20140405 122586 protein-coding NCBI-supplied PMID: 10710307 MUTATION: ilvI mutant is attenuated in rats [PMID:11062540]. 3026 acetolactate synthase isozyme III large subunit ilvI Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 904226 NMB1929 20130709 122586 protein-coding NCBI-supplied PMID: 10710307 MUTATION: lgtA mutant is attenuated in rats [PMID:11062540]. 3027 lacto-N-neotetraose biosynthesis glycosyl transferase lgtA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 904357 Cj0019c 20140315 192222 protein-coding NCBI-supplied PMID: 10688204; 17565669 MUTATION: a Cj0019c C. jejuni mutant was attenuated for colonization of the chick caeca [PMID:15066034] 802 MCP-domain signal transduction protein Cj0019c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 904360 Cj0020c 20140222 192222 protein-coding NCBI-supplied PMID: 10688204; 17565669 MUTATION: a Cj0020c C. jejuni mutant was attenuated for colonization of the chick caeca [PMID:15066034] 803 cytochrome C551 peroxidase Cj0020c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 904393 Cj0061c 20140222 192222 protein-coding NCBI-supplied PMID: 10688204; 17565669; 17768253 MUTATION: fliA mutants showed reduced motility (25% that of the wild type) and did not colonize a chicken cecum [PMID:17761334] 804 flagellar biosynthesis sigma factor fliA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 904574 Cj0248 20140222 192222 protein-coding NCBI-supplied PMID: 10688204; 16287129; 17565669 MUTATION: a Cj0248 C. jejuni mutant was attenuated for colonization of the chick caeca [PMID:15066034] 805 hypothetical protein Cj0248 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 904660 Cj0336c 20140329 192222 protein-coding NCBI-supplied PMID: 10688204; 17565669; 23678739 MUTATION: a Cj0336c mutant C. jejuni was attenuated for colonization of the chicken caeca [PMID:15066034] 806 flagellar motor protein MotB motB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 904661 Cj0337c 20140405 192222 protein-coding NCBI-supplied PMID: 10688204; 17565669; 23678739 MUTATION: a Cj0337c C. jejuni mutant was attenuated for colonization of the chicken caeca [PMID:15066034] 807 flagellar motor protein MotA motA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 904739 Cj0415 20140405 192222 protein-coding NCBI-supplied PMID: 10688204; 17565669 MUTATION: a cj0415 mutant was impaired in establishing chicken colonization [PMID:18284594] 808 GMC oxidoreductase subunit Cj0415 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 904777 Cj0454c 20130526 192222 protein-coding NCBI-supplied PMID: 10688204; 17565669 MUTATION: a Cj0454c C. jejuni mutant was attenuated for colonziation of the chick caeca [PMID:15066034] 809 hypothetical protein Cj0454c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 904779 Cj0456c 20130526 192222 protein-coding NCBI-supplied PMID: 10688204; 17565669 MUTATION: a Cj0456c C. jejuni mutant was attenuated for colonization of the chick caeca [PMID:15066034] 810 hypothetical protein Cj0456c MUTATION: a Cj0618 C. jejuni mutant was attenuated for the colonization of the chick caeca [PMID:15066034] 811 MUTATION: Cj0629 (capA) mutant had a significantly reduced capacity for association with and invasion of Caco-2 cells and failed to colonize and persist in chickens [PMID:17172331]. 812 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 904991 Cj0670 20140222 192222 protein-coding NCBI-supplied PMID: 10688204; 17565669 MUTATION: rpoN mutant cells lacked the spiral shape of C. jejuni and motility was reduced to 10% of the wild-type, mutants also showed significant colonization defects of a chicken cecum [PMID:17761334] 813 RNA polymerase factor sigma-54 rpoN Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 905007 Cj0688 20140405 192222 protein-coding NCBI-supplied PMID: 10688204; 17565669 MUTATION: a Cj0688 C. jejuni mutant was attenuated for colonization of the chick caeca [PMID:15066034] 814 phosphate acetyltransferase pta Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 905038 Cj0720c 20140405 192222 protein-coding NCBI-supplied PMID: 10688204; 17565669 MUTATION: Invasion of HEp-2 cells by flaC null mutants was reduced to a level of 14% compared with wild type [PMID:15228533] 815 flagellin flaC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 905201 Cj0903c 20140406 192222 protein-coding NCBI-supplied PMID: 10688204; 17565669 MUTATION: a Cj0903c C. jejuni mutant was attenuated for colonization of the chick caeca [PMID:15066034] 816 amino acid transport protein Cj0903c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 905214 Cj0914c 20130905 192222 protein-coding NCBI-supplied PMID: 10688204; 17565669 MUTATION: C. jejuni ciaB null mutants had a significant reduction in internalization [PMID:10361274] 817 invasion antigen CiaB ciaB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 905232 Cj0938c 20140215 192222 protein-coding NCBI-supplied PMID: 10688204; 17565669 MUTATION: a Cj0938c (aas) C. jejuni mutant was attenuated for colonization of the chick caeca [PMID:15066034] 818 2-acylglycerophosphoethanolamine acyltransferase aas Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 905268 Cj0977 20130526 192222 protein-coding NCBI-supplied PMID: 10688204; 16369037; 17565669 MUTATION: A Cj0977 mutant strain is fully motile but significantly reduced in the invasion of intestinal epithelial cells in vitro [PMID:18835274] 819 hypothetical protein Cj0977 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 905311 Cj1019c 20140405 192222 protein-coding NCBI-supplied PMID: 10688204; 17565669 MUTATION: a Cj1019c (livJ) C. jejuni mutant was attenuated for colonization of the chick caeca [PMID:15066034] 820 branched-chain amino acid ABC transporter substrate-binding protein livJ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 905409 Cj1118c 20140315 192222 protein-coding NCBI-supplied PMID: 10688204; 17565669 MUTATION: a Cj1118c (cheY) C. jejuni mutant was attenuated for the colonization of chick caeca [PMID:15066034] 821 chemotaxis regulatory protein cheY Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 905411 Cj1120c 20140322 192222 protein-coding NCBI-supplied PMID: 10688204; 17565669 MUTATION: a Cj1120c C. jejuni mutant was attenuated for colonization of the chick caeca [PMID:15066034] 822 UDP-GlcNAc C4,6 dehydratase pglF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 905412 Cj1121c 20140322 192222 protein-coding NCBI-supplied PMID: 10688204; 16690622; 17565669 UDP-4-keto-6-deoxy-GlcNAc C4 aminotransferase pglE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 905420 Cj1129c 20140322 192222 protein-coding NCBI-supplied PMID: 10688204; 17565669 MUTATION: a Cj1129c C. jejuni mutant was attenuated for colonization of the chick caeca [PMID:15066034] 824 GalNAc transferase/polymerase pglH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 905469 Cj1179c 20140222 192222 protein-coding NCBI-supplied PMID: 10688204; 17565669 MUTATION: a Cj1179c C. jejuni mutant was attenuated for colonization of the chick caeca [PMID:15066034] 825 flagellar biosynthesis protein FliR fliR Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 905513 Cj1223c 20130526 192222 protein-coding NCBI-supplied PMID: 10688204; 17565669; 20348251 MUTATION: A DeltadccR (Delta Cj1223c) response regulator mutant exhibited significantly reduced colonization of immunocompetent limited flora (I-LF) mice [PMID:15554967] 826 two-component regulator dccR Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 905521 Cj1230 20140222 192222 protein-coding NCBI-supplied PMID: 10688204; 17565669; 19850618 MUTATION: hspR mutant was unable to form colonies at 44 degrees C [PMID:15758235] 827 heat shock transcriptional regulator hspR Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 905551 Cj1260c 20140406 192222 protein-coding NCBI-supplied PMID: 10688204; 17565669 MUTATION: a C. jejuni DnaJ mutant was unable to colonize newly hatched Leghorn chickens [PMID:9673247] 828 molecular chaperone DnaJ dnaJ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 905570 Cj1279c 20140222 192222 protein-coding NCBI-supplied PMID: 10688204; 17565669 MUTATION: Cj1279c mutants had a significantly reduced adherence to chicken epithelial cells [PMID:19349427] 829 fibronectin domain-containing lipoprotein Cj1279c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 905608 Cj1316c 20140215 192222 protein-coding NCBI-supplied PMID: 10688204; 17565669 MUTATION: Mutation of Cj1316c or pseA had been shown to result in loss of PseAm. C jejuni that produced flagella lacking PseAm failed to autoagglutinate. Mutants (81-176) defective in autoagglutination showed a modest reduction in adherence and invasion of INT407 cells [PMID:16573682] 830 pseudaminic acid biosynthesis PseA protein pseA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 905613 Cj1321 20130905 192222 pseudo NCBI-supplied MUTATION: colonization of chick ceca by a Δ(Cj1321-Cj1325/6) mutant was reduced [PMID:19307210] 831 pseudo Cj1321 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 905614 Cj1322 20130905 192222 pseudo NCBI-supplied pseudo Cj1322 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 905616 Cj1324 20140222 192222 protein-coding NCBI-supplied PMID: 10688204; 17565669; 19307210 MUTATION: A motile ΔCj1324 mutant with intact flagella was considerably less hydrophobic, less able to autoagglutinate and form biofilms, and less able to colonize chickens than the parent strain [PMID:19307210] 834 hypothetical protein Cj1324 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 905617 Cj1325 20140315 192222 protein-coding NCBI-supplied PMID: 10688204; 17565669 methyltransferase Cj1325 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 905630 Cj1338c 20140329 192222 protein-coding NCBI-supplied PMID: 10688204; 17565669 flagellin flaB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 905631 Cj1339c 20140322 192222 protein-coding NCBI-supplied PMID: 10688204; 17340996; 17565669; 20936115; 21158479 MUTATION: nonflagellated, nonmotile (flaA flaB Mot-) mutants of C. jejuni had a 30%-40% decrease in INT 407 cell internalization [PMID:8478066] 838 flagellin flaA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 905641 Cj1349c 20140217 192222 protein-coding NCBI-supplied PMID: 10688204; 17565669 MUTATION: Cj1349c mutants had a significantly reduced ability to colonize chicken epithelial cells [PMID:19349427] 839 fibronectin/fibrinogen-binding protein Cj1349c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 905643 Cj1351 20140406 192222 protein-coding NCBI-supplied PMID: 10688204; 17565669 MUTATION: a mutation in the pldA gene impairs the ability of C. jejuni to colonize the cecum [PMID:11569726] 840 phospholipase A pldA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 905749 Cj1461 20140405 192222 protein-coding NCBI-supplied PMID: 10688204; 17565669 MUTATION: A Deltacj1461 mutant was sevenfold more adherent to but 50-fold less invasive of INT-407 human epithelial cells than the wild type [PMID:18689478] 841 DNA methylase Cj1461 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 905754 Cj1466 20130526 192222 protein-coding NCBI-supplied PMID: 10688204; 17565669 MUTATION: a flgK mutant of C. jejuni expressing only the hook filament junction protein showed diminished motility and was completely attenuated for cecal colonization in chickens [PMID:17761334] 842 flagellar hook-associated protein FlgK flgK Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 905864 Cj1565c 20140406 192222 protein-coding NCBI-supplied PMID: 10688204; 17565669 paralysed flagellum protein pflA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 905896 Cj1624c 20140406 192222 protein-coding NCBI-supplied PMID: 10688204; 17565669 MUTATION: sdaA mutants completely failed to colonize 3-week-old chickens as assayed both by cloacal swabs taken over a 6-week period and by cecal colony counts postmortem [PMID:14688104] 844 L-serine dehydratase sdaA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 906008 Cj0921c 20140215 192222 protein-coding NCBI-supplied PMID: 10688204; 16689801; 17565669; 17631313 MUTATION: reduced adherence to epithelial cells, attenuated in mice [PMID:9488379]. 845 bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein peb1A Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 906200 NMA0185 20140222 122587 protein-coding NCBI-supplied PMID: 10761919; 15378741 MUTATION: lipB mutant is attenuated in rats [PMID:11062540]. 2947 capsule polysaccharide modification protein NMA0185 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 906284 NMA0275 20140322 122587 protein-coding NCBI-supplied PMID: 10761919; 15378741 MUTATION: metG mutant is attenuated in rats [PMID:11062540]. 2948 methionyl-tRNA synthetase metG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 906394 NMA0391 20130526 122587 protein-coding NCBI-supplied PMID: 10761919; 15378741 MUTATION: ptsH mutant is attenuated in rats [PMID:11062540]. 2949 sugar transport PTS system phosphocarrier protein HPR NMA0391 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 906395 NMA0392 20140406 122587 protein-coding NCBI-supplied PMID: 10761919; 15378741 MUTATION: ptsI mutant is attenuated in rats [PMID:11062540]. 2950 phosphoenolpyruvate-protein phosphotransferase NMA0392 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 906445 NMA0445 20140405 122587 protein-coding NCBI-supplied PMID: 10761919; 15378741 MUTATION: purL mutant is attenuated in rats [PMID:11062540]. 2951 phosphoribosylformylglycinamidine synthase purL Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 906518 NMA0524 20140406 122587 protein-coding NCBI-supplied PMID: 10761919; 15378741 MUTATION: lgtA mutant is attenuated in rats [PMID:11062540]. 2952 lacto-N-neotetraose biosynthesis glycosyl transferase NMA0524 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 906580 NMA0587 20140406 122587 protein-coding NCBI-supplied PMID: 10761919; 15378741 MUTATION: fba mutant is attenuated in rats [PMID:11062540]. 2953 fructose-1,6-bisphosphate aldolase fba Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 906612 NMA0617 20140405 122587 protein-coding NCBI-supplied PMID: 10761919; 15378741 MUTATION: fhs mutant is attenuated in rats [PMID:11062540] 2954 formate--tetrahydrofolate ligase fhs Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 906642 NMA0647 20140405 122587 protein-coding NCBI-supplied PMID: 10761919; 15378741 MUTATION: aroB mutant is attenuated in rats [PMID:11062540]. 2955 3-dehydroquinate synthase aroB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 906644 NMA0650 20140222 122587 protein-coding NCBI-supplied PMID: 10761919; 15378741 MUTATION: pilQ mutant were unable to colonize human nasopharyngeal tissue in an organ culture model [PMID:18936183]. 2956 pilus secretin NMA0650 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 906788 NMA0798 20140222 122587 protein-coding NCBI-supplied PMID: 10761919; 15378741 MUTATION: NMA0798 (phoP) mutant is avirulent in mice [PMID:14688113]. 2957 two-component system regulator NMA0798 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 906836 NMA0848 20140405 122587 protein-coding NCBI-supplied PMID: 10761919; 15378741 MUTATION: galU mutant is attenuated in rats [PMID:11062540]. 2958 UTP--glucose-1-phosphate uridylyltransferase NMA0848 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 906854 NMA0867 20140222 122587 protein-coding NCBI-supplied PMID: 10761919; 15378741 MUTATION: ampD mutant is attenuated in rats [PMID:11062540]. 2959 N-acetyl-anhydromuranmyl-L-alanine amidase ampD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 906875 NMA0888 20140406 122587 protein-coding NCBI-supplied PMID: 10761919; 15378741 MUTATION: rnc mutant is attenuated in rats [PMID:11062540]. 2960 ribonuclease III rnc Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 907010 NMA1034 20140222 122587 protein-coding NCBI-supplied PMID: 10761919; 15378741 MUTATION: rfaE mutant is attenuated in rats [PMID:11062540]. 2961 DP-heptose synthetase NMA1034 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 907108 NMA1139 20140405 122587 protein-coding NCBI-supplied PMID: 10761919; 15378741 MUTATION: metF mutant is attenuated in rats [PMID:11062540]. 2962 5,10-methylenetetrahydrofolate reductase metF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 907187 NMA1964 20140405 122587 protein-coding NCBI-supplied PMID: 10761919; 15378741 MUTATION: gdhA mutant is attenuated in rats [PMID:11062540]. 2963 glutamate dehydrogenase gdhA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 907267 NMA2180 20140405 122587 protein-coding NCBI-supplied PMID: 10761919; 15378741 MUTATION: aroG mutant is attenuated in rats [PMID:11062540]. 2964 phospho-2-dehydro-3-deoxyheptonate aldolase aroG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 907288 NMA2159 20140222 122587 protein-coding NCBI-supplied PMID: 10761919; 15378741 MUTATION: pilF mutant were unable to colonize human nasopharyngeal tissue in an organ culture model [PMID:18936183]. 2965 type IV pilus assembly protein NMA2159 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 907318 NMA2129 20140405 122587 protein-coding NCBI-supplied PMID: 10761919; 15378741 MUTATION: aroE mutant is attenuated in rats [PMID:11062540]. 2966 shikimate dehydrogenase NMA2129 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 907353 NMA2090 20140406 122587 protein-coding NCBI-supplied PMID: 10761919; 15378741 MUTATION: NadA mutation decreases epithelial adhesion of capsulate N. meningitidis and invasion by acapsulate N. meningitidis [PMID:19481311]. 2967 quinolinate synthetase nadA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 907455 NMA1985 20140222 122587 protein-coding NCBI-supplied PMID: 10761919; 15378741 MUTATION: tonB mutant is unable to replicate within human epithelial cells [PMID:11854233]. 2968 TonB protein NMA1985 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 907458 NMA1983 20140222 122587 protein-coding NCBI-supplied PMID: 10761919; 15378741 MUTATION: exbD mutant is attenuated in rats [PMID:11062540]. 2969 biopolymer transport protein NMA1983 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 907459 NMA1984 20130526 122587 protein-coding NCBI-supplied PMID: 10761919; 15378741 MUTATION: exbB mutant is attenuated in rats [PMID:11062540]. 2970 biopolymer transport protein NMA1984 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 907476 NMA1959 20140406 122587 protein-coding NCBI-supplied PMID: 10761919; 15378741 MUTATION: rfaK mutant is attenuated in rats [PMID:11062540]. 2971 alpha 1,2 N-acetylglucosamine transferase NMA1959 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 907493 NMA1939 20140405 122587 protein-coding NCBI-supplied PMID: 10761919; 15378741 MUTATION: aroC mutant is attenuated in rats [PMID:11062540]. 2972 chorismate synthase aroC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 907554 NMA1250 20130526 122587 protein-coding NCBI-supplied PMID: 10761919; 15378741 MUTATION: dedA mutant is attenuated in rats [PMID:11062540]. 2973 DedA protein NMB_orthologue NMA1250 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 907555 NMA1251 20130526 122587 protein-coding NCBI-supplied PMID: 10761919; 15378741; 16006553; 18076035 outer membrane protein NMA1251 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 907658 NMA1766 20140405 122587 protein-coding NCBI-supplied PMID: 10761919; 15378741 MUTATION: ilvI mutant is attenuated in rats [PMID:11062540]. 2975 acetolactate synthase isozyme III large subunit NMA1766 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 907768 NMA1361 20140406 122587 protein-coding NCBI-supplied PMID: 10761919; 15378741 MUTATION: ilvD mutant is attenuated in rats [PMID:11062540]. 2976 dihydroxy-acid dehydratase ilvD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 907882 NMA1488 20140329 122587 protein-coding NCBI-supplied PMID: 10761919; 15378741 MUTATION: mltB mutant is attenuated in rats [PMID:11062540]. 2977 murein hydrolase NMA1488 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 908048 NMA1659 20140329 122587 protein-coding NCBI-supplied PMID: 10761919; 15378741 MUTATION: aroD mutant is attenuated in rats [PMID:11062540]. 2978 3-dehydroquinate dehydratase aroD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 908116 NMA1727 20140301 122587 protein-coding NCBI-supplied PMID: 10761919; 15378741 MUTATION: rfaF mutant is attenuated in rats [PMID:11062540]. 2979 ADP-heptose--LPS heptosyltransferase NMA1727 MUTATION: VP35 mutant is avirulent in guinea pigs [PMID:20071589]. 4530 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 912086 OpmnVgp129 20140215 262177 protein-coding NCBI-supplied PMID: 9126251 polyhedral envelope protein OpmnVgp129 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 915134 ECs4770 20140217 386585 protein-coding NCBI-supplied PMID: 10734605; 11108008; 11111050; 11258796; 17967175 MUTATION: attenuated in mice [PMID:12117951]. 2123 transcriptional activator RfaH rfaH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 919662 CPj0898 20140222 138677 protein-coding NCBI-supplied PMID: 10839753; 10871362 MUTATION: mutant showed attenuated virulence in lungs of mice [PMID:10736106]. 3948 heat shock protein-60 groEL_3 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 920146 PestiV2gp1 20140406 11096 protein-coding NCBI-supplied PMID: 14659557; 16022897; 16908042; 16917742; 17108025; 17447110; 17928086; 17947522; 17969857; 18485511; 18632959; 18987150; 19093875; 19185595; 19264773; 19710255; 19713054; 19767841; 19782108; 19906943; 19951725; 20558217; 20631090; 20637813; 21318239; 21400206; 21680532; 21945636; 21968199; 22258858; 22261205; 22496228; 22674973; 22727685; 22795973; 23487454 MUTATION: A E2 mutant in Classical swine fever virus is attenuated in pigs [PMID:15837238]. 4960 polyprotein PestiV2gp1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 922492 MT3385 20140222 83331 protein-coding NCBI-supplied PMID: 12218036; 19099550 MUTATION: sigF mutant is attenuated in mice [PMID:14977982]. 57 RNA polymerase sigma factor SigF sigF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 922599 MT3911 20140222 83331 protein-coding NCBI-supplied PMID: 12218036; 19099550 MUTATION: fbpA mutant is attenuated in mice [PMID:15557632]. 58 esterase, , antigen 85-A fbpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 922795 MT3706.1 20140405 83331 protein-coding NCBI-supplied PMID: 12218036; 19099550 MUTATION: panCD mutant is attenuated in mice [PMID:12219086]. 59 aspartate alpha-decarboxylase panD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 922907 MT3320 20140217 83331 protein-coding NCBI-supplied PMID: 12218036; 19099550; 22235255 MUTATION: sigH mutant has diminished immunopathology and is nonlethal in mice [PMID:12060776]. 60 RNA polymerase sigma factor RpoE sigH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 923111 MT3523 20140217 83331 protein-coding NCBI-supplied PMID: 12218036; 15659067; 19099550 MUTATION: sigD mutant is attenuated in human macrophages and mice [PMID:15659067]. 61 RNA polymerase sigma factor SigD MT3523 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 923491 MT2018 20140222 83331 protein-coding NCBI-supplied PMID: 12218036; 19099550 MUTATION: mce-3 mutant is strongly attenuated in BALB/c mice [PMID:16388878]. 4917 virulence factor mce-3 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 923545 MT0368 20140215 83331 protein-coding NCBI-supplied PMID: 12218036; 19099550 MUTATION: hspR mutant is attenuated in mice [PMID:11385512]. 62 transcriptional regulator HspR hspR Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 923602 MT1959 20140329 83331 protein-coding NCBI-supplied PMID: 12218036; 19099550 MUTATION: katG mutant is attenuated in mice and guinea pigs [PMID:9534978]. 63 catalase-peroxidase katG from M. tuberculosis CDC1551 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 923760 MT0447 20140406 83331 protein-coding NCBI-supplied PMID: 12218036; 19099550 MUTATION: sodC mutant is more susceptible to killing by activated murine macrophages than the wild type [PMID:11447176]. 64 superoxide dismutase sodC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 923776 MT1859 20140406 83331 protein-coding NCBI-supplied PMID: 12218036; 19099550 MUTATION: mgtC mutant is attenuated in human macrophages and mice [PMID:10760138]. 65 Mg2+ transport protein mgtC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 923873 MT0509 20140222 83331 protein-coding NCBI-supplied PMID: 12218036; 19099550 MUTATION: senX3-regX3 deletion mutant is attenuated in mice [PMID:12777483]. 66 sensor histidine kinase SenX3 senX3 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 923874 MT0510 20130330 83331 protein-coding NCBI-supplied PMID: 12218036; 19099550 MUTATION: senX3-regX3 deletion mutant is attenuated in mice [PMID:12777483]. 67 DNA-binding response regulator RegX3 regX3 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 923905 MT0520 20140405 83331 protein-coding NCBI-supplied PMID: 12218036; 19099550 MUTATION: proC mutant is attenuated in mice [PMID:11160012]. 68 pyrroline-5-carboxylate reductase proC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 924178 MT2248 20140405 83331 protein-coding NCBI-supplied PMID: 12218036; 19099550 MUTATION: trpD mutant is attenuated in mice [PMID:11160012]. 69 anthranilate phosphoribosyltransferase trpD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 924361 MT1591 20130420 83331 protein-coding NCBI-supplied PMID: 12218036; 19099550 MUTATION: lspA mutant is attenuated in mice [PMID:18832305]. 70 lipoprotein signal peptidase lspA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 924601 MT2129 20140222 83331 protein-coding NCBI-supplied PMID: 12218036; 18798983; 19099550 MUTATION: sigC mutant is attenuated in mice [PMID:15049808]. 71 ECF subfamily RNA polymerase sigma factor sigC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 924814 MT1259 20140406 83331 protein-coding NCBI-supplied PMID: 12218036; 19099550 MUTATION: sigE mutant is unable to grow in unactivated human and murine macrophages and is more susceptible to killing by activated macrophages than the wild type [PMID:11489128]. 72 RNA polymerase sigma factor SigE sigE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 925014 MT0618 20140222 83331 protein-coding NCBI-supplied PMID: 12218036; 19099550 MUTATION: a mce-2 mutant is a strongly attenuated in BALB/c mice [PMID:16388878]. 4916 virulence factor mce-2 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 925207 MT3065 20140405 83331 protein-coding NCBI-supplied PMID: 12218036; 19099550 MUTATION: leuD mutant is attenuated in mice [PMID:10768986]. 73 isopropylmalate isomerase small subunit leuD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 925657 MT2660 20140406 83331 protein-coding NCBI-supplied PMID: 12218036; 19099550 MUTATION: Long-term survival of the relA mutant during in vitro starvation or nutrient run out in normal media was significantly impaired compared to that in the wild type. In addition, the mutant was significantly less able to survive extended anaerobic incubation than the wild-type virulent organism [PMID:10940033]. 74 GTP pyrophosphokinase relA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 925827 MT2503 20140222 83331 protein-coding NCBI-supplied PMID: 12218036; 19099550 MUTATION: ahpC mutant has decreased survival in unactivated macrophages compared to the wild type [PMID:12368447]. 75 alkyl hydroperoxide reductase ahpC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 925884 MT2462 20140405 83331 protein-coding NCBI-supplied PMID: 12218036; 19099550 MUTATION: cysH mutant is attenuated in mice [PMID:16553880]. 76 phosphoadenosine phosphosulfate reductase cysH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 925954 MT0670 20140406 83331 protein-coding NCBI-supplied PMID: 12218036; 19099550 MUTATION: mma4 mutant is attenuated in mice [PMID:10844652]. 77 methoxy mycolic acid synthase 4 mma4 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 926053 MT0759 20131108 83331 protein-coding NCBI-supplied PMID: 12218036; 19099550 MUTATION: sigL mutant is attenuated in mice [PMID:16199577]. 78 RNA polymerase sigma factor SigL sigL Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 926330 MT3917 20111129 83331 protein-coding NCBI-supplied PMID: 12218036; 19099550 MUTATION: erp mutant is attenuated in mice [PMID:9784137]. 79 exported repetitive protein erp Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 926524 MT3707 20140405 83331 protein-coding NCBI-supplied PMID: 12218036; 19099550 MUTATION: panCD mutant is attenuated in mice [PMID:12219086]. 80 pantoate--beta-alanine ligase panC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 926547 MT3491.1 20111129 83331 protein-coding NCBI-supplied PMID: 12218036; 19099550 MUTATION: MT3491.1 mutant is attenuated in survival within macrophages [PMID:15340136]. 81 hypothetical protein MT3491.1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 929770 SP_0023 20121123 170187 pseudo NCBI-supplied MUTATION: radA mutant is attenuated in mice [PMID:12207705]. 3132 pseudo radA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 929784 SP_1976 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1976 mutant is attenuated in mice [PMID:12207705]. 3133 pyruvate formate-lyase-activating enzyme SP_1976 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 929800 SP_2239 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_2239 mutant is attenuated in mice [PMID:12207705]. 3134 serine protease SP_2239 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 929801 SP_0049 20140215 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0049 mutant is attenuated in mice [PMID:12207705]. 3135 vanZ protein SP_0049 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 929804 SP_0050 20140405 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: purH mutant is attenuated in mice [PMID:12207705]. 3136 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase purH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 929812 SP_0057 20140405 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0057 mutant is attenuated in mice [PMID:12207705]. 3137 beta-N-acetylhexosaminidase SP_0057 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 929823 SP_0063 20140405 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0063 mutant is attenuated in mice [PMID:12207705]. 3138 PTS system transporter subunit IID SP_0063 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 929826 SP_2231 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_2231 mutant is attenuated in mice [PMID:12207705]. 3139 ABC transporter permease SP_2231 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 929838 SP_0071 20130609 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0071 mutant is attenuated in mice [PMID:12207705]. 3140 immunoglobulin A1 protease SP_0071 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 929848 SP_0078 20130609 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0078 mutant is attenuated in mice [PMID:12207705]. 3141 Trk family potassium uptake protein SP_0078 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 929865 SP_2210 20140405 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_2210 mutant is attenuated in mice [PMID:12207705]. 3142 cysteine synthase SP_2210 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 929866 SP_0092 20140217 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0092 mutant is attenuated in mice [PMID:12207705]. 3143 ABC transporter substrate-binding protein SP_0092 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 929869 SP_0095 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0095 mutant is attenuated in mice [PMID:12207705]. 3144 hypothetical protein SP_0095 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 929875 SP_0100 20140217 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0100 mutant is attenuated in mice [PMID:12207705]. 3145 hypothetical protein SP_0100 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 929877 SP_0102 20140217 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0102 mutant is attenuated in mice [PMID:12207705]. 3146 glycosyl transferase family protein SP_0102 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 929888 SP_0110 20140215 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0110 mutant is attenuated in mice [PMID:12207705]. 3147 hypothetical protein SP_0110 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 929896 SP_0117 20140406 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: pspA mutant is attenuated in mice [PMID:12207705]. 3148 surface protein A SP_0117 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 929900 SP_0121 20130609 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0121 mutant is attenuated in mice [PMID:12207705]. 3149 metallo-beta-lactamase superfamily protein SP_0121 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 929911 SP_0128 20130609 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0128 mutant is attenuated in mice [PMID:12207705]. 3150 ribosomal-protein-alanine acetyltransferase SP_0128 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 929922 SP_0136 20140215 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0136 mutant is attenuated in mice [PMID:12207705]. 3151 glycosyl transferase family protein SP_0136 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 929928 SP_0141 20140405 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0141 mutant is attenuated in mice [PMID:12207705]. 3152 transcriptional regulator SP_0141 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 929933 SP_0145 20130609 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0145 mutant is attenuated in mice [PMID:12207705]. 3153 hypothetical protein SP_0145 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 929934 SP_0146 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0146 mutant is attenuated in mice [PMID:12207705]. 3154 hypothetical protein SP_0146 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 929938 SP_0150 20140406 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0150 mutant is attenuated in mice [PMID:12207705]. 3155 hypothetical protein SP_0150 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 929947 SP_0156 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0156 mutant is attenuated in mice [PMID:12207705]. 3156 DNA-binding response regulator SP_0156 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 929948 SP_0157 20121123 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0157 mutant is attenuated in mice [PMID:12207705]. 3157 hypothetical protein SP_0157 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 929951 SP_0160 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0160 mutation is attenuated in mice [PMID:12207705]. 3158 hypothetical protein SP_0160 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 929957 SP_1964 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1964 mutant is attenuated in mice [PMID:12207705]. 3159 DNA-entry nuclease SP_1964 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 929969 SP_0177 20140329 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0177 mutant is attenuated in mice [PMID:12207705]. 3160 riboflavin synthase subunit alpha SP_0177 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 929993 SP_0198 20140406 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0198 mutant is attenuated in mice [PMID:12207705]. 3161 hypothetical protein SP_0198 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 929994 SP_0199 20140405 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0199 mutant is attenuated in mice [PMID:12207705]. 3162 cardiolipin synthetase SP_0199 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930040 SP_0240 20140405 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0240 mutant is attenuated in mice [PMID:12207705]. 3163 phosphoglycerate mutase SP_0240 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930043 SP_0242 20130609 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0242 mutant is attenuated in mice [PMID:12207705]. 3164 ABC transporter ATP-binding protein SP_0242 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930048 SP_0246 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0246 mutant is attenuated in mice [PMID:12207705]. 3165 DeoR family transcriptional regulator SP_0246 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930049 SP_0247 20130609 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0247 mutant is attenuated in mice [PMID:12207705]. 3166 transcriptional regulator SP_0247 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930053 SP_0251 20140405 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0251 mutant is attenuated in mice [PMID:12207705]. 3167 formate acetyltransferase SP_0251 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930055 SP_0253 20140405 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: gldA mutant is attenuated in mice [PMID:12207705]. 3168 glycerol dehydrogenase gldA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930056 SP_0254 20140215 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: leuS mutant is attenuated in mice [PMID:12207705]. 3169 leucyl-tRNA synthetase leuS Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930071 SP_0265 20140406 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0625 mutant is attenuated in mice [PMID:12207705]. 3170 glycosyl hydrolase SP_0265 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930074 SP_0267 20140406 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0267 mutant is attenuated in mice [PMID:12207705]. 3171 hypothetical protein SP_0267 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930075 SP_0268 20140329 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0268 mutant is attenuated in mice [PMID:12207705]. 3172 alkaline amylopullulanase SP_0268 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930082 SP_0274 20140405 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: polC mutant is attenuated in mice [PMID:12207705]. 3173 DNA polymerase III PolC polC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930110 SP_0298 20140215 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0298 mutant is attenuated in mice [PMID:12207705]. 3174 hypothetical protein SP_0298 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930119 SP_0306 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0306 mutant is attenuated in mice [PMID:12207705]. 3175 transcriptional regulator SP_0306 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930125 SP_0312 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0312 mutant is attenuated in mice [PMID:12207705]. 3176 glycosyl hydrolase SP_0312 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930127 SP_0314 20140217 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0314 mutant is attenuated in mice [PMID:12207705]. 3177 hyaluronidase SP_0314 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930133 SP_0320 20130609 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0320 mutant is attenuated in mice [PMID:12207705]. 3178 gluconate 5-dehydrogenase SP_0320 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930147 SP_0332 20140406 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0332 mutant is attenuated in mice [PMID:12207705]. 3179 hypothetical protein SP_0332 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930156 SP_0338 20140215 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0338 mutant is attenuated in mice [PMID:12207705]. 3180 ATP-dependent Clp protease ATP-binding subunit SP_0338 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930192 SP_2175 20140406 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: dltB mutant is attenuated in mice [PMID:12207705]. 3181 dltB protein SP_2175 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930196 SP_2170 20130609 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_2170 mutant is attenuated [PMID:12207705]. 3182 zinc ABC transporter permease SP_2170 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930201 SP_2164 20140405 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_2164 mutant is attenuated in mice [PMID:12207705]. 3183 PTS system transporter subunit IIA SP_2164 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930202 SP_2162 20140322 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_2162 mutant is attenuated in mice [PMID:12207705]. 3184 PTS system transporter subunit IIC SP_2162 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930213 SP_2145 20140217 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_2145 mutant is attenuated in mice [PMID:12207705]. 3185 cell wall antigen SP_2145 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930214 SP_2143 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_2143 mutant is attenuated in mice [PMID:12207705]. 3186 hypothetical protein SP_2143 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930222 SP_2128 20140405 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_2128 mutant is attenuated in mice [PMID:12207705]. 3187 transketolase SP_2128 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930238 SP_2108 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_2108 mutant is attenuated in mice [PMID:12207705]. 3188 maltose/maltodextrin ABC transporter maltose/maltodextrin-binding protein SP_2108 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930243 SP_2101 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_2101 mutant is attenuated in mice [PMID:12207705]. 3189 cation transporter E1-E2 family ATPase SP_2101 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930245 SP_2098 20140217 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_2098 mutant is attenuated in mice [PMID:12207705]. 3190 hypothetical protein SP_2098 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930248 SP_2095 20140405 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_2095 mutant is attenuated in mice [PMID:12207705]. 3191 5-formyltetrahydrofolate cyclo-ligase SP_2095 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930262 SP_2076 20121123 170187 pseudo NCBI-supplied MUTATION: SP_2076 mutant is attenuated in mice [PMID:12207705]. 3192 pseudo SP_2076 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930283 SP_1952 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1952 mutant is attenuated in mice [PMID:12207705] 3193 hypothetical protein SP_1952 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930291 SP_0377 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: cbpC mutant is attenuated in mice [PMID:12207705]. 3194 choline binding protein C SP_0377 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930301 SP_0385 20130609 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0385 mutant is attenuated in mice [PMID:12207705]. 3195 hypothetical protein SP_0385 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930330 SP_0396 20140405 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0396 mutant is attenuated in mice [PMID:12207705]. 3196 PTS system mannitol-specific transporter subunit IIA SP_0396 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930383 SP_0445 20140405 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0445 mutant is attenuated in mice [PMID:12207705]. 3197 acetolactate synthase catalytic subunit SP_0445 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930392 SP_0454 20140215 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0454 mutant is attenuated in mice [PMID:12207705]. 3198 hypothetical protein SP_0454 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930399 SP_0461 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0461 mutant is attenuated in mice [PMID:12207705]. 3199 transcriptional regulator SP_0461 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930406 SP_0468 20140215 170187 protein-coding NCBI-supplied PMID: 11463916; 19153457; 22122269 MUTATION: SP_0468 mutant is attenuated in mice [PMID:12207705]. 3200 sortase SP_0468 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930412 SP_0474 20140329 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0474 mutant is attenuated in mice [PMID:12207705]. 3201 PTS system cellobiose-specific transporter subunit IIC SP_0474 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930416 SP_0478 20140329 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0478 mutant is attenuated in mice [PMID:12207705]. 3202 PTS system lactose-specific transporter subunit IIBC SP_0478 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930417 SP_0479 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0479 mutant is attenuated in mice [PMID:12207705]. 3203 Trk family potassium uptake protein SP_0479 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930429 SP_0492 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0492 mutant is attenuated in mice [PMID:12207705]. 3204 hypothetical protein SP_0492 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930432 SP_0494 20140405 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0494 mutant is attenuated in mice [PMID:12207705]. 3205 CTP synthase Other designations: CTP synthetase pyrG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930436 SP_0498 20130609 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0498 mutant is attenuated in mice [PMID:12207705]. 3206 endo-beta-N-acetylglucosaminidase SP_0498 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930448 SP_0510 20130609 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0510 mutant is attenuated in mice [PMID:12207705]. 3207 type I restriction-modification system, R subunit SP_0510 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930470 SP_0530 20121123 170187 pseudo NCBI-supplied MUTATION: blpA mutant is attenuated in mice [PMID:12207705]. 3208 pseudo blpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930515 SP_0571 20140215 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0571 mutant is attenuated in mice [PMID:12207705]. 3209 cell filamentation protein Fic-like protein SP_0571 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930532 SP_0586 20140406 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0586 mutant is attenuated in mice [PMID:12207705]. 3210 5,10-methylenetetrahydrofolate reductase SP_0586 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930541 SP_0595 20130609 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0595 mutant is attenuated in mice [PMID:12207705]. 3211 hypothetical protein SP_0595 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930547 SP_0600 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: vexp2 mutant is attenuated in mice [PMID:12207705]. 3212 ABC transporter ATP-binding protein SP_0600 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930563 SP_0614 20140215 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0614 mutant is attenuated in mice [PMID:12207705]. 3213 tributyrin esterase SP_0614 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930571 SP_0622 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0622 mutant is attenuated in mice [PMID:12207705]. 3214 nitroreductase SP_0622 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930582 SP_0633 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0633 mutant is attenuated in mice [PMID:12207705]. 3215 hypothetical protein SP_0633 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930590 SP_0641 20140217 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0641 mutant is attenuated in mice [PMID:12207705]. 3216 serine protease SP_0641 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930594 SP_0645 20140405 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0645 mutation is attenuated in mice [PMID:12207705]. 3217 PTS system transporter subunit IIA SP_0645 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930597 SP_0648 20140405 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0648 mutant is attenuated in mice [PMID:12207705]. 3218 beta-galactosidase SP_0648 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930604 SP_0655 20130609 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0655 mutant is attenuated in mice [PMID:12207705]. 3219 sodium/hydrogen exchanger family protein SP_0655 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930610 SP_0661 20140215 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0661 mutant is attenuated in mice [PMID:12207705]. 3220 DNA-binding response regulator SP_0661 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930612 SP_0663 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0663 mutant is attenuated in mice [PMID:12207705]. 3221 hypothetical protein SP_0663 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930613 SP_0664 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0664 mutant is attenuated in mice [PMID:12207705]. 3222 zinc metalloprotease ZmpB SP_0664 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930614 SP_0665 20130609 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0665 mutant is attenuated in mice [PMID:12207705]. 3223 chorismate binding protein SP_0665 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930636 SP_0686 20140405 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0686 mutant is attenuated in mice [PMID:12207705]. 3224 hypothetical protein SP_0686 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930640 SP_0690 20140215 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0690 mutant is attenuated in mice [PMID:12207705]. 3225 cell division protein DivIB SP_0690 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930669 SP_0719 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0719 mutant is attenuated in mice [PMID:12207705]. 3226 hypothetical protein SP_0719 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930670 SP_0720 20130609 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0720 mutant is attenuated in mice [PMID:12207705]. 3227 ABC transporter ATP-binding protein SP_0720 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930676 SP_0726 20140329 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0736 mutant is attenuated in mice [PMID:12207705]. 3228 phosphomethylpyrimidine kinase SP_0726 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930678 SP_0728 20140405 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0728 mutant is attenuated in mice [PMID:12207705]. 3229 hypothetical protein SP_0728 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930679 SP_0729 20140405 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0729 mutant is attenuated in mice [PMID:12207705]. 3230 cation transporter E1-E2 family ATPase SP_0729 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930696 SP_0746 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: clpP mutant is attenuated in mice [PMID:15664911]. 3231 ATP-dependent Clp protease proteolytic subunit clpP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930716 SP_0766 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0766 mutant is attenuated in mice [PMID:12207705]. 3232 superoxide dismutase, manganese-dependent SP_0766 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930717 SP_0767 20140406 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0767 mutant is attenuated in mice [PMID:12207705]. 3233 hypothetical protein SP_0767 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930724 SP_0774 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0774 mutant is attenuated in mice [PMID:12207705]. 3234 hypothetical protein SP_0774 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930735 SP_0785 20140215 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0785 mutant is attenuated in mice [PMID:12207705]. 3235 hypothetical protein SP_0785 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930739 SP_0789 20140215 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0789 mutant is attenuated in mice [PMID:12207705]. 3236 hypothetical protein SP_0789 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930747 SP_0797 20140329 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0797 mutant is attenuated in mice [PMID:12207705]. 3237 aminopeptidase SP_0797 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930757 SP_0807 20140217 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0807 mutant is attenuated in mice [PMID:12207705]. 3238 septation ring formation regulator EzrA SP_0807 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930779 SP_0829 20140308 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0829 mutant is attenuated in mice [PMID:12207705]. 3239 phosphopentomutase SP_0829 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930792 SP_0842 20140405 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0842 mutant is attenuated in mice [PMID:12207705]. 3240 pyrimidine-nucleoside phosphorylase SP_0842 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930806 SP_0856 20140405 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0856 mutant is attenuated in mice [PMID:12207705]. 3241 branched-chain amino acid aminotransferase SP_0856 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930830 SP_0877 20140405 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0877 mutant is attenuated [PMID:12207705]. 3242 PTS system fructose specific transporter subunit IIABC SP_0877 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930839 SP_0886 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0886 mutant is attenuated in mice [PMID:12207705]. 3243 type I restriction-modification system, M subunit SP_0886 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930840 SP_0887 20140406 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0887 mutant is attenuated in mice [PMID:12207705]. 3244 type I restriction-modification system subunit S SP_0887 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930845 SP_0892 20130609 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0892 mutant is attenuated in mice [PMID:12207705]. 3245 type I restriction-modification system, R subunit SP_0892 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930869 SP_0916 20140329 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0916 mutant is attenuated in mice [PMID:12207705]. 3246 lysine decarboxylase SP_0916 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930880 SP_0927 20140406 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0927 is attenuated in mice [PMID:12207705]. 3247 LysR family transcriptional regulator SP_0927 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930892 SP_0939 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0939 mutant is attenuated in mice [PMID:12207705]. 3248 hypothetical protein SP_0939 Bin Zhao, Oliver He gid WEB: http://www.ncbi.nlm.nih.gov/gene 930896 SP_0943 20140215 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: gid mutant is attenuated in mice [PMID:12207705]. 3249 tRNA (uracil-5-)-methyltransferase Gid - SP_0943 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930933 SP_1889 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: AmiD mutant is attenuated in mice [PMID:12207705]. 3250 oligopeptide ABC transporter permease AmiD SP_1889 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930935 SP_1898 20140405 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1898 mutant is attenuated in mice [PMID:12207705]. 3251 alpha-galactosidase SP_1898 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930937 SP_1896 20140215 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1896 mutant is attenuated in mice [PMID:12207705]. 3252 sugar ABC transporter permease SP_1896 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930941 SP_1890 20140215 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: AmiC mutant is attenuated in mice [PMID:12207705]. 3253 oligopeptide ABC transporter permease AmiC SP_1890 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930943 SP_1891 20140215 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: AmiA mutant is attenuated in mice [PMID:12207705]. 3254 oligopeptide ABC transporter oligopeptide-binding protein AmiA SP_1891 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930953 SP_1879 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1879 mutant is attenuated in mice [PMID:12207705]. 3255 hypothetical protein SP_1879 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930959 SP_1869 20130609 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1869 mutant is attenuated in mice [PMID:12207705]. 3256 iron ABC transporter permease SP_1869 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930972 SP_1861 20140405 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1861 mutant is attenuated in mice [PMID:12207705]. 3257 choline transporter SP_1861 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930975 SP_1859 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1859 mutant is attenuated in mice [PMID:12207705]. 3258 transporter SP_1859 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930978 SP_1856 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1856 mutant is attenuated in mice [PMID:12207705]. 3259 MerR family transcriptional regulator SP_1856 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930979 SP_1855 20140406 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1855 mutation is attenuated in mice [PMID:12207705]. 3260 zinc-containing alcohol dehydrogenase SP_1855 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930980 SP_1854 20140215 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1854 mutant is attenuated in mice [PMID:12207705]. 3261 galactose operon repressor SP_1854 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 930985 SP_1847 20140406 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1847 mutant is attenuated in mice [PMID:12207705]. 3262 xanthine phosphoribosyltransferase SP_1847 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931005 SP_1830 20140217 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1830 mutant is attenuated in mice [PMID:12207705]. 3263 phosphate transport system regulatory protein PhoU SP_1830 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931018 SP_1817 20140405 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1817 mutant is attenuated in mice [PMID:12207705]. 3264 anthranilate synthase component I SP_1817 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931019 SP_1800 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1800 mutant is attenuated in mice [PMID:12207705]. 3265 transcriptional activator SP_1800 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931020 SP_1816 20140329 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1816 mutant is attenuated in mice [PMID:12207705]. 3266 anthranilate synthase component II SP_1816 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931021 SP_1815 20140405 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: trpD mutant is attenuated in mice [PMID:12207705]. 3267 anthranilate phosphoribosyltransferase trpD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931039 SP_1793 20130609 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1793 mutant is attenuated in mice [PMID:12207705]. 3268 hypothetical protein SP_1793 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931052 SP_1770 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1770 mutant is attenuated in mice [PMID:12207705]. 3269 glycosyl transferase family protein SP_1770 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931054 SP_1780 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1780 mutant is attenuated in mice [PMID:12207705]. 3270 oligoendopeptidase F SP_1780 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931055 SP_1771 20130609 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1771 mutant is attenuated in mice [PMID:12207705]. 3271 glycosyl transferase family protein SP_1771 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931057 SP_1779 20140215 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1779 mutant is attenuated in mice [PMID:12207705]. 3272 hypothetical protein SP_1779 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931060 SP_1772 20140215 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1772 mutant is attenuated in mice [PMID:12207705]. 3273 cell wall surface anchor family protein SP_1772 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931073 SP_1760 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1760 mutant is attenuated in mice [PMID:12207705]. 3274 hypothetical protein SP_1760 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931115 SP_1717 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1717 mutant is attenuated in mice [PMID:12207705]. 3275 ABC transporter ATP-binding protein SP_1717 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931117 SP_1715 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1715 mutant is attenuated in mice [PMID:12207705]. 3276 hypothetical protein SP_1715 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931126 SP_1706 20130609 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: Sp_1706 mutant is attenuated in mice [PMID:12207705]. 3277 hypothetical protein SP_1706 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931175 SP_1652 20130518 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1652 mutant is attenuated in mice [PMID:12207705]. 3278 hypothetical protein SP_1652 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931185 SP_1654 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1654 mutant is attenuated in mice [PMID:12207705]. 3279 hypothetical protein SP_1654 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931191 SP_1646 20140215 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1646 mutant is attenuated in mice [PMID:12207705]. 3280 metallo-beta-lactamase superfamily protein SP_1646 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931192 SP_1645 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1645 mutant is attenuated in mice [PMID:12207705]. 3281 GTP pyrophosphokinase SP_1645 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931205 SP_1636 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1636 mutant is attenuated in mice [PMID:12207705]. 3282 Rrf2 family protein SP_1636 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931206 SP_1633 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1633 mutant is attenuated in mice [PMID:12207705]. 3283 DNA-binding response regulator SP_1633 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931254 SP_1591 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1591 mutant is attenuated in mice [PMID:12207705]. 3284 proline dipeptidase SP_1591 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931258 SP_1580 20130609 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1580 mutant is attenuated in mice [PMID:12207705]. 3285 sugar ABC transporter ATP-binding protein SP_1580 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931265 SP_1573 20130609 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: lytC mutant have reduced colonization of rat nasopharynx compared to wild type [PMID:10992472]. 3286 lysozyme lytC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931286 SP_0966 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0966 mutant is attenuated [PMID:12207705]. 3287 adherence and virulence protein A SP_0966 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931296 SP_1544 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1544 mutant is attenuated in mice [PMID:12207705]. 3288 aspartate aminotransferase SP_1544 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931302 SP_1538 20130609 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1538 mutant is attenuated in mice [PMID:12207705]. 3289 Cof family protein/peptidyl-prolyl cis-trans isomerase, cyclophilin type SP_1538 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931308 SP_1529 20140215 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1529 mutant is attenuated in mice [PMID:12207705]. 3290 polysaccharide biosynthesis protein SP_1529 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931319 SP_1518 20140215 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1518 mutant is attenuated in mice [PMID:12207705]. 3291 hypothetical protein SP_1518 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931359 SP_1483 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1483 mutant is attenuated in mice [PMID:12207705]. 3292 DEAD/DEAH box helicase SP_1483 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931406 SP_1433 20140215 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1433 mutant is attenuated in mice [PMID:12207705]. 3293 AraC family transcriptional regulator SP_1433 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931407 SP_1434 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1434 mutant is attenuated in mice [PMID:12207705]. 3294 ABC transporter ATP-binding protein/permease SP_1434 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931411 SP_1431 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1431 mutant is attenuated in mice [PMID:12207705]. 3295 type II DNA modification methyltransferase SP_1431 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931432 SP_1400 20140329 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1400 mutant is attenuated in mice [PMID:12207705]. 3296 phosphate ABC transporter substrate-binding protein SP_1400 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931438 SP_1399 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1339 mutant is attenuated in mice [PMID:12207705]. 3297 phosphate ABC transporter permease SP_1399 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931439 SP_1398 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1398 mutant is attenuated in mice [PMID:12207705]. 3298 phosphate ABC transporter permease SP_1398 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931441 SP_1396 20140406 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1396 mutant is attenuated in mice [PMID:12207705]. 3299 phosphate transporter ATP-binding protein SP_1396 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931450 SP_1378 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1378 mutant is attenuated in mice [PMID:12207705]. 3300 hypothetical protein SP_1378 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931456 SP_1382 20140405 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1382 mutant is attenuated in mice [PMID:12207705]. 3301 alpha-amylase SP_1382 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931457 SP_1377 20140406 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: aroD mutant is attenuated in mice [PMID:12207705]. 3302 3-dehydroquinate dehydratase aroD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931491 SP_0978 20140215 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: CoiA mutant is attenuated in mice [PMID:12207705]. 3303 competence protein CoiA SP_0978 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931492 SP_0979 20140406 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_0979 mutant is attenuated in mice [PMID:12207705]. 3304 oligoendopeptidase F SP_0979 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931514 SP_1001 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1001 mutant is attenuated in mice [PMID:12207705]. 3305 amino acid permease SP_1001 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931516 SP_1003 20130609 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1003 mutant is attenuated in mice [PMID:12207705]. 3306 hypothetical protein SP_1003 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931532 SP_1018 20140405 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1018 mutant is attenuated in mice [PMID:12207705]. 3307 thymidine kinase SP_1018 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931537 SP_1023 20140406 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1023 mutant is attenuated in mice [PMID:12207705]. 3308 acetyltransferase SP_1023 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931543 SP_1029 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1029 mutant is attenuated in mice [PMID:12207705]. 3309 RNA methyltransferase SP_1029 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931546 SP_1032 20140217 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1032 mutant is attenuated in mice [PMID:12207705]. 3310 iron-compound ABC transporter iron compound-binding protein SP_1032 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931554 SP_1040 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1040 mutant is attenuated in mice [PMID:12207705]. 3311 resolvase family site-specific recombinase SP_1040 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931557 SP_1043 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: Sp_1043 (phgA) mutant is attenuated in mice [PMID:15271918]. 3312 hypothetical protein SP_1043 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931559 SP_1045 20130609 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1045 (phgC) mutant is attenuated in mice [PMID:15271918]. 3313 hypothetical protein SP_1045 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931603 SP_1089 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1089 mutant is attenuated in mice [PMID:12207705]. 3314 glutamine amidotransferase SP_1089 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931625 SP_1111 20140406 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1111 mutant is attenuated in mice [PMID:12207705]. 3315 hypothetical protein SP_1111 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931626 SP_1112 20130609 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1112 mutant is attenuated in mice [PMID:12207705]. 3316 degV family protein SP_1112 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931629 SP_1115 20140406 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1115 mutant is attenuated in mice [PMID:12207705]. 3317 transcriptional regulator MutR SP_1115 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931632 SP_1118 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1118 mutant is attenuated in mice [PMID:12207705]. 3318 pullulanase SP_1118 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931635 SP_1121 20140405 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1121 mutant is attenuated in mice [PMID:12207705]. 3319 glycogen branching protein SP_1121 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931641 SP_1127 20140217 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1127 mutant is attenuated in mice [PMID:12207705]. 3320 hypothetical protein SP_1127 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931657 SP_1143 20140215 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1143 mutant is attenuated in mice [PMID:12207705]. 3321 hypothetical protein SP_1143 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931667 SP_1153 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1153 mutant is attenuated in mice [PMID:12207705]. 3322 hypothetical protein SP_1153 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931668 SP_1154 20140215 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1154 mutant is attenuated in mice [PMID:12207705]. 3323 immunoglobulin A1 protease SP_1154 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931670 SP_1156 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: rnhB mutant is attenuated in mice [PMID:12207705]. 3324 ribonuclease HII rnhB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931688 SP_1174 20140405 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1174 mutant is attenuated in mice [PMID:12207705]. 3325 hypothetical protein SP_1174 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931689 SP_1175 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1175 mutant is attenuated in mice [PMID:12207705]. 3326 hypothetical protein SP_1175 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931707 SP_1193 20140406 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: LacA mutant is attenuated in mice [PMID:12207705]. 3327 galactose-6-phosphate isomerase subunit LacA SP_1193 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931716 SP_1202 20140217 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: RecN mutant is attenuated in mice [PMID:12207705]. 3328 DNA repair protein RecN SP_1202 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931792 SP_1278 20140322 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1278 mutant is attenuated in mice [PMID:12207705]. 3329 bifunctional pyrimidine regulatory protein PyrR/uracil phosphoribosyltransferase SP_1278 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931795 SP_1281 20121123 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1281 mutant is attenuated in mice [PMID:12207705]. 3330 hypothetical protein SP_1281 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931799 SP_1285 20130609 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: gidB mutant is attenuated in mice [PMID:12207705]. 3331 16S rRNA methyltransferase GidB gidB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931800 SP_1286 20140406 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1286 mutant is attenuated in mice [PMID:12207705]. 3332 uracil permease SP_1286 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931806 SP_1292 20130609 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1292 mutant is attenuated in mice [PMID:12207705]. 3333 SAP domain-containing protein SP_1292 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931837 SP_1321 20140322 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1321 mutant is attenuated in mice [PMID:12207705]. 3334 V-type ATP synthase subunit K SP_1321 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931845 SP_1328 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1328 mutant is attenuated in mice [PMID:12207705]. 3335 sodium:solute symporter family protein SP_1328 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931860 SP_1343 20130508 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1343 mutant is attenuated in mice [PMID:12207705]. 3336 prolyl oligopeptidase SP_1343 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931861 SP_1344 20130609 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1344 mutant is attenuated in mice [PMID:12207705]. 3337 hypothetical protein SP_1344 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931883 SP_1941 20130609 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1941 mutant is attenuated in mice [PMID:12207705]. 3338 competence damage-inducible protein A SP_1941 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931885 SP_1970 20140405 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1970 mutant is attenuated in mice [PMID:12207705]. 3339 asparagine synthetase AsnA SP_1970 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931895 SP_1998 20140406 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1988 mutant is attenuated in mice [PMID:12207705]. 3340 L-asparaginase SP_1998 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931907 SP_2201 20140406 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: cbpD mutant is attenuated in mice [PMID:12207705]. 3341 choline binding protein D SP_2201 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931908 SP_2236 20130609 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_2236 mutant is attenuated in mice [PMID:12207705]. 3342 sensor histidine kinase ComD SP_2236 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931915 SP_1923 20131123 170187 protein-coding NCBI-supplied PMID: 11463916; 16339781; 20049723; 24051749 MUTATION: pneumolysin mutant is attenuated in mice [PMID:12207705]. 3343 pneumolysin SP_1923 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931916 SP_1956 20140215 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION:SP_1956 mutant is attenuated in mice [PMID:12207705]. 3344 hypothetical protein SP_1956 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931921 SP_2190 20140406 170187 protein-coding NCBI-supplied PMID: 11463916; 15616594; 16597618 MUTATION: SP_2190 mutant is attenuated in mice [PMID:12207705]. 3345 choline binding protein A SP_2190 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931927 SP_2176 20140217 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_2176 mutant is attenuated in mice [PMID:12207705]. 3346 D-alanine--poly(phosphoribitol) ligase subunit 1 SP_2176 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931928 SP_2182 20130609 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_2182 mutant is attenuated in mice [PMID:12207705]. 3347 hypothetical protein SP_2182 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931931 SP_2167 20130609 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: fucK mutant is attenuated in mice [PMID:12207705]. 3348 L-fuculose kinase fucK SP_2167 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931935 SP_2159 20140217 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_2159 mutant is attenuated in mice [PMID:12207705]. 3349 fucolectin-like protein SP_2159 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931940 SP_2146 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_2146 mutant is attenuated in mice [PMID:12207705]. 3350 hypothetical protein SP_2146 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931944 SP_2142 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_2142 mutant is attenuated in mice [PMID:12207705]. 3351 ROK family protein SP_2142 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931946 SP_2136 20130609 170187 protein-coding NCBI-supplied PMID: 11463916; 22796387 MUTATION: PcpA mutant is attenuated in mice [PMID:12207705]. 3352 choline binding protein PcpA SP_2136 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931948 SP_2131 20130508 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_2131 mutant is attenuated in mice [PMID:12207705]. 3353 BglG family transcriptional regulator SP_2131 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931957 SP_2105 20140215 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_2105 mutant is attenuated in mice [PMID:12207705]. 3354 hypothetical protein SP_2105 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931966 SP_2086 20140222 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_2086 mutant is attenuated in mice [PMID:12207705]. 3355 phosphate ABC transporter permease SP_2086 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931978 SP_2060 20140217 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_2060 mutant is attenuated in mice [PMID:12207705]. 3356 pyrrolidone-carboxylate peptidase SP_2060 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931979 SP_2052 20140217 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: CglB mutant is attenuated in mice [PMID:12207705]. 3357 competence protein CglB SP_2052 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931984 SP_1939 20130609 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_1939 mutant is attenuated in mice [PMID:12207705]. 3358 MATE efflux family protein DinF SP_1939 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 931986 SP_2002 20140215 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_2002 mutant is attenuated in mice [PMID:12207705]. 3359 hypothetical protein SP_2002 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 932016 SP_2017 20140329 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_2017 mutant is attenuated in mice [PMID:12207705]. 3360 hypothetical protein SP_2017 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 932024 SP_2022 20140405 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_2022 mutant is attenuated in mice [PMID:12207705]. 3361 PTS system transporter subunit IIC SP_2022 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 932042 SP_2039 20130609 170187 protein-coding NCBI-supplied PMID: 11463916 MUTATION: SP_2039 mutant is attenuated in mice [PMID:12207705]. 3362 hypothetical protein SP_2039 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 932066 MYXV_gp132 20140215 10273 protein-coding NCBI-supplied PMID: 10562494; 16356857 integrin-associated protein homolog Other designations: CD47-like protein m128L Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 932849 spr0623 20140222 171101 protein-coding NCBI-supplied PMID: 11544234 MUTATION: glnP mutant is attenuated in mice [PMID:18174343]. 3096 amino acid ABC transporter permease glnP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 932894 spr0121 20140406 171101 protein-coding NCBI-supplied PMID: 11544234; 16237028; 19419534; 21696869 MUTATION: pspA mutant is attenuated in mice [PMID:10603379]. 3097 surface protein pspA pspA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 932908 spr0624 20140222 171101 protein-coding NCBI-supplied PMID: 11544234 MUTATION: glnP mutant is attenuated in mice [PMID:18174343]. 3098 amino acid ABC transporter permease glnP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 933003 spr1494 20140215 171101 protein-coding NCBI-supplied PMID: 11544234 MUTATION: psaA mutant is attenuated in mice [PMID:8945574]. 3099 manganese ABC transporter substrate-binding protein psaA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 933037 spr1054 20140406 171101 protein-coding NCBI-supplied PMID: 11544234 MUTATION: mutX mutant is attenuated in mice [PMID:9826334]. 3100 8-oxodGTP nucleoside triphosphatase mutX Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 933163 spr1431 20130724 171101 protein-coding NCBI-supplied PMID: 11544234; 15943581; 16109966; 18667432; 19389766 MUTATION: lytC mutant have reduced colonization of rat nasopharynx compared to wild type [PMID:10992472]. 3101 1,4-beta-N-acetylmuramidase lytC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 933274 spr0581 20140222 171101 protein-coding NCBI-supplied PMID: 11544234; 16776657 MUTATION: zmpB mutant is attenuated in mice [PMID:12841855]. 3102 zinc metalloprotease zmpB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 933352 spr1639 20140222 171101 protein-coding NCBI-supplied PMID: 11544234 MUTATION: ccpA mutant is attenuated in mice [PMID:16321938]. 3103 catabolite control protein ccpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 933482 spr0532 20140406 171101 protein-coding NCBI-supplied PMID: 11544234 MUTATION: glnP mutant is attenuated in mice [PMID:18174343]. 3104 amino acid ABC transporter permease glnP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 933485 spr0533 20140217 171101 protein-coding NCBI-supplied PMID: 11544234 MUTATION: glnP mutant is attenuated in mice [PMID:18174343]. 3105 amino acid ABC transporter permease glnP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 933487 spr1995 20140217 171101 protein-coding NCBI-supplied PMID: 11544234 MUTATION: pspC mutant had reduced ability to colonize the nasopharynx of mice [PMID:17261599]. 3106 choline binding protein A pspC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 933600 spr1813 20130826 171101 protein-coding NCBI-supplied PMID: 11544234 MUTATION: ccpA mutant is attenuated in mice [PMID:16321938]. 3107 catabolite control protein A ccpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 933669 spr1754 20140215 171101 protein-coding NCBI-supplied PMID: 11544234; 17439951; 19389766 MUTATION: lytA mutant is attenuated in mice [PMID:10603379]. 3108 N-acetylmuramoyl-L-alanine amidase lytA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 933687 spr1739 20140222 171101 protein-coding NCBI-supplied PMID: 11544234 MUTATION: ply mutant is attenuated in mice [PMID:10603379]. 3109 pneumolysin ply Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 933751 spr1493 20130826 171101 protein-coding NCBI-supplied PMID: 11544234 MUTATION: psaC mutant is attenuated in mice [PMID:11988523]. 3110 manganese ABC transporter permease psaC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 933772 spr1492 20140217 171101 protein-coding NCBI-supplied PMID: 11544234 MUTATION: psaB mutant is attenuated in mice [PMID:11988523]. 3111 manganese ABC transporter ATP-binding protein psaB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 933902 spr1536 20140405 171101 protein-coding NCBI-supplied PMID: 11544234 MUTATION: nanA mutant is attenuated in mice [PMID:9826334]. 3112 neuraminidase A nanA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 933909 spr1042 20140217 171101 protein-coding NCBI-supplied PMID: 11544234 MUTATION: iga mutant is attenuated in mice [PMID:12841855]. 3113 immunoglobulin A1 protease iga Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 933916 spr1439 20140215 171101 protein-coding NCBI-supplied PMID: 11544234 MUTATION: codY mutant has lower bacterial loads during infection in mice compared to the wild type and have a diminished ability to adhere to nasopharangeal cells in vitro [PMID:18024519]. 3114 transcriptional repressor CodY codY Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 933969 spr1098 20140215 171101 protein-coding NCBI-supplied PMID: 11544234 MUTATION: The srtA mutant colonized the nasopharynx of chinchillas at a significantly lower level than the wild type [PMID:16246506]. 3115 sortase srtA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 934028 spr1120 20131105 171101 protein-coding NCBI-supplied PMID: 11544234 MUTATION: glnP mutant is attenuated in mice [PMID:18174343]. 3116 amino acid ABC transporter substrate-binding protein glnP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 934181 spr0642 20140329 171101 protein-coding NCBI-supplied PMID: 11544234; 15576764 MUTATION: spxB mutant has a loss in the ability to attach eukayrotic cells and is attenuated in rabbits [PMID:8820650]. 3117 pyruvate oxidase spxB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 934194 spr0656 20140222 171101 protein-coding NCBI-supplied PMID: 11544234; 15701650 MUTATION: clpP is attenuated in mice [PMID:15664911]. 3118 ATP-dependent Clp protease proteolytic subunit clpP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 934215 spr0674 20140222 171101 protein-coding NCBI-supplied PMID: 11544234 MUTATION: sodA mutant is attenuated in mice [PMID:10768978]. 3119 superoxide dismutase sodA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 934251 spr0707 20140301 171101 protein-coding NCBI-supplied PMID: 11544234; 16484208; 17725562; 21422763; 21903754; 23710838 MUTATION: ciaR mutant is attenuated in mice [PMID:15292127]. 3120 DNA-binding response regulator CiaR ciaR Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 934267 spr0727 20130724 171101 protein-coding NCBI-supplied PMID: 11544234 MUTATION: glnP mutant is attenuated in mice [PMID:18174343]. 3121 amino acid ABC transporter permease glnP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 934406 spr0867 20140222 171101 protein-coding NCBI-supplied PMID: 11544234 MUTATION: lytB has reduced colonization of nasopharynx of rats compared to wild type [PMID:10992472]. 3122 endo-beta-N-acetylglucosaminidase lytB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 934459 spr1243 20140222 171101 protein-coding NCBI-supplied PMID: 11544234 MUTATION: potD mutant is attenuated in pulmonary and systemic models of infection in mice [PMID:16368990]. 3123 spermidine/putrescine ABC transporter substrate-binding protein potD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 934540 spr1323 20140217 171101 protein-coding NCBI-supplied PMID: 11544234 MUTATION: nox mutant is attenuated in mice [PMID:11158360]. 3124 NADH oxidase nox Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 934547 spr1333 20140215 171101 protein-coding NCBI-supplied PMID: 11544234 MUTATION: pgdA mutant is attenuated in mice [PMID:12438406]. 3125 peptidoglycan GlcNAc deacetylase pgdA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 934570 spr1355 20140222 171101 protein-coding NCBI-supplied PMID: 11544234 MUTATION: glnP mutant is attenuated in mice [PMID:18174343]. 3126 amino acid ABC transporter permease glnP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 934722 spr0298 20130724 171101 protein-coding NCBI-supplied PMID: 11544234 MUTATION: regR mutant is attenuated in mice [PMID:12704136]. 3127 GalR family transcription regulator regR Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 934756 spr0308 20140329 171101 protein-coding NCBI-supplied PMID: 11544234 MUTATION: luxS mutant has defective ability to persist in the nasopharyngeal tissues of mice [PMID:15102809]. 3128 S-ribosylhomocysteinase luxS Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 934783 spr0444 20140405 171101 protein-coding NCBI-supplied PMID: 11544234; 16787930 MUTATION: glnA mutant had significantly reduced adhesion to Detroit 562 human pharyngeal epithelial cells [PMID:16787930]. 3129 glutamine synthetase, type I glnA MUTATION: cbpG has reduced colonization of nasopharynx of rats and reduced adherence to human epithelial cells [PMID:10992472]. 3130 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 934859 spr2006 20140406 171101 protein-coding NCBI-supplied PMID: 11544234; 19389766 MUTATION: cbpD has reduced colonization of nasopharynx of rats compared to the wild type [PMID:10992472]. 3131 choline binding protein D cbpD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 944630 SPPV_19 20140406 10266 protein-coding NCBI-supplied PMID: 12021338; 17686843 hypothetical protein SPPV_19 Bin Zhao, Oliver He ECK0034 JW0031 cap pyrA WEB: http://www.ncbi.nlm.nih.gov/gene 944775 b0033 20140406 511145 protein-coding NCBI-supplied GO_0006221; GO_0006526 PMID: 179975; 189806; 229896; 240389; 1630901; 1737023; 2682645; 3525565; 3549732; 4358555; 5339592; 6162837; 6308632; 6330744; 6377309; 6451616; 7577987; 7616563; 7648201; 8794775; 9174345; 9242657; 9278503; 9624689; 9636022; 10029528; 10047492; 10089390; 10428826; 10625457; 10727215; 10843852; 11943174; 14718657; 14741201; 15081891; 15322282; 15690043; 16397293; 16621816; 16820464; 16937252; 17012394; 17187058; 17209549; 17919280; 18458150; 18535147; 18852508; 19569682 MUTATION: A carAB mutant is attenuated in turkeys [PMID:8063392]. 4910 carbamoyl-phosphate synthase large subunit EcoGene:EG10135 carB Bin Zhao, Oliver He ECK0948 JW0940 con tolG tut WEB: http://www.ncbi.nlm.nih.gov/gene 945571 b0957 20140406 511145 protein-coding NCBI-supplied GO_0009274; GO_0009279 PMID: 323051; 330500; 340230; 340280; 367782; 1107024; 1370426; 1370823; 1644765; 1695894; 1757995; 2473377; 3047120; 3047121; 3311813; 3902787; 6086577; 6205157; 6253901; 6256604; 6260961; 6298577; 6374024; 7001445; 7001461; 7021177; 7024253; 7499313; 7517935; 8106193; 8537339; 8626345; 8740179; 8855933; 8905232; 9278503; 9298646; 9383162; 9629924; 9701827; 9808047; 9826663; 10213603; 10368142; 10636850; 10757971; 10764596; 10809669; 11118595; 11248102; 11274469; 11276254; 11532450; 11698382; 11872715; 11906175; 12107143; 12441110; 12486715; 12509434; 12750409; 12771143; 12850204; 12860457; 12949068; 12950181; 14513830; 14530384; 14561880; 14595348; 14623313; 14640415; 14644420; 15004283; 15130122; 15215418; 15249060; 15362847; 15476881; 15584713; 15595387; 15705572; 15736961; 15743961; 15823570; 15850404; 15852340; 15911532; 15951436; 15956183; 16079137; 16080708; 16204185; 16302275; 16313626; 16317765; 16336047; 16352602; 16381841; 16391137; 16397293; 16513633; 16556233; 16575570; 16581049; 16601117; 16606699; 16719475; 16858726; 16888722; 16937252; 16980421; 17007876; 17015657; 17040898; 17041590; 17115690; 17122336; 17224606; 17260943; 17264113; 17267407; 17379704; 17426813; 17497900; 17559395; 17564441; 17601489; 17659252; 17675366; 17699162; 17928002; 18287020; 18317746; 18318713; 18504019; 18641391; 18662321; 18968447; 19158385; 19181847; 19244616; 19382746; 19500339; 19569227; 19571368; 19601955; 19656854; 19737520; 19780589; 19877613; 20004640; 20170640; 20851887; 21069910; 21148506; 21782315; 21840983; 22963587; 23763479; 24077225 MUTATION: OmpA− strains are unable to cause actin condensation needed for invasion of brain epithelial cells [PMID:10531228]. 2256 outer membrane protein A (3a;II*;G;d) EcoGene:EG10669 ompA Bin Zhao, Oliver He ECK1246 JW5195 T1rec exbA WEB: http://www.ncbi.nlm.nih.gov/gene 945843 b1252 20140406 511145 protein-coding NCBI-supplied GO_0009274; GO_0019866 PMID: 126991; 135755; 327077; 390162; 1885532; 1937006; 2089218; 2670904; 2836373; 2985285; 4897798; 5330218; 5330517; 6310567; 6989802; 7654405; 7665457; 8022270; 8039672; 8039674; 8100348; 8316079; 8316087; 8316089; 8344918; 8588889; 8631671; 9159515; 9278503; 9353297; 9811664; 10209752; 10323233; 10441470; 10485884; 11029413; 11087740; 11292793; 11328822; 11344156; 11418549; 11501670; 11566987; 11705387; 11790740; 11872715; 11895294; 11934617; 11967085; 12193634; 12427941; 12618451; 12823822; 12840109; 12873727; 12890026; 12896986; 12957834; 12958215; 13129945; 14651622; 14665631; 14668326; 15109731; 15213392; 15351721; 15522863; 15612934; 15644214; 15736954; 15824450; 15993072; 16005896; 16381841; 16397293; 16414071; 16718599; 16741124; 16741125; 16820681; 16928679; 17225063; 17225934; 17277053; 17449669; 17483231; 17578453; 17628143; 17803902; 17803904; 17908684; 17927700; 18083710; 18390658; 18653801; 19432807; 19627500; 19708689; 21179522; 21665976; 21905676; 21984795; 22100395; 22237011 MUTATION: attenuated in mice [PMID:11553558]. 2257 membrane spanning protein in TonB-ExbB-ExbD transport complex EcoGene:EG11012 tonB Bin Zhao, Oliver He ECK0564 JW0561 ibeB silC ylcB WEB: http://www.ncbi.nlm.nih.gov/gene 946288 b0572 20140406 511145 protein-coding NCBI-supplied GO_0009274; GO_0009279 PMID: 9278503; 9324262; 10225861; 10493123; 11004187; 11222619; 11283292; 11566977; 11739772; 12374972; 12813074; 12829268; 12829273; 12829274; 12876315; 15174130; 15659689; 15659690; 15686558; 15770503; 15773991; 16060662; 16166532; 16381841; 16397293; 16820466; 16964970; 17189367; 17467658; 17893146; 17893365; 18157124; 18202673; 18419149; 18847219 MUTATION: ibeB mutant is unable to invade BMEC and was attenuated in a newborn rat model [PMID:10225861]. 2258 copper/silver efflux system, outer membrane component EcoGene:EG14233 cusC Bin Zhao, Oliver He ECK3531 JW3513 alu dpp fpp WEB: http://www.ncbi.nlm.nih.gov/gene 948062 b3544 20140406 511145 protein-coding NCBI-supplied GO_0009063; GO_0042597 PMID: 368023; 1478454; 1702779; 1956284; 3520334; 4126826; 6389518; 6389761; 7033214; 7536291; 8041620; 8444807; 8496961; 8527431; 8563629; 8789466; 9278503; 9298646; 9600841; 9740056; 10537211; 10726772; 10972807; 11513805; 11683869; 12654735; 14342337; 14726535; 15176868; 16397293; 16905647; 17122063; 17187058; 17264113; 18287020; 18312576; 18557941; 19118352 MUTATION: dppA mutant was attenuated 10- to 50-fold compared to the wild type for colonization of the bladders and kidneys of mice [PMID:17074858]. 2259 dipeptide transporter EcoGene:EG10248 dppA Bin Zhao, Oliver He ECK3612 JW3597 rfaL WEB: http://www.ncbi.nlm.nih.gov/gene 948148 b3622 20140406 511145 protein-coding NCBI-supplied GO_0009244; GO_0009274; GO_0019866; GO_0042280 PMID: 1385388; 1577693; 1624462; 1938935; 7504166; 7517391; 8041620; 8157607; 8478319; 9157235; 9278503; 9535865; 9791168; 12045108; 15919996; 16120447; 16397293; 17227761; 18559433; 19019161; 19019162; 23614028 MUTATION: rfaL mutant is attenuated in rats [PMID:11430402]. 2260 O-antigen ligase EcoGene:EG11424 waaL Bin Zhao, Oliver He ECK3649 JW3633 yicK WEB: http://www.ncbi.nlm.nih.gov/gene 948177 b3659 20140406 511145 protein-coding NCBI-supplied GO_0009274; GO_0019866 PMID: 7686882; 8438231; 9278503; 9529885; 10209755; 10438463; 10943556; 15919996; 16120447; 16381841; 16397293; 16842212 putative arabinose efflux transporter EcoGene:EG11687 setC Bin Zhao, Oliver He ECK3834 JW3818 hlyT sfrB WEB: http://www.ncbi.nlm.nih.gov/gene 948327 b3842 20140406 511145 protein-coding NCBI-supplied GO_0005737; GO_0009244; GO_0009289; GO_0009297; GO_0016563; GO_0042280 PMID: 383690; 1379743; 1584020; 1655711; 1860828; 2437101; 3009418; 6111554; 6192244; 6230355; 7007352; 7504166; 8606157; 8820641; 8951819; 9171395; 9278503; 9426123; 9711858; 10660066; 11682190; 11983161; 12007406; 12045108; 12117951; 12480883; 14643636; 15503145; 15727837; 16397293; 16452414; 17012804; 17122336; 17434131; 17543954; 17711918; 19096362; 20132437; 22817892; 23131843; 23990324; 24163336 MUTATION: attenuated in mice [PMID:12117951]. 2262 DNA-binding transcriptional antiterminator EcoGene:EG10839 rfaH Bin Zhao, Oliver He ECK3852 JW3832 dsf iarA ppfA WEB: http://www.ncbi.nlm.nih.gov/gene 948353 b3860 20140406 511145 protein-coding NCBI-supplied GO_0006457; GO_0006950; GO_0042597 PMID: 1429594; 1465440; 1740115; 1934062; 7487336; 7568240; 7615498; 7628442; 7693702; 7814337; 7830566; 7881552; 7909462; 7972100; 8110795; 8155639; 8180227; 8188592; 8218303; 8277944; 8346018; 8411164; 8413591; 8430071; 8478925; 8483456; 8494885; 8503954; 8521518; 8977120; 9140064; 9159398; 9159399; 9194175; 9278503; 9298646; 9300489; 9534151; 9572841; 9655827; 10047491; 10210188; 10227169; 10234837; 10633106; 10682851; 10781078; 10841975; 11080145; 11157926; 11157944; 11208797; 11285220; 11868275; 11967064; 12006488; 12032077; 12107143; 12193604; 12198560; 12498799; 12564920; 12787348; 12853466; 13129941; 13678528; 14534316; 14612576; 14634016; 14726535; 14739460; 14747707; 15057279; 15220477; 15347648; 15380548; 15502869; 15515098; 15687215; 15687218; 15755450; 15838024; 15937162; 15937881; 16027117; 16087673; 16357193; 16397293; 16446111; 16606699; 16676581; 16720693; 17019443; 17110337; 17122336; 17267399; 17366881; 17456749; 17543954; 17642268; 17702751; 18036138; 18067575; 18082634; 18315846; 18325532; 18406599; 18421137; 18504019; 18642678; 18692066; 18695247; 18775700; 19214188; 19389711; 19567379; 19766568; 19906178; 20615876; 23416557 MUTATION: mutation of dsbA led to degradation of bundilin and an absence of localized adherence to host cells in EPEC [PMID:9224871]. 2263 periplasmic protein disulfide isomerase I EcoGene:EG11297 dsbA Bin Zhao, Oliver He ECK3946 JW3927 cptA yijP WEB: http://www.ncbi.nlm.nih.gov/gene 948458 b3955 20140406 511145 protein-coding NCBI-supplied GO_0009274 PMID: 8265357; 9278503; 10456927; 15215418; 15795227; 15866924; 15919996; 16397293; 16514146; 17362200 MUTATION: yijP mutant had reduced invasion of BMEC [PMID:10456927]. 2264 predicted LPS core phosphoethanolamine transferase EcoGene:EG11914 eptC Bin Zhao, Oliver He ECK4311 JW4283 WEB: http://www.ncbi.nlm.nih.gov/gene 948847 b4320 20140406 511145 protein-coding NCBI-supplied GO_0009101; GO_0009289 PMID: 1355769; 1363735; 1648076; 1686292; 1970114; 1971261; 1977736; 2863818; 2878917; 2886490; 2890081; 2890622; 2894612; 2900235; 2904111; 7610040; 7892228; 7905476; 7916011; 8101185; 8121417; 8878036; 9108285; 9278503; 9545231; 9791174; 10446051; 10768955; 10869080; 10908657; 10913698; 11532135; 11580845; 11597451; 11739641; 12270717; 12417198; 12700251; 12876315; 15039312; 15174130; 15387828; 15546670; 15659162; 15920478; 16036224; 16094085; 16238022; 16397293; 16624825; 16672475; 16930149; 16933977; 17028033; 17122336; 17189376; 17222190; 17378923; 17502398; 17567583; 17589887; 17602628; 17696543; 17697252; 18174167; 18292092; 18438011; 18485865; 18485872; 18627459; 18664574; 19057665; 19325559; 19552773; 19577575; 20018753; 20067530; 20478255; 21768279; 22290143; 23220068; 23795713 MUTATION: attenuated in humans and mice [PMID:18482721]. 2265 minor component of type 1 fimbriae EcoGene:EG10315 fimH Bin Zhao, Oliver He ECK3794 JW3773 atsA gppB WEB: http://www.ncbi.nlm.nih.gov/gene 949015 b3801 20140406 511145 protein-coding NCBI-supplied GO_0005737; GO_0006790 PMID: 361719; 415041; 1379743; 6307972; 8432711; 9278503; 9710560; 10359304; 10948126; 15493058; 16397293 MUTATION: disruption mutant was less invasive in an in vitro HBMEC invasion assay than the wild-type E. coli K1 [PMID:10948126]. 2266 acrylsulfatase-like enzyme EcoGene:EG10089 aslA Bin Zhao, Oliver He ECK0033 JW0030 arg cap pyrA WEB: http://www.ncbi.nlm.nih.gov/gene 949025 b0032 20140406 511145 protein-coding NCBI-supplied GO_0006221; GO_0006526 PMID: 84616; 179975; 189806; 229896; 240389; 1334233; 1630901; 1737023; 1827118; 2464695; 2682645; 3525565; 3549732; 3894020; 4358555; 5319709; 5339592; 6162837; 6308632; 6330744; 6377309; 6451616; 7616563; 7648201; 8282707; 8794775; 9174345; 9242657; 9278503; 9298646; 9457878; 9624689; 9636022; 9740056; 10029528; 10047492; 10089390; 10428826; 10587438; 10625457; 10727215; 11943174; 14718657; 14741201; 15081891; 15322282; 15690043; 16381862; 16397293; 16606699; 16621816; 16858726; 17012394; 17187058; 17209549; 17919280; 18458150; 18535147; 19569682 MUTATION: A carAB mutant is attenuated in turkeys [PMID:8063392]. 4909 carbamoyl phosphate synthetase small subunit, glutamine amidotransferase EcoGene:EG10134 carA Bin Zhao, Oliver He ECK1922 H JW1908 flaF hag WEB: http://www.ncbi.nlm.nih.gov/gene 949101 b1923 20140406 511145 protein-coding NCBI-supplied GO_0009296; GO_0019861; GO_0042330 PMID: 2659972; 3536885; 6305924; 8002586; 8407796; 9097040; 9119048; 9278503; 9298646; 9449357; 9545371; 9600841; 9791174; 10320579; 10498711; 10667798; 10972838; 11118149; 11169117; 11268201; 11872702; 12500982; 12700273; 14625308; 14673116; 15130122; 15170399; 15276183; 15663798; 15806100; 15911532; 16024789; 16397293; 16397770; 16499606; 17122336; 17283097; 17489638; 17702465; 17925449; 18227166; 18819156; 19016776; 19134113; 19200386; 19656466; 23220068 MUTATION: fliC deletion mutants had reduced adherence in bovine tissue compared to the wild type EHEC and EPEC strains [PMID:17693516]. 2267 flagellar filament structural protein (flagellin) EcoGene:EG10321 fliC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 949374 HI0364 20140215 71421 protein-coding NCBI-supplied PMID: 7542800; 7542802; 8805245; 9719565; 10675023; 11156613 MUTATION: HI0364 mutant is attenuated in rats [PMID:12473436]. 2842 penicillin-binding protein 7 HI0364 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 949442 HI0330 20140406 71421 protein-coding NCBI-supplied PMID: 7542800; 7542802; 8805245; 9719565; 10675023; 11156613 MUTATION: oapA mutant has significantly reduced binding to Chang epithelial cells than the wild type [PMID:10417187]. 2843 opacity associated protein oapA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 949460 HI1018 20110216 71421 pseudo NCBI-supplied MUTATION: HI1018 mutant is attenuated in rats [PMID:12473436]. 2844 pseudo HI1018 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 949505 HI0406 20140405 71421 protein-coding NCBI-supplied PMID: 7542800; 7542802; 8805245; 9719565; 10675023; 11156613 MUTATION: accA mutant is attenuated in rats [PMID:12473436]. 2845 acetyl-CoA carboxylase carboxyltransferase subunit alpha accA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 949531 HI0432 20140322 71421 protein-coding NCBI-supplied PMID: 7542800; 7542802; 8805245; 9719565; 10675023; 11156613 MUTATION: nudC mutant is attenuated in rats [PMID:12473436]. 2846 NADH pyrophosphatase nudC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 949562 HI1245 20140406 71421 protein-coding NCBI-supplied PMID: 7542800; 7542802; 8805245; 9719565; 10675023; 11156613 MUTATION: HI1245 mutant is attenuated in rats [PMID:12473436] 2847 malic enzyme HI1245 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 949590 HI0527 20140322 71421 protein-coding NCBI-supplied PMID: 7542800; 7542802; 8805245; 9719565; 10675023; 11156613 MUTATION: fdx-2 mutant is attenuated in rats [PMID:12473436]. 2848 ferredoxin fdx-2 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 949701 HI0661 20140222 71421 protein-coding NCBI-supplied PMID: 7542800; 7542802; 8805245; 9719565; 10675023; 11156613 MUTATION: oapA mutant has significantly reduced binding to Chang epithelial cells than the wild type [PMID:10417187]. 2849 hemoglobin-binding protein oapA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 949725 HI0700 20130708 71421 protein-coding NCBI-supplied PMID: 7542800; 7542802; 8805245; 9719565; 10675023; 11156613 MUTATION: HI0700 mutant is attenuated in rats [PMID:12473436]. 2850 hypothetical protein HI0700 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 949839 HI0884 20140406 71421 protein-coding NCBI-supplied PMID: 7542800; 7542802; 8805245; 9719565; 10675023; 11156613; 11717280 MUTATION: arcA mutant is attenuated in mice [PMID:12496162]. 2851 two-component response regulator arcA Bin Zhao, Oliver He cgtA obg yhbZ WEB: http://www.ncbi.nlm.nih.gov/gene 949885 HI0877 20140322 71421 protein-coding NCBI-supplied PMID: 7542800; 7542802; 8805245; 9719565; 10675023; 11156613 MUTATION: obgE mutant is attenuated in rats [PMID:12473436]. 2852 GTPase ObgE - obgE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 949904 HI0898 20140222 71421 protein-coding NCBI-supplied PMID: 7542800; 7542802; 8805245; 9719565; 10675023; 11156613 MUTATION: emrA mutant is attenuated in rats [PMID:12473436]. 2853 multidrug resistance protein A emrA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 949926 HI0928 20140329 71421 protein-coding NCBI-supplied PMID: 7542800; 7542802; 8805245; 9719565; 10675023; 11156613 MUTATION: htkE mutant has attenuated virulence in interperitioneal infection of infant rats [PMID:7927766]. 2854 catalase hktE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 949980 HI1275 20140322 71421 protein-coding NCBI-supplied PMID: 7542800; 7542802; 8805245; 9719565; 10675023; 11156613 MUTATION: tehB mutant is attenuated in rats [PMID:20075041]. 2855 tellurite resistance protein TehB tehB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 950115 HI1152 20140322 71421 protein-coding NCBI-supplied PMID: 7542800; 7542802; 8805245; 9719565; 10675023; 11156613 MUTATION: pmbA mutant is attenuated in rats [PMID:12473436]. 2856 hypothetical protein pmbA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 950124 HI1164 20140405 71421 protein-coding NCBI-supplied PMID: 7542800; 7542802; 8805245; 9719565; 10675023; 11156613 MUTATION: ompA mutant had reduced adherence to human oropharyngeal cells in vitro, augmented clearance from the tympanum post-transbullar inoculation, and significantly reduced induction of OM post-intranasal inoculation in a chinchilla model compared to the wild type [PMID:7909539]. 2857 outer membrane protein P5 ompA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 950165 HI1215 20140222 71421 protein-coding NCBI-supplied PMID: 7542800; 7542802; 8805245; 9719565; 10675023; 11156613 MUTATION: dsbA mutant is attenuated in mice [PMID:18212083]. 2858 thiol-disulfide interchange protein dsbA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 950224 HI0561 20140222 71421 protein-coding NCBI-supplied PMID: 7542800; 7542802; 8805245; 9719565; 10675023; 11156613 MUTATION: HI0561 mutant is attenuated in rats [PMID:12473436]. 2859 hypothetical protein HI0561 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 950350 HI1459 20140222 71421 protein-coding NCBI-supplied PMID: 7542800; 7542802; 8805245; 9719565; 10675023; 11156613 MUTATION: HI1459 mutant is attenuated in rats [PMID:12473436]. 2860 RNA polymerase sigma factor HI1459 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 950390 HI1528 20140215 71421 protein-coding NCBI-supplied PMID: 7542800; 7542802; 8805245; 9719565; 10675023; 11156613 MUTATION: parE mutant is attenuated in rats [PMID:12473436]. 2861 DNA topoisomerase IV subunit B parE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 950399 HI1537 20140329 71421 protein-coding NCBI-supplied PMID: 7542800; 7542802; 8805245; 9719565; 10675023; 11156613 MUTATION: licA mutant is attenuated in rats [PMID:12473436]. 2862 lic-1 operon protein licA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 950454 HI1598 20140322 71421 protein-coding NCBI-supplied PMID: 7542800; 7542802; 8805245; 9719565; 10675023; 11156613 MUTATION: HI1598 mutant is attenuated in rats [PMID:12473436]. 2863 hypothetical protein HI1598 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 950673 HI1368 20140222 71421 protein-coding NCBI-supplied PMID: 7542800; 7542802; 8805245; 9719565; 10675023; 11156613 MUTATION: HI1368 mutant is attenuated in rats [PMID:12473436]. 2864 zinc protease HI1368 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 950731 HI0936 20140215 71421 protein-coding NCBI-supplied PMID: 7542800; 7542802; 8805245; 9719565; 10675023; 11156613 MUTATION: HI0936 mutant is attenuated in rats [PMID:12473436]. 2865 cytochrome C-type biogenesis HI0936 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 950748 HI1218 20140322 71421 protein-coding NCBI-supplied PMID: 7542800; 7542802; 8805245; 9719565; 10675023; 11156613 MUTATION: lctP mutant is attenuated in rats [PMID:12473436]. 2866 L-lactate permease lctP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 950776 HI0814 20140406 71421 protein-coding NCBI-supplied PMID: 7542800; 7542802; 8805245; 9719565; 10675023; 11156613 MUTATION: alaS mutant is attenuated in rats [PMID:12473436]. 2867 alanyl-tRNA synthetase alaS Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 950801 HI0628 20140322 71421 protein-coding NCBI-supplied PMID: 7542800; 7542802; 8805245; 9719565; 10675023; 11156613 MUTATION: ropE mutants are unable to survive intracellularly in macrophages [PMID:11796603]. 2868 RNA polymerase sigma factor RpoE rpoE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 950809 HI0428 20140406 71421 protein-coding NCBI-supplied PMID: 7542800; 7542802; 8805245; 9719565; 10675023; 11156613 MUTATION: dsbB mutant is attenuated in rats [PMID:12473436]. 2869 disulfide bond formation protein B dsbB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 950862 HI1677 20140322 71421 protein-coding NCBI-supplied PMID: 7542800; 7542802; 8805245; 9719565; 10675023; 11156613 MUTATION: Compared to the wild-type strain, the ytfE (HI1677) mutant exhibited decreased survival when exposed to macrophages, a defect that was more pronounced after prior stimulation of macrophages with IFN-gamma or lipopolysaccharide. Complementation restored survival of the mutant to the level in the parental strain [PMID:19289513]. 2870 iron-sulfur cluster repair di-iron protein HI1677 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 950872 HI1712 20140406 71421 protein-coding NCBI-supplied PMID: 7542800; 7542802; 8805245; 9719565; 10675023; 11156613 MUTATION: ptsl mutant is attenuated in mice [PMID:12949188]. 2871 phosphoenolpyruvate-protein phosphotransferase ptsI Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 950878 HI1732 20110216 71421 other NCBI-supplied MUTATION: HI1732 mutant is attenuated in rats [PMID:12473436]. 2872 HI1732 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 950982 HI0086 20140405 71421 protein-coding NCBI-supplied PMID: 7542800; 7542802; 8805245; 9719565; 10675023; 11156613 MUTATION: metB mutant is attenuated in rats [PMID:12473436]. 2873 cystathionine gamma-synthase metB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 951037 HI0129 20140222 71421 protein-coding NCBI-supplied PMID: 7542800; 7542802; 8805245; 9719565; 10675023; 11156613 MUTATION: afuB mutant is attenuated in rats [PMID:12473436]. 2874 ferric transport system permease-like protein afuB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 951048 HI0139 20140405 71421 protein-coding NCBI-supplied PMID: 7542800; 7542802; 8805245; 9719565; 10675023; 11156613 MUTATION: the introduction of functional NTHI ompP2 gene into the avirulent Hib ompP2 mutant restored the virulence of this strain to wild-type levels [PMID:7689543]. P2 mutants are unable to produce detectable bacteremia in infant rats [PMID:7689543]. 2875 outer membrane protein P2 ompP2 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 951117 HI0209 20140322 71421 protein-coding NCBI-supplied PMID: 7542800; 7542802; 8805245; 9719565; 10675023; 11156613 MUTATION: dam mutants is attenuated in invasion of of human brain microvascular endothelial cells (HBMECs) and human respiratory epithelial cells (NCI-H292) [PMID:15228541]. 2876 DNA adenine methylase dam Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 951501 ECTVgp018 20140217 12643 protein-coding NCBI-supplied PMID: 7747448; 9495531; 10725549 kelch-like protein EVM018 Bin Zhao, Oliver He EVM167 WEB: http://www.ncbi.nlm.nih.gov/gene 951519 ECTVgp168 20130525 12643 protein-coding NCBI-supplied PMID: 7747448; 9495531; 10725549; 18221766 MUTATION: deletions of one to four genes of kelch family both individually (single mutants) and in different combinations (double, triple and quadruple mutants). It was shown that deletion of any of the three genes EVMO18, EVM027 or EVM167 resulted in reduction of 50% lethal dose (LD50) by five and more orders in outbred white mice infected intraperitoneally. Deletion of mousepox kelch-gene EVM150 did not influence the virus virulence. Two or more kelch-genes deletion also resulted in high level of attenuation, which could evidently be due to the lack of three genes EVM167, EVM018 and/or EVM027 identified as virulence factors. [PMID:19807023] 5100 hypothetical protein - C13R Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 951567 ECTVgp027 20140406 12643 protein-coding NCBI-supplied PMID: 7747448; 9495531; 10725549 Kelch-like protein EVM027 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 956528 FLUAVs7gp2 20140208 211044 protein-coding NCBI-supplied PMID: 6927841; 15731254; 15831957; 15919950; 19217395; 19837376; 20713739; 21775472; 24027311; 24168642 MUTATION: Mutant influenza virus that lacks the transmembrane and cytoplasmic tail domains of M2 (M2 knockout [M2KO]) from Influenza A virus (A/Puerto Rico/8/34(H1N1)) is attenuated in both cell culture and mice [PMID:19321619]. 4984 M2 Other designations: matrix protein 2 M2 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 956533 FLUAVs8gp2 20140405 211044 protein-coding NCBI-supplied PMID: 7208353; 7241645; 7385583; 7465426; 17053203; 17079289; 17881440; 18029356; 18039687; 19454344; 19454348; 19717515; 19726611; 19917317; 20463066; 21085662; 21163951; 21411677; 22022552; 22171255; 22174864; 22398291; 22563505; 22744180; 22951840; 22973032; 22993153; 23418535; 23468495; 24027311; 24220336; 24277853 MUTATION: Influenza virus with a deletion of the NS1 gene were highly attenuated in mice [PMID:9878611]. 4832 nonstructural protein NS1 NS1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 956534 FLUAVs2gp1 20120703 211044 protein-coding NCBI-supplied PMID: 6281731; 18182088; 18660801; 19461581; 21837415 MUTATION: mutations eliminating expression of PB1F2 without afffecting the PB1 open reading frame were attenuating following intranasal inoculation [PMID:16873254]. 4833 polymerase 1 PB1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 956555 LACVsMgp1 20140215 11577 protein-coding NCBI-supplied G1/G2 membrane polyprotein M MUTATION: NSs mutant virus is avirulent in mice [PMID:18225953]. 1917 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 956702 Z3343 20140215 155864 protein-coding NCBI-supplied PMID: 11206551; 21203383 shiga-like toxin 1 subunit B encoded within prophage CP-933V stx1B Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 956892 Z0178 20130330 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: map mutant is attenuated in calves [PMID:15528651]. 2125 methionine aminopeptidase map Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 956966 Z3341 20130508 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: Z3341 mutant is attenuated in calves [PMID:15528651]. 2126 hypothetical protein Z3341 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 956968 Z3344 20140222 155864 protein-coding NCBI-supplied PMID: 11206551 shiga-like toxin 1 subunit A encoded within prophage CP-933V stx1A Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 957027 Z0275 20140222 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: Z0275 mutant is attenuated in calves [PMID:15528651]. 2128 hypothetical protein Z0275 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 957084 Z3399 20140222 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: sanA mutant is attenuated in calves [PMID:15528651]. 2129 hypothetical protein sanA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 957113 Z3404 20130508 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: mglA mutant is attenuated in calves [PMID:15731074]. 2130 galactose/methyl galaxtoside transporter ATP-binding protein mglA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 957204 Z0390 20130226 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: Z0390 mutant is attenuated in calves [PMID:15528651]. 2131 hypothetical protein Z0390 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 957222 Z3496 20130226 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: Z3496 mutant is attenuated in calves [PMID:15528651]. 2132 hypothetical protein Z3496 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 957315 Z0469 20130508 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: Z0469 mutant is attenuated in calves [PMID:15528651]. 2133 hypothetical protein Z0469 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 957342 Z0492 20140222 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: rdgC mutant is attenuated in calves [PMID:15528651]. 2134 recombination associated protein rdgC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 957466 Z0609 20140217 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: Z0609 mutant is attenuated in calves [PMID:15528651]. 2135 hypothetical protein Z0609 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 957555 Z3632 20140222 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: evgS mutant is attenuated in calves [PMID:15731074]. 2136 hybrid sensory histidine kinase in two-component regulatory system with EvgA evgS Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 957907 Z3841 20140215 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: yfhH mutant is attenuated in calves [PMID:15528651]. 2137 DNA-binding transcriptional regulator yfhH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 957981 Z3867 20130330 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: trxC mutant is attenuated in calves [PMID:15528651]. 2138 thioredoxin trxC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 957986 Z0990 20140406 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: Z0990 mutant is attenuated in calves [PMID:15528651]. 2139 hypothetical protein Z0990 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 958085 Z3950 20130226 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: Z3950 mutant is attenuated in calves [PMID:15528651]. 2140 hypothetical protein Z3950 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 958288 Z4136 20140222 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: recD mutant is attenuated in calves [PMID:15731074]. 2141 exonuclease V subunit alpha recD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 958313 Z4163 20140222 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: kduI mutant is attenuated in calves [PMID:15528651]. 2142 5-keto-4-deoxyuronate isomerase kduI Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 958343 Z4200 20140222 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: z4200 (pkgA) mutant is attenuated in calves [PMID:15731074]. 2143 hypothetical protein Z4200 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 958378 Z3635 20140215 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: z3635 (yfdV) mutant is attenuated in calves [PMID:15731074]. 2144 transporter YfdV Z3635 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 958414 Z4282 20130226 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: z4282 mutant is attenuated in calves [PMID:15731074]. 2145 hypothetical protein Z4282 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 958416 Z4283 20140405 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: speA mutant is attenuated in calves [PMID:15731074]. 2146 arginine decarboxylase speA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 958457 Z4318 20140215 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: Z4318 mutant is attenuated in calves [PMID:15528651]. 2147 hypothetical protein Z4318 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 958466 Z4341 20130826 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: pitB mutant is attenuated in calves [PMID:15731074]. 2148 transporter pitB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 958522 Z1126 20130613 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: Z1126 mutant is attenuated in calves [PMID:15528651]. 2149 hypothetical protein Z1126 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 958525 Z1129 20140215 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: z1129 mutant is attenuated in calves [PMID:15731074]. 2150 helicase Z1129 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 958549 Z4466 20140405 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: tdcE mutant is attenuated in calves [PMID:15731074]. 2151 formate acetyltransferase 3 tdcE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 958755 Z1182 20130613 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: Z1182 mutant is attenuated in calves [PMID:15528651]. 2152 hypothetical protein Z1182 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 958789 Z1202 20130826 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: Z1202 mutant is attenuated in calves [PMID:15528651]. 2153 hypothetical protein Z1202 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 958846 Z1232 20140308 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: trxB mutant is attenuated in calves [PMID:15731074]. 2154 thioredoxin reductase trxB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 958948 Z1307 20140405 155864 protein-coding NCBI-supplied PMID: 11206551; 20693671 MUTATION: OmpA− strains are unable to cause actin condensation needed for invasion of brain epithelial cells [PMID:10531228]. 2155 outer membrane protein OmpA ompA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 958973 Z1328 20130226 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: Z1328 mutant is attenuated in calves [PMID:15528651]. 2156 hypothetical protein Z1328 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 958999 Z4168 20140222 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: ygeJ mutant is attenuated in calves [PMID:15528651]. 2157 hypothetical protein yqeJ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 959050 Z1403 20140406 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: ymcC mutant is attenuated in calves [PMID:15528651]. 2158 regulator ymcC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 959107 Z1465 20140406 155864 protein-coding NCBI-supplied PMID: 11206551 shiga-like toxin II B subunit encoded by bacteriophage BP-933W stx2B Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 959162 Z1526 20140215 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: ycdS mutant is attenuated in calves [PMID:15528651]. 2160 outer membrane protein PgaA pgaA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 959220 Z4492 20140405 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: agaB mutant is attenuated in calves [PMID:15528651]. 2161 PTS system N-acetylgalactosamine-specific transporter subunit IIB agaB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 959379 Z1681 20140406 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: mdoC (ymdD) mutant is attenuated in calves [PMID:15731074]. 2162 glucans biosynthesis protein mdoC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 959506 Z3948 20140222 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: ypjA mutant is attenuated in calves [PMID:15528651]. 2163 ABC transporter ATP-binding protein ypjA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 959584 Z4251 20140405 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: serA mutant is attenuated in calves [PMID:15731074]. 2164 D-3-phosphoglycerate dehydrogenase serA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 959588 Z1829 20140215 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: z1829 mutant is attenuated in calves [PMID:15731074]. 2165 hypothetical protein Z1829 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 959707 Z5946 20130508 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: Z5946 mutant is attenuated in calves [PMID:15528651]. 2166 restriction modification enzyme S subunit Z5946 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 959733 Z5918 20140406 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: attenuated in mice and humans [PMID:18482721]. 2167 minor fimbrial subunit, D-mannose specific adhesin fimH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 959740 Z5911 20130420 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: fimE mutant is attenuated in calves [PMID:15731074]. 2168 tyrosine recombinase fimE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 959744 Z5905 20140215 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: yjhS mutant is attenuated in calves [PMID:15528651]. 2169 hypothetical protein yjhS Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 959763 Z5886 20140215 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: Z5886 mutant is attenuated in calves [PMID:15528651]. 2170 hypothetical protein Z5886 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 959802 Z5848 20140405 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: nrdD mutant is attenuated in calves [PMID:15731074]. 2171 anaerobic ribonucleoside triphosphate reductase nrdD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 959880 Z1930 20140222 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: Z1930 mutant is attenuated in calves [PMID:15528651]. 2172 protease encoded within prophage CP-933X Z1930 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 959978 Z5750 20130226 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: yjeJ mutant is attenuated in calves [PMID:15528651]. 2173 hypothetical protein yjeJ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 960058 Z5665 20140215 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: yjcF mutant is attenuated in calves [PMID:15528651]. 2174 hypothetical protein yjcF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 960113 Z5608 20130508 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: arp mutant is attenuated in calves [PMID:15528651]. 2175 regulator of acetyl CoA synthetase arp Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 960248 Z5444 20130226 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: Z5444 mutant is attenuated in calves [PMID:15528651]. 2176 glycoporin Z5444 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 960300 Z5392 20140406 155864 protein-coding NCBI-supplied PMID: 11206551; 18067575 MUTATION: mutation of dsbA led to degradation of bundilin and an absence of localized adherence to host cells in EPEC [PMID:9224871]. 2177 protein disulfide isomerase dsbA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 960318 Z5362 20140217 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: attenuated in mice [PMID:12117951]. 2178 transcriptional activator RfaH rfaH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 960401 Z5279 20140406 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: ilvG mutant is attenuated in calves [PMID:15528651]. 2179 acetolactate synthase 2 catalytic subunit ilvG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 960477 Z2001 20140406 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: narG mutant is attenuated in calves [PMID:15731074]. 2180 nitrate reductase 1 subunit alpha narG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 960504 Z2030 20130518 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: attenuated in mice [PMID:11553558]. 2181 transporter tonB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 960527 Z2056 20140217 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: z2056 mutant is attenuated in calves [PMID:15731074]. 2182 hypothetical protein Z2056 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 960608 Z2142 20140222 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: z2142 mutant is attenuated in calves [PMID:15731074]. 2183 tail component of prophage CP-933O Z2142 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 960610 Z2144 20140222 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: Z2144 mutant is attenuated in calves [PMID:15528651]. 2184 tail component of prophage CP-933O Z2144 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 960615 Z2149 20130226 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: Z2149 mutant is attenuated in calves [PMID:15528651]. 2185 hypothetical protein Z2149 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 960638 Z2176 20130226 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: z2176 mutant is attenuated in calves [PMID:15731074]. 2186 hypothetical protein Z2176 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 960656 Z2195 20140217 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: ydeK mutant is attenuated in calves [PMID:15731074]. 2187 lipoprotein ydeK Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 960662 Z2203 20140217 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: Z2203 mutation is attenuated in calves [PMID:15528651]. 2188 fimbrial usher protein Z2203 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 960664 Z2205 20140222 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: z2205 mutant is attenuated in calves [PMID:15731074]. 2189 fimbrial-like protein Z2205 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 960666 Z2207 20140405 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: z2207 mutant is attenuated in calves [PMID:15731074]. 2190 oxidoreductase Z2207 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 960672 Z2212 20140222 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: yddA mutant is attenuated in calves [PMID:15731074]. 2191 ABC transporter ATP-binding protein yddA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 960719 Z5214 20140222 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: Z5214 mutant is attenuated in calves [PMID:15528651]. 2192 hypothetical protein Z5214 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 960725 Z5212 20130226 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: Z5212 mutant is attenuated in calves [PMID:15528651]. 2193 hypothetical protein Z5212 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 960841 Z5131 20140222 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: Z5131 mutant is attenuated in calves [PMID:15528651]. 2194 hypothetical protein Z5131 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 960846 Z5126 20131002 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: escC mutant is attenuated in calves [PMID:15528651]. 2195 hypothetical protein escC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 960851 Z5121 20131002 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: z5121(st22) mutant is attenuated in calves [PMID:15731074]. 2196 hypothetical protein Z5121 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 960852 Z5120 20140215 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: escV mutant is attenuated in calves [PMID:15528651]. 2197 hypothetical protein escV Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 960853 Z5119 20140222 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: deletion of escN abolished pathogenicity in infant rabbits compared to wild-type EHEC [PMID:15731044]. 2198 hypothetical protein escN Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 960856 Z5116 20140222 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: sepQ mutant is attenuated in calves [PMID:15528651]. 2199 hypothetical protein sepQ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 960858 Z5114 20131002 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: Z5114 (cesF) mutant is attenuated in calves [PMID:15528651]. 2200 hypothetical protein Z5114 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 960860 Z5112 20140222 155864 protein-coding NCBI-supplied PMID: 11206551; 15527496; 16228285; 16954405; 17521329; 21567195 MUTATION: tir deletion strains are unable to adhere to tissue in an in vitro organ culture [PMID:17474908]. 2201 translocated intimin receptor protein tir Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 960862 Z5110 20140222 155864 protein-coding NCBI-supplied PMID: 11206551; 21179574; 21206020; 22658748 MUTATION: attenuated in humans [PMID:8376594]. 2202 intimin adherence protein eae Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 960865 Z5107 20140217 155864 protein-coding NCBI-supplied PMID: 11206551; 16707687; 18178741; 21075691; 23043360 MUTATION: deletion of espA in STEC abolished ability to attach to HeLa cells and induce actin rearrangements [PMID:9786192]. 2203 hypothetical protein espA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 960866 Z5106 20140406 155864 protein-coding NCBI-supplied PMID: 11206551; 21651628; 23043360 MUTATION: espD deletion mutant of the enterohemorrhagic E. coli (EHEC) strain EDL933 had impaired attachment to HeLa cells [PMID:10456938]. 2204 hypothetical protein espD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 960867 Z5105 20140406 155864 protein-coding NCBI-supplied PMID: 11206551; 23043360 MUTATION: deletion mutant attenuated in humans compared to wild-type EPEC [PMID:10816529]. 2205 hypothetical protein espB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 960871 Z5100 20140406 155864 protein-coding NCBI-supplied PMID: 11206551; 18067584 MUTATION: espF EPEC mutant is deficient in its ability to disrupt electrical resistance across a polarized monolayer of intestinal epithelial cells, suggesting that EspF is an effector molecule required for disrupting intestinal epithelial barrier function [PMID:11238563]. 2206 hypothetical protein espF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 960931 Z5042 20140406 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: yibD mutant is attenuated in calves [PMID:15528651]. 2207 glycosyl transferase yibD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 960959 Z5014 20140406 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: rhsA mutant is attenuated in calves [PMID:15731074]. 2208 rhsA protein in rhs element rhsA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 961000 Z2313 20140222 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: hrpA mutant is attenuated in calves [PMID:15528651]. 2209 ATP-dependent RNA helicase HrpA hrpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 961004 Z2318 20140405 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: Z2318 mutant is attenuated in calves [PMID:15528651]. 2210 phosphatidate cytidylyltransferase Z2318 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 961074 Z4961 20140405 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: dppA mutant was attenuated 10- to 50-fold compared to the wild type for colonization of the bladders and kidneys of mice [PMID:17074858]. 2211 dipeptide transport protein dppA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 961092 Z4942 20130508 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: dctA mutant is attenuated in calves [PMID:15528651]. 2212 C4-dicarboxylate transporter DctA dctA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 961108 Z2368 20130226 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: Z2368 mutant is attenuated in calves [PMID:15528651]. 2213 hypothetical protein Z2368 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 961176 Z4911 20140215 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: chuA mutant unable to grow on iron-depleted medium containing heme [PMID:9157252]. 2214 outer membrane heme/hemoglobin receptor chuA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 961212 Z4887 20140215 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: yhiJ mutant is attenuated in calves [PMID:15528651]. 2215 hypothetical protein yhiJ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 961230 Z3620 20130226 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: Z3620 mutant is attenuated in calves [PMID:15528651]. 2216 hypothetical protein Z3620 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 961311 Z2463 20140215 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: ycjV mutant is attenuated in calves [PMID:15731074]. 2217 ABC transporter ATP-binding protein ycjV Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 961382 Z2532 20140405 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: acnA mutant is attenuated in calves [PMID:15731074]. 2218 aconitate hydratase acnA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 961399 Z2550 20140405 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: trpB mutant is attenuated in calves [PMID:15731074]. 2219 tryptophan synthase subunit beta trpB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 961413 Z6010 20140217 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: Z6010 mutant is attenuated in calves [PMID:15528651]. 2220 hypothetical protein Z6010 Bin Zhao, Oliver He sapG WEB: http://www.ncbi.nlm.nih.gov/gene 961474 Z4660 20140222 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: trkA mutant is attenuated in calves [PMID:15731074]. 2221 potassium transporter peripheral membrane protein - trkA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 961645 Z2702 20140215 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: Z2702 mutant is attenuated in calves [PMID:15528651]. 2222 hypothetical protein Z2702 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 961691 Z2749 20130508 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: z2749 mutant is attenuated in calves [PMID:15731074]. 2223 hypothetical protein Z2749 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 961692 Z2751 20140215 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: z2751 mutant is attenuated in calves [PMID:15731074]. 2224 hypothetical protein Z2751 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 961704 Z2764 20140222 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: celF mutant is attenuated in calves [PMID:15528651]. 2225 6-phospho-beta-glucosidase celF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 961796 Z2868 20130330 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: cspC mutant is attenuated in calves [PMID:15528651]. 2226 cold shock-like protein CspC cspC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 961896 Z2984 20140222 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: Z2984 mutant is attenuated in calves [PMID:15528651]. 2227 serine acetlyltransferase of prophage CP-933T Z2984 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 961914 Z3004 20140217 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: sidA mutant is attenuated in calves [PMID:15528651]. 2228 DNA-binding transcriptional activator SdiA sdiA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 961921 Z3013 20140405 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: fliC deletion mutants had reduced adherence in bovine tissue compared to the wild type EHEC and EPEC strains [PMID:17693516]. 2229 flagellin fliC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 961931 Z3022 20140222 155864 protein-coding NCBI-supplied PMID: 11206551 hypothetical protein yedL Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 961932 Z3023 20140222 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: Z3023 mutant is attenuated in calves [PMID:15528651]. 2231 hypothetical protein Z3023 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 961934 Z3026 20140222 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: Z3026 mutant is attenuated in calves [PMID:15528651]. 2232 hypothetical protein Z3026 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 961974 Z3062 20140329 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: z3062 mutant is attenuated in calves [PMID:15731074]. 2233 hypothetical protein Z3062 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 962089 Z3194 20140405 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: manB mutant is attenuated in calves [PMID:15528651]. 2234 phosphomannomutase manB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 962090 Z3195 20140405 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: manC mutant is attenuated in calves [PMID:15528651]. 2235 mannose-1-phosphate guanylyltransferase manC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 962092 Z3197 20140405 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: fcl mutant is attenuated in calves [PMID:15528651]. 2236 fucose synthetase fcI Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 962094 Z3199 20140215 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: wbdP mutant is attenuated in calves [PMID:15528651]. 2237 glycosyl transferase wbdP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 962095 Z3200 20140215 155864 protein-coding NCBI-supplied PMID: 11206551 MUTATION: per mutant is attenuated in calves [PMID:15528651]. 2238 perosamine synthetase per Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 984498 lmo0558 20140406 169963 protein-coding NCBI-supplied PMID: 11679669; 16428782; 19448609 MUTATION: pgl mutant exhibited a 15 to 30 fold defect in growth in vivo [PMID:19398547]. 498 hypothetical protein lmo0558 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 984504 lmo2821 20140402 169963 protein-coding NCBI-supplied PMID: 11679669; 16428782; 19448609 MUTATION: mutant attenuated in virulence after intravenous infection of mice [PMID:16177371]. 499 internalin lmo2821 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 984795 lmo2067 20140405 169963 protein-coding NCBI-supplied PMID: 11679669; 16428782; 19448609 MUTATION: deletion of bsh decreased resistance to bile, bacterial faecal carriage in guinea pigs and liver colonization in mice [PMID:12180927]. 500 bile acid hydrolase lmo2067 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 984958 lmo2549 20140322 169963 protein-coding NCBI-supplied PMID: 11679669; 16428782; 18192405; 19448609 MUTATION: a gtcA mutant was attenuated in mice [PMID:11254558] 501 wall teichoic acid glycosylation protein GtcA gtcA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 985015 lmo0674 20140401 169963 protein-coding NCBI-supplied PMID: 11679669; 16428782; 19448609 MUTATION: mogR deletion mutant has a 250-fold decrease in virulence in mice and has reduced capacity for cell-to-cell spread [PMID:15302931]. 4904 lmo0674 Other designations: hypothetical protein lmo0674 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 985032 lmo0692 20140405 169963 protein-coding NCBI-supplied PMID: 11679669; 16428782; 19448609 MUTATION: mutant reduced invasion of Caco-2 cells compared to wild type [PMID:15155625]. 502 two-component sensor histidine kinase CheA cheA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 985049 lmo0691 20140402 169963 protein-coding NCBI-supplied PMID: 11679669; 16428782; 19448609 MUTATION: mutant reduced invasion of Caco-2 cells compared to wild type [PMID:15155625]. 503 chemotaxis response regulator CheY cheY Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 985073 lmo1273 20140405 169963 protein-coding NCBI-supplied PMID: 11679669; 16428782; 19246760; 19448609 MUTATION: mutant attenuated in mice, multiplication was significantly impaired [PMID:19246760]. 504 ribonuclease HII rnhB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 985087 lmo1269 20140224 169963 protein-coding NCBI-supplied PMID: 11679669; 16428782; 19448609 MUTATION: lmo1269 (sipX) is attenuated in mice [PMID:14982622]. 505 type I signal peptidase lmo1269 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 985089 lmo1271 20140406 169963 protein-coding NCBI-supplied PMID: 11679669; 16428782; 19448609 MUTATION: lmo1271 (sipZ) mutant is attenuated in mice [PMID:14982622]. 506 type I signal peptidase lmo1271 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 985096 lmo1267 20140402 169963 protein-coding NCBI-supplied PMID: 11679669; 16428782; 19448609 MUTATION: mutant showed reduced capacity to persist in spleens and livers of infected mice [PMID:17021213]. 507 trigger factor tig Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 985140 lmo0582 20140224 169963 protein-coding NCBI-supplied PMID: 11679669; 14527997; 16321943; 16428782; 19448609 MUTATION: mutant is strongly attenuated in mice, deletion led to abnormal cell division and loss of motility [PMID:12761132]. 508 invasion associated secreted endopeptidase iap Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 985151 lmo0433 20140402 169963 protein-coding NCBI-supplied PMID: 11679669; 16332872; 16428782; 16751490; 17566579; 18806773; 18840511; 19309566; 19448609; 20066101; 21144051; 23317868; 23376167 MUTATION: attenuated in mice [PMID:7558297]. 509 internalin A inlA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 985307 lmo1600 20140405 169963 protein-coding NCBI-supplied PMID: 11679669; 16428782; 19448609 MUTATION: attenuated in mice [PMID:16790768]. 510 bifunctional 3-deoxy-7-phosphoheptulonate synthase/chorismate mutase aroA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 985416 lmo2206 20140406 169963 protein-coding NCBI-supplied PMID: 11679669; 16428782; 19448609 MUTATION: mutant displayed 100 fold decrease in virulence in bacteria, also attenuated in mice [PMID:14762012]. 511 Clp protease subunit B clpB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 985561 lmo1745 20140224 169963 protein-coding NCBI-supplied PMID: 11679669; 16428782; 19448609 MUTATION: VirR deletion severely decreased virulence in mice and invasion in cell culture [PMID:16102006]. 512 two-component response regulator lmo1745 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 985618 lmo1695 20140224 169963 protein-coding NCBI-supplied PMID: 11679669; 16428782; 19448609 MUTATION: attenuated in mice [PMID:17042784]. 513 hypothetical protein lmo1695 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 985753 lmo1927 20140406 169963 protein-coding NCBI-supplied PMID: 11679669; 16428782; 19448609 MUTATION: attenuated in mice [PMID:16790768]. 514 3-dehydroquinate synthase aroB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 985887 lmo1829 20140406 169963 protein-coding NCBI-supplied PMID: 11679669; 16428782; 19448609 MUTATION: FbpA mutant attenuated in mice [PMID:15228540]. 515 fibronectin-binding proteins lmo1829 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 985901 lmo1821 20140402 169963 protein-coding NCBI-supplied PMID: 11679669; 16428782; 19448609 MUTATION: mutant attenuated in mice [PMID:15813732]. 516 phosphoprotein phosphatase lmo1821 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 985945 lmo1786 20140224 169963 protein-coding NCBI-supplied PMID: 11679669; 16428782; 19448609; 20855622; 23403554 MUTATION: attenuated virulence in mice [PMID:8878044]. 517 internalin C inlC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 986264 lmo1076 20140224 169963 protein-coding NCBI-supplied PMID: 11679669; 16428782; 19210622; 19448609 MUTATION: aut deletion mutants show reduced invasiveness and virulence in mice and guinea pigs [PMID:15009888]. 518 autolysin lmo1076 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 986269 lmo1072 20140405 169963 protein-coding NCBI-supplied PMID: 11679669; 16428782; 19448609; 20097852 MUTATION: pycA mutant unable to replicate in mammalian cells, attenuated in mice [PMID:20097852]. 519 pyruvate carboxylase pycA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 986449 lmo0974 20140402 169963 protein-coding NCBI-supplied PMID: 11679669; 16428782; 19448609 MUTATION: mutant displayed impaired adherence to various cell lines in vitro, and impaired virulence in mice [PMID:11849532]. 520 D-alanine--poly(phosphoribitol) ligase subunit 1 dltA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 986568 lmo0931 20140405 169963 protein-coding NCBI-supplied PMID: 11679669; 16428782; 19448609 MUTATION: mutant strain defective for growth, less virulent in animals by a factor of 300 [PMID:14564012]. 521 lipoate protein ligase A lmo0931 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 986748 lmo0135 20140224 169963 protein-coding NCBI-supplied PMID: 11679669; 16428782; 19448609 MUTATION: deletion mutant showed reduced bacterial adherence to host cells, severely attenuated in mice [PMID:19818015]. 522 peptide ABC transporter substrate-binding protein lmo0135 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 986780 lmo0997 20140224 169963 protein-coding NCBI-supplied PMID: 11679669; 16428782; 19448609 MUTATION: mutant strain was avirulent in mice, eliminated in the liver, affected cell division [PMID:9987121]. 523 ATP-dependent protease clpE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 986791 lmo1439 20140402 169963 protein-coding NCBI-supplied PMID: 11679669; 16428782; 19448609 MUTATION: deletion mutant attenuated in mice [PMID:16905535]. 524 superoxide dismutase sod Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 986847 lmo0943 20140402 169963 protein-coding NCBI-supplied PMID: 11679669; 15758237; 16428782; 19448609; 23176286 MUTATION: mutant was impaired in ability to survive in macrophage cells and was attenuated in mice [PMID:15758237]. 525 non-heme iron-binding ferritin fri Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 986892 lmo0434 20140402 169963 protein-coding NCBI-supplied PMID: 11679669; 16428782; 16469057; 16751490; 17662939; 18156467; 18806773; 18840511; 19234302; 19448609; 20670691; 20823205; 21722201; 22887347; 23376167 MUTATION: attenuated in mice [PMID:7558297]. 526 internalin B inlB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 987031 lmo0200 20140322 169963 protein-coding NCBI-supplied PMID: 11679669; 15686563; 16428782; 17379709; 19448609 MUTATION: attenuated in mice [PMID:1729245]. 527 listeriolysin positive regulatory protein prfA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 987032 lmo0201 20140401 169963 protein-coding NCBI-supplied PMID: 11679669; 16428782; 19448609 MUTATION: mutant had attenuated virulence in mice, failed to grow in host tissues [PMID:1847723]. 528 phosphatidylinositol-specific phospholipase c plcA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 987033 lmo0202 20140402 169963 protein-coding NCBI-supplied PMID: 11679669; 16428782; 16622046; 18523249; 19448609; 20008285; 20194588; 21220348; 21482680; 23006849 MUTATION: mutant strain resulted in a 100-fold virulence defect in mice, prematurely killed host cell [PMID:11901168]. 529 listeriolysin O precursor hly Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 987034 lmo0203 20140401 169963 protein-coding NCBI-supplied PMID: 11679669; 16428782; 19448609 MUTATION: attenuated in mice [PMID:1311708]. 530 Zinc metalloproteinase precursor mpl Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 987035 lmo0204 20140402 169963 protein-coding NCBI-supplied PMID: 8861907; 11679669; 16428782; 17118980; 19448609; 21846725 MUTATION: mutant impaired in cell to cell spread, attenuated in maternal organs [PMID:15871123]. 531 actin-assembly inducing protein precursor actA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 987036 lmo0205 20140405 169963 protein-coding NCBI-supplied PMID: 11679669; 16428782; 19448609 MUTATION: deletion mutants showed reduced virulence in mice, escape from vacuole and cell-to-cell spread [PMID:7591052]. 532 phospholipase C plcB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 987167 lmo0690 20140405 169963 protein-coding NCBI-supplied PMID: 11679669; 15790072; 16428782; 19448609 MUTATION: mutant strain impaired colonization in plant tissue [PMID:19357783]. 533 flagellin flaA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 987203 lmo0232 20140406 169963 protein-coding NCBI-supplied PMID: 11679669; 16428782; 19448609 MUTATION: mutant strain showed a restricted capacity to grow in bone-marrow-derived macrophages, and an attenuated virulence in mice [PMID:8885268]. 534 endopeptidase Clp ATP-binding chain C clpC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 987254 lmo2558 20140224 169963 protein-coding NCBI-supplied PMID: 11679669; 16428782; 19448609 MUTATION: mutant strains showed a significant reduction in adherence to several cell types, attenuated in mice [PMID:11251838]. 535 autolysin, amidase ami Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 987350 lmo0262 20140224 169963 protein-coding NCBI-supplied PMID: 11679669; 16428782; 19448609 MUTATION: mutant showed loss in virulence, reduced numbers of viable bacteria in both liver and spleen of mice [PMID:9862466]. 536 internalin G inlG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 987355 lmo0263 20140224 169963 protein-coding NCBI-supplied PMID: 11679669; 16428782; 19448609; 20176794 MUTATION: mutant showed loss in virulence, reduced numbers of viable bacteria in both liver and spleen of mice [PMID:9862466]. 537 internalin H inlH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 987358 lmo0264 20140224 169963 protein-coding NCBI-supplied PMID: 11679669; 16428782; 19448609 MUTATION: mutant showed loss in virulence, reduced numbers of viable bacteria in both liver and spleen of mice [PMID:9862466]. 538 internalin E inlE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 987364 lmo2468 20140402 169963 protein-coding NCBI-supplied PMID: 11679669; 16428782; 19448609 MUTATION: mutant strain showed reduced bacterial escape from phagosomes of macrophages and attenuated virulence in mice [PMID:10760131]. 539 ATP-dependent Clp protease proteolytic subunit clpP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 987455 lmo0292 20140224 169963 protein-coding NCBI-supplied PMID: 11679669; 16085809; 16428782; 19448609 MUTATION: attenuated in mice [PMID:16369036]. 540 heat-shock protein htrA serine protease lmo0292 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 987487 lmo2537 20140405 169963 protein-coding NCBI-supplied PMID: 11679669; 16428782; 16952950; 19448609 MUTATION: mutant avirulent in mice [PMID:16952950]. 541 UDP-N-acetylglucosamine 2-epimerase lmo2537 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 987534 lmo0317 20140406 169963 protein-coding NCBI-supplied PMID: 11679669; 16428782; 19181806; 19448609 MUTATION: knockout inhibited growth in mMWB and reduced spread in epithelial cells [PMID:19181806]. 542 phosphomethylpyrimidine kinase lmo0317 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 987788 lmo1523 20140406 169963 protein-coding NCBI-supplied PMID: 11679669; 16428782; 17302820; 19448609 MUTATION: impaired growth, avirulent in a murine model [PMID:11790730]. 543 (p)ppGpp synthetase relA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 987823 lmo0415 20140224 169963 protein-coding NCBI-supplied PMID: 11679669; 16428782; 19448609 MUTATION: lmo0415 (pgdA) is attenuated in mice [PMID:17215377]. 544 endo-1,4-beta-xylanase lmo0415 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 988262 CPE0036 20140405 195102 protein-coding NCBI-supplied PMID: 11792842; 15919667; 16923791; 22079896 MUTATION: plc mutant is attenuated in mice [PMID:7746141]. 852 phospholipase C plc Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 988404 CPE0163 20140222 195102 protein-coding NCBI-supplied PMID: 11792842; 15797734; 18404211; 22079896 perfringolysin O pfoA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 989810 CPE1500 20140222 195102 protein-coding NCBI-supplied PMID: 11792842; 18790863; 19363118; 19513115 MUTATION: virS mutant is attenuated in mice [PMID:8052128]. 854 sensor histidine kinase VirS virS Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 993646 spyM18_1239 20140406 186103 protein-coding NCBI-supplied PMID: 11917108; 12122206 exotoxin SpeM spyM18_1239 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 994087 spyM18_1238 20140222 186103 protein-coding NCBI-supplied PMID: 11917108; 12122206 exotoxin SpeL spyM18_1238 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 994370 spyM18_2077 20130518 186103 protein-coding NCBI-supplied PMID: 11917108; 12122206; 15937178 MUTATION: mga mutant is attenuated in a humanized mouse model for superficial skin infection [PMID:18588968]. 4315 positive regulatory protein Mga mga Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 994764 spyM18_2074 20140406 186103 protein-coding NCBI-supplied PMID: 11917108; 12122206 MUTATION: scpA mutant is attenuated in mouse pneumonia model [PMID:9119483]. 4316 C5A peptidase scpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 995014 spyM18_0393 20140217 186103 protein-coding NCBI-supplied PMID: 11917108; 12122206; 15295110; 16428778 exotoxin type A speA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 995250 spyM18_0799 20121222 186103 protein-coding NCBI-supplied PMID: 11917108; 12122206 MUTATION: sagA mutant is attenuated in mice [PMID:9529097]. 4318 streptolysin S associated protein sagA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1003381 MW1269 20140222 196620 protein-coding NCBI-supplied PMID: 12044378; 19374556 MUTATION: mutant attenuated in murine infection model [PMID:15664928]. 4319 oligopeptide transporter permease opp-2C Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1003409 MW1297 20140406 196620 protein-coding NCBI-supplied PMID: 12044378; 19374556 MUTATION: mutant attenuated in murine infection model [PMID:15664928]. 4320 branched-chain amino acid carrier protein braB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1003457 MW1345 20140222 196620 protein-coding NCBI-supplied PMID: 12044378; 19374556 MUTATION: mutant attenuated in murine infection model [PMID:15664928]. 4321 ATP-dependent DNA helicase dinG dinG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1008327 SpyM3_0013 20140406 198466 protein-coding NCBI-supplied PMID: 12122206 MUTATION: SpyM3_0013 mutant is attenuated in zebrafish [PMID:19223485]. 4322 amino acid permease SpyM3_0013 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1008418 SpyM3_0104 20130518 198466 protein-coding NCBI-supplied PMID: 12122206; 14749329 MUTATION: F2 like fibronectin-binding protein mutant had attenuated attachment to to HEp-2 epithelial cells [PMID:14749329]. 4323 protein F2 like fibronectin-binding protein SpyM3_0104 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1008444 SpyM3_0130 20140215 198466 protein-coding NCBI-supplied PMID: 12122206 MUTATION: slo mutant was attenuated in mice [PMID:11035749]. 4324 streptolysin O slo Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1008547 SpyM3_0233 20140222 198466 protein-coding NCBI-supplied PMID: 12122206 MUTATION: atmB mutant is attenuated in zebrafish [PMID:19223485]. 4325 ABC transporter substrate-binding protein atmB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1008699 SpyM3_0385 20140405 198466 protein-coding NCBI-supplied PMID: 12122206 MUTATION: SpyM3_0385 mutant is attenuated in zebrafish [PMID:19223485]. 4326 UDP-glucose 6-dehydrogenase SpyM3_0385 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1008700 SpyM3_0386 20140217 198466 protein-coding NCBI-supplied PMID: 12122206 MUTATION: SpyM3_0386 mutant is attenuated in zebrafish [PMID:19223485]. 4327 efflux protein SpyM3_0386 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1008870 SpyM3_0556 20140222 198466 protein-coding NCBI-supplied PMID: 12122206 MUTATION: lsp mutant is attenuated in a murine model of soft tissue infection [PMID:19398546]. 4328 lipoprotein signal peptidase lsp Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1009964 SpyM3_1649 20140222 198466 protein-coding NCBI-supplied PMID: 12122206 MUTATION: salT mutant is attenuated in zebrafish [PMID:19223485]. 4329 salivaricin A modification enzyme salT Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1010041 SpyM3_1726 20140406 198466 protein-coding NCBI-supplied PMID: 12122206 MUTATION: scpA mutant is attenuated in mouse pneumonia model [PMID:9119483]. 4330 C5A peptidase precursor scpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1010042 SpyM3_1727 20121222 198466 protein-coding NCBI-supplied PMID: 12122206 MUTATION: emm3 mutant has reduced adherence to and internalization into HEp-2 cells compared to the wild type [PMID:14522456]. 4331 antiphagocytic M protein, type 3 emm3 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1010043 SpyM3_1728 20140222 198466 protein-coding NCBI-supplied PMID: 12122206; 23980109 MUTATION: mga mutant is attenuated in a humanized mouse model for superficial skin infection [PMID:18588968]. 4332 M protein trans-acting positive regulator, multi-gene activator mga Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1010057 SpyM3_1742 20130526 198466 protein-coding NCBI-supplied PMID: 12122206 MUTATION: Mice infected by M1, M3 and M49 speB mutants, through air pouch or intraperitoneal challenge, showed less mortality compared with that of the wild-type strains [PMID:18796357]. 4333 pyrogenic exotoxin B speB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1010110 SpyM3_1795 20140215 198466 protein-coding NCBI-supplied PMID: 12122206 MUTATION: SpyM3_1795 mutant is attenuated in zebrafish [PMID:19223485]. 4334 hypothetical protein SpyM3_1795 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1010166 SpyM3_1851 20140406 198466 protein-coding NCBI-supplied PMID: 12122206 MUTATION: hasA mutant is attenuated in zebrafish [PMID:19223485]. 4335 hyaluronan synthase hasA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1013087 SAG0298 20140329 208435 protein-coding NCBI-supplied PMID: 12200547; 17057092 MUTATION: pbp1A mutant is attenuated in rats [PMID:10998175]. 4336 penicillin-binding protein 1A pbp1A Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1013789 SAG0985 20130330 208435 protein-coding NCBI-supplied PMID: 12200547 MUTATION: ciaR mutant had a significant decrease in intracellular survival within neutrophils, murine macrophages, and human BMEC [PMID:19114476]. 4337 DNA-binding response regulator CiaR ciaR Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1014041 SAG1234 20140222 208435 protein-coding NCBI-supplied PMID: 12200547 MUTATION: lmb mutant has reduced invasion of human brain microvascular endothelial cells compared to the wildtype [PMID:17400016]. 4338 laminin-binding surface protein lmb Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1014433 SAG1624 20140222 208435 protein-coding NCBI-supplied PMID: 12200547; 18203834; 19542277 MUTATION: csrS mutant is attenuated in mice [PMID:15659687]. 4339 sensor histidine kinase CsrS csrS Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1014434 SAG1625 20140406 208435 protein-coding NCBI-supplied PMID: 12200547; 18203834; 19542277 MUTATION: csrR mutant is attenuated in mice [PMID:15659687]. 4340 DNA-binding response regulator CsrR csrR Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1023373 SF1684 20120928 198214 protein-coding NCBI-supplied PMID: 12384590 MUTATION: sodB mutant is extremely sensitive to killing by phagocytes compared to the wild-type, and causes only mild damage in infection of rabbit ileal loops [PMID:2404874]. 859 superoxide dismutase sodB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1023438 SF3931 20140222 198214 protein-coding NCBI-supplied PMID: 12384590 MUTATION: dsbA mutants are less invasive to MK-2 cell monolayers compared to the wild-type [PMID:7761426]. 860 periplasmic protein disulfide isomerase I dsbA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1023875 SF0903 20140405 198214 protein-coding NCBI-supplied PMID: 12384590 MUTATION: aroA deletion mutants are attenuated in HeLa cells [PMID:8757833]. 861 3-phosphoshikimate 1-carboxyvinyltransferase aroA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1024087 SF1149 20130406 198214 protein-coding NCBI-supplied PMID: 12384590 MUTATION: phoP mutants were resolved more quickly than wild type in animal models, and are more susceptible to killing by PMNs [PMID:11207599]. 862 DNA-binding transcriptional regulator PhoP phoP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1024200 SF1255 20140222 198214 protein-coding NCBI-supplied PMID: 12384590 MUTATION: tonB mutant is able to invade epithelial cells but is incapable of cell to cell spread [PMID:11035742]. 863 transporter tonB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1024213 SF1236 20140405 198214 protein-coding NCBI-supplied PMID: 12384590 MUTATION: galU mutant is attenuated in cell to cell spread in He La cells [PMID:7528731]. 864 UTP-glucose-1-phosphate uridylyltransferase galU Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1024218 SF3930 20130508 198214 protein-coding NCBI-supplied PMID: 12384590 MUTATION: yihE mutant is unable to cause keratoconjunctivitis in guinea pigs [PMID:15073317]. 865 serine/threonine protein kinase yihE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1024343 SF1365 20140222 198214 protein-coding NCBI-supplied PMID: 12384590 MUTATION: sitA mutant is attenuated in mice [PMID:19289511]. 866 iron ABC transporter substrate-binding protein sitA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1024405 SF2424 20140406 198214 protein-coding NCBI-supplied PMID: 12384590 MUTATION: vacJ mutants are incapable of intercellular spread of epithelial cells [PMID:8145644]. 867 ABC transporter outer membrane lipoprotein vacJ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1024482 SF0137 20140222 198214 protein-coding NCBI-supplied PMID: 12384590 MUTATION: dksA mutants are able to invade cultured cell monlayers but are incapable of cell to cell spread [PMID:11500451]. 868 RNA polymerase-binding transcription factor dksA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1024578 SF0050 20140406 198214 protein-coding NCBI-supplied PMID: 12384590 MUTATION: surA mutant is able to infect epithelial cells but is incapable of cell to cell spread [PMID:20447864]. 869 peptidyl-prolyl cis-trans isomerase SurA surA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1024864 SF1723 20140406 198214 protein-coding NCBI-supplied PMID: 12384590 MUTATION: aroD deletion led to attenuation in HeLa cells and monkeys [PMID:8356844]. 870 3-dehydroquinate dehydratase aroD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1025367 SF3424 20140215 198214 protein-coding NCBI-supplied PMID: 12384590 MUTATION: mutant of the ompB locus (both the envZ and ompR genes) showed attenuated virulence in HeLa cells, and a weak response to a Serany test [PMID:2121709]. 871 osmolarity response regulator ompR Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1025395 SF4334 20140222 198214 protein-coding NCBI-supplied PMID: 12384590 MUTATION: vacB mutants had attenuated invasion of MK2 cells compared to the wild-type strain [PMID:1400189]. 872 hypothetical protein vacB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1025630 SF2553 20140405 198214 protein-coding NCBI-supplied PMID: 12384590 MUTATION: guaAguaB mutants are attenuated in HeLa cells [PMID:8757833]. 873 GMP synthase guaA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1025853 SF4327 20140222 198214 protein-coding NCBI-supplied PMID: 12384590 MUTATION: hfq deletion mutants are attenuated in guinea pig eye infection model (Sereny test) [PMID:20080057]. 874 RNA-binding protein Hfq hfq Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1026035 SF3858 20140222 198214 protein-coding NCBI-supplied PMID: 12384590 MUTATION: rfe mutant is attenuated in cell to cell spread in He La cells [PMID:7528731]. 875 undecaprenyl-phosphate alpha-N-acetylglucosaminyl 1-phosphate transferase rfe Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1026065 SF2968 20140222 198214 protein-coding NCBI-supplied PMID: 12384590 MUTATION: sigA mutant is attenuated in rabbit ileal loop infection model [PMID:10768931]. 876 serine protease sigA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1026141 SF3718 20140405 198214 protein-coding NCBI-supplied PMID: 12384590 MUTATION: iuc mutants are attenuated in chicken embryos and rabbit ileal loops [PMID:19130265]. 877 lysine:N6-hydroxylase iucD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1026151 SF3717 20140329 198214 protein-coding NCBI-supplied PMID: 12384590 MUTATION: iuc mutants are attenuated in chicken embryos and rabbit ileal loops [PMID:19130265]. 878 siderophore biosynthesis protein iucC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1026161 SF3715 20140308 198214 protein-coding NCBI-supplied PMID: 12384590 MUTATION: iuc mutants are attenuated in chicken embryos and rabbit ileal loops [PMID:19130265]. 879 siderophore biosynthesis protein iucA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1026206 SF3719 20140222 198214 protein-coding NCBI-supplied PMID: 12384590 MUTATION: mutants of the iuc locus and the aerobactin receptor, iutA were attenuated in chicken embryos [PMID:3028962]. 880 ferric siderophore receptor iutA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1026481 SF3423 20140222 198214 protein-coding NCBI-supplied PMID: 12384590 MUTATION: envZ insertion mutant is able to invade cells but has decreased virulence due to the inability to survive intracellularly [PMID:2121709]. 881 osmolarity sensor protein envZ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1026756 SF2299 20140215 198214 protein-coding NCBI-supplied PMID: 12384590 MUTATION: ompC mutants were attenuated in their ability to spread cell to cell and kill epithelial cells, and had a negative Sereny test [PMID:8359885]. 882 porin ompC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1026857 SF4326 20140329 198214 protein-coding NCBI-supplied PMID: 12384590 MUTATION: miaA mutants had reduced ability to invade and spread in MK2 cell monolayers compared to the wildtype [PMID:9294434]. 883 tRNA delta(2)-isopentenylpyrophosphate transferase miaA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1026896 SF3716 20140329 198214 protein-coding NCBI-supplied PMID: 12384590 MUTATION: iuc mutants are attenuated in chicken embryos and rabbit ileal loops [PMID:19130265]. 884 siderophore biosynthesis protein iucB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1027589 SF2554 20140406 198214 protein-coding NCBI-supplied PMID: 12384590 MUTATION: guaAguaB mutants are attenuated in HeLa cells [PMID:8757833]. 885 inosine 5'-monophosphate dehydrogenase guaB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1030007 gbs1020 20130330 211110 protein-coding NCBI-supplied PMID: 12354221; 19568429 MUTATION: gbs1020 (CiaR) mutant had a significant decrease in intracellular survival within neutrophils, murine macrophages, and human BMEC [PMID:19114476]. 4341 DNA-binding response regulator CiaR gbs1020 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1030264 gbs1244 20140222 211110 protein-coding NCBI-supplied PMID: 12354221; 19568429 MUTATION:cpsD mutant results in an unencapsulated strain which is avirulent in a neonatal rat model of sepsis compared to the wild type strain, and is also sensitive to killing by human phagocytes in vitro [PMID:8355611]. 4342 capsular polysaccharide chain length regulator/exporter cpsD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1030333 gbs1307 20140217 211110 protein-coding NCBI-supplied PMID: 12354221; 19568429 MUTATION: lmb mutant has reduced invasion of human brain microvascular endothelial cells compared to wildtype [PMID:17400016]. 4343 laminin-binding surface protein lmb Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1030336 gbs1308 20130330 211110 protein-coding NCBI-supplied PMID: 12354221; 19568429 MUTATION: scpB mutant has significantly reduced invasion of HEp2 and A549 human cell lines [PMID:11953377]. 4344 streptococcal C5a peptidase scpB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1030444 gbs1402 20140222 211110 protein-coding NCBI-supplied PMID: 12354221; 19568429; 20421944 MUTATION: gbs1402 (pefR) mutant is attenuated in mice [PMID:20421944]. 4345 MarR family transcriptional regulator gbs1402 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1030552 gbs1477 20140217 211110 protein-coding NCBI-supplied PMID: 12354221; 19568429 MUTATION: gbs1477 (pilB) mutant had significantly reduced invasion of hBMECs [PMID:17041051]. 4346 hypothetical protein gbs1477 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1030619 gbs1529 20140215 211110 protein-coding NCBI-supplied PMID: 12354221; 19568429 MUTATION: Deletion of srr1(gbs1529) in NCTC 10/84 resulted in a significant decrease in adherence to and invasion of hBMECs [PMID:19392623]. 4347 cell wall surface anchor family protein gbs1529 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1034931 c1250 20140222 199310 protein-coding NCBI-supplied PMID: 12471157 MUTATION: iroA gene cluster mutants were unable to resist Lcn2 in mouse serum [PMID:17060628]. 2088 outer membrane receptor FepA iroN Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1034933 c1252 20140222 199310 protein-coding NCBI-supplied PMID: 12471157 MUTATION: attenuated in chicks [PMID:18541653]. 2089 ferric enterochelin esterase iroD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1034934 c1253 20140406 199310 protein-coding NCBI-supplied PMID: 12471157 MUTATION: attenuated in chicks [PMID:18541653]. 2090 ABC transporter ATP-binding protein iroC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1034935 c1254 20140406 199310 protein-coding NCBI-supplied PMID: 12471157; 15598734 MUTATION: attenuated in chicks [PMID:18541653]. 2091 glucosyltransferase iroB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1035499 c1717 20140406 199310 protein-coding NCBI-supplied PMID: 12471157 MUTATION: attenuated in mice [PMID:11553558]. 2092 transport protein TonB tonB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1035566 c1780 20140406 199310 protein-coding NCBI-supplied PMID: 12471157 MUTATION: ycjM mutant is attenuated in chickens [PMID:15845486]. 2093 sucrose phosphorylase ycjM Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1035846 c4789 20140222 199310 protein-coding NCBI-supplied PMID: 12471157 MUTATION: attenuated in mice [PMID:12117951]. 2094 transcriptional activator RfaH rfaH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1036493 c4711 20140215 199310 protein-coding NCBI-supplied PMID: 12471157 MUTATION: wecE mutant is attenuated in mice [PMID:12180926]. 2095 TDP-4-oxo-6-deoxy-D-glucose transaminase wecE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1036525 c4804 20140406 199310 protein-coding NCBI-supplied PMID: 12471157; 19376849 MUTATION: mutation of dsbA led to degradation of bundilin and an absence of localized adherence to host cells in EPEC [PMID:9224871]. 2096 periplasmic protein disulfide isomerase I dsbA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1036891 c1239 20140217 199310 protein-coding NCBI-supplied PMID: 12471157 MUTATION: focA deletion mutants were unable to bind to brain glycolipids [PMID:8098039]. 2097 F1C major fimbrial subunit focA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1036977 c2338 20140322 199310 protein-coding NCBI-supplied PMID: 12471157 MUTATION: fliC deletion mutants had reduced adherence in bovine tissue compared to the wild type EHEC and EPEC strains [PMID:17693516]. 2098 flagellin fliC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1037196 c4308 20140405 199310 protein-coding NCBI-supplied PMID: 12471157 MUTATION: chuA mutant unable to grow on iron-depleted medium containing heme [PMID:9157252]. 2099 outer membrane heme/hemoglobin receptor chuA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1037233 c5400 20140222 199310 protein-coding NCBI-supplied PMID: 12471157; 17177088; 19462430 MUTATION: attenuated in mice and humans [PMID:18482721]. 2100 FimH protein fimH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1037237 c5397 20140405 199310 protein-coding NCBI-supplied PMID: 12471157 MUTATION: fimF mutant is attenuated in mice [PMID:12180926]. 2101 FimF protein fimF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1037242 c5396 20140406 199310 protein-coding NCBI-supplied PMID: 12471157 MUTATION: fimD mutant is attenuated in mice [PMID:12180926]. 2102 outer membrane usher protein fimD fimD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1037243 c5395 20130613 199310 protein-coding NCBI-supplied PMID: 12471157 MUTATION: fimC mutant is attenuated in mice [PMID:12180926]. 2103 chaperone protein fimC fimC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1037245 c5394 20130508 199310 protein-coding NCBI-supplied PMID: 12471157 MUTATION: fimI mutant is attenuated in mice [PMID:12180926]. 2104 fimbrin-like protein fimI fimI Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1037250 c5391 20140222 199310 protein-coding NCBI-supplied PMID: 12471157 MUTATION: fimB mutant is attenuated in mice [PMID:12180926]. 2105 tyrosine recombinase fimB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1037335 c4361 20140405 199310 protein-coding NCBI-supplied PMID: 12471157 MUTATION: dppA mutant was attenuated 10- to 50-fold compared to the wild type for colonization of the bladders and kidneys of mice [PMID:17074858]. 2106 periplasmic dipeptide transport protein dppA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1037835 c2557 20140406 199310 protein-coding NCBI-supplied PMID: 12471157 MUTATION: manB mutant is attenuated in mice [PMID:12180926]. 2107 phosphomannomutase manB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1038245 c4450 20140222 199310 protein-coding NCBI-supplied PMID: 12471157 MUTATION: waaW mutant is attenuated in chickens [PMID:15845486]. 2108 UDP-galactose:(galactosyl) LPS alpha1,2-galactosyltransferase waaW Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1039495 c3569 20140406 199310 protein-coding NCBI-supplied PMID: 12471157 MUTATION: hlyC is required for the acylation and therefore activation of the toxin hemolysin which has the ability to lyse several different types of cells [PMID:8793877]. 2109 hemolysin C hlyC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1039496 c3570 20140222 199310 protein-coding NCBI-supplied PMID: 12471157 MUTATION: attenuated in zebra fish [PMID:20019794]. 2110 hemolysin A hlyA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1039518 c3583 20140406 199310 protein-coding NCBI-supplied PMID: 12471157 MUTATION: attenuated to human neutrophils in vitro [PMID:7960108]. 2111 PapG protein papG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1039530 c3592 20140406 199310 protein-coding NCBI-supplied PMID: 12471157 MUTATION: mutant papA in wild-type smooth strains do not mediate Gal-Gal adherence [PMID:1672263]. 2112 PapA protein papA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1039573 c3619 20140222 199310 protein-coding NCBI-supplied PMID: 12471157 MUTATION: Sat elicits cytopathic activity that damages host tissue and may increase the ability of E. coli to propagate [PMID:12117966]. 2113 secreted auto transporter toxin sat Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1039578 c3623 20130508 199310 protein-coding NCBI-supplied PMID: 12471157 MUTATION: mutant attenuated in mice competition assay [PMID:11553558]. 2114 IutA protein iutA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1039579 c3624 20140329 199310 protein-coding NCBI-supplied PMID: 12471157 MUTATION: attenuated in mice [PMID:2973985]. 2115 IucD protein iucD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1039580 c3625 20140405 199310 protein-coding NCBI-supplied PMID: 12471157 MUTATION: attenuated in mice [PMID:2973985]. 2116 IucC protein iucC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1039581 c3626 20140405 199310 protein-coding NCBI-supplied PMID: 12471157 MUTATION: attenuated in mice [PMID:2973985]. 2117 IucB protein iucB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1039582 c3627 20140405 199310 protein-coding NCBI-supplied PMID: 12471157 MUTATION: attenuated in mice [PMID:2973985]. 2118 IucA protein iucA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1039730 c3690 20140222 199310 protein-coding NCBI-supplied PMID: 12471157 MUTATION: kpsC mutant is attenuated in mice [PMID:12180926]. 2119 KpsC protein kpsC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1039998 c1081 20140329 199310 protein-coding NCBI-supplied PMID: 12471157 MUTATION: pyrD mutant is attenuated in mice [PMID:12180926]. 2120 dihydroorotate dehydrogenase 2 pyrD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1039999 c1093 20130508 199310 protein-coding NCBI-supplied PMID: 12471157 MUTATION: OmpA− strains are unable to cause actin condensation needed for invasion of brain epithelial cells [PMID:10531228]. 2121 outer membrane protein A ompA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1040241 c4648 20130420 199310 protein-coding NCBI-supplied PMID: 12471157 MUTATION: phoU mutant is attenuated in mice [PMID:12180926]. 2122 transcriptional regulator PhoU phoU Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1060232 CTC01888 20140222 212717 protein-coding NCBI-supplied PMID: 12552129 tetanolysin O CTC01888 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1061073 pE88_34 20140406 212717 protein-coding NCBI-supplied PMID: 23703618 MUTATION: colT is a collagenase that catalyzes the hydrolysis of collagen in host tissues [PMID:16701501]. 2824 collagenase ColT colT Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1061100 pE88_60 20140406 212717 protein-coding NCBI-supplied PMID: 19602728; 22079193 tetanus toxin tetX tetX Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1065796 SPs0560 20140215 193567 protein-coding NCBI-supplied PMID: 12799345 protein SpeA SPs0560 MUTATION: cstA mutants have reduced epithelial cell invasion and reduced transepithelial migration of PMN compared to the wild type [PMID:15182677]. 2301 MUTATION: leuO mutant exhibited wild-type levels of epithelial invasion but highly reduced transepithelial migration of PMN [PMID:15182677]. 2302 MUTATION: tdcA mutant is less invasive of cultured epithelial cells and attenuated in mice [PMID:19812899]. 2303 MUTATION: invE mutants were unable to penetrate Henle-407 human intestinal cells and Madin-Darby canine kidney cells [PMID:1631083]. 2304 MUTATION: invH mutants are attenuated in calves [PMID:9529064]. 2305 MUTATION: invI mutants are defective for entry into cultured epithelial cells [PMID:7752894]. 2306 MUTATION: spaR mutant is severely impaired in entry to Henle-407 cells [PMID:8751894]. 2307 MUTATION: spaQ mutant is severely impaired in entry to Henle-407 cells [PMID:8751894]. 2308 MUTATION: spaO mutant is severely impaired in entry to Henle-407 cells [PMID:8751894]. 2309 MUTATION: invJ mutants are defective for entry into cultured epithelial cells [PMID:7752894]. 2310 MUTATION: spaP mutant is severely impaired in entry to Henle-407 cells [PMID:8751894]. 2311 MUTATION: spaS mutant was 30-fold reduced for invasion into HEp-2 cells when compared with the wild-type strain [PMID:10692170]. 2312 MUTATION: A SipC nucleation-deficient mutant, which maintained its effector translocation activity, had significantly reduced ability to induce actin cytoskeleton rearrangements, resulting in lower bacterial invasion into HeLa cells [PMID:15720547]. 2313 MUTATION: orgA mutants are attenuated in their ability to invade HEp-2 cells [PMID:10816487]. 2314 MUTATION: prgK mutants are attenuated in their ability to invade HEp-2 cells [PMID:10816487]. 2315 MUTATION: prgJ mutants are attenuated in their ability to invade HEp-2 cells [PMID:10816487]. 2316 MUTATION: orgA mutants are attenuated in their ability to invade HEp-2 cells [PMID:10816487]. 2317 MUTATION: waaP mutant is avirulent in mice [PMID:10899846]. 2318 MUTATION: cstA mutants have reduced epithelial cell invasion and reduced transepithelial migration of PMN compared to the wild type [PMID:15182677]. 2319 MUTATION: fliC mutants were attenuated in orally inoculated chicks [PMID:11731137]. 2320 MUTATION: spiC mutant cannot survive within macrophages and is attenuated in mice [PMID:10406797]. 2321 MUTATION: sseC mutant is attenuated in mice [PMID:11159962]. 2322 MUTATION: sseD mutant is attenuated in mice [PMID:11159962]. 2323 MUTATION: ssaM mutant is attenuated in mice [PMID:15491354]. 2324 MUTATION: ssaV and aroC double mutants are attenuated in humans [PMID:19745519]. 2325 MUTATION: pcgL mutant is attenuated in pigs [PMID:17526851]. 2326 MUTATION: sigD mutant is less invasive than the wild type in both HEp-2 and CHO cell lines [PMID:9537377]. 2327 MUTATION: sigE mutant is less invasive than the wild type in both HEp-2 and CHO cell lines [PMID:9537377]. 2328 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1076439 S0052 20140406 198215 protein-coding NCBI-supplied PMID: 12704152 MUTATION: surA mutant is able to infect epithelial cells but is incapable of cell to cell spread [PMID:20447864]. 928 peptidyl-prolyl cis-trans isomerase SurA surA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1076574 S0140 20140222 198215 protein-coding NCBI-supplied PMID: 12704152; 23035718 MUTATION: dksA mutants are able to invade cultured cell monlayers but are incapable of cell to cell spread [PMID:11500451]. 929 DnaK transcriptional regulator DksA dksA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1077373 S0967 20140405 198215 protein-coding NCBI-supplied PMID: 12704152 MUTATION: aroA deletion mutants are attenuated in HeLa cells [PMID:8757833]. 930 3-phosphoshikimate 1-carboxyvinyltransferase aroA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1077630 S1232 20131002 198215 protein-coding NCBI-supplied PMID: 12704152 MUTATION: phoP mutants were resolved more quickly than wild type in animal models, and are more susceptible to killing by PMNs [PMID:11207599]. 931 DNA-binding transcriptional regulator PhoP phoP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1077674 S1322 20140405 198215 protein-coding NCBI-supplied PMID: 12704152 MUTATION: galU mutant is attenuated in cell to cell spread in He La cells [PMID:7528731]. 932 UTP--glucose-1-phosphate uridylyltransferase subunit GalU galU Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1077715 S1341 20140222 198215 protein-coding NCBI-supplied PMID: 12704152 MUTATION: tonB mutant is able to invade epithelial cells but is incapable of cell to cell spread [PMID:11035742]. 933 transporter tonB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1078189 S1855 20140406 198215 protein-coding NCBI-supplied PMID: 12704152 MUTATION: aroD deletion led to attenuation in HeLa cells and monkeys [PMID:8356844]. 934 3-dehydroquinate dehydratase aroD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1078262 S1931 20140405 198215 protein-coding NCBI-supplied PMID: 12704152 lipid A biosynthesis (KDO)2-(lauroyl)-lipid IVA acyltransferase msbB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1078295 S1964 20140222 198215 protein-coding NCBI-supplied PMID: 12704152 MUTATION: sitA mutant is attenuated in mice [PMID:19289511]. 936 Iron transport protein sitA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1078521 S2219 20131002 198215 protein-coding NCBI-supplied PMID: 12704152 MUTATION: rfc mutant is attenuated in invasion of T84 cell monolayer and adhesion to epithelial cells [PMID:11854195]. 937 O-antigen polymerase rfc Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1078841 S2559 20140406 198215 protein-coding NCBI-supplied PMID: 12704152 MUTATION: vacJ mutants are incapable of intercellular spread of epithelial cells [PMID:8145644]. 939 lipoprotein precursor vacJ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1078991 S2725 20140322 198215 protein-coding NCBI-supplied PMID: 12704152 MUTATION: guaAguaB mutants are attenuated in HeLa cells [PMID:8757833]. 940 GMP synthase guaA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1078993 S2726 20140406 198215 protein-coding NCBI-supplied PMID: 12704152 MUTATION: guaAguaB mutants are attenuated in HeLa cells [PMID:8757833]. 941 inosine 5'-monophosphate dehydrogenase guaB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1079354 S1816 20131002 198215 protein-coding NCBI-supplied PMID: 12704152 MUTATION: sodB mutant is extremely sensitive to killing by phagocytes compared to the wild-type, and causes only mild damage in infection of rabbit ileal loops [PMID:2404874]. 942 superoxide dismutase sodB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1079436 S4824 20140222 198215 protein-coding NCBI-supplied PMID: 12704152 MUTATION: sigA mutant is attenuated in rabbit ileal loop infection model [PMID:10768931]. 943 serine protease sigA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1079793 S4594 20140405 198215 protein-coding NCBI-supplied PMID: 12704152 MUTATION: miaA mutants had reduced ability to invade and spread in MK2 cell monolayers compared to the wildtype [PMID:9294434]. 944 tRNA delta(2)-isopentenylpyrophosphate transferase miaA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1080031 S3816 20140222 198215 protein-coding NCBI-supplied PMID: 12704152 MUTATION: dsbA mutants are less invasive to MK-2 cell monolayers compared to the wild-type [PMID:7761426]. 945 periplasmic protein disulfide isomerase I dsbA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1080032 S3817 20131002 198215 protein-coding NCBI-supplied PMID: 12704152 MUTATION: yihE mutant is unable to cause keratoconjunctivitis in guinea pigs [PMID:15073317]. 946 serine/threonine protein kinase yihE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1080258 S4052 20140222 198215 protein-coding NCBI-supplied PMID: 12704152 MUTATION: mutants of the iuc locus and the aerobactin receptor, iutA were attenuated in chicken embryos [PMID:3028962]. 947 ferric siderophore receptor iutA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1080259 S4053 20140405 198215 protein-coding NCBI-supplied PMID: 12704152 MUTATION: iuc mutants are attenuated in chicken embryos and rabbit ileal loops [PMID:19130265]. 948 lysine:N6-hydroxylase iucD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1080260 S4054 20140329 198215 protein-coding NCBI-supplied PMID: 12704152 MUTATION: iuc mutants are attenuated in chicken embryos and rabbit ileal loops [PMID:19130265]. 949 siderophore biosynthesis protein iucC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1080261 S4055 20140329 198215 protein-coding NCBI-supplied PMID: 12704152 MUTATION: iuc mutants are attenuated in chicken embryos and rabbit ileal loops [PMID:19130265]. 950 siderophore biosynthesis protein iucB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1080262 S4056 20140405 198215 protein-coding NCBI-supplied PMID: 12704152 MUTATION: iuc mutants are attenuated in chicken embryos and rabbit ileal loops [PMID:19130265]. 951 siderophore biosynthesis protein iucA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1080544 S4339 20140215 198215 protein-coding NCBI-supplied PMID: 12704152 MUTATION: mutant of the ompB locus (both the envZ and ompR genes) showed attenuated virulence in HeLa cells, and a weak response to a Serany test [PMID:2121709]. 952 osmolarity response regulator ompR Bin Zhao, Oliver He ompB WEB: http://www.ncbi.nlm.nih.gov/gene 1080545 S4340 20140222 198215 protein-coding NCBI-supplied PMID: 12704152 MUTATION: envZ insertion mutant is able to invade cells but has decreased virulence due to the inability to survive intracellularly [PMID:2121709]. 953 osmolarity sensor protein - envZ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1080803 S4602 20140222 198215 protein-coding NCBI-supplied PMID: 12704152 MUTATION: vacB mutants had attenuated invasion of MK2 cells compared to the wild-type strain [PMID:1400189]. 954 exoribonuclease R vacB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1080960 S4595 20140222 198215 protein-coding NCBI-supplied PMID: 12704152 MUTATION: hfq deletion mutants are attenuated in guinea pig eye infection model (Sereny test) [PMID:20080057]. 955 RNA-binding protein Hfq hfq Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1080962 S3902 20140222 198215 protein-coding NCBI-supplied PMID: 12704152 MUTATION: rfe mutant is attenuated in cell to cell spread in He La cells [PMID:7528731]. 956 UDP-GlcNAc:undecaprenylphosphate GlcNAc-1-phosphate transferase rfe Bin Zhao, Oliver He BA4704 WEB: http://www.ncbi.nlm.nih.gov/gene 1083685 BA_4704 20140215 198094 protein-coding NCBI-supplied GO_0006508 (EC: ISS, PMID: 12721629) PMID: 12721629 MUTATION: clpX deletion mutant is attenuated in mice [PMID:20375606]. 855 ATP-dependent protease ATP-binding subunit ClpX - clpX Bin Zhao, Oliver He BA5139 WEB: http://www.ncbi.nlm.nih.gov/gene 1084508 BA_5139 20140222 198094 protein-coding NCBI-supplied GO_0019430 (EC: ISS, PMID: 12721629) PMID: 12721629 MUTATION: A quadruple-knockout strain (Delta sod15 Delta sodA1 Delta sodC Delta sodA2) was attenuated more than 40-fold upon intranasal challenge of mice compared to the wild type [PMID:18955476]. 856 superoxide dismutase, Cu-Zn - sodC Bin Zhao, Oliver He BA3966 WEB: http://www.ncbi.nlm.nih.gov/gene 1086802 BA_3966 20140222 198094 protein-coding NCBI-supplied GO_0003700 (EC: ISS, PMID: 12721629); GO_0006355 (EC: ISS, PMID: 12721629) PMID: 12721629 MUTATION: codY mutant is attenuated in mice [PMID:19651859]. 857 transcriptional repressor CodY - codY Bin Zhao, Oliver He BA0992 WEB: http://www.ncbi.nlm.nih.gov/gene 1088960 BA_0992 20140215 198094 protein-coding NCBI-supplied GO_0006352 (EC: IMP, PMID: 10960085); GO_0016987 (EC: IMP, PMID: 10960085) PMID: 10960085; 12721629 MUTATION: sigB mutant is less virulent in mice than the parent strain [PMID:10960085]. 858 RNA polymerase sigma factor SigB - sigB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1089767 MGA_0161 20140405 710127 protein-coding NCBI-supplied PMID: 12949158; 16428737 MUTATION: An lpd mutant is highly attenuated in chickens [PMID:18342996]. 4898 dihydrolipoamide dehydrogenase (E3) component of pyruvate dehydrogenase complex lpd Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1090081 MGA_0674 20140222 710127 protein-coding NCBI-supplied PMID: 12949158 MUTATION: MGA_0674 mutant is attenuated in chickens [PMID:20515935]. 3982 mycoplasma specific lipoprotein A MGA_0674 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1090269 MGA_1107 20140222 710127 protein-coding NCBI-supplied PMID: 12949158 MUTATION: MGA_1107 mutant is attenuated in chickens [PMID:20123709]. 3983 hypothetical protein MGA_1107 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1121382 SAV1407 20140406 158878 protein-coding NCBI-supplied PMID: 11418146; 15141945 MUTATION: mutant attenuated in murine infection model [PMID:15664928]. 4311 branched-chain amino acid carrier protein braB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1122975 SA0198 20130826 158879 protein-coding NCBI-supplied PMID: 11418146; 11717293; 15205410; 15231800; 15576791; 15870358; 16428416; 16484201; 16885446; 16980462; 16980476; 18793396 MUTATION: attenuated in murine model [PMID:9383163]. 4286 oligopeptide transport ATP-binding protein oppF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1123664 SA0847 20130628 158879 protein-coding NCBI-supplied PMID: 11418146; 11717293; 15205410; 15231800; 15576791; 15870358; 16428416; 16484201; 16885446; 16980462; 16980476; 18793396 MUTATION: attenuated in murine model [PMID:9383163]. 4287 oligopeptide transport system ATP-binding protein OppD homologue Other designations: hypothetical protein oppD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1123744 SA0921 20140406 158879 protein-coding NCBI-supplied PMID: 11418146; 11717293; 15205410; 15231800; 15576791; 15870358; 16428416; 16484201; 16885446; 16980462; 16980476; 18793396 MUTATION: attenuated in murine model [PMID:9383163]. 4288 phosphoribosylformylglycinamidine synthase II purL Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1123893 SA1062 20140222 158879 protein-coding NCBI-supplied PMID: 11418146; 11717293; 15205410; 15231800; 15576791; 15870358; 16428416; 16484201; 16885446; 16980462; 16980476; 18793396 MUTATION: SA1062 (stp1) mutant is attenuated in mice [PMID:20552019]. 4289 hypothetical protein SA1062 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1123894 SA1063 20140215 158879 protein-coding NCBI-supplied PMID: 11418146; 11717293; 15205410; 15231800; 15576791; 15870358; 16428416; 16484201; 16885446; 16980462; 16980476; 18793396 MUTATION: stk1 (SA1063) mutant is attenuated in mice [PMID:19395491]. 4290 protein kinase SA1063 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1123959 SA1128 20140406 158879 protein-coding NCBI-supplied PMID: 11418146; 11717293; 15205410; 15231800; 15576791; 15870358; 16428416; 16484201; 16885446; 16980462; 16980476; 18793396 MUTATION: attenuated in murine model [PMID:9383163]. 4291 recombinase A recA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1124002 SA1166 20140405 158879 protein-coding NCBI-supplied PMID: 11418146; 11717293; 15205410; 15231800; 15576791; 15870358; 16428416; 16484201; 16885446; 16980462; 16980476; 18793396 MUTATION: attenuated in murine model [PMID:9383163]. 4292 homoserine kinase homolog Other designations: homoserine kinase thrB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1124021 SA1184 20140405 158879 protein-coding NCBI-supplied PMID: 11418146; 11717293; 15205410; 15231800; 15576791; 15870358; 16428416; 16484201; 16885446; 16980462; 16980476; 18793396 MUTATION: attenuated in murine model [PMID:9383163]. 4293 aconitate hydratase citB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1124032 SA1194 20140222 158879 protein-coding NCBI-supplied PMID: 11418146; 11717293; 15205410; 15231800; 15576791; 15870358; 16428416; 16484201; 16885446; 16980462; 16980476; 18793396 MUTATION: attenuated in murine model [PMID:9383163]. 4294 peptide methionine sulfoxide reductase homolog Other designations: methionine sulfoxide reductase A msrA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1124033 SA1195 20140406 158879 protein-coding NCBI-supplied PMID: 11418146; 11717293; 15205410; 15231800; 15576791; 15870358; 16428416; 16484201; 16885446; 16980462; 16980476; 18793396 MUTATION: mutant displayed reduced ability to colonize and reduced virulence in nematodes and rat endocarditis [PMID:19459977]. 4295 peptide methionine sulfoxide reductase msrR Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1124040 SA1201 20140405 158879 protein-coding NCBI-supplied PMID: 11418146; 11717293; 15205410; 15231800; 15576791; 15870358; 16428416; 16484201; 16885446; 16980462; 16980476; 18793396 MUTATION: attenuated in murine model [PMID:9383163]. 4296 anthranilate phosphoribosyltransferase trpD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1124043 SA1204 20140405 158879 protein-coding NCBI-supplied PMID: 11418146; 11717293; 15205410; 15231800; 15576791; 15870358; 16428416; 16484201; 16885446; 16980462; 16980476; 18793396 MUTATION: attenuated in murine model [PMID:9383163]. 4297 tryptophan synthase subunit beta trpB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1124044 SA1205 20140405 158879 protein-coding NCBI-supplied PMID: 11418146; 11717293; 15205410; 15231800; 15576791; 15870358; 16428416; 16484201; 16885446; 16980462; 16980476; 18793396 MUTATION: attenuated in murine model [PMID:9383163]. 4298 tryptophan synthase subunit alpha trpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1124045 SA1206 20140308 158879 protein-coding NCBI-supplied PMID: 11418146; 11717293; 15205410; 15231800; 15576791; 15870358; 16428416; 16484201; 16885446; 16980462; 16980476; 18793396 MUTATION: attenuated in murine model [PMID:9383163]. 4299 factor essential for expression of methicillin resistance femA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1124046 SA1207 20140329 158879 protein-coding NCBI-supplied PMID: 11418146; 11717293; 15205410; 15231800; 15576791; 15870358; 16428416; 16484201; 16885446; 16980462; 16980476; 18793396 MUTATION: attenuated in murine model [PMID:9383163]. 4300 FemB protein femB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1124052 SA1213 20140405 158879 protein-coding NCBI-supplied PMID: 11418146; 11717293; 15205410; 15231800; 15576791; 15870358; 16428416; 16484201; 16885446; 16980462; 16980476; 18793396 MUTATION: mutant attenuated in murine infection model [PMID:15664928]. 4301 oligopeptide transporter permease opp-2C Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1124065 SA1226 20140405 158879 protein-coding NCBI-supplied PMID: 11418146; 11717293; 15205410; 15231800; 15576791; 15870358; 16428416; 16484201; 16885446; 16980462; 16980476; 18793396 MUTATION: attenuated in murine model [PMID:9383163]. 4302 aspartate semialdehyde dehydrogenase asd Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1124071 SA1232 20140405 158879 protein-coding NCBI-supplied PMID: 11418146; 11717293; 15205410; 15231800; 15576791; 15870358; 16428416; 16484201; 16885446; 16980462; 16980476; 18793396 MUTATION: attenuated in murine model [PMID:9383163]. 4303 diaminopimelate decarboxylase lysA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1124078 SA1239 20140406 158879 protein-coding NCBI-supplied PMID: 11418146; 11717293; 15205410; 15231800; 15576791; 15870358; 16428416; 16484201; 16885446; 16980462; 16980476; 18793396 MUTATION: mutant attenuated in murine infection model [PMID:15664928]. 4304 branched-chain amino acid carrier protein braB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1124083 SA1244 20140405 158879 protein-coding NCBI-supplied PMID: 11418146; 11717293; 15205410; 15231800; 15576791; 15870358; 16428416; 16484201; 16885446; 16980462; 16980476; 18793396 MUTATION: attenuated in murine model [PMID:9383163]. 4305 dihydrolipoamide succinyltransferase odhB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1124100 SA1262 20140222 158879 protein-coding NCBI-supplied PMID: 11418146; 11717293; 15205410; 15231800; 15576791; 15870358; 16428416; 16484201; 16885446; 16980462; 16980476; 18793396 MUTATION: SA1262 (cvfC3) mutant is attenuated in silkworms [PMID:20347953]. 4306 hypothetical protein SA1262 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1124126 SA1288 20140406 158879 protein-coding NCBI-supplied PMID: 11418146; 11717293; 15205410; 15231800; 15576791; 15870358; 16428416; 16484201; 16885446; 16980462; 16980476; 18793396 MUTATION: attenuated in murine model [PMID:15664928]. 4307 ATP-dependent DNA helicase DinG dinG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1124296 SA1453 20140222 158879 protein-coding NCBI-supplied PMID: 11418146; 11717293; 15205410; 15231800; 15576791; 15870358; 16428416; 16484201; 16885446; 16980462; 16980476; 18793396 MUTATION: SA1453 (cymR) mutant is attenuated in mice [PMID:20485570]. 4308 hypothetical protein SA1453 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1124343 SA1498 20140405 158879 protein-coding NCBI-supplied PMID: 11418146; 11717293; 15205410; 15231800; 15576791; 15870358; 16428416; 16484201; 16885446; 16980462; 16980476; 18793396 MUTATION: attenuated in murine model [PMID:9383163]. 4309 ATP-dependent protease ATP-binding subunit ClpX clpX Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1125231 SA2304 20140405 158879 protein-coding NCBI-supplied PMID: 11418146; 11717293; 15205410; 15231800; 15576791; 15870358; 16428416; 16484201; 16885446; 16980462; 16980476; 18793396 MUTATION: attenuated in murine model [PMID:15664928]. 4310 fructose-bisphosphatase fbp Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1145050 y0103 20130508 187410 protein-coding NCBI-supplied PMID: 12142430 MUTATION: relA spoT deletion mutants are attenuated in mice [PMID:19701461]. 759 bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase spoT Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1145449 y0502 20140406 187410 protein-coding NCBI-supplied PMID: 12142430 MUTATION: purH mutant is attenuated in mice [PMID:14742535]. 760 AICAR formyltransferase; IMP cyclohydrolase Other designations: bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase purH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1145577 y0630 20130227 187410 protein-coding NCBI-supplied PMID: 12142430 MUTATION: hfq mutant is highly attenuated in mice after subcutaneous or intravenous injection and has attenuated survival in macrophages [PMID:19593436]. 761 RNA-binding protein Hfq hfq Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1145626 y0679 20140222 187410 protein-coding NCBI-supplied PMID: 12142430 MUTATION: greA mutants are attenuated in mice [PMID:14742535]. 762 transcription elongation factor GreA greA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1145758 y0811 20140406 187410 protein-coding NCBI-supplied PMID: 12142430 MUTATION: relA spoT deletion mutants are attenuated in mice [PMID:19701461]. 763 GDP/GTP pyrophosphokinase relA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1145779 y0832 20140222 187410 protein-coding NCBI-supplied PMID: 12142430 MUTATION: pcm mutant is attenuated in mice [PMID:14742535]. 764 protein-L-isoaspartate O-methyltransferase pcm Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1145780 y0833 20140215 187410 protein-coding NCBI-supplied PMID: 12142430 MUTATION: nlpD mutant is attenuated in mice [PMID:19759820]. 765 lipoprotein NlpD nlpD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1146049 y1102 20140406 187410 protein-coding NCBI-supplied PMID: 12142430 MUTATION: purK mutant is attenuated in mice [PMID:14742535]. 766 AIR carboxylase, CO(2)-fixing subunit Other designations: phosphoribosylaminoimidazole carboxylase ATPase subunit purK Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1146083 y1136 20130508 187410 protein-coding NCBI-supplied PMID: 12142430 MUTATION: y1136 mutant is attenuated in mice [PMID:14742535]. 767 hypothetical protein y1136 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1146205 y1258 20140405 187410 protein-coding NCBI-supplied PMID: 12142430 MUTATION: pgm mutant of Y. pestis is attenuated in mice [PMID:12009274]. 768 phosphoglucomutase pgm Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1146271 y1324 20140222 187410 protein-coding NCBI-supplied PMID: 12142430; 17768237; 18025094 MUTATION: ompX mutants are attenuated in their ability to attach to and invade HeLa cells [PMID:17768237]. 769 attachment invasion locus protein ompX Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1146382 y1436 20140222 187410 protein-coding NCBI-supplied PMID: 12142430 MUTATION: y1436 mutant is attenuated in mice [PMID:14742535]. 770 hypothetical protein y1436 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1146484 y1537 20140222 187410 protein-coding NCBI-supplied PMID: 12142430 MUTATION: y1537 mutant is attenuated in mice [PMID:14742535]. 771 hypothetical protein y1537 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1146629 y1682 20140217 187410 protein-coding NCBI-supplied PMID: 12142430 MUTATION: ompX mutants are attenuated in their ability to attach to and invade HeLa cells [PMID:17768237]. 772 outer membrane protein X ompX Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1146665 y1718 20130227 187410 protein-coding NCBI-supplied PMID: 12142430 MUTATION: y1718 mutant is attenuated in mice [PMID:14742535]. 773 hypothetical protein y1718 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1146741 y1794 20140222 187410 protein-coding NCBI-supplied PMID: 12142430; 19025559 MUTATION: phoP mutants have a reduced ability to survive in J774 macrophage cell cultures and under conditions of low pH and oxidative stress in vitro. The mean lethal dose of the phoP mutant in mice was increased 75-fold in comparison with that of the wild-type strain [PMID:10816493]. 774 DNA-binding transcriptional regulator PhoP phoP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1146767 y1820 20140217 187410 protein-coding NCBI-supplied PMID: 12142430 MUTATION: mgtC mutants are defective in early intracellular survival in macrophages compared to wild type Y. pestis [PMID:16790745]. 775 magnesium ABC transporter ATPase mgtC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1146843 y1896 20140222 187410 protein-coding NCBI-supplied PMID: 12142430 MUTATION: yfeAB mutant is attenuated when given subcutaneously to mice and is avirulent when given to mice intravenously [PMID:10231495]. 776 ATP-binding transport protein yfeB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1146844 y1897 20140222 187410 protein-coding NCBI-supplied PMID: 12142430 MUTATION: yfeAB mutant is attenuated when given subcutaneously to mice and is avirulent when given to mice intravenously [PMID:10231495]. 777 periplasmic-binding protein yfeA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1146981 y2034 20140222 187410 protein-coding NCBI-supplied PMID: 12142430 MUTATION: ompX mutants are attenuated in their ability to attach to and invade HeLa cells [PMID:17768237]. 778 attachment invasion locus protein precursor ompX Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1147194 y2247 20140405 187410 protein-coding NCBI-supplied PMID: 12142430; 16452420 MUTATION: lpxM (msbB) mutant is avirulent in mice and guinea pigs [PMID:17913308]. 779 lipid A biosynthesis (KDO)2-(lauroyl)-lipid IVA acyltransferase msbB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1147232 y2285 20130508 187410 protein-coding NCBI-supplied PMID: 12142430 MUTATION: YchM mutant is attenuated in mice [PMID:14742535]. 780 sulfate transporter YchM y2285 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1147263 y2316 20130227 187410 protein-coding NCBI-supplied PMID: 12142430 MUTATION: y2316 mutant is attenuated in mice [PMID:14742535]. 781 hypothetical protein y2316 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1147344 y2397 20140217 187410 protein-coding NCBI-supplied PMID: 12142430 MUTATION: ybtP mutant is avirulent in mouse bubonic plague model [PMID:10231486]. 782 permease and ATP-binding protein of yersiniabactin-iron ABC transporter ybtP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1147346 y2399 20140222 187410 protein-coding NCBI-supplied PMID: 12142430 MUTATION: irp2 mutants are unable to grow at 37 degrees in iron deficient media [PMID:7896707]. 783 HMWP2 nonribosomal peptide synthetase irp2 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1147351 y2404 20140217 187410 protein-coding NCBI-supplied PMID: 12142430 MUTATION: psn mutant is unable to grow on iron-deficient media at 37 degrees C [PMID:7896707]. 784 pesticin/yersiniabactin outer membrane receptor psn Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1147732 y2785 20140217 187410 protein-coding NCBI-supplied PMID: 12142430 MUTATION: yadBC mutant is attenuated in mice and is less invasive of HeLa cells than the wild-type [PMID:18025093]. 785 hypothetical protein y2785 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1147733 y2786 20140406 187410 protein-coding NCBI-supplied PMID: 12142430 MUTATION: yadBC mutant is attenuated in mice and is less invasive of HeLa cells than the wild-type [PMID:18025093]. 786 hypothetical protein y2786 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1147829 y2882 20140222 187410 protein-coding NCBI-supplied PMID: 12142430; 15557646 MUTATION: psaA mutants have a 100-fold reduced 50% lethal dose in mice [PMID:2164509]. 787 pH 6 antigen precursor (antigen 4) (adhesin) psaA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1147831 y2884 20140215 187410 protein-coding NCBI-supplied PMID: 12142430 MUTATION: psaE mutants are attenuated in mice [PMID:2164509]. 788 regulator psaE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1147957 y3010 20140222 187410 protein-coding NCBI-supplied PMID: 12142430 MUTATION: y3010 mutant is attenuated in mice [PMID:14742535]. 789 hypothetical protein y3010 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1148026 y3079 20130227 187410 protein-coding NCBI-supplied PMID: 12142430 MUTATION: smpB ssrA mutant is attenuated in mice [PMID:20065026]. 790 SsrA-binding protein smpB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1148067 y3120 20140406 187410 protein-coding NCBI-supplied PMID: 12142430 MUTATION: dnaE mutant is attenuated in mice [PMID:14742535]. 791 DNA polymerase III subunit alpha dnaE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1148342 y3395 20130227 187410 protein-coding NCBI-supplied PMID: 12142430 MUTATION: y3395 mutant is attenuated in mice [PMID:14742535]. 792 hypothetical protein y3395 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1148666 y3719 20140215 187410 protein-coding NCBI-supplied PMID: 12142430 MUTATION: y3719 mutant is attenuated in mice [PMID:14742535]. 793 thr operon leader peptide thrL Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1148792 y3845 20140215 187410 protein-coding NCBI-supplied PMID: 12142430 MUTATION: yapE mutant is attenuated in mice and has impaired colonization in bubonic plague model [PMID:18936182]. 794 autotransporter protein yapE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1148804 y3857 20140215 187410 protein-coding NCBI-supplied PMID: 12142430 MUTATION: y3857 mutant is attenuated in mice [PMID:14742535]. 795 metalloprotease y3857 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1148884 y3937 20140222 187410 protein-coding NCBI-supplied PMID: 12142430 MUTATION: dam mutant is attenuated in mice [PMID:16188402]. 796 DNA adenine methylase dam Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1148903 y3956 20140222 187410 protein-coding NCBI-supplied PMID: 12142430; 17933899 MUTATION: crp mutant is attenuated in mice [PMID:20086087]. 797 cAMP-regulatory protein crp Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1149093 D744_p6060 20140215 632 protein-coding NCBI-supplied PMID: 9748454 MUTATION: caf1A mutants are attenuated in mice [PMID:14711524]. 2534 F1 capsule anchoring protein caf1A Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1149094 D744_p6059 20140215 632 protein-coding NCBI-supplied PMID: 9748454 MUTATION: caf1M mutants are attenuated in mice [PMID:14711524]. 2535 Caf1M caf1M MUTATION: The LD50 for the mouse of the yscH mutant was 10-fold higher than that of the parental strain indicating that YopR is involved in pathogenesis [PMID:8709853]. 2522 MUTATION: lcrF mutant is attenuated in mice [PMID:14742535]. 2523 MUTATION: lcrV mutants are avirulent in mice [PMID:7730287]. 2524 MUTATION: lcrH mutant is avirulent in mice [PMID:2707857]. 2525 MUTATION: yopB mutant is avirulent in mouse model, fails to elicit a cytotoxic response in cultured HeLa cells and is unable to inhibit phagocytosis by macrophage-like J774 cells [PMID:8918459]. 2526 MUTATION: yopD mutants are unable to induce cytotoxicity in HeLa cells [PMID:1937815]. 2527 MUTATION: yopM mutant is attenuated in mice compared to the wild type [PMID:2401564]. 2528 MUTATION: yopK mutant has an increased LD50 dose in mice, and infected mice died after 5 days as compared to mice infected with the wild type died after just 3 days [PMID:3002984]. 2529 MUTATION: yopE mutants are attenuated after oral or intraperitoneal infection in mice, but are not attenuated after intravenous infection in mice [PMID:2191183]. 2530 MUTATION: ypkA mutants of Y. pseudotuberculosis are attenuated in mice [PMID:8441468]. 2531 MUTATION: yopH mutants are unable to resist phagocytosis by J774 cells, while wild type Yersinia is able to resist phagocytosis [PMID:8809758]. 2532 MUTATION: pla mutant is attenuated in mice [PMID:1439793]. 2521 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1149242 Y1098 20140217 187410 protein-coding NCBI-supplied PMID: 9826348 MUTATION: caf1M mutants are attenuated in mice [PMID:14711524]. 798 F1 capsule caf1M Bin Zhao, Oliver He Y0009 WEB: http://www.ncbi.nlm.nih.gov/gene 1149271 D744_p5008 20140215 632 protein-coding NCBI-supplied PMID: 9746557 MUTATION: ypkA mutants of Y. pseudotuberculosis are attenuated in mice [PMID:8441468]. 2509 secreted protein kinase - ypkA Bin Zhao, Oliver He Y0013 WEB: http://www.ncbi.nlm.nih.gov/gene 1149274 D744_p5011 20140222 632 protein-coding NCBI-supplied PMID: 9746557 MUTATION: yopH mutants are unable to resist phagocytosis by J774 cells, while wild type Yersinia is able to resist phagocytosis [PMID:8809758]. 2510 targeted effector protein - yopH Bin Zhao, Oliver He Y0024 WEB: http://www.ncbi.nlm.nih.gov/gene 1149284 D744_p5021 20140406 632 protein-coding NCBI-supplied PMID: 9746557 MUTATION: The LD50 for the mouse of the yscH mutant was 10-fold higher than that of the parental strain indicating that YopR is involved in pathogenesis [PMID:8709853]. 2511 secreted protein - yscH Bin Zhao, Oliver He Y0032 WEB: http://www.ncbi.nlm.nih.gov/gene 1149292 D744_p5029 20130918 632 protein-coding NCBI-supplied PMID: 9746557 MUTATION: lcrF mutant is attenuated in mice [PMID:14742535]. 2512 LCR activator - lcrF Bin Zhao, Oliver He Y0050 WEB: http://www.ncbi.nlm.nih.gov/gene 1149310 D744_p5047 20140208 632 protein-coding NCBI-supplied PMID: 9746557; 17438030; 23695558 MUTATION: lcrV mutants are avirulent in mice [PMID:7730287]. 2513 Yop secretion and targeting control protein - lcrV Bin Zhao, Oliver He Y0051 WEB: http://www.ncbi.nlm.nih.gov/gene 1149311 D744_p5048 20140406 632 protein-coding NCBI-supplied PMID: 9746557 MUTATION: lcrH mutant is avirulent in mice [PMID:2707857]. 2514 YopBD chaperone - lcrH Bin Zhao, Oliver He Y0052 WEB: http://www.ncbi.nlm.nih.gov/gene 1149312 D744_p5049 20130918 632 protein-coding NCBI-supplied PMID: 9746557 MUTATION: yopB mutant is avirulent in mouse model, fails to elicit a cytotoxic response in cultured HeLa cells and is unable to inhibit phagocytosis by macrophage-like J774 cells [PMID:8918459]. 2515 Yop targeting protein - yopB Bin Zhao, Oliver He Y0053 WEB: http://www.ncbi.nlm.nih.gov/gene 1149313 D744_p5050 20140406 632 protein-coding NCBI-supplied PMID: 9746557 MUTATION: yopD mutants are unable to induce cytotoxicity in HeLa cells [PMID:1937815]. 2516 Yop targeting negative regulator - yopD Bin Zhao, Oliver He Y0059 WEB: http://www.ncbi.nlm.nih.gov/gene 1149317 D744_p5054 20140222 632 protein-coding NCBI-supplied PMID: 2670888; 9746557 MUTATION: yopM mutant is attenuated in mice compared to the wild type [PMID:2401564]. 2517 Yop targeted effector protein - yopM Bin Zhao, Oliver He Y0065 WEB: http://www.ncbi.nlm.nih.gov/gene 1149322 D744_p5059 20140406 632 protein-coding NCBI-supplied PMID: 9746557 Yop targeted effector - yopT Bin Zhao, Oliver He Y0066 WEB: http://www.ncbi.nlm.nih.gov/gene 1149323 D744_p5060 20140111 632 protein-coding NCBI-supplied PMID: 9746557; 23205707; 23633954 MUTATION: yopK mutant has an increased LD50 dose in mice, and infected mice died after 5 days as compared to mice infected with the wild type died after just 3 days [PMID:3002984]. 2519 Yop targeting protein - yopK Bin Zhao, Oliver He Y0077 WEB: http://www.ncbi.nlm.nih.gov/gene 1149332 D744_p5069 20140215 632 protein-coding NCBI-supplied PMID: 9746557; 21653834 MUTATION: yopE mutants are attenuated after oral or intraperitoneal infection in mice, but are not attenuated after intravenous infection in mice [PMID:2191183]. 2520 targeted effector - yopE Bin Zhao, Oliver He LA0615 WEB: http://www.ncbi.nlm.nih.gov/gene 1149958 LA_0615 20111126 189518 I protein-coding NCBI-supplied PMID: 12712204 hypothetical protein - LA_0615 Bin Zhao, Oliver He LA1641 WEB: http://www.ncbi.nlm.nih.gov/gene 1150984 LA_1641 20111126 189518 I protein-coding NCBI-supplied PMID: 12712204 hypothetical protein - LA_1641 Bin Zhao, Oliver He LB186 WEB: http://www.ncbi.nlm.nih.gov/gene 1153745 LB_186 20140405 189518 II protein-coding NCBI-supplied PMID: 12712204 MUTATION: hemO mutant is attenuated in hamsters [PMID:19114124]. 4815 heme oxygenase - LB_186 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1158705 BXA0146 20140406 191218 protein-coding NCBI-supplied PMID: 12004073 MUTATION: atxA mutant is avirulent in mice [PMID:12224521]. 799 pXO1-119 Other designations: transcriptional activator AtxA atxA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1158723 BXA0164 20140222 191218 protein-coding NCBI-supplied PMID: 12004073; 15473701 MUTATION: pagA mutant is non-lethal in mice [PMID:1910002]. 800 protective antigen pagA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1158731 BXA0172 20140217 191218 protein-coding NCBI-supplied PMID: 12004073; 16293620 MUTATION: lef mutants are non-lethal in mice [PMID:1910002]. 801 lethal factor lef Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1164441 BRA0005 20140222 204722 II protein-coding NCBI-supplied PMID: 12271122 ribokinase BRA0005 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1164473 BRA0037 20140222 204722 II protein-coding NCBI-supplied PMID: 12271122 magnesium ion-transporting ATPase E1-E2 family protein BRA0037 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1164477 BRA0041 20140215 204722 II protein-coding NCBI-supplied PMID: 12271122 sensor histidine kinase BRA0041 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1164492 BRA0055 20140405 204722 II protein-coding NCBI-supplied PMID: 12271122 MUTATION: gltD encodes the small subunit of glutamate synthase. It is required for B. abortus growth as shown in signature-tagged transposon mutagenesis. It suggests that glutamate may serve as carbon and/or nitrogen sources during growth of B abortus [PMID:10858227]. 960 glutamate synthase subunit beta gltD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1164496 BRA0059 20140405 204722 II protein-coding NCBI-supplied PMID: 12271122; 16730027 MUTATION: The virB11 mutation experiment confirms that a complete VirB apparatus is required for their secretion [PMID:15312849]. 961 type IV secretion system protein VirB11 BRA0059 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1164497 BRA0060 20140222 204722 II protein-coding NCBI-supplied PMID: 12271122; 16648257; 21763312 MUTATION: Mutants with polar and nonpolar mutations introduced in irB10 showed different behaviors in mice and in the HeLa cell infection assay, suggesting that virB10 per se is necessary for the correct function of this type IV secretion apparatus [PMID:11260139]. A B. abortus virB10 mutant showed a decrease of intracellular live bacteria comparable to that of the wild-type strain until 4 h after infection, indicating that a functional VirB system is not required for the short-term survival of Brucella inside macrophages. At later time points, the number of live virB10 mutants progressively decreased. Hence, the Brucella virB10 strain did not replicate, but rather was killed. Although the virB10 mutants are capable of short-term survival, they can not evade long-term degradation through fusion with lysosomes [PMID:11260139]. B abortus virB1 and virB10 mutants are unable to persist in mouse spleens after i.p. inoculation, suggest that attenuation in the animal model is due to an inability of these strains to grow intracellularly [PMID:11260139]. A B abortus virB10 mutant lost the ability to multiply in HeLa cells and was not recovered from the spleens of infected BALBc mice [PMID:11260139]. The non polar virB10 mutant was able to block the acquisition of cathepsin D, but was not able to translocate to the replication compartment [PMID:11260139]. The virB10 non-polar mutants were capable of avoiding interactions with the endocytic pathway but , diverging to wild-type Brucella, were unable to reach the endoplasmic reticulum to establish their intracellular replication niche and seemed to be recycled to the cell surface [PMID:11260139]. 962 type IV secretion system protein VirB10 BRA0060 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1164498 BRA0061 20140222 204722 II protein-coding NCBI-supplied PMID: 12271122 MUTATION: Uptake in the presence or absence of Ca2 and Mg2 did not influence the subsequent intracellular survival of wild-type Brucella, whereas the decrease in the number of surviving virB9 mutant cells was delayed in the absence of Ca2 and Mg2. Possibly two types of adhesion molecules promoted uptake of Brucella, one being Ca2 and Mg2 dependent and the other not, and that both types participate in the uptake of wild-type bacteria but only the latter type participates in the uptake of the virB9 mutant [PMID:12414149]. Four independent mutants in virB5, virB9 or virB10 were highly attenuated in an in vitro infection model with human macrophages [PMID:12414149]. The intracellular fate of three virB mutants (virB2, virB4 and virB9) in HeLa cells by immunofluorescence was examined. The three VirB proteins are not necessary for penetration and the inhibition of phago-lysosomal fusion within non-professional phagocytes. Rather, the virB mutants are unable to reach the replicative niche and reside in a membrane -bound vacuole expressing the late endosomal marker, LAMP1, and the sec61beta protein from the ER membrane, proteins that are present in autophagic vesicles originating from the ER [PMID:12414149]. Attenuated non-polar virB2, virB4, virB8, virB9 and virB10 Brucella mutants are capable of penetrating cells as the same rate as the virulent wild-type Brucella, transit through EEA1 -positive early compartments and then localize in LAMP1-positive compartments at early times of infection [PMID:12414149]. 963 type IV secretion system protein VirB9 BRA0061 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1164499 BRA0062 20140222 204722 II protein-coding NCBI-supplied PMID: 12271122; 15764702; 16648257; 21763312 MUTATION: virB8 mutant was attenuated by a mini-Tn5 transposon mutagenesis [PMID:12414149]. Attenuated non-polar virB2, virB4, virB8, virB9 and virB10 Brucella mutants are capable of penetrating cells as the same rate as the virulent wild-type Brucella, transit through EEA1-positive early compartments and then localize in LAMP1-positive compartments at early times of infection [PMID:12414149]. 964 type IV secretion system protein VirB8 BRA0062 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1164501 BRA0064 20130611 204722 II protein-coding NCBI-supplied PMID: 12271122 type IV secretion system protein VirB6 BRA0064 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1164502 BRA0065 20140406 204722 II protein-coding NCBI-supplied PMID: 12271122 MUTATION: A comparison of the VirB8 and VirB5 contents after induction of the B suis wild type and of virB5 and virB12 mutants further confirmed that the virB5 and virB12 genes belong to the same operon [PMID:10510235]. Smooth strains of Brucella unable to replicate (ie, killed B suis or the avirulent mutant B suis virB5) exhibit delayed phagosome-lysosome fusion [PMID:10510235]. Polar mutations in the operon upstream of virB5 exert a greater effect on the expression of virB5 than they do on the expression of the downstream gene virB12. It indicates that in B abortus , regulatory elements other than the virB promoter may influence VirB12 protein levels [PMID:10510235]. Four independent mutants in virB5, virB9 or virB10 were highly attenuated in an in vitro infection model with human macrophages [PMID:10510235]. 966 type IV secretion system protein VirB5 BRA0065 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1164503 BRA0066 20140222 204722 II protein-coding NCBI-supplied PMID: 12271122; 16648257 MUTATION: A mutant strain of B abortus that contains an in-frame deletion in virB4 is unable to replicate in macrophages and survives in mice [PMID:15135535]. ntracellular replication was inhibited in wild-type B abortus after introducing a plasmid expressing a mutant VirB4 altered in the NTP -binding region. VirB4 containing the intact NTP -binding region is essential for evasion of fusion with lysosomes (11988518). The ruffling associated with internalization of the virB4 mutant results in a more rapid uptake than for the wild-type strain. The virB4 mutant shows primarily small regions of phalloidin staining at the sites of binding. Macrophages incubated simultaneously with B abortus and the fluid-phase marker tetramethyl rhodamine isothiocyanate (TRITC)-dextran accumulate the marker in large vacuoles containing the wild-type strain, but little or no marker accumulates in phagosomes containing the virB4 mutant. Similarly, phase-contrast micrographs have shown the wild-type strain in large phase-transparent compartments, but the virB4 mutant is in much smaller compartments (14738898). Intracellular growth-defective virB4 mutant and attenuated vaccine strain S19 did not induce abortion [PMID:15135535]. The B abortus virB4 mutant was completely cleared from the spleens of mice after 4 weeks, while the pncA mutant showed a 1.5-log reduction of the number of bacteria isolated from spleens after 10 weeks. Splenomegaly was not observed at all in mice infected with virB4 mutant [PMID:15135535]. 967 type IV secretion system protein VirB4 BRA0066 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1164504 BRA0067 20130611 204722 II protein-coding NCBI-supplied PMID: 12271122 MUTATION: The B abortus virB3 gene is found to be essential for intracellular growth inside HeLa cells [PMID:12761078]. 968 type IV secretion system protein VirB3 BRA0067 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1164505 BRA0068 20140406 204722 II protein-coding NCBI-supplied PMID: 12271122 MUTATION: The Brucella abortus virB operon, encoding a type IV secretion system (T4SS), is required for intracellular replication and persistent infection in the mouse model. The products of the first two genes of the virB operon, virB1 and virB2, are predicted to be localized at the bacterial surface. Both mutants were shown to be nonpolar, as demonstrated by their ability to express the downstream gene virB5 during stationary phase of growth in vitro. Both VirB1 and VirB2 were essential for intracellular replication in J774 macrophages. The nonpolar virB2 mutant was unable to cause persistent infection in the mouse model, demonstrating the essential role of VirB2 in the function of the T4SS apparatus during infection [PMID:16113325]. Polar mutations in the virB1 to virB2 intergenic region or in virB2 reduced the detection of VirB5 to a greater extent than they did that of VirB12. A virB1 mutation also eliminates the transcription of virB12 in B suis [PMID:16113325]. 969 type IV secretion system protein VirB2 BRA0068 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1164506 BRA0069 20140222 204722 II protein-coding NCBI-supplied PMID: 12271122 MUTATION: The Brucella abortus virB operon, encoding a type IV secretion system (T4SS), is required for intracellular replication and persistent infection in the mouse model. The products of the first two genes of the virB operon, virB1 and virB2, are predicted to be localized at the bacterial surface. Both mutants were shown to be nonpolar, as demonstrated by their ability to express the downstream gene virB5 during stationary phase of growth in vitro. Both VirB1 and VirB2 were essential for intracellular replication in J774 macrophages. The nonpolar virB1 mutant persisted at wild-type levels, showing that the function of VirB1 is dispensable in the mouse model of persistent infection [PMID:16272371]. A B abortus polar virB1 mutant failed to replicate in HeLa cells, indicating that the virB operon plays a critical role in intracellular multiplication [PMID:16272371]. Polar mutations in the virB1 to virB2 intergenic region or in virB2 reduced the detection of VirB5 to a greater extent than they did that of VirB12. A virB1 mutation also eliminates the transcription of virB12 in B suis [PMID:16272371]. An infection assay with signature-tagged Brucella abortus mutants demonstrated that mutagenesis of the virB1 gene causes attenuation of virulence [PMID:16272371]. 970 type IV secretion system protein VirB1 BRA0069 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1164513 BRA0076 20140405 204722 II protein-coding NCBI-supplied PMID: 12271122 ferrochelatase hemH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1164514 BRA0077 20130611 204722 II protein-coding NCBI-supplied PMID: 12271122 lipoprotein Omp10 omp10 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1164548 BRA0111 20140405 204722 II protein-coding NCBI-supplied PMID: 12271122 MUTATION: gnd is involved in pentose phosphate pathway. It is essential for intracellular growth inside HeLa cells as shown by its Brucella suis miniTn5Km2 transposon mutation analysis. The mutant is attenuated in the mouse model [PMID:12761078]. 973 6-phosphogluconate dehydrogenase gnd Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1164556 BRA0119 20130611 204722 II protein-coding NCBI-supplied PMID: 12271122 LuxR family transcriptional regulator BRA0119 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1164572 BRA0135 20140217 204722 II protein-coding NCBI-supplied PMID: 12271122 glycosyl transferase group 2 family protein BRA0135 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1164583 BRA0146 20130611 204722 II protein-coding NCBI-supplied PMID: 12271122 DeoR family transcriptional regulator BRA0146 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1164593 BRA0156 20140215 204722 II protein-coding NCBI-supplied PMID: 12271122 flagellar basal body P-ring biosynthesis protein FlgA flgI Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1164614 BRA0177 20130611 204722 II protein-coding NCBI-supplied PMID: 12271122 GntR family transcriptional regulator BRA0177 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1164627 BRA0190 20111207 204722 II other NCBI-supplied gluP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1164661 BRA0224 20140222 204722 II protein-coding NCBI-supplied PMID: 12271122 CAIB/BAIF family protein BRA0224 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1164683 BRA0246 20140215 204722 II protein-coding NCBI-supplied PMID: 12271122 cytochrome c oxidase subunit III BRA0246 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1164688 BRA0251 20140217 204722 II protein-coding NCBI-supplied PMID: 12271122 MUTATION: A mutant of Brucella suis bearing a Tn5 insertion in norD , the last gene of the operon norEFCBQD, encoding nitric oxide reductase, was unable to survive under anaerobic denitrifying conditions (more-than-5log reduction in viable counts). As a consequence of the norD mutation , NO might not be further reduced to N2O by the NO reductase and it could become toxic for the bacteria. The infection of resting macrophages showed that the norD mutant and the wild-type strain displayed similar rates of multiplication. On the contrary, activation of J774A.1 cells by LPS and IFN was accompanied by a more-thantenfold attenuation of the norD mutant at 48 h p. i. [PMID:16495577]. 982 norD protein norD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1164736 BRA0299 20140406 204722 II protein-coding NCBI-supplied PMID: 12271122 MUTATION: The narG gene encodes for an essential component of the dissimilatory nitrate reductase complex. This complex is encoded by the narGHIJ locus, which is present in the B suis genome together with the gene of the nitrite extrusion protein, narK. The narG mutant was unable to produce nitrite from nitrate [PMID:12438693]. A study with miniTn5 mutants of B. suis constitutively expressing gfp indicates that B. suis xx gene is required for intracellular multiplication in human macrophage THP-1 cells [PMID:12438693]. 983 respiratory nitrate reductase subunit alpha narG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1164751 BRA0314 20140222 204722 II protein-coding NCBI-supplied PMID: 12271122 glutaredoxin-like protein nrdH nrdH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1164785 BRA0347 20140405 204722 II protein-coding NCBI-supplied PMID: 12271122 mannose-1-phosphate guanylyltransferase BRA0347 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1164786 BRA0348 20140405 204722 II protein-coding NCBI-supplied PMID: 12271122 phosphoglucomutase BRA0348 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1164792 BRA0354 20140405 204722 II protein-coding NCBI-supplied PMID: 12271122 MUTATION: The transcription product of Brucella abortus oxyR binds to the B abortus catalase promoter region. A gene replacementdeletion Brucella oxyR mutant exhibits increased sensitivity to prolonged exposure to H2O2 and is unable to adapt to H2O2 in the environment [PMID:10986275]. 987 transcriptional regulator OxyR oxyR Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1164823 BRA0385 20140222 204722 II protein-coding NCBI-supplied PMID: 12271122 phosphoketolase xfp Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1164881 BRA0443 20140322 204722 II protein-coding NCBI-supplied PMID: 12271122 glycerol kinase glpK Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1164905 BRA0467 20140217 204722 II protein-coding NCBI-supplied PMID: 12271122 taurine ABC transporter permease BRA0467 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1164946 BRA0508 20140222 204722 II protein-coding NCBI-supplied PMID: 12271122 MUTATION: The cydB and cydD mutants are also defective for the intracellular growth of B abortus and B suis, suggesting that functional cytochrome bd oxidase is required for growth in an intracellular environment [PMID:12761078]. 991 ABC transporter ATP-binding protein CydD cydD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1164947 BRA0509 20140217 204722 II protein-coding NCBI-supplied PMID: 12271122 ABC transporter ATP-binding/permease BRA0509 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1164949 BRA0511 20140329 204722 II protein-coding NCBI-supplied PMID: 12271122 MUTATION: cydB is a gene that is part of the cydAB operon encoding cytochrome bd oxidase , which catalyzes an alternate terminal electron transport step in bacterial respiration. Transposon (Tn5) mutagenesis of B abortus cydB was severely attenuated for intracellular survival. Unlike the virulent strain 2308, the Brucella cydB::Tn5 mutant was severely compromised for survival in the spleens of inoculated mice [PMID:11274104]. The cydB and cydD mutants are also defective for the intracellular growth of B abortus and B suis, suggesting that functional cytochrome bd oxidase is required for growth in an intracellular environment [PMID:11274104]. 993 cytochrome d ubiquinol oxidase subunit II cydB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1165007 BRA0568 20140215 204722 II protein-coding NCBI-supplied PMID: 12271122 ABC transporter permease BRA0568 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1165011 BRA0572 20140215 204722 II protein-coding NCBI-supplied PMID: 12271122 MUTATION: The role of Phosphatidylcholine (PC) in Brucella abortus was examined by generating mutants in pcs (BApcs) and pmtA (BApmtA), which encode key enzymes of the two bacterial PC biosynthetic routes, the choline and methyl-transferase pathways. In rich medium, BApcs and the double mutant BApcspmtA but not BApmtA displayed reduced growth, increased phosphatidylethanolamine and no PC, showing that Pcs is essential for PC synthesis under these conditions. In minimal medium, the parental strain, BApcs and BApmtA showed reduced but significant amounts of PC suggesting that PmtA may also be functional Probing with phage Tb, antibiotics, polycations and serum demonstrated that all mutants had altered envelopes. In macrophages, BApcs and BApcspmtA showed reduced ability to evade fusion with lysosomes and establish a replication niche. In mice, BApcs showed attenuation only at early times after infection, BApmtA at later stages and BApcspmtA throughout. The results suggest that Pcs and PmtA have complementary roles in vivo related to nutrient availability and that PC and the membrane properties that depend on this typical eukaryotic phospholipid are essential for Brucella virulence [PMID:16882035]. 995 phosphatidylcholine synthase pcs Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1165038 BRA0598 20140405 204722 II protein-coding NCBI-supplied PMID: 12271122 acyl-CoA dehydrogenase BRA0598 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1165039 BRA0599 20140329 204722 II protein-coding NCBI-supplied PMID: 12271122 aspartate carbamoyltransferase pyrB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1165052 BRA0612 20130611 204722 II protein-coding NCBI-supplied PMID: 12271122 polar differentiation response regulator divK Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1165097 BRA0655 20140215 204722 II protein-coding NCBI-supplied PMID: 12271122 MUTATION: B suis ugpB mutant does not contain SP41 protein. Mutants lacking SP41 production are less invasive, but proliferate in HeLa cells. An isogenic DeltaugpB mutant showed a significant inhibitory effect on Brucella adherence and invasion of human cultured epithelial cells and this effect could be reversed by restoration of the ugpB on a plasmid. [PMID:16817909]. 999 glycerol-3-phosphate ABC transporter periplasmic glycerol-3-phosphate-binding protein ugpB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1165098 BRA0656 20140222 204722 II protein-coding NCBI-supplied PMID: 12271122 MUTATION: UgpA is one of the attenuated Signature-Tagged Mutagenesis mutants of Brucella melitensis identified during the acute phase of infection in mice [PMID:14638795]. 1000 glycerol-3-phosphate ABC transporter permease ugpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1165134 BRA0692 20130831 204722 II protein-coding NCBI-supplied PMID: 12271122 MUTATION: UgpA is one of the attenuated Signature-Tagged Mutagenesis mutants of Brucella melitensis identified during the acute phase of infection in mice [PMID:14638795]. 1001 sugar ABC transporter permease BRA0692 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1165142 BRA0700 20130611 204722 II protein-coding NCBI-supplied PMID: 12271122 iron ABC transporter substrate-binding protein BRA0700 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1165145 BRA0703 20140215 204722 II protein-coding NCBI-supplied PMID: 12271122 superoxide dismutase, Cu-Zn sodC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1165154 BRA0712 20140222 204722 II protein-coding NCBI-supplied PMID: 12271122 SIS domain-containing protein BRA0712 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1165167 BRA0725 20140405 204722 II protein-coding NCBI-supplied PMID: 12271122 glycine dehydrogenase gcvP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1165169 BRA0727 20140405 204722 II protein-coding NCBI-supplied PMID: 12271122 MUTATION: A study with miniTn5 mutants of B. suis constitutively expressing gfp indicates that B. suis gcvT gene is required for intracellular multiplication in human macrophage THP-1 cells [PMID:12438693]. 1006 glycine cleavage system aminomethyltransferase T gcvT Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1165206 BRA0764 20130611 204722 II protein-coding NCBI-supplied PMID: 12271122 exodeoxyribonuclease VII large subunit xseA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1165220 BRA0778 20140406 204722 II protein-coding NCBI-supplied PMID: 12271122 MUTATION: Brucella abortus zwf mutant via mini-Tn5Km2 transposon mutagenesis has intracellular growth defect inside HeLa cells and macrophages [PMID:12761078]. 1008 glucose-6-phosphate 1-dehydrogenase zwf Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1165246 BRA0804 20140222 204722 II protein-coding NCBI-supplied PMID: 12271122 nickel ABC transporter nickel-binding protein BRA0804 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1165248 BRA0806 20130611 204722 II protein-coding NCBI-supplied PMID: 12271122 UxaA family hydrolase BRA0806 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1165308 BRA0865 20140406 204722 II protein-coding NCBI-supplied PMID: 12271122 MUTATION: EryB is an erythritol phosphate dehydrogenase. The vaccine strain B abortus B19 is the only known B abortus isolate whose growth is inhibited by erythritol. The B abortus B19 strain is an eryCD double mutant. The defect in B19 was complemented in trans by plasmids containing the complete ery region and by plasmids with Tn1725 insertions in eryA, eryB and eryD. Plasmids with Tn1725 insertions in eryC were the only ones that failed to complement the Ery phenotype of B19 [PMID:10708387]. The B. suis eryB mutant by Tn5 transposon mutagenesis was attenuated in the human macrophage -like THP-1 cells. This mutant is sensitive to erythritol and mimics the erythritol sensitive response of the B19 strain [PMID:10708387]. 1011 glycerol-3-phosphate dehydrogenase eryB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1165309 BRA0866 20140406 204722 II protein-coding NCBI-supplied PMID: 12271122; 16177356 MUTATION: The eryC gene encodes for enzyme Derythrulose-1-phosphate dehydrogenase. The vaccine strain B abortus B19 is the only known B abortus isolate whose growth is inhibited by erythritol. The B abortus B19 strain is an eryCD double mutant. The defect in B19 was complemented in trans by plasmids containing the complete ery region and by plasmids with Tn1725 insertions in eryA, eryB and eryD. Plasmids with Tn1725 insertions in eryC were the only ones that failed to complement the Ery phenotype of B19 [PMID:10708387]. Allelic exchange mutants in eryC of Brucella suis were erythritol sensitive in vitro with a MIC of 1 to 5 mM of erythritol. Their multiplication in macrophage-like cells was 50 to 90- fold reduced , but complementation of the mutant restored wild-type levels of intracellular multiplication and the capacity to use erythritol as a sole carbon source. In vivo, the eryC mutant colonized the spleens of infected BALBc mice to a significantly lower extent than the wild type and the complemented strain. Interestingly, eryC mutants that were in addition spontaneously erythritol tolerant nevertheless exhibited wild-type-like intramacrophagic and intramurine replication. In conclusion, erythritol was not an essential carbon source for the pathogen in the macrophage host cell but that the inactivation of the eryC gene significantly reduced the intramacrophagic and intramurine fitness of B suis [PMID:10708387]. 1012 D-erythrulose-1-phosphate dehydrogenase eryC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1165363 BRA0919 20140217 204722 II protein-coding NCBI-supplied PMID: 12271122 molybdopterin-binding oxidoreductase BRA0919 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1165380 BRA0936 20140222 204722 II protein-coding NCBI-supplied PMID: 12271122 sugar ABC transporter ATP-binding protein BRA0936 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1165391 BRA0947 20130611 204722 II protein-coding NCBI-supplied PMID: 12271122 D-aminopeptidase BRA0947 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1165431 BRA0987 20140215 204722 II protein-coding NCBI-supplied PMID: 12271122 MUTATION: A study with miniTn5 mutants of B. suis constitutively expressing gfp indicates that B. suis cobW gene is required for intracellular multiplication in human macrophage THP-1 cells [PMID:12438693]. 1016 cobalamin synthesis protein/P47K family protein BRA0987 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1165456 BRA1012 20140222 204722 II protein-coding NCBI-supplied PMID: 12271122 ABC transporter periplasmic substrate-binding protein BRA1012 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1165575 BRA1122 20140222 204722 II protein-coding NCBI-supplied PMID: 12271122 MUTATION: Brucella abortus znuA mutant via mini-Tn5Km2 transposon mutagenesis has intracellular growth defect inside HeLa cells [PMID:12761078]. High-affinity zinc uptake system protein mutant (znuA mutant) showed reduced growth in zinc chelated medium, and failed to replicate in HeLa cells and mouse bone marrow-derived macrophages. Transformation of znuA mutant with a shuttle vector pBBR1MCS-4 containing znuA gene restored the growth in zinc chelated medium and intracellular replication in HeLa cells and macrophages to a level comparable to that of wild-type strain. Bacterial internalization into HeLa cells and macrophages and co-localization with either late endosomes or lysosomes of znuA mutant were not different from those of wild-type strain. These results suggest that znuA does not contribute to intracellular trafficking of B abortus, but contributes to utilization of zinc required for intracellular growth [PMID:12761078]. 1018 zinc ABC transporter periplasmic zinc-binding protein znuA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1165576 BRA1123 20140406 204722 II protein-coding NCBI-supplied PMID: 12271122 zinc ABC transporter ATP-binding protein znuC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1165592 BRA1139 20140406 204722 II protein-coding NCBI-supplied PMID: 12271122 flagellar hook protein FlgE flgE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1165597 BRA1144 20140405 204722 II protein-coding NCBI-supplied PMID: 12271122 flagellar motor protein MotB motB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1165599 BRA1146 20140215 204722 II protein-coding NCBI-supplied PMID: 12271122 flagellar MS-ring protein fliF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1165684 BR0027 20140222 204722 I protein-coding NCBI-supplied PMID: 12271122 MUTATION: rpsA is a B. suis gene identified by signature-tagged mutagenesis [PMID:10678941]. 1023 30S ribosomal protein S1 rpsA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1165694 BR0037 20140405 204722 I protein-coding NCBI-supplied PMID: 12271122 MUTATION: The product of pheA gene is specifically dedicated to the biosynthesis of phenylalanine. The B. abortus pheA mutant with mini-Tn5 disruption displays nutritional defects in vitro. Experimental findings with the B abortus ilvD, trpB, and pheA mutants suggest that tryptophan and phenylalanine are available to the brucellae in their intracellular niche but that other amino acids (eg, leucine, isoleucine, or valine) are not. The pheA::miniTn5 mutant displayed attenuation in macrophages but not in mice [PMID:15271960]. 1024 prephenate dehydratase pheA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1165715 BR0058 20140405 204722 I protein-coding NCBI-supplied PMID: 12271122 MUTATION: Brucella pgm encodes the phosphoglucomutase. The B. abortus pgm mutant (B2211) lacks the O antigen. However, the core region of the mutant LPS migrated in Tricine-PAGE electrophoresis in a position that was indistinguishable from that of the wild type core. Although the exponential intracellular replication of the pgm mutant was delayed by approximately 20 h with respect to that of the wild type, the high number of recoverable bacteria at 48 h postinfection indicates that mutant strain B2211 replicates inside HeLa host cells [PMID:10992476]. B abortus phosphoglucomutase (pgm) insertional mutants were attenuated in vivo but not in vitro [PMID:10992476]. 1025 phosphoglucomutase pgm Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1165756 BR0099 20140405 204722 I protein-coding NCBI-supplied PMID: 12271122 dihydroxy-acid dehydratase ilvD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1165768 BR0111 20140222 204722 I protein-coding NCBI-supplied PMID: 12271122 cyclic beta 1-2 glucan synthetase BR0111 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1165801 BR0144 20140222 204722 I protein-coding NCBI-supplied PMID: 12271122 PII uridylyl-transferase BR0144 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1165838 BR0181 20140405 204722 I protein-coding NCBI-supplied PMID: 12271122 sulfite reductase (NADPH) hemoprotein subunit beta cysI Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1165845 BR0188 20140406 204722 I protein-coding NCBI-supplied PMID: 12271122 B12-dependent methionine synthase metH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1165896 BR0238 20140222 204722 I protein-coding NCBI-supplied PMID: 12271122 sugar ABC transporter ATP-binding protein BR0238 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1165911 BR0252 20140406 204722 I protein-coding NCBI-supplied PMID: 12271122; 22196018 histidinol dehydrogenase hisD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1165946 BR0285 20140406 204722 I protein-coding NCBI-supplied PMID: 12271122 glucose-6-phosphate isomerase pgi Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1165972 BR0311 20140406 204722 I protein-coding NCBI-supplied PMID: 12271122 MUTATION: B. suis pyrD mutation study indicated that pyrimidine synthesis pathway contributes to intracellular growth [PMID:12761078]. 1034 dihydroorotate dehydrogenase 2 pyrD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1165977 BR0316 20140406 204722 I protein-coding NCBI-supplied PMID: 12271122 sensor histidine kinase/response regulator BR0316 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1166033 BR0372 20130611 204722 I protein-coding NCBI-supplied PMID: 12271122 MUTATION: B abortus bacA mutant exhibited decreased survival in macrophages and greatly accelerated clearance from experimentally infected mice compared to the virulent parental strain [PMID:10741969]. R meliloti bacA gene encodes a putative cytoplasmic membrane transport protein required for symbiosis [PMID:10741969]. The BacA protein is essential for the long-term survival of Sinorhizobium meliloti and Brucella abortus within acidic compartments in plant and animal cells , respectively. Mutation study showed that B. abortus BacA affects the distribution of LPS fatty acids, including a very-long-chain fatty acid thought to be unique to the alpha-proteobacteria[PMID:10741969]. 1036 transport protein bacA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1166075 BR0414 20140405 204722 I protein-coding NCBI-supplied PMID: 12271122 phosphoribosylamine--glycine ligase purD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1166089 BR0428 20140405 204722 I protein-coding NCBI-supplied PMID: 12271122 chorismate synthase aroC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1166103 BR0442 20140215 204722 I protein-coding NCBI-supplied PMID: 12271122 ABC transporter ATP-binding/permease BR0442 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1166107 BR0446 20140405 204722 I protein-coding NCBI-supplied PMID: 12271122 MUTATION: A B. suis purF mutation experiment suggests that the purine biosynthesis pathway contributes to intracellular growth [PMID:12761078]. 1040 amidophosphoribosyltransferase purF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1166126 BR0465 20140217 204722 I protein-coding NCBI-supplied PMID: 12271122 tldD protein BR0465 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1166145 BR0484 20140405 204722 I protein-coding NCBI-supplied PMID: 12271122 threonine synthase thrC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1166157 BR0496 20140215 204722 I protein-coding NCBI-supplied PMID: 12271122 twin-arginine translocation pathway signal sequence domain-containing protein BR0496 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1166172 BR0511 20140222 204722 I protein-coding NCBI-supplied PMID: 12271122 glycosyl transferase group 4 family protein BR0511 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1166180 BR0518 20130611 204722 I protein-coding NCBI-supplied PMID: 12271122 MUTATION: No function has been assigned to the B. melitensis 16M wbkB gene either by homology search or functionally, because deletion of wbkB did not interfere with the O-antigen structure [PMID:11081580]. 1045 wbkB protein wbkB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1166182 BR0520 20140215 204722 I protein-coding NCBI-supplied PMID: 12271122 O-antigen export system permease RfbD rfbD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1166183 BR0521 20140215 204722 I protein-coding NCBI-supplied PMID: 12271122 perosamine synthase BR0521 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1166184 BR0522 20140406 204722 I protein-coding NCBI-supplied PMID: 12271122 MUTATION: gmd may be involved in perosamine synthesis. It has been shown to be in LPS synthesis since its B. melitensis mutation induces rough phenotype [PMID:15099501]. 1048 GDP-mannose 4,6-dehydratase gmd Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1166191 BR0529 20140215 204722 I protein-coding NCBI-supplied PMID: 12271122 mannosyltransferase BR0529 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1166199 BR0537 20140405 204722 I protein-coding NCBI-supplied PMID: 12271122 phosphomannomutase BR0537 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1166202 BR0540 20140222 204722 I protein-coding NCBI-supplied PMID: 12271122 group 1 glycosyl transferase BR0540 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1166266 BR0604 20140222 204722 I protein-coding NCBI-supplied PMID: 12271122 DNA-binding response regulator BR0604 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1166267 BR0605 20130611 204722 I protein-coding NCBI-supplied PMID: 12271122 sensor histidine kinase BR0605 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1166273 BR0611 20130611 204722 I protein-coding NCBI-supplied PMID: 12271122 serine protease BR0611 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1166277 BR0615 20140222 204722 I protein-coding NCBI-supplied PMID: 12271122 hypothetical protein BR0615 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1166279 BR0617 20140215 204722 I protein-coding NCBI-supplied PMID: 12271122 MUTATION: A single mutation of PepN leads to a significant decrease in the growth rate, thus PepN seems to play a more prominent role than do the other proteases [PMID:12933870]. 1056 aminopeptidase pepN Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1166315 BR0652 20140222 204722 I protein-coding NCBI-supplied PMID: 12271122 RelA/SpoT family protein BR0652 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1166364 BR0701 20140215 204722 I protein-coding NCBI-supplied PMID: 12271122; 17635859 outer-membrane protein Omp25 omp25 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1166372 BR0709 20140405 204722 I protein-coding NCBI-supplied PMID: 12271122 MUTATION: B. abortus purN gene is essential for intracellular growth in HeLa cells as shown from transposon mutagenesis study [PMID:12761078]. 1059 phosphoribosylglycinamide formyltransferase purN Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1166373 BR0710 20140405 204722 I protein-coding NCBI-supplied PMID: 12271122 phosphoribosylaminoimidazole synthetase purM Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1166378 BR0715 20140406 204722 I protein-coding NCBI-supplied PMID: 12271122 epimerase BR0715 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1166430 BR0765 20140405 204722 I protein-coding NCBI-supplied PMID: 12271122 serine hydroxymethyltransferase glyA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1166505 BR0837 20140405 204722 I protein-coding NCBI-supplied PMID: 12271122 phosphoribosylformylglycinamidine synthase II purL Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1166567 BR0898 20140406 204722 I protein-coding NCBI-supplied PMID: 12271122 trigger factor tig Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1166578 BR0909 20140406 204722 I protein-coding NCBI-supplied PMID: 12271122 hypothetical protein BR0909 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1166584 BR0915 20140406 204722 I protein-coding NCBI-supplied PMID: 12271122 N-acetylmuramoyl-L-alanine amidase BR0915 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1166599 BR0930 20140329 204722 I protein-coding NCBI-supplied PMID: 12271122 cysteine desulfurase BR0930 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1166602 BR0933 20130611 204722 I protein-coding NCBI-supplied PMID: 12271122 hypothetical protein BR0933 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1166625 BR0955 20140222 204722 I protein-coding NCBI-supplied PMID: 12271122 amino acid ABC transporter substrate-binding protein BR0955 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1166655 BR0982 20140222 204722 I protein-coding NCBI-supplied PMID: 12271122 group 1 glycosyl transferase BR0982 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1166677 BR1004 20140405 204722 I protein-coding NCBI-supplied PMID: 12271122 MUTATION: A study with miniTn5 mutants of B. suis constitutively expressing gfp indicates that B. suis glnA gene is required for intracellular multiplication in human macrophage THP-1 cells [PMID:12438693]. 1071 glutamine synthetase glnA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1166727 BR1053 20140406 204722 I protein-coding NCBI-supplied PMID: 12271122 cysteine synthase A BR1053 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1166760 BR1084 20140215 204722 I protein-coding NCBI-supplied PMID: 12271122 CAIB/BAIF family protein BR1084 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1166780 BR1104 20140222 204722 I protein-coding NCBI-supplied PMID: 12271122 excinuclease ABC subunit A uvrA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1166782 BR1106 20140222 204722 I protein-coding NCBI-supplied PMID: 12271122 ATP-dependent protease La lon Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1166787 BR1111 20130611 204722 I protein-coding NCBI-supplied PMID: 12271122 RNA-binding protein Hfq hfq Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1166792 BR1116 20130611 204722 I protein-coding NCBI-supplied PMID: 12271122 MUTATION: The NtrY protein is a sensor of an ntr-related regulon which may be part of the glnALG operon. This mutant has a weakly attenuated phenotype (reduction of 1.2 log units versus the wild type at 48 h postinfection) which could be explained by a pleiotropic effect on the ntr regulon, since the ntrC mutant did not show such a phenotype [PMID:10678941]. 1077 nitrogen regulation protein NtrY ntrY Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1166793 BR1117 20140222 204722 I protein-coding NCBI-supplied PMID: 12271122 MUTATION: ntrC encodes for a response regulator subfamily (NtrC). A B suis ntrC isogenic mutant was constructed which showed no significant differences in growth rates compared to the wild-type strain when grown at different temperatures in vitro. However, the mutant exhibited a reduction in metabolic activity in the presence of many amino acids. The mutation did not affect survival or multiplication of B suis in macrophages, but during the initial stages of infection in the murine brucellosis model, the ntrC mutant showed a reduced ability to multiply rapidly in splenic tissue [PMID:10373105]. 1078 nitrogen regulation protein NtrC ntrC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1166815 BR1139 20140222 204722 I protein-coding NCBI-supplied PMID: 12271122 rotamase BR1139 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1166834 BR1158 20140315 204722 I protein-coding NCBI-supplied PMID: 12271122 undecaprenyl pyrophosphate synthase uppS Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1166878 BR1202 20140406 204722 I protein-coding NCBI-supplied PMID: 12271122 recombinase A recA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1166885 BR1209 20140329 204722 I protein-coding NCBI-supplied PMID: 12271122 DNA-directed RNA polymerase subunit alpha rpoA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1166947 BR1268 20140215 204722 I protein-coding NCBI-supplied PMID: 12271122 lactoylglutathione lyase gloA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1166977 BR1296 20140301 204722 I protein-coding NCBI-supplied PMID: 12271122 cobyrinic acid a,c-diamide synthase cobB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1167060 BR1378 20130611 204722 I protein-coding NCBI-supplied PMID: 12271122 class I aminotransferase BR1378 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1167062 BR1380 20140405 204722 I protein-coding NCBI-supplied PMID: 12271122 ketol-acid reductoisomerase ilvC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1167072 BR1390 20140329 204722 I protein-coding NCBI-supplied PMID: 12271122 tRNA delta(2)-isopentenylpyrophosphate transferase miaA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1167073 BR1391 20140406 204722 I protein-coding NCBI-supplied PMID: 12271122 MUTATION: A study with miniTn5 mutants of B. suis constitutively expressing gfp indicates that B. suis serB gene is required for intracellular multiplication in human macrophage THP-1 cells [PMID:12438693]. 1088 phosphoserine phosphatase serB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1167146 BR1464 20140405 204722 I protein-coding NCBI-supplied PMID: 12271122 MUTATION: Brucella abortus pnc mutant via mini-Tn5Km2 transposon mutagenesis has intracellular growth defect inside HeLa cells [PMID:12761078]. Nicotinamidasepyrazinamidase mutant (pncA mutant) of Brucella abortus failed to replicate in HeLa cells, and showed a lower rate of intracellular replication than that of wild-type strain in macrophages [PMID:12761078]. The pncA mutant was not co-localizing with either late endosomes or lysosomes. The pncA mutant showed a 1.5-log reduction of the number of bacteria isolated from mouse spleens after 10 weeks [PMID:12761078]. It indicates that the mutant has reduced virulence in mice. 1089 pyrazinamidase/nicotinamidase pncA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1167147 BR1465 20130611 204722 I protein-coding NCBI-supplied PMID: 12271122 MUTATION: Brucella abortus pnc mutant via mini-Tn5Km2 transposon mutagenesis has intracellular growth defect inside HeLa cells [PMID:15135535]. Nicotinamidasepyrazinamidase mutant (pncA mutant) of Brucella abortus failed to replicate in HeLa cells, and showed a lower rate of intracellular replication than that of wild-type strain in macrophages [PMID:15135535]. The pncA mutant was not co-localizing with either late endosomes or lysosomes. The pncA mutant showed a 1.5-log reduction of the number of bacteria isolated from mouse spleens after 10 weeks [PMID:15135535]. It indicates that the mutant has reduced virulence in mice. 1090 hypothetical protein BR1465 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1167178 BR1495 20140406 204722 I protein-coding NCBI-supplied PMID: 12271122 MUTATION: aspC encodes for an aminotransferase. B.abortus aspC mutant obtained from randomized miniTn5Km2 transposon mutagenesis showed decreased intracellular survival inside HeLa cells. So B. abortus aspC gene is essential for HeLa cell intracellular growth [PMID:12761078]. 1091 aspartate aminotransferase aspC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1167181 BR1498 20140222 204722 I protein-coding NCBI-supplied PMID: 12271122 LysR family transcriptional regulator BR1498 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1167219 BR1536 20140406 204722 I protein-coding NCBI-supplied PMID: 12271122 peptidyl-tRNA hydrolase pth Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1167249 BR1566 20140405 204722 I protein-coding NCBI-supplied PMID: 12271122 2-isopropylmalate synthase leuA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1167334 BR1642 20140217 204722 I protein-coding NCBI-supplied PMID: 12271122 disulfide bond formation protein B BR1642 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1167338 BR1646 20140222 204722 I protein-coding NCBI-supplied PMID: 12271122 base-excision DNA repair protein BR1646 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1167364 BR1671 20140222 204722 I protein-coding NCBI-supplied PMID: 12271122 HlyD family secretion protein BR1671 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1167368 BR1675 20140405 204722 I protein-coding NCBI-supplied PMID: 12271122 deoxyuridine 5'-triphosphate nucleotidohydrolase dut Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1167369 BR1676 20140222 204722 I protein-coding NCBI-supplied PMID: 12271122 AsnC family transcriptional regulator BR1676 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1167437 BR1744 20140405 204722 I protein-coding NCBI-supplied PMID: 12271122 phosphoribosylaminoimidazole carboxylase, catalytic subunit purE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1167474 BR1781 20140405 204722 I protein-coding NCBI-supplied PMID: 12271122 MUTATION: pyc is one B. suis gene identified by signature-tagged mutagenesis. It is essential for survival and mulitplication in macrophages [PMID:10678941]. 1101 pyruvate carboxylase pyc Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1167484 BR1791 20140215 204722 I protein-coding NCBI-supplied PMID: 12271122 branched-chain amino acid ABC transporter permease BR1791 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1167509 BR1816 20140405 204722 I protein-coding NCBI-supplied PMID: 12271122 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase purH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1167606 BR1906 20140405 204722 I protein-coding NCBI-supplied PMID: 12271122 isopropylmalate isomerase large subunit leuC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1167607 BR1907 20130611 204722 I protein-coding NCBI-supplied PMID: 12271122 50S ribosomal protein L19 rplS Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1167630 BR1930 20140406 204722 I protein-coding NCBI-supplied PMID: 12271122 lipoprotein Omp19 omp19 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1167668 BR1967 20111205 204722 I pseudo NCBI-supplied pseudo cysK Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1167684 BR1983 20140405 204722 I protein-coding NCBI-supplied PMID: 12271122 MUTATION: A study with miniTn5 mutants of B. suis constitutively expressing gfp indicates that B. suis lysA gene is required for intracellular multiplication in human macrophage THP-1 cells [PMID:12438693]. 1108 diaminopimelate decarboxylase lysA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1167686 BR1985 20140405 204722 I protein-coding NCBI-supplied PMID: 12271122 hypoxanthine-guanine phosphoribosyltransferase hpt Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1167688 BR1987 20140405 204722 I protein-coding NCBI-supplied PMID: 12271122 histidinol-phosphate aminotransferase hisC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1167788 BR2085 20140405 204722 I protein-coding NCBI-supplied PMID: 12271122 imidazole glycerol phosphate synthase subunit HisF hisF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1167793 BR2090 20140222 204722 I protein-coding NCBI-supplied PMID: 12271122 MUTATION: The two-component BvrSBvrR system is essential for Brucella abortus virulence. Disruption of BvrSBvrR damages the outer membrane, thus contributing to the severe attenuation manifested by bvrS and bvrR mutants. The bvrS and bvrR mutants are avirulent in mice, show reduced invasiveness to epithelial cells and macrophages, and are incapable of inhibiting lysosome fusion and replicating intracellularly [PMID:12218183]. Mutations in the bvrR or bvrS genes hamper the penetration of B abortus in non-phagocytic cells and impairs intracellular trafficking and virulence. BvrRBvrS mutants do not recruit small GTPases of the Rho subfamily required for actin polymerization and penetration to cells. Dysfunction of the BvrRBvrS system alters the outer membrane permeability, the expression of several group 3 outer membrane proteins and the pattern of lipid A acylation. Constructs of virulent B abortus chimeras containing heterologous LPS from the bvrS(-) mutant demonstrated an altered permeability to cationic peptides similar to that of the BvrRBvrS mutants. It is hypothesized that the Brucella BvrRBvrS is a system devoted to the homeostasis of the outer membrane and, therefore in the interface for cell invasion and mounting the required structures for intracellular parasitism [PMID:12218183]. In contrast to S2308 and S19, bvrS and bvrR mutant strains poorly invade HeLa cells and are rapidly targeted to cathepsin D- containing compartments [PMID:12218183]. B abortus bvrS bvrR mutants display reduced invasiveness and virulence [PMID:12218183]. Brucella bvrS and bvrR null mutants are defective in several outer membrane proteins, mainly Omp3a (former Omp25) and Omp3b as well as in the structure of the LPS molecule, but the O chain seems to be intact [PMID:12218183]. Because bvrR and bvrS mutants are also altered in cell-surface hydrophobicity, permeability, and sensitivity to surface- targeted bactericidal peptides, it is proposed that BvrRBvrS controls cell envelope changes necessary to transit between extracellular and intracellular environments [PMID:12218183]. BvrR/BvrS mutants are avirulent in mice, show reduced invasiveness in cells, and are unable to inhibit lysosome fusion and to replicate intracellularly [PMID:12218183]. 1112 DNA-binding response regulator BvrR BR2090 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1167794 BR2091 20140215 204722 I protein-coding NCBI-supplied PMID: 12271122 MUTATION: The two-component BvrSBvrR system is essential for Brucella abortus virulence. Disruption of BvrSBvrR damages the outer membrane, thus contributing to the severe attenuation manifested by bvrS and bvrR mutants. The bvrS and bvrR mutants are avirulent in mice, show reduced invasiveness to epithelial cells and macrophages, and are incapable of inhibiting lysosome fusion and replicating intracellularly [PMID:12218183]. Mutations in the bvrR or bvrS genes hamper the penetration of B abortus in non-phagocytic cells and impairs intracellular trafficking and virulence. BvrRBvrS mutants do not recruit small GTPases of the Rho subfamily required for actin polymerization and penetration to cells. Dysfunction of the BvrRBvrS system alters the outer membrane permeability, the expression of several group 3 outer membrane proteins and the pattern of lipid A acylation. Constructs of virulent B abortus chimeras containing heterologous LPS from the bvrS(-) mutant demonstrated an altered permeability to cationic peptides similar to that of the BvrRBvrS mutants. It is hypothesized that the Brucella BvrRBvrS is a system devoted to the homeostasis of the outer membrane and, therefore in the interface for cell invasion and mounting the required structures for intracellular parasitism [PMID:12218183]. In contrast to S2308 and S19, bvrS and bvrR mutant strains poorly invade HeLa cells and are rapidly targeted to cathepsin D- containing compartments [PMID:12218183]. B abortus bvrS bvrR mutants display reduced invasiveness and virulence [PMID:12218183]. Brucella bvrS and bvrR null mutants are defective in several outer membrane proteins, mainly Omp3a (former Omp25) and Omp3b as well as in the structure of the LPS molecule, but the O chain seems to be intact [PMID:12218183]. Because bvrR and bvrS mutants are also altered in cell-surface hydrophobicity, permeability, and sensitivity to surface- targeted bactericidal peptides, it is proposed that BvrRBvrS controls cell envelope changes necessary to transit between extracellular and intracellular environments [PMID:12218183]. BvrR/BvrS mutants are avirulent in mice, show reduced invasiveness in cells, and are unable to inhibit lysosome fusion and to replicate intracellularly [PMID:12218183]. 1113 sensor histidine kinase BvrS BR2091 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1167828 BR2125 20140215 204722 I protein-coding NCBI-supplied PMID: 12271122 molecular chaperone DnaK dnaK Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1167830 BR2127 20140406 204722 I protein-coding NCBI-supplied PMID: 12271122 MUTATION: The role of Phosphatidylcholine (PC) in Brucella abortus was examined by generating mutants in pcs (BApcs) and pmtA (BApmtA), which encode key enzymes of the two bacterial PC biosynthetic routes, the choline and methyl-transferase pathways. In rich medium, BApcs and the double mutant BApcspmtA but not BApmtA displayed reduced growth, increased phosphatidylethanolamine and no PC, showing that Pcs is essential for PC synthesis under these conditions. In minimal medium, the parental strain, BApcs and BApmtA showed reduced but significant amounts of PC suggesting that PmtA may also be functional Probing with phage Tb, antibiotics, polycations and serum demonstrated that all mutants had altered envelopes. In macrophages, BApcs and BApcspmtA showed reduced ability to evade fusion with lysosomes and establish a replication niche. In mice, BApcs showed attenuation only at early times after infection, BApmtA at later stages and BApcspmtA throughout. The results suggest that Pcs and PmtA have complementary roles in vivo related to nutrient availability and that PC and the membrane properties that depend on this typical eukaryotic phospholipid are essential for Brucella virulence [PMID:16882035]. 1115 phospholipid N-methyltransferase pmtA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1167886 BR2183 20140222 204722 I protein-coding NCBI-supplied PMID: 12271122 formamidopyrimidine-DNA glycosylase mutM Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1172643 YPPCP1.07 20140405 214092 protein-coding NCBI-supplied PMID: 11586360; 17255510; 19589835; 23701256 MUTATION: pla mutant is attenuated in mice [PMID:1439793]. 1117 outer membrane protease pla Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1172651 YPCD1.06 20140215 214092 protein-coding NCBI-supplied PMID: 11586360 MUTATION: yopE mutants are attenuated after oral or intraperitoneal infection in mice, but are not attenuated after intravenous infection in mice [PMID:2191183]. 1118 putative outer membrane virulence protein yopE Bin Zhao, Oliver He yopK WEB: http://www.ncbi.nlm.nih.gov/gene 1172664 YPCD1.19c 20120205 214092 protein-coding NCBI-supplied PMID: 11586360 MUTATION: yopK mutant has an increased LD50 dose in mice, and infected mice died after 5 days as compared to mice infected with the wild type died after just 3 days [PMID:3002984]. 1119 Yop targeting protein - yopQ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1172665 YPCD1.20 20140406 214092 protein-coding NCBI-supplied PMID: 11586360 Yop targeted effector yopT Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1172671 YPCD1.26c 20140222 214092 protein-coding NCBI-supplied PMID: 11586360 MUTATION: yopM mutant is attenuated in mice compared to the wild type [PMID:2401564]. 1121 secreted effector protein yopM Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1172673 YPCD1.28c 20140406 214092 protein-coding NCBI-supplied PMID: 11586360 MUTATION: yopD mutants are unable to induce cytotoxicity in HeLa cells [PMID:1937815]. 1122 secreted effector protein yopD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1172674 YPCD1.29c 20130508 214092 protein-coding NCBI-supplied PMID: 11586360 MUTATION: yopB mutant is avirulent in mouse model, fails to elicit a cytotoxic response in cultured HeLa cells and is unable to inhibit phagocytosis by macrophage-like J774 cells [PMID:8918459]. 1123 secreted effector protein yopB Bin Zhao, Oliver He lcrH WEB: http://www.ncbi.nlm.nih.gov/gene 1172675 YPCD1.30c 20140406 214092 protein-coding NCBI-supplied PMID: 11586360 MUTATION: lcrH mutant is avirulent in mice [PMID:2707857]. 1124 secretion chaperone - sycD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1172676 YPCD1.31c 20111126 214092 protein-coding NCBI-supplied PMID: 11586360; 18854239; 19249344 MUTATION: lcrV mutants are avirulent in mice [PMID:7730287]. 1125 secreted effector protein lcrV Bin Zhao, Oliver He lcrF WEB: http://www.ncbi.nlm.nih.gov/gene 1172694 YPCD1.49 20130508 214092 protein-coding NCBI-supplied PMID: 11586360 MUTATION: lcrF mutant is attenuated in mice [PMID:14742535]. 1126 transcriptional regulator - virF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1172712 YPCD1.67c 20140222 214092 protein-coding NCBI-supplied PMID: 11586360; 20565713 MUTATION: yopH mutants are unable to resist phagocytosis by J774 cells, while wild type Yersinia is able to resist phagocytosis [PMID:8809758]. 1127 putative secreted protein-tyrosine phosphatase yopH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1172717 YPCD1.72c 20140217 214092 protein-coding NCBI-supplied PMID: 11586360 MUTATION: ypkA mutants of Y. pseudotuberculosis are attenuated in mice [PMID:8441468]. 1128 secreted protein kinase ypkA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1172837 YPMT1.82 20140217 214092 protein-coding NCBI-supplied PMID: 11274119; 11586360 MUTATION: caf1M mutants are attenuated in mice [PMID:14711524]. 1129 putative F1 chaperone protein caf1M Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1172838 YPMT1.83 20140217 214092 protein-coding NCBI-supplied PMID: 11274119; 11586360 MUTATION: caf1A mutants are attenuated in mice [PMID:14711524]. 1130 putative F1 capsule anchoring protein caf1A Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1172888 YPO0038 20130905 214092 protein-coding NCBI-supplied PMID: 11586360; 12834539; 19055764 MUTATION: relA spoT deletion mutants are attenuated in mice [PMID:19701461]. 1131 bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase spoT Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1173000 YPO0154 20140222 214092 protein-coding NCBI-supplied PMID: 11586360; 12834539; 19055764 MUTATION: dam mutant is attenuated in mice [PMID:16188402]. 1132 DNA adenine methylase dam Bin Zhao, Oliver He csm WEB: http://www.ncbi.nlm.nih.gov/gene 1173020 YPO0175 20140222 214092 protein-coding NCBI-supplied PMID: 11586360; 12834539; 19055764; 19703315; 21345179 MUTATION: crp mutant is attenuated in mice [PMID:20086087]. 1133 cAMP-regulatory protein - crp Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1173219 YPO0373 20130526 214092 protein-coding NCBI-supplied PMID: 11586360; 12834539; 19055764; 22924957 MUTATION: hfq mutant is highly attenuated in mice after subcutaneous or intravenous injection and has attenuated survival in macrophages [PMID:19593436]. 1134 RNA-binding protein Hfq hfq Bin Zhao, Oliver He cpxC dye fexA msp seg sfrA WEB: http://www.ncbi.nlm.nih.gov/gene 1173302 YPO0458 20130905 214092 protein-coding NCBI-supplied PMID: 11586360; 12834539; 19055764 MUTATION: arcA mutant is attenuated in mice [PMID:14742535]. 1135 two-component response regulator - arcA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1173841 YPO1003 20130526 214092 protein-coding NCBI-supplied PMID: 11586360; 12834539; 19055764 MUTATION: YPO1003 mutant is attenuated in mice [PMID:14742535]. 1136 hypothetical protein YPO1003 Bin Zhao, Oliver He polC WEB: http://www.ncbi.nlm.nih.gov/gene 1173899 YPO1059 20140406 214092 protein-coding NCBI-supplied PMID: 11586360; 12834539; 19055764 MUTATION: dnaE mutant is attenuated in mice [PMID:14742535]. 1137 DNA polymerase III subunit alpha - dnaE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1173948 YPOs04 20111205 214092 miscRNA NCBI-supplied PMID: 20065026 MUTATION: smpB ssrA mutant is attenuated in mice [PMID:20065026]. 1138 miscRNA ssrA Bin Zhao, Oliver He smqB WEB: http://www.ncbi.nlm.nih.gov/gene 1173949 YPO1101 20140406 214092 protein-coding NCBI-supplied PMID: 11586360; 12834539; 19055764; 20065026 MUTATION: smpB ssrA mutant is attenuated in mice [PMID:20065026]. 1139 SsrA-binding protein - smpB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1174028 YPO1179 20140222 214092 protein-coding NCBI-supplied PMID: 11586360; 12834539; 19055764 MUTATION: YPO1179 mutant is attenuated in mice [PMID:14742535]. 1140 hypothetical protein YPO1179 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1174143 YPO1301 20140217 214092 protein-coding NCBI-supplied PMID: 11586360; 12834539; 19055764 MUTATION: psaE mutants are attenuated in mice [PMID:2164509]. 1141 regulatory protein psaE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1174145 YPO1303 20140217 214092 protein-coding NCBI-supplied PMID: 11586360; 12834539; 19055764 MUTATION: psaA mutants have a 100-fold reduced 50% lethal dose in mice [PMID:2164509]. 1142 pH 6 antigen (antigen 4) (adhesin) psaA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1174228 YPO1387 20140406 214092 protein-coding NCBI-supplied PMID: 11586360; 12834539; 19055764 MUTATION: yadBC mutant (yadB is YPO1387) is attenuated in mice and is less invasive to HeLa cells than the wildtype [PMID:18025093]. 1143 hypothetical protein YPO1387 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1174229 YPO1388 20140217 214092 protein-coding NCBI-supplied PMID: 11586360; 12834539; 19055764 MUTATION: yadBC (yadC is YPO1388) mutant is attenuated in mice and is less invasive of HeLa cells than the wild-type [PMID:18025093]. 1144 hypothetical protein YPO1388 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1174473 YPO1634 20140222 214092 protein-coding NCBI-supplied PMID: 11586360; 12834539; 15710615; 16790745; 19055764 MUTATION: phoP mutants have a reduced ability to survive in J774 macrophage cell cultures and under conditions of low pH and oxidative stress in vitro. The mean lethal dose of the phoP mutant in mice was increased 75-fold in comparison with that of the wild-type strain [PMID:10816493]. 1145 DNA-binding transcriptional regulator PhoP phoP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1174499 YPO1660 20140215 214092 protein-coding NCBI-supplied PMID: 11586360; 12834539; 19055764 MUTATION: mgtC mutants are defective in early intracellular survival in macrophages compared to wild type Y. pestis [PMID:16790745]. 1146 Mg(2+) transport ATPase protein C mgtC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1174696 YPO1860 20140222 214092 protein-coding NCBI-supplied PMID: 11586360; 12834539; 19055764 MUTATION: a Y. pestis ail deletion mutant was rapidly killed by sera from all mammals tested except mice [PMID:18025094]. 1147 attachment invasion locus protein ail Bin Zhao, Oliver He psn WEB: http://www.ncbi.nlm.nih.gov/gene 1174745 YPO1906 20140215 214092 protein-coding NCBI-supplied PMID: 11586360; 12834539; 19055764 MUTATION: psn mutant is unable to grow on iron-deficient media at 37 degrees C [PMID:7896707]. 1148 pesticin/yersiniabactin receptor protein - fyuA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1174750 YPO1911 20140222 214092 protein-coding NCBI-supplied PMID: 11586360; 12834539; 19055764 MUTATION: irp2 mutants are unable to grow at 37 degrees in iron deficient media [PMID:7896707]. 1149 yersiniabactin biosynthetic protein irp2 Bin Zhao, Oliver He ybtP WEB: http://www.ncbi.nlm.nih.gov/gene 1174752 YPO1913 20140222 214092 protein-coding NCBI-supplied PMID: 11586360; 12834539; 19055764 MUTATION: ybtP mutant is avirulent in mouse bubonic plague model [PMID:10231486]. 1150 lipoprotein inner membrane ABC transporter - irp6 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1174831 YPO1994 20130905 214092 protein-coding NCBI-supplied PMID: 11586360; 12834539; 19055764 MUTATION: YPO1994 mutant is attenuated in mice [PMID:14742535]. 1151 hypothetical protein YPO1994 MUTATION: YPO2027 mutant is attenuated in mice [PMID:14742535]. 1152 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1174901 YPO2063 20140405 214092 protein-coding NCBI-supplied PMID: 11586360; 12834539; 19055764; 23275092 MUTATION: lpxM (msbB) mutant is avirulent in mice and guinea pigs [PMID:17913308]. 1153 lipid A biosynthesis (KDO)2-(lauroyl)-lipid IVA acyltransferase msbB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1175024 YPO2190 20140222 214092 protein-coding NCBI-supplied PMID: 11586360; 12834539; 19055764 MUTATION: a Y. pestis ail deletion mutant was rapidly killed by sera from all mammals tested except mice [PMID:18025094]. 1154 attachment invasion locus protein ail Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1175206 YPO2374 20140215 214092 protein-coding NCBI-supplied PMID: 11586360; 12834539; 19055764 MUTATION: slyA (rovA) mutant is attenuated in mice [PMID:16938880]. 1155 transcriptional regulator SlyA slyA Bin Zhao, Oliver He mlpA WEB: http://www.ncbi.nlm.nih.gov/gene 1175228 YPO2394 20140215 214092 protein-coding NCBI-supplied PMID: 11586360; 12834539; 19055764; 19589835 MUTATION: lpp deletion mutant is attenuated in mice [PMID:19737605]. 1156 major outer membrane lipoprotein - lpp Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1175273 YPO2439 20140222 214092 protein-coding NCBI-supplied PMID: 11586360; 12834539; 19055764 MUTATION: yfeAB mutant is attenuated when given subcutaneously to mice and is avirulent when given to mice intravenously [PMID:10231495]. 1157 substrate-binding protein yfeA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1175274 YPO2440 20140222 214092 protein-coding NCBI-supplied PMID: 11586360; 12834539; 19055764 MUTATION: yfeAB mutant is attenuated when given subcutaneously to mice and is avirulent when given to mice intravenously [PMID:10231495]. 1158 ATP-binding transport protein yfeB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1175305 YPO2471 20130526 214092 protein-coding NCBI-supplied PMID: 11586360; 12834539; 19055764 MUTATION: YPO2471 mutant is attenuated in mice [PMID:14742535]. 1159 hypothetical protein YPO2471 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1175340 YPO2506 20130526 214092 protein-coding NCBI-supplied PMID: 11586360; 12834539; 19055764; 20837715 MUTATION: ompX mutants are attenuated in their ability to attach to and invade HeLa cells [PMID:17768237]. 1160 outer membrane protein X ompX Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1175516 YPO2686 20140406 214092 protein-coding NCBI-supplied PMID: 11586360; 12834539; 19055764 MUTATION: pgm mutant of Y. pestis is attenuated in mice [PMID:12009274]. 1161 phosphoglucomutase pgm Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1175620 YPO2793 20130905 214092 protein-coding NCBI-supplied PMID: 11586360; 12834539; 19055764 MUTATION: YPO2793 mutant is attenuated in mice [PMID:14742535]. 1162 hypothetical protein YPO2793 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1175694 YPO2870 20140329 214092 protein-coding NCBI-supplied PMID: 11586360; 12834539; 19055764 MUTATION: guaBA operon mutant is highly attenuated in mice [PMID:20096773]. 1163 GMP synthase guaA Bin Zhao, Oliver He guaR WEB: http://www.ncbi.nlm.nih.gov/gene 1175695 YPO2871 20140322 214092 protein-coding NCBI-supplied PMID: 11586360; 12834539; 19055764 MUTATION: guaBA operon mutant is highly attenuated in mice [PMID:20096773]. 1164 inosine 5'-monophosphate dehydrogenase - guaB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1175729 YPO2905 20140222 214092 protein-coding NCBI-supplied PMID: 11586360; 12834539; 19055764; 20883662; 21969002; 22078566 MUTATION: a Y. pestis ail deletion mutant was rapidly killed by sera from all mammals tested except mice [PMID:18025094]. 1165 attachment invasion locus protein ail Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1175766 YPO2947 20140222 214092 protein-coding NCBI-supplied PMID: 11586360; 12834539; 19055764 MUTATION: YPO2947 mutant is attenuated in mice [PMID:14742535]. 1166 hypothetical protein YPO2947 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1175866 YPO3045 20140222 214092 protein-coding NCBI-supplied PMID: 11586360; 12834539; 19055764 MUTATION: YP03045 mutant is attenuated in mice [PMID:14742535]. 1167 hypothetical protein ybcI Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1175898 YPO3077 20140406 214092 protein-coding NCBI-supplied PMID: 11586360; 12834539; 19055764 MUTATION: purK mutant is attenuated in mice [PMID:14742535]. 1168 phosphoribosylaminoimidazole carboxylase ATPase subunit purK Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1176173 YPO3356 20140215 214092 protein-coding NCBI-supplied PMID: 11586360; 12834539; 19055764 MUTATION: nlpD mutant is attenuated in mice [PMID:19759820]. 1169 lipoprotein NlpD nlpD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1176174 YPO3357 20140222 214092 protein-coding NCBI-supplied PMID: 11586360; 12834539; 19055764 MUTATION: pcm mutant is attenuated in mice [PMID:14742535]. 1170 protein-L-isoaspartate O-methyltransferase pcm Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1176197 YPO3380 20140406 214092 protein-coding NCBI-supplied PMID: 11586360; 12834539; 19055764 MUTATION: relA spoT deletion mutants are attenuated in mice [PMID:19701461]. 1171 GDP/GTP pyrophosphokinase relA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1176215 YPO3398 20140215 214092 protein-coding NCBI-supplied PMID: 11586360; 12834539; 19055764 MUTATION: yadBC double mutant is less invasive of HeLa cells compared to the wild type and decreased virulence in bubonic plague in mice [PMID:18025093]. 1172 glutamyl-Q tRNA(Asp) synthetase yadB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1176324 YPO3505 20140222 214092 protein-coding NCBI-supplied PMID: 11586360; 12834539; 19055764 MUTATION: greA mutants are attenuated in mice [PMID:14742535]. 1173 transcription elongation factor GreA greA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1176554 YPO3728 20140406 214092 protein-coding NCBI-supplied PMID: 11586360; 12834539; 19055764 MUTATION: purH mutant is attenuated in mice [PMID:14742535]. 1174 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase purH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1176811 YPO3973 20140215 214092 protein-coding NCBI-supplied PMID: 11586360; 12834539; 19055764 MUTATION: YPO3973 mutant is attenuated in mice [PMID:14742535]. 1175 metalloprotease YPO3973 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1176822 YPO3984 20140301 214092 protein-coding NCBI-supplied PMID: 11586360; 12834539; 18936182; 19055764; 23701256 MUTATION: yapE mutant is attenuated in mice and has impaired colonization in bubonic plague model [PMID:18936182]. 1176 autotransporter protein yapE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1194858 BB_0022 20140322 224326 protein-coding NCBI-supplied PMID: 9403685 MUTATION: mutant showed attenuated virulence in C3H/HeN mice [PMID:19997622]. 4190 Holliday junction DNA helicase RuvB ruvB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1194859 BB_0023 20140215 224326 protein-coding NCBI-supplied PMID: 9403685 MUTATION: mutant showed attenuated virulence in C3H/HeN mice [PMID:19997622]. 4191 Holliday junction DNA helicase RuvA ruvA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1194934 BB_0098 20140406 224326 protein-coding NCBI-supplied PMID: 9403685 MUTATION: mutant showed attenuated virulence in C3H/HeN mice [PMID:19997622]. 4192 recombination and DNA strand exchange inhibitor protein BB_0098 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1194988 BB_0153 20131127 224326 protein-coding NCBI-supplied PMID: 9403685; 19040638 MUTATION: sodA mutant showed complete attenuation in C3H/HeN mice compared with control strains [PMID:19040638]. 4193 superoxide dismutase [Mn] (General stress protein 24)(GSP24) BB_0153 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1195033 BB_0198 20131127 224326 protein-coding NCBI-supplied PMID: 9403685 MUTATION: rel(Bbu) deletion mutant eliminated virulence in mice [PMID:16041012]. 4194 guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase BB_0198 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1195047 BB_0210 20140406 224326 protein-coding NCBI-supplied PMID: 9403685; 20696833 MUTATION: deletion severely impaired mutant's ability to persist and induce disease in murine tissues [PMID:19266024]. 4195 hypothetical protein BB_0210 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1195056 BB_0219 20140222 224326 protein-coding NCBI-supplied PMID: 9403685 MUTATION: bmtA mutant attenuated in mice [PMID:19218460]. 4196 gufA protein BB_0219 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1195105 BB_0268 20140322 224326 protein-coding NCBI-supplied PMID: 9403685; 20815822 MUTATION: mutant not infectious in murine model [PMID:20815822]. 4197 hypothetical protein BB_0268 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1195160 BB_0323 20130614 224326 protein-coding NCBI-supplied PMID: 9403685 MUTATION: deletion mutant unable to infect mice or ticks [PMID:19754308] 4198 hypothetical protein BB_0323 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1195200 BB_0363 20140222 224326 protein-coding NCBI-supplied PMID: 9403685; 20444101 MUTATION: mutant not infectious in mice, showed decreased motility [PMID:20444101]. 4199 hypothetical protein BB_0363 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1195655 BB_0797 20140322 224326 protein-coding NCBI-supplied PMID: 9403685 MUTATION: mutant showed attenuated virulence in C3H/HeN mice [PMID:19997622]. 4200 DNA mismatch repair protein MutS mutS Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1195778 BMEI0066 20140217 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122; 19742243 MUTATION: BMEI0066 deletion mutant fails to replicated in murine macrophages and is rapidly cleared from the spleens of experimentally infected BALB/c mice [PMID:19742243]. 4890 two component response regulator BMEI0066 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1195794 BMEI0082 20140329 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 hypoxanthine-guanine phosphoribosyltransferase BMEI0082 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1195796 BMEI0084 20140405 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 MUTATION: A study with miniTn5 mutants of B. suis constitutively expressing gfp indicates that B. suis lysA gene is required for intracellular multiplication in human macrophage THP-1 cells [PMID:12438693]. 1203 diaminopimelate decarboxylase BMEI0084 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1195797 BMEI0085 20140222 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 hypothetical protein BMEI0085 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1195847 BMEI0135 20140406 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 outer membrane lipoprotein BMEI0135 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1195868 BMEI0156 20130611 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 50S ribosomal protein L19 rplS Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1195869 BMEI0157 20140405 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 isopropylmalate isomerase large subunit BMEI0157 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1195881 BMEI0169 20140222 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 GntR family transcriptional regulator BMEI0169 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1195902 BMEI0190 20140217 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 phosphoenolpyruvate-protein phosphotransferase PTSP BMEI0190 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1195945 BMEI0233 20140405 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase purH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1195970 BMEI0258 20140406 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 high-affinity branched-chain amino acid transport system permease livH BMEI0258 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1195978 BMEI0266 20140405 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 MUTATION: pyc is one B. suis gene identified by signature-tagged mutagenesis. It is essential for survival and mulitplication in macrophages [PMID:10678941]. 1212 pyruvate carboxylase BMEI0266 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1195979 BMEI0267 20140217 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 hypothetical protein BMEI0267 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1195987 BMEI0275 20130518 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 ATP-dependent DNA helicase BMEI0275 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196007 BMEI0296 20140405 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 phosphoribosylaminoimidazole carboxylase catalytic subunit BMEI0296 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196016 BMEI0305 20140215 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 DeoR family transcriptional regulator BMEI0305 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196031 BMEI0320 20140217 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 GntR family transcriptional regulator BMEI0320 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196068 BMEI0357 20140217 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 AsnC family transcriptional regulator BMEI0357 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196069 BMEI0358 20140329 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 deoxyuridine 5'-triphosphate nucleotidohydrolase dut Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196070 BMEI0359 20140217 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 periplasmic protein of efflux system BMEI0359 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196093 BMEI0382 20140222 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 DNA-3-methyladenine glycosidase BMEI0382 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196095 BMEI0384 20140215 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 disulfide bond formation protein B BMEI0384 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196141 BMEI0430 20140406 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 nodulation protein NOLR BMEI0430 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196144 BMEI0433 20140329 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 periplasmic dipeptide transport protein BMEI0433 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196162 BMEI0451 20140405 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 2-isopropylmalate synthase BMEI0451 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196166 BMEI0455 20140215 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 glutathione S-transferase BMEI0455 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196191 BMEI0480 20140406 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 peptidyl-tRNA hydrolase BMEI0480 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196220 BMEI0509 20130526 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 lipopolysaccharide core biosynthesis mannosyltransferase LPCC BMEI0509 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196223 BMEI0512 20140405 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 thioredoxin reductase BMEI0512 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196224 BMEI0513 20140222 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 LysR family transcriptional regulator BMEI0513 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196227 BMEI0516 20140405 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 MUTATION: aspC encodes for an aminotransferase. B.abortus aspC mutant obtained from randomized miniTn5Km2 transposon mutagenesis showed decreased intracellular survival inside HeLa cells. So B. abortus aspC gene is essential for HeLa cell intracellular growth [PMID:12761078]. 1231 aspartate aminotransferase BMEI0516 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196237 BMEI0526 20140406 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 carbamoyl phosphate synthase small subunit BMEI0526 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196256 BMEI0545 20130518 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 MUTATION: Brucella abortus pnc mutant via mini-Tn5Km2 transposon mutagenesis has intracellular growth defect inside HeLa cells [PMID:15135535]. Nicotinamidasepyrazinamidase mutant (pncA mutant) of Brucella abortus failed to replicate in HeLa cells, and showed a lower rate of intracellular replication than that of wild-type strain in macrophages [PMID:15135535]. The pncA mutant was not co-localizing with either late endosomes or lysosomes. The pncA mutant showed a 1.5-log reduction of the number of bacteria isolated from mouse spleens after 10 weeks [PMID:15135535]. It indicates that the mutant has reduced virulence in mice. 1233 hypothetical protein BMEI0545 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196316 BMEI0605 20140217 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 bicyclomycin resistance protein BMEI0605 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196326 BMEI0615 20140405 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 MUTATION: A study with miniTn5 mutants of B. suis constitutively expressing gfp indicates that B. suis serB gene is required for intracellular multiplication in human macrophage THP-1 cells [PMID:12438693]. 1235 phosphoserine phosphatase BMEI0615 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196327 BMEI0616 20140405 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 tRNA delta(2)-isopentenylpyrophosphate transferase miaA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196328 BMEI0617 20140405 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 acetolactate synthase 3 catalytic subunit BMEI0617 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196335 BMEI0624 20140405 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 ketol-acid reductoisomerase BMEI0624 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196337 BMEI0626 20130518 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 GntR family transcriptional regulator BMEI0626 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196382 BMEI0671 20130526 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 integral membrane protein / hemolysin BMEI0671 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196416 BMEI0705 20140405 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 cobyrinic acid a,c-diamide synthase BMEI0705 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196436 BMEI0725 20140405 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 homoserine dehydrogenase BMEI0725 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196441 BMEI0730 20140222 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 lactoylglutathione lyase BMEI0730 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196492 BMEI0781 20140405 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 DNA-directed RNA polymerase subunit alpha BMEI0781 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196498 BMEI0787 20140405 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 recombinase A recA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196538 BMEI0827 20140329 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 undecaprenyl pyrophosphate synthase BMEI0827 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196556 BMEI0845 20140215 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 peptidyl-prolyl cis-trans isomerase D BMEI0845 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196578 BMEI0867 20140406 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 MUTATION: The NtrY protein is a sensor of an ntr-related regulon which may be part of the glnALG operon. This mutant has a weakly attenuated phenotype (reduction of 1.2 log units versus the wild type at 48 h postinfection) which could be explained by a pleiotropic effect on the ntr regulon, since the ntrC mutant did not show such a phenotype [PMID:10678941]. 1248 nitrogen regulation protein NTRY BMEI0867 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196583 BMEI0872 20130611 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 RNA-binding protein Hfq hfq Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196587 BMEI0876 20130518 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 ATP-dependent protease LA BMEI0876 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196589 BMEI0878 20140215 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 excinuclease ABC subunit A uvrA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196592 BMEI0881 20140222 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 GntR family transcriptional regulator BMEI0881 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196609 BMEI0898 20140222 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 acyl-CoA transferase BMEI0898 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196644 BMEI0933 20140405 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 cysteine synthase A BMEI0933 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196690 BMEI0979 20140405 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 MUTATION: A study with miniTn5 mutants of B. suis constitutively expressing gfp indicates that B. suis glnA gene is required for intracellular multiplication in human macrophage THP-1 cells [PMID:12438693]. 1255 glutamine synthetase BMEI0979 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196708 BMEI0997 20140222 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 mannosyltransferase BMEI0997 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196730 BMEI1019 20140322 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 molybdenum cofactor biosynthesis protein A moaA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196751 BMEI1040 20140222 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 ABC transporter ATP-binding protein BMEI1040 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196754 BMEI1043 20140322 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 NifS protein BMEI1043 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196767 BMEI1056 20140215 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 N-acetylmuramoyl-L-alanine amidase BMEI1056 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196771 BMEI1060 20140215 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 hypothetical protein BMEI1060 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196780 BMEI1069 20140222 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 trigger factor tig Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196815 BMEI1104 20140215 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 arginine/ornithine-binding periplasmic protein precursor BMEI1104 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196827 BMEI1116 20140405 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 ribulose-phosphate 3-epimerase BMEI1116 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196838 BMEI1127 20140329 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 phosphoribosylformylglycinamidine synthase II BMEI1127 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196903 BMEI1192 20140406 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 serine hydroxymethyltransferase BMEI1192 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196940 BMEI1229 20130611 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 exonuclease BMEI1229 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196948 BMEI1237 20140405 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 UDP-glucose 4-epimerase BMEI1237 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196951 BMEI1240 20140329 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 phosphoribosylaminoimidazole synthetase BMEI1240 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196952 BMEI1241 20140405 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 MUTATION: B. abortus purN gene is essential for intracellular growth in HeLa cells as shown from transposon mutagenesis study [PMID:12761078]. 1270 phosphoribosylglycinamide formyltransferase purN Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196960 BMEI1249 20140405 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 hypothetical protein BMEI1249 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196969 BMEI1258 20140215 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 ABC transporter ATP-binding protein BMEI1258 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1196992 BMEI1281 20140322 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 dihydroorotase BMEI1281 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197007 BMEI1296 20140215 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase BMEI1296 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197037 BMEI1326 20140406 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 hypothetical protein BMEI1326 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197041 BMEI1330 20140222 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 protease Do BMEI1330 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197047 BMEI1336 20140222 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 sensor protein PHOQ BMEI1336 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197048 BMEI1337 20140405 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 transcriptional regulatory protein PhoP BMEI1337 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197050 BMEI1339 20120912 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 hypothetical protein BMEI1339 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197072 BMEI1361 20120912 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 hypothetical protein BMEI1361 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197104 BMEI1393 20140222 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 mannosyltransferase BMEI1393 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197107 BMEI1396 20140405 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 phosphomannomutase BMEI1396 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197115 BMEI1404 20140217 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 mannosyltransferase BMEI1404 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197124 BMEI1413 20140406 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 GDP-mannose 4,6-dehydratase BMEI1413 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197125 BMEI1414 20140406 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 perosamine synthetase BMEI1414 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197137 BMEI1426 20140222 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 undecaprenyl-phosphate alpha-N-acetylglucosaminyltransferase BMEI1426 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197151 BMEI1440 20140215 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 thiol:disulfide interchange protein DsbA BMEI1440 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197154 BMEI1443 20140405 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 2-haloalkanoic acid dehalogenase BMEI1443 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197159 BMEI1448 20140222 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 c-di-GMP phosphodiesterase A-related protein BMEI1448 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197161 BMEI1450 20140405 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 threonine synthase BMEI1450 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197179 BMEI1468 20130526 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 TLDD protein BMEI1468 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197199 BMEI1488 20140405 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 MUTATION: A B. suis purF mutation experiment suggests that the purine biosynthesis pathway contributes to intracellular growth [PMID:12761078]. 1292 amidophosphoribosyltransferase BMEI1488 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197209 BMEI1498 20140405 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 1-deoxy-D-xylulose-5-phosphate synthase BMEI1498 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197217 BMEI1506 20140405 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 chorismate synthase BMEI1506 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197230 BMEI1519 20140405 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 phosphoribosylamine--glycine ligase BMEI1519 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197242 BMEI1531 20140222 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 hypothetical protein BMEI1531 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197264 BMEI1553 20140222 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 MUTATION: B abortus bacA mutant exhibited decreased survival in macrophages and greatly accelerated clearance from experimentally infected mice compared to the virulent parental strain [PMID:12270820]. R meliloti bacA gene encodes a putative cytoplasmic membrane transport protein required for symbiosis [PMID:12270820]. The BacA protein is essential for the long-term survival of Sinorhizobium meliloti and Brucella abortus within acidic compartments in plant and animal cells , respectively. Mutation study showed that B. abortus BacA affects the distribution of LPS fatty acids, including a very-long-chain fatty acid thought to be unique to the alpha-proteobacteria[PMID:12270820]. 1297 transporter BMEI1553 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197284 BMEI1573 20140222 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 LysR family transcriptional regulator BMEI1573 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197317 BMEI1606 20140215 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 sensory transduction histidine kinase BMEI1606 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197322 BMEI1611 20140329 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 MUTATION: B. suis pyrD mutation study indicated that pyrimidine synthesis pathway contributes to intracellular growth [PMID:12761078]. 1300 dihydroorotate dehydrogenase 2 BMEI1611 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197347 BMEI1636 20140405 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 glucose-6-phosphate isomerase pgi Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197369 BMEI1658 20130611 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 hypothetical protein BMEI1658 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197379 BMEI1668 20140405 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 histidinol dehydrogenase hisD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197424 BMEI1713 20140215 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 maltose ABC transporter ATP-binding protein BMEI1713 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197453 BMEI1742 20130508 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 ABC transporter ATP-binding protein BMEI1742 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197470 BMEI1759 20140405 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 B12-dependent methionine synthase metH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197477 BMEI1766 20140405 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 sulfite reductase (ferredoxin) BMEI1766 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197497 BMEI1786 20140406 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 nitrogen regulatory IIA protein BMEI1786 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197515 BMEI1804 20140215 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 PII uridylyl-transferase BMEI1804 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197520 BMEI1809 20140215 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 hypothetical protein BMEI1809 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197548 BMEI1837 20130518 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 cellobiose-phosphorylase BMEI1837 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197555 BMEI1844 20140406 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 hypothetical protein BMEI1844 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197559 BMEI1848 20140405 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 dihydroxy-acid dehydratase BMEI1848 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197560 BMEI1849 20140222 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 thiol:disulfide interchange protein CYCY precursor BMEI1849 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197570 BMEI1859 20130526 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 hypothetical protein BMEI1859 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197590 BMEI1879 20130526 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 hypothetical protein BMEI1879 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197597 BMEI1886 20140405 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 MUTATION: Brucella pgm encodes the phosphoglucomutase. The B. abortus pgm mutant (B2211) lacks the O antigen. However, the core region of the mutant LPS migrated in Tricine-PAGE electrophoresis in a position that was indistinguishable from that of the wild type core. Although the exponential intracellular replication of the pgm mutant was delayed by approximately 20 h with respect to that of the wild type, the high number of recoverable bacteria at 48 h postinfection indicates that mutant strain B2211 replicates inside HeLa host cells [PMID:12525425]. B abortus phosphoglucomutase (pgm) insertional mutants were attenuated in vivo but not in vitro [PMID:12525425]. 1317 phosphoglucomutase BMEI1886 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197613 BMEI1902 20140215 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 molybdopterin biosynthesis protein BMEI1902 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197624 BMEI1913 20140222 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 LysR family transcriptional regulator BMEI1913 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197626 BMEI1915 20140222 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 MUTATION: rpsA is a B. suis gene identified by signature-tagged mutagenesis [PMID:10678941]. 1320 30S ribosomal protein S1 rpsA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197657 BMEI1946 20140406 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 formamidopyrimidine-DNA glycosylase BMEI1946 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197713 BMEI2002 20140217 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 molecular chaperone DnaK dnaK Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197746 BMEI2035 20140217 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 MUTATION: The two-component BvrSBvrR system is essential for Brucella abortus virulence. Disruption of BvrSBvrR damages the outer membrane, thus contributing to the severe attenuation manifested by bvrS and bvrR mutants. The bvrS and bvrR mutants are avirulent in mice, show reduced invasiveness to epithelial cells and macrophages, and are incapable of inhibiting lysosome fusion and replicating intracellularly [PMID:11401996]. Mutations in the bvrR or bvrS genes hamper the penetration of B abortus in non-phagocytic cells and impairs intracellular trafficking and virulence. BvrRBvrS mutants do not recruit small GTPases of the Rho subfamily required for actin polymerization and penetration to cells. Dysfunction of the BvrRBvrS system alters the outer membrane permeability, the expression of several group 3 outer membrane proteins and the pattern of lipid A acylation. Constructs of virulent B abortus chimeras containing heterologous LPS from the bvrS(-) mutant demonstrated an altered permeability to cationic peptides similar to that of the BvrRBvrS mutants. It is hypothesized that the Brucella BvrRBvrS is a system devoted to the homeostasis of the outer membrane and, therefore in the interface for cell invasion and mounting the required structures for intracellular parasitism [PMID:11401996]. In contrast to S2308 and S19, bvrS and bvrR mutant strains poorly invade HeLa cells and are rapidly targeted to cathepsin D- containing compartments [PMID:11401996]. B abortus bvrS bvrR mutants display reduced invasiveness and virulence [PMID:11401996]. Brucella bvrS and bvrR null mutants are defective in several outer membrane proteins, mainly Omp3a (former Omp25) and Omp3b as well as in the structure of the LPS molecule, but the O chain seems to be intact [PMID:11401996]. Because bvrR and bvrS mutants are also altered in cell-surface hydrophobicity, permeability, and sensitivity to surface- targeted bactericidal peptides, it is proposed that BvrRBvrS controls cell envelope changes necessary to transit between extracellular and intracellular environments [PMID:11401996]. BvrR/BvrS mutants are avirulent in mice, show reduced invasiveness in cells, and are unable to inhibit lysosome fusion and to replicate intracellularly [PMID:11401996]. 1323 sensor protein CHVG BMEI2035 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197747 BMEI2036 20140222 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 MUTATION: The two-component BvrSBvrR system is essential for Brucella abortus virulence. Disruption of BvrSBvrR damages the outer membrane, thus contributing to the severe attenuation manifested by bvrS and bvrR mutants. The bvrS and bvrR mutants are avirulent in mice, show reduced invasiveness to epithelial cells and macrophages, and are incapable of inhibiting lysosome fusion and replicating intracellularly [PMID:11401996]. Mutations in the bvrR or bvrS genes hamper the penetration of B abortus in non-phagocytic cells and impairs intracellular trafficking and virulence. BvrRBvrS mutants do not recruit small GTPases of the Rho subfamily required for actin polymerization and penetration to cells. Dysfunction of the BvrRBvrS system alters the outer membrane permeability, the expression of several group 3 outer membrane proteins and the pattern of lipid A acylation. Constructs of virulent B abortus chimeras containing heterologous LPS from the bvrS(-) mutant demonstrated an altered permeability to cationic peptides similar to that of the BvrRBvrS mutants. It is hypothesized that the Brucella BvrRBvrS is a system devoted to the homeostasis of the outer membrane and, therefore in the interface for cell invasion and mounting the required structures for intracellular parasitism [PMID:11401996]. In contrast to S2308 and S19, bvrS and bvrR mutant strains poorly invade HeLa cells and are rapidly targeted to cathepsin D- containing compartments [PMID:11401996]. B abortus bvrS bvrR mutants display reduced invasiveness and virulence [PMID:11401996]. Brucella bvrS and bvrR null mutants are defective in several outer membrane proteins, mainly Omp3a (former Omp25) and Omp3b as well as in the structure of the LPS molecule, but the O chain seems to be intact [PMID:11401996]. Because bvrR and bvrS mutants are also altered in cell-surface hydrophobicity, permeability, and sensitivity to surface- targeted bactericidal peptides, it is proposed that BvrRBvrS controls cell envelope changes necessary to transit between extracellular and intracellular environments [PMID:11401996]. BvrR/BvrS mutants are avirulent in mice, show reduced invasiveness in cells, and are unable to inhibit lysosome fusion and to replicate intracellularly [PMID:11401996]. 1324 transcriptional regulatory protein chvI BMEI2036 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197752 BMEI2041 20140405 224914 I protein-coding NCBI-supplied PMID: 11756688; 12271122 imidazole glycerol phosphate synthase subunit HisF BMEI2041 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197788 BMEII0017 20130611 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 outer membrane lipoprotein BMEII0017 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197789 BMEII0018 20140405 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 ferrochelatase hemH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197796 BMEII0025 20140217 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 MUTATION: The Brucella abortus virB operon, encoding a type IV secretion system (T4SS), is required for intracellular replication and persistent infection in the mouse model. The products of the first two genes of the virB operon, virB1 and virB2, are predicted to be localized at the bacterial surface. Both mutants were shown to be nonpolar, as demonstrated by their ability to express the downstream gene virB5 during stationary phase of growth in vitro. Both VirB1 and VirB2 were essential for intracellular replication in J774 macrophages. The nonpolar virB1 mutant persisted at wild-type levels, showing that the function of VirB1 is dispensable in the mouse model of persistent infection [PMID:15322008]. A B abortus polar virB1 mutant failed to replicate in HeLa cells, indicating that the virB operon plays a critical role in intracellular multiplication [PMID:15322008]. Polar mutations in the virB1 to virB2 intergenic region or in virB2 reduced the detection of VirB5 to a greater extent than they did that of VirB12. A virB1 mutation also eliminates the transcription of virB12 in B suis [PMID:15322008]. An infection assay with signature-tagged Brucella abortus mutants demonstrated that mutagenesis of the virB1 gene causes attenuation of virulence [PMID:15322008]. 1328 attachment mediating protein VIRB1-like protein BMEII0025 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197797 BMEII0026 20140406 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 MUTATION: The Brucella abortus virB operon, encoding a type IV secretion system (T4SS), is required for intracellular replication and persistent infection in the mouse model. The products of the first two genes of the virB operon, virB1 and virB2, are predicted to be localized at the bacterial surface. Both mutants were shown to be nonpolar, as demonstrated by their ability to express the downstream gene virB5 during stationary phase of growth in vitro. Both VirB1 and VirB2 were essential for intracellular replication in J774 macrophages. The nonpolar virB2 mutant was unable to cause persistent infection in the mouse model, demonstrating the essential role of VirB2 in the function of the T4SS apparatus during infection [PMID:15322008]. Polar mutations in the virB1 to virB2 intergenic region or in virB2 reduced the detection of VirB5 to a greater extent than they did that of VirB12. A virB1 mutation also eliminates the transcription of virB12 in B suis [PMID:15322008]. 1329 VirB2 BMEII0026 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197798 BMEII0027 20130611 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 MUTATION: The B abortus virB3 gene is found to be essential for intracellular growth inside HeLa cells [PMID:12761078]. 1330 VirB3 BMEII0027 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197799 BMEII0028 20140215 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 MUTATION: A mutant strain of B abortus that contains an in-frame deletion in virB4 is unable to replicate in macrophages and survives in mice [PMID:11988518]. ntracellular replication was inhibited in wild-type B abortus after introducing a plasmid expressing a mutant VirB4 altered in the NTP -binding region. VirB4 containing the intact NTP -binding region is essential for evasion of fusion with lysosomes (11988518). The ruffling associated with internalization of the virB4 mutant results in a more rapid uptake than for the wild-type strain. The virB4 mutant shows primarily small regions of phalloidin staining at the sites of binding. Macrophages incubated simultaneously with B abortus and the fluid-phase marker tetramethyl rhodamine isothiocyanate (TRITC)-dextran accumulate the marker in large vacuoles containing the wild-type strain, but little or no marker accumulates in phagosomes containing the virB4 mutant. Similarly, phase-contrast micrographs have shown the wild-type strain in large phase-transparent compartments, but the virB4 mutant is in much smaller compartments (14738898). Intracellular growth-defective virB4 mutant and attenuated vaccine strain S19 did not induce abortion [PMID:11988518]. The B abortus virB4 mutant was completely cleared from the spleens of mice after 4 weeks, while the pncA mutant showed a 1.5-log reduction of the number of bacteria isolated from spleens after 10 weeks. Splenomegaly was not observed at all in mice infected with virB4 mutant [PMID:11988518]. 1331 ATPase VIRB4-like protein BMEII0028 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197800 BMEII0029 20130611 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 MUTATION: A comparison of the VirB8 and VirB5 contents after induction of the B suis wild type and of virB5 and virB12 mutants further confirmed that the virB5 and virB12 genes belong to the same operon [PMID:12595417]. Smooth strains of Brucella unable to replicate (ie, killed B suis or the avirulent mutant B suis virB5) exhibit delayed phagosome-lysosome fusion [PMID:12595417]. Polar mutations in the operon upstream of virB5 exert a greater effect on the expression of virB5 than they do on the expression of the downstream gene virB12. It indicates that in B abortus , regulatory elements other than the virB promoter may influence VirB12 protein levels [PMID:12595417]. Four independent mutants in virB5, virB9 or virB10 were highly attenuated in an in vitro infection model with human macrophages [PMID:12595417]. 1332 VirB5 BMEII0029 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197801 BMEII0030 20140222 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 channel protein VIRB6-like protein BMEII0030 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197803 BMEII0032 20140222 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 MUTATION: virB8 mutant was attenuated by a mini-Tn5 transposon mutagenesis [PMID:10678941]. Attenuated non-polar virB2, virB4, virB8, virB9 and virB10 Brucella mutants are capable of penetrating cells as the same rate as the virulent wild-type Brucella, transit through EEA1-positive early compartments and then localize in LAMP1-positive compartments at early times of infection [PMID:10678941]. 1334 VirB8 BMEII0032 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197804 BMEII0033 20140222 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 MUTATION: Uptake in the presence or absence of Ca2 and Mg2 did not influence the subsequent intracellular survival of wild-type Brucella, whereas the decrease in the number of surviving virB9 mutant cells was delayed in the absence of Ca2 and Mg2. Possibly two types of adhesion molecules promoted uptake of Brucella, one being Ca2 and Mg2 dependent and the other not, and that both types participate in the uptake of wild-type bacteria but only the latter type participates in the uptake of the virB9 mutant [PMID:11349069]. Four independent mutants in virB5, virB9 or virB10 were highly attenuated in an in vitro infection model with human macrophages [PMID:11349069]. The intracellular fate of three virB mutants (virB2, virB4 and virB9) in HeLa cells by immunofluorescence was examined. The three VirB proteins are not necessary for penetration and the inhibition of phago-lysosomal fusion within non-professional phagocytes. Rather, the virB mutants are unable to reach the replicative niche and reside in a membrane -bound vacuole expressing the late endosomal marker, LAMP1, and the sec61beta protein from the ER membrane, proteins that are present in autophagic vesicles originating from the ER [PMID:11349069]. Attenuated non-polar virB2, virB4, virB8, virB9 and virB10 Brucella mutants are capable of penetrating cells as the same rate as the virulent wild-type Brucella, transit through EEA1 -positive early compartments and then localize in LAMP1-positive compartments at early times of infection [PMID:11349069]. 1335 channel protein VIRB9-like protein BMEII0033 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197805 BMEII0034 20140222 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 MUTATION: Mutants with polar and nonpolar mutations introduced in irB10 showed different behaviors in mice and in the HeLa cell infection assay, suggesting that virB10 per se is necessary for the correct function of this type IV secretion apparatus [PMID:11401996]. A B. abortus virB10 mutant showed a decrease of intracellular live bacteria comparable to that of the wild-type strain until 4 h after infection, indicating that a functional VirB system is not required for the short-term survival of Brucella inside macrophages. At later time points, the number of live virB10 mutants progressively decreased. Hence, the Brucella virB10 strain did not replicate, but rather was killed. Although the virB10 mutants are capable of short-term survival, they can not evade long-term degradation through fusion with lysosomes [PMID:11401996]. B abortus virB1 and virB10 mutants are unable to persist in mouse spleens after i.p. inoculation, suggest that attenuation in the animal model is due to an inability of these strains to grow intracellularly [PMID:11401996]. A B abortus virB10 mutant lost the ability to multiply in HeLa cells and was not recovered from the spleens of infected BALBc mice [PMID:11401996]. The non polar virB10 mutant was able to block the acquisition of cathepsin D, but was not able to translocate to the replication compartment [PMID:11401996]. The virB10 non-polar mutants were capable of avoiding interactions with the endocytic pathway but , diverging to wild-type Brucella, were unable to reach the endoplasmic reticulum to establish their intracellular replication niche and seemed to be recycled to the cell surface [PMID:11401996]. 1336 channel protein VIRB10-like protein BMEII0034 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197806 BMEII0035 20130508 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 MUTATION: The virB11 mutation experiment confirms that a complete VirB apparatus is required for their secretion [PMID:15312849]. 1337 ATPase VIRB11-like protein BMEII0035 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197810 BMEII0039 20140405 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 glutamate synthase subunit beta gltD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197811 BMEII0040 20140405 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 MUTATION: gltD encodes the small subunit of glutamate synthase. It is required for B. abortus growth as shown in signature-tagged transposon mutagenesis. It suggests that glutamate may serve as carbon and/or nitrogen sources during growth of B abortus [PMID:10858227]. 1339 glutamate synthase [NADPH] large chain BMEII0040 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197823 BMEII0052 20140222 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 sensory transduction histidine kinase BMEII0052 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197827 BMEII0056 20130526 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 magnesium ABC transporter ATPase BMEII0056 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197848 BMEII0077 20140405 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 isochorismate synthase BMEII0077 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197860 BMEII0089 20140215 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 ribokinase BMEII0089 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197887 BMEII0116 20140215 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 GntR family transcriptional regulator BMEII0116 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197899 BMEII0128 20140215 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 hypothetical protein BMEII0128 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197907 BMEII0136 20130518 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 homoprotocatechuate 2,3-dioxygenase BMEII0136 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197921 BMEII0150 20140405 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 flagellin BMEII0150 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197922 BMEII0151 20140222 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 flagellar M-ring protein FLIF BMEII0151 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197925 BMEII0154 20140329 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 flagellar motor protein MotB motB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197929 BMEII0158 20140222 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 MUTATION: FtcR is required in B melitensis 16M for the transcription of the fliF gene during vegetative and intracellular growth, and for the production of the two structural flagellar components FlgE and FliC during vegetative growth. A ftcR mutant has the same virulence phenotype as previously found with structural flagellar mutants. In HeLa cells and bovine macrophages, no attenuation of the ftcR mutant was observed compared to the WT parental strain. In BALB/c mice, the ftcR mutant was not attenuated after 1 week of infection but was attenuated after 4 weeks of infection. FtcR acts as a flagellar master regulator in B melitensis and perhaps in other related alpha-proteobacteria [PMID:17056750]. 1350 two component response regulator BMEII0158 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197930 BMEII0159 20140329 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 flagellar hook protein FlgE flgE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197937 BMEII0166 20140215 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 flagellar biosynthetic protein FlhA BMEII0166 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197948 BMEII0177 20140215 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 high-affinity zinc uptake system ATP-binding protein ZNUC BMEII0177 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1197949 BMEII0178 20140215 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 MUTATION: Brucella abortus znuA mutant via mini-Tn5Km2 transposon mutagenesis has intracellular growth defect inside HeLa cells [PMID:15472468]. High-affinity zinc uptake system protein mutant (znuA mutant) showed reduced growth in zinc chelated medium, and failed to replicate in HeLa cells and mouse bone marrow-derived macrophages. Transformation of znuA mutant with a shuttle vector pBBR1MCS-4 containing znuA gene restored the growth in zinc chelated medium and intracellular replication in HeLa cells and macrophages to a level comparable to that of wild-type strain. Bacterial internalization into HeLa cells and macrophages and co-localization with either late endosomes or lysosomes of znuA mutant were not different from those of wild-type strain. These results suggest that znuA does not contribute to intracellular trafficking of B abortus, but contributes to utilization of zinc required for intracellular growth [PMID:15472468]. 1354 high-affinity zinc uptake system protein ZNUA BMEII0178 Bin Zhao, Oliver He yihA ysxC WEB: http://www.ncbi.nlm.nih.gov/gene 1198045 BMEII0274 20140406 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 ribosome biogenesis GTP-binding protein YsxC - engB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1198072 BMEII0300 20140406 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 ribose ABC transporter ATP-binding protein BMEII0300 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1198080 BMEII0308 20140222 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 MUTATION: A study with miniTn5 mutants of B. suis constitutively expressing gfp indicates that B. suis cobW gene is required for intracellular multiplication in human macrophage THP-1 cells [PMID:12438693]. 1357 zinc transporter BMEII0308 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1198090 BMEII0318 20140217 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 6-aminohexanoate-dimer hydrolase BMEII0318 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1198108 BMEII0336 20140222 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 ABC transporter permease BMEII0336 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1198122 BMEII0350 20140406 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 D-aminopeptidase BMEII0350 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1198133 BMEII0361 20140222 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 sugar transport ATP-binding protein BMEII0361 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1198150 BMEII0378 20140222 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 formate dehydrogenase alpha chain BMEII0378 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1198162 BMEII0390 20130508 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 LysR family transcriptional regulator BMEII0390 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1198200 BMEII0428 20140405 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 MUTATION: The eryC gene encodes for enzyme Derythrulose-1-phosphate dehydrogenase. The vaccine strain B abortus B19 is the only known B abortus isolate whose growth is inhibited by erythritol. The B abortus B19 strain is an eryCD double mutant. The defect in B19 was complemented in trans by plasmids containing the complete ery region and by plasmids with Tn1725 insertions in eryA, eryB and eryD. Plasmids with Tn1725 insertions in eryC were the only ones that failed to complement the Ery phenotype of B19 [PMID:16177356]. Allelic exchange mutants in eryC of Brucella suis were erythritol sensitive in vitro with a MIC of 1 to 5 mM of erythritol. Their multiplication in macrophage-like cells was 50 to 90- fold reduced , but complementation of the mutant restored wild-type levels of intracellular multiplication and the capacity to use erythritol as a sole carbon source. In vivo, the eryC mutant colonized the spleens of infected BALBc mice to a significantly lower extent than the wild type and the complemented strain. Interestingly, eryC mutants that were in addition spontaneously erythritol tolerant nevertheless exhibited wild-type-like intramacrophagic and intramurine replication. In conclusion, erythritol was not an essential carbon source for the pathogen in the macrophage host cell but that the inactivation of the eryC gene significantly reduced the intramacrophagic and intramurine fitness of B suis [PMID:16177356]. 1364 D-erythrulose 4-phosphate dehydrogenase BMEII0428 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1198201 BMEII0429 20140215 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 MUTATION: EryB is an erythritol phosphate dehydrogenase. The vaccine strain B abortus B19 is the only known B abortus isolate whose growth is inhibited by erythritol. The B abortus B19 strain is an eryCD double mutant. The defect in B19 was complemented in trans by plasmids containing the complete ery region and by plasmids with Tn1725 insertions in eryA, eryB and eryD. Plasmids with Tn1725 insertions in eryC were the only ones that failed to complement the Ery phenotype of B19 [PMID:16177356]. The B. suis eryB mutant by Tn5 transposon mutagenesis was attenuated in the human macrophage -like THP-1 cells. This mutant is sensitive to erythritol and mimics the erythritol sensitive response of the B19 strain [PMID:16177356]. 1365 glycerol-3-phosphate dehydrogenase BMEII0429 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1198247 BMEII0475 20140406 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 GntR family transcriptional regulator BMEII0475 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1198257 BMEII0485 20140222 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 D-galactarate dehydratase BMEII0485 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1198259 BMEII0487 20130611 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 nickel-binding periplasmic protein precursor BMEII0487 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1198285 BMEII0513 20140405 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 MUTATION: Brucella abortus zwf mutant via mini-Tn5Km2 transposon mutagenesis has intracellular growth defect inside HeLa cells and macrophages [PMID:12761078]. 1369 glucose-6-phosphate 1-dehydrogenase BMEII0513 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1198299 BMEII0527 20140222 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 exodeoxyribonuclease VII large subunit xseA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1198342 BMEII0570 20140329 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 sugar phosphate isomerase/epimerase IolE BMEII0570 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1198345 BMEII0573 20140405 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 RPIR family transcriptional regulator BMEII0573 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1198353 BMEII0581 20140222 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 superoxide dismutase (Cu-Zn) BMEII0581 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1198356 BMEII0584 20140222 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 iron(III)-binding periplasmic protein precursor BMEII0584 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1198363 BMEII0591 20140406 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 MUTATION: UgpA is one of the attenuated Signature-Tagged Mutagenesis mutants of Brucella melitensis identified during the acute phase of infection in mice [PMID:14638795]. 1375 sugar transport system permease BMEII0591 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1198396 BMEII0624 20130611 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 MUTATION: UgpA is one of the attenuated Signature-Tagged Mutagenesis mutants of Brucella melitensis identified during the acute phase of infection in mice [PMID:14638795]. 1376 SN-glycerol-3-phosphate transport system permease UGPA BMEII0624 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1198398 BMEII0626 20130611 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 membrane dipeptidase BMEII0626 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1198431 BMEII0659 20130611 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 two component response regulator BMEII0659 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1198441 BMEII0669 20140405 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 dihydroorotase BMEII0669 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1198442 BMEII0670 20140405 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 aspartate carbamoyltransferase pyrB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1198443 BMEII0671 20140222 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 acyl-CoA dehydrogenase BMEII0671 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1198473 BMEII0701 20130518 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 ribose ABC transporter permease BMEII0701 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1198531 BMEII0759 20140405 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 MUTATION: cydB is a gene that is part of the cydAB operon encoding cytochrome bd oxidase , which catalyzes an alternate terminal electron transport step in bacterial respiration. Transposon (Tn5) mutagenesis of B abortus cydB was severely attenuated for intracellular survival. Unlike the virulent strain 2308, the Brucella cydB::Tn5 mutant was severely compromised for survival in the spleens of inoculated mice [PMID:11274104]. The cydB and cydD mutants are also defective for the intracellular growth of B abortus and B suis, suggesting that functional cytochrome bd oxidase is required for growth in an intracellular environment [PMID:11274104]. 1383 cytochrome D ubiquinol oxidase subunit II BMEII0759 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1198533 BMEII0761 20130518 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 transport ATP-binding protein CYDC BMEII0761 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1198534 BMEII0762 20130611 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 MUTATION: The cydB and cydD mutants are also defective for the intracellular growth of B abortus and B suis, suggesting that functional cytochrome bd oxidase is required for growth in an intracellular environment [PMID:12761078]. 1385 transport ATP-binding protein CYDD BMEII0762 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1198571 BMEII0799 20140222 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 nitrate transport permease NRTB BMEII0799 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1198595 BMEII0823 20140405 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 glycerol kinase BMEII0823 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1198653 BMEII0881 20140406 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 phosphoketolase BMEII0881 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1198671 BMEII0899 20140405 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 phosphomannomutase BMEII0899 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1198672 BMEII0900 20140405 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 mannose-6-phosphate isomerase BMEII0900 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1198695 BMEII0923 20130526 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 spermidine/putrescine-binding periplasmic protein BMEII0923 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1198703 BMEII0931 20140215 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 ribonucleotide reductase stimulatory protein nrdI Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1198704 BMEII0932 20140222 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 glutaredoxin BMEII0932 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1198707 BMEII0935 20140215 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 nickel resistance protein BMEII0935 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1198722 BMEII0950 20140405 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 MUTATION: The narG gene encodes for an essential component of the dissimilatory nitrate reductase complex. This complex is encoded by the narGHIJ locus, which is present in the B suis genome together with the gene of the nitrite extrusion protein, narK. The narG mutant was unable to produce nitrite from nitrate [PMID:12438693]. A study with miniTn5 mutants of B. suis constitutively expressing gfp indicates that B. suis xx gene is required for intracellular multiplication in human macrophage THP-1 cells [PMID:12438693]. 1395 nitrate reductase alpha chain BMEII0950 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1198773 BMEII1001 20140215 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 heme-copper oxidase subunit III BMEII1001 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1198809 BMEII1037 20140222 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 zinc protease BMEII1037 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1198817 BMEII1045 20130511 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 HAD superfamily protein involved in N-acetyl-glucosamine catabolism BMEII1045 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1198825 BMEII1053 20140215 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 glucose/galactose transporter BMEII1053 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1198838 BMEII1066 20140406 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 pyruvate dehydrogenase complex repressor BMEII1066 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1198856 BMEII1084 20140215 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 flagellar basal body P-ring biosynthesis protein FlgA flgI Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1198865 BMEII1093 20130611 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 glycerol-3-phosphate regulon repressor BMEII1093 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1198873 BMEII1101 20140215 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 bactoprenol glucosyl transferase / bactoprenol apolipoprotein N-acyltransferase BMEII1101 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1198888 BMEII1116 20130508 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 LuxR family transcriptional regulator BMEII1116 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1198896 BMEII1124 20140405 224914 II protein-coding NCBI-supplied PMID: 11756688; 12271122 MUTATION: gnd is involved in pentose phosphate pathway. It is essential for intracellular growth inside HeLa cells as shown by its Brucella suis miniTn5Km2 transposon mutation analysis. The mutant is attenuated in the mouse model [PMID:12761078]. 1405 6-phosphogluconate dehydrogenase BMEII1124 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1199135 EF0243 20140322 226185 protein-coding NCBI-supplied PMID: 12663927; 15917518; 19725962 MUTATION: brnQ mutant is attenuated in killing C. elegans [PMID:17307944]. 4795 branched-chain amino acid ABC transporter brnQ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1199295 EF0376 20140322 226185 protein-coding NCBI-supplied PMID: 12663927; 15917518; 19725962 MUTATION: EF0376 mutant is attenuated in killing C. elegans [PMID:17307944]. 4807 hypothetical protein EF0376 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1199301 EF0382 20140322 226185 protein-coding NCBI-supplied PMID: 12663927; 15917518; 19725962 MUTATION: EF0382 mutant is attenuated in killing C. elegans [PMID:17307944]. 4790 hypothetical protein EF0382 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1199634 EF0737 20140405 226185 protein-coding NCBI-supplied PMID: 12663927; 15917518; 19725962 MUTATION: EF0737 mutant is attenuated in killing C. elegans [PMID:17307944]. 4802 amidase EF0737 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1199754 EF0861 20140322 226185 protein-coding NCBI-supplied PMID: 12663927; 15917518; 19725962 MUTATION: EF0861 mutant is attenuated in killing C. elegans [PMID:17307944]. 4808 acetyltransferase EF0861 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1199842 EF0954 20140322 226185 protein-coding NCBI-supplied PMID: 12663927; 15917518; 19725962 MUTATION: bopD mutant has delayed colonization in murine intestinal tract [PMID:16834772]. 4787 LacI family sugar-binding transcriptional regulator EF0954 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1199996 EF1094 20140322 226185 protein-coding NCBI-supplied PMID: 12663927; 15917518; 17016560; 19286802; 19725962 MUTATION: bps (srtC) mutant is attenuated in mice [PMID:17785477]. 4774 sortase EF1094 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1200199 EF1302 20140322 226185 protein-coding NCBI-supplied PMID: 12663927; 15917518; 19725962 MUTATION: EF1302 mutant is attenuated in killing C. elegans [PMID:17307944]. 4791 transcriptional regulator EF1302 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1200416 EF1513 20140406 226185 protein-coding NCBI-supplied PMID: 12663927; 15917518; 19725962 MUTATION: EF1513 mutant is attenuated in killing C. elegans [PMID:17307944]. 4796 pheromone binding protein EF1513 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1200442 EF1542 20140322 226185 protein-coding NCBI-supplied PMID: 12663927; 15917518; 19725962 MUTATION: EF1542 mutant is attenuated in killing C. elegans [PMID:17307944]. 4809 hypothetical protein EF1542 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1200445 EF1545 20140222 226185 protein-coding NCBI-supplied PMID: 12663927; 15917518; 19725962 MUTATION: recQ-1 mutant is attenuated in killing C. elegans and is attenuated in mice [PMID:17307944]. 4798 ATP-dependent DNA helicase RecQ recQ-1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1200469 EF1569 20140322 226185 protein-coding NCBI-supplied PMID: 12663927; 15917518; 19725962 MUTATION: psr mutant is attenuated in killing C. elegans [PMID:17307944]. 4792 transcriptional regulator, PSR protein psr Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1200476 EF1576 20140405 226185 protein-coding NCBI-supplied PMID: 12663927; 15917518; 19725962 MUTATION: thyA mutant is attenuated in killing C. elegans [PMID:17307944]. 4805 thymidylate synthase thyA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1200489 EF1590 20140322 226185 protein-coding NCBI-supplied PMID: 12663927; 15917518; 19725962 MUTATION: EF1590 mutant is attenuated in killing C. elegans and is attenuated in mice [PMID:17307944]. 4810 protease synthase and sporulation negative regulatory protein pai 1 EF1590 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1200497 EF1598 20140322 226185 protein-coding NCBI-supplied PMID: 12663927; 15917518; 19725962 MUTATION: phrB mutant is attenuated in killing C. elegans and is attenuated in mice [PMID:17307944]. 4799 deoxyribodipyrimidine photolyase phrB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1200501 EF1603 20140405 226185 protein-coding NCBI-supplied PMID: 12663927; 15917518; 19725962 MUTATION: scrB mutant is avirulent in C. elegans and attenuated in mice [PMID:17307944]. MUTATION: scrB-1 mutant is attenuated in killing C. elegans and is attenuated in mice [PMID:17307944]. 4780 sucrose-6-phosphate dehydrogenase scrB-1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1200502 EF1604 20140222 226185 protein-coding NCBI-supplied PMID: 12663927; 15917518; 19725962 MUTATION: scrR-1 mutant is attenuated in killing C. elegans [PMID:17307944]. 4793 sucrose operon repressor ScrR scrR-1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1200521 EF1623 20140322 226185 protein-coding NCBI-supplied PMID: 12663927; 15917518; 19725962 MUTATION: EF1623 mutant is attenuated in killing C. elegans [PMID:17307944]. 4804 microcompartment protein EF1623 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1200671 EF1782 20140406 226185 protein-coding NCBI-supplied PMID: 12663927; 15917518; 19725962 MUTATION: purL mutant is attenuated in mice [PMID:9780263]. 4781 phosphoribosylformylglycinamidine synthase II purL Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1200680 EF1792 20140222 226185 protein-coding NCBI-supplied PMID: 12663927; 15917518; 19725962 MUTATION: EF1792 mutant is attenuated in killing C. elegans [PMID:17307944]. 4811 hypothetical protein EF1792 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1200706 EF1821 20140322 226185 protein-coding NCBI-supplied PMID: 12663927; 15917518; 19725962 MUTATION: fsrB (agrBfs) mutant is attenuated in killing C. elegans and is attenuated in mice [PMID:17307944]. 4794 agrBfs protein agrBfs Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1201076 EF2200 20140405 226185 protein-coding NCBI-supplied PMID: 12663927; 15917518; 19725962; 23767698 MUTATION: map mutant is attenuated in killing C. elegans [PMID:17307944]. 4806 methionine aminopeptidase map Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1201351 EF2487 20140406 226185 protein-coding NCBI-supplied PMID: 12663927; 15917518; 19725962 MUTATION: cpsI mutant is rapidly cleared from murine cutaneous infection sites compared to the wild type [PMID:11830672]. 4786 UDP-galactopyranose mutase glf Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1201452 EF2591 20140215 226185 protein-coding NCBI-supplied PMID: 12663927; 15917518; 19725962 MUTATION: EF2591 mutant is attenuated in killing C. elegans [PMID:17307944]. 4801 glyoxalase EF2591 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1201458 EF2598 20140322 226185 protein-coding NCBI-supplied PMID: 12663927; 15917518; 19725962 MUTATION: EF2598 mutant is attenuated in killing C. elegans [PMID:17307944]. 4797 PTS system beta-glucoside-specific transporter subunit IIABC EF2598 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1201532 EF2675 20140322 226185 protein-coding NCBI-supplied PMID: 12663927; 15917518; 19725962 MUTATION: EF2675 mutant is attenuated in killing C. elegans [PMID:17307944]. 4812 competence protein EF2675 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1201809 EF2957 20140405 226185 protein-coding NCBI-supplied PMID: 12663927; 15917518; 19725962 MUTATION: EF2957 mutant is attenuated in killing C. elegans [PMID:17307944]. 4813 hexapeptide repeat-containing acetyltransferase EF2957 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1201902 EF3056 20140322 226185 protein-coding NCBI-supplied PMID: 12663927; 15917518; 19286802; 19725962 MUTATION: srtA mutant is attenuated in murine urinary tract infection model [PMID:20696830]. 4788 sortase EF3056 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1202157 EF3314 20140406 226185 protein-coding NCBI-supplied PMID: 12663927; 15917518; 19725962; 19856273 MUTATION: EF3314 deletion mutant is attenuated in attachment to HeLa cells, survival within macrophages and in a C. elegans killing model [PMID:19856273]. 4772 cell wall surface anchor family protein EF3314 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1202219 EFA0047 20140322 226185 protein-coding NCBI-supplied PMID: 12663927 MUTATION: asa1 deletion mutant has reduced adherence to macrophages, and an AS negative strain had decreased survival in macrophages compared to a AS positive strain [PMID:10948103]. 4785 aggregation substance Asa1 asa1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1208012 CBU_0141 20140215 227377 protein-coding NCBI-supplied GO_0000910 (EC: ISS, PMID: 12704232); GO_0003924 (EC: ISS, PMID: 12704232) PMID: 12704232; 19047403 MUTATION: ftsZ mutant had a significantly lower growth rate than wild-type bacteria and frequently appeared as filamentous forms displaying incomplete cell division septa. The latter phenotype correlated with a deficiency in generating infectious foci on a per-genome basis compared to wild-type organisms in vero cells [PMID:19114492]. 1406 cell division protein FtsZ ftsZ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1237991 CP0123 20140222 198214 protein-coding NCBI-supplied PMID: 12384590 MUTATION: virB mutants have an avirulent phenotype and do not invade host cells [PMID:8385666]. 886 transcriptional activator VirB virB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1237992 CP0181 20140329 198214 protein-coding NCBI-supplied PMID: 12384590; 22939626 MUTATION: virA mutants did not move within the host cytoplasm and failed to move into adjacent cells [PMID:17095701]. 887 VirA protein virA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1237998 CP0149 20140222 198214 protein-coding NCBI-supplied PMID: 12384590 MUTATION: spa47 mutants form needle-less type III structure which is defective, and thus incapable of invasion of host cells [PMID:10921870]. 888 ATP synthase SpaL spa47 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1238000 CP0152 20140215 198214 protein-coding NCBI-supplied PMID: 12384590 MUTATION: spa33 mutants are unable to secrete effectors necessary to cell invasion [PMID:16246841]. 889 Mxi-Spa secretion machinery protein Spa33 spa33 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1238001 CP0151 20130611 198214 protein-coding NCBI-supplied PMID: 12384590 MUTATION: spa32 mutants are unable to invade HeLa cells and do not secrete type III effectors [PMID:11844752]. 890 Mxi-Spa secretion machinery protein Spa32 spa32 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1238004 CP0148 20140215 198214 protein-coding NCBI-supplied PMID: 12384590 MUTATION: spa15 mutant was attenuated in entry into epithelial cells compared to the wild-type [PMID:11952903]. 891 Mxi-Spa secretion machinery protein Spa15 spa15 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1238005 CP0070 20140406 198214 protein-coding NCBI-supplied PMID: 12384590 MUTATION: sepA mutant has attenuated virulence in ligated rabbit ileal loop model [PMID:7476198]. 892 extracellular serine protease SepA sepA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1238010 CP0227 20140406 198214 protein-coding NCBI-supplied PMID: 12384590 MUTATION: Upon infection of ileal loops in rabbits, the ospG mutant induced a stronger inflammatory response than the wild-type strain, indicating that OspG negatively controls the host innate response induced by S. flexneri upon invasion of the epithelium [PMID:16162672]. 893 protein OspG ospG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1238011 CP0010 20140406 198214 protein-coding NCBI-supplied PMID: 12384590 MUTATION: ospF mutants had reduced PMN transepithelial migration when compared to wild-type infection, PMN transepithelial migration is necessary for virulence of Shigella [PMID:16988276]. 894 OspF ospF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1238012 CP0093 20140215 198214 protein-coding NCBI-supplied PMID: 12384590 MUTATION: sen deletion mutant elicited lower rises in mucosal short-circuit current than the wild type, suggesting that the senA/ospD3 gene encodes an enterotoxin of Shigella [PMID:7591128]. 895 hypothetical protein ospD3 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1238020 CP0237 20140217 198214 protein-coding NCBI-supplied PMID: 12384590 MUTATION: virK mutants have attenuated ability for intracellular spreading in host cells [PMID:15664968]. 896 hypothetical protein virK Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1238022 CP0046 20140406 198214 protein-coding NCBI-supplied PMID: 12384590 MUTATION: virF knockouts are non-invasive to host cells [PMID:20237205]. 897 transcriptional activator VirF virF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1238025 CP0094 20140406 198214 protein-coding NCBI-supplied PMID: 12384590 MUTATION: ospC1 mutants had reduced PMN transepithelial migration when compared to wild-type infection, PMN transepithelial migration is necessary for virulence of Shigella [PMID:16988276]. 898 protein OspC1 ospC1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1238026 CP0003 20130611 198214 protein-coding NCBI-supplied PMID: 12384590 MUTATION: ospB mutants had reduced PMN transepithelial migration when compared to wild-type infection, PMN transepithelial migration is necessary for virulence of Shigella [PMID:19017275]. 899 OspB protein ospB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1238027 CP0141 20140217 198214 protein-coding NCBI-supplied PMID: 12384590 MUTATION: mxiN mutants were unable to invade HeLa cells [PMID:12864857]. 900 Mxi-Spa secretion machinery protein MxiN mxiN Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1238028 CP0143 20140406 198214 protein-coding NCBI-supplied PMID: 12384590; 15775974; 18940609 MUTATION: mxiM mutants are phenotypically avirulent, and also unable to invade semiconfluent L2 cell monolayers [PMID:10085046]. 901 Mxi-Spa secretion machinery protein MxiM mxiM Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1238030 CP0140 20140217 198214 protein-coding NCBI-supplied PMID: 12384590 MUTATION: mxiK mutants are unable to invade HeLa cells [PMID:12864857]. 902 Mxi-Spa secretion machinery protein MxiK mxiK Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1238031 CP0139 20140222 198214 protein-coding NCBI-supplied PMID: 12384590 MUTATION: mxiJ mutant was unable to invade HeLa cells, to induce the formation of plaques on confluent monolayers of HeLa cells, and to provoke keratoconjunctivitis in guinea pigs [PMID:1332940]. 903 Mxi-Spa secretion machinery protein MxiJ mxiJ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1238032 CP0136 20140222 198214 protein-coding NCBI-supplied PMID: 12384590 MUTATION: mxiG mutant was unable to enter HeLa cells and to provoke keratoconjunctivitis in guinea-pigs [PMID:8559065]. 904 MxiG protein mxiG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1238033 CP0144 20140222 198214 protein-coding NCBI-supplied PMID: 12384590; 18192384 MUTATION: mxiE deletion mutants are unable to block apoptosis of host epithelial cells [PMID:17339354]. 905 AraC-like family protein MxiE mxiE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1238034 CP0145 20140222 198214 protein-coding NCBI-supplied PMID: 12384590; 18940609 MUTATION: mxiD mutant is unable to invade HeLa cells or to provoke keratoconjunctivitis in guinea-pigs [PMID:8437520]. 906 outermembrane protein MxiD mxiD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1238035 CP0146 20140222 198214 protein-coding NCBI-supplied PMID: 12384590; 19017268 MUTATION: mxiC mutant has a 10-fold decrease in efficiency in invading epithelial cells [PMID:19017268]. 907 Mxi-Spa secretion machinery protein mxiC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1238036 CP0147 20140215 198214 protein-coding NCBI-supplied PMID: 12384590 MUTATION: mxiA mutants were attenuated in invasion of HeLa cells [PMID:2037361]. 908 Mxi-Spa secretion machinery protein MxiA mxiA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1238042 CP0133 20140406 198214 protein-coding NCBI-supplied PMID: 12384590 MUTATION: ipgD mutant is unable to dephosphorylate phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P2] and induces shorter filapodia in host cells [PMID:12356723]. 909 hypothetical protein ipgD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1238043 CP0129 20140222 198214 protein-coding NCBI-supplied PMID: 12384590; 18192384 MUTATION: ipgC mutant attenuated in infecting Caco-2 cells monolayer [PMID:11207551]. 910 IpgC, cytoplasmic chaperone for IpaB and IpaC ipgC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1238044 CP0024 20140405 198214 protein-coding NCBI-supplied PMID: 12384590; 16413487; 20363740 MUTATION: ipgB2 mutant had entry into polarized cells reduced by 70% compared to the wild-type [PMID:18316224]. 911 hypothetical protein ipgB2 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1238045 CP0130 20140406 198214 protein-coding NCBI-supplied PMID: 12384590; 16413487 MUTATION: The invasiveness of the ipgB1 mutant was decreased to less than 50% of the wild-type level (100%) in a gentamicin protection or plaque forming assay [PMID:15849186]. 912 secreted by the Mxi-Spa machinery, function unknown Other designations: protein IpgB1 ipgB1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1238046 CP0131 20130611 198214 protein-coding NCBI-supplied PMID: 12384590 MUTATION: transposon mutants of ipgA cannot invade epithelial cells and cannot induce keratoconjunctivitis in mice [PMID:8376337]. 913 chaperone IpgA ipgA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1238048 CP0226 20140325 198214 protein-coding NCBI-supplied PMID: 12384590; 20831869 MUTATION: ipaH9.8 deletion mutant caused more severe inflammatory responses with increased pro-inflammatory cytokine production levels than did wild-type Shigella, which resulted in a 30-fold decrease in bacterial colonization in murine lungs [PMID:15950937]. 914 invasion plasmid antigen, secreted by the Mxi-Spa secretion machinery ipaH9.8 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1238049 CP0078 20140222 198214 protein-coding NCBI-supplied PMID: 12384590 MUTATION: ipaH7.8 mutants had a lower rate of exit from the endocytic vacuoles into the cytoplasm in mouse macrophages than the wild-type strain [PMID:10816519]. 915 invasion plasmid antigen ipaH7.8 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1238053 CP0126 20140406 198214 protein-coding NCBI-supplied PMID: 12384590; 16946465; 17110044 MUTATION: ipaD mutants are completely unable to invade cultured cells or lyse RBCs [PMID:15731041]. 916 hypothetical protein ipaD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1238054 CP0127 20140405 198214 protein-coding NCBI-supplied PMID: 12384590; 12800254 MUTATION: ipaC mutants cannot invade cultured cells or lyse red blood cells [PMID:18656530]. 917 IpaC, secreted by the Mxi-Spa secretion machinery, required for entry into epithelial cells ipaC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1238055 CP0128 20140329 198214 protein-coding NCBI-supplied PMID: 12384590; 15819617 MUTATION: ipaB mutant is unable to infect HeLa cells [PMID:20086081]. 918 IpaB, secreted by the Mxi-Spa secretion machinery, required for entry into epithelial cells ipaB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1238056 CP0125 20140329 198214 protein-coding NCBI-supplied PMID: 12384590; 16826238 MUTATION: ipaA mutants are attenuated in invasion of HeLa cells [PMID:9184218]. 919 hypothetical protein ipaA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1238057 CP0132 20130611 198214 protein-coding NCBI-supplied PMID: 12384590; 15576571 MUTATION: icsB mutants are attenuated in guinea pig eyes [PMID:12753186]. 920 IcsB, invasion protein icsB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1238061 CP0004 20140406 198214 protein-coding NCBI-supplied PMID: 12384590; 16452446 MUTATION: phoN2/apy mutant is attenuated for growth in HeLa and Caco-2 cells [PMID:16452446]. 921 PhoN2 (Apy), periplasmic phosphatase, apyrase, ATP diphosphohydrolase phoN2/apy Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1238256 CP0137 20140215 198214 protein-coding NCBI-supplied PMID: 12384590; 16227202 MUTATION: mxiH mutants are unable to invade HeLa cells [PMID:11169106]. 922 Mxi-Spa secretion machinery protein MxiH mxiH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1238257 CP0138 20140406 198214 protein-coding NCBI-supplied PMID: 12384590 MUTATION: mxiI mutant is unable to invade HeLa cells [PMID:11169106]. 923 Mxi-Spa secretion machinery protein MxiI mxiI MUTATION: bfpA deletion mutant of EPEC was less virulent in humans than the wild-type EPEC [PMID:9641917]. 2026 MUTATION: bfpB mutant EPEC is unable to form BFP which is a major virulence factor of EPEC [PMID:8932312]. 2027 MUTATION: bfpE mutant strain of EPEC fails to form detectable BFP and fails to carry out autoaggregation and localized adherence to HEp-2 epithelial cells in tissue culture [PMID:11443077]. 2028 MUTATION: bfpF mutant colonized the human intestine but was about 200-fold less virulent than the wild-type EPEC [PMID:9641917]. 2029 MUTATION: mutation in bfpP blocks BFP biogenesis and localized adherence to host cells by EPEC [PMID:10762251]. 2030 MUTATION: bfpT (perA) disruption mutant of EPEC was less virulent in humans than the wild-type EPEC [PMID:9641917]. 2031 MUTATION: yopP mutant is attenuated in mice [PMID:10216859]. 3938 MUTATION: lcrV mutant is attenuated in mice [PMID:10216859]. 3939 MUTATION: yscR mutant is attenuated in mice [PMID:10216859]. 3940 MUTATION: yscU mutant is attenuated in mice [PMID:10216859]. 3941 MUTATION: virG mutant is attenuated in mice [PMID:10216859]. 3942 MUTATION: virF mutant is attenuated in mice [PMID:10216859]. 3943 MUTATION: yscC mutant is attenuated in mice [PMID:10216859]. 3944 MUTATION: yscL mutant is attenuated in mice [PMID:10216859]. 3945 MUTATION: sycH mutant is attenuated in mice [PMID:12654794]. 3946 MUTATION: yadA mutant is attenuated in mice [PMID:12654794]. 3947 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1239183 pYVa12790_p47 20140406 630 protein-coding NCBI-supplied MUTATION: sycH mutant is attenuated in mice [PMID:12654794]. 3972 SycH sycH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1239194 pYVa12790_p12 20130525 630 protein-coding NCBI-supplied PMID: 16239347 MUTATION: lcrV mutant is attenuated in mice [PMID:10216859]. 3973 LcrV lcrV Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1239200 pYVa12790_p29 20140406 630 protein-coding NCBI-supplied PMID: 11402007 MUTATION: yscU mutant is attenuated in mice [PMID:10216859]. 3974 YscU yscU Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1239201 pYVa12790_p34 20140222 630 protein-coding NCBI-supplied PMID: 11402007 MUTATION: yscC mutant is attenuated in mice [PMID:10216859]. 3975 hypothetical protein yscC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1239208 pYVa12790_p26 20140222 630 protein-coding NCBI-supplied PMID: 11402007 MUTATION: yscR mutant is attenuated in mice [PMID:10216859]. 3976 type III secretion system protein yscR Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1239212 pYVa12790_p44 20140215 630 protein-coding NCBI-supplied MUTATION: yscL mutant is attenuated in mice [PMID:10216859]. 3977 type III secretion system protein yscL Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1239217 pYVa12790_p30 20140215 630 protein-coding NCBI-supplied PMID: 11402007 MUTATION: virG mutant is attenuated in mice [PMID:10216859]. 3978 VirG virG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1239218 pYVa12790_p31 20140406 630 protein-coding NCBI-supplied PMID: 11402007 MUTATION: virF mutant is attenuated in mice [PMID:10216859]. 3979 VirF virF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1239224 pYVa12790_p60 20140215 630 protein-coding NCBI-supplied PMID: 2592347; 11080146; 12813066; 14527656 MUTATION: yadA mutant is attenuated in mice [PMID:12654794]. 3980 adhesin YadA yadA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1239242 pYVa12790_p68 20140217 630 protein-coding NCBI-supplied PMID: 17624595 MUTATION: yopP mutant is attenuated in mice [PMID:10216859]. 3981 YopP yopP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1243367 PM0020 20140405 272843 protein-coding NCBI-supplied PMID: 11248100 MUTATION: purN mutant is attenuated in chickens and mice [PMID:12933901]. 4495 phosphoribosylglycinamide formyltransferase purN Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1243393 PM0046 20140215 272843 protein-coding NCBI-supplied PMID: 11248100 MUTATION: dsbB mutant is attenuated in mice [PMID:10873488]. 4507 disulfide bond formation protein B dsbB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1243428 PM0081 20140222 272843 protein-coding NCBI-supplied PMID: 11248100 MUTATION: PM0081 mutant is attenuated in chickens [PMID:12933901]. 4500 hypothetical protein PM0081 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1243570 PM0223 20140217 272843 protein-coding NCBI-supplied PMID: 11248100 MUTATION: dcaA mutant is attenuated in chickens and mice [PMID:12933901]. 4492 protein DcaA dcaA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1243640 PM0293 20140322 272843 protein-coding NCBI-supplied PMID: 11248100 MUTATION: guaA mutant is attenuated in mice [PMID:10873488]. 4503 GMP synthase guaA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1243991 PM0644 20130518 272843 protein-coding NCBI-supplied PMID: 11248100 MUTATION: ponC mutant is attenuated in chickens [PMID:12933901]. 4499 protein PonC ponC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1244048 PM0701 20140405 272843 protein-coding NCBI-supplied PMID: 11248100 MUTATION: purF mutant is attenuated in mice [PMID:10873488]. 4502 amidophosphoribosyltransferase purF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1244144 PM0797 20140222 272843 protein-coding NCBI-supplied PMID: 11248100 MUTATION: pyrF mutant is attenuated in chickens [PMID:12933901]. 4498 OMP decarboxylase; OMPDCase; OMPdecase Other designations: orotidine 5'-phosphate decarboxylase pyrF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1244202 PM0855 20140222 272843 protein-coding NCBI-supplied PMID: 11248100 MUTATION: PM0855 mutant is attenuated in chickens and mice [PMID:12933901]. 4493 hypothetical protein PM0855 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1244416 PM1069 20140222 272843 protein-coding NCBI-supplied PMID: 11248100 MUTATION: PM1069 mutant is attenuated in chickens [PMID:12933901]. 4496 hypothetical protein PM1069 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1244569 PM1222 20140215 272843 protein-coding NCBI-supplied PMID: 11248100 MUTATION: dam mutant is attenauted in mice [PMID:12904568]. 4501 hypothetical protein dam Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1244641 PM1294 20140222 272843 protein-coding NCBI-supplied PMID: 11248100 MUTATION: PM1294 mutant is attenuated in chickens and mice [PMID:12933901]. 4494 hypothetical protein PM1294 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1244690 PM1343 20130616 272843 protein-coding NCBI-supplied PMID: 11248100 MUTATION: deoC mutant is attenuated in chickens [PMID:12933901]. 4497 deoxyribose-phosphate aldolase deoC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1244813 PM1466 20140406 272843 protein-coding NCBI-supplied PMID: 11248100 MUTATION: atpG mutant is attenuated in mice [PMID:10873488]. 4505 hypothetical protein PM1466 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1244840 PM1493 20140322 272843 protein-coding NCBI-supplied PMID: 11248100 MUTATION: atpG mutant is attenuated in mice [PMID:10873488]. 4504 F0F1 ATP synthase subunit gamma atpG Bin Zhao, Oliver He leuO WEB: http://www.ncbi.nlm.nih.gov/gene 1246630 STY0134 20140406 220341 protein-coding NCBI-supplied PMID: 11677608; 17908208; 18156266 MUTATION: leuO mutant exhibited wild-type levels of epithelial invasion but highly reduced transepithelial migration of PMN [PMID:15182677]. 1177 leuABCD operon activator protein - STY0134 Bin Zhao, Oliver He gmhA WEB: http://www.ncbi.nlm.nih.gov/gene 1246837 STY0355 20140406 220341 protein-coding NCBI-supplied PMID: 11677608 MUTATION: gmhA mutants have reduced epithelial cell invasion and reduced transepithelial migration of PMN compared to the wild type [PMID:15182677]. 1178 phosphoheptose isomerase - STY0355 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1247108 STY0644 20140405 220341 protein-coding NCBI-supplied PMID: 11677608 MUTATION: cstA mutants have reduced epithelial cell invasion and reduced transepithelial migration of PMN compared to the wild type [PMID:15182677]. 1179 carbon starvation protein A cstA Bin Zhao, Oliver He pipC WEB: http://www.ncbi.nlm.nih.gov/gene 1247535 STY1120 20140222 220341 protein-coding NCBI-supplied PMID: 11677608 MUTATION: sigE mutant is less invasive than the wild type in both HEp-2 and CHO cell lines [PMID:9537377]. 1180 cell invasion protein - sigE Bin Zhao, Oliver He sopB WEB: http://www.ncbi.nlm.nih.gov/gene 1247536 STY1121 20140406 220341 protein-coding NCBI-supplied PMID: 11677608 MUTATION: sigD mutant is less invasive than the wild type in both HEp-2 and CHO cell lines [PMID:9537377]. 1181 cell invasion protein - sigD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1247855 STY1465 20140225 220341 protein-coding NCBI-supplied PMID: 11677608 MUTATION: pcgL mutant is attenuated in pigs [PMID:17526851]. 1182 D-alanyl-D-alanine dipeptidase pcgL Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1248080 STY1706 20140406 220341 protein-coding NCBI-supplied PMID: 11677608 MUTATION: ssaV and aroC double mutants are attenuated in humans [PMID:19745519]. 1183 type III secretion protein ssaV Bin Zhao, Oliver He ssaM WEB: http://www.ncbi.nlm.nih.gov/gene 1248081 STY1707 20140222 220341 protein-coding NCBI-supplied PMID: 11677608 MUTATION: ssaM mutant is attenuated in mice [PMID:15491354]. 1184 pathogenicity island protein - STY1707 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1248093 STY1719 20140215 220341 protein-coding NCBI-supplied PMID: 11677608 MUTATION: sseD mutant is attenuated in mice [PMID:11159962]. 1185 pathogenicity island effector protein sseD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1248094 STY1720 20140215 220341 protein-coding NCBI-supplied PMID: 11677608 MUTATION: sseC mutant is attenuated in mice [PMID:11159962]. 1186 pathogenicity island effector protein sseC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1248101 STY1727 20140222 220341 protein-coding NCBI-supplied PMID: 11677608; 19737903 MUTATION: spiC mutant cannot survive within macrophages and is attenuated in mice [PMID:10406797]. 1187 pathogenicity island 2 secreted effector protein spiC Bin Zhao, Oliver He flaG WEB: http://www.ncbi.nlm.nih.gov/gene 1248507 STY2167 20140405 220341 protein-coding NCBI-supplied PMID: 11677608 MUTATION: fliC mutants were attenuated in orally inoculated chicks [PMID:11731137]. 1188 flagellin - fliC Bin Zhao, Oliver He aroC WEB: http://www.ncbi.nlm.nih.gov/gene 1248939 STY2616 20140405 220341 protein-coding NCBI-supplied PMID: 11677608 MUTATION: ssaV and aroC double mutants are attenuated in humans [PMID:19745519]. 1189 chorismate synthase - STY2616 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1249300 STY2992 20140406 220341 protein-coding NCBI-supplied PMID: 11677608 MUTATION: prgK mutants are attenuated in their ability to invade HEp-2 cells [PMID:10816487]. 1190 pathogenicity 1 island effector protein prgK Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1249301 STY2993 20140222 220341 protein-coding NCBI-supplied PMID: 11677608 MUTATION: prgJ mutants are attenuated in their ability to invade HEp-2 cells [PMID:10816487]. 1191 pathogenicity 1 island effector protein prgJ Bin Zhao, Oliver He sspC WEB: http://www.ncbi.nlm.nih.gov/gene 1249313 STY3007 20140405 220341 protein-coding NCBI-supplied PMID: 11677608 MUTATION: A SipC nucleation-deficient mutant, which maintained its effector translocation activity, had significantly reduced ability to induce actin cytoskeleton rearrangements, resulting in lower bacterial invasion into HeLa cells [PMID:15720547]. 1192 pathogenicity island 1 effector protein - sipC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1249316 STY3010 20140225 220341 protein-coding NCBI-supplied PMID: 11677608 MUTATION: spaS mutant was 30-fold reduced for invasion into HEp-2 cells when compared with the wild-type strain [PMID:10692170]. 1193 secretory protein spaS Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1249317 STY3011 20140225 220341 protein-coding NCBI-supplied PMID: 11677608 MUTATION: spaR mutant is severely impaired in entry to Henle-407 cells [PMID:8751894]. 1194 secretory protein spaR Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1249318 STY3012 20140225 220341 protein-coding NCBI-supplied PMID: 11677608 MUTATION: spaQ mutant is severely impaired in entry to Henle-407 cells [PMID:8751894]. 1195 secretory protein spaQ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1249319 STY3013 20140225 220341 protein-coding NCBI-supplied PMID: 11677608 MUTATION: spaP mutant is severely impaired in entry to Henle-407 cells [PMID:8751894]. 1196 secretory protein spaP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1249320 STY3014 20140225 220341 protein-coding NCBI-supplied PMID: 11677608 MUTATION: spaO mutant is severely impaired in entry to Henle-407 cells [PMID:8751894]. 1197 surface presentation of antigens protein spaO Bin Zhao, Oliver He invJ WEB: http://www.ncbi.nlm.nih.gov/gene 1249321 STY3015 20140205 220341 protein-coding NCBI-supplied PMID: 11677608 MUTATION: invJ mutants are defective for entry into cultured epithelial cells [PMID:7752894]. 1198 surface presentation of antigens protein - spaN Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1249322 STY3016 20140225 220341 protein-coding NCBI-supplied PMID: 11677608 MUTATION: invI mutants are defective for entry into cultured epithelial cells [PMID:7752894]. 1199 secretory protein spaM Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1249329 STY3023 20140205 220341 protein-coding NCBI-supplied PMID: 11677608; 23159244 MUTATION: invH mutants are attenuated in calves [PMID:9529064]. 1200 cell adherance/invasion protein invH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1251088 STY4890 20140217 220341 protein-coding NCBI-supplied PMID: 11677608 MUTATION: cstA mutants have reduced epithelial cell invasion and reduced transepithelial migration of PMN compared to the wild type [PMID:15182677]. 1201 carbon starvation protein cstA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1251534 STM0016 20140406 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: STM0016 mutant is attenuated in mice [PMID:16518469]. 2588 hypothetical protein STM0016 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1251548 STM0030 20140222 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: STM0030 mutant is attenuated in mice [PMID:16518469]. 2589 transcriptional regulator STM0030 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1251554 STM0036 20140222 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: STM0036 mutant is attenuated in pigs [PMID:17526851]. 2590 arylsulfatase regulator STM0036 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1251610 STM0092 20140406 99287 protein-coding NCBI-supplied PMID: 11677609; 20232248 MUTATION: A surA mutant (BRD1115) is attenuated in BALB/c mice [PMID:10678914]. 5007 peptidyl-prolyl cis-trans isomerase SurA surA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1251633 STM0115 20140324 99287 protein-coding NCBI-supplied PMID: 11677609; 15711009 MUTATION: leuO mutant exhibited wild-type levels of epithelial invasion but highly reduced transepithelial migration of PMN [PMID:15182677]. 2591 leucine transcriptional activator leuO Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1251726 STM0208 20140222 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: dgt mutant is attenuated in mice [PMID:16518469]. 2592 deoxyguanosinetriphosphate triphosphohydrolase dgt Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1251780 STM0262 20140222 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: yagS mutant is attenuated in mice [PMID:16518469]. 2593 SAM-dependent methyltransferase yafS Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1251817 STM0298 20140125 99287 pseudo NCBI-supplied MUTATION: STM0298 mutant is attenuated in mice [PMID:16518469]. 2594 pseudo STM0298 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1251818 STM0299 20140222 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: safA mutant is attenuated in pigs [PMID:17526851]. 2595 major pilus subunit SafA safA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1251829 STM0310 20140406 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: gmhA mutants have reduced epithelial cell invasion and reduced transepithelial migration of PMN compared to the wild type [PMID:15182677]. 2596 phosphoheptose isomerase gmhA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1251832 STM0313 20140322 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: dinP mutant is attenuated in mice [PMID:16518469]. 2597 DNA polymerase IV dinP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1251847 STM0328.s 20140301 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: STM0328 mutant is attenuated in pigs [PMID:17526851]. 2598 permease STM0328.s Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1251856 STM0337 20131204 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: stbD mutant is attenuated in pigs [PMID:17526851]. 2599 fimbrial usher stbD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1251857 STM0338 20140125 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: stbC mutant is attenuated in pigs [PMID:17526851]. 2600 fimbrial usher stbC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1251892 STM0373 20140324 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: yaiU mutant is attenuated in pigs [PMID:17526851]. 2601 flagellar protein yaiU Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1251915 STM0396 20140125 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: sbcD mutant is attenuated in pigs [PMID:17526851]. 2602 exonuclease subunit SbcD sbcD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1251958 STM0438 20140222 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: STM0438 mutant is attenuated in pigs [PMID:17526851]. 2603 hypothetical protein STM0438 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1251962 STM0442 20140322 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: cyoB mutant is attenuated in mice [PMID:16518469]. 2604 cytochrome o ubiquinol oxidase subunit I cyoB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1251968 STM0448 20140322 99287 protein-coding NCBI-supplied PMID: 11677609; 18245288; 22380597; 23676436 MUTATION: clpP mutant is attenuated in mice [PMID:7618105]. 2605 ATP-dependent Clp protease proteolytic subunit clpP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1251970 STM0450 20140222 99287 protein-coding NCBI-supplied PMID: 11677609; 15661008 MUTATION: lon mutant is attenuated in mice [PMID:12496146]. 4924 DNA-binding ATP-dependent protease La lon Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1251994 STM0474 20140406 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: ybaJ mutant is attenuated in pigs [PMID:17526851]. 2606 hypothetical protein ybaJ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252038 STM0518 20140406 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: gip mutant is attenuated in mice [PMID:16518469]. 2607 hydroxypyruvate isomerase gip Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252040 STM0520 20140222 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: STM0520 mutant is attenuated in mice [PMID:16518469]. 2608 permease STM0520 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252048 STM0528 20140322 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: allD mutant is attenuated in mice [PMID:16518469]. 2609 ureidoglycolate dehydrogenase allD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252063 STM0543 20140322 99287 protein-coding NCBI-supplied PMID: 11677609; 23938383 MUTATION: fimA mutants are attenuated in mice and swine [PMID:14573666]. 2610 fimbrin fimA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252067 STM0547 20140322 99287 protein-coding NCBI-supplied PMID: 11677609; 19383701 MUTATION: fimH mutants were impaired in binding and internalization of HeLa cells [PMID:17379714]. 2611 minor fimbrial subunit fimH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252072 STM0552 20140215 99287 protein-coding NCBI-supplied PMID: 11677609; 19218381 MUTATION: fimW mutant is attenuated in mice [PMID:16518469]. 2612 fimbrial protein fimW Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252077 STM0557 20131204 99287 protein-coding NCBI-supplied PMID: 11677609; 18826410 MUTATION: STM0557 mutant is attenuated in pigs [PMID:17526851]. 2613 inner membrane protein STM0557 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252079 STM0559 20131204 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: rfbl mutant is attenuated in pigs [PMID:17526851]. 2614 glycosyl translocase rfbI Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252098 STM0578 20140322 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: nfnB mutant is attenuated in mice [PMID:16518469]. 2615 nitroreductase nfnB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252105 STM0585 20140405 99287 protein-coding NCBI-supplied PMID: 11677609; 23959718 MUTATION: fepA mutant is attenuated in pigs [PMID:17526851]. 2616 outer membrane receptor FepA fepA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252120 STM0600 20140222 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: cstA mutants have reduced epithelial cell invasion and reduced transepithelial migration of PMN compared to the wild type [PMID:15182677]. 2617 carbon starvation protein cstA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252144 STM0624 20140222 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: citC mutant is attenuated in pigs [PMID:17526851]. 2618 citrate lyase synthetase citC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252146 STM0626 20140222 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: dpiA mutant is attenuated in pigs [PMID:17526851]. 2619 two-component response regulator DpiA dpiA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252149 STM0629 20131204 99287 protein-coding NCBI-supplied PMID: 11677609; 20054119 MUTATION: cspE mutant is attenuated in mice [PMID:16518469]. 2620 cold shock protein CspE cspE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252179 STM0659 20140125 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: hscC mutant is attenuated in pigs [PMID:17526851]. 2621 heatshock protein hscC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252243 STM0723 20140215 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: STM0723 mutant is attenuated in mice [PMID:16518469]. 2622 polysaccharide/polyol phosphate ABC transporter ATPase STM0723 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252267 STM0747 20140222 99287 protein-coding NCBI-supplied PMID: 11677609; 19118362; 21252278 MUTATION: A tolA mutant is attenuated in mice [PMID:19118362]. 4933 cell envelope integrity inner membrane protein TolA tolA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252285 STM0765 20140222 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: STM0765 mutant is attenuated in pigs [PMID:17526851]. 2623 cation transporter STM0765 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252320 STM0800 20140222 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: slrP mutant is attenuated in mice [PMID:10569754]. 2624 E3 ubiquitin-protein ligase SlrP slrP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252328 STM0808 20140406 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: ybhM mutant is attenuated in pigs [PMID:17526851]. 2625 integral membrane protein ybhM Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252385 STM0866 20140222 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: mdfA mutant is attenuated in pigs [PMID:17526851]. 2626 multidrug translocase mdfA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252488 STM0970 20140329 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: pflA mutant is attenuated in pigs [PMID:17526851]. 2627 pyruvate formate lyase-activating enzyme 1 pflA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252490 STM0972 20140125 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: STM0972 mutant is attenuated in mice [PMID:16518469]. 2628 Secreted effector protein SopD2 STM0972 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252492 STM0974 20140222 99287 protein-coding NCBI-supplied PMID: 11677609; 21493860 MUTATION: focA mutant is attenuated in mice [PMID:16518469]. 2629 formate transporter focA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252520 STM1002 20140322 99287 protein-coding NCBI-supplied PMID: 11677609; 22904288 MUTATION: STM1002 mutant is attenuated in mice [PMID:16518469]. 2630 diaminopropionate ammonia-lyase STM1002 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252569 STM1051 20140324 99287 protein-coding NCBI-supplied PMID: 11677609; 19956712; 21767808 MUTATION: sseI mutant is attenuated in mice [PMID:16518469]. 2631 required for maintaining a long-term systemic infection Other designations: secreted effector protein sseI Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252576 STM1058 20140405 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: pyrD mutant is attenuated in pigs [PMID:17526851]. 2632 dihydroorotate dehydrogenase 2 pyrD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252587 STM1069 20140324 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: ycbG mutant is attenuated in mice [PMID:16518469]. 2633 hypothetical protein ycbG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252605 STM1087 20140217 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: pipA mutants have reduced epithelial cell invasion and reduced transepithelial migration of PMN compared to the wild type [PMID:15182677]. 2634 pathogenicity island-encoded protein A pipA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252608 STM1090 20140405 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: pipC mutant is attenuated in pigs [PMID:17526851]. 2635 pathogenicity island-encoded protein C pipC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252609 STM1091 20140405 99287 protein-coding NCBI-supplied PMID: 11677609; 15205533; 15642738; 16153243; 16869830; 17379731; 17389247; 19379694; 19614667; 19662166; 20542249; 21498643; 21555401; 21779406; 24075929 MUTATION: sopB mutants induce significantly less fluid accumulation in bovine ligated ileal loops than the wild-type [PMID:12065528]. 2636 inositol phosphate phosphatase SopB sopB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252612 STM1094 20140222 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: pipD mutant is attenuated in mice [PMID:16518469]. 2637 dipeptidase pipD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252613 STM1095 20140222 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: copS mutant is attenuated in mice [PMID:16518469]. 2638 copper resistance protein copS Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252658 STM1140 20140324 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: csgF mutant is attenuated in mice [PMID:16518469]. 2639 curli assembly protein CsgF csgF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252660 STM1142 20140324 99287 protein-coding NCBI-supplied PMID: 11677609; 16842367; 19376870; 19897646; 20545866 MUTATION: csgD mutant is attenuated in mice [PMID:16518469]. 2640 DNA-binding transcriptional regulator CsgD csgD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252663 STM1145 20140406 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: csgC mutant is attenuated in mice [PMID:16518469]. 2641 autoagglutination protein csgC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252678 STM1160 20140406 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: solA mutant is attenuated in mice [PMID:16518469]. 2642 N-methyltryptophan oxidase solA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252742 STM1224 20140325 99287 protein-coding NCBI-supplied PMID: 11677609; 15469435; 15710609; 15905402; 18996344; 19801640 MUTATION: sifA mutants are attenuated in mice and don't induce Salmonella-produced filaments in epithelial cells [PMID:8861213]. 2643 secreted effector protein SifA sifA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252764 STM1246 20140325 99287 protein-coding NCBI-supplied PMID: 11677609; 16279195; 18620040 MUTATION: pagC mutant is attenuated in mice [PMID:16518469]. 2644 virulence membrane protein PAGC precursor pagC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252801 STM1283 20140222 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: yeaJ mutant is attenuated in mice [PMID:16518469]. 2645 methyl-accepting chemotaxis protein yeaJ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252814 STM1296 20131204 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: ydjA mutant is attenuated in pigs [PMID:17526851]. 2646 hypothetical protein ydjA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252830 STM1312 20140325 99287 protein-coding NCBI-supplied PMID: 11677609 PTS system N,N'-diacetylchitobiose-specific transporter subunit IIB celA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252834 STM1316 20140222 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: celF mutant is attenuated in pigs [PMID:17526851]. 2648 phospho-beta-glucosidase/cellobiose-6-phosphate hydrolase celF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252861 STM1343 20140124 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: nlpC mutant is attenuated in mice [PMID:16518469]. 2649 lipoprotein nlpC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252882 STM1364 20140222 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: ydiK mutant is attenuated in mice [PMID:16518469]. 2650 inner membrane protein ydiK Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252909 STM1391 20140222 99287 protein-coding NCBI-supplied PMID: 11677609; 15491370; 16904940; 17630976; 19245712; 20660761; 21059960 MUTATION: ssrB mutant is attenuated in pigs [PMID:17526851]. 2651 transcriptional activator ssrB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252910 STM1392 20140215 99287 protein-coding NCBI-supplied PMID: 11677609; 16904940; 16999831 MUTATION: ssrA mutant is attenuated in pigs [PMID:17526851]. 2652 sensor kinase ssrA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252911 STM1393 20140124 99287 protein-coding NCBI-supplied PMID: 11677609; 19520723 MUTATION: ssaB mutant is attenuated in pigs [PMID:17526851]. 2653 secreted effector protein ssaB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252912 STM1394 20140222 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: ssaC mutant is attenuated in murine macrophages [PMID:16113260]. 2654 outer membrane secretin precursor ssaC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252913 STM1395 20131204 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: ssaD mutant is attenuated in pigs [PMID:17526851]. 2655 virulence protein ssaD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252914 STM1396 20140406 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: ssaE mutant is attenuated in mice [PMID:16518469]. 2656 secretion system effector ssaE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252915 STM1397 20140325 99287 protein-coding NCBI-supplied PMID: 11677609; 15256549 secretion system chaperone protein SseA sseA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252916 STM1398 20140325 99287 protein-coding NCBI-supplied PMID: 11677609; 15256549 MUTATION: sseB mutant is attenuated in mice [PMID:16518469]. 2658 translocation machinery protein SseB sseB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252918 STM1400 20140215 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: sseC mutant is attenuated in mice [PMID:11159962]. 2659 translocation machinery protein SseC sseC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252919 STM1401 20140325 99287 protein-coding NCBI-supplied PMID: 11677609; 15256549; 17524577; 20377892 MUTATION: sseD mutant is attenuated in mice [PMID:11159962]. 2660 translocation machinery protein SseD sseD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252920 STM1402 20140215 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: sseE mutant is defective for replication in murine macrophages [PMID:16113260]. 2661 secreted effector protein sseE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252922 STM1404 20131204 99287 protein-coding NCBI-supplied PMID: 11677609; 22529968 MUTATION: sseF mutant is defective for replication in murine macrophages [PMID:16113260]. 2662 secreted effector protein sseF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252923 STM1405 20140406 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: sseG mutant has a defect in replication in murine macrophages [PMID:16113260]. 2663 secreted effector protein sseG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252924 STM1406 20140222 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: ssaG mutant is attenuated in pigs [PMID:17526851]. 2664 type III secretion system apparatus protein ssaG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252927 STM1409 20140325 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: ssaJ mutant is attenuated in pigs [PMID:17526851]. 2665 needle complex inner membrane lipoprotein ssaJ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252929 STM1411 20140406 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: ssaK mutant is attenuated in pigs [PMID:17526851]. 2666 type III secretion system apparatus protein ssaK Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252930 STM1412 20140325 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: ssaL mutant is attenuated in pigs [PMID:17526851]. 2667 type III secretion system apparatus protein ssaL Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252931 STM1413 20140322 99287 protein-coding NCBI-supplied PMID: 11677609; 15491354 MUTATION: ssaM mutant is attenuated in mice [PMID:15491354]. 2668 type III secretion system apparatus protein ssaM Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252933 STM1415 20140406 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: ssaN mutant is attenuated in mice [PMID:16518469]. 2669 type III secretion system ATPase ssaN Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252936 STM1418 20140325 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: ssaQ mutant is attenuated in pigs [PMID:17526851]. 2670 type III secretion system protein ssaQ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252937 STM1419 20140125 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: ssaR mutant is attenuated in pigs [PMID:17526851]. 2671 type III secretion system protein ssaR Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252938 STM1420 20140322 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: ssaS mutant is attenuated in pigs [PMID:17526851]. 2672 type III secretion system apparatus protein SsaS ssaS Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252940 STM1422 20140325 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: ssaU mutant is attenuated in mice [PMID:16518469]. 2673 secretion system apparatus protein SsaU ssaU Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1252962 STM1444 20140301 99287 protein-coding NCBI-supplied PMID: 11677609; 17259627; 18678876; 19204896; 21550983 MUTATION: slyA mutant is attenuated in mice [PMID:8290552]. 2674 transcriptional regulator SlyA slyA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1253000 STM1482 20140325 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: ydgF mutant is attenuated in mice [PMID:16518469]. 2675 multidrug efflux system protein MdtJ ydgF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1253045 STM1527 20140215 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: STM1527 mutant is attenuated in pigs [PMID:17526851]. 2676 inner membrane protein STM1527 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1253067 STM1549 20140406 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: STM1549 mutant is attenuated in mice [PMID:16518469]. 2677 translation initiation inhibitor STM1549 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1253082 STM1564 20140325 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: yddX mutant is attenuated in mice [PMID:16518469]. 2678 biofilm-dependent modulation protein yddX Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1253090 STM1572 20140325 99287 protein-coding NCBI-supplied PMID: 11677609; 19767429; 21646491 MUTATION: nmpC (ompD) mutant is attenuated in swine [PMID:17296750]. 4929 outer membrane porin precursor nmpC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1253101 STM1583 20140322 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: STM1583 mutant is attenuated in mice [PMID:16518469]. 2679 hypothetical protein STM1583 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1253107 STM1589 20140325 99287 protein-coding NCBI-supplied PMID: 11677609 NADP-dependent oxidoreductase yncB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1253149 STM1631 20140406 99287 protein-coding NCBI-supplied PMID: 11677609; 18333886; 18757801; 18996344; 21138562 MUTATION: sseJ mutants are defective in intracellular replication in cultured epithelial cells and are attenuated in mice [PMID:16177296]. 2681 deacylase activity Other designations: secreted effector protein SseJ sseJ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1253170 STM1652 20140325 99287 protein-coding NCBI-supplied PMID: 11677609; 18007050 MUTATION: ynaF mutant is attenuated in pigs [PMID:17526851]. 2682 universal stress protein ynaF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1253186 STM1668 20140124 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: STM1668 mutant is attenuated in pigs [PMID:17526851]. 2683 antivirulence protein ZirS STM1668 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1253187 STM1669 20140222 99287 protein-coding NCBI-supplied PMID: 11677609; 18389060 MUTATION: STM1669 mutant is attenuated in mice [PMID:16518469]. 2684 invasin-like protein STM1669 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1253225 STM1706 20140325 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: yciH mutant is attenuated in mice [PMID:16518469]. 2685 translation initiation factor Sui1 yciH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1253248 STM1729 20140325 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: yciF mutant is attenuated in pigs [PMID:17526851]. 2686 hypothetical protein yciF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1253270 STM1751 20140222 99287 protein-coding NCBI-supplied PMID: 11677609; 15966862; 16763111; 18039769; 18160484; 19521501; 20444106; 21075923 MUTATION: hns mutant is attenuated in pigs [PMID:17526851]. 2687 global DNA-binding transcriptional dual regulator H-NS hns Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1253337 STM1818 20140405 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: fadD mutant is attenuated in mice [PMID:16518469]. 2688 long-chain-fatty-acid--CoA ligase fadD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1253356 STM1837 20140325 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: cspC mutant is attenuated in mice [PMID:16518469]. 2689 cold shock-like protein CspC cspC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1253374 STM1855 20140405 99287 protein-coding NCBI-supplied PMID: 11677609; 16359332; 16869830; 17379731; 19662166; 19683679 MUTATION: sopE2 mutant has reduced ability to invade HeLa cells compared to wild-type [PMID:10735884]. 2690 type III-secreted effector protein sopE2 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1253381 STM1862 20140325 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: pagO mutant is attenuated in pigs [PMID:17526851]. 2691 integral membrane protein pagO Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1253383 STM1864 20140215 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: STM1864 mutant is attenuated in pigs [PMID:17526851]. 2692 inner membrane protein STM1864 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1253386 STM1867 20140222 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: pagK mutant is attenuated in pigs [PMID:17526851]. 2693 PagK pagK Bin Zhao, Oliver He yebL WEB: http://www.ncbi.nlm.nih.gov/gene 1253412 STM1891 20140329 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: znuABC mutant is attenuated in mice [PMID:21219981]. 2694 high-affinity zinc transporter periplasmic protein - znuA Bin Zhao, Oliver He yebM WEB: http://www.ncbi.nlm.nih.gov/gene 1253413 STM1892.S 20140301 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: znuABC mutant is attenuated in mice [PMID:21219981]. 2695 high-affinity zinc transporter ATPase - znuC Bin Zhao, Oliver He yebI WEB: http://www.ncbi.nlm.nih.gov/gene 1253414 STM1893 20140222 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: znuABC mutant is attenuated in mice [PMID:21219981]. 2696 high-affinity zinc transporter membrane protein - znuB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1253415 STM1894 20140325 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: A ruvB mutant is attenuated in mice [PMID:20670908]. 4932 Holliday junction DNA helicase RuvB ruvB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1253417 STM1896 20131204 99287 protein-coding NCBI-supplied PMID: 11677609 hypothetical protein STM1896 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1253455 STM1934 20131204 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: STM1934 mutant is attenuated in mice [PMID:16518469]. 2698 outer membrane lipoprotein STM1934 Bin Zhao, Oliver He sirA WEB: http://www.ncbi.nlm.nih.gov/gene 1253468 STM1947 20140222 99287 protein-coding NCBI-supplied PMID: 11677609; 17635868; 21518393 MUTATION: sirA mutant is defective for intracellular replication, invasion of epithelial cells and defective in murine macrophages [PMID:16113260]. 2699 response regulator - uvrY Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1253480 STM1959 20140325 99287 protein-coding NCBI-supplied PMID: 11677609; 15501801; 15944299; 16179598; 16803592; 16844786; 17292856; 20868693; 22516952; 23012363; 23624387 MUTATION: fliC mutants were attenuated in orally inoculated chicks [PMID:11731137]. 2700 flagellin fliC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1253501 STM1980 20140325 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: fliQ mutant is attenuated in mice [PMID:7618105]. 2701 flagellar biosynthesis protein FliQ fliQ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1253522 STM2001 20140322 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: yeeI mutant is attenuated in pigs [PMID:17526851]. 2702 inner membrane protein yeeI Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1253587 STM2066 20140322 99287 protein-coding NCBI-supplied PMID: 11677609; 16176924; 17076670; 17379731; 19191875 MUTATION: sopA mutants induce significantly less fluid accumulation in bovine ligated ileal loops than the wild-type [PMID:12065528]. 2703 E3 ubiquitin-protein ligase SopA sopA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1253601 STM2080 20140405 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: udg mutant is attenuated in mice [PMID:16518469]. 2704 UDP-glucose/GDP-mannose dehydrogenase udg Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1253603 STM2082 20140322 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: rfbP mutant is attenuated in mice [PMID:16518469]. 2705 undecaprenol-phosphate galactosephosphotransferase/O-antigen transferase rfbP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1253604 STM2083 20140405 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: rfbK mutant is attenuated in pigs [PMID:17526851]. 2706 phosphomannomutase rfbK Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1253605 STM2084 20140405 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: rfbM mutant is attenuated in mice [PMID:7618105]. 2707 mannose-1-phosphate guanylyltransferase rfbM Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1253606 STM2085 20140322 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: rfbN mutant is attenuated in pigs [PMID:17526851]. 2708 rhamnosyl transferase rfbN Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1253611 STM2090 20140325 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: rfbH mutant is attenuated in pigs [PMID:17526851]. 2709 CDP-6-deoxy-D-xylo-4-hexulose-3-dehydrase rfbH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1253614 STM2093 20140405 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: rfbI mutant is attenuated in pigs [PMID:17526851]. 2710 CDP-6-deoxy-delta-3,4-glucoseen reductase rfbI Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1253615 STM2094 20140406 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: rfbC mutant is attenuated in mice [PMID:16518469]. 2711 dTDP-4-deoxyrhamnose 3,5 epimerase rfbC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1253616 STM2095 20140405 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: rfbA mutant is attenuated in mice [PMID:16518469]. 2712 dTDP-glucose pyrophosphorylase rfbA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1253617 STM2096 20140405 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: rfbD mutant is attenuated in mice [PMID:7618105]. 2713 dTDP-4-dehydrorhamnose reductase rfbD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1253618 STM2097 20140405 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: rfbB mutant is attenuated in mice [PMID:7618105]. 2714 dTDP-glucose-4,6-dehydratase rfbB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1253619 STM2098 20140405 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: galF mutant is attenuated in mice [PMID:16518469]. 2715 UTP--glucose-1-phosphate uridylyltransferase subunit GalF galF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1253620 STM2099 20140325 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: wcaM mutant is attenuated in mice [PMID:16518469]. 2716 colanic acid biosynthesis protein wcaM Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1253632 STM2111 20140222 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: wcaE mutant is attenuated in pigs [PMID:17526851]. 2717 glycosyl transferase family protein wcaE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1253657 STM2136 20140222 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: yegQ mutant is attenuated in mice [PMID:16518469]. 2718 protease yegQ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1253658 STM2137 20140215 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: STM2137 mutant is attenuated in mice [PMID:16518469]. 2719 hypothetical protein STM2137 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1253670 STM2149 20140215 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: stcD mutant is attenuated in mice [PMID:16518469]. 2720 outer membrane lipoprotein stcD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1253671 STM2150 20140125 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: stcC mutant is attenuated in mice [PMID:16518469]. 2721 outer membrane protein stcC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1253688 STM2166 20140405 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: bglX mutant is attenuated in mice [PMID:16518469]. 2722 periplasmic beta-D-glucoside glucohydrolase bglX Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1253709 STM2187 20140405 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: yeiA mutant is attenuated in mice [PMID:16518469]. 2723 dihydropyrimidine dehydrogenase yeiA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1253719 STM2197 20140406 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: STM2197 mutant is attenuated in mice [PMID:16518469]. 2724 phosphoserine phosphatase STM2197 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1253765 STM2243 20140124 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: STM2243 mutant is attenuated in pigs [PMID:17526851]. 2725 tail fiber protein of phage STM2243 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1253767 STM2245 20131204 99287 protein-coding NCBI-supplied PMID: 11677609; 18567660 MUTATION: STM2245 mutant is attenuated in pigs [PMID:17526851]. 2726 outer membrane protein STM2245 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1253794 STM2272 20140322 99287 protein-coding NCBI-supplied PMID: 11677609; 16166547; 16431864; 16585773; 22916023 MUTATION: A gyrA-cpxA-rpoB Salmonella Typhimurium mutant was attenuated in pigs [PMID:15542179]. 5003 DNA gyrase subunit A gyrA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1253895 STM2373 20131204 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: STM2373 mutant is attenuated in mice [PMID:16518469]. 2727 hypothetical protein STM2373 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1254023 STM2501 20140406 99287 protein-coding NCBI-supplied PMID: 11677609; 15838036 MUTATION: ppk mutant is attenuated in pigs [PMID:17526851]. 2728 polyphosphate kinase ppk Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1254025 STM2503 20140125 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: STM2503 mutant is attenuated in pigs [PMID:17526851]. 2729 diguanylate cyclase STM2503 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1254035 STM2513 20140222 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: shdA mutants exhibit a shedding defect in mice [PMID:12540539]. 2730 AIDA autotransporter-like protein shdA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1254036 STM2514 20140222 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: ratB mutant are unable to colonize the cecum in mice, but are still able to colonize the eyer's patches, mesenteric lymph nodes, and spleen of mice [PMID:12540539]. 2731 outer membrane protein ratB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1254080 STM2558 20140222 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: cadB mutant is attenuated in pigs [PMID:17526851]. 2732 lysine/cadaverine antiporter cadB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1254096 STM2574 20140124 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: STM2574 mutant is attenuated in pigs [PMID:17526851]. 2733 permease STM2574 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1254098 STM2576 20140222 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: yfhL mutant is attenuated in mice [PMID:16518469]. 2734 ferredoxin yfhL Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1254107 STM2585 20140125 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: STM2585 mutant is attenuated in mice [PMID:16518469]. 2735 transposase-like protein STM2585 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1254183 STM2660 20140215 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: clpB mutant is attenuated in pigs [PMID:17526851]. 2736 protein disaggregation chaperone clpB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1254203 STM2680 20131204 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: STM2680 mutant is attenuated in mice [PMID:16518469]. 2737 hypothetical protein STM2680 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1254212 STM2689 20131204 99287 pseudo NCBI-supplied PMID: 16313619 MUTATION: STM2689 (bapA) mutant strain showed a significantly lower colonization rate at the intestinal cell barrier and consequently a decreased efficiency for organ invasion compared with the wild-type strain in mice [PMID:16313619]. 2738 pseudo STM2689 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1254293 STM2770 20140325 99287 protein-coding NCBI-supplied PMID: 11677609; 16844786 MUTATION: fljA mutant is attenuated in pigs [PMID:17526851]. 2739 phase-1 flagellin repressor fljA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1254305 STM2782 20140222 99287 protein-coding NCBI-supplied PMID: 11677609; 15661016 MUTATION: mig-14 mutants are cleared by mice compared to the wild type which is fatal to mice in the doses given [PMID:11083839]. 2740 transcriptional activator mig-14 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1254319 STM2796 20140222 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: ygaE mutant is attenuated in mice [PMID:16518469]. 2741 transporter yqaE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1254390 STM2867 20140406 99287 protein-coding NCBI-supplied PMID: 11677609; 15661008; 18160484; 18245288 MUTATION: hilC mutants have decreased invasion of HEp-2 cells compared to the wild type [PMID:10320584]. 2742 invasion regulatory protein hilC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1254392 STM2869 20140215 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: orgB mutants are attenuated in their ability to invade HEp-2 cells [PMID:10816487]. 2743 needle complex export protein orgB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1254393 STM2870 20140222 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: orgA mutants are attenuated in their ability to invade HEp-2 cells [PMID:10816487]. 2744 invasion protein OrgA orgA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1254394 STM2871 20140215 99287 protein-coding NCBI-supplied PMID: 11677609; 20368966; 21385715 MUTATION: prgK mutants are attenuated in their ability to invade HEp-2 cells [PMID:10816487]. 2745 needle complex inner membrane lipoprotein prgK Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1254395 STM2872 20140329 99287 protein-coding NCBI-supplied PMID: 11677609; 24379359 MUTATION: prgJ mutants are attenuated in their ability to invade HEp-2 cells [PMID:10816487]. 2746 needle complex minor subunit prgJ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1254396 STM2873 20140325 99287 protein-coding NCBI-supplied PMID: 11677609; 16501225; 17617421; 19823588 MUTATION: prgI mutants are attenuated in their ability to invade HEp-2 cells [PMID:10816487]. 2747 needle complex major subunit prgI Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1254397 STM2874 20140322 99287 protein-coding NCBI-supplied PMID: 11677609; 20368966; 21385715 MUTATION: prgH mutants are attenuated in their ability to invade HEp-2 cells [PMID:10816487]. 2748 needle complex inner membrane protein prgH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1254398 STM2875 20140322 99287 protein-coding NCBI-supplied PMID: 11677609; 15661008; 18160484; 18245288; 20190046; 20889744; 21518393 MUTATION: hilD mutants have decreased invasion of HEp-2 cells compared to the wild type [PMID:10320584]. 2749 invasion protein regulatory protein hilD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1254399 STM2876 20140222 99287 protein-coding NCBI-supplied PMID: 11677609; 16443238; 16585772; 17635868; 18092431; 18160484; 20190046; 21075923 MUTATION: hilA mutants have reduced ability to invade HEp-2 cells and to colonize murine Peyer’s patches [PMID:10456944]. 2750 invasion protein regulator hilA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1254401 STM2878 20140405 99287 protein-coding NCBI-supplied PMID: 11677609; 19286132; 21801239; 24332031 MUTATION: sptP mutants have reduced epithelial cell invasion and reduced transepithelial migration of PMN compared to the wild type. Competition experiments indicate that sptP mutants fail to colonize the spleen of mice when coinoculated with wild-type S. enterica [PMID:15182677]. 2751 protein tyrosine phosphatase/GTPase activating protein sptP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1254404 STM2881 20140406 99287 protein-coding NCBI-supplied PMID: 11677609; 21263021 acyl carrier protein iacP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1254405 STM2882 20140405 99287 protein-coding NCBI-supplied PMID: 11677609; 16107539; 16507363; 16869830; 17379731; 17697195; 18005682; 18076120; 19046340; 19114119; 19411325; 20947770; 21899702; 22186610 MUTATION: sipA mutants have a decreased invasion of MDCK cells as compared to the wild type [PMID:19046340]. 2753 cell invasion protein SipA sipA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1254407 STM2884 20140329 99287 protein-coding NCBI-supplied PMID: 11677609; 19364837 MUTATION: A SipC nucleation-deficient mutant, which maintained its effector translocation activity, had significantly reduced ability to induce actin cytoskeleton rearrangements, resulting in lower bacterial invasion into HeLa cells [PMID:15720547]. 2754 cell invasion protein SipC sipC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1254409 STM2886 20140325 99287 protein-coding NCBI-supplied PMID: 11677609; 17768243; 21045315 MUTATION: sicA mutants are unable to invade cultured epithelial cells [PMID:7608068]. 2755 secretion chaperone SicA sicA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1254410 STM2887 20140217 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: spaS mutant was 30-fold reduced for invasion into HEp-2 cells when compared with the wild-type strain [PMID:10692170]. 2756 surface presentation of antigens protein SpaS spaS Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1254411 STM2888 20140325 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: spaR mutant is severely impaired in entry to Henle-407 cells [PMID:8751894]. 2757 needle complex export protein spaR Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1254412 STM2889 20140325 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: spaQ mutant is severely impaired in entry to Henle-407 cells [PMID:8751894]. 2758 needle complex export protein spaQ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1254413 STM2890 20140217 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: spaP mutant is severely impaired in entry to Henle-407 cells [PMID:8751894]. 2759 surface presentation of antigens protein SpaP spaP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1254414 STM2891 20140325 99287 protein-coding NCBI-supplied PMID: 11677609; 21292939 MUTATION: spaO mutant is severely impaired in entry to Henle-407 cells [PMID:8751894]. 2760 surface presentation of antigens protein SpaO spaO Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1254415 STM2892 20140325 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: invJ mutants are defective for entry into cultured epithelial cells [PMID:7752894]. 2761 needle length control protein invJ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1254416 STM2893 20140325 99287 protein-coding NCBI-supplied PMID: 11677609; 19260965 MUTATION: invI mutants are defective for entry into cultured epithelial cells [PMID:7752894]. 2762 needle complex assembly protein invI Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1254417 STM2894 20140322 99287 protein-coding NCBI-supplied PMID: 11677609; 17524577; 20185511 MUTATION: invC mutants are attenuated in chicks infected orally but not intraperitoneally [PMID:9087319]. 2763 ATP synthase SpaL invC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1254418 STM2895 20140222 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: In the absence of InvB, the ΔsopB ΔsopE2 strain was severely defective in its ability to invade cultured intestinal cells, indicating that InvB is required for the translocation of SopE into host cells [PMID:14645290]. 2764 secretion chaperone invB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1254419 STM2896 20140405 99287 protein-coding NCBI-supplied PMID: 11677609; 20306492 MUTATION: invA mutants are attenuated in chicks infected orally but not intraperitoneally [PMID:9087319]. 2765 needle complex export protein invA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1254420 STM2897 20140222 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: invE mutants were unable to penetrate Henle-407 human intestinal cells and Madin-Darby canine kidney cells [PMID:1631083]. 2766 invasion protein invE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1254421 STM2898 20140325 99287 protein-coding NCBI-supplied PMID: 11677609; 20368966; 21385715 MUTATION: invG mutants have reduced ability to enter into cultured epithelial cells [PMID:7997169]. 2767 outer membrane secretin InvG invG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1254422 STM2899 20140215 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: invF mutants have reduced ability to enter into cultured epithelial cells [PMID:7997169]. 2768 invasion regulatory protein invF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1254423 STM2900 20140406 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: invH mutants are attenuated in calves [PMID:9529064]. 2769 needle complex outer membrane lipoprotein precursor invH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1254468 STM2945 20140222 99287 protein-coding NCBI-supplied PMID: 11677609; 15554961; 17379731; 20185511 MUTATION: sopD mutants induce significantly less fluid accumulation in bovine ligated ileal loops than the wild-type [PMID:12065528]. 2770 secreted effector protein SopD sopD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1254481 STM2958 20140215 99287 protein-coding NCBI-supplied PMID: 11677609; 21518393 MUTATION: barA mutant is inefficient in invasion of HEp-2 epithelial cells [PMID:16113260]. 2771 hybrid sensory histidine kinase BarA barA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1254541 STM3018 20140322 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: kdul mutant is attenuated in pigs [PMID:17526851]. 2772 5-keto-4-deoxyuronate isomerase kduI Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1254559 STM3036 20131204 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: STM3036 mutant is attenuated in mice [PMID:16518469]. 2773 inner membrane protein STM3036 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1254651 STM3128 20140315 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: STM3128 mutant is attenuated in mice [PMID:16518469]. 2774 oxidoreductase STM3128 MUTATION: STM3192 mutant is attenuated in mice [PMID:16518469]. 2775 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1254768 STM3245 20140215 99287 protein-coding NCBI-supplied PMID: 11677609; 18600042; 19812899; 21464594 MUTATION: tdcA mutant is less invasive of cultured epithelial cells and attenuated in mice [PMID:19812899]. 2776 DNA-binding transcriptional activator TdcA tdcA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1254865 STM3342 20131204 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: sspA mutants are not able to cause lethal infection in calves, however these mutants are still able to cause diarrhea in calves [PMID:10816458]. 2777 stringent starvation protein A sspA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1254976 STM3453 20140406 99287 protein-coding NCBI-supplied PMID: 11677609; 20232248 MUTATION: fkpA mutant exhibited a reduced ability to survive intracellularly in J774.A1 cells [PMID:9009347]. 2778 FKBP-type peptidyl-prolyl cis-trans isomerase fkpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1254978 STM3455 20140222 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: slyD mutant is attenuated in pigs [PMID:17526851]. 2779 FKBP-type peptidyl-prolyl cis-trans isomerase slyD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1254989 STM3466 20140217 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: crp deletion mutants are attenuated in mice [PMID:3291452]. 2780 cAMP-regulatory protein crp Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1255007 STM3484 20140325 99287 protein-coding NCBI-supplied PMID: 11677609; 15796979; 19191875; 20132031; 20487280 MUTATION: Lack of Dam methylation causes severe attenuation in animal models. Defects in virulence in dam mutants include such as impaired expression and secretion of invasion proteins, reduced cytotoxicity on M cells , inefficient colonization of Peyer’s patches and mesenteric lymph nodes, sensitivity to components of innate immunity, envelope instability and changes in LPS expression [PMID:19762965]. 2781 DNA adenine methylase dam Bin Zhao, Oliver He ompB WEB: http://www.ncbi.nlm.nih.gov/gene 1255024 STM3501 20140325 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: envZ mutant is attenuated in mice [PMID:7618105]. 2782 osmolarity sensor protein - envZ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1255125 STM3602 20140325 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: STM3602 mutant is attenuated in pigs [PMID:17526851]. 2783 regulatory protein STM3602 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1255197 STM3673 20140222 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: yiaO mutant is attenuated in mice [PMID:16518469]. 2784 periplasmic dicarboxylate-binding protein yiaO Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1255214 STM3690 20140222 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: STM3690 mutant is attenuated in mice [PMID:16518469]. 2785 inner membrane lipoprotein STM3690 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1255231 STM3707 20140215 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: yibD mutant is attenuated in mice [PMID:16518469]. 2786 glycosyl transferase family protein yibD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1255238 STM3714 20140405 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: rfaK mutant is attenuated in pigs [PMID:17526851]. 2787 hexose transferase rfaK Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1255239 STM3715 20140325 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: rfaZ mutant is attenuated in mice [PMID:16518469]. 2788 lipopolysaccharide core biosynthesis protein rfaZ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1255243 STM3719 20140325 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: rfaB mutant is attenuated in pigs [PMID:17526851]. 2789 UDP-D-galactose:(glucosyl)lipopolysaccharide-1,6-D-galactosyltransferase rfaB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1255246 STM3722 20140406 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: rfaG mutant is attenuated in pigs [PMID:17526851]. 2790 glucosyltransferase I rfaG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1255277 STM3753 20140125 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: sugR mutant is attenuated in pigs [PMID:17526851]. 2791 ATP-binding protein sugR Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1255279 STM3755 20140222 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: rhuM mutant has diminished capacity to invade cultured epithelial cells compared to the wild type [PMID:15182677]. 2792 hypothetical protein rhuM Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1255281 STM3757 20140406 99287 protein-coding NCBI-supplied PMID: 11677609; 15948960; 17351045 MUTATION: misL mutant is attenuated in mice [PMID:15948960]. 2793 autotransporter misL Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1255283 STM3759.S 20140406 99287 protein-coding NCBI-supplied PMID: 11677609; 17351045 MUTATION: marT mutant is attenuated in mice [PMID:16518469]. 2794 transcriptional regulator marT Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1255288 STM3764 20140322 99287 protein-coding NCBI-supplied PMID: 11677609; 17176255; 18620040 MUTATION: mgtC mutant is attenuated in pigs [PMID:17526851]. 2795 protein MgtC mgtC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1255336 STM3809.S 20140325 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: ibpA mutant is attenuated in mice [PMID:16518469]. 2796 heat shock protein IbpA ibpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1255348 STM3821 20140325 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: torD mutant is attenuated in mice [PMID:16518469]. 2797 chaperone protein TorD torD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1255394 STM3867 20140406 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: An atpA mutant is attenuated in mice [PMID:19649318]. 5000 F0F1 ATP synthase subunit alpha atpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1255433 STM3907 20140406 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: STM3907 mutant is attenuated in mice [PMID:16518469]. 2798 hypothetical protein STM3907 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1255436 STM3910 20140325 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: ppiC mutant is attenuated in mice [PMID:16518469]. 2799 peptidyl-prolyl cis-trans isomerase C ppiC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1255441 STM3915 20140325 99287 protein-coding NCBI-supplied PMID: 11677609; 16926406; 19767428; 19884329 MUTATION: trxA mutant is attenuated in mice [PMID:19884329]. 2800 thioredoxin trxA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1255451 STM3925 20140325 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: wecE mutant is attenuated in pigs [PMID:17526851]. 2801 TDP-4-oxo-6-deoxy-D-glucose transaminase wecE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1255479 STM3953 20140406 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: yigF mutant is attenuated in pigs [PMID:17526851]. 2802 inner membrane protein yigF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1255480 STM3954 20140325 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: yigG mutant is attenuated in mice [PMID:16518469]. 2803 hypothetical protein yigG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1255506 STM3980 20140325 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: STM3980 mutant is attenuated in mice [PMID:16518469]. 2804 outer membrane protein STM3980 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1255578 STM4051 20131204 99287 protein-coding NCBI-supplied PMID: 11677609 outer membrane protein STM4051 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1255585 STM4058 20131204 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: cpxA mutants are attenuated in mice [PMID:15271926]. 5001 two-component sensor protein cpxA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1255605 STM4078 20140325 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: yneB mutant is attenuated in mice [PMID:16518469]. 2806 autoinducer-2 (AI-2) modifying protein LsrF STM4078 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1255606 STM4079.S 20140301 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: yneC mutant is attenuated in mice [PMID:16518469]. 2807 autoinducer-2 (AI-2) modifying protein LsrG STM4079.S Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1255679 STM4153 20140405 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: A gyrA-cpxA-rpoB Salmonella Typhimurium mutant was attenuated in pigs [PMID:15542179]. 5006 DNA-directed RNA polymerase subunit beta rpoB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1255681 STM4155 20140325 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: STM4155 mutant is attenuated in mice [PMID:16518469]. 2808 inner membrane protein STM4155 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1255684 STM4158 20140325 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: STM4158 mutant is attenuated in mice [PMID:16518469]. 2809 hypothetical protein STM4158 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1255695 STM4169 20140325 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: yjaG mutant is attenuated in mice [PMID:16518469]. 2810 hypothetical protein yjaG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1255701 STM4175 20140405 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: purD mutant is attenuated in mice [PMID:7618105]. 2811 phosphoribosylamine--glycine ligase purD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1255708 STM4182 20140405 99287 protein-coding NCBI-supplied PMID: 11677609; 15838036 MUTATION: metA mutant is attenuated in mice [PMID:16518469]. 2812 homoserine O-succinyltransferase metA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1255724 STM4198 20131204 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: STM4198 mutant is attenuated in pigs [PMID:17526851]. 2813 hypothetical protein STM4198 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1255732 STM4206 20131204 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: STM4206 mutant is attenuated in mice [PMID:16518469]. 2814 phage glucose translocase STM4206 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1255786 STM4260 20140217 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: STM4260 mutant is attenuated in mice [PMID:16518469]. 2815 cation efflux pump STM4260 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1255787 STM4261 20140217 99287 protein-coding NCBI-supplied PMID: 11677609; 22102234 MUTATION: STM4261 mutant is attenuated in mice [PMID:16518469]. 2816 non-fimbrial adhesin SiiE STM4261 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1255819 STM4293 20140325 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: yjdB mutant is attenuated in mice [PMID:16518469]. 2817 phosphoethanolamine transferase eptA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1255842 STM4316 20131204 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: STM4316 mutant is attenuated in pigs [PMID:17526851]. 2818 hypothetical protein STM4316 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1255845 STM4319 20140405 99287 protein-coding NCBI-supplied PMID: 11677609; 17263560 MUTATION: phoN mutant is attenuated in mice [PMID:16518469]. 2819 non-specific acid phosphatase phoN Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1255858 STM4332 20131204 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: yjeJ mutant is attenuated in mice [PMID:16518469]. 2820 inner membrane protein yjeJ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1255870 STM4344 20140222 99287 protein-coding NCBI-supplied PMID: 11677609; 21348575 MUTATION: A poxA mutant is attenuated in mice [PMID:9826331]. 5005 lysyl-tRNA synthetase yjeA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1255959 STM4433 20140405 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: STM4433 mutant is attenuated in pigs [PMID:17526851]. 2821 myo-inositol 2-dehydrogenase STM4433 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1256011 STM4485 20140405 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: idnK mutant is attenuated in mice [PMID:16518469]. 2822 D-gluconate kinase idnK Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1256120 STM4594 20140215 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: sthA mutant is attenuated in mice [PMID:16518469]. 2823 fimbrial chaperone sthA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1256164 PSLT072 20140325 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: PSLT072 mutant is attenuated in mice [PMID:16518469]. 2580 putative transglycosylase PSLT072 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1256197 PSLT041 20140325 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: spvR mutant is attenuated in mice [PMID:7618105]. 2581 regulator of spv operon spvR Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1256199 PSLT039 20140406 99287 protein-coding NCBI-supplied PMID: 11677609; 21036103 MUTATION: spvB mutants are attenuated in mice [PMID:11260464]. TOXIN: spvB encodes an ADP-ribosylating enzyme that uses actin as a substrate and depolymerizes actin filaments when expressed in CHO cells [PMID:11260464]. 2582 hydrophilic protein spvB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1256200 PSLT040 20140325 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: spvA mutant is attenuated in mice [PMID:7618105]. 2583 outer membrane protein spvA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1256201 PSLT038 20140325 99287 protein-coding NCBI-supplied PMID: 11677609; 18284579; 21036103; 22188134 MUTATION: The spvBC-bearing plasmid was capable of replacing all of the spv genes, as well as the entire virulence plasmid, of serovar Typhimurium for causing systemic infection in BALB/c mice after subcutaneous, but not oral, inoculation. A point mutation in the spvBC plasmid preventing translation but not transcription of spvC eliminated the ability of the plasmid to confer virulence [PMID:11443102]. 2584 hydrophilic protein spvC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1256202 PSLT037 20140325 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: spvD mutant is attenuated in mice [PMID:7618105]. 2585 hydrophilic protein spvD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1256222 PSLT017 20140325 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: pefC mutants are attenuated in mice [PMID:8557375]. 2586 usher protein pefC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1256230 PSLT009 20140325 99287 protein-coding NCBI-supplied PMID: 11677609 MUTATION: rck mutants reduces serum resistance and eukaryotic cell invasion [PMID:8675302]. 2587 resistance to complement killing rcK Bin Zhao, Oliver He AcOrf-138 WEB: http://www.ncbi.nlm.nih.gov/gene 1403971 ACNVgp139 20140406 46015 protein-coding NCBI-supplied PMID: 8030224; 18796706; 19264658; 20007360; 20610731; 21849453 p74 - Other designations: occlusion-derived virus envelope protein Ac-p74 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1446509 p165897_034 20140410 562 protein-coding NCBI-supplied PMID: 17220406 MUTATION: traT mutants have altered membrane permeability and are sensitive to hydrophobic antibiotics [PMID:3323837]. 2297 conjugal transfer surface exclusion protein TraT traT Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1446522 p165897_049 20140410 562 protein-coding NCBI-supplied PMID: 16113321; 16436373; 17220406 MUTATION: tir deletion strains are unable to adhere to tissue in an in vitro organ culture [PMID:17474908]. 2298 hypothetical protein tir Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1449458 pYVe8081_p09 20140217 630 protein-coding NCBI-supplied PMID: 11402007; 15919371; 16254184 MUTATION: lcrV mutant is attenuated in mice [PMID:10216859]. 3984 control of Yop release Other designations: LcrV lcrV Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1449471 pYVe8081_p22 20140222 630 protein-coding NCBI-supplied PMID: 11402007 MUTATION: yscR mutant is attenuated in mice [PMID:10216859]. 3985 required for Yop secretion Other designations: type III secretion system protein yscR Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1449474 pYVe8081_p25 20140406 630 protein-coding NCBI-supplied PMID: 11402007; 18452514; 18976663 MUTATION: yscU mutant is attenuated in mice [PMID:10216859]. 3986 required for Yop secretion Other designations: YscU yscU Bin Zhao, Oliver He yscW WEB: http://www.ncbi.nlm.nih.gov/gene 1449475 pYVe8081_p26 20140215 630 protein-coding NCBI-supplied PMID: 11402007 MUTATION: virG mutant is attenuated in mice [PMID:10216859]. 3987 required for localization of YscC - Other designations: VirG virG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1449476 pYVe8081_p27 20140406 630 protein-coding NCBI-supplied PMID: 11402007 MUTATION: virF mutant is attenuated in mice [PMID:10216859]. 3988 transcriptional activator VirF virF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1449479 pYVe8081_p30 20140222 630 protein-coding NCBI-supplied PMID: 11402007 MUTATION: yscC mutant is attenuated in mice [PMID:10216859]. 3989 required for Yop secretion Other designations: hypothetical protein yscC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1449488 pYVe8081_p39 20140215 630 protein-coding NCBI-supplied PMID: 11402007; 16672607 MUTATION: yscL mutant is attenuated in mice [PMID:10216859]. 3990 required for Yop secretion Other designations: type III secretion system protein yscL Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1449491 pYVe8081_p42 20140222 630 protein-coding NCBI-supplied PMID: 11402007 MUTATION: sycH mutant is attenuated in mice [PMID:12654794]. 3991 YopH chaperone SycH sycH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1449501 pYVe8081_p52 20140222 630 protein-coding NCBI-supplied PMID: 11402007; 17921300; 18625735; 19812190; 21170337 MUTATION: yadA mutant is attenuated in mice [PMID:12654794]. 3992 Adhesin Other designations: adhesin YadA yadA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1449509 pYVe8081_p61 20140215 630 protein-coding NCBI-supplied PMID: 11402007 MUTATION: yopP mutant is attenuated in mice [PMID:10216859]. 3993 Yop effector YopP yopP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1467017 CpB0334 20140222 182082 protein-coding NCBI-supplied MUTATION: knock out mutant showed growth inhibition in yeast and mammalian cells [PMID:18830244]. 3994 CopN copN Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1485896 CPXV021 20121122 10243 protein-coding NCBI-supplied PMID: 2014645; 2309453; 6961398; 8091665 MUTATION: Higher doses of VGF- virus than WT virus were required for intracranial lethality in mice and for production of skin lesions in rabbits. Thus, expression of the VGF gene is important to the virulence of vaccinia virus [PMID:3339716]. 5035 similar to viral growth factor (C11R vaccinia virus Copenhagen) Other designations: CPXV021 protein or CPXV VGF protein VGF Bin Zhao, Oliver He SFGF T-10 WEB: http://www.ncbi.nlm.nih.gov/gene 1486856 SFV_s010L 20121122 10271 protein-coding NCBI-supplied PMID: 1660196; 2173269; 6323741; 10562495 Epidermal growth factor - Other designations: gp010L SFV_s010L Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1487308 HHV2gp26 20130525 10310 protein-coding NCBI-supplied PMID: 9499055 nuclear protein UL24 UL24 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1487355 HHV2gp66 20140222 10310 protein-coding NCBI-supplied PMID: 9499055; 15958677; 16815072; 19740999; 19945726; 21430051 tegument protein; phosphorylates nuclear egress lamina protein; mediates phosphorylation of HDAC1 and HDAC2 and other cellular and viral proteins Other designations: serine/threonine protein kinase US3 US3 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1487364 BoHV1_gp35 20140215 10320 protein-coding NCBI-supplied PMID: 9010995; 15494213; 15557224; 15784882; 16760386; 17215277; 18842710; 19176627; 19553330; 20410286; 21689696; 22160940; 23926348 contains a RING finger; disrupts ND10; proteasome-dependent degradation of several cellular proteins Other designations: ubiquitin E3 ligase ICP0 BICP0 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1487380 BoHV1_gp21 20140406 10320 protein-coding NCBI-supplied PMID: 9010995 MUTATION: A thymidine kinase-deficient mutant (B8-D53) showed no detectable thymidine kinase-inducing activity and was attenuated in calves [PMID:2994602]. 4953 thymidine kinase UL23 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1487395 BoHV1_gp07 20131116 10320 protein-coding NCBI-supplied PMID: 9010995; 17005680; 19692545; 19864376; 22542975; 23926348 modulates transactivating tegument protein VP16; RNA-binding protein Other designations: tegument protein VP13/14 UL47 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1487407 BoHV1_gp42 20140215 10320 protein-coding NCBI-supplied PMID: 9010995; 18480434 MUTATION: Strain A of the virus has a mutation in the glycoprotein E gene, and is avirulent in calves [PMID:8023552]. MUTATION: the Za strain of BHV1 is attenuated by a deletion of the gE gene and is used as a live attenuated vaccine [PMID:8023552]. 4893 type 1 membrane protein; contains a signal peptide; complexed with envelope glycoprotein I to form an Fc-receptor Other designations: envelope glycoprotein E US8 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1487675 HHV3_gp12 20140406 10335 protein-coding NCBI-supplied PMID: 3018124; 21755366 MUTATION: deletion of ORF10 reduced viral titers and the extent of cutaneous lesions significantly in SCIDhu skin xenografts in vivo [PMID:16537591]. 3363 transactivates immediate early genes Other designations: transactivating tegument protein VP16 ORF10 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1488656 Bmnpvgp026 20130525 271108 protein-coding NCBI-supplied PMID: 9185864; 10355780; 15284481; 18611420 AcMNPV orf32 Other designations: FGF fgf Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1488687 Bmnpvgp059 20121124 271108 protein-coding NCBI-supplied PMID: 9185864; 10355780 AcMNPV orf68 Orf_56 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1488760 Bmnpvgp136 20140217 271108 protein-coding NCBI-supplied PMID: 9185864; 10355780 AcMNPV orf153 Other designations: PE38 pe38 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1488815 ASFVgp045 20140217 10497 protein-coding NCBI-supplied PMID: 1309282; 1316688; 1583732; 1994575; 2325202; 2325203; 2327074; 2389555; 3763393; 7856088; 7933107; 8102411; 8139051; 8178480; 8245848; 8262374; 8266720; 8293992; 8335009; 8382399; 8393914; 8438592; 8474154; 8503790; 8506138; 9049318; 11831707 thymidine kinase K196R MUTATION: An E mutant is attenuated in hamsters [PMID:18463152]. 5008 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1489707 RRVgp2 20140222 11029 protein-coding NCBI-supplied PMID: 2833022; 23514884 structural polyprotein RRVgp2 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1489802 MeVgp6 20140222 11234 protein-coding NCBI-supplied PMID: 2041073; 2924348; 3754588; 3882996; 10949953; 15351217; 19198563; 24003217 MUTATION: The L gene from the attenuated Edmonston strain replaced the L protein of a virulent clinical isolate IC-B of the measles virus and grown in Vero cells. The recombinant viruses had had growth disadvantage in CD150-positive lymphoid B95a cells compared to the wild type IC-B [PMID:16306593]. 1914 large subunit of RNA dependent RNA polymerase (RdRp); RNA synthesis, capping, and polyadenylation Other designations: large polymerase protein L Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1489803 MeVgp3 20130323 11234 protein-coding NCBI-supplied PMID: 2041073; 2924348; 3754588; 3882996; 10949953; 16731933; 17374768; 19198563; 19397874; 19656884; 19826940; 23221571 MUTATION: The M gene from the attenuated Edmonston strain replaced the M protein of a virulent clinical isolate IC-B of the measles virus and grown in Vero cells. The recombinant viruses had had growth disadvantage in CD150-positive lymphoid B95a cells compared to the wild type IC-B [PMID:16306593]. 1915 hydrophobic protein on inner leaflet of membrane; inhibits transcription Other designations: matrix protein M Bin Zhao, Oliver He P WEB: http://www.ncbi.nlm.nih.gov/gene 1489805 MeVgp2 20140406 11234 protein-coding NCBI-supplied PMID: 2041073; 2924348; 3754588; 3882996; 9035364; 10949953; 15351217; 15866077; 15919937; 16046624; 17166428; 18234267; 19004947; 19198563; 21071089; 21270162; 21477834; 21994456; 22072748; 22887965; 23022562; 23856440; 24003217 MUTATION: V and C protein mutants (encoded by the P gene) are attenuated in Rhesus monkeys [PMID:18385234]. 1916 subunit of RNA dependent RNA polymerase (RdRp); chaperone for Measles virus nucleocapsid protein - Other designations: C protein|V protein|phosphoprotein P/V/C Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1489807 BovRSVgp01 20121122 11246 protein-coding NCBI-supplied PMID: 9847328 NS1 Other designations: nonstructural protein 1 NS1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1489808 BovRSVgp02 20140215 11246 protein-coding NCBI-supplied PMID: 9847328 NS2 Other designations: nonstructural protein 2 NS2 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1489813 BovRSVgp07 20140222 11246 protein-coding NCBI-supplied PMID: 9847328 MUTATION: A glycoprotein G deletion in bovine respiratory syncytial virus(rBRSV) and recombinant rBRSV was attenuated in calves [PMID:12414977]. 4954 G Other designations: attachment glycoprotein G Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1489849 IHNVgp5 20140406 11290 protein-coding NCBI-supplied PMID: 8578857 MUTATION: A mutation in the non-virion protein of IHNV causes attenuated growth in rainbow trout [PMID:15047826]. 4983 non-virion protein NV Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1489853 RABVgp1 20140222 11292 protein-coding NCBI-supplied PMID: 3407152; 3459163; 16494915; 16778023; 20130065; 20875468; 23607781 MUTATION: The N protein of the virulent Nishigahara strain was placed in the background of the avirulent Ni-CE rabies virus to create a chimeric rabies virus. The chimera killed mice after intracereberal inoculation, compared to the Ni-CE strain which is avirulent in mice [PMID:17010466]. 3028 nucleoprotein N RABVgp1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1489854 RABVgp2 20140217 11292 protein-coding NCBI-supplied PMID: 3407152; 3459163; 19031691 MUTATION: The P protein of the virulent NIshigahara strain was placed in the background of the avirulent Ni-CE rabies virus to create a chimeric rabies virus. The chimera killed mice after intracereberal inoculation, compared to the Ni-CE strain which is avirulent in mice [PMID:1489854]. 3029 phosphoprotein M1 RABVgp2 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1489855 RABVgp3 20140406 11292 protein-coding NCBI-supplied PMID: 3407152; 3459163; 18667490 MUTATION: The M protein of the virulent NIshigahara strain was placed in the background of the avirulent Ni-CE rabies virus to create a chimeric rabies virus. The chimera killed mice after intracereberal inoculation, compared to the Ni-CE strain which is avirulent in mice [PMID:17010466]. 3030 M2 protein RABVgp3 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1489856 RABVgp4 20140221 11292 protein-coding NCBI-supplied PMID: 3407152; 3459163; 15557743; 16099913; 16188341; 16473429; 20086240; 20377742; 20538851; 21068252; 22248643; 22438951; 23114627 MUTATION: G protein from the virulent Nishigahara strain was recombined with the RC-HL genome an attenuated rabies virus. The chimeric virus killed mice when given by intracerebral inoculation. The RC-HL rabies virus normally is attenuated in mice, and therefore the G protein can be considered a virulence factor of rabies virus [PMID:11533176]. 3031 transmembrane glycoprotein G RABVgp4 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1490008 SIVgp7 20140222 11723 protein-coding NCBI-supplied PMID: 2024476; 11861836; 15542684; 16448682; 16611907; 16728715; 18489774; 19012413; 19358735; 19436700; 20147394; 20594957; 20617930; 21366921; 21625568; 21841125; 23853598 MUTATION: A SIV nef mutant is attenuated in rhesus monkeys [PMID:1470917]. 5009 nef protein nef Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1670230 MYXV_gp168 20140222 10273 protein-coding NCBI-supplied PMID: 1651597; 10562494; 16356857 MUTATION: Although the T2-minus recombinant myxoma virus grew normally in tissue culture, upon infection of susceptible rabbits the viral disease was observed to be significantly attenuated [PMID:1651597]. 5031 TNF receptor Other designations: M-T2 MYXV_gp168 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1724707 FIVgp4 20121122 11673 protein-coding NCBI-supplied PMID: 2762293; 2813380 MUTATION: Feline immunodeficiency virus (FIV) made defective in the accessory gene ORF-A were previously shown to be greatly attenuated in its ability to replicate in lymphocytes but to grow normally or near normally in other cell types [PMID:15680433]. 4895 ORF 2 Other designations: hypothetical protein FIVgp4 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1724709 FIVgp3 20140406 11673 protein-coding NCBI-supplied PMID: 2762293; 2813380 MUTATION: A vif mutant in feline immunodeficiency virus was attenuated in cats [PMID:10891409]. 4964 ORF 1 Other designations: hypothetical protein FIVgp3 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1789667 pO157p58 20140222 386585 protein-coding NCBI-supplied PMID: 9628576 MUTATION: toxB mutants had attenuated adherence to Caco-2 cells [PMID:11598035]. 2274 toxin B toxB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1789686 pO157p18 20130508 386585 protein-coding NCBI-supplied PMID: 9628576 MUTATION: attenuated in zebra fish [PMID:20019794]. 2275 hemolysin A hlyA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1789689 pO157p17 20130508 386585 protein-coding NCBI-supplied PMID: 9628576 MUTATION: hlyC is required for the acylation and therefore activation of the toxin hemolysin which has the ability to lyse several different types of cells [PMID:8793877]. 2276 hemolysin C hlyC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 1789732 pO157p78 20140222 386585 protein-coding NCBI-supplied PMID: 9628576; 17451446; 18047580; 20876094; 21646511; 23874912; 24165126 MUTATION: espP mutant is attenuated in calves [PMID:17451446]. 2277 EspP espP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2612154 VCA0688 20140222 243277 II protein-coding NCBI-supplied PMID: 10952301 MUTATION: VCA0688 mutant is attenuated in mice [PMID:11952899]. 2383 polyhydroxyalkanoic acid synthase VCA0688 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2612226 VCA0910 20140222 243277 II protein-coding NCBI-supplied PMID: 10952301 MUTATION: VCA0910 mutant is attenuated in mice [PMID:11952899]. 2384 TonB1 protein VCA0910 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2612229 VCA0006 20140222 243277 II protein-coding NCBI-supplied PMID: 10952301 MUTATION: VCA0006 mutant is attenuated in mice [PMID:11952899]. 2385 hypothetical protein VCA0006 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2612274 VCA0903 20140405 243277 II protein-coding NCBI-supplied PMID: 10952301 MUTATION: VCA0903 mutant is attenuated in mice [PMID:11952899]. 2386 hypothetical protein VCA0903 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2612623 VCA0896 20140405 243277 II protein-coding NCBI-supplied PMID: 10952301 MUTATION: VCA0896 mutant is attenuated in mice [PMID:11952899]. 2387 glucose-6-phosphate 1-dehydrogenase VCA0896 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2612672 VCA0600 20140222 243277 II protein-coding NCBI-supplied PMID: 10952301 MUTATION: VCA0600 mutant is attenuated in mice [PMID:11952899]. 2388 repressor protein PhnR VCA0600 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2612692 VCA0578 20130330 243277 II protein-coding NCBI-supplied PMID: 10952301 MUTATION: VCA0578 mutant is attenuated in mice [PMID:11952899]. 2389 hypothetical protein VCA0578 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2612700 VCA0530 20140329 243277 II protein-coding NCBI-supplied PMID: 10952301 MUTATION: VCA0530 mutant is attenuated in mice [PMID:11952899]. 2390 pyruvate-flavoredoxin oxidoreductase VCA0530 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2612870 VCA0583 20140222 243277 II protein-coding NCBI-supplied PMID: 10952301 MUTATION: VCA0583 mutant is attenuated in mice [PMID:11952899]. 2391 hypothetical protein VCA0583 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2612901 VCA0930 20140329 243277 II protein-coding NCBI-supplied PMID: 10952301 MUTATION: VCA0930 mutant is attenuated in mice [PMID:11952899]. 2392 hypothetical protein VCA0930 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2612960 VC0028 20140405 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC0028 mutant was attenuated in mice [PMID:11952899]. 2393 dihydroxy-acid dehydratase VC0028 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2612962 VC0122 20140406 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: cyaA mutant is attenuated in mice [PMID:11952899]. 2394 adenylate cyclase cyaA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2612968 VC2426 20140322 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC2426 (pilD/vcpD) mutant is attenuated in mice [PMID:9781884]. 2395 leader peptidase PilD VC2426 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2612975 VC2433 20140222 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC2433 mutant is attenuated in mice [PMID:11952899]. 2396 cyclic 3',5'-adenosine monophosphate phosphodiesterase VC2433 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2612978 VC2436 20140406 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: tolC mutant is deficient in intestinal colonization of mice [PMID:11402016]. 2397 outer membrane channel protein tolC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2612979 VC2437 20130326 243277 I pseudo NCBI-supplied MUTATION: VC2437 mutant is attenuated in mice [PMID:11952899]. 2398 pseudo VC2437 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2612995 VC2453 20140222 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: barA mutant is attenuated in mice [PMID:11952899]. 2399 hybrid sensory histidine kinase BarA VC2453 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2612997 VC2455 20111206 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC2455 mutant is attenuated in mice [PMID:11952899]. 2400 hypothetical protein VC2455 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2612999 VC2457 20140322 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: acpS mutant is attenuated in mice [PMID:11952899]. 2401 4'-phosphopantetheinyl transferase acpS Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2613001 VC2459 20130827 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: recO mutant is attenuated in mice [PMID:11952899]. 2402 DNA repair protein RecO recO Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2613058 VC2389 20140405 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: carB mutant is attenuated in mice [PMID:11952899]. 2403 carbamoyl phosphate synthase large subunit carB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2613059 VC2390 20140405 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC2390 mutant is attenuated in mice [PMID:11952899]. 2404 carbamoyl phosphate synthase small subunit VC2390 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2613082 VC2413 20140405 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: aceF mutant is attenuated in mice [PMID:11952899]. 2405 dihydrolipoamide acetyltransferase aceF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2613091 VC2295 20130508 243277 I protein-coding NCBI-supplied PMID: 10952301; 15870079 MUTATION: VC2295 mutant is attenuated in mice [PMID:11952899]. 2406 Na(+)-translocating NADH-quinone reductase subunit A VC2295 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2613116 VC2320 20130330 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC2320 mutant is attenuated in mice [PMID:11952899]. 2407 exodeoxyribonuclease V VC2320 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2613212 VC2290 20140222 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC2290 mutant is attenuated in mice [PMID:11952899]. 2408 Na(+)-translocating NADH-quinone reductase subunit F VC2290 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2613213 VC2291 20140322 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC2291 mutant is attenuated in mice [PMID:11952899]. 2409 Na(+)-translocating NADH-quinone reductase subunit E VC2291 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2613246 VC2206 20140222 243277 I protein-coding NCBI-supplied PMID: 10952301; 19592588 MUTATION: VC2206 (flgP) mutant is defective in intestinal colonization of mice [PMID:17981980]. 2410 hypothetical protein VC2206 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2613362 VC2106 20140406 243277 I protein-coding NCBI-supplied PMID: 10952301; 19400801; 21750152 MUTATION: fur mutant is attenuated in mice [PMID:11952899]. 2411 ferric uptake regulator fur Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2613400 VC2021 20140405 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: fabG mutant is attenuated in mice [PMID:11952899]. 2412 3-ketoacyl-ACP reductase fabG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2613409 VC2030 20140222 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC2030 mutant is attenuated in mice [PMID:11952899]. 2413 ribonuclease E VC2030 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2613423 VC2042 20130330 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: aphA mutant is attenuated in mice [PMID:11489126]. 2414 histone deacetylase/AcuC/AphA family protein VC2042 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2613432 VC2052 20140322 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC2052 mutant is attenuated in mice [PMID:11952899]. 2415 cytochrome c-type biogenesis protein CcmF VC2052 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2613447 VC2067 20140222 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC2067 mutant is attenuated in mice [PMID:11952899]. 2416 MinD-like protein VC2067 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2613590 VC1836 20130827 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: tolB mutant is attenuated in mice [PMID:11952899]. 2417 translocation protein TolB tolB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2613641 VC1887 20140222 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC1887 mutant is attenuated in mice [PMID:11952899]. 2418 hypothetical protein VC1887 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2613651 VC1771 20111206 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC1771 mutant is attenuated in mice [PMID:11952899]. 2419 hypothetical protein VC1771 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2613719 VC1714 20140322 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: mukB mutant is attenuated in mice [PMID:11952899]. 2420 cell division protein MukB mukB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2613720 VC1715 20140222 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC1715 mutant is attenuated in mice [PMID:11952899]. 2421 condesin subunit E VC1715 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2613721 VC1716 20140406 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC1716 mutant is attenuated in mice [PMID:11952899]. 2422 condesin subunit F VC1716 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2613770 VC1639 20130508 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC1639 mutant is attenuated in mice [PMID:11952899]. 2423 sensor histidine kinase VC1639 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2613806 VC1675 20140215 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC1675 mutant is attenuated in mice [PMID:11952899]. 2424 multidrug resistance protein VC1675 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2613848 VC1594 20140406 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: galM mutant is attenuated in mice [PMID:11952899]. 2425 aldose 1-epimerase galM Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2613849 VC1595 20140405 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC1595 mutant is attenuated in mice [PMID:11952899]. 2426 galactokinase VC1595 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2614180 VC0257 20140406 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC0257 mutant is attenuated in mice [PMID:11952899]. 2427 transposase OrfAB subunit B VC0257 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2614218 VC0965 20140222 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC0965 mutant is attenuated in mice [PMID:11952899]. 2428 phosphoenolpyruvate-protein phosphotransferase VC0965 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2614257 VC1004 20140405 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC1004 mutant is attenuated in mice [PMID:11952899]. 2429 amidophosphoribosyltransferase VC1004 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2614265 VC1012 20140322 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC1012 mutant is attenuated in mice [PMID:11952899]. 2430 electron transport complex protein RsxE VC1012 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2614274 VC0251 20140222 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC0251 mutant is attenuated in mice [PMID:11952899]. 2431 acyl protein synthase/acyl-CoA reductase RfbN VC0251 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2614277 VC0249 20140217 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: rfbL mutant is attenuated in mice [PMID:11952899]. 2432 RfbL protein VC0249 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2614278 VC0250 20140222 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC0250 mutant is attenuated in mice [PMID:11952899]. 2433 iron-containing alcohol dehydrogenase VC0250 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2614291 VC1021 20140322 243277 I protein-coding NCBI-supplied PMID: 10952301; 16376028 MUTATION: luxO mutant is defective in colonization of infant mouse intestine [PMID:11854465]. 2434 LuxO repressor protein VC1021 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2614345 VC1075 20140215 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC1075 mutant is attenuated in mice [PMID:11952899]. 2435 hypothetical protein VC1075 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2614368 VC1098 20140405 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC1098 mutant is attenuated in mice [PMID:11952899]. 2436 acetate kinase VC1098 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2614419 VC0051 20140405 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC0051 mutant is attenuated in mice [PMID:11952899]. 2437 phosphoribosylaminoimidazole carboxylase ATPase subunit VC0051 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2614466 VC0032 20140406 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC0032 mutant is attenuated in mice [PMID:11952899]. 2438 ComM-like protein VC0032 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2614481 VC0036 20140329 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC0036 mutant is attenuated in mice [PMID:11952899]. 2439 FixG-like protein VC0036 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2614493 VC0826 20140217 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: tcpP mutant is attenuated in mice [PMID:11952899]. 2440 toxin co-regulated pilus biosynthesis protein P VC0826 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2614495 VC0828 20140329 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC0828 mutant is attenuated in mice [PMID:11952899]. 2441 toxin co-regulated pilin VC0828 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2614498 VC0831 20140405 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC0831 mutant is attenuated in mice [PMID:11952899]. 2442 toxin co-regulated pilus biosynthesis outer membrane protein C VC0831 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2614502 VC0835 20140322 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC0835 mutant is attenuated in mice [PMID:11952899]. 2443 toxin co-regulated pilus biosynthesis protein T VC0835 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2614503 VC0836 20140405 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: tcpE mutant is attenuated in mice [PMID:11952899]. 2444 toxin co-regulated pilus biosynthesis protein E VC0836 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2614504 VC0837 20140405 243277 I protein-coding NCBI-supplied PMID: 10952301; 17320105 MUTATION: tcpF mutant is attenuated in mice [PMID:11952899]. 2445 toxin co-regulated pilus biosynthesis protein F VC0837 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2614536 VC0869 20140322 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC0869 mutant is attenuated in mice [PMID:11952899]. 2446 phosphoribosylformylglycinamidine synthase VC0869 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2614565 VC0247 20140222 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC0247 mutant is attenuated in mice [PMID:11952899]. 2447 lipopolysaccharide/O-antigen transport protein VC0247 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2614566 VC0244 20140322 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC0244 mutant is attenuated in mice [PMID:11952899]. 2448 perosamine synthase VC0244 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2614595 VC1162 20140215 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC1162 mutant is attenuated in mice [PMID:11952899]. 2449 hypothetical protein VC1162 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2614606 VC1173 20140322 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC1173 mutant is attenuated in mice [PMID:11952899]. 2450 anthranilate synthase component II VC1173 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2614701 VC0192 20140222 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC0192 mutant is attenuated in mice [PMID:11952899]. 2451 AraC family transcriptional regulator VC0192 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2614702 VC0212 20140405 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC0212 mutant is attenuated in mice [PMID:11952899]. 2452 lipid A biosynthesis (KDO)2-(lauroyl)-lipid IVA acyltransferase VC0212 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2614705 VC0242 20140406 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC0242 mutant is attenuated in mice [PMID:11952899]. 2453 phosphomannomutase VC0242 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2614706 VC0243 20140405 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC0243 mutant is attenuated in mice [PMID:11952899]. 2454 GDP-mannose 4,6-dehydratase VC0243 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2614707 VC0239 20140406 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC0239 mutant is attenuated in mice [PMID:11952899]. 2455 hypothetical protein VC0239 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2614834 VC1380 20111206 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC1380 mutant is attenuated in mice [PMID:11952899]. 2456 hypothetical protein VC1380 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2614849 VC0238 20140215 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC0238 mutant is attenuated in mice [PMID:11952899]. 2457 hexapaptide repeat-containing transferase VC0238 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2614878 VC0260 20140215 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC0260 mutant is attenuated in mice [PMID:11952899]. 2458 mannosyltransferase VC0260 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2615060 VC0347 20130827 243277 I protein-coding NCBI-supplied PMID: 10952301; 22484176 MUTATION: hfq mutant fails to colonize the suckling mouse intestine [PMID:15225327]. 2459 RNA-binding protein Hfq hfq Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2615121 VC0459 20140222 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC0459 mutant is attenuated in mice [PMID:11952899]. 2460 hypothetical protein VC0459 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2615130 VC0468 20140405 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC0468 mutant is attenuated in mice [PMID:11952899]. 2461 glutathione synthetase VC0468 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2615170 VC2506 20140322 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC2506 mutant is attenuated in mice [PMID:11952899]. 2462 ATP-dependent helicase HepA VC2506 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2615253 VC0576 20130330 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: sspA mutant is attenuated in mice [PMID:11952899]. 2463 stringent starvation protein A sspA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2615261 VC0259 20140222 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC0259 mutant is attenuated in mice [PMID:11952899]. 2464 lipopolysaccharide biosynthesis protein RfbV VC0259 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2615279 VC0485 20140405 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC0485 mutant is attenuated in mice [PMID:11952899]. 2465 pyruvate kinase VC0485 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2615366 VC0125 20140406 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC0125 mutant is attenuated in mice [PMID:11952899]. 2466 diaminopimelate decarboxylase VC0125 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2615384 VC0596 20140215 243277 I protein-coding NCBI-supplied PMID: 10952301; 22904284 MUTATION: VC0596 mutant is attenuated in mice [PMID:11952899]. 2467 dnaK suppressor protein VC0596 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2615427 VC0639 20140405 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC0639 mutant is attenuated in mice [PMID:11952899]. 2468 phosphoglucosamine mutase glmM Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2615437 VC0647 20140405 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC0647 mutant is attenuated in mice [PMID:11952899]. 2469 polynucleotide phosphorylase VC0647 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2615561 VC2544 20140405 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC2544 mutant is attenuated in mice [PMID:11952899]. 2470 fructose-1,6-bisphosphatase VC2544 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2615664 VC2647 20140222 243277 I protein-coding NCBI-supplied PMID: 10952301; 21926235 MUTATION: VC2347 mutant is attenuated in mice [PMID:11952899]. 2471 hypothetical protein VC2647 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2615675 VC2658 20140405 243277 I protein-coding NCBI-supplied PMID: 10952301 fumarate reductase subunit C VC2658 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2615677 VC2660 20130527 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC2660 mutant is attenuated in mice [PMID:11952899]. 2473 elongation factor P VC2660 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2615733 VC0724 20130330 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC0724 mutant is attenuated in mice [PMID:11952899]. 2474 phosphate ABC transporter permease VC0724 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2615736 VC0727 20140222 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: phoU mutant is attenuated in mice [PMID:11952899]. 2475 transcriptional regulator PhoU VC0727 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2615814 VC0523 20140405 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC0523 mutant is attenuated in mice [PMID:11952899]. 2476 glycerol-3-phosphate acyltransferase PlsY VC0523 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2615822 VC0095 20140405 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC0095 mutant is attenuated in mice [PMID:11952899]. 2477 chorismate--pyruvate lyase VC0095 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2615825 VC0132 20130330 243277 I protein-coding NCBI-supplied PMID: 10952301 MUTATION: VC0132 mutant is attenuated in mice [PMID:11952899]. 2478 hypothetical protein VC0132 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2650114 DIP2010 20140301 257309 protein-coding NCBI-supplied PMID: 14602910 MUTATION: spaC (DIP2010) mutant has diminished adherence to human pharyngeal epithelial cells [PMID:17376076]. 3364 surface-anchored membrane protein DIP2010 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2650115 DIP2011 20140301 257309 protein-coding NCBI-supplied PMID: 14602910 MUTATION: spaB (DIP2011) mutant has diminished adherence to human pharyngeal epithelial cells [PMID:17376076]. 3365 surface anchored protein DIP2011 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2650491 DIP0222 20140222 257309 protein-coding NCBI-supplied PMID: 14602910; 15680246; 17584737; 20050921; 20398220 diphtheria toxin tox Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2659145 BB3469 20140405 257310 protein-coding NCBI-supplied PMID: 12910271; 15130135; 19015265 MUTATION: Inactivation of the aroA gene highly attenuates B. bronchiseptica, severely impairing its ability to colonize and survive in the respiratory tract of mice [PMID:12009288]. 4892 3-phosphoshikimate 1-carboxyvinyltransferase aroA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2661538 BB3978 20140222 257310 protein-coding NCBI-supplied PMID: 12910271; 15130135; 19015265 MUTATION: A dnt mutant in Bordetella Bronchiseptica was attenuated in guinea pigs [PMID:3182989]. 4948 dermonecrotic toxin dnt Bin Zhao, Oliver He cya WEB: http://www.ncbi.nlm.nih.gov/gene 2661688 BB0324 20140322 257310 protein-coding NCBI-supplied PMID: 12910271; 15130135; 19015265; 22473603; 23381998 MUTATION: A double mutant strain of Bordetella Bronchiseptica lacking adenylate cyclase(cyaA gene) and type III secretion(bscN gene) is attenuated in mice [PMID:17452472]. 4947 bifunctional hemolysin-adenylate cyclase - cyaA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2662485 BB1628 20140222 257310 protein-coding NCBI-supplied PMID: 12910271; 15130135; 19015265 MUTATION: A double mutant strain of Bordetella Bronchiseptica lacking adenylate cyclase(cyaA gene) and type III secretion(bscN gene) is attenuated in mice [PMID:17452472]. 4946 type III secretion system ATPase bscN Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2664030 BP0347 20140222 257313 protein-coding NCBI-supplied PMID: 12910271 MUTATION: attenuated in mice [PMID:16495546]. 3949 outer membrane heme receptor bhuR Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2664290 BP1054 20140222 257313 protein-coding NCBI-supplied PMID: 12910271; 20306653 MUTATION: mutant was 30% to 40% less efficient at adhering to CHO cells and to human HeLa cells compared to parent [PMID:1988935]. 3950 pertactin prn Bin Zhao, Oliver He HlyC WEB: http://www.ncbi.nlm.nih.gov/gene 2664491 BP0758 20140222 257313 protein-coding NCBI-supplied PMID: 12910271 MUTATION: cyaC mutant had toxin activities less than 1% of the wild type [PMID:1987161]. 3951 cyclolysin-activating lysine-acyltransferase - cyaC Bin Zhao, Oliver He cya WEB: http://www.ncbi.nlm.nih.gov/gene 2664492 BP0760 20140322 257313 protein-coding NCBI-supplied PMID: 12910271; 15528345; 15845471; 16002668; 16552051; 16627468; 17148436; 17927697; 18375764; 19348784; 20438736; 20521845; 20610650; 22231172; 24064217; 24297899 MUTATION: mutant strain was unable to multiply as fast and is avirulent in murine respiratory models [PMID:1614333]. 3952 bifunctional hemolysin-adenylate cyclase - cyaA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2664891 BP3493 20140222 257313 protein-coding NCBI-supplied PMID: 12910271 MUTATION: attenuated in infant mice [PMID:11348687]. 3953 serum resistance protein brkB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2664892 BP3494 20140322 257313 protein-coding NCBI-supplied PMID: 12910271 MUTATION: attenuated in infant mice [PMID:11348687]. 3954 serum resistance protein brkA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2664931 BP3531 20140217 257313 protein-coding NCBI-supplied PMID: 12910271 MUTATION: tonB exb double mutant is attenuated in mice [PMID:10722583]. 3955 siderophore-mediated iron transport protein tonB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2664932 BP3532 20140217 257313 protein-coding NCBI-supplied PMID: 12910271 MUTATION: tonB exbB double mutant is attenuated in mice [PMID:10722583]. 3956 MotA/TolQ/ExbB proton channel family protein exbB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2665068 BP3783 20140215 257313 protein-coding NCBI-supplied PMID: 12910271 MUTATION: deletion mutant displayed a significant defect in respiratory tract colonization in mice [PMID:15155640]. 3957 toxin subunit 1 ptxA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2665069 BP3784 20140322 257313 protein-coding NCBI-supplied PMID: 12910271; 15879099; 16689799; 19380820 MUTATION: deletion mutant displayed a significant defect in respiratory tract colonization in mice [PMID:15155640]. 3958 toxin subunit 2 ptxB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2665353 BP0123 20140222 257313 protein-coding NCBI-supplied PMID: 12910271 MUTATION: deletion mutant avirulent in the infant mouse model [PMID:2877614]. 3959 cAMP phosphodiesterase BP0123 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2665596 BP1568 20140222 257313 protein-coding NCBI-supplied PMID: 12910271 MUTATION: deletion mutant showed significantly reduced ability to colonize in the trachea of a mouse respiratory infection model [PMID:1350044]. 3960 serotype 3 fimbrial subunit fim3 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2666331 BP3072 20140329 257313 protein-coding NCBI-supplied PMID: 12910271 MUTATION: lpxL1 deficient mutant displayed defect in infection of human macrophages [PMID:17967899]. 3961 lipid A biosynthesis lauroyl acyltransferase BP3072 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2666888 BP1201 20140406 257313 protein-coding NCBI-supplied PMID: 12910271 MUTATION: TcfA mutation reduced bacteria by 10 fold compared to parent strain [PMID:7476158]. 3962 tracheal colonization factor tcfA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2666936 BP3439 20140222 257313 protein-coding NCBI-supplied PMID: 12910271 MUTATION: deletion mutant attenuated in mice [PMID:18762220]. 3963 dermonecrotic toxin dnt Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2667056 BP1876 20140406 257313 protein-coding NCBI-supplied PMID: 12910271 MUTATION: mutant showed reduced colonization in mice compared to wild-type [PMID:11348687]. 3964 regulatory protein BvgR bvgR Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2667057 BP1877 20140329 257313 protein-coding NCBI-supplied PMID: 12910271 MUTATION: mutant displayed reduced virulence, and lost ability to express some Bvg+-phase factors [PMID:9194696]. 3965 virulence sensor protein bvgS Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2667058 BP1878 20140322 257313 protein-coding NCBI-supplied PMID: 12910271; 23489959 MUTATION: mutant strain showed growth inhibition and reduced colonization [PMID:9573202]. 3966 virulence factors transcription regulator bvgA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2667059 BP1879 20140222 257313 protein-coding NCBI-supplied PMID: 12910271; 16771844; 19043589; 19220744 MUTATION: FhaB mutation abolished bacterial adhesion to Chinese Hamster Ovary cells [PMID:8415678]. 3967 filamentous hemagglutinin/adhesin fhaB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2667132 BP2245 20140215 257313 protein-coding NCBI-supplied PMID: 12910271 MUTATION: deletion mutant showed a decrease in cytotoxicity and secretion of proteins in vitro as well as reduced colonization in the trachea of a rat infection model [PMID:9663681]. 3968 type III secretion system ATPase bscN Bin Zhao, Oliver He fhaE WEB: http://www.ncbi.nlm.nih.gov/gene 2667435 BP1883 20140222 257313 protein-coding NCBI-supplied PMID: 12910271 MUTATION: FimD mutant strain showed reduced colonization in the lungs and trachea of mice [PMID:11348687]. 3969 fimbrial adhesin - fimD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2667436 BP1884 20140215 257313 protein-coding NCBI-supplied PMID: 12910271; 16771844 MUTATION: mutation strongly reduced binding to CHO cells [PMID:8415678]. 3970 hemolysin activator-like protein fhaC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2667469 BP2463 20140406 257313 protein-coding NCBI-supplied PMID: 12910271 MUTATION: fauA mutant is attenuated in mice [PMID:17724074]. 3971 ferric alcaligin siderophore receptor fauA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2700720 BoHV5_gp34 20140301 35244 protein-coding NCBI-supplied PMID: 12970418 TK Other designations: thymidine kinase UL23 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2703361 HHV1gp057 20140222 10298 protein-coding NCBI-supplied PMID: 2839594; 21697465 ribonucleotide reductase subunit 1 UL39 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2703365 HHV1gp060 20140217 10298 protein-coding NCBI-supplied PMID: 2839594; 15564467; 16095647; 16477041; 16940547; 17005689; 17620619; 17670820; 18321964; 19584246; 20174621; 20357089; 20427534; 21430045; 22951838; 23077305; 23302873; 23388723; 23589852; 24067977; 24109211 MUTATION: Viruses lacking UL41 (vhs) are attenuated in mice [PMID:10729135]. 4529 mRNA-specific RNase Other designations: tegument host shutoff protein UL41 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2703374 HHV1gp034 20140329 10298 protein-coding NCBI-supplied PMID: 2839594; 15996701; 16927131; 17522225; 20113192; 20819721; 21761115; 22024514; 22096991; 22155911; 23289583; 23354806; 23877048; 24374341; 24466749 MUTATION: A thymidine kinase-deficient (UL23) mutant was found to be attenuated in mice [PMID:212476]. 4978 thymidine kinase UL23 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2703383 HHV1gp018 20140222 10298 protein-coding NCBI-supplied PMID: 2839594; 16095647; 16415024; 17913541; 18272572 tegument serine/threonine protein kinase UL13 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2703390 HHV1gp082 20140406 10298 protein-coding NCBI-supplied PMID: 2839594; 11752173; 15194749; 15494213; 15824310; 15897453; 16537602; 16764725; 17126870; 17258208; 18057247; 18321553; 18497856; 18590780; 18715910; 18945770; 18952891; 19073918; 19264774; 19264778; 19508374; 19535445; 19706544; 19828605; 20075863; 20098619; 20147399; 20164220; 20164233; 20454685; 20660182; 20686034; 20876123; 21191021; 21248039; 21411540; 21471243; 21609490; 21632771; 21698222; 21937654; 21949651; 22013039; 22158881; 22278229; 22405594; 22438555; 22875967; 22993145; 23135716; 23221554; 23283962; 23785201; 23864622; 23938468; 24027338; 24067962; 24089549; 24089555 MUTATION: ICP0 null HSV-1 mutant is avirulent in mice [PMID:16764725]. 4526 contains a RING finger; disrupts ND10; proteasome-dependent degradation of several cellular proteins Other designations: ubiquitin E3 ligase ICP0 RL2 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2703396 HHV1gp083 20140406 10298 protein-coding NCBI-supplied PMID: 2839594; 18005679; 19759141; 21248029; 22072757; 22171259; 23073763 MUTATION: ICP34.5 mutant virus is avirulent in mice [PMID:12663769]. 4528 virion protein; inhibits stress-induced translational arrest; related to eIF2 phosphatase regulatory subunit GADD34; binds protein phosphatase 1 to form a holoenzyme capable of dephosphorylating eIF2-alpha Other designations: neurovirulence protein ICP34.5 RL1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2703399 HHV1gp087 20140406 10298 protein-coding NCBI-supplied PMID: 2839594; 12663780 possibly envelope-associated; interacts with cytokeratin 18 Other designations: virion protein US2 US2 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2703406 HHV1gp094 20140222 10298 protein-coding NCBI-supplied PMID: 2839594; 15731277; 15972328; 16987059; 17360490; 17405920; 17959661; 19357164; 20826693; 21411539; 22239829; 23152509 MUTATION: A HSV-1 strain with mutatinos in the gD gene is attenuated for virulence in mice [PMID:18243431]. 4527 type 1 membrane protein; contains a signal peptide; binds cell surface receptors Other designations: envelope glycoprotein D|envelope glycoprotein J US5 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2703439 HHV1gp107 20140406 10298 protein-coding NCBI-supplied PMID: 2839594; 12915535; 16246910; 17229694; 18395766; 20633584; 22130536; 22301138; 23115300; 23773021; 24067967 dsRNA-binding protein; antagonizes PKR; inhibits stress-induced translational arrest Other designations: tegument protein US11 US11 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2703444 HHV1gp096 20140111 10298 protein-coding NCBI-supplied PMID: 2839594; 15557552; 17485527; 18032483; 18076965; 18671825; 20089288; 24049165 protein-coding US6 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2703446 HHV1gp098 20140217 10298 protein-coding NCBI-supplied PMID: 2839594; 18753205; 19570876; 23077321 type 1 membrane protein; contains a signal peptide; complexed with envelope glycoprotein E to form an Fc-receptor Other designations: envelope glycoprotein I US7 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2703448 HHV1gp101 20140406 10298 protein-coding NCBI-supplied PMID: 2839594; 16997344; 17035313; 18480440; 18753205; 19279114; 19357164; 19570876; 21228231; 21734040; 21734044; 23077321; 23322573 MUTATION: An HSV-1 gE (US8) deletion strain is attenuated in mice [PMID:18562543]. 4976 type 1 membrane protein; contains a signal peptide; complexed with envelope glycoprotein I to form an Fc-receptor Other designations: envelope glycoprotein E US8 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2703458 HHV1gp41.5 20140406 10298 protein-coding NCBI-supplied PMID: 2839594; 15140983; 18497856; 20585571; 22205745; 22491472 MUTATION: A UL29 mutant is attenuated in mice [PMID:8289372]. 4977 contains a zinc-finger Other designations: single-stranded DNA-binding protein UL29 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2716459 pC15-1a_084 20140410 562 protein-coding NCBI-supplied PMID: 15388431 MUTATION: traT mutants have altered membrane permeability and are sensitive to hydrophobic antibiotics [PMID:3323837]. 2295 conjugal transfer surface exclusion protein TraT traT Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2716469 pC15-1a_100 20140410 562 protein-coding NCBI-supplied PMID: 15388431 MUTATION: tir deletion strains are unable to adhere to tissue in an in vitro organ culture [PMID:17474908]. 2296 hypothetical protein tir Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2717869 MAP1047 20140301 262316 protein-coding NCBI-supplied PMID: 16116077; 18192416 MUTATION: A M. avium relA mutant is attenuated in calves and goats [PMID:21565243]. 4985 RelA relA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2763750 YP_1973 20140405 229193 protein-coding NCBI-supplied PMID: 15262951; 15368893 MUTATION: ugd mutant had defects in intracellular survival in macrophages [PMID:16790745]. 2536 nucleotide sugar dehydrogenase ugd Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2763931 YP_0330 20140222 229193 protein-coding NCBI-supplied PMID: 15262951; 15368893 MUTATION: pcm mutant is attenuated in mice [PMID:14742535]. 2537 protein-L-isoaspartate O-methyltransferase pcm Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2764073 YP_0529 20120618 229193 protein-coding NCBI-supplied PMID: 15262951; 15368893 MUTATION: hfq mutant is highly attenuated in mice after subcutaneous or intravenous injection and has attenuated survival in macrophages [PMID:19593436]. 2538 RNA-binding protein Hfq hfq Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2764186 YP_0578 20140222 229193 protein-coding NCBI-supplied PMID: 15262951; 15368893 MUTATION: greA mutants are attenuated in mice [PMID:14742535]. 2539 transcription elongation factor GreA greA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2764362 YP_2321 20140215 229193 protein-coding NCBI-supplied PMID: 15262951; 15368893 MUTATION: ompX mutants are attenuated in their ability to attach to and invade HeLa cells [PMID:17768237]. 2540 outer membrane protein X ompX Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2764482 YP_s4 20111206 229193 miscRNA NCBI-supplied MUTATION: smpB ssrA mutant is attenuated in mice [PMID:20065026]. 2541 miscRNA ssrA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2764498 YP_1055 20111206 229193 protein-coding NCBI-supplied PMID: 15262951; 15368893 MUTATION: smpB ssrA mutant is attenuated in mice [PMID:20065026]. 2542 SsrA-binding protein smpB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2764801 YP_2227 20140222 229193 protein-coding NCBI-supplied PMID: 15262951; 15368893 MUTATION: yfeAB mutant is attenuated when given subcutaneously to mice and is avirulent when given to mice intravenously [PMID:10231495]. 2543 periplasmic-binding protein yfeA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2764839 YP_2228 20140222 229193 protein-coding NCBI-supplied PMID: 15262951; 15368893 MUTATION: yfeAB mutant is attenuated when given subcutaneously to mice and is avirulent when given to mice intravenously [PMID:10231495]. 2544 ATP-binding transport protein yfeB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2764925 YP_1656 20140215 229193 protein-coding NCBI-supplied PMID: 15262951; 15368893 MUTATION: ybtP mutant is avirulent in mouse bubonic plague model [PMID:10231486]. 2545 permease and ATP-binding protein of yersiniabactin-iron ABC transporter ybtP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2764958 YP_1654 20140215 229193 protein-coding NCBI-supplied PMID: 15262951; 15368893 MUTATION: irp2 mutants are unable to grow at 37 degrees in iron deficient media [PMID:7896707]. 2546 yersiniabactin biosynthetic protein irp2 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2764984 YP_1649 20140217 229193 protein-coding NCBI-supplied PMID: 15262951; 15368893 MUTATION: psn (fyuA) mutant is unable to grow on iron-deficient media at 37 degrees C [PMID:7896707]. 2547 pesticin/yersiniabactin receptor protein fyuA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2765067 YP_3347 20140217 229193 protein-coding NCBI-supplied PMID: 15262951; 15368893 MUTATION: yapE mutant is attenuated in mice and has impaired colonization in bubonic plague model [PMID:18936182]. 2548 autotransporter protein yapE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2765450 YP_2488 20140405 229193 protein-coding NCBI-supplied PMID: 15262951; 15368893 MUTATION: pgm mutant of Y. pestis is attenuated in mice [PMID:12009274]. 2549 phosphoglucomutase pgm Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2765473 YP_2181 20140215 229193 protein-coding NCBI-supplied PMID: 15262951; 15368893 MUTATION: lpp deletion mutant is attenuated in mice [PMID:19737605]. 2550 major outer membrane lipoprotein lpp Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2765634 YP_0847 20140406 229193 protein-coding NCBI-supplied PMID: 15262951; 15368893 MUTATION: purK mutant is attenuated in mice [PMID:14742535]. 2551 phosphoribosylaminoimidazole carboxylase ATPase subunit purK Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2765673 YP_3091 20140406 229193 protein-coding NCBI-supplied PMID: 15262951; 15368893 MUTATION: purH mutant is attenuated in mice [PMID:14742535]. 2552 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase purH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2765857 YP_1764 20140222 229193 protein-coding NCBI-supplied PMID: 15262951; 15368893 MUTATION: phoP mutants have a reduced ability to survive in J774 macrophage cell cultures and under conditions of low pH and oxidative stress in vitro. The mean lethal dose of the phoP mutant in mice was increased 75-fold in comparison with that of the wild-type strain [PMID:10816493]. 2553 DNA-binding transcriptional regulator PhoP phoP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2766044 YP_1906 20140405 229193 protein-coding NCBI-supplied PMID: 15262951; 15368893 MUTATION: lpxM (msbB) mutant is attenuated in mice and guinea pigs [PMID:17913308]. 2554 lipid A biosynthesis (KDO)2-(lauroyl)-lipid IVA acyltransferase msbB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2766170 YP_1289 20140222 229193 protein-coding NCBI-supplied PMID: 15262951; 15368893 MUTATION: psaA mutants have a 100-fold reduced 50% lethal dose in mice [PMID:2164509]. 2555 adhesin psaA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2766260 YP_0039 20130508 229193 protein-coding NCBI-supplied PMID: 15262951; 15368893 MUTATION: relA spoT deletion mutants are attenuated in mice [PMID:19701461]. 2556 bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase spoT Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2766450 YP_1790 20140301 229193 protein-coding NCBI-supplied PMID: 15262951; 15368893 MUTATION: mgtC mutants are defective in early intracellular survival in macrophages compared to wild type Y. pestis [PMID:16790745]. 2557 Mg(2+) transport ATPase protein C mgtC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2766547 YP_0156 20140222 229193 protein-coding NCBI-supplied PMID: 15262951; 15368893 MUTATION: dam mutant is attenuated in mice [PMID:16188402]. 2558 DNA adenine methylase dam Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2766548 YP_1291 20140215 229193 protein-coding NCBI-supplied PMID: 15262951; 15368893 MUTATION: psaE mutants are attenuated in mice [PMID:2164509]. 2559 regulatory protein psaE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2766682 YP_0306 20140406 229193 protein-coding NCBI-supplied PMID: 15262951; 15368893 MUTATION: relA spoT deletion mutants are attenuated in mice [PMID:19701461]. 2560 GDP/GTP pyrophosphokinase relA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2767357 YP_0174 20140222 229193 protein-coding NCBI-supplied PMID: 15262951; 15368893 MUTATION: crp mutant is attenuated in mice [PMID:20086087]. 2561 cAMP-regulatory protein crp Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2767486 YP_pCD53 20140406 229193 protein-coding NCBI-supplied PMID: 15262951; 15368893 MUTATION: lcrH (sycD) mutant is avirulent in mice [PMID:2707857]. 2497 putative yopB/yopD chaperone SycD sycD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2767487 YP_pCD54 20130827 229193 protein-coding NCBI-supplied PMID: 15262951; 15368893 MUTATION: yopB mutant is avirulent in mouse model, fails to elicit a cytotoxic response in cultured HeLa cells and is unable to inhibit phagocytosis by macrophage-like J774 cells [PMID:8918459]. 2498 putative Yop targeting protein YopB yopB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2767507 YP_pCD55 20140405 229193 protein-coding NCBI-supplied PMID: 15262951; 15368893 MUTATION: yopD mutants are unable to induce cytotoxicity in HeLa cells [PMID:1937815]. 2499 putative Yop negative regulation/targeting component YopD yopD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2767512 YP_pCD67 20140405 229193 protein-coding NCBI-supplied PMID: 15262951; 15368893 putative cytotoxic effector protein YopT yopT Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2767526 YP_pCD17 20140222 229193 protein-coding NCBI-supplied PMID: 15262951; 15368893; 15615724 MUTATION: yopH mutants are unable to resist phagocytosis by J774 cells, while wild type Yersinia is able to resist phagocytosis [PMID:8809758]. 2501 putative protein-tyrosine phosphatase Yop effector YopH yopH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2767532 YP_pCD52 20130827 229193 protein-coding NCBI-supplied PMID: 15262951; 15368893; 21179438 MUTATION: lcrV mutants are avirulent in mice [PMID:7730287]. 2502 V antigen LcrV lcrV Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2767553 YP_pCD68 20130827 229193 protein-coding NCBI-supplied PMID: 15262951; 15368893 MUTATION: yopK (yopQ) mutant has an increased LD50 dose in mice, and infected mice died after 5 days as compared to mice infected with the wild type died after just 3 days [PMID:3002984]. 2503 putative virulence determinant protein YopQ yopQ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2767558 YP_pCD34 20130827 229193 protein-coding NCBI-supplied PMID: 15262951; 15368893 MUTATION: lcrF mutant is attenuated in mice [PMID:14742535]. 2504 putative thermoregulatory protein VirF virF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2767571 YP_pCD13 20140215 229193 protein-coding NCBI-supplied PMID: 15262951; 15368893; 17475872 MUTATION: ypkA mutants of Y. pseudotuberculosis are attenuated in mice [PMID:8441468]. 2505 putative targeted effector protein kinase YpkA ypkA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2767574 YP_pCD60 20140301 229193 protein-coding NCBI-supplied PMID: 15262951; 15368893; 21764506 MUTATION: yopM mutant is attenuated in mice compared to the wild type [PMID:2401564]. 2506 putative targeted effector protein YopM yopM Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2767576 YP_pCD26 20140406 229193 protein-coding NCBI-supplied PMID: 15262951; 15368893 MUTATION: The LD50 for the mouse of the yscH mutant was 10-fold higher than that of the parental strain indicating that YopR is involved in pathogenesis [PMID:8709853]. 2507 putative type III secretion protein YscH yscH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2767578 YP_pCD81 20140217 229193 protein-coding NCBI-supplied PMID: 15262951; 15368893 MUTATION: yopE mutants are attenuated after oral or intraperitoneal infection in mice, but are not attenuated after intravenous infection in mice [PMID:2191183]. 2508 putative outer membrane virulence protein YopE yopE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2767618 YP_pMT084 20140222 229193 protein-coding NCBI-supplied PMID: 15262951; 15368893 MUTATION: caf1M mutants are attenuated in mice [PMID:14711524]. 2494 putative F1 chaperone protein caf1M Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2767657 YP_pMT083 20140215 229193 protein-coding NCBI-supplied PMID: 15262951; 15368893 MUTATION: caf1A mutants are attenuated in mice [PMID:14711524]. 2495 putative F1 capsule anchoring protein caf1A Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2767661 YP_pMT119 20140217 229193 protein-coding NCBI-supplied PMID: 15262951; 15368893 MUTATION: ymt mutants are unable to block X. cheopsis fleas and have low survival rates in the flea gut [PMID:11976454]. 2496 toxin ymt Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2797078 LMOf2365_0216 20140405 265669 protein-coding NCBI-supplied GO_0004629 (EC: ISS, PMID: 15115801); GO_0009405 (EC: ISS, PMID: 15115801); GO_0019836 (EC: ISS, PMID: 15115801) PMID: 15115801 MUTATION: deletion mutants showed reduced virulence in mice, escape from vacuole and cell-to-cell spread [PMID:7591052]. 1419 phospholipase C plcB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2797098 LMOf2365_0213 20140222 265669 protein-coding NCBI-supplied GO_0009405 (EC: ISS, PMID: 15115801); GO_0015485 (EC: ISS, PMID: 15115801); GO_0019835 (EC: ISS, PMID: 15115801); GO_0019836 (EC: ISS, PMID: 15115801) PMID: 15115801; 18322222 MUTATION: mutant strain resulted in a 100-fold virulence defect in mice, prematurely killed host cell [PMID:11901168]. 1420 listeriolysin O hly Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2797137 LMOf2365_2488 20140222 265669 protein-coding NCBI-supplied GO_0000155 (EC: ISS, PMID: 15115801); GO_0000160 (EC: ISS, PMID: 15115801); GO_0006355 (EC: ISS, PMID: 15115801) PMID: 15115801; 19796338 MUTATION: mutant strain showed reduction in motility, attenuated in mice [PMID:16213668]. 1421 DNA-binding response regulator DegU degU Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2797185 LMOf2365_0429 20130615 265669 protein-coding NCBI-supplied GO_0003824 (EC: ISS, PMID: 15115801); GO_0009405 (EC: ISS, PMID: 15115801) PMID: 15115801 MUTATION: deletion mutant avirulent in mice [PMID:9791184]. 1422 internalin inlF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2797731 LMOf2365_2745 20130615 265669 protein-coding NCBI-supplied GO_0004003 (EC: ISS, PMID: 15115801); GO_0006310 (EC: ISS, PMID: 15115801) PMID: 15115801 MUTATION: a recQ mutant was attenuated in mice [PMID:11254558] 1423 ATP-dependent DNA helicase RecQ recQ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2798471 LMOf2365_0094 20130527 265669 protein-coding NCBI-supplied GO_0003674 (EC: ND); GO_0008150 (EC: ND) PMID: 15115801 MUTATION: attenuated in mice [PMID:14638794]. 1424 pentapeptide repeat-containing protein LMOf2365_0094 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2798475 LMOf2365_0471 20130527 265669 protein-coding NCBI-supplied GO_0003674 (EC: ND); GO_0009405 (EC: ISS, PMID: 15115801); GO_0030260 (EC: ISS, PMID: 15115801) PMID: 15115801 MUTATION: attenuated in mice [PMID:7558297]. 1425 internalin A inlA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2798554 LMOf2365_1971 20130527 265669 protein-coding NCBI-supplied GO_0004003 (EC: ISS, PMID: 15115801); GO_0006310 (EC: ISS, PMID: 15115801) PMID: 15115801 MUTATION: a recQ mutant was attenuated in mice [PMID:11254558] 1426 ATP-dependent DNA helicase RecQ LMOf2365_1971 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2798680 LMOf2365_2522 20140215 265669 protein-coding NCBI-supplied GO_0003674 (EC: ND); GO_0019350 (EC: ISS, PMID: 15115801) PMID: 15115801 MUTATION: a gtca mutant showed diminished ability to invade intestinal epithelial cells, was attenuated in mice [PMID:11254558]. 1427 cell wall teichoic acid glycosylation protein GtcA gtcA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2798696 LMOf2365_0060 20140406 265669 protein-coding NCBI-supplied GO_0000156 (EC: ISS, PMID: 15115801); GO_0000160 (EC: ISS, PMID: 15115801) PMID: 15115801 MUTATION: virulence of a agrA mutant was attenuated in a mouse [PMID:12874326]. 1428 accessory gene regulator protein A agrA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2799022 LMOf2365_0214 20140222 265669 protein-coding NCBI-supplied GO_0004222 (EC: ISS, PMID: 15115801); GO_0006508 (EC: ISS, PMID: 15115801); GO_0008270 (EC: ISS, PMID: 15115801) PMID: 15115801 MUTATION: attenuated in mice [PMID:1311708]. 1429 zinc metallopeptidase mpl Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2799165 LMOf2365_0241 20140222 265669 protein-coding NCBI-supplied GO_0006355 (EC: ISS, PMID: 15115801); GO_0006950 (EC: ISS, PMID: 15115801) PMID: 15115801; 16332826 MUTATION: attenuated virulence in spleens of mice [PMID:12940983]. 1430 CtsR family transcriptional regulator ctsR Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2799227 LMOf2365_0472 20130527 265669 pseudo NCBI-supplied GO_0003674 (EC: ND); GO_0009405 (EC: ISS, PMID: 15115801); GO_0030260 (EC: ISS, PMID: 15115801) PMID: 15115801 MUTATION: attenuated in mice [PMID:7558297]. 1431 pseudo inlB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2799457 LMOf2365_0211 20140222 265669 protein-coding NCBI-supplied GO_0009405 (EC: ISS, PMID: 15115801) PMID: 15115801; 15686548; 16239554; 16707681; 17566579 MUTATION: attenuated in mice [PMID:1729245]. 1432 listeriolysin regulatory protein prfA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2799536 LMOf2365_2441 20140215 265669 protein-coding NCBI-supplied GO_0004176 (EC: ISS, PMID: 15115801); GO_0004252 (EC: ISS, PMID: 15115801); GO_0009368 (EC: ISS, PMID: 15115801) PMID: 15115801 MUTATION: mutant strain showed reduced bacterial escape from phagosomes of macrophages and virulence in mice [PMID:10760131]. 1433 ATP-dependent Clp protease proteolytic subunit clpP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2799631 LMOf2365_2252 20130615 265669 protein-coding NCBI-supplied GO_0003755 (EC: ISS, PMID: 15115801); GO_0006457 (EC: ISS, PMID: 15115801) PMID: 15115801 MUTATION: mutant attenuated in mice, impaired cell to cell spread in host cells [PMID:19451247]. 1434 protein export protein prsA-2 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2814654 GBAA_0992 20140215 261594 protein-coding NCBI-supplied PMID: 18952800 MUTATION: sigB mutant is less virulent in mice than the parental strain [PMID:10960085]. 1409 RNA polymerase sigma factor SigB sigB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2815836 GBAA_4766 20140222 261594 protein-coding NCBI-supplied PMID: 18952800 MUTATION: fpuA (GBAA4766) mutant is attenuated in mice [PMID:20487286]. 1410 iron ABC transporter substrate-binding protein GBAA_4766 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2816065 GBAA_4704 20140215 261594 protein-coding NCBI-supplied PMID: 18952800 MUTATION: clpX deletion mutant is attenuated in mice [PMID:20375606]. 1411 ATP-dependent protease ATP-binding subunit ClpX clpX Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2817231 GBAA_0552 20140329 261594 protein-coding NCBI-supplied PMID: 18952800 MUTATION: GBAA0552 mutant is attenuated in mice [PMID:19768119]. 1412 internalin GBAA_0552 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2819662 GBAA_5139 20140222 261594 protein-coding NCBI-supplied PMID: 18952800 MUTATION: A quadruple-knockout strain (Delta sod15 Delta sodA1 Delta sodC Delta sodA2) was attenuated more than 40-fold upon intranasal challenge of mice compared to the wild type [PMID:18955476]. 1413 superoxide dismutase, Cu-Zn sodC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2819695 GBAA_1340 20140406 261594 protein-coding NCBI-supplied PMID: 18952800 MUTATION: phnX (GBAA1340) mutant is attenuated in mice [PMID:19768119]. 1414 phosphonoacetaldehyde hydrolase phnX Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2820095 GBAA_3966 20140222 261594 protein-coding NCBI-supplied PMID: 18952800; 19651859; 21911592; 23292769 MUTATION: codY mutant is attenuated in mice [PMID:19651859]. 1415 transcriptional repressor CodY codY Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2820148 GBAA_pXO1_0172 20140215 261594 protein-coding NCBI-supplied PMID: 15530370; 15871122; 17339348; 18222626; 18276157; 18356299; 18490752; 18667583; 18831046; 18952800; 19103170; 19307216; 19343203; 19349425; 19359249; 19720758; 20534570; 21518787; 21791242; 22526673; 23313942; 23423542; 23818853 MUTATION: lef mutant is non-lethal in mice [PMID:1910002]. 1416 lethal factor lef Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2820165 GBAA_pXO1_0164 20140222 261594 protein-coding NCBI-supplied PMID: 15871122; 16051798; 16141341; 16188881; 16460675; 16473908; 16475827; 17107945; 17251181; 18222626; 18490752; 18667583; 18952800; 19349425; 20061382; 20221438; 20359529; 22526673; 22855243 MUTATION: pagA mutant is non-lethal in mice [PMID:1910002]. 1417 protective antigen pagA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2820309 GBAA_pXO1_0146 20140406 261594 protein-coding NCBI-supplied PMID: 17302798; 18676674; 18952800; 20359529 MUTATION: atxA mutant is avirulent in mice [PMID:12224521]. 1418 transcriptional activator AtxA atxA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2851842 BAS4369 20140215 260799 protein-coding NCBI-supplied PMID: 20375606 MUTATION: clpX deletion mutant is attenuated in mice [PMID:20375606]. 1407 ATP-dependent protease ATP-binding subunit ClpX clpX MUTATION: BAS4929 (ccpA) mutant is attenuated in mice [PMID:20971911]. 1408 Bin Zhao, Oliver He fmtC WEB: http://www.ncbi.nlm.nih.gov/gene 2861306 SAR1372 20140406 282458 protein-coding NCBI-supplied PMID: 15213324; 19183815 MUTATION: mprF mutant is attenuated in mice [PMID:11342591]. 4312 hypothetical protein - mprF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2865827 BH13280 20140217 283166 protein-coding NCBI-supplied PMID: 15210978; 15231811; 18037886 MUTATION: virB4 mutant is attenuated in the capacity to grow in co-culture with, invade into, or survive within endothelial cells [PMID:15049812]. 4581 virB4 protein virB4 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2873843 AN2855.2 20140301 227321 VI protein-coding NCBI-supplied PMID: 16372000 MUTATION: pacC mutant is attenuated in mice [PMID:15686555]. 4567 similar to S54308 DNA binding protein - Emericella nidulans Other designations: hypothetical protein AN2855.2 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2887693 CAGL0F09097g 20140406 284593 F protein-coding NCBI-supplied PMID: 15229592; 19693686 MUTATION: skn7 deletion mutant is attenuated in mice [PMID:19693686]. 4705 hypothetical protein CAGL0F09097g Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2888485 CAGL0H08558g 20140406 284593 H protein-coding NCBI-supplied PMID: 15229592 MUTATION: CgAtg11 mutant is killed more efficiently by macrophages than the wildtype [PMID:19811500]. 4698 hypothetical protein CAGL0H08558g Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2890566 CAGL0L00605g 20140405 284593 L protein-coding NCBI-supplied PMID: 15229592 MUTATION: cnb1 mutant is attenuated in mice [PMID:20100876]. 4700 hypothetical protein CAGL0L00605g Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2891693 CAGL0M06831g 20140406 284593 M protein-coding NCBI-supplied PMID: 15229592 MUTATION: crz1 mutant is attenuated in mice [PMID:20100876]. 4701 hypothetical protein CAGL0M06831g Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2941480 M6_Spy0741 20130518 286636 protein-coding NCBI-supplied PMID: 15272401 SpeA variant M6_Spy0741 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2943079 HTNVsMgp1 20140301 11599 protein-coding NCBI-supplied PMID: 3103329; 17267477; 17342054; 19143481; 19767836 MUTATION: Two Hantaan virus strains, clone 1 (cl-1), which is virulent in newborn mice, and its attenuated mutant (mu11E10), were used to examine the pathogenesis of Hantaan virus infection in a mouse model and identify virus factors relating to virulence. After subcutaneous inoculation of newborn BALB/c mice, cl-1 caused fatal disease with high viral multiplication in peripheral organs, but mu11E10 produced nonfatal infection with a low level of virus multiplication. Sequence comparison detected a single deduced amino acid change (cl-1 Ile to mu11E10 Thr) at amino acid number 515 in glycoprotein G1. In mouse brain microvascular endothelial cells in vitro, viruses possessing a cl-1-derived M segment grew more rapidly than viruses containing a mu11E10-derived M segment. These results suggest that the single amino acid change in the glycoprotein alters peripheral growth, which affects invasion of the central nervous system in mice [PMID:10982372]. 2877 precursor structural polyprotein Other designations: hypothetical protein HTNVsMgp1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2943185 PCV2_gp3 20140222 85708 protein-coding NCBI-supplied PMID: 15564454; 21733152; 21859462; 22492916; 24210099 capsid protein ORF2 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2943186 PCV2_gp1 20140301 85708 protein-coding NCBI-supplied PMID: 20030061 replicase ORF1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2952517 SuHV1_gp70 20140222 10345 protein-coding NCBI-supplied PMID: 14671123; 17131935 type 1 membrane protein; contains a signal peptide; complexed with envelope glycoprotein I to form an Fc-receptor Other designations: envelope glycoprotein E US8 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2952522 SuHV1_gp27 20130525 10345 protein-coding NCBI-supplied PMID: 14671123 MUTATION: A UL41 mutant is highly attenuated in mice [PMID:20448414]. 4525 mRNA-specific RNase Other designations: tegument host shutoff protein UL41 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2952537 SuHV1_gp07 20140222 10345 protein-coding NCBI-supplied PMID: 14671123 MUTATION: A UL50 mutant is attenuated in pigs [PMID:9228681]. 4998 deoxyuridine triphosphatase UL50 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2952540 SuHV1_gp63 20130525 10345 protein-coding NCBI-supplied PMID: 14671123; 22532685 MUTATION: A gp50+gp63 deletion mutant in Pseudorabies virus was attenuated in pigs [PMID:8178562]. 4993 transcriptional regulator ICP4 IE180 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2952541 SuHV1_gp37 20140222 10345 protein-coding NCBI-supplied PMID: 14671123; 17079290 interacts with microtubules Other designations: tegument protein UL21 UL21 MUTATION: A gp50 null mutant is attenuated in pigs [PMID:8178562]. 4992 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2952552 SuHV1_gp71 20140301 10345 protein-coding NCBI-supplied PMID: 14671123; 17686845; 18483549; 19420087; 22448044; 23245325; 23527020; 23804637 type 2 membrane protein; tegument-associated; localizes envelope proteins Other designations: membrane protein US9 US9 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2952559 SuHV1_gp35 20140301 10345 protein-coding NCBI-supplied PMID: 14671123 MUTATION: a thymidine kinase PRV mutant is attenuated in pigs [PMID:12488067]. MUTATION: A UL23 mutant, in combination with mutations in glycoproteins G and E, is attenuated in raccoons [PMID:12488067]. 4997 thymidine kinase UL23 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2952561 SuHV1_gp65 20140222 10345 protein-coding NCBI-supplied PMID: 14671123; 17499381; 20053819; 21093504; 23365433 MUTATION: US3 mutant is attenuated in pigs [PMID:7975253]. 4999 tegument protein; phosphorylates nuclear egress lamina protein; mediates phosphorylation of HDAC1 and HDAC2 and other cellular and viral proteins Other designations: serine/threonine protein kinase US3 US3 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2952940 pYV0047 20130518 273123 protein-coding NCBI-supplied PMID: 15358858; 22547545 MUTATION: yopM mutant has attenuated colonization of mouse tissues [PMID:20368345]. 3995 yopM; targeted effector protein pYV0047 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2952967 pYV0074 20140217 273123 protein-coding NCBI-supplied PMID: 15358858; 18424518; 19395493 MUTATION: yscU mutant is attenuated in mice [PMID:11292689]. 3996 yscU; type III secretion protein pYV0074 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2952977 pYV0084 20130616 273123 protein-coding NCBI-supplied PMID: 15358858 MUTATION: yscH mutant is attenuated in mice [PMID:11292689]. 3997 yscH, yopR, lcrP; type III secretion protein pYV0084 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2952987 pYV0094 20140222 273123 protein-coding NCBI-supplied PMID: 15358858 MUTATION: yopH mutant is attenuated in mice [PMID:12542470]. 3998 yopH; protein-tyrosine phosphatase Yop effector pYV0094 Bin Zhao, Oliver He nov WEB: http://www.ncbi.nlm.nih.gov/gene 2955341 YPTB2111 20140322 273123 protein-coding NCBI-supplied PMID: 15358858; 19055764 MUTATION: cls mutant is attenuated in mice [PMID:11292689]. 3999 cardiolipin synthetase - cls Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2955440 YPTB1001 20140406 273123 protein-coding NCBI-supplied PMID: 15358858; 19055764 MUTATION: ddhC mutant is attenuated in mice [PMID:11292689]. 4000 CDP-4-keto-6-deoxy-D-glucose-3-dehydratase ddhC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2955730 YPTB1009 20140405 273123 protein-coding NCBI-supplied PMID: 15358858; 19055764 MUTATION: gmd mutant is attenuated in mice [PMID:11292689]. 4001 GDP-D-mannose dehydratase gmd Bin Zhao, Oliver He rsmA WEB: http://www.ncbi.nlm.nih.gov/gene 2955927 YPTB0633 20130827 273123 protein-coding NCBI-supplied PMID: 15358858; 19055764 MUTATION: ksgA mutant is attenuated in mice [PMID:11292689]. 4002 dimethyladenosine transferase - ksgA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2956268 YPTB2434 20140222 273123 protein-coding NCBI-supplied PMID: 15358858; 19055764 MUTATION: A phoP mutant in Yersinia pseudotuberculosis (Yptb) was attenuated in mice [PMID:17194509]. 5016 DNA-binding transcriptional regulator PhoP phoP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2956900 YPTB1004 20130226 273123 protein-coding NCBI-supplied PMID: 15358858; 19055764 MUTATION: wzx mutant is attenuated in mice [PMID:11292689]. 4003 O-unit flippase wzx Bin Zhao, Oliver He wzx WEB: http://www.ncbi.nlm.nih.gov/gene 2956901 YPTB0176 20130518 273123 protein-coding NCBI-supplied PMID: 15358858; 19055764 MUTATION: wzx mutant is attenuated in mice [PMID:11292689]. 4004 PST family o-antigen export protein - wzxE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 2957096 YPTB0425 20130616 273123 protein-coding NCBI-supplied PMID: 15358858; 19055764; 20231416 MUTATION: hfq mutant is attenuated in mice [PMID:20231416]. 4005 RNA-binding protein Hfq hfq Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3077319 pG8786_122 20140215 632 protein-coding NCBI-supplied PMID: 15385458 MUTATION: ymt mutants are unable to block X. cheopsis fleas and have low survival rates in the flea gut [PMID:11976454]. 2491 toxin protein ymt Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3077339 pG8786_073 20140217 632 protein-coding NCBI-supplied PMID: 15385458 MUTATION: caf1A mutants are attenuated in mice [PMID:14711524]. 2492 F1 capsule anchoring protein caf1A Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3077340 pG8786_074 20140222 632 protein-coding NCBI-supplied PMID: 15385458; 17376079 MUTATION: caf1M mutants are attenuated in mice [PMID:14711524]. 2493 F1 capsule protein caf1M Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3078198 lpg0742 20140329 272624 protein-coding NCBI-supplied PMID: 15448271 MUTATION: ldsA (lpg0742) mutant is attenuated in mouse macrophages [PMID:16997951]. 1435 hypothetical protein lpg0742 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3078361 lpg1438 20140222 272624 protein-coding NCBI-supplied PMID: 15448271; 18192394 MUTATION: cpxR mutant is attenuated in mouse macrophages [PMID:16997951]. 1436 transcriptional regulatory protein CpxR cpxR Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3078495 lpg0791 20140329 272624 protein-coding NCBI-supplied PMID: 15448271; 21794054 MUTATION: mip mutants are approximately 50- to 100-fold less infective for A. castellanii and for human mononuclear phagocytes in vitro compared with their isogenic Mip-positive parental strains [PMID:7591108]. 1437 macrophage infectivity potentiator (Mip) mip Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3078951 lpg1905 20140329 272624 protein-coding NCBI-supplied PMID: 15448271; 23830739 MUTATION: lpg1905 mutant is attenuated in macrophages and human alveolar cells [PMID:17388784]. 1438 ectonucleoside triphosphate diphosphohydrolase I lpg1905 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3078981 lpg2155 20130616 272624 protein-coding NCBI-supplied PMID: 15448271; 17101649 MUTATION: sidJ (lpg2155) mutant is attenuated in macrophages [PMID:17101649]. 1439 hypothetical protein lpg2155 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3079093 lpg2689 20140222 272624 protein-coding NCBI-supplied PMID: 15448271 MUTATION: icmX mutant is attenuated in guinea pigs [PMID:10393970]. 1440 intracellular multiplication protein IcmX icmX Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3079177 lpg2639 20140329 272624 protein-coding NCBI-supplied PMID: 15448271; 22901537 MUTATION: enhC mutant is attenuated in mouse macrophages [PMID:18549456]. 1441 enhanced entry protein EnhC enhC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3079449 lpg2676 20140329 272624 protein-coding NCBI-supplied PMID: 15448271 MUTATION: dotB mutant is attenuated in guinea pigs [PMID:10393970]. 1442 ATPase dotB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3079451 lpg2686 20140329 272624 protein-coding NCBI-supplied PMID: 15448271 MUTATION: dotA mutant is unable to replicate in mouse macrophages [PMID:16997951]. 1443 defect in organelle trafficking protein DotA dotA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3079487 lpg2657 20140329 272624 protein-coding NCBI-supplied PMID: 15448271; 20036663 MUTATION: feoB mutant is attenuated in human macrophages [PMID:12228295]. 1444 ferrous iron transport protein B feoB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3079830 lpg2871 20140329 272624 protein-coding NCBI-supplied PMID: 15448271 MUTATION: ptsP mutant is attenuated in guinea pigs [PMID:11447151]. 1445 phosphoenolpyruvate protein phosphotransferase PtsP ptsP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3079958 lpg0452 20140406 272624 protein-coding NCBI-supplied PMID: 15448271 MUTATION: icmG mutant is attenuated in guinea pigs [PMID:10393970]. 1446 IcmG protein icmG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3080126 lpg0456 20140406 272624 protein-coding NCBI-supplied PMID: 15448271 MUTATION: icmB mutant is attenuated in guinea pigs [PMID:10393970]. 1447 IcmB protein icmB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3080381 lpg1284 20140329 272624 protein-coding NCBI-supplied PMID: 15448271 MUTATION: rpoS mutant is defective in intracellular replication in its protozoan host [PMID:19218380]. 1448 stationary phase specific sigma factor RpoS rpoS Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3080541 lpg2341 20140406 272624 protein-coding NCBI-supplied PMID: 15448271 MUTATION: djlA mutant is attenuated in mouse macrophages [PMID:16997951]. 1449 Dna-J like membrane chaperone protein djlA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3080592 lpg2515 20130528 272624 protein-coding NCBI-supplied PMID: 15448271 MUTATION: rtxA mutant is attenuated in mice and does not replicate as well as the wild type in monocytes [PMID:11119544]. 1450 structural toxin protein (hemagglutinin/hemolysin) RtxA lpg2515 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3086085 BMAA0739 20140329 243160 2 protein-coding NCBI-supplied PMID: 15377793 MUTATION: BMAA0739 (tssE) is attenuated in hamsters [PMID:17555434]. 2020 hypothetical protein BMAA0739 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3086187 BMAA0743 20130511 243160 2 protein-coding NCBI-supplied PMID: 15377793 MUTATION: BMAA0743 (tssB) mutant is attenuated in hamsters [PMID:17555434]. 2021 hypothetical protein BMAA0743 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3086213 BMAA0746 20140329 243160 2 protein-coding NCBI-supplied PMID: 15377793 MUTATION: virG mutant is avirulent in hamsters [PMID:15377793]. 2022 DNA-binding response regulator virG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3086253 BMAA0742 20130511 243160 2 protein-coding NCBI-supplied PMID: 15377793 MUTATION: BMAA0742 (hcp1) mutant is attenuated in hamsters [PMID:17555434]. 2023 hypothetical protein BMAA0742 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3086328 BMAA0649 20140329 243160 2 protein-coding NCBI-supplied PMID: 15377793 MUTATION: boaA (BMAA0649) mutant has reduced adherence to human epithelial cell lines, specifically HEp2 (laryngeal cells) and A549 (type II pneumocytes), as well as to cultures of normal human bronchial epithelium (NHBE) compared to the wild type [PMID:20920184]. 2024 hemagluttinin motif-containing protein BMAA0649 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3086415 BMAA0740 20130511 243160 2 protein-coding NCBI-supplied PMID: 15377793 MUTATION: BMAA0740 (tssD) mutant is attenuated in hamsters [PMID:17555434]. 2025 hypothetical protein BMAA0740 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3091509 BPSL1039 20130511 272560 1 protein-coding NCBI-supplied PMID: 15377794 MUTATION: BPSL1039 mutant is attenuated in mice [PMID:17189432]. 1991 ABC transporter membrane protein BPSL1039 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3091526 BPSL1263 20130518 272560 1 protein-coding NCBI-supplied PMID: 15377794 MUTATION: BPSL1263 (cdpA) mutant has a 3-fold reduction in invasion of human lung epithelial cells and a 6-fold reduction in cytotoxicity on human macrophage cells [PMID:20194589]. 1992 hypothetical protein BPSL1263 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3091586 BPSL0413 20140322 272560 1 protein-coding NCBI-supplied PMID: 15377794 MUTATION: lipB mutant is attenuated in mice [PMID:16714590]. 1993 lipoate-protein ligase B lipB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3091767 BPSL3133 20140405 272560 1 protein-coding NCBI-supplied PMID: 15377794 MUTATION: hisF mutant is attenuated in mice and has intracellular growth defects [PMID:16714590]. 1994 imidazole glycerol phosphate synthase subunit HisF hisF Bin Zhao, Oliver He gmhC WEB: http://www.ncbi.nlm.nih.gov/gene 3091825 BPSL2793 20140406 272560 1 protein-coding NCBI-supplied PMID: 15377794 MUTATION: wcbN mutant is attenuated in mice [PMID:17189432]. 1995 D-glycero-d-manno-heptose 1,7-bisphosphate phosphatase - wcbN Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3091847 BPSL2825 20130518 272560 1 protein-coding NCBI-supplied PMID: 15377794 MUTATION: BPSL2825 mutant is attenuated in mice [PMID:16714590]. 1996 hypothetical protein BPSL2825 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3092290 BPSL0634 20130518 272560 1 protein-coding NCBI-supplied PMID: 15377794 MUTATION: BPSL0634 mutant is attenuated in mice [PMID:17189432]. 1997 oxidoreductase BPSL0634 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3092312 BPSL1528 20121017 272560 1 protein-coding NCBI-supplied PMID: 15377794 MUTATION: Inactivation of gene BPSL1528 leads to impaired actin tail formation, reduced intracellular survival, and high-grade attenuation of virulence in mice [PMID:16714590]. 1998 hypothetical protein BPSL1528 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3092462 BPSL3168 20140405 272560 1 protein-coding NCBI-supplied PMID: 15377794 MUTATION: aroB mutant is attenuated in mice [PMID:17189432]. 1999 3-dehydroquinate synthase aroB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3092485 BPSL3051 20140405 272560 1 protein-coding NCBI-supplied PMID: 15377794 MUTATION: trpG mutant is attenuated in mice [PMID:17189432]. 2000 anthranilate synthase component II trpG Bin Zhao, Oliver He purG WEB: http://www.ncbi.nlm.nih.gov/gene 3092877 BPSL2818 20140405 272560 1 protein-coding NCBI-supplied PMID: 15377794 MUTATION: purM mutant is avirulent in mice [PMID:20404077]. 2001 phosphoribosylaminoimidazole synthetase - purM Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3092878 BPSL0908 20140405 272560 1 protein-coding NCBI-supplied PMID: 15377794 MUTATION: purN mutant is attenuated in mice [PMID:16714590]. 2002 phosphoribosylglycinamide formyltransferase purN Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3093047 BPSL2808 20130518 272560 1 protein-coding NCBI-supplied PMID: 15377794 MUTATION: wcbB mutant is attenuated in mice [PMID:17189432]. 2003 capsular polysaccharide glycosyltransferase biosynthesis protein wcbB Bin Zhao, Oliver He cpxD WEB: http://www.ncbi.nlm.nih.gov/gene 3093048 BPSL2807 20140222 272560 1 protein-coding NCBI-supplied PMID: 15377794 MUTATION: wcbC mutation is attenuated in mice [PMID:11119486]. 2004 capsular polysaccharide biosynthesis/export protein - wcbC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3093395 BPSL1103 20130330 272560 1 protein-coding NCBI-supplied PMID: 15377794 MUTATION: nth mutant is attenuated in mice [PMID:17189432]. 2005 endonuclease III nth Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3093782 BPSL0872 20130511 272560 1 protein-coding NCBI-supplied PMID: 15377794 MUTATION: BPSLO872 (mviN) mutant displayed an increased LD50 value in the hamster infection model and a loss of the ability to invade human lung epithelial cells [PMID:17110975]. 2006 MviN-like protein BPSL0872 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3093846 BPSL0395 20130330 272560 1 protein-coding NCBI-supplied PMID: 15377794 MUTATION: BPSL0395 mutant is attenuated in mice [PMID:16714590]. 2007 cytidylyltransferase BPSL0395 Bin Zhao, Oliver He bexB WEB: http://www.ncbi.nlm.nih.gov/gene 3093941 BPSL2805 20140222 272560 1 protein-coding NCBI-supplied PMID: 15377794 MUTATION: wzm mutant is attenuated in mice [PMID:17189432]. 2008 capsular polysaccharide export ABC transporter transmembrane protein - wzm Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3093947 BPSL1196 20140405 272560 1 protein-coding NCBI-supplied PMID: 15377794 MUTATION: ilvI mutant is attenuated in mice [PMID:12183585]. 2009 acetolactate synthase 3 catalytic subunit ilvI Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3094015 BPSL3319 20140405 272560 1 protein-coding NCBI-supplied PMID: 15377794 MUTATION: fliC mutant is attenuated in mice [PMID:12654773]. 2010 flagellin fliC Bin Zhao, Oliver He bexC WEB: http://www.ncbi.nlm.nih.gov/gene 3094162 BPSL2806 20140222 272560 1 protein-coding NCBI-supplied PMID: 15377794 MUTATION: wcbD mutant is attenuated in mice [PMID:17189432]. 2011 capsule polysaccharide export ABC transporter transmembrane protein - wcbD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3094200 BPSL3147 20130511 272560 1 protein-coding NCBI-supplied PMID: 15377794 MUTATION: BPSL3147 mutant is attenuated in mice [PMID:17189432]. 2012 lipoprotein BPSL3147 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3094241 BPSL2519 20140405 272560 1 protein-coding NCBI-supplied PMID: 15377794 MUTATION: serC mutant is attenuated in mice [PMID:16997946]. 2013 phosphoserine aminotransferase serC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3094325 BPSL0776 20130330 272560 1 protein-coding NCBI-supplied PMID: 15377794 MUTATION: recA mutant is attenuated in mice [PMID:17189432]. 2014 recombinase A recA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3094734 BPSL1876 20140405 272560 1 protein-coding NCBI-supplied PMID: 15377794 MUTATION: BPSL1876 mutant is attenuated in mice [PMID:16988221]. 2015 phospholipase BPSL1876 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3094881 BPSL1705 20130518 272560 1 protein-coding NCBI-supplied PMID: 15377794 MUTATION: boaB (BPSL1705) mutant has reduced attachment to respiratory cells, and a boaA boaB double mutant was attenuated in murine macrophages [PMID:20920184]. 2016 hypothetical protein BPSL1705 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3094947 BPSS1705 20140405 272560 2 protein-coding NCBI-supplied PMID: 15377794 MUTATION: leuB mutant is attenuated in mice [PMID:17189432]. 1980 3-isopropylmalate dehydrogenase leuB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3095047 BPSS1509 20130511 272560 2 protein-coding NCBI-supplied PMID: 15377794 MUTATION: BPSS1509 mutant is attenuated in mice [PMID:16714590]. 1981 hypothetical protein BPSS1509 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3095565 BPSS1400 20130511 272560 2 protein-coding NCBI-supplied PMID: 15377794 MUTATION: sctU mutant is attenuated in hamsters [PMID:15621426]. 1982 type III secretion system protein HrcU sctU Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3095712 BPSS2074 20130511 272560 2 protein-coding NCBI-supplied PMID: 15377794 MUTATION: BPSS2074 (lpfA) mutant is attenuated in hamsters [PMID:16987331]. 1983 senescence marker protein-30 (SMP-30) family protein BPSS2074 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3096115 BPSS1529 20140322 272560 2 protein-coding NCBI-supplied PMID: 15377794; 16880550; 16946464; 16950399; 17077085 MUTATION: bipD mutant was attenuated in mice [PMID:16714590]. 1984 membrane antigen bipD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3096285 BPSS1539 20121017 272560 2 protein-coding NCBI-supplied PMID: 15377794 MUTATION: BPSS1539 mutant is attenuated in mice [PMID:16714590]. 1985 hypothetical protein BPSS1539 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3096393 BPSS1525 20140322 272560 2 protein-coding NCBI-supplied PMID: 15377794 MUTATION: bopE mutant is attenuated in mice [PMID:15289563]. 1986 G-nucleotide exchange factor bopE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3096627 BPSS1534 20131226 272560 2 protein-coding NCBI-supplied PMID: 15377794 MUTATION: bsaZ mutant is attenuated in mouse macrophages [PMID:12410823]. 1987 surface presentation of antigens protein SpaS bsaZ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3096819 BPSS0067 20140405 272560 2 protein-coding NCBI-supplied PMID: 15377794 MUTATION: BPSS0067 mutant is attenuated in mice [PMID:16988221]. 1988 phospholipase C precursor BPSS0067 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3096991 BPSS2053 20130518 272560 2 protein-coding NCBI-supplied PMID: 15377794 MUTATION: BPSS2053 mutant had reduced microbial adherence to human epithelial cells [PMID:18927621]. 1989 cell surface protein BPSS2053 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3097087 BPSS0885 20140222 272560 2 protein-coding NCBI-supplied PMID: 15377794 MUTATION: pmll mutant is attenuated in mice [PMID:15060030]. 1990 N-acylhomoserine lactone synthase pmlI Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3113555 lpl1422 20130616 297245 protein-coding NCBI-supplied PMID: 15467720 MUTATION: plaB mutant is attenuated in guinea pigs [PMID:20153694]. 1452 phospholipase plaB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3113668 lpl2784 20140329 297245 protein-coding NCBI-supplied PMID: 15467720 MUTATION: ptsP mutant is attenuated in guinea pigs [PMID:11447151]. 1453 phosphoenolpyruvate-protein phosphotransferase PtsP ptsP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3113684 lpl2613 20140329 297245 protein-coding NCBI-supplied PMID: 15467720 MUTATION: dotA mutant is unable to replicate in mouse macrophages [PMID:16997951]. 1454 defect in organelle trafficking protein DotA dotA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3113813 lpl2262 20140329 297245 protein-coding NCBI-supplied PMID: 15467720 MUTATION: djlA mutant is attenuated in mouse macrophages [PMID:16997951]. 1455 Dna-J like membrane chaperone protein djlA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3114023 lpl2616 20130616 297245 protein-coding NCBI-supplied PMID: 15467720 MUTATION: icmX mutant is attenuated in guinea pigs [PMID:10393970]. 1456 intracellular multiplication protein IcmX icmX Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3114223 lpl0681 20140329 297245 protein-coding NCBI-supplied PMID: 15467720 MUTATION: rtxA mutant is attenuated in mice and doesn't grow as well in monocytes as the wild type [PMID:11119544]. 1457 structural toxin protein RtxA rtxA-2 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3114458 lpl0829 20130616 297245 protein-coding NCBI-supplied PMID: 15467720 MUTATION: mip mutants are approximately 50- to 100-fold less infective for A. castellanii and for human mononuclear phagocytes in vitro compared with their isogenic Mip-positive parental strains [PMID:7591108]. 1458 macrophage infectivity potentiator mip Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3114487 lpl1293 20140405 297245 protein-coding NCBI-supplied PMID: 15467720 MUTATION: flaA mutant is less invasive of HL-60 cells than the wild type [PMID:11254565]. 1459 flagellin flaA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3114575 lpl0414 20140406 297245 protein-coding NCBI-supplied PMID: 15467720 MUTATION: fur mutant has attenuated intracellular growth within U937 cell monolayers [PMID:12228295]. 1460 ferric uptake regulation protein fur Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3114696 lpl0419 20121209 297245 protein-coding NCBI-supplied PMID: 15467720; 17124169 MUTATION: sdhA mutant is attenuated in mouse macrophages [PMID:17124169]. 1461 SdhA, substrate of the Dot/Icm system sdhA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3114737 lpl2603 20140222 297245 protein-coding NCBI-supplied PMID: 15467720 MUTATION: dotB mutant is attenuated in guinea pigs [PMID:10393970]. 1462 defect in organelle trafficking protein DotB (ATPase) dotB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3114746 lpl0784 20140222 297245 protein-coding NCBI-supplied PMID: 15467720 MUTATION: iraA mutant is attenuated in guinea pigs [PMID:10678909]. 1463 small-molecule methyltransferase IraA iraA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3114978 lpl1247 20140329 297245 protein-coding NCBI-supplied PMID: 15467720 MUTATION: rpoS mutant is defective in intracellular replication in its protozoan host [PMID:19218380]. 1464 RNA polymerase sigma factor RpoS rpoS Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3115099 lpl0571 20130528 297245 protein-coding NCBI-supplied PMID: 15467720 MUTATION: lvgA mutant is attenuated in guinea pigs [PMID:12704109]. 1465 hypothetical protein lvgA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3115566 lpl1603 20140222 297245 protein-coding NCBI-supplied PMID: 15467720 MUTATION: cpxR mutant is attenuated in mouse macrophages [PMID:16997951]. 1466 transcriptional regulatory protein CpxR cpxR Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3115599 lpl2584 20140329 297245 protein-coding NCBI-supplied PMID: 15467720 MUTATION: feoB mutant is attenuated in human macrophages [PMID:12228295]. 1467 ferrous iron transport protein B feoB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3116520 lpp1568 20130528 297246 protein-coding NCBI-supplied PMID: 15467720; 19400772 MUTATION: plaB mutant is attenuated in guinea pigs [PMID:20153694]. 1468 phospholipase plaB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3116645 lpp0813 20140222 297246 protein-coding NCBI-supplied PMID: 15467720; 19400772 MUTATION: iraA mutant is attenuated in guinea pigs [PMID:10678909]. 1469 small-molecule methyltransferase IraA iraA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3116728 lpp0590 20121017 297246 protein-coding NCBI-supplied PMID: 15467720; 16803597; 19400772 MUTATION: lvgA mutant is attenuated in guinea pigs [PMID:12704109]. 1470 hypothetical protein lvgA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3117391 lpp1247 20140329 297246 protein-coding NCBI-supplied PMID: 15467720; 19400772 MUTATION: rpoS mutant has defective intracellular replication in its protozoan host [PMID:19218380]. 1471 RNA polymerase sigma factor RpoS rpoS Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3117483 lpp0699 20140329 297246 protein-coding NCBI-supplied PMID: 15467720; 19400772 MUTATION: rtxA mutant is attenuated in mice and doesn't grow as well in monocytes as the wild type [PMID:11119544]. 1472 structural toxin protein RtxA rtxA-1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3117748 lpp0443 20121017 297246 protein-coding NCBI-supplied PMID: 15467720; 19400772 MUTATION: sdhA mutant is attenuated in mouse macrophages [PMID:17124169]. 1473 SdhA, substrate of the Dot/Icm system sdhA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3117985 lpp2740 20140329 297246 protein-coding NCBI-supplied PMID: 15467720; 19400772 MUTATION: dotA mutant is unable to replicate in mouse macrophages [PMID:16997951]. 1474 defect in organelle trafficking protein DotA dotA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3117986 lpp2730 20140329 297246 protein-coding NCBI-supplied PMID: 15467720; 19400772 MUTATION: dotB mutant is attenuated in guinea pigs [PMID:10393970]. 1475 defect in organelle trafficking protein DotB (ATPase) dotB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3118177 lpp2743 20140329 297246 protein-coding NCBI-supplied PMID: 15467720; 19400772 MUTATION: icmX mutant is attenuated in guinea pigs [PMID:10393970]. 1476 intracellular multiplication protein IcmX icmX Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3118718 lpp1393 20140329 297246 protein-coding NCBI-supplied PMID: 15467720; 19400772 MUTATION: cpxR mutant is attenuated in mouse macrophages [PMID:16997951]. 1477 transcriptional regulatory protein CpxR cpxR Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3118937 lpp2930 20140406 297246 protein-coding NCBI-supplied PMID: 15467720; 19400772 MUTATION: ptsP mutant is attenuated in guinea pigs [PMID:11447151]. 1478 phosphoenolpyruvate-protein phosphotransferase PtsP ptsP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3119216 lpp0438 20140405 297246 protein-coding NCBI-supplied PMID: 15467720; 19400772 MUTATION: fur mutant is attenuated in growth within U937 cell monolayers[PMID:8975903]. 1479 ferric uptake regulation protein fur Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3119248 lpp0855 20140406 297246 protein-coding NCBI-supplied PMID: 15467720; 19400772 MUTATION: mip mutants are approximately 50- to 100-fold less infective for A. castellanii and for human mononuclear phagocytes in vitro compared with their isogenic Mip-positive parental strains [PMID:7591108]. 1480 macrophage infectivity potentiator mip Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3119310 lpp2711 20140329 297246 protein-coding NCBI-supplied PMID: 15467720; 19400772 MUTATION: feoB mutant is attenuated in human macrophages [PMID:12228295]. 1481 ferrous iron transport protein B feoB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3119334 lpp1294 20140405 297246 protein-coding NCBI-supplied PMID: 15467720; 19400772 MUTATION: flaA mutant is less invasive of HL-60 cells than the wild type [PMID:11254565]. 1482 flagellin flaA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3119498 lpp2289 20140329 297246 protein-coding NCBI-supplied PMID: 15467720; 19400772 MUTATION: djlA mutant is attenuated in mouse macrophages [PMID:16997951]. 1483 Dna-J like membrane chaperone protein djlA MUTATION: sigE mutant is less invasive than the wild type in both HEp-2 and CHO cell lines [PMID:9537377]. 2567 MUTATION: spiC mutant cannot survive within macrophages and is attenuated in mice [PMID:10406797]. 2568 MUTATION: invJ mutants are defective for entry into cultured epithelial cells [PMID:7752894]. 2569 MUTATION: invI mutants are defective for entry into cultured epithelial cells [PMID:7752894]. 2570 MUTATION: sopE2 mutant has reduced ability to invade HeLa cells compared to wild-type [PMID:10735884]. 2571 MUTATION: sigD mutant is less invasive than the wild type in both HEp-2 and CHO cell lines [PMID:9537377]. 2572 MUTATION: slyA mutant is attenuated in mice [PMID:8290552]. 2573 MUTATION: sodC mutant is attenuated in mice [PMID:19577637]. 2574 MUTATION: sopE mutant is attenuated in mice [PMID:19577637]. 2575 MUTATION: ssaV and aroC double mutants are attenuated in humans [PMID:19745519]. 2576 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3190705 FTT_0054 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: FTT0054 mutant is attenuated in mouse spleen [PMID:17389372]. 545 ATPase FTT_0054 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3190713 FTT_0068 20140406 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: sodB mutant is attenuated in mice [PMID:16923916]. 546 superoxide dismutase sodB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3190728 FTT_0684c 20140405 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a sthA mutant was attenuated for infection in a mouse lung [PMID:17420240] 547 soluble pyridine nucleotide transhydrogenase sthA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3190738 FTT_0504c 20140405 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a sucC mutant was attenuated for infection in a mouse lung [PMID:17420240] 548 succinyl-CoA synthetase subunit beta sucC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3190739 FTT_0077 20140405 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: sucB mutant is attenuated in mouse spleen [PMID:17389372]. 549 dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex sucB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3190740 FTT_0503c 20140405 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a sucD mutant was attenuated for infection in a mouse lung [PMID:17420240] 550 succinyl-CoA synthetase subunit alpha sucD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3190742 FTT_0469 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: ksgA mutant is attenuated in mouse spleen [PMID:17389372]. 551 dimethyladenosine transferase ksgA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3190745 FTT_0468 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: surA mutant is attenuated in mouse spleen [PMID:17389372]. 552 peptidyl-prolyl cis-trans isomerase surA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3190746 FTT_0105c 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a FTT0105c mutant was attenuated for infection of a mouse lung [PMID:17420240] 553 AcrB/AcrD/AcrF family transporter FTT_0105c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3190751 FTT_0444 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a tet mutant was attenuated for infection in a mouse lung [PMID:17420240] 554 multidrug transporter tet Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3190770 FTT_0413c 20140405 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a glgB mutant was attenuated for infection in a mouse lung [PMID:17420240] 555 glycogen branching protein glgB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3190771 FTT_0134 20130905 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION; FTT0134 mutant is attenuated in mouse spleen [PMID:17389372]. 556 hypothetical protein FTT_0134 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3190785 FTT_0623 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a tig mutant was attenuated for infection in a mouse lung [PMID:17420240] 557 trigger factor tig Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3190796 FTT_1441 20140325 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a FTT1441 mutant was attenuated for infection in a mouse lung [PMID:17420240] 558 hypothetical protein FTT_1441 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3190802 FTT_0626 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a lon mutant was attenuated for infection in a mouse lung [PMID:17420240] 559 DNA-binding, ATP-dependent protease La lon Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3190834 FTT_0904 20130905 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: lpnB mutant is attenuated in mouse spleen [PMID:17389372]. 560 lipoprotein lpnB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3190835 FTT_1489 20130905 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: FTT1489 mutant is attenuated in mouse spleen [PMID:17389372]. 561 hypothetical protein FTT_1489 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3190879 FTT_1400c 20120712 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a FTT1400c mutant was attenuated for infection in a mouse lung [PMID:17420240] 562 hypothetical protein FTT_1400c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3190902 FTT_0975 20130905 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a FTT0975 mutant was attenuated for infection in a mouse lung [PMID:17420240] 563 hypothetical protein FTT_0975 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3190914 FTT_0920 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a isftu1 mutant was attenuated for infection in a mouse lung [PMID:17420240] 564 transposase isftu1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3190931 FTT_1125 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a metlQ mutant was attenuated for infection in a mouse lung [PMID:17420240] 565 D-methionine ABC transporter permease/substrate-binding protein metIQ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3190942 FTT_1748 20140405 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a glpe mutant was attenuated for infection in a mouse lung [PMID:17420240] 566 thiosulfate sulfurtransferase glpe Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3190950 FTT_0963c 20140405 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a aroG mutant was attenuated for infection in a mouse lung [PMID:17420240] 567 phospho-2-dehydro-3-deoxyheptonate aldolase aroG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3190956 FTT_0884c 20140405 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a aspC1 mutant was attenuated for infection in a mouse lung [PMID:17420240] 568 aspartate aminotransferase aspC1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3190961 FTT_1327 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: cdd mutant is attenuated in mouse spleen [PMID:17389372]. 569 cytidine deaminase cdd Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3190963 FTT_0934c 20140405 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a bioD mutant was attenuated for infection in a mouse lung [PMID:17420240] 570 dethiobiotin synthetase bioD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3190965 FTT_0935c 20140329 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a bioC mutant was attenuated for infection in a mouse lung [PMID:17420240] 571 biotin synthesis protein BioC bioC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3190966 FTT_1179 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a bipA mutant was attenuated for infection in a mouse lung [PMID:17420240] 572 GTP binding translational elongation factor Tu and G family protein bipA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3190967 FTT_0415 20130905 177416 pseudo NCBI-supplied MUTATION: a glgC mutant was attenuated for infection in a mouse lung [PMID:17420240] 573 pseudo glgC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3190968 FTT_0937c 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: bioB mutant is attenuated in mouse spleen [PMID:17389372]. 574 biotin synthase bioB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3190971 FTT_0805 20140322 177416 protein-coding NCBI-supplied PMID: 15640799; 20651039 MUTATION: a capB mutant was attenuated for infection in a mouse lung [PMID:17420240] 575 capsule biosynthesis protein CapB capB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3190975 FTT_0936c 20140405 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a bioF mutant was attenuated for infection in a mouse lung [PMID:17420240] 576 8-amino-7-oxononanoate synthase bioF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3190985 FTT_0946 20140405 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: trpG mutant is attenuated in mouse spleen [PMID:17389372]. 577 anthranilate synthase subunit II trpG1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191024 FTT_0708 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a FTT0708 mutant was attenuated for infection in a mouse lung [PMID:17420240] 578 major facilitator transporter FTT_0708 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191036 FTT_0685c 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: FTT0685c mutant is attenuated in mouse spleen [PMID:17389372]. 579 potassium channel protein FTT_0685c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191053 FTT_0667 20130905 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: FTT0667 mutant is attenuated in mouse spleen [PMID:17389372]. 580 hypothetical protein FTT_0667 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191066 FTT_0645c 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: FTT0645c mutant is attenuated in mouse spleen [PMID:17389372]. 581 hypothetical protein FTT_0645c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191074 FTT_1663 20140405 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: carA mutant is attenuated in mouse spleen [PMID:17389372]. 582 carbamoyl phosphate synthase small subunit carA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191087 FTT_1633c 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: FTT1633c mutant is attenuated in mouse spleen [PMID:17389372]. 583 amino acid transporter FTT_1633c MUTATION: FTT1640c mutant is attenuated in mouse spleen [PMID:17389372]. 584 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191109 FTT_1314c 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a FTT1314c mutant was attenuated for infection in a mouse lung [PMID:17420240] 585 Type IV pili fiber building block protein FTT_1314c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191122 FTT_1611 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a FTT1611 mutant was attenuated for infection in a mouse lung [PMID:17420240] 586 hypothetical protein FTT_1611 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191128 FTT_1334c 20120712 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: FTT1334c mutant is attenuated in mouse spleen [PMID:17389372]. 587 hypothetical protein FTT_1334c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191148 FTT_0615c 20140322 177416 protein-coding NCBI-supplied PMID: 15640799; 21670171 MUTATION: FTT0615c mutant is attenuated in mice [PMID:17389372]. 588 metal ion transporter protein FTT_0615c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191174 FTT_0589 20130905 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: FTT0589 mutant is attenuated in mouse spleen [PMID:17389372]. 589 hypothetical protein FTT_0589 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191177 FTT_0584 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: FTT0584 mutant is severely attenuated in mice [PMID:17389372]. 590 hypothetical protein FTT_0584 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191217 FTT_1359c 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: an iglA mutant was attenuated for infection in a mouse lung [PMID:17420240] 591 intracellular growth locus subunit A iglA1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191238 FTT_0118 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: prfC mutant is attenuated in mouse spleen [PMID:17389372]. 592 peptide chain release factor 3 prfC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191243 FTT_1117c 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a FTT1117c mutant was attenuated for infection in a mouse lung [PMID:17420240] 593 isochorismatase hydrolase family protein FTT_1117c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191248 FTT_0397 20140329 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: mtn mutant is attenuated in mouse spleen [PMID:17389372]. 594 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase mtn Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191250 FTT_1103 20140322 177416 protein-coding NCBI-supplied PMID: 15640799; 18981253 MUTATION: a FTT1103 mutant was attenuated for infection in a mouse lung [PMID:17420240] 595 lipoprotein FTT_1103 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191253 FTT_1102 20130905 177416 pseudo NCBI-supplied MUTATION: a FTT1102 mutant was attenuated for infection in a mouse lung [PMID:17420240] 596 pseudo FTT_1102 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191264 FTT_0390c 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a rpsU mutant was attenuated for infection in a mouse lung [PMID:17420240] 597 30S ribosomal protein S21 rpsU Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191271 FTT_0406 20140405 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: cadA mutant is attenuated in mouse spleen [PMID:17389372]. 598 lysine decarboxylase, inducable cadA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191278 FTT_0463 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a yibK mutant was attenuated for infection in a mouse lung [PMID:17420240] 599 tRNA/rRNA methyltransferase yibK Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191290 FTT_1563 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: pcs mutant is attenuated in mouse spleen [PMID:17389372]. 600 phosphatidylcholine synthase pcs Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191291 FTT_1013c 20130905 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: ruvB mutant is attenuated in mouse spleen [PMID:17389372]. 601 Holliday junction DNA helicase RuvB ruvB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191293 FTT_0295 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: FTT0295 mutant is attenuated in mouse spleen [PMID:17389372]. 602 hypothetical protein FTT_0295 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191294 FTT_1344 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: pdpA mutant is attenuated in mouse spleen [PMID:17389372]. 603 hypothetical protein pdpA1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191301 FTT_1345 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: pdpB mutant is attenuated in mouse spleen [PMID:17389372]. 604 hypothetical protein pdpB1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191321 FTT_0288c 20140329 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: pdxY mutant is attenuated in mouse spleen [PMID:17389372]. 605 pyridoxal kinase pdxY Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191322 FTT_0256c 20130330 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: FTT0256c mutant is attenuated in mice [PMID:17389372]. 606 lipopolysaccharide protein FTT_0256c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191350 FTT_0209c 20130330 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a FTT0209c mutant was attenuated for infection in a mouse lung [PMID:17420240] 607 periplasmic solute binding family protein FTT_0209c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191363 FTT_0414 20140405 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: pgm mutant is attenuated in mouse spleen [PMID:17389372]. 608 phosphoglucomutase pgm Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191380 FTT_0509c 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: FTT0509c mutant is attenuated in mouse spleen [PMID:17389372]. 609 hypothetical protein FTT_0509c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191400 FTT_0072 20140405 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: sdhC mutant is attenuated in mouse spleen [PMID:17389372]. 610 succinate dehydrogenase cytochrome b556 sdhC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191408 FTT_0455c 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: FTT0455c mutant is attenuated in mouse spleen [PMID:17389372]. 611 dolichyl-phosphate-mannose-protein mannosyltransferase family protein FTT_0455c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191409 FTT_0908 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a parB mutant was attenuated for infection in a mouse lung [PMID:17420240] 612 chromosome partition protein B parB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191411 FTT_0453c 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: FTT0453c mutant is attenuated in mouse spleen [PMID:17389372]. 613 hypothetical protein FTT_0453c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191417 FTT_0443 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a FTT0443 mutant was attenuated for infection in a mouse lung [PMID:17420240] 614 hypothetical protein FTT_0443 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191430 FTT_0398c 20120712 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: FTT0398c mutant is mildly attenuated in mice [PMID:17389372]. 615 hypothetical protein FTT_0398c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191433 FTT_0399c 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: FTT0399c mutant is attenuated in mouse spleen [PMID:17389372]. 616 BNR/Asp-box repeat-containing protein FTT_0399c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191452 FTT_0296 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: pcp mutant is attenuated in mouse spleen [PMID:17389372]. 617 pyrrolidone-carboxylate peptidase pcp Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191474 FTT_1258 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: FTT1258 mutant is attenuated in mouse spleen [PMID:17389372]. 618 outer membrane efflux protein FTT_1258 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191490 FTT_0356 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: htpG mutant is strongly attenuated in mice [PMID:17389372]. 619 heat shock protein 90 htpG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191508 FTT_1471c 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a deaD mutant was attenuated for infection in a mosue lung [PMID:17420240] 620 cold-shock DEAD-box protein A deaD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191510 FTT_1223 20130905 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: dedA1 mutant is attenuated in mouse spleen [PMID:17389372]. 621 DedA family protein dedA1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191513 FTT_0113 20140405 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: deoB mutant is attenuated in mouse spleen [PMID:17389372]. 622 phosphopentomutase deoB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191517 FTT_0766 20140405 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a deoD mutant was attenuated for infection in a mouse lung [PMID:17420240] 623 purine nucleoside phosphorylase deoD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191534 FTT_1600c 20140405 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a fumA mutant was attenuated for infection in a mouse lung [PMID:17420240] 624 fumerate hydratase fumA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191540 FTT_0108c 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: cca mutant is attenuated in mouse spleen [PMID:17389372]. 625 tRNA CCA-pyrophosphorylase cca Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191543 FTT_0107c 20140322 177416 protein-coding NCBI-supplied PMID: 15640799; 18458069 MUTATION: dsbB mutant is attenuated in mouse spleen [PMID:17389372]. 626 disulfide bond formation protein dsbB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191553 FTT_0408 20140405 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: gcvH mutant is attenuated in mouse spleen [PMID:17389372]. 627 glycine cleavage system H protein gcvH1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191558 FTT_0654 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a elbB mutant was attenuated for infection in a mouse lung [PMID:17420240] 628 isoprenoid biosynthesis protein with amidotransferase-like domain elbB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191564 FTT_1358c 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: an iglB mutant was attenuated for infection in a mouse lung [PMID:17420240] 629 intracellular growth locus subunit B iglB1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191568 FTT_1503 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: xerC mutant is attenuated in mouse spleen [PMID:17389372]. 630 integrase/recombinase XerC xerC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191584 FTT_0791 20140405 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: galE mutant is attenuated in mouse spleen [PMID:17389372]. 631 UDP-glucose 4-epimerase galE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191591 FTT_1357c 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: an iglC mutant was attenuated for infection in a mouse lung [PMID:17420240] 632 intracellular growth locus subunit C iglC1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191616 FTT_0055 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: rluC mutant is attenuated in mouse spleen [PMID:17389372]. 633 ribosomal large subunit pseudouridine synthase C rluC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191617 FTT_1056c 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a rluB mutant was attenuated for infection in a mouse lung [PMID:17420240] 634 ribosomal large subunit pseudouridine synthase B rluB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191625 FTT_1672 20140329 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: ribB mutant is attenuated in mouse spleen [PMID:17389372]. 635 riboflavin synthase subunit alpha ribB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191626 FTT_1673 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: ribA mutant is attenuated in mouse spleen [PMID:17389372]. 636 riboflavin biosynthesis protein ribA/GTP-cyclohydrolase II ribA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191632 FTT_1508c 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: relA mutant is attenuated in mouse spleen [PMID:17389372]. 637 GTP pyrophosphokinase relA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191642 FTT_1394c 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: recB mutant is attenuated in mouse spleen [PMID:17389372]. 638 exodeoxyribonuclease V subunit beta recB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191643 FTT_1750 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a recA mutant was attenuated for infection in a mouse lung [PMID:17420240] 639 recombinase A recA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191646 FTT_0051 20130905 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: rbfA mutant is attenuated in mouse spleen [PMID:17389372]. 640 ribosome-binding factor A rbfA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191649 FTT_0094c 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: qseC mutant is attenuated in mouse spleen [PMID:17389372]. 641 sensor histidine kinase qseC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191650 FTT_0315 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: pyrH mutant is attenuated in mouse spleen [PMID:17389372]. 642 uridylate kinase pyrH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191652 FTT_1648c 20140405 177416 protein-coding NCBI-supplied PMID: 15640799; 20385757 MUTATION: pyrF mutant is attenuated in mouse spleen [PMID:17389372]. 643 orotidine 5'-phosphate decarboxylase pyrF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191654 FTT_1647c 20140329 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: pyrD mutant is attenuated in mouse spleen [PMID:17389372]. 644 diyroorotate dehydrogenase pyrD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191656 FTT_1665 20140405 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: pyrB mutant is attenuated in mouse spleen [PMID:17389372]. 645 aspartate carbamoyltransferase pyrB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191660 FTT_1150c 20140405 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: putA mutant is attenuated in mouse spleen [PMID:17389372]. 646 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase putA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191663 FTT_0895 20140405 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: purN mutant is attenuated in mouse spleen [PMID:17389372]. 647 phosphoribosylglycinamide formyltransferase purN Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191664 FTT_0893 20140405 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: purM mutant is attenuated in mouse spleen [PMID:17389372]. 648 phosphoribosylaminoimidazole synthetase purM Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191665 FTT_1720c 20140405 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: purL mutant is attenuated in mouse spleen [PMID:17389372]. 649 phosphoribosylformylglycinamidine synthase purL Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191667 FTT_0203c 20140405 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: purH mutant is attenuated in mouse spleen [PMID:17389372]. 650 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase purH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191669 FTT_1721c 20140405 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: purF mutant is attenuated in mouse spleen [PMID:17389372]. 651 amidophosphoribosyltransferase purF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191675 FTT_0896 20140405 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: purE mutant is attenuated in mouse spleen [PMID:17389372]. 652 phosphoribosylaminoimidazole carboxylase catalyic subunit purE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191681 FTT_1151c 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: FTT1151c mutant is attenuated in mouse spleen [PMID:17389372]. 653 hypothetical protein FTT_1151c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191684 FTT_0918 20140322 177416 protein-coding NCBI-supplied PMID: 15640799; 19651867 MUTATION: a FTT0918 mutant was attenuated for infection in a mouse lung [PMID:17420240] 654 hypothetical protein FTT_0918 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191688 FTT_0910 20140329 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a FTT0910 mutant was attenuated for infection in a mouse lung [PMID:17420240] 655 hypothetical protein FTT_0910 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191692 FTT_0905 20140322 177416 protein-coding NCBI-supplied PMID: 15640799; 21804002 MUTATION: FTT0905 mutant is attenuated in mouse spleen [PMID:17389372]. 656 Type IV pili glycosylation protein FTT_0905 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191693 FTT_0903 20130905 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: FTT0903 mutant is attenuated in mouse spleen [PMID:17389372]. 657 hypothetical protein FTT_0903 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191695 FTT_0138 20140405 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a secE mutant was attenuated for infection in a mouse lung [PMID:17420240] 658 preprotein translocase subunit SecE secE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191699 FTT_0891 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: FTT0891 mutant is attenuated in mouse spleen [PMID:17389372]. 659 hypothetical protein FTT_0891 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191712 FTT_0881c 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a FTT0881c mutant was attenuated for infection in a mouse lung [PMID:17420240] 660 amino acid permease FTT_0881c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191730 FTT_1129c 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: FTT1129c mutant is attenuated in mouse spleen [PMID:17389372]. 661 hypothetical protein FTT_1129c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191744 FTT_0843 20130905 177416 pseudo NCBI-supplied MUTATION: a FTT0843 mutant was attenuated for infection in a mouse lung [PMID:17420240] 662 pseudo FTT_0843 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191766 FTT_1747 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a FTT1747 mutant was attenuated for infection in a mouse lung [PMID:17420240] 663 hypothetical protein FTT_1747 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191768 FTT_0078 20140405 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: apt mutant is attenuated in mouse spleen [PMID:17389372]. 664 adenine phosphoribosyltransferase apt Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191788 FTT_0617c 20130508 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: phoH mutant is attenuated in mouse spleen [PMID:17389372]. 665 phoH-like protein phoH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191792 FTT_0901 20130905 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a FTT0901 mutant was attenuated for infection in a mouse lung [PMID:17420240] 666 lipoprotein lpnA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191793 FTT_1568c 20140405 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a lpxB mutant was attenuated for infection in a mouse lung [PMID:17420240] 667 lipid-A-disaccharide synthase lpxB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191810 FTT_0800 20130905 177416 protein-coding NCBI-supplied PMID: 15640799; 21803994 MUTATION: FTT0800 mutant is attenuated in mouse spleen [PMID:17389372]. 668 haloacid dehalogenase FTT_0800 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191811 FTT_0799 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: FTT0799 mutant is attenuated in mouse spleen [PMID:17389372]. 669 glycosyl transferases group 1 family protein FTT_0799 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191812 FTT_0798 20140322 177416 protein-coding NCBI-supplied PMID: 15640799; 21803994 MUTATION: FTT0798 mutant is attenuated in mice [PMID:17389372]. 670 glycosyl transferase family protein FTT_0798 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191818 FTT_0793 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: FTT0793 mutant is attenuated in mouse spleen [PMID:17389372]. 671 ABC transporter ATP-binding protein/permease FTT_0793 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191819 FTT_0790 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: FTT0790 mutant is attenuated in mouse spleen [PMID:17389372]. 672 sugar transferase FTT_0790 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191827 FTT_0797 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: FTT0797 mutant is attenuated in mouse spleen [PMID:17389372]. 673 glycosyl transferase family protein FTT_0797 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191829 FTT_0807 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a FTT0807 mutant was attenuated for infection in a mouse lung [PMID:17420240] 674 hypothetical protein FTT_0807 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191841 FTT_0759 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a FTT0759 mutant was attenuated for infection in a mouse lung [PMID:17420240] 675 hypothetical protein FTT_0759 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191845 FTT_0792 20130905 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: FTT0792 mutant is attenuated in mouse spleen [PMID:17389372]. 676 glycosyl transferase family protein FTT_0792 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191851 FTT_0748 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: FTT0748 mutant is strongly attenuated in mice [PMID:17389372]. 677 hypothetical protein FTT_0748 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191870 FTT_1254 20140405 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: fadD1 mutant is attenuated in mouse spleen [PMID:17389372]. 678 acyl-CoA synthetase fadD1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191871 FTT_1530 20140405 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATIONO: a fadB/acbP mutant was attenuated for infection in a mouse lung [PMID:17420240] 679 bifunctional 3-hydroxacyl-CoA dehydrogenase/acyl-CoA-binding protein fadB/acbP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191885 FTT_0249 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a feoB mutant was attenuated for infection in a mouse lung [PMID:17420240] 680 ferrous iron transport protein feoB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191887 FTT_0802 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a cphB mutant was attenuated for infection in a mouse lung [PMID:17420240] 681 cyanophycinase cphB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191888 FTT_1130c 20140324 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: cphA mutant is attenuated in mouse spleen [PMID:17389372]. 682 cyanophycin synthetase cphA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191913 FTT_1312c 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a uvrA mutant was attenuated for infection in a mouse lung [PMID:17420240] 683 DNA excision repair protein subunit A uvrA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191917 FTT_0282 20140329 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: cyoB mutant is attenuated in mouse spleen [PMID:17389372]. 684 cytochrome O ubiquinol oxidase subunit I cyoB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191921 FTT_0283 20140405 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a cyoC mutant was attenuated for infection in a mouse lung [PMID:17420240] 685 cytochrome O ubiquinol oxidase subunit III cyoC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191924 FTT_0284 20140405 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: cyoD mutant is attenuated in mice [PMID:17389372]. 686 cytochrome O ubiquinol oxidase subunit IV cyoD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191934 FTT_0892 20140329 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: folD mutant is attenuated in mouse spleen [PMID:17389372]. 687 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/5,10-methylene-tetrahydrofolate cyclohydrolase folD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191939 FTT_1464c 20140301 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a wbtA mutant was attenuated for infection in a mouse lung [PMID:17420240] 688 dTDP-glucose 4,6-dehydratase wbtA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191965 FTT_1416c 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a FTT1416c mutant was attenuated for infection in a mouse lung [PMID:17420240] 689 lipoprotein FTT_1416c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191976 FTT_0183c 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a rpsA mutant was attenuated for infection in a mouse lung [PMID:17420240] 690 30S ribosomal protein S1 rpsA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191983 FTT_1442c 20140405 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a rpoA2 mutant was attenuated for infection in a mouse lung [PMID:17420240] 691 DNA-directed RNA polymerase subunit alpha rpoA2 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191985 FTT_0346 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a rpmJ mutant was attenuated for infection in a mouse lung [PMID:17420240] 692 50S ribosomal protein L36 rpmJ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191996 FTT_0773 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a rpmA mutant was attenuated for infection in a mouse lung [PMID:17420240] 693 50S ribosomal protein L27 rpmA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191997 FTT_0675 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a rplY mutant was attenuated for infection in a mouse lung [PMID:17420240] 694 50S ribosomal protein L25 rplY Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3191999 FTT_0327 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: rplW mutant is attenuated in mouse spleen [PMID:17389372]. 695 50S ribosomal protein L23 rplW Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192002 FTT_0820 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a rplT mutant was attenuated for infection in a mouse lung [PMID:17420240] 696 50S ribosomal protein L20 rplT Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192005 FTT_0583 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a fopA mutant was attenuated for infection in a mouse lung [PMID:17420240] 697 outer membrane associated protein fopA1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192007 FTT_0351 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: rplQ mutant is attenuated in mouse spleen [PMID:17389372]. 698 50S ribosomal protein L17 rplQ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192020 FTT_0326 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: rplD mutant is attenuated in mouse spleen [PMID:17389372]. 699 50S ribosomal protein L4 rplD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192037 FTT_1048c 20120712 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: FTT1048c mutant is mildly attenuated in mice [PMID:17389372]. 700 hypothetical protein FTT_1048c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192038 FTT_1047c 20120712 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: FTT1047c mutant is attenuated in mouse spleen [PMID:17389372]. 701 hypothetical protein FTT_1047c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192056 FTT_1015 20140324 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a FTT1015 mutant was attenuated for infection in a mouse lung [PMID:17420240] 702 hypothetical protein FTT_1015 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192077 FTT_0769 20140405 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a secA mutant was attenuated for infection in a mouse lung [PMID:17420240] 703 preprotein translocase subunit SecA secA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192078 FTT_1461c 20140301 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: wbtD mutant is attenuated in mouse spleen [PMID:17389372]. 704 galacturonosyl transferase wbtD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192079 FTT_1459c 20140405 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a wbtF mutant was attenuated for infection in a mouse lung [PMID:17420240] 705 NAD dependent epimerase wbtF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192084 FTT_1457c 20140301 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: wbtG mutant is attenuated in mouse spleen [PMID:17389372]. 706 glycosyl transferase family protein wbtG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192087 FTT_1456c 20140405 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: wbtH mutant is attenuated in mouse spleen [PMID:17389372]. 707 asparagine synthase wbtH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192098 FTT_0721c 20140406 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a katG mutant was attenuated for infection in a mouse lung [PMID:17420240] 708 peroxidase/catalase katG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192117 FTT_0480c 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: xasA mutant is attenuated in mouse spleen [PMID:17389372]. 709 glutamate:gamma-aminobutyric acid antiporter family protein xasA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192118 FTT_0154 20130905 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: xerD mutant is attenuated in mouse spleen [PMID:17389372]. 710 integrase/recombinase xerD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192141 FTT_0028c 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: FTT0028c mutant is attenuated in mice [PMID:17389372]. 711 hypothetical protein FTT_0028c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192145 FTT_0029c 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a FTT0029c mutant was attenuated for infection in a mouse lung [PMID:17420240] 712 hypothetical protein FTT_0029c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192151 FTT_0057 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: FTT0057 mutant is attenuated in mouse spleen [PMID:17389372]. 713 hypothetical protein FTT_0057 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192152 FTT_0053 20130905 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: FTT0053 mutant is attenuated in mouse spleen [PMID:17389372]. 714 major facilitator transporter FTT_0053 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192153 FTT_0056c 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: FTT0056c mutant is attenuated in mouse spleen [PMID:17389372]. 715 major facilitator transporter FTT_0056c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192162 FTT_1726 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a yegQ mutant was attenuated for infection in a mouse lung [PMID:17420240] 716 protease yegQ yegQ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192163 FTT_0101 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a FTT0101 mutant was attenuated for infection in a mouse lung [PMID:17420240] 717 hypothetical protein FTT_0101 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192164 FTT_0454 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: yfdH mutant is attenuated in mouse spleen [PMID:17389372]. 718 glycosyl transferase family protein yfdH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192179 FTT_1152 20130905 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a FTT1152 mutant was attenuated for infection in a mouse lung [PMID:17420240] 719 hypothetical protein FTT_1152 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192184 FTT_1472c 20140222 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a ppiC mutant was attenuated for infection in a mouse lung [PMID:17420240] 720 peptidyl-prolyl cis-trans isomerase ppiC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192199 FTT_0405 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: lolD mutant is attenuated in mouse spleen [PMID:17389372]. 721 lipoprotein releasing system ABC transporter ATP-binding protein lolD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192211 FTT_1238c 20120712 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: FTT1238c mutant is attenuated in mouse spleen [PMID:17389372]. 722 hypothetical protein FTT_1238c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192217 FTT_1239 20130905 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: FTT1239 mutant is attenuated in mouse spleen [PMID:17389372]. 723 hypothetical protein FTT_1239 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192220 FTT_1236 20130905 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: FTT1236 mutant is attenuated in mouse spleen [PMID:17389372]. 724 hypothetical protein FTT_1236 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192224 FTT_1237 20140324 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: FTT1237 mutant is attenuated in mouse spleen [PMID:17389372]. 725 glycosyl transferase family protein FTT_1237 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192229 FTT_1221 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a FTT1221 mutant was attenuated for infection in a mouse lung [PMID:17420240] 726 hypothetical protein FTT_1221 MUTATION: a FTTt19 mutant was attenuated for infection in a mouse lung [PMID:17420240] 727 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192273 FTT_1447c 20140405 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: manB mutant is attenuated in mouse spleen [PMID:17389372]. 728 phosphomannomutase manB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192274 FTT_r07 20100320 177416 rRNA NCBI-supplied MUTATION: a FTTr07 mutant was attenuated for infection in a mouse lung [PMID:17420240] 729 16S rRNA FTT_r07 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192305 FTT_0027c 20140405 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: lysA mutant is attenuated in mice [PMID:17389372]. 730 diaminopimelate decarboxylase lysA1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192308 FTT_1562 20140405 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: ispA mutant is attenuated in mouse spleen [PMID:17389372]. 731 geranyltranstransferase ispA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192333 FTT_0938 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: bioA mutant is attenuated in mouse spleen [PMID:17389372]. 732 adenosylmethionine-8-amino-7-oxononanoate aminotransferase bioA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192360 FTT_1257 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: emrA1 mutant is attenuated in mouse spleen [PMID:17389372]. 733 HlyD family secretion protein emrA1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192361 FTT_0624 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a clpP mutant was attenuated for infection in a mouse lung [PMID:17420240] 734 ATP-dependent Clp protease proteolytic subunit clpP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192366 FTT_0806 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a capC mutant was attenuated for infection in a mouse lung [PMID:17420240] 735 capsule biosynthesis protein CapC capC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192368 FTT_1676 20130905 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a FTT1676 mutant was attenuated for infection in a mouse lung [PMID:17420240] 736 hypothetical protein FTT_1676 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192377 FTT_0712c 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: sdaC1 mutant is attenuated in mouse spleen [PMID:17389372]. 737 serine transporter sdaC1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192393 FTT_1782c 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a yjjK mutant was attenuated for infection in a mouse lung [PMID:17420240] 738 ABC transporter ATP-binding protein yjjK Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192426 FTT_0633 20130905 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a hflK mutant was attenuated for infection in a mouse lung [PMID:17420240] 739 hypothetical protein hflK Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192427 FTT_0631 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a hflX mutant was attenuated for infection in a mouse lung [PMID:17420240] 740 protease GTP-binding subunit hflX Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192430 FTT_0052 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: hisS mutant is attenuated in mouse spleen [PMID:17389372]. 741 histidyl-tRNA synthetase hisS Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192433 FTT_0968c 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a FTT0968c mutant was attenuated for infection in a mouse lung [PMID:17420240] 742 amino acid antiporter FTT_0968c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192434 FTT_1606 20140324 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a minD mutant was attenuated for infection in a mouse lung [PMID:17420240] 743 septum site-determining protein MinD minD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192454 FTT_0945 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: FTT0945 mutant is attenuated in mouse spleen [PMID:17389372]. 744 chorismate binding family protein FTT_0945 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192455 FTT_0944 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: FTT0944 mutant is attenuated in mouse spleen [PMID:17389372]. 745 AMP-binding protein FTT_0944 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192456 FTT_0941c 20140329 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a FTT0941c mutant was attenuated for infection in a mouse lung[PMID:17420240] 746 lipase/esterase FTT_0941c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192457 FTT_0940c 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: FTT0940c mutant is attenuated in mouse spleen [PMID:17389372]. 747 hypothetical protein FTT_0940c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192464 FTT_0928c 20140329 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: FTT0928c mutant is attenuated in mouse spleen [PMID:17389372]. 748 beta-glucosidase FTT_0928c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192486 FTT_1605 20130905 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a minC mutant was attenuated for infection in a mouse lung [PMID:17420240] 749 septum site-determining protein MinC minC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192487 FTT_0162 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: ampD mutant is attenuated in mouse spleen [PMID:17389372]. 750 N-acetyl-anhydromuranmyl-L-alanine amidase ampD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192492 FTT_1490 20130905 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: FTT1490 mutant is attenuated in mouse spleen [PMID:17389372]. 751 Na+/H+ antiporter FTT_1490 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192502 FTT_0409 20140405 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: gcvP1 mutant is attenuated in mouse spleen [PMID:17389372]. 752 glycine dehydrogenase subunit 1 gcvP1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192507 FTT_0625 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a clpX mutant was attenuated for infection in a mouse lung [PMID:17420240] 753 ATP-dependent protease ATP-binding subunit ClpX clpX Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192509 FTT_1769c 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a clpB mutant was attenuated for infection in a mouse lung [PMID:17420240] 754 ClpB protein clpB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192518 FTT_0407 20140405 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: gcvT mutant is attenuated in mouse spleen [PMID:17389372]. 755 glycine cleavage system aminomethyltransferase T gcvT Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192524 FTT_0165c 20140322 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: FTT0165c mutant is attenuated in mouse spleen [PMID:17389372]. 756 lipoprotein FTT_0165c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192538 FTT_1165c 20140405 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a aspC2 mutant was attenuated for infection in a mouse lung [PMID:17420240] 757 aspartate aminotransferase aspC2 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3192549 FTT_1631c 20140405 177416 protein-coding NCBI-supplied PMID: 15640799 MUTATION: a glpX mutant was attenuated for infection in a mouse lung [PMID:17420240] 758 fructose 1,6-bisphosphatase II glpX Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3231503 CJE0992 20130613 195099 protein-coding NCBI-supplied GO_0008233 (EC: ISS, PMID: 15660156); GO_0009306 (EC: ISS, PMID: 15660156); GO_0009405 (EC: ISS, PMID: 15660156); GO_0030260 (EC: ISS, PMID: 15660156) PMID: 15660156 invasion antigen B ciaB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3231508 CJE0997 20140222 195099 protein-coding NCBI-supplied GO_0006865 (EC: ISS, PMID: 15660156); GO_0007155 (EC: ISS, PMID: 15660156); GO_0042626 (EC: ISS, PMID: 15660156) PMID: 15660156 MUTATION: PEP1 mutants had a significantly reduced in vivo colonization of broiler chicks [PMID:19349427] 847 amino acid ABC transporter permease PEB1 CJE0997 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3231509 CJE0998 20140217 195099 protein-coding NCBI-supplied GO_0006865 (EC: ISS, PMID: 15660156); GO_0007155 (EC: ISS, PMID: 15660156); GO_0042626 (EC: ISS, PMID: 15660156) PMID: 15660156 MUTATION: PEB1 mutants had a significantly reduced in vivo colonization of broiler chicks [PMID:19349427] 848 amino acid ABC transporter permease PEB1 CJE0998 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3231511 CJE1000 20140222 195099 protein-coding NCBI-supplied GO_0006865 (EC: ISS, PMID: 15660156); GO_0007155 (EC: ISS, PMID: 15660156); GO_0015424 (EC: ISS, PMID: 15660156); GO_0042626 (EC: ISS, PMID: 15660156) PMID: 15660156 MUTATION: PEB1 mutants had a significantly reduced in vivo colinization of broiler chickens [PMID:19349427] 849 amino acid ABC transporter ATP-binding protein PEB1 pebC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3231574 CJE1065 20130508 195099 protein-coding NCBI-supplied GO_0003674 (EC: ND); GO_0009986 (EC: ISS, PMID: 15660156); GO_0016337 (EC: ISS, PMID: 15660156) PMID: 15660156 MUTATION: adherence of deletion mutants of jlpA to HEp-2 epithelial cells was reduced compared with that of parental C. jejuni [PMID:11251839] 850 surface-exposed lipoprotein jlpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3231778 CJE1271 20130613 195099 protein-coding NCBI-supplied GO_0006487 (EC: ISS, PMID: 15660156); GO_0016757 (EC: ISS, PMID: 15660156) PMID: 15660156 MUTATION: reduce ability to adhere to human epithelial Caco-2 cells [PMID:15184581]. 851 general glycosylation pathway protein pglH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3239035 GaHV1_gp17 20140406 10386 protein-coding NCBI-supplied PMID: 16873243 MUTATION: A thymidine-kinase mutant is attenuated in chickens [PMID:12021870]. 4974 thymidine kinase UL23 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3239037 GaHV1_gp60 20110310 10386 protein-coding NCBI-supplied PMID: 16873243 MUTATION: A UL0 mutant mutant was attenuated in chickens [PMID:14645915]. 4973 protein UL0 UL0 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3239064 GaHV1_gp67 20140215 10386 protein-coding NCBI-supplied PMID: 16873243 MUTATION: a UL47 mutant is attenuated in chickens [PMID:17325345]. 4975 modulates transactivating tegument protein VP16; RNA-binding protein Other designations: tegument protein VP13/14 sORF1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3239078 GaHV1_gp05 20110310 10386 protein-coding NCBI-supplied PMID: 16873243 deoxyuridine triphosphatase UL50 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3244810 O2R_18 20140410 562 protein-coding NCBI-supplied PMID: 16251312 MUTATION: traT mutants have altered membrane permeability and are sensitive to hydrophobic antibiotics [PMID:3323837]. 2 plays a role in APEC complement resistance; similar to protein family HMM PF05818 Other designations: conjugal transfer surface exclusion protein TraT traT MUTATION: The divergent Pka2 catalytic subunit was found to regulate mating, haploid fruiting, and virulence factor production in serotype D strains [PMID:14871933]. 5346 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3253516 CNA03280 20120818 214684 1 protein-coding NCBI-supplied GO_0000124; GO_0004402; GO_0005671; GO_0016568; GO_0016573 PMID: 15653466 MUTATION: gcn5 mutant is avirulent in mice [PMID:20581290]. 4731 transcriptional activator gcn5 CNA03280 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3253764 CNA07740 20140406 214684 1 protein-coding NCBI-supplied GO_0003987; GO_0005829; GO_0006085 PMID: 15653466 MUTATION: acs1 mutant is attenuated in mice [PMID:18673460]. 4713 acetate--CoA ligase CNA07740 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3254663 CNK02540 20140406 214684 11 protein-coding NCBI-supplied GO_0000145; GO_0000910; GO_0006893; GO_0006897; GO_0006904; GO_0006906; GO_0007121 PMID: 15653466 MUTATION: sec6 RNAi mutant strains of C. neoformans were defective in a number of virulence factors and demonstrated attenuated virulence in mice [PMID:19210702]. 4742 vesicle fusion-related protein CNK02540 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3254698 CNK02740 20120817 214684 11 protein-coding NCBI-supplied GO_0004672; GO_0005624 PMID: 15653466 MUTATION: kin1 mutant is attenuated in mice [PMID:19151325]. 4734 protein kinase kin1 CNK02740 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3254820 CNL04550 20140406 214684 12 protein-coding NCBI-supplied GO_0000175; GO_0000289; GO_0005737; GO_0006357; GO_0030015 PMID: 15653466; 17430900 MUTATION: ccr4 mutant is attenuated in mice [PMID:17646356]. 4723 ccr4-not transcription complex, subunit 7 CNL04550 MUTATION: This gene (USX1) encodes the previously identified UDP-xylose synthase. We demonstrated that it is necessary for both capsule xylosylation and C. neoformans virulence [PMID:12139628]. 5384 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3255024 CNL06630 20140406 214684 12 protein-coding NCBI-supplied GO_0003926; GO_0005798; GO_0005829; GO_0006888; GO_0006891 PMID: 15653466; 17430900 MUTATION: cps1 mutant is attenuated in C. elegans killing assay [PMID:17545316]. 4728 put. CPS1 protein CNL06630 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3256195 CNC01830 20120818 214684 3 protein-coding NCBI-supplied GO_0003930; GO_0005886; GO_0007189; GO_0007265; GO_0008283 PMID: 15653466; 17233829 MUTATION: ras1 mutant is avirulent in rabbit model of cryptococcal meningitis [PMID:10792722]. 4741 RAS1 CNC01830 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3256405 CNC01260 20130705 214684 3 protein-coding NCBI-supplied GO_0000921; GO_0004672; GO_0005935; GO_0006468; GO_0007117; GO_0007120 PMID: 15653466; 20719250; 21866697 MUTATION: snf1 mutant is attenuated in mice [PMID:18673460]. 4743 SNF1 family protein kinase CNC01260 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3257282 CND02400 20140406 214684 4 protein-coding NCBI-supplied PMID: 15653466 MUTATION: apt1 mutant is attenuated in mouse inhalation model of cryptococcosis [PMID:19949048]. 4716 hypothetical protein CND02400 MUTATION: Deletion of XRN1 impairs uni- and bisexual mating [PMID:25267175]. 5389 MUTATION: This gene, HEM15, is predicted to encode a ferrochelatase that catalyses the final step in haem biosynthesis from highly photoreactive porphyrins. HEM15 is regulated by light and the mutants are photosensitive and exhibit reduced virulence [PMID:20488877]. 5316 MUTATION: The Δall1 mutants of two serotypes produced a shorter exo-PS with less branching and structural complexity than the parental strains;Δall1 mutant strains manifested differences in epitope expression and significant resistance to phagocytosis [PMID:18955480][PMID:18955480]. 5264 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3258511 CNG03730 20140329 214684 7 protein-coding NCBI-supplied GO_0004588; GO_0005634; GO_0005737; GO_0019856 PMID: 15653466 MUTATION: ura5 mutant is attenuated in mice [PMID:1541525]. 4769 orotidine monophosphate pyrophosphorylase (URA5) CNG03730 MUTATION: Analysis of cell wall composition of the AGS1 deletion mutant demonstrated complete loss of alpha glucan accompanied by a compensatory increase in chitin/chitosan and a redistribution of beta glucan between cell wall fractions. The mutants were unable to growing mouse model of infection, but caused death in nematodes [PMID:17244196]. 5262 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3259176 CNH02280 20140406 214684 8 protein-coding NCBI-supplied PMID: 15653466; 16741577 MUTATION: gcs1 mutant is attenuated in mice [PMID:17664261]. 4732 hypothetical protein CNH02280 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3259238 CNH02380 20140406 214684 8 protein-coding NCBI-supplied PMID: 15653466 MUTATION: mpf3 mutant is attenuated in mice [PMID:15765146]. 4756 hypothetical protein CNH02380 MUTATION: sopB mutants induce significantly less fluid accumulation in bovine ligated ileal loops than the wild-type [PMID:12065528]. 2578 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3267210 pCF10_16 20140217 1351 protein-coding NCBI-supplied PMID: 1938961; 7545961; 8349565; 8693026; 15659682 MUTATION: prgB mutant is attenuated in rabbit model of endocarditis [PMID:18955479]. 4789 aggregation substance Other designations: PrgB prgB MUTATION: sseC mutant is attenuated in mice [PMID:11159962]. 1639 MUTATION: sseD mutant is attenuated in mice [PMID:11159962]. 1640 MUTATION: ssaM mutant is attenuated in mice [PMID:15491354]. 1641 MUTATION: ssaV and aroC double mutants are attenuated in humans [PMID:19745519]. 1642 MUTATION: sopE2 mutant has reduced ability to invade HeLa cells compared to wild-type [PMID:10735884]. 1643 MUTATION: sptP mutants have reduced epithelial cell invasion and reduced transepithelial migration of PMN compared to the wild type. Competition experiments indicate that sptP mutants fail to colonize the spleen of mice when coinoculated with wild-type S. enterica [PMID:15182677]. 1644 MUTATION: spaR mutant is severely impaired in entry to Henle-407 cells [PMID:8751894]. 1645 MUTATION: spaQ mutant is severely impaired in entry to Henle-407 cells [PMID:8751894]. 1646 MUTATION: tdcA mutant is less invasive of cultured epithelial cells and attenuated in mice [PMID:19812899]. 1647 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3376122 cgd6_1760 20140405 353152 6 protein-coding NCBI-supplied PMID: 15044751 MUTATION: P13K mutant is attenuated in invasion of H69 cells [PMID:15133042]. 2019 phosphatidylinositol 3-kinase; PI3ka plus PI3Kc domains cgd6_1760 Bin Zhao, Oliver He 77.t00030 WEB: http://www.ncbi.nlm.nih.gov/gene 3407934 EHI_098210 20121017 294381 protein-coding NCBI-supplied PMID: 15729342 MUTATION: parasites with blocked expression of kerp1 are attenuated in causing liver abscesses in hamsters [PMID:17711481]. 4533 lysine and glutamic acid-rich protein 1 (KERP1) Pathema:EHI_098210 EHI_098210 Bin Zhao, Oliver He 18.t00027 WEB: http://www.ncbi.nlm.nih.gov/gene 3410347 EHI_118270 20140222 294381 protein-coding NCBI-supplied PMID: 15729342 MUTATION: Ehap-a gene was silenced resulting in a nonvirulent phenotype in hamsters [PMID:18493998]. 4534 amoebapore C Pathema:EHI_118270 EHI_118270 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3424772 PB000799.01.0 20140322 5823 protein-coding NCBI-supplied PMID: 15637271 MUTATION: P36p-deficient Plasmodium berghei is attenuated in mice [PMID:17604034]. 4988 P36-like protein PB000799.01.0 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3429565 NTHI0225 20140322 281310 protein-coding NCBI-supplied PMID: 15102813; 15968074 MUTATION: the introduction of functional NTHI ompP2 gene into the avirulent Hib ompP2 mutant restored the virulence of this strain to wild-type levels [PMID:7689543]. P2 mutants are unable to produce detectable bacteremia in infant rats [PMID:7689543]. 2827 OMP P2 Other designations: outer membrane protein P2 ompP2 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3429634 NTHI0307 20140406 281310 protein-coding NCBI-supplied PMID: 15102813; 15968074 MUTATION: dam mutants is attenuated in invasion of of human brain microvascular endothelial cells (HBMECs) and human respiratory epithelial cells (NCI-H292) [PMID:15228541]. 2828 deoxyadenosyl-methyltransferase; DNA adenine methyltransferase; M.HindIV Other designations: DNA adenine methylase dam Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3429690 NTHI0365 20140322 281310 protein-coding NCBI-supplied PMID: 15102813; 15968074; 16966407 MUTATION: lgtC mutant is attenuated in infant rat model [PMID:8855319]. 2829 UDP-galactose--lipooligosaccharide galactosyltransferase lgtC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3429769 NTHI0448 20140322 281310 protein-coding NCBI-supplied PMID: 15102813; 15968074 MUTATION: oapA mutant has significantly reduced binding to Chang epithelial cells than the wild type [PMID:10417187]. 2830 opacity associated protein oapA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3429791 NTHI0472 20140406 281310 protein-coding NCBI-supplied PMID: 15102813; 15968074 MUTATION: lic3A mutant is attenuated in chinchilla [PMID:12855765]. 2831 CMP-Neu5Ac--lipooligosaccharide alpha 2-3 sialyltransferase lic3A Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3429845 NTHI0528 20140405 281310 protein-coding NCBI-supplied PMID: 15102813; 15968074 MUTATION: accA mutant is attenuated in rats [PMID:12473436]. 2832 acetyl-CoA carboxylase carboxyltransferase subunit alpha accA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3430027 NTHI0719 20140315 281310 protein-coding NCBI-supplied PMID: 15102813; 15968074 MUTATION: ropE mutants are unable to survive intracellularly in macrophages [PMID:11796603]. 2833 Sigma-24 Other designations: RNA polymerase sigma factor RpoE rpoE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3430211 NTHI0899 20140405 281310 protein-coding NCBI-supplied PMID: 15102813; 15968074 MUTATION: pgmB mutant is had reduced adherence and invasion of human bronchial epithelial cells (16HBE14) [PMID:10931302]. 2834 phosphoglucomutase pgmB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3430315 NTHI1012 20140222 281310 protein-coding NCBI-supplied PMID: 15102813; 15968074 MUTATION: dsbA mutant is attenuated in mice [PMID:18212083]. 2835 thiol:disulfide interchange protein DsbA dsbA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3430322 NTHI1021 20140322 281310 protein-coding NCBI-supplied PMID: 15102813; 15968074; 19451029 MUTATION: hbpA mutant is attenuated in mice [PMID:18212083]. 2836 hemin-binding lipoprotein Other designations: heme-binding protein A hbpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3430392 NTHI1099 20140405 281310 protein-coding NCBI-supplied PMID: 15102813; 15968074 MUTATION: ktkE mutant has attenuated virulence in interperitoneal infection in infant rats [PMID:7927766]. 2837 catalase hktE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3430833 NTHI1594 20140322 281310 protein-coding NCBI-supplied PMID: 15102813; 15968074 MUTATION: licD mutant is more rapidly cleared in mouse pulmonary infection than the wild type [PMID:18347044]. 2838 phosphorylcholine transferase licD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3431148 NTHI1891 20140405 281310 protein-coding NCBI-supplied PMID: 15102813; 15968074 MUTATION: siaB mutant is attenuated in chinchillas [PMID:12855765]. 2839 CMP-N-acetylneuraminic acid synthetase; CMP-NeuNAc synthetase; CMP-sialic acid synthetase Other designations: acylneuraminate cytidylyltransferase siaB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3431152 NTHI1895 20140322 281310 protein-coding NCBI-supplied PMID: 15102813; 15968074 MUTATION: tehB mutant is attenuated in rats [PMID:20075041]. 2840 tellurite resistance protein TehB tehB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3431268 NTHI2021 20140406 281310 protein-coding NCBI-supplied PMID: 15102813; 15968074 MUTATION: ptsI is attenuated in mice [PMID:12949188]. 2841 phosphotransferase system, enzyme I Other designations: phosphoenolpyruvate-protein phosphotransferase ptsI Bin Zhao, Oliver He Afu6g04820 WEB: http://www.ncbi.nlm.nih.gov/gene 3505208 AFUA_6G04820 20121210 330879 6 protein-coding NCBI-supplied PMID: 16372009 MUTATION: pabaA mutant is attenauted in mice [PMID:10931287]. 4555 para-aminobenzoate synthase PabaA - AFUA_6G04820 Bin Zhao, Oliver He Afu6g01970 WEB: http://www.ncbi.nlm.nih.gov/gene 3505289 AFUA_6G01970 20121210 330879 6 protein-coding NCBI-supplied PMID: 16372009 MUTATION: areA mutant has delayed onset of pulmonary aspergillosis in mice compared to the wild type [PMID:9669338]. 4539 GATA transcriptional activator AreA - AFUA_6G01970 Bin Zhao, Oliver He Afu3g03420 WEB: http://www.ncbi.nlm.nih.gov/gene 3506154 AFUA_3G03420 20121210 330879 3 protein-coding NCBI-supplied PMID: 16372009 MUTATION: sidD mutant is attenuated in D. melanogaster [PMID:20370364]. 4565 nonribosomal peptide synthase SidD - AFUA_3G03420 Bin Zhao, Oliver He Afu1g06900 WEB: http://www.ncbi.nlm.nih.gov/gene 3507698 AFUA_1G06900 20121210 330879 1 protein-coding NCBI-supplied PMID: 16372009 MUTATION: crzA mutant is attenuated in mice [PMID:18298443]. 4545 C2H2 transcription factor Crz1 - AFUA_1G06900 Bin Zhao, Oliver He Afu6g09660 WEB: http://www.ncbi.nlm.nih.gov/gene 3508160 AFUA_6G09660 20121210 330879 6 protein-coding NCBI-supplied PMID: 16372009; 17574915; 17601876; 17630330 MUTATION: gliP mutant is attenuated in mice immunosuppressed by hydrocortisone [PMID:17601876]. 4549 nonribosomal peptide synthase GliP - AFUA_6G09660 Bin Zhao, Oliver He Afu6g10240 WEB: http://www.ncbi.nlm.nih.gov/gene 3508218 AFUA_6G10240 20121210 330879 6 protein-coding NCBI-supplied PMID: 16372009 MUTATION: fos-1 is attenuated in mice [PMID:12146755]. 4546 sensor histidine kinase/response regulator Fos-1/TcsA - AFUA_6G10240 Bin Zhao, Oliver He Afu4g12470 WEB: http://www.ncbi.nlm.nih.gov/gene 3509491 AFUA_4G12470 20140222 330879 4 protein-coding NCBI-supplied PMID: 16372009; 18249572 MUTATION: cpcA mutant is attenauted in mice [PMID:15101984]. 4544 bZIP transcription factor CpcA - AFUA_4G12470 Bin Zhao, Oliver He Afu1g14660 WEB: http://www.ncbi.nlm.nih.gov/gene 3509858 AFUA_1G14660 20130323 330879 1 protein-coding NCBI-supplied PMID: 16372009; 17630330; 23022264 MUTATION: laeA mutant is attenuated in mice [PMID:16151250]. 4551 regulator of secondary metabolism LaeA - AFUA_1G14660 Bin Zhao, Oliver He Afu1g12930 WEB: http://www.ncbi.nlm.nih.gov/gene 3510275 AFUA_1G12930 20121210 330879 1 protein-coding NCBI-supplied PMID: 16372009 MUTATION: gpaB mutant is almost avirulent in a low-dose murine inhalation model [PMID:15322014]. 4550 G protein complex alpha subunit GpaB - AFUA_1G12930 Bin Zhao, Oliver He Afu1g10080 WEB: http://www.ncbi.nlm.nih.gov/gene 3510549 AFUA_1G10080 20121210 330879 1 protein-coding NCBI-supplied PMID: 16372009 MUTATION: zafA mutant is attenuated in a murine model of invasive aspergillosis [PMID:17542914]. 4566 C2H2 transcription factor - AFUA_1G10080 Bin Zhao, Oliver He Afu1g10380 WEB: http://www.ncbi.nlm.nih.gov/gene 3510659 AFUA_1G10380 20121210 330879 1 protein-coding NCBI-supplied PMID: 16372009; 16759234 MUTATION: pes1 mutant is attenuated in Galleria mellonella model system [PMID:16759234]. 4556 nonribosomal peptide synthase Pes1 - AFUA_1G10380 Bin Zhao, Oliver He Afu5g10760 WEB: http://www.ncbi.nlm.nih.gov/gene 3510739 AFUA_5G10760 20121210 330879 5 protein-coding NCBI-supplied PMID: 16372009 MUTATION: kre2 (afmnt1) mutant is attenuated in mice [PMID:18708564]. 4536 alpha-1,2-mannosyltransferase (Kre2) - AFUA_5G10760 Bin Zhao, Oliver He Afu5g09360 WEB: http://www.ncbi.nlm.nih.gov/gene 3511045 AFUA_5G09360 20140322 330879 5 protein-coding NCBI-supplied PMID: 16372009; 16835453; 18456861; 18606829; 21107627; 22066998; 22634424; 23990785 MUTATION: cnaA mutant is attenuated in mice [PMID:16835453]. 4543 calcineurin catalytic subunit CnaA - AFUA_5G09360 Bin Zhao, Oliver He Afu5g08890 WEB: http://www.ncbi.nlm.nih.gov/gene 3511364 AFUA_5G08890 20140405 330879 5 protein-coding NCBI-supplied PMID: 16372009 homoaconitase LysF - AFUA_5G08890 Bin Zhao, Oliver He Afu5g05480 WEB: http://www.ncbi.nlm.nih.gov/gene 3511630 AFUA_5G05480 20140215 330879 5 protein-coding NCBI-supplied PMID: 16372009 MUTATION: rhbA mutant is attenuated in mice [PMID:12704156]. 4563 Rheb small monomeric GTPase RhbA - AFUA_5G05480 Bin Zhao, Oliver He Afu2g07770 WEB: http://www.ncbi.nlm.nih.gov/gene 3513137 AFUA_2G07770 20121210 330879 2 protein-coding NCBI-supplied PMID: 16372009 MUTATION: rasB mutant is attenuated in mice [PMID:16339716]. 4561 Ras small monomeric GTPase RasB - AFUA_2G07770 Bin Zhao, Oliver He Afu2g08360 WEB: http://www.ncbi.nlm.nih.gov/gene 3513211 AFUA_2G08360 20140308 330879 2 protein-coding NCBI-supplied PMID: 16372009; 17406500 MUTATION: pyrG mutant is avirulent in mice [PMID:8926121]. 4560 orotidine 5'-phosphate decarboxylase PyrG - AFUA_2G08360 Bin Zhao, Oliver He Afu2g17600 WEB: http://www.ncbi.nlm.nih.gov/gene 3513291 AFUA_2G17600 20121210 330879 2 protein-coding NCBI-supplied PMID: 16372009; 17630330 MUTATION: alb1 mutant is attenauted in mice [PMID:9620950]. 4538 conidial pigment polyketide synthase PksP/Alb1 - AFUA_2G17600 Bin Zhao, Oliver He Afu2g12330 WEB: http://www.ncbi.nlm.nih.gov/gene 3513314 AFUA_2G12330 20121210 330879 2 protein-coding NCBI-supplied PMID: 16372009 MUTATION: acuM mutant is attenuated in G. mellonella and murine models of invasive aspergillosis [PMID:21062375]. 4535 Zn cluster transcription factor Rds2 - AFUA_2G12330 Bin Zhao, Oliver He Afu2g12200 WEB: http://www.ncbi.nlm.nih.gov/gene 3513486 AFUA_2G12200 20121210 330879 2 protein-coding NCBI-supplied PMID: 16372009; 21210869 MUTATION: pkaC1 mutant is almost avirulent in a low-dose murine inhalation model [PMID:15322014]. 4557 cAMP-dependent protein kinase catalytic subunit PkaC1 - AFUA_2G12200 Bin Zhao, Oliver He Afu2g07680 WEB: http://www.ncbi.nlm.nih.gov/gene 3513640 AFUA_2G07680 20140405 330879 2 protein-coding NCBI-supplied PMID: 16372009; 20614882; 22465572; 22928747; 24072704; 24321106 MUTATION: sidA mutant is attenuated in D. melanogaster [PMID:20370364]. 4564 L-ornithine N5-oxygenase SidA - AFUA_2G07680 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3533424 Tc00.1047053504593.10 20140315 353153 protein-coding NCBI-supplied PMID: 16020724; 16020725; 21162542 MUTATION: T. cruzi isolates that express and shed higher amounts of trans-sialidase are more virulent in mice [PMID:15181573]. 4461 trans-sialidase Tc00.1047053504593.10 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3571047 M5005_Spy_1838 20130905 293653 protein-coding NCBI-supplied PMID: 16088826 MUTATION: gidA mutant is highly attenuated in the murine ulcer model of soft tissue infection [PMID:18426891]. 4354 tRNA uridine 5-carboxymethylaminomethyl modification protein GidA gidA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3571136 M5005_Spy_1735 20140405 293653 protein-coding NCBI-supplied PMID: 16088826; 20805338 MUTATION: Mice infected by M1, M3 and M49 speB mutants, through air pouch or intraperitoneal challenge, showed less mortality compared with that of the wild-type strains [PMID:18796357]. 4355 exotoxin B speB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3571155 M5005_Spy_1715 20140329 293653 protein-coding NCBI-supplied PMID: 16088826 MUTATION: scpA mutant is attenuated in mouse pneumonia model [PMID:9119483]. 4356 C5A peptidase scpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3571160 M5005_Spy_1720 20140215 293653 protein-coding NCBI-supplied PMID: 16088826; 18005100; 22773785 MUTATION: mga mutant is attenuated in a humanized mouse model for superficial skin infection [PMID:18588968]. 4357 trans-acting positive regulator mga Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3571180 M5005_Spy_1702 20140222 293653 protein-coding NCBI-supplied PMID: 16088826 MUTATION: smeZ mutant is attenuated in zebrafish [PMID:19223485]. 4358 mitogenic exotoxin Z smeZ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3571297 M5005_Spy_1607 20140405 293653 protein-coding NCBI-supplied PMID: 16088826 MUTATION: fba mutant showed diminished invasive capabilities to HEp-2 cells and low mortality in mice following skin infection [PMID:11679068]. 4359 fructose-bisphosphate aldolase fba Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3571619 M5005_Spy_1305 20140406 293653 protein-coding NCBI-supplied PMID: 16088826 MUTATION: In a murine skin infection model, an insertion mutation in the response regulator gene, trxR (M5005_Spy_1305), led to a significant reduction in lesion size, lesion severity, and lethality [PMID:18678666]. 4360 two-component response regulator M5005_Spy_1305 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3571808 M5005_Spy_1106 20140405 293653 protein-coding NCBI-supplied PMID: 16088826 MUTATION: grab mutant is attenuated in mice when injected intraperitoneally [PMID:10336419]. 4361 protein G-related alpha 2M-binding protein grab Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3571853 M5005_Spy_1073 20140329 293653 protein-coding NCBI-supplied PMID: 16088826 MUTATION: dltA mutant was diminished in its ability to adhere to and invade cultured human pharyngeal epithelial cells [PMID:16166534]. 4362 D-alanine--poly(phosphoribitol) ligase subunit 1 dltA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3572266 M5005_Spy_0637 20140222 293653 protein-coding NCBI-supplied PMID: 16088826 MUTATION: lsp mutant is attenuated in a murine model of soft tissue infection [PMID:19398546]. 4363 lipoprotein signal peptidase lsp Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3572347 M5005_Spy_0562 20130905 293653 protein-coding NCBI-supplied PMID: 16088826 MUTATION: sagA mutant is attenuated in mice [PMID:9529097]. 4364 streptolysin S sagA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3572479 M5005_Spy_0424 20140215 293653 protein-coding NCBI-supplied PMID: 16088826; 18490461; 20333240 MUTATION: ccpA mutant is attenuated in mice [PMID:20333240]. 4365 catabolite control protein A ccpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3572567 M5005_Spy_0356 20130905 293653 protein-coding NCBI-supplied PMID: 16088826 exotoxin type J speJ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3572612 M5005_Spy_0283 20140329 293653 protein-coding NCBI-supplied PMID: 16088826 MUTATION: covS mutant has reduced capacity to bind to epithelial cell layers [PMID:20507231]. 4367 transmembrane histidine kinase covS Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3572677 M5005_Spy_0249 20140329 293653 protein-coding NCBI-supplied PMID: 16088826 MUTATION: oppA mutant caused less mortality and tissue damage than the wild-type strain when inoculated into BALB/c mice via an air pouch [PMID:15845494]. 4368 oligopeptide-binding protein oppA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3572745 M5005_Spy_0161 20140406 293653 protein-coding NCBI-supplied PMID: 16088826 MUTATION: perR mutant is attenuated in mouse air sac model [PMID:12183543]. 4369 ferric uptake regulation protein perR Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3573258 M28_Spy0345 20140329 319701 protein-coding NCBI-supplied PMID: 16088825 exotoxin type J precursor speJ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3574429 M28_Spy1700 20140329 319701 protein-coding NCBI-supplied PMID: 16088825 MUTATION: scpA mutant is attenuated in mouse pneumonia model [PMID:9119483]. 4351 C5A peptidase precursor scpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3574433 M28_Spy1704 20140329 319701 protein-coding NCBI-supplied PMID: 16088825 MUTATION: mga mutant is attenuated in a humanized mouse model for superficial skin infection [PMID:18588968]. 4352 M protein trans-acting positive regulator (Mga) mga Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3574788 M28_Spy0617 20140222 319701 protein-coding NCBI-supplied PMID: 16088825 MUTATION: lsp mutant is attenuated in a murine model of soft tissue infection [PMID:19398546]. 4353 lipoprotein signal peptidase lsp Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3635197 CaO19.6001 20140222 237561 3 protein-coding NCBI-supplied PMID: 15123810 MUTATION: sap3 mutant is attenuated in mice and guinea pigs [PMID:9284116]. 4677 secretory aspartyl proteinase SAP3p SAP3 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3635261 CaO19.5908 20140406 237561 3 protein-coding NCBI-supplied PMID: 15123810; 22438817 MUTATION: The deletion of the CaTEC1 gene attenuates virulence of C. albicans in a systemic model of murine candidiasis [PMID:11069668]. 4605 potential TEA/ATTS domain protein; similar to TEA/ATTS domain of S. cerevisiae TEC1 (YBR083W) regulator of Ty1 expression Other designations: potential TEA/ATTS type DNA binding protein TEC1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3636332 CaO19.11492 20140406 237561 5 protein-coding NCBI-supplied PMID: 15123810 MUTATION: cnb1 mutants are attenuated in mice [PMID:12796287]. 4621 Calcineurin regulatory (B) subunit Other designations: hypothetical protein CNB1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3636585 CaO19.1665 20140222 237561 3 protein-coding NCBI-supplied PMID: 15123810 MUTATION: mnt1p mutant has reduced ability to adhere to human buccal epithelial cells and to rat vaginal epithelial cells, and is attenuated in guinea pig and mouse models of systemic candidosis [PMID:9636208]. 4592 mannosyltransferase similar to S. cerevisiae KTR1p Other designations: hypothetical protein MNT1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3636648 CaO19.1715 20120906 237561 3 protein-coding NCBI-supplied PMID: 15123810 MUTATION: IRO1 mutant is attenuated in mice [PMID:16237272]. 4641 potential transcription factor; version of putative iron utilization gene IRO1 with an N terminal extension; IRO1 rescues S. cerevisiae aft1 (YGL071W) mutant although not structurally similar; 3' half is deleted in CAI4 strain Other designations: putative transcription factor IRO1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3636747 CaO19.9240 20140406 237561 3 protein-coding NCBI-supplied PMID: 15123810 MUTATION: csf4 (UTR2) mutant has reduction in adherence to mammalian cells and attenuated virulence in an immunocompetent mouse model of disseminated candidiasis [PMID:15042589]. 4623 Cell wall protein Other designations: hypothetical protein UTR2 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3636877 CaO19.2972 20140406 237561 1 protein-coding NCBI-supplied PMID: 15123810 MUTATION: pde2 mutant is attenuated in mice [PMID:17614954]. 4658 similar to S. cerevisiae PDE2 (YOR360C) cAMP phosphodiesterase; same as cosmid orf Ca49C10.20c Other designations: hypothetical protein PDE2 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3636892 CaO19.3038 20140322 237561 1 protein-coding NCBI-supplied PMID: 15123810 MUTATION: CaTPS2 mutant is attenuated in a mouse model of systemic infection [PMID:11895938]. 4606 trehalose-6-phosphate phosphatase; similar to S. cerevisiae TPS2 (YDR074W) involved in stress response Other designations: hypothetical protein TPS2 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3637217 CaO19.8424 20140406 237561 2 protein-coding NCBI-supplied PMID: 15123810 MUTATION: vma7 null mutant is avirulent in a mouse model of systemic candidiasis [PMID:15870472]. 4694 vacuolar membrane ATPase subunit F Other designations: hypothetical protein VMA7 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3637270 CaO19.8514 20140406 237561 2 protein-coding NCBI-supplied PMID: 15123810; 23171549 MUTATION: hog1 mutant is attenuated in mice [PMID:10322006]. 4636 MAP kinase involved in osmoregulation; identified by functional complementation of S. cerevisiae hog1 (YLR113W) deletion mutant. Other designations: likely protein kinase HOG1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3637397 CaO19.837 20140406 237561 2 protein-coding NCBI-supplied PMID: 15123810; 17588177; 20719741 MUTATION: gna1 null mutant is significantly attenuated in mice [PMID:10878139]. 4633 potential glucosamine phosphate N-acetyl tranferase (GNAT family) similar to S. cerevisiae GNA1 (YFL017C) involved in UDP-N-acetylglucosamine synthesis Other designations: potential glucosamine phosphate N-acetyl tranferase (GNAT family) GNA1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3637595 CaO19.11733 20140406 237561 5 protein-coding NCBI-supplied PMID: 15123810 MUTATION: disruption of INT1 gene in C. albicans suppressed hyphal growth, adhesion to epithelial cells, and virulence in mice [PMID:9478896]. 4640 Integrin-like protein; potential pleckstrin homology domain; similar to S. cerevisiae BUD4 Other designations: integrin-like protein INT1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3637661 CaO19.11717 20140406 237561 5 protein-coding NCBI-supplied PMID: 15123810 MUTATION: CST20 mutant cells were less virulent in a mouse model for systemic candidiasis [PMID:8917571]. 4627 likely signal transduction kinase; can functionally substitute for S. cerevisiae STE20 (YHL007C) kinase involved in pheromone response pathway Other designations: likely signal transduction kinase CST20 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3637703 CaO19.4339 20140406 237561 5 protein-coding NCBI-supplied PMID: 15123810; 18814053; 19819358 MUTATION: vps4 mutant is greatly attenuated for virulence in a mouse model of disseminated candidiasis [PMID:18814053]. 4695 likely AAA ATPase similar to S. cerevisiae VPS4 (YPR173C) AAA ATPase involved in vacuolar sorting Other designations: potential vacuolar sorting ATPase VPS4 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3638043 CaO19.7089 20140405 237561 7 protein-coding NCBI-supplied PMID: 15123810; 15843378 MUTATION: pmr1 mutant was severely attenuated in virulence in a murine model of systemic infection [PMID:15843378]. 4663 Ca++-Pump, ATPase Other designations: hypothetical protein CaO19.7089 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3638247 CaO19.7922 20140406 237561 3 protein-coding NCBI-supplied PMID: 15123810 MUTATION: C. albicans KRE5 homozygous mutant strains exhibit a 50% reduction in adhesion to human epithelial cells and are completely avirulent in a mouse model of systemic infection [PMID:15590817]. 4645 similar to S. pombe stress-induced UDP-glucose-glycoprotein glucosyltransferase gpt1 (SPBPJ4664.06); similar to S. cerevisiae KRE5 (YOR336W) involved in beta-1,6 glucan biosynthesis Other designations: potential glycoprotein glucosyltransferase GPT1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3638466 CaO19.6763 20140406 237561 3 protein-coding NCBI-supplied PMID: 15123810; 22438817 MUTATION: ker1 mutant had attenuated virulence in systemic mouse infections [PMID:15289560]. 4643 lysine/glutamic acid-rich protein Other designations: hypothetical protein CaO19.6763 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3638538 CaO19.6812 20140406 237561 3 protein-coding NCBI-supplied PMID: 15123810 MUTATION: pmt2 mutant has attenuated virulence in a mouse model of hematogenously disseminated candidiasis (HDC) [PMID:16040968]. 4665 similar to dolichyl-P-mannose:protein mannosyltransferase involved in mannosylation of serine and threonine residues Other designations: hypothetical protein PMT2 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3638702 CaO19.9607 20140406 237561 2 protein-coding NCBI-supplied PMID: 15123810 MUTATION: sod5 mutant is attenuated in mice [PMID:14617819]. 4686 one of three potential Cu/Zn superoxide dismutase genes similar to N. crassa NCU03013.1; weak similarity to S. cerevisiae SOD1 (YJR104C); contains potential signal peptide Other designations: potential secreted Cu/Zn superoxide dismutase SOD31 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3638977 CaO19.7622 20140406 237561 R protein-coding NCBI-supplied PMID: 15123810; 22438817 MUTATION: spt3 mutant is avirulent in mice [PMID:12072450]. 4688 transcription factor Spt3 Other designations: hypothetical protein SPT3 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3638983 CaO19.7551 20140406 237561 R protein-coding NCBI-supplied PMID: 15123810 MUTATION: alo1 mutant is attenuated in mice [PMID:11349062]. 4586 D-arabinono-1,4-lactone oxidase Other designations: hypothetical protein ALO1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3639011 CaO19.7549 20140405 237561 R protein-coding NCBI-supplied PMID: 15123810 MUTATION: pmt5 mutant was less virulent in engineered human oral mucosa (EHOM) and in a mouse model of hematogenously disseminated candidiasis (HDC) [PMID:16040968]. 4667 similar to dolichyl-P-mannose:protein mannosyltransferase involved in mannosylation of serine and threonine residues; second orf similar to PMT1 Other designations: hypothetical protein CaO19.7549 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3639229 CaO19.5542 20140406 237561 6 protein-coding NCBI-supplied PMID: 15123810; 21646240; 23430844 MUTATION: a sap4/sap5/sap6 null mutant is attenuated in guinea pigs and mice [PMID:9284116]. 4680 secretory aspartyl proteinase SAP6p SAP6 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3639268 CaO19.5585 20140406 237561 6 protein-coding NCBI-supplied PMID: 15123810; 21646240; 23430844 MUTATION: a sap4/sap5/sap6 null mutant is attenuated in guinea pigs and mice [PMID:9284116]. 4679 secretory aspartyl proteinase SAP5p SAP5 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3639328 CaO19.6033 20140406 237561 1 protein-coding NCBI-supplied PMID: 15123810; 22438817 MUTATION: cmp1 (CNA1)mutant is strongly attenuated in mice [PMID:12933882]. 4619 similar to calcineurin-like protein serine/threonine protein phosphatase Other designations: hypothetical protein CNA1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3639342 CaO19.6091 20140405 237561 1 protein-coding NCBI-supplied PMID: 15123810 MUTATION: rim8 mutant is attenuated in a mouse model of hematogenously disseminated systemic candidiasis [PMID:10992507]. 4673 positive regulator of alkaline-induced genes via proteolysis of RIM101 transcription factor; contains potential Arrestin domains; similar to S. cerevisiae RIM8 (YGL045W) Regulator of IME2 Other designations: positive regulator of alkaline-induced genes RIM8 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3639349 CaO19.6028 20140406 237561 1 protein-coding NCBI-supplied PMID: 15071502; 15123810 MUTATION: hgc1 (CLN3) mutant is has markedly reduced virulence in the kidneys of systemically infected mice [PMID:15071502]. 4635 similar to S. cerevisiae cyclin-dependent protein kinase CLN2 (YPL256C) involved in re-entry into mitotic cell cycle after pheromone arrest Other designations: hypothetical protein CLN3 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3639369 CaO19.6109 20140406 237561 1 protein-coding NCBI-supplied PMID: 15123810; 16998076; 22438817; 23543672 MUTATION: tup1 mutant is significantly reduced in the ability to invade and injure endothelial cells [PMID:10816502]. 4693 transcriptional repressor of filamentous growth; similar to S. cerevisiae TUP1 (YCR084C); eight potential WD domains Other designations: transcriptional repressor of filamentous growth TUP1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3639406 CaO19.13454 20140406 237561 1 protein-coding NCBI-supplied PMID: 15123810 MUTATION: CNA mutant is attenuated in mice [PMID:12753189]. 4620 potential calcineurin-like protein serine/threonine protein phosphatase Other designations: hypothetical protein CNA1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3639789 CaO19.9980 20140406 237561 1 protein-coding NCBI-supplied PMID: 15123810 MUTATION: chs7 mutant had reduced virulence and a high clearance rate in mice [PMID:16079341]. 4617 involved in chitin synthesis Other designations: hypothetical protein CHS7 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3640256 CaO19.5714 20140222 237561 6 protein-coding NCBI-supplied PMID: 15123810 MUTATION: sap1 mutant is attenuated in mice and guinea pigs [PMID:9284116]. 4675 secretory aspartyl proteinase SAP1p SAP1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3640365 CaO19.13139 20140406 237561 6 protein-coding NCBI-supplied PMID: 15123810; 21646240; 23430844 MUTATION: a sap4/sap5/sap6 null mutant is attenuated in guinea pigs and mice [PMID:9284116]. 4678 secretory aspartyl proteinase SAP4p SAP4 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3640536 CaO19.5389 20140406 237561 3 protein-coding NCBI-supplied PMID: 15123810 MUTATION: fkh2 mutant are unable to damage human epithelial or endothelial cells in vitro [PMID:12455696]. 4631 potential forkhead-like transcription factor similar to S. cerevisiae FKH2 (YNL068C) involved in pseudohyphal growth Other designations: potential forkhead-like transcriptional regulator FKH2 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3640763 CaO19.5107 20140406 237561 1 protein-coding NCBI-supplied PMID: 15123810; 16239513 MUTATION: NOT5 mutant had reduced adherence to epithelial cells and has attenuated virulence in mice [PMID:14500538]. 4657 one of two genes similar to S. cerevisiae NOT3 (YIL038C) and NOT5 (YPR072W) components of the cytoplasmic mRNA deadenylase and CCR4-NOT transcription factor complex Other designations: potential mRNA deadenylase and CCR4-NOT complex subunit Not5p NOT5 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3640905 CaO19.8183 20140222 237561 R protein-coding NCBI-supplied PMID: 15123810 MUTATION: cdc10 mutant is attenuated in mice [PMID:12819094]. 4607 septin Other designations: hypothetical protein CDC10 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3641249 CaO19.5343 20140222 237561 2 protein-coding NCBI-supplied PMID: 15123810 MUTATION: ash1p mutant is attenuated for virulence in a mouse model of disseminated candidiasis [PMID:12446785]. 4589 GATA-type Zn finger protein that asymmetrically localizes to daughter cell nucleus and to growing hyphal tips Other designations: hypothetical protein ASH1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3641393 CaO19.5171 20120906 237561 7 protein-coding NCBI-supplied PMID: 15123810 MUTATION: Homozygous pmt1 mutants were avirulent in a mouse model of systemic infection, while heterozygous PMT1/pmt1 strains showed reduced virulence [PMID:9694829]. 4664 similar to dolichyl-P-mannose:protein mannosyltransferase involved in mannosylation of serine and threonine residues Other designations: hypothetical protein PMT1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3641499 CaO19.8586 20140406 237561 5 protein-coding NCBI-supplied PMID: 15123810 MUTATION: skn7 mutant is mildly attenuated in mice [PMID:15039366]. 4684 HSF-type DNA binding and Response regulator receiver domains similar to S. cerevisiae SKN1 (YHR206W) involved in osmotic stress response Other designations: potential HSF-type DNA binding transcription factor SKN7 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3642307 CaO19.2179 20140406 237561 2 protein-coding NCBI-supplied PMID: 15123810 MUTATION: sit1(ARN1) mutant was defective in infection of a reconstituted human epithelium as a model for human oral mucosa [PMID:12183576]. 4682 ferrichrome-type siderophore transporter transcriptionally regulated in response to iron; similar to S. cerevisiae ARN1 (YHL040C) Other designations: ferrichrome-type siderophore transporter ARN1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3642557 CaO19.10362 20140329 237561 R protein-coding NCBI-supplied PMID: 15123810 MUTATION: RHO1 mutant is unable to colonize murine kidneys and cause disease in mice [PMID:12702298]. 4671 Ras-like GTP-binding protein; PKC1 pathway; regulatory subunit of GSC1 glucan synthase; can functionally substitute for S. cerevisiae RHO1 (YPR165W) Other designations: Ras family GTP-binding protein Rho1p RHO1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3642789 CaO19.2886 20140406 237561 4 protein-coding NCBI-supplied PMID: 15123810; 19542310; 20384695; 20719741; 21249169; 21375589; 23139737 MUTATION: disruption of the CEK1 gene adversely affects the growth of serum-induced mycelial colonies and attenuates virulence in a mouse model for systemic candidiasis [PMID:9596738]. 4610 MAP kinase-like orf; aka CEK1; one of two protein kinase genes similar to S. cerevisiae MAP kinases FUS3 (YBL016W) and KSS1 (YGR040W) involved in pheromone signal transduction Other designations: likely protein kinase ERK1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3642986 CaO19.5798 20140406 237561 2 protein-coding NCBI-supplied PMID: 15123810 MUTATION: deletion of one or both copies of LIG4 resulted in attenuation of virulence in a murine model of candidiasis [PMID:11119499]. 4646 ATP-dependent DNA ligase implicated in dsDNA break repair via nonhomologous end-joining Other designations: dsDNA break repair ligase LIG4 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3643218 CaO19.4401 20140406 237561 R protein-coding NCBI-supplied PMID: 15123810 MUTATION: yvh1 has attenuated virulence in mice [PMID:16000712]. 4697 potential dual specificity phosphatase similar to S. cerevisiae YVH1 (YIR026C) nitrogen starvation-induced tyrosine phosphatase Other designations: potential dual specificity phosphatase YVH1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3643280 CaO19.7247 20140406 237561 1 protein-coding NCBI-supplied PMID: 15123810; 18627379; 20375342; 20870932; 21457451; 22427429 MUTATION: rim101 mutant is attenuated in a mouse model of hematogenously disseminated systemic candidiasis [PMID:10992507]. 4672 proteolytically activated regulator of alkaline-induced filamentation; zinc finger protein similar to S. cerevisiae RIM101 (YHL027W) transcriptional activator needed for entry into meiosis Other designations: proteolytically activated regulator of alkaline-induced filamentation RIM101 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3643971 CaO19.9345 20140406 237561 2 protein-coding NCBI-supplied PMID: 15123810; 20875088 MUTATION: camp65 mutants are attenuated in mice [PMID:17217426]. 4593 Mannoprotein MP65; similar to S. cerevisiae soluble cell wall protein SCW10 (YMR305C) glucosidase involved in conjugation with cellular fusion; match to COG5309, Exo-beta-1,3-glucanase (Carbohydrate transport and metabolism) Other designations: potential glycosyl hydrolase CMP65 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3644089 CaO19.4077 20140405 237561 2 protein-coding NCBI-supplied PMID: 15123810 MUTATION: mit1(SUR1) mutant was less virulent during both the acute and chronic phases of systemic infection in mice [PMID:15347680]. 4651 mannosylation of inositolphosphorylceramide Other designations: hypothetical protein SUR1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3644096 CaO19.4109 20140406 237561 2 protein-coding NCBI-supplied PMID: 15123810 MUTATION: pmt4 mutant is attenuated in mice [PMID:15659169]. 4666 similar to dolichyl-P-mannose:protein mannosyltransferase involved in mannosylation of serine and threonine residues Other designations: hypothetical protein PMT4 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3644665 CaO19.8642 20140406 237561 1 protein-coding NCBI-supplied PMID: 15123810 MUTATION: mad2 mutant is attenuated in mice [PMID:12100546]. 4647 spindle-assembly checkpoint protein Other designations: hypothetical protein MAD2 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3644735 CaO19.8376 20140406 237561 1 protein-coding NCBI-supplied PMID: 15123810 MUTATION: sap7 mutant is attenuated in an intravenous model of systemic candidiasis in mice [PMID:16177393]. 4681 secretory aspartyl proteinase SAP7p SAP7 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3645329 CaO19.1161 20140406 237561 1 protein-coding NCBI-supplied PMID: 15123810 MUTATION: pld1(SPO14) mutants are unable to survive in internal organs after intravenous challenge, and are not lethal for immunodeficient mice after oral challenge [PMID:15552646]. 4661 Phospholipase D:required for commitment to meiosis Other designations: hypothetical protein SPO14 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3645650 CaO19.6953 20140406 237561 3 protein-coding NCBI-supplied PMID: 15123810; 18957583 MUTATION: an irs4 null mutant strain was associated with attenuated mortality, diminished tissue burdens, less extensive infections, impaired C. albicans hyphal formation and decreased kidney damage in mice [PMID:16151204]. 4642 similar to S. cerevisiae IRS4p involved in chromatin silencing at rDNA loci Other designations: hypothetical protein CaO19.6953 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3645961 CaO19.2151 20140406 237561 6 protein-coding NCBI-supplied PMID: 15123810 MUTATION: CaNAG6 mutant is attenuated in mice [PMID:12076781]. 4599 similar to S. cerevisiae SEY1 involved in vesicular traffic in stressed cells; similarity in the N-terminal region to human interferon-induced guanylate binding protein GBP1 Other designations: hypothetical protein NAG6 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3645978 CaO19.2160 20140405 237561 6 protein-coding NCBI-supplied PMID: 15123810 MUTATION: CaNAG4 mutant is attenuated in mice [PMID:12076781]. 4597 potential transporter similar to S. cerevisiae TPO3 (YPR156C) and TPO2 (YGR138C) plasma membrane polyamine transporters Other designations: potential polyamine transporter NAG4 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3645995 CaO19.13543 20140406 237561 R protein-coding NCBI-supplied PMID: 15123810 MUTATION: ace2 mutant is virulent in a mouse model [PMID:15255906]. 4583 potential zinc finger protein similar to S. cerevisiae ACE2 (YLR131C) cell cycle-specific transcriptional regulator of CUP1 Other designations: potential zinc finger transcription factor ACE2 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3646114 CaO19.9701 20140406 237561 6 protein-coding NCBI-supplied PMID: 15123810; 23341961 MUTATION: a DAC1/NAG1/HXK1(NAG5) mutant is highly attenuated in a murine systemic candidiasis model and was less adherent to human buccal epithelial cells in vitro [PMID:11705974]. 4638 N-acetylglucosamine kinase; recognizes glucose and mannose as substrates; similar to S. cerevisiae HXK1 (YFR053C) Other designations: N-acetylglucosamine kinase NAG5 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3646116 CaO19.9703 20140406 237561 6 protein-coding NCBI-supplied PMID: 15123810 MUTATION: a DAC1/NAG1/HXK1 mutant is highly attenuated in a murine systemic candidiasis model and was less adherent to human buccal epithelial cells in vitro [PMID:11705974]. 4655 C. albicans glucosamine-6-phosphate deaminase (EC 3.5.99.6) Other designations: hypothetical protein NAG1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3646118 CaO19.9705 20140406 237561 6 protein-coding NCBI-supplied PMID: 15123810 MUTATION: CaNAG3 mutant is attenuated in mice [PMID:12076781]. 4596 potential transporter similar to S. cerevisiae TPO3 (YPR156C) and TPO2 (YGR138C) plasma membrane polyamine transporters Other designations: potential polyamine transporter NAG3 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3646146 CaO19.6844 20140405 237561 protein-coding NCBI-supplied PMID: 15123810 MUTATION: Candida albicans mutants lacking ICL1 are markedly less virulent in mice than the wild type [PMID:11452311]. 4639 isocitrate lyase capable of functionally substituting for S. cerevisiae ICL1 (YER065C); gluconeogenesis Other designations: hypothetical protein ICL1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3646212 CaO19.13961 20140329 237561 1 protein-coding NCBI-supplied PMID: 15123810 MUTATION: Mice inoculated with 10(6) CFU of the tps1/tps1 mutant did not show visible symptoms of infection 16 days after inoculation, while those similarly inoculated with wild-type cells were dead 12 days after inoculation [PMID:9683476]. 4692 trehalose-6-phosphate synthase cloned by functional complementation of a S. cerevisiae tps1 (YBR126C) mutant Other designations: hypothetical protein TPS1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3646770 CaO19.13719 20140406 237561 protein-coding NCBI-supplied PMID: 15123810 MUTATION: spa2Delta exhibited no virulence in the mouse systemic candidiasis model [PMID:12940995]. 4687 spindle pole antigen Other designations: hypothetical protein SPA2 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3646776 CaO19.10874 20140405 237561 4 protein-coding NCBI-supplied PMID: 15123810 MUTATION: csh3 (SHR3) mutant is attenuated is avirulent in mice [PMID:14756779]. 4625 Protein required for amino acid permeases Other designations: hypothetical protein SHR3 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3647353 CaO19.3707 20140406 237561 R protein-coding NCBI-supplied PMID: 15123810 MUTATION: CaYHB1 mutant is still lethal in mice but has reduced virulence compared to the wild type [PMID:15189992]. 4696 one of three likely flavohemoproteins similar to S. pombe SPAC869.02c and S. cerevisiae YHB1 (YGR234W) NADPH-dependent flavohemoglobin implicated in the oxidative stress response Other designations: likely flavohemoglobin YHB1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3647663 CaO19.11547 20140405 237561 protein-coding NCBI-supplied PMID: 15123810 MUTATION: gpi7 mutant is attenuated for virulence in mice and has reduced survival in the gastrointestinal environment of mice [PMID:11994163]. 4634 N terminal fragment of fungal cell wall-specific GPI anchor synthesis protein Gpi7p; similar to of S. cerevisiae LAS21 (YJL062W); truncation due to end of contig, other end of GPI7 is at end of contig19-10020, CaP19.60 Other designations: fungal cell wall GPI anchor synthesis protein Gpi7p fragment GPI7 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3647888 CaO19.5691 20140406 237561 protein-coding NCBI-supplied PMID: 15123810; 15449307 MUTATION: cdc11 mutant is attenuated in mice [PMID:12819094]. 4608 Septin, component of 10nm filaments of mother-bud neck Other designations: hypothetical protein CDC11 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3647982 CaO19.12667 20140406 237561 R protein-coding NCBI-supplied PMID: 15123810 MUTATION: sit4 mutant is attenuated in mice [PMID:14731272]. 4683 calcineurin-like phosphoesterase similar to S. cerevisiae SIT4 (YDL047W) type 2A-related protein phosphatase Other designations: potential type 2A-related protein phosphatase SIT4 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3654467 LH0131 20140329 562 protein-coding NCBI-supplied PMID: 14573650 MUTATION: traT mutants have altered membrane permeability and are sensitive to hydrophobic antibiotics [PMID:3323837]. 3 conjugal transfer surface exclusion protein TraT traT Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3654480 LH0144 20140329 562 protein-coding NCBI-supplied PMID: 14573650; 16377616; 17382555; 20637130; 22326301; 22379807 hemolysin A ehxA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3654481 LH0145 20140329 562 protein-coding NCBI-supplied PMID: 14573650 hemolysin C ehxC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3654615 FLUAVH5N1_s1gp1 20140406 93838 protein-coding NCBI-supplied PMID: 10484749; 18305037; 19066626; 19119420; 20211480; 21367983 polymerase PB2 PB2 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3654617 FLUAVH5N1_s3gp1 20140406 93838 protein-coding NCBI-supplied PMID: 10484749; 18615018; 19194458; 19587036; 20211480; 21177821; 23901080 polymerase PA PA MUTATION: PEX2 RNA silenced mutant of the bloodstream form rapidly dies [PMID:12077356]. 4464 Bin Zhao, Oliver He SSO_1750 WEB: http://www.ncbi.nlm.nih.gov/gene 3666430 SSON_1750 20140406 300269 protein-coding NCBI-supplied PMID: 16275786 MUTATION: sitA mutant is attenuated in mice [PMID:19289511]. 1578 periplasmic-binding protein - Other designations: Iron transport protein sitA Bin Zhao, Oliver He SSO_1500 WEB: http://www.ncbi.nlm.nih.gov/gene 3666606 SSON_1500 20121017 300269 protein-coding NCBI-supplied PMID: 16275786 MUTATION: sodB mutant is extremely sensitive to killing by phagocytes compared to the wild-type, and causes only mild damage in infection of rabbit ileal loops [PMID:2404874]. 1579 superoxide dismutase - sodB Bin Zhao, Oliver He SSO_2403 WEB: http://www.ncbi.nlm.nih.gov/gene 3667111 SSON_2403 20121017 300269 protein-coding NCBI-supplied PMID: 16275786 MUTATION: vacJ mutants are incapable of intercellular spread of epithelial cells [PMID:8145644]. 1580 lipoprotein - vacJ Bin Zhao, Oliver He SSO_3535 ompB WEB: http://www.ncbi.nlm.nih.gov/gene 3667244 SSON_3535 20140222 300269 protein-coding NCBI-supplied PMID: 16275786 MUTATION: envZ insertion mutant is able to invade cells but has decreased virulence due to the inability to survive intracellularly [PMID:2121709]. 1581 osmolarity sensor protein - envZ Bin Zhao, Oliver He SSO_3536 WEB: http://www.ncbi.nlm.nih.gov/gene 3667245 SSON_3536 20140215 300269 protein-coding NCBI-supplied PMID: 16275786 MUTATION: mutant of the ompB locus (both the envZ and ompR genes) showed attenuated virulence in HeLa cells, and a weak response to a Serany test [PMID:2121709]. 1582 sensor; EnvZ - Other designations: osmolarity response regulator ompR Bin Zhao, Oliver He SSO_2273 WEB: http://www.ncbi.nlm.nih.gov/gene 3667899 SSON_2273 20130508 300269 protein-coding NCBI-supplied PMID: 16275786 MUTATION: ompC mutants were attenuated in their ability to spread cell to cell and kill epithelial cells, and had a negative Sereny test [PMID:8359885]. 1583 porin - ompC Bin Zhao, Oliver He SSO_2589 WEB: http://www.ncbi.nlm.nih.gov/gene 3668044 SSON_2589 20140405 300269 protein-coding NCBI-supplied PMID: 16275786 MUTATION: guaAguaB mutants are attenuated in HeLa cells [PMID:8757833]. 1584 glutamine-hydrolyzing - Other designations: GMP synthase guaA Bin Zhao, Oliver He SSO_2590 WEB: http://www.ncbi.nlm.nih.gov/gene 3668045 SSON_2590 20140406 300269 protein-coding NCBI-supplied PMID: 16275786 MUTATION: guaAguaB mutants are attenuated in HeLa cells [PMID:8757833]. 1585 inosine 5'-monophosphate dehydrogenase - guaB Bin Zhao, Oliver He SSO_1914 WEB: http://www.ncbi.nlm.nih.gov/gene 3668089 SSON_1914 20130420 300269 protein-coding NCBI-supplied PMID: 16275786 MUTATION: tonB mutant is able to invade epithelial cells but is incapable of cell to cell spread [PMID:11035742]. 1586 energy transducer; uptake of iron, cyanocobalimin; sensitivity to phages, colicins - Other designations: transporter tonB Bin Zhao, Oliver He SSO_2665 WEB: http://www.ncbi.nlm.nih.gov/gene 3668265 SSON_2665 20130508 300269 protein-coding NCBI-supplied PMID: 16275786 enterotoxin - senB Bin Zhao, Oliver He SSO_4356 WEB: http://www.ncbi.nlm.nih.gov/gene 3668476 SSON_4356 20140406 300269 protein-coding NCBI-supplied PMID: 16275786 MUTATION: miaA mutants had reduced ability to invade and spread in MK2 cell monolayers compared to the wildtype [PMID:9294434]. 1588 tRNA delta(2)-isopentenylpyrophosphate transferase - miaA Bin Zhao, Oliver He SSO_4357 WEB: http://www.ncbi.nlm.nih.gov/gene 3668477 SSON_4357 20140222 300269 protein-coding NCBI-supplied PMID: 16275786; 19476612 MUTATION: hfq deletion mutants are attenuated in guinea pig eye infection model (Sereny test) [PMID:20080057]. 1589 RNA-binding protein Hfq - hfq Bin Zhao, Oliver He SSO_4364 WEB: http://www.ncbi.nlm.nih.gov/gene 3668484 SSON_4364 20140406 300269 protein-coding NCBI-supplied PMID: 16275786 MUTATION: vacB mutants had attenuated invasion of MK2 cells compared to the wild-type strain [PMID:1400189]. 1590 exoribonuclease R - vacB Bin Zhao, Oliver He SSO_0157 WEB: http://www.ncbi.nlm.nih.gov/gene 3668675 SSON_0157 20140222 300269 protein-coding NCBI-supplied PMID: 16275786 MUTATION: dksA mutants are able to invade cultured cell monlayers but are incapable of cell to cell spread [PMID:11500451]. 1591 RNA polymerase-binding transcription factor - dksA Bin Zhao, Oliver He SSO_0061 WEB: http://www.ncbi.nlm.nih.gov/gene 3668735 SSON_0061 20140406 300269 protein-coding NCBI-supplied PMID: 16275786 MUTATION: surA mutant is able to infect epithelial cells but is incapable of cell to cell spread [PMID:20447864]. 1592 peptidyl-prolyl cis-trans isomerase SurA - surA Bin Zhao, Oliver He SSO_4031 WEB: http://www.ncbi.nlm.nih.gov/gene 3669620 SSON_4031 20130508 300269 protein-coding NCBI-supplied PMID: 16275786 MUTATION: yihE mutant is unable to cause keratoconjunctivitis in guinea pigs [PMID:15073317]. 1593 serine/threonine protein kinase - yihE Bin Zhao, Oliver He SSO_1148 WEB: http://www.ncbi.nlm.nih.gov/gene 3670177 SSON_1148 20130406 300269 protein-coding NCBI-supplied PMID: 16275786 MUTATION: phoP mutants were resolved more quickly than wild type in animal models, and are more susceptible to killing by PMNs [PMID:11207599]. 1594 DNA-binding transcriptional regulator PhoP - phoP Bin Zhao, Oliver He SSO_0909 WEB: http://www.ncbi.nlm.nih.gov/gene 3670343 SSON_0909 20140405 300269 protein-coding NCBI-supplied PMID: 16275786 MUTATION: aroA deletion mutants are attenuated in HeLa cells [PMID:8757833]. 1595 3-phosphoshikimate 1-carboxyvinyltransferase - aroA Bin Zhao, Oliver He SSO_3602 WEB: http://www.ncbi.nlm.nih.gov/gene 3670426 SSON_3602 20140315 300269 protein-coding NCBI-supplied PMID: 16275786 MUTATION: iuc mutants are attenuated in chicken embryos and rabbit ileal loops [PMID:19130265]. 1596 siderophore biosynthesis protein - iucB Bin Zhao, Oliver He SSO_3603 WEB: http://www.ncbi.nlm.nih.gov/gene 3670427 SSON_3603 20140329 300269 protein-coding NCBI-supplied PMID: 16275786 MUTATION: iuc mutants are attenuated in chicken embryos and rabbit ileal loops [PMID:19130265]. 1597 siderophore biosynthesis protein - iucC Bin Zhao, Oliver He SSO_3604 WEB: http://www.ncbi.nlm.nih.gov/gene 3670428 SSON_3604 20140405 300269 protein-coding NCBI-supplied PMID: 16275786 MUTATION: iuc mutants are attenuated in chicken embryos and rabbit ileal loops [PMID:19130265]. 1598 lysine:N6-hydroxylase - iucD Bin Zhao, Oliver He SSO_3605 WEB: http://www.ncbi.nlm.nih.gov/gene 3670429 SSON_3605 20130518 300269 protein-coding NCBI-supplied PMID: 16275786 MUTATION: mutants of the iuc locus and the aerobactin receptor, iutA were attenuated in chicken embryos [PMID:3028962]. 1599 ferric siderophore receptor - iutA Bin Zhao, Oliver He SSO_3601 WEB: http://www.ncbi.nlm.nih.gov/gene 3670519 SSON_3601 20140322 300269 protein-coding NCBI-supplied PMID: 16275786 MUTATION: iuc mutants are attenuated in chicken embryos and rabbit ileal loops [PMID:19130265]. 1600 siderophore biosynthesis protein - iucA Bin Zhao, Oliver He SSO_1461 WEB: http://www.ncbi.nlm.nih.gov/gene 3670791 SSON_1461 20140405 300269 protein-coding NCBI-supplied PMID: 16275786 MUTATION: aroD deletion led to attenuation in HeLa cells and monkeys [PMID:8356844]. 1601 3-dehydroquinate dehydratase - aroD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3670805 SSON_P003 20130616 300269 protein-coding NCBI-supplied PMID: 16122562; 16275786 MUTATION: ospB mutants had reduced PMN transepithelial migration when compared to wild-type infection, PMN transepithelial migration is necessary for virulence of Shigella [PMID:19017275]. 1602 protein secreted by the Mxi-Spa secretion machinery Other designations: OspB ospB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3670811 SSON_P009 20130616 300269 protein-coding NCBI-supplied PMID: 16122562; 16275786 MUTATION: ospF mutants had reduced PMN transepithelial migration when compared to wild-type infection, PMN transepithelial migration is necessary for virulence of Shigella [PMID:16988276]. 1603 OspF ospF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3670829 SSON_P085 20140222 300269 protein-coding NCBI-supplied PMID: 16122562; 16275786 MUTATION: virB mutants have an avirulent phenotype and do not invade host cells [PMID:8385666]. 1604 transcriptional activator required for tanscription of the ipa, mxi, and spa operons Other designations: VirB virB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3670831 SSON_P087 20140405 300269 protein-coding NCBI-supplied PMID: 16122562; 16275786 MUTATION: ipaA mutants are attenuated in invasion of HeLa cells [PMID:9184218]. 1605 secreted by the Mxi-Spa machinery; modulates entry of bacteria into epithelial cells Other designations: IpaA ipaA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3670832 SSON_P088 20140405 300269 protein-coding NCBI-supplied PMID: 16122562; 16275786 MUTATION: ipaD mutants are completely unable to invade cultured cells or lyse RBCs [PMID:15731041]. 1606 secreted by the Mxi-Spa machinery; required for entry of bacteria into epithelial cells Other designations: IpaD ipaD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3670833 SSON_P089 20140322 300269 protein-coding NCBI-supplied PMID: 16122562; 16275786 MUTATION: ipaC mutants cannot invade cultured cells or lyse red blood cells [PMID:18656530]. 1607 secreted by the Mxi-Spa secretion machinery; required for entry into epithelial cells Other designations: IpaC ipaC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3670834 SSON_P090 20140322 300269 protein-coding NCBI-supplied PMID: 16122562; 16275786 MUTATION: ipaB mutant is unable to infect HeLa cells [PMID:20086081]. 1608 secreted by the Mxi-Spa secretion machinery; required for entry into epithelial cells Other designations: IpaB ipaB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3670835 SSON_P091 20140222 300269 protein-coding NCBI-supplied PMID: 16122562; 16275786 MUTATION: ipgC mutant attenuated in infecting Caco-2 cells monolayer [PMID:11207551]. 1609 cytoplasmic chaperone for IpaB and IpaC Other designations: IpgC ipgC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3670836 SSON_P092 20140405 300269 protein-coding NCBI-supplied PMID: 16122562; 16275786 MUTATION: The invasiveness of the ipgB1 mutant was decreased to less than 50% of the wild-type level (100%) in a gentamicin protection or plaque forming assay [PMID:15849186]. 1610 secreted by the Mxi-Spa machinery Other designations: IpgB1 ipgB1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3670837 SSON_P093 20130616 300269 protein-coding NCBI-supplied PMID: 16122562; 16275786 MUTATION: transposon mutants of ipgA cannot invade epithelial cells and cannot induce keratoconjunctivitis in mice [PMID:8376337]. 1611 similar to IpgE; putative chaperone Other designations: IpgA ipgA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3670838 SSON_P094 20130616 300269 protein-coding NCBI-supplied PMID: 16122562; 16275786 MUTATION: icsB mutants are attenuated in guinea pig eyes [PMID:12753186]. 1612 invasion protein Other designations: IcsB icsB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3670839 SSON_P095 20140406 300269 protein-coding NCBI-supplied PMID: 16122562; 16275786 MUTATION: ipgD mutant is unable to dephosphorylate phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P2] and induces shorter filapodia in host cells [PMID:12356723]. 1613 secreted by the Mxi-Spa machinery; modulates entry of bacteria into epithelial cells Other designations: IpgD ipgD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3670842 SSON_P098 20140222 300269 protein-coding NCBI-supplied PMID: 16122562; 16275786 MUTATION: mxiG mutant was unable to enter HeLa cells and to provoke keratoconjunctivitis in guinea-pigs [PMID:8559065]. 1614 component of the Mxi-Spa secretion machinery, contains one transmembrane segment Other designations: MxiG mxiG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3670843 SSON_P099 20140215 300269 protein-coding NCBI-supplied PMID: 16122562; 16275786 MUTATION: mxiH mutants are unable to invade HeLa cells [PMID:11169106]. 1615 component of the Mxi-Spa secretion machinery Other designations: MxiH mxiH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3670844 SSON_P100 20140405 300269 protein-coding NCBI-supplied PMID: 16122562; 16275786 MUTATION: mxiI mutant is unable to invade HeLa cells [PMID:11169106]. 1616 component of the Mxi-Spa secretion machinery Other designations: MxiI mxiI Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3670845 SSON_P101 20140215 300269 protein-coding NCBI-supplied PMID: 16122562; 16275786 MUTATION: mxiJ mutant was unable to invade HeLa cells, to induce the formation of plaques on confluent monolayers of HeLa cells, and to provoke keratoconjunctivitis in guinea pigs [PMID:1332940]. 1617 lipoprotein, component of the Mxi-Spa secretion machinery Other designations: MxiJ mxiJ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3670846 SSON_P102 20140215 300269 protein-coding NCBI-supplied PMID: 16122562; 16275786 MUTATION: mxiK mutants are unable to invade HeLa cells [PMID:12864857]. 1618 putative component of the Mxi-Spa secretion machinery Other designations: MxiK mxiK Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3670847 SSON_P103 20140215 300269 protein-coding NCBI-supplied PMID: 16122562; 16275786 MUTATION: mxiN mutants were unable to invade HeLa cells [PMID:12864857]. 1619 putative component of the Mxi-Spa secretion machinery Other designations: MxiN mxiN Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3670849 SSON_P105 20140406 300269 protein-coding NCBI-supplied PMID: 16122562; 16275786 MUTATION: mxiM mutants are phenotypically avirulent, and also unable to invade semiconfluent L2 cell monolayers [PMID:10085046]. 1620 lipoprotein; component of the Mxi-Spa secretion machinery Other designations: MxiM mxiM Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3670850 SSON_P106 20140222 300269 protein-coding NCBI-supplied PMID: 16122562; 16275786 MUTATION: mxiE deletion mutants are unable to block apoptosis of host epithelial cells [PMID:17339354]. 1621 similar to transcriptional activators of the AraC family Other designations: MxiE mxiE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3670851 SSON_P107 20130616 300269 protein-coding NCBI-supplied PMID: 16122562; 16275786 MUTATION: mxiD mutant is unable to invade HeLa cells or to provoke keratoconjunctivitis in guinea-pigs [PMID:8437520]. 1622 outermembrane protein of the secretin family; component of the Mxi-Spa secretion machinery Other designations: MxiD mxiD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3670852 SSON_P108 20140222 300269 protein-coding NCBI-supplied PMID: 16122562; 16275786; 19476612 MUTATION: mxiC mutant has a 10-fold decrease in efficiency in invading epithelial cells [PMID:19017268]. 1623 secreted by and putative component of the Mxi-Spa secretion machinery; similar to YopN (secreted by the type III secretion machinery of Yersinia enterocoltica) Other designations: MxiC mxiC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3670853 SSON_P109 20140215 300269 protein-coding NCBI-supplied PMID: 16122562; 16275786 MUTATION: mxiA mutants were attenuated in invasion of HeLa cells [PMID:2037361]. 1624 innermembrane protein; component of the Mxi-Spa secretion machinery Other designations: MxiA mxiA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3670854 SSON_P110 20140215 300269 protein-coding NCBI-supplied PMID: 16122562; 16275786 MUTATION: spa15 mutant was attenuated in entry into epithelial cells compared to the wild-type [PMID:11952903]. 1625 putative component of the Mxi-Spa secretion machinery Other designations: Spa15 spa15 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3670855 SSON_P111 20130616 300269 protein-coding NCBI-supplied PMID: 16122562; 16275786 MUTATION: spa47 mutants form needle-less type III structure which is defective, and thus incapable of invasion of host cells [PMID:10921870]. 1626 component of the Mxi-Spa secretion machinery; putative ATPase Other designations: ATP synthase SpaL spa47 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3670857 SSON_P113 20130616 300269 protein-coding NCBI-supplied PMID: 16122562; 16275786 MUTATION: spa32 mutants are unable to invade HeLa cells and do not secrete type III effectors [PMID:11844752]. 1627 secreted by and component of the Mxi-Spa machinery Other designations: Spa32 spa32 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3670858 SSON_P114 20130616 300269 protein-coding NCBI-supplied PMID: 16122562; 16275786 MUTATION: spa33 mutants are unable to secrete effectors necessary to cell invasion [PMID:16246841]. 1628 component of the Mxi-Spa secretion machinery Other designations: Spa33 spa33 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3670886 SSON_P142 20140322 300269 protein-coding NCBI-supplied PMID: 16122562; 16275786 MUTATION: virA mutants did not move within the host cytoplasm and failed to move into adjacent cells [PMID:17095701]. 1629 secreted by the Mxi-Spa secretion machinery Other designations: VirA virA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3670911 SSON_P167 20130827 300269 protein-coding NCBI-supplied PMID: 16122562; 16275786 MUTATION: ipaH9.8 deletion mutant caused more severe inflammatory responses with increased pro-inflammatory cytokine production levels than did wild-type Shigella, which resulted in a 30-fold decrease in bacterial colonization in murine lungs [PMID:15950937]. 1630 secreted by the Mxi-Spa secretion machinery Other designations: invasion plasmid antigen ipaH9.8 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3670914 SSON_P170 20140406 300269 protein-coding NCBI-supplied PMID: 16122562; 16275786 MUTATION: Upon infection of ileal loops in rabbits, the ospG mutant induced a stronger inflammatory response than the wild-type strain, indicating that OspG negatively controls the host innate response induced by S. flexneri upon invasion of the epithelium [PMID:16162672]. 1631 secreted by the Mxi-Spa secretion machinery Other designations: OspG ospG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3670925 SSON_P181 20130616 300269 protein-coding NCBI-supplied PMID: 16122562; 16275786 MUTATION: virK mutants have attenuated ability for intracellular spreading in host cells [PMID:15664968]. 1632 required for proper localization of IcsA (VirG) at the surface of bacteria Other designations: VirK virK Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3670995 SSON_P024 20140405 300269 protein-coding NCBI-supplied PMID: 16122562; 16275786 MUTATION: ipgB2 mutant had entry into polarized cells reduced by 70% compared to the wild-type [PMID:18316224]. 1633 probably secreted by the Mxi-Spa secretion machinery Other designations: IpgB2 ipgB2 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3671012 SSON_P041 20140405 300269 protein-coding NCBI-supplied PMID: 16122562; 16275786 MUTATION: virF knockouts are non-invasive to host cells [PMID:20237205]. 1634 member of the AraC family of transcriptional activators; required for transcription of virB and icsA Other designations: VirF virF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3671015 SSON_P044 20130616 300269 protein-coding NCBI-supplied PMID: 16122562; 16275786 MUTATION: ospE mutants had attenuated adhesion to HeLa cells than the wild-type [PMID:19489119]. 1635 secreted by the Mxi-Spa secretion machinery Other designations: OspE2 ospE2 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3671020 SSON_P049 20130616 300269 protein-coding NCBI-supplied PMID: 16122562; 16275786 MUTATION: ospC1 mutants had reduced PMN transepithelial migration when compared to wild-type infection, PMN transepithelial migration is necessary for virulence of Shigella [PMID:16988276]. 1636 secreted by the Mxi-Spa secretion machinery Other designations: OspC1 ospC1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3671021 SSON_P050 20130616 300269 protein-coding NCBI-supplied PMID: 16122562; 16275786 MUTATION: sen deletion mutant elicited lower rises in mucosal short-circuit current than the wild type, suggesting that the senA/ospD3 gene encodes an enterotoxin of Shigella [PMID:7591128]. 1637 SenA; probably secreted by the Mxi-Spa secretion machinery Other designations: OspD3 ospD3 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3671029 SSON_P058 20130616 300269 protein-coding NCBI-supplied PMID: 16122562; 16275786 MUTATION: ipaH7.8 mutants had a lower rate of exit from the endocytic vacuoles into the cytoplasm in mouse macrophages than the wild-type strain [PMID:10816519]. 1638 probably secreted by the Mxi-Spa machinery Other designations: invasion plasmid antigen ipaH7.8 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3683719 L7020 20140222 155864 protein-coding NCBI-supplied PMID: 9722640; 16262782; 20688909; 21352460 MUTATION: espP mutant is attenuated in calves [PMID:17451446]. 2292 putative exoprotein-precursor espP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3683746 L7047 20140215 155864 protein-coding NCBI-supplied PMID: 9722640 MUTATION: hlyC is required for the acylation and therefore activation of the toxin hemolysin which has the ability to lyse several different types of cells [PMID:8793877]. 2293 hemolysin transport protein EHEC-hlyC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3683747 L7048 20130826 155864 protein-coding NCBI-supplied PMID: 9722640 MUTATION: hlyA mutant is attenuated in calves [PMID:15731074]. 2294 hemolysin toxin protein EHEC-hlyA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3685108 SAK_1744 20140329 205921 protein-coding NCBI-supplied PMID: 16172379 MUTATION: pepX mutant is attenuated in rats [PMID:10998175]. 4370 x-prolyl-dipeptidyl aminopeptidase pepX Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3685696 SAK_1750 20140405 205921 protein-coding NCBI-supplied PMID: 16172379 MUTATION: cydA mutant is attenuated in rats [PMID:15813741]. 4371 cytochrome d ubiquinol oxidase, subunit II cydA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3685706 SAK_0893 20140405 205921 protein-coding NCBI-supplied PMID: 16172379 MUTATION: murF mutant is attenuated in rats [PMID:10998175]. 4372 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase murF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3685802 SAK_1080 20130526 205921 protein-coding NCBI-supplied PMID: 16172379 MUTATION: ciaR mutant had a significant decrease in intracellular survival within neutrophils, murine macrophages, and human BMEC [PMID:19114476]. 4373 DNA-binding response regulator CiaR ciaR Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3685804 SAK_0517 20140222 205921 protein-coding NCBI-supplied PMID: 16172379 MUTATION: C protein alpha antigen mutant is attenuated in mice [PMID:9371832]. 4374 C protein alpha-antigen SAK_0517 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3685811 SAK_1319 20140215 205921 protein-coding NCBI-supplied PMID: 16172379 MUTATION: lmb mutant has reduced invasion of human brain microvascular endothelial cells compared to the wildtype [PMID:17400016]. 4375 laminin-binding surface protein lmb Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3686058 SAK_1132 20140405 205921 protein-coding NCBI-supplied PMID: 16172379 MUTATION: carB mutant is attenuated in rats [PMID:10998175]. 4376 carbamoyl phosphate synthase large subunit carB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3686098 SAK_1320 20130526 205921 protein-coding NCBI-supplied PMID: 16172379 MUTATION: scpB mutant had significantly reduced invasion of HEp2 and A549 human cell lines [PMID:11953377]. 4377 C5a peptidase ScpB scpB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3686142 SAK_1022 20140222 205921 protein-coding NCBI-supplied PMID: 16172379 MUTATION: lepA mutant is attenuated in rats [PMID:10998175]. 4378 GTP-binding protein LepA lepA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3686267 SAK_1703 20140405 205921 protein-coding NCBI-supplied PMID: 16172379 MUTATION: scrB mutant is attenuated in rats [PMID:10998175]. 4379 sucrose-6-phosphate hydrolase scrB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3686398 SAK_0156 20140405 205921 protein-coding NCBI-supplied PMID: 16172379 MUTATION: rpoE mutant is attenuated in rats [PMID:16513739]. 4380 DNA-directed RNA polymerase subunit delta rpoE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3686453 SAK_1263 20140329 205921 protein-coding NCBI-supplied PMID: 16172379 MUTATION: An isogenic strain bearing a kanamycin insertion in mtaR (cpsY) was attenuated for survival in a neonatal-rat model of sepsis and grew poorly in human plasma [PMID:14594832]. 4381 CpsY family transcriptional regulator cpsY Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3686784 SAK_1081 20140405 205921 protein-coding NCBI-supplied PMID: 16172379 MUTATION: pepN mutant is attenuated in rats [PMID:10998175]. 4382 aminopeptidase pepN Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3686789 SAK_0797 20130526 205921 protein-coding NCBI-supplied PMID: 16172379 MUTATION: cylE mutant has decreased invasion of lung epithelial cells [PMID:11807693]. 4383 CylE protein cylE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3686928 SAK_1062 20140322 205921 protein-coding NCBI-supplied PMID: 16172379 MUTATION: guaA mutant is attenuated in rats [PMID:10998175]. 4384 glutamine-hydrolyzing Other designations: GMP synthase guaA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3687119 SAK_0863 20140222 205921 protein-coding NCBI-supplied PMID: 16172379; 19383708 MUTATION: lgt mutant has a significant reduction in adherence to human endothelial cells of fetal origin [PMID:19383708]. 4385 prolipoprotein diacylglyceryl transferase lgt Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3690536 BURPS1710b_1867 20140329 320372 I protein-coding NCBI-supplied MUTATION: aroC mutant is attenuated in mice [PMID:19323044]. 1973 chorismate synthase aroC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3690587 BURPS1710b_3318 20140329 320372 I protein-coding NCBI-supplied MUTATION: pabB mutant is attenuated in mice [PMID:19121696]. 1974 chorismate binding protein pabB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3693839 BURPS1710b_A0427 20140329 320372 II protein-coding NCBI-supplied MUTATION: sctU mutant is attenuated in mice [PMID:15621426]. 1970 type III secretion system protein HrcU sctU Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3694081 BURPS1710b_A0562 20130617 320372 II protein-coding NCBI-supplied MUTATION: BopA mutant was attenuated in mice [PMID:16714590]. 1971 BopA protein bopA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3694226 BURPS1710b_A0680 20140329 320372 II protein-coding NCBI-supplied MUTATION: sctU mutant is attenuated in mice [PMID:15621426]. 1972 type III secretion system protein HrcU sctU Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3707508 VACWR051 20140405 10245 protein-coding NCBI-supplied PMID: 19052096 temporal expression: early Other designations: EEV maturation protein F12L Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3707532 VACWR134 20140406 10245 protein-coding NCBI-supplied hydrophobic IMV membrane protein A14.5L Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3707550 VACWR094 20140215 10245 protein-coding NCBI-supplied PMID: 17062140; 17065088 temporal expression: early Other designations: thymidine kinase J2R Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3707557 VACWR101 20140222 10245 protein-coding NCBI-supplied temporal expression: late Other designations: IMV heparin binding surface protein H3L Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3707571 VACWR115 20140406 10245 protein-coding NCBI-supplied PMID: 17283339; 19210265; 20639534 temporal expression: late Other designations: contains mutT-like motif of NTP-phosphohydrolase for DNA repair D10R Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3707582 VACWR205 20130525 10245 protein-coding NCBI-supplied MUTATION: C12L mutant is attenuated in BALB/c mice when infected intranasally [PMID:12388820]. 1909 temporal expression: early Other designations: serine protease inhibitor-like SPI-1 C12L Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3707592 VACWR059 20130525 10245 protein-coding NCBI-supplied PMID: 17959656; 17984076; 18502465; 18715932; 19369349; 20519457; 21957283; 22174864; 22419806 MUTATION: VVDeltaE3L mutant is apathogenic in mice [PMID:11134298]. 1910 temporal expression: early Other designations: double-strand RNA-binding protein E3L Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3707601 VACWR068 20140406 10245 protein-coding NCBI-supplied PMID: 22171261 Hypothetical protein O1L Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3707643 VACWR028 20140215 10245 protein-coding NCBI-supplied PMID: 16387679; 17123957; 17485524; 22013032; 22194685 MUTATION: Deletion of N1L results in attenuation in culture and in intracranially infected mice [PMID:20441222]. 1911 temporal expression: early/late Other designations: putative virulence factor N1L Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3707644 VACWR029 20140222 10245 protein-coding NCBI-supplied temporal expression: early Other designations: putative alpha aminitin-sensitive protein N2L Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3707652 VACWR181 20140222 10245 protein-coding NCBI-supplied PMID: 19036815; 21715594; 21901096 temporal expression: early/late Other designations: hemagglutinin A56R Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3707658 VACWR187 20140215 10245 protein-coding NCBI-supplied PMID: 20378144 temporal expression: early/late Other designations: EEV membrane glycoprotein B5R Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3707660 VACWR189 20121122 10245 protein-coding NCBI-supplied hypothetical protein B7R Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3707661 VACWR190 20140222 10245 protein-coding NCBI-supplied temporal expression: early Other designations: soluble interferon-gamma receptor-like protein B8R Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3707687 VACWR157 20140215 10245 protein-coding NCBI-supplied PMID: 17553539; 18094183; 18094186; 23255618 temporal expression: late Other designations: IEV and EEV membrane glycoprotein A34R Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3707688 VACWR158 20130525 10245 protein-coding NCBI-supplied PMID: 19828608; 19954808 hypothetical protein A35R Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3707689 VACWR159 20140406 10245 protein-coding NCBI-supplied PMID: 19052096; 20093437; 20195521; 21915095; 22980329; 22980331 temporal expression: early/late Other designations: IEV transmembrane phosphoprotein A36R Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3707698 VACWR168 20130724 10245 protein-coding NCBI-supplied putative type-I membrane glycoprotein A43R Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3707702 VACWR172 20140222 10245 protein-coding NCBI-supplied PMID: 22593572 MUTATION: Vaccinia virus lacking the A46R gene was attenuated in a murine intranasal model [PMID:15767367]. 1913 Toll/IL1-receptor A46R Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3707710 VACWR179 20130525 10245 protein-coding NCBI-supplied secreted TNF-receptor-like protein A53R Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3773132 HRCV_s3gp1 20140222 36427 protein-coding NCBI-supplied PMID: 8091676 MUTATION: Reassortant viruses with the RRV VP4 entered cultured mouse cholangiocytes more efficiently than did those with UK VP4 [PMID:21191030]. 3032 outer capsid spike protein VP4 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3776469 SDY_P013 20140406 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: ospF mutants had reduced PMN transepithelial migration when compared to wild-type infection, PMN transepithelial migration is necessary for virulence of Shigella [PMID:16988276]. 1484 OspF ospF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3776481 SDY_P025 20140406 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: ipgB2 mutant had entry into polarized cells reduced by 70% compared to the wild-type [PMID:18316224]. 1485 probably secreted by the Mxi-Spa secretion machinery Other designations: IpgB2 ipgB2 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3776491 SDY_P211 20140406 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: virA mutants did not move within the host cytoplasm and failed to move into adjacent cells [PMID:17095701]. 1486 secreted by the Mxi-Spa secretion machinery Other designations: VirA virA Bin Zhao, Oliver He virG WEB: http://www.ncbi.nlm.nih.gov/gene 3776494 SDY_P214 20140406 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: virG mutants are able to replicate in cells, but cell to cell spread is attenuated in monkey kidney epithelial cells [PMID:2644195]. 1487 VirG; outermembrane protein exposed to the bacterial surface by a C-terminal autotransporter domain and involved in the movement of intracellular bacteria by binding to N-WASP - Other designations: IcsA icsA Bin Zhao, Oliver He sopA WEB: http://www.ncbi.nlm.nih.gov/gene 3776504 SDY_P224 20140406 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: sopA mutant was able to infect HeLa cells, but was attenuated in its ability to spread to other cells compared to the wild type [PMID:9076742]. 1488 SopA; outermembrane protease of the OmpP family, involved in cleavage of surface exposed IcsA - Other designations: outer membrane protease icsP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3776506 SDY_P189 20130616 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: spa32 mutants are unable to invade HeLa cells and do not secrete type III effectors [PMID:11844752]. 1489 secreted by and component of the Mxi-Spa machinery Other designations: Spa32 spa32 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3776507 SDY_P190 20140406 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: spa33 mutants are unable to secrete effectors necessary to cell invasion [PMID:16246841]. 1490 component of the Mxi-Spa secretion machinery Other designations: Spa33 spa33 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3776525 SDY_P169 20130616 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: transposon mutants of ipgA cannot invade epithelial cells and cannot induce keratoconjunctivitis in mice [PMID:8376337]. 1491 similar to IpgE, putative chaperone Other designations: IpgA ipgA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3776526 SDY_P170 20130616 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: icsB mutants are attenuated in guinea pig eyes [PMID:12753186]. 1492 invasion protein Other designations: IcsB icsB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3776527 SDY_P171 20140405 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: ipgD mutant is unable to dephosphorylate phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P2] and induces shorter filapodia in host cells [PMID:12356723]. 1493 secreted by the Mxi-Spa machinery, modulates entry of bacteria into epithelial cells Other designations: IpgD ipgD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3776530 SDY_P174 20140406 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: mxiG mutant was unable to enter HeLa cells and to provoke keratoconjunctivitis in guinea-pigs [PMID:8559065]. 1494 component of the Mxi-Spa secretion machinery, contains one transmembrane segment Other designations: MxiG mxiG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3776531 SDY_P175 20140406 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: mxiH mutants are unable to invade HeLa cells [PMID:11169106]. 1495 component of the Mxi-Spa secretion machinery Other designations: MxiH mxiH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3776532 SDY_P176 20140406 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: mxiI mutant is unable to invade HeLa cells [PMID:11169106]. 1496 component of the Mxi-Spa secretion machinery Other designations: MxiI mxiI Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3776533 SDY_P177 20140406 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: mxiJ mutant was unable to invade HeLa cells, to induce the formation of plaques on confluent monolayers of HeLa cells, and to provoke keratoconjunctivitis in guinea pigs [PMID:1332940]. 1497 lipoprotein, component of the Mxi-Spa secretion machinery Other designations: MxiJ mxiJ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3776534 SDY_P178 20140406 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: mxiK mutants are unable to invade HeLa cells [PMID:12864857]. 1498 putative component of the Mxi-Spa secretion machinery Other designations: MxiK mxiK Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3776535 SDY_P179 20140406 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: mxiN mutants were unable to invade HeLa cells [PMID:12864857]. 1499 putative component of the Mxi-Spa secretion machinery Other designations: MxiN mxiN Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3776537 SDY_P181 20140406 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: mxiM mutants are phenotypically avirulent, and also unable to invade semiconfluent L2 cell monolayers [PMID:10085046]. 1500 lipoprotein, component of the Mxi-Spa secretion machinery Other designations: MxiM mxiM Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3776538 SDY_P182 20140406 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: mxiE deletion mutants are unable to block apoptosis of host epithelial cells [PMID:17339354]. 1501 similar to transcriptional activators of the AraC family Other designations: MxiE mxiE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3776539 SDY_P183 20140406 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: mxiD mutant is unable to invade HeLa cells or to provoke keratoconjunctivitis in guinea-pigs [PMID:8437520]. 1502 outermembrane protein of the secretin family, component of the Mxi-Spa secretion machinery Other designations: MxiD mxiD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3776540 SDY_P184 20140406 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: mxiC mutant has a 10-fold decrease in efficiency in invading epithelial cells [PMID:19017268]. 1503 secreted by and putative component of the Mxi-Spa secretion machinery, similar to YopN (secreted by the type III secretion machinery of Yersinia enterocoltica) Other designations: MxiC mxiC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3776541 SDY_P185 20140406 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: mxiA mutants were attenuated in invasion of HeLa cells [PMID:2037361]. 1504 innermembrane protein, component of the Mxi-Spa secretion machinery Other designations: MxiA mxiA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3776542 SDY_P186 20140406 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: spa15 mutant was attenuated in entry into epithelial cells compared to the wild-type [PMID:11952903]. 1505 putative component of the Mxi-Spa secretion machinery Other designations: Spa15 spa15 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3776543 SDY_P187 20140406 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: spa47 mutants form needle-less type III structure which is defective, and thus incapable of invasion of host cells [PMID:10921870]. 1506 component of the Mxi-Spa secretion machinery, putative ATPase Other designations: ATP synthase SpaL spa47 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3776546 SDY_P003 20130616 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: ospB mutants had reduced PMN transepithelial migration when compared to wild-type infection, PMN transepithelial migration is necessary for virulence of Shigella [PMID:19017275]. 1507 protein secreted by the Mxi-Spa secretion machinery Other designations: OspB ospB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3776565 SDY_P161 20140222 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: virB mutants have an avirulent phenotype and do not invade host cells [PMID:8385666]. 1508 transcriptional activator required for tanscription of the ipa, mxi, and spa operons Other designations: VirB virB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3776567 SDY_P163 20140406 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: ipaA mutants are attenuated in invasion of HeLa cells [PMID:9184218]. 1509 secreted by the Mxi-Spa machinery, modulates entry of bacteria into epithelial cells Other designations: IpaA ipaA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3776568 SDY_P164 20140406 300267 protein-coding NCBI-supplied PMID: 16275786; 23731655 MUTATION: ipaD mutants are completely unable to invade cultured cells or lyse RBCs [PMID:15731041]. 1510 secreted by the Mxi-Spa machinery, required for entry of bacteria into epithelial cells Other designations: IpaD ipaD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3776569 SDY_P165 20140406 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: ipaC mutants cannot invade cultured cells or lyse red blood cells [PMID:18656530]. 1511 secreted by the Mxi-Spa secretion machinery, required for entry into epithelial cells Other designations: IpaC ipaC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3776570 SDY_P166 20140406 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: ipaB mutant is unable to infect HeLa cells [PMID:20086081]. 1512 secreted by the Mxi-Spa secretion machinery, required for entry into epithelial cells Other designations: IpaB ipaB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3776571 SDY_P167 20140222 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: ipgC mutant attenuated in infecting Caco-2 cells monolayer [PMID:11207551]. 1513 cytoplasmic chaperone for IpaB and IpaC Other designations: IpgC ipgC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3776572 SDY_P168 20140406 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: The invasiveness of the ipgB1 mutant was decreased to less than 50% of the wild-type level (100%) in a gentamicin protection or plaque forming assay [PMID:15849186]. 1514 secreted by the Mxi-Spa machinery Other designations: IpgB1 ipgB1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3776601 SDY_P099 20140405 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: ipaH9.8 deletion mutant caused more severe inflammatory responses with increased pro-inflammatory cytokine production levels than did wild-type Shigella, which resulted in a 30-fold decrease in bacterial colonization in murine lungs [PMID:15950937]. 1515 secreted by the Mxi-Spa secretion machinery Other designations: invasion plasmid antigen ipaH9.8 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3776603 SDY_P101 20140405 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: Upon infection of ileal loops in rabbits, the ospG mutant induced a stronger inflammatory response than the wild-type strain, indicating that OspG negatively controls the host innate response induced by S. flexneri upon invasion of the epithelium [PMID:16162672]. 1516 secreted by the Mxi-Spa secretion machinery Other designations: OspG ospG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3776611 SDY_P109 20130616 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: virK mutants have attenuated ability for intracellular spreading in host cells [PMID:15664968]. 1517 required for proper localization of IcsA (VirG) at the surface of bacteria Other designations: VirK virK Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3776622 SDY_P140 20140406 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: ipaH mutant is attenuated in mice [PMID:17214743]. 1518 invasion plasmid antigen, fragment ipaH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3776637 SDY_P038 20140406 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: ipaH7.8 mutants had a lower rate of exit from the endocytic vacuoles into the cytoplasm in mouse macrophages than the wild-type strain [PMID:10816519]. 1519 probably secreted by the Mxi-Spa machinery Other designations: invasion plasmid antigen ipaH7.8 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3776645 SDY_P046 20130616 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: ospE mutants had attenuated adhesion to HeLa cells than the wild-type [PMID:19489119]. 1520 secreted by the Mxi-Spa secretion machinery Other designations: OspE1 ospE1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3776650 SDY_P055 20140406 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: ospC1 mutants had reduced PMN transepithelial migration when compared to wild-type infection, PMN transepithelial migration is necessary for virulence of Shigella [PMID:16988276]. 1521 secreted by the Mxi-Spa secretion machinery Other designations: OspC1 ospC1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3776651 SDY_P056 20140406 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: sen deletion mutant elicited lower rises in mucosal short-circuit current than the wild type, suggesting that the senA/ospD3 gene encodes an enterotoxin of Shigella [PMID:7591128]. 1522 SenA; probably secreted by the Mxi-Spa secretion machinery Other designations: OspD3 ospD3 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3776711 SBO_P113 20140406 300268 protein-coding NCBI-supplied PMID: 16275786 MUTATION: ipaH9.8 deletion mutant caused more severe inflammatory responses with increased pro-inflammatory cytokine production levels than did wild-type Shigella, which resulted in a 30-fold decrease in bacterial colonization in murine lungs [PMID:15950937]. 1545 secreted by the Mxi-Spa secretion machinery Other designations: invasion plasmid antigen ipaH9.8 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3776716 SBO_P118 20140222 300268 protein-coding NCBI-supplied PMID: 16275786 MUTATION: virK mutants have attenuated ability for intracellular spreading in host cells [PMID:15664968]. 1546 required for proper localization of IcsA (VirG) at the surface of bacteria Other designations: VirK protein virK Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3776752 SBO_P005 20121017 300268 protein-coding NCBI-supplied PMID: 16275786 MUTATION: ospB mutants had reduced PMN transepithelial migration when compared to wild-type infection, PMN transepithelial migration is necessary for virulence of Shigella [PMID:19017275]. 1547 protein secreted by the Mxi-Spa secretion machinery Other designations: OspB ospB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3776764 SBO_P017 20140222 300268 protein-coding NCBI-supplied PMID: 16275786 MUTATION: ospF mutants had reduced PMN transepithelial migration when compared to wild-type infection, PMN transepithelial migration is necessary for virulence of Shigella [PMID:16988276]. 1548 OspF ospF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3776781 SBO_P033 20140222 300268 protein-coding NCBI-supplied PMID: 16275786 MUTATION: ipgB2 mutant had entry into polarized cells reduced by 70% compared to the wild-type [PMID:18316224]. 1549 probably secreted by the Mxi-Spa secretion machinery Other designations: IpgB2 ipgB2 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3776800 SBO_P052 20140406 300268 protein-coding NCBI-supplied PMID: 16275786 MUTATION: virF knockouts are non-invasive to host cells [PMID:20237205]. 1550 member of the AraC family of transcriptional activators; required for transcription of virB and icsA Other designations: VirF virF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3776815 SBO_P067 20140406 300268 protein-coding NCBI-supplied PMID: 16275786 MUTATION: ipaH7.8 mutants had a lower rate of exit from the endocytic vacuoles into the cytoplasm in mouse macrophages than the wild-type strain [PMID:10816519]. 1551 probably secreted by the Mxi-Spa machinery Other designations: invasion plasmid antigen ipaH7.8 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3776824 SBO_P076 20140406 300268 protein-coding NCBI-supplied PMID: 16275786 MUTATION: sen deletion mutant elicited lower rises in mucosal short-circuit current than the wild type, suggesting that the senA/ospD3 gene encodes an enterotoxin of Shigella [PMID:7591128]. 1552 SenA; probably secreted by the Mxi-Spa secretion machinery Other designations: OspD3 ospD3 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3776825 SBO_P077 20140222 300268 protein-coding NCBI-supplied PMID: 16275786 MUTATION: ospC1 mutants had reduced PMN transepithelial migration when compared to wild-type infection, PMN transepithelial migration is necessary for virulence of Shigella [PMID:16988276]. 1553 secreted by the Mxi-Spa secretion machinery, function unknown Other designations: OspC1 ospC1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3779009 SBO_0134 20140222 300268 protein-coding NCBI-supplied PMID: 12117952; 16275786 MUTATION: dksA mutants are able to invade cultured cell monlayers but are incapable of cell to cell spread [PMID:11500451]. 1554 RNA polymerase-binding transcription factor dksA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3779925 SBO_0042 20140406 300268 protein-coding NCBI-supplied PMID: 12117952; 16275786 MUTATION: surA mutant is able to infect epithelial cells but is incapable of cell to cell spread [PMID:20447864]. 1555 peptidyl-prolyl cis-trans isomerase SurA surA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3780421 SBO_1438 20140405 300268 protein-coding NCBI-supplied PMID: 12117952; 16275786 MUTATION: aroD deletion led to attenuation in HeLa cells and monkeys [PMID:8356844]. 1556 3-dehydroquinate dehydratase aroD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3780458 SBO_1475 20121017 300268 protein-coding NCBI-supplied PMID: 12117952; 16275786 MUTATION: sodB mutant is extremely sensitive to killing by phagocytes compared to the wild-type, and causes only mild damage in infection of rabbit ileal loops [PMID:2404874]. 1557 superoxide dismutase sodB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3780674 SBO_1691 20140405 300268 protein-coding NCBI-supplied PMID: 12117952; 16275786 MUTATION: sitA mutant is attenuated in mice [PMID:19289511]. 1558 Iron transport protein, periplasmic-binding protein sitA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3780796 SBO_1813 20140222 300268 protein-coding NCBI-supplied PMID: 12117952; 16275786 MUTATION: tonB mutant is able to invade epithelial cells but is incapable of cell to cell spread [PMID:11035742]. 1559 energy transducer; uptake of iron, cyanocobalimin; sensitivity to phages, colicins Other designations: transporter tonB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3780892 SBO_1909 20130406 300268 protein-coding NCBI-supplied PMID: 12117952; 16275786 MUTATION: phoP mutants were resolved more quickly than wild type in animal models, and are more susceptible to killing by PMNs [PMID:11207599]. 1560 DNA-binding transcriptional regulator PhoP phoP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3781075 SBO_2092 20140215 300268 protein-coding NCBI-supplied PMID: 12117952; 16275786 MUTATION: ompC mutants were attenuated in their ability to spread cell to cell and kill epithelial cells, and had a negative Sereny test [PMID:8359885]. 1561 outer membrane porin protein C ompC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3781177 SBO_2194 20140405 300268 protein-coding NCBI-supplied PMID: 12117952; 16275786 MUTATION: aroA deletion mutants are attenuated in HeLa cells [PMID:8757833]. 1562 3-phosphoshikimate 1-carboxyvinyltransferase aroA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3781371 SBO_2388 20121017 300268 protein-coding NCBI-supplied PMID: 12117952; 16275786 MUTATION: vacJ mutants are incapable of intercellular spread of epithelial cells [PMID:8145644]. 1563 lipoprotein vacJ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3781514 SBO_2531 20140405 300268 protein-coding NCBI-supplied PMID: 12117952; 16275786 MUTATION: guaAguaB mutants are attenuated in HeLa cells [PMID:8757833]. 1564 glutamine-hydrolyzing Other designations: GMP synthase guaA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3781515 SBO_2532 20140405 300268 protein-coding NCBI-supplied PMID: 12117952; 16275786 MUTATION: guaAguaB mutants are attenuated in HeLa cells [PMID:8757833]. 1565 inosine 5'-monophosphate dehydrogenase guaB Bin Zhao, Oliver He ompB WEB: http://www.ncbi.nlm.nih.gov/gene 3782374 SBO_3391 20140222 300268 protein-coding NCBI-supplied PMID: 12117952; 16275786 MUTATION: envZ insertion mutant is able to invade cells but has decreased virulence due to the inability to survive intracellularly [PMID:2121709]. 1566 protein histidine kinase/phosphatase sensor for OmpR, modulates expression of ompF and ompC - Other designations: osmolarity sensor protein envZ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3782375 SBO_3392 20140215 300268 protein-coding NCBI-supplied PMID: 12117952; 16275786 MUTATION: mutant of the ompB locus (both the envZ and ompR genes) showed attenuated virulence in HeLa cells, and a weak response to a Serany test [PMID:2121709]. 1567 response regulator (sensor, EnvZ) affecting transcription of ompC and ompF: outer membrane protein synthesis Other designations: osmolarity response regulator ompR Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3782854 SBO_3871 20140406 300268 protein-coding NCBI-supplied PMID: 12117952; 16275786 MUTATION: yihE mutant is unable to cause keratoconjunctivitis in guinea pigs [PMID:15073317]. 1568 serine/threonine protein kinase yihE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3783260 SBO_4277 20140406 300268 protein-coding NCBI-supplied PMID: 12117952; 16275786 MUTATION: vacB mutants had attenuated invasion of MK2 cells compared to the wild-type strain [PMID:1400189]. 1569 exoribonuclease R vacB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3783267 SBO_4284 20140222 300268 protein-coding NCBI-supplied PMID: 12117952; 16275786 MUTATION: hfq deletion mutants are attenuated in guinea pig eye infection model (Sereny test) [PMID:20080057]. 1570 a growth-related protein Other designations: RNA-binding protein Hfq hfq Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3783268 SBO_4285 20140406 300268 protein-coding NCBI-supplied PMID: 12117952; 16275786 MUTATION: miaA mutants had reduced ability to invade and spread in MK2 cell monolayers compared to the wildtype [PMID:9294434]. 1571 tRNA delta(2)-isopentenylpyrophosphate transferase miaA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3783320 SBO_4337 20140405 300268 protein-coding NCBI-supplied PMID: 12117952; 16275786 MUTATION: iuc mutants are attenuated in chicken embryos and rabbit ileal loops [PMID:19130265]. 1572 siderophore biosynthesis protein iucA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3783321 SBO_4338 20140329 300268 protein-coding NCBI-supplied PMID: 12117952; 16275786 MUTATION: iuc mutants are attenuated in chicken embryos and rabbit ileal loops [PMID:19130265]. 1573 siderophore biosynthesis protein iucB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3783322 SBO_4339 20140405 300268 protein-coding NCBI-supplied PMID: 12117952; 16275786 MUTATION: iuc mutants are attenuated in chicken embryos and rabbit ileal loops [PMID:19130265]. 1574 siderophore biosynthesis protein iucC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3783323 SBO_4340 20140405 300268 protein-coding NCBI-supplied PMID: 12117952; 16275786 MUTATION: iuc mutants are attenuated in chicken embryos and rabbit ileal loops [PMID:19130265]. 1575 lysine:N6-hydroxylase iucD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3783324 SBO_4341 20130406 300268 protein-coding NCBI-supplied PMID: 12117952; 16275786 MUTATION: mutants of the iuc locus and the aerobactin receptor, iutA were attenuated in chicken embryos [PMID:3028962] . 1576 ferric siderophore receptor iutA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3786978 BAB1_0188 20140405 359391 I protein-coding NCBI-supplied PMID: 16299333 B12-dependent methionine synthase metH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3787092 BAB1_0316 20140405 359391 I protein-coding NCBI-supplied PMID: 16299333 glucose-6-phosphate isomerase pgi Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3787589 BAB1_0917 20130511 359391 I protein-coding NCBI-supplied PMID: 16299333 trigger factor tig Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3787776 BAB1_1128 20130702 359391 I protein-coding NCBI-supplied PMID: 16299333 excinuclease ABC subunit A uvrA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3787973 BAB1_1409 20140405 359391 I protein-coding NCBI-supplied PMID: 16299333 tRNA delta(2)-isopentenylpyrophosphate transferase miaA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3788256 BAB1_1742 20140405 359391 I protein-coding NCBI-supplied PMID: 16299333 MUTATION: A pgk mutant is attenuated in mice [PMID:20194591]. 4958 phosphoglycerate kinase pgk Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3788622 BAB1_0454 20140405 359391 I protein-coding NCBI-supplied PMID: 16299333 chorismate synthase aroC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3788626 BAB1_1514 20140405 359391 I protein-coding NCBI-supplied PMID: 16299333 MUTATION: aspC encodes for an aminotransferase. B.abortus aspC mutant obtained from randomized miniTn5Km2 transposon mutagenesis showed decreased intracellular survival inside HeLa cells. So B. abortus aspC gene is essential for HeLa cell intracellular growth [PMID:12761078]. 1710 aspartate aminotransferase aspC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3788635 BAB1_0402 20121017 359391 I protein-coding NCBI-supplied PMID: 16299333 MUTATION: B abortus bacA mutant exhibited decreased survival in macrophages and greatly accelerated clearance from experimentally infected mice compared to the virulent parental strain [PMID:10741969]. R meliloti bacA gene encodes a putative cytoplasmic membrane transport protein required for symbiosis [PMID:10741969]. The BacA protein is essential for the long-term survival of Sinorhizobium meliloti and Brucella abortus within acidic compartments in plant and animal cells , respectively. Mutation study showed that B. abortus BacA affects the distribution of LPS fatty acids, including a very-long-chain fatty acid thought to be unique to the alpha-proteobacteria[PMID:10741969]. 1711 transporter bacA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3788677 BAB1_0181 20140406 359391 I protein-coding NCBI-supplied PMID: 16299333 nitrite/sulfite reductase ferredoxin subunit cysI Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3788687 BAB1_1687 20140405 359391 I protein-coding NCBI-supplied PMID: 16299333 deoxyuridine 5'-triphosphate nucleotidohydrolase dut Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3788725 BAB1_1023 20140405 359391 I protein-coding NCBI-supplied PMID: 16299333 MUTATION: A study with miniTn5 mutants of B. suis constitutively expressing gfp indicates that B. suis glnA gene is required for intracellular multiplication in human macrophage THP-1 cells [PMID:12438693]. 1714 glutamine synthetase glnA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3788728 BAB1_1286 20140217 359391 I protein-coding NCBI-supplied PMID: 16299333 glyoxalase/bleomycin resistance protein/dioxygenase gloA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3788734 BAB1_0787 20140405 359391 I protein-coding NCBI-supplied PMID: 16299333 serine hydroxymethyltransferase glyA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3788735 BAB1_0545 20140406 359391 I protein-coding NCBI-supplied PMID: 16299333 MUTATION: gmd may be involved in perosamine synthesis. It has been shown to be in LPS synthesis since its B. melitensis mutation induces rough phenotype [PMID:15099501]. 1717 short-chain dehydrogenase gmd Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3788748 BAB1_1134 20130702 359391 I protein-coding NCBI-supplied PMID: 16299333 RNA-binding protein Hfq hfq Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3788751 BAB1_1988 20140405 359391 I protein-coding NCBI-supplied PMID: 16299333 histidinol-phosphate aminotransferase hisC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3788752 BAB1_0285 20140405 359391 I protein-coding NCBI-supplied PMID: 16299333 histidinol dehydrogenase hisD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3788754 BAB1_2086 20140405 359391 I protein-coding NCBI-supplied PMID: 16299333 imidazole glycerol phosphate synthase subunit HisF hisF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3788755 BAB1_1986 20140405 359391 I protein-coding NCBI-supplied PMID: 16299333 phosphoribosyltransferase hpt Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3788763 BAB1_0096 20140405 359391 I protein-coding NCBI-supplied PMID: 16299333 dihydroxy-acid dehydratase ilvD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3788771 BAB1_1583 20140406 359391 I protein-coding NCBI-supplied PMID: 16299333 2-isopropylmalate synthase leuA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3788772 BAB1_1905 20140405 359391 I protein-coding NCBI-supplied PMID: 16299333 isopropylmalate isomerase large subunit leuC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3788788 BAB1_1984 20140405 359391 I protein-coding NCBI-supplied PMID: 16299333 MUTATION: A study with miniTn5 mutants of B. suis constitutively expressing gfp indicates that B. suis lysA gene is required for intracellular multiplication in human macrophage THP-1 cells [PMID:12438693]. 1726 diaminopimelate decarboxylase lysA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3788792 BAB1_0562 20111201 359391 I pseudo NCBI-supplied MUTATION: a manAB double mutant is attenuated in mice [PMID:16790778]. 4957 pseudo manA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3788817 BAB1_1140 20140222 359391 I protein-coding NCBI-supplied PMID: 16299333 MUTATION: ntrC encodes for a response regulator subfamily (NtrC). A B suis ntrC isogenic mutant was constructed which showed no significant differences in growth rates compared to the wild-type strain when grown at different temperatures in vitro. However, the mutant exhibited a reduction in metabolic activity in the presence of many amino acids. The mutation did not affect survival or multiplication of B suis in macrophages, but during the initial stages of infection in the murine brucellosis model, the ntrC mutant showed a reduced ability to multiply rapidly in splenic tissue [PMID:10373105]. 1727 response regulator receiver ntrC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3788818 BAB1_1139 20130508 359391 I protein-coding NCBI-supplied PMID: 16299333; 22582926 MUTATION: The NtrY protein is a sensor of an ntr-related regulon which may be part of the glnALG operon. This mutant has a weakly attenuated phenotype (reduction of 1.2 log units versus the wild type at 48 h postinfection) which could be explained by a pleiotropic effect on the ntr regulon, since the ntrC mutant did not show such a phenotype [PMID:10678941]. 1728 PAS/histidine kinase/ATPase domain-containing protein ntrY Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3788831 BAB1_1930 20140406 359391 I protein-coding NCBI-supplied PMID: 16299333; 18761420 lipoprotein Omp19 omp19 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3788843 BAB1_0641 20140405 359391 I protein-coding NCBI-supplied PMID: 16299333 MUTATION: A single mutation of PepN leads to a significant decrease in the growth rate, thus PepN seems to play a more prominent role than do the other proteases [PMID:12933870]. 1730 aminopeptidase N pepN Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3788847 BAB1_0055 20140405 359391 I protein-coding NCBI-supplied PMID: 16299333 MUTATION: Brucella pgm encodes the phosphoglucomutase. The B. abortus pgm mutant (B2211) lacks the O antigen. However, the core region of the mutant LPS migrated in Tricine-PAGE electrophoresis in a position that was indistinguishable from that of the wild type core. Although the exponential intracellular replication of the pgm mutant was delayed by approximately 20 h with respect to that of the wild type, the high number of recoverable bacteria at 48 h postinfection indicates that mutant strain B2211 replicates inside HeLa host cells [PMID:10992476]. B abortus phosphoglucomutase (pgm) insertional mutants were attenuated in vivo but not in vitro [PMID:10992476]. 1731 phosphoglucomutase pgm Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3788850 BAB1_0034 20140329 359391 I protein-coding NCBI-supplied PMID: 16299333 MUTATION: The product of pheA gene is specifically dedicated to the biosynthesis of phenylalanine. The B. abortus pheA mutant with mini-Tn5 disruption displays nutritional defects in vitro. Experimental findings with the B abortus ilvD, trpB, and pheA mutants suggest that tryptophan and phenylalanine are available to the brucellae in their intracellular niche but that other amino acids (eg, leucine, isoleucine, or valine) are not. The pheA::miniTn5 mutant displayed attenuation in macrophages but not in mice [PMID:15271960]. 1732 prephenate dehydratase pheA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3788869 BAB1_1552 20140406 359391 I protein-coding NCBI-supplied PMID: 16299333 peptidyl-tRNA hydrolase pth Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3788874 BAB1_0442 20140322 359391 I protein-coding NCBI-supplied PMID: 16299333 phosphoribosylamine--glycine ligase purD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3788875 BAB1_0472 20140405 359391 I protein-coding NCBI-supplied PMID: 16299333 MUTATION: A B. suis purF mutation experiment suggests that the purine biosynthesis pathway contributes to intracellular growth [PMID:12761078]. 1735 amidophosphoribosyltransferase purF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3788876 BAB1_1824 20140405 359391 I protein-coding NCBI-supplied PMID: 16299333 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase purH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3788878 BAB1_0731 20140405 359391 I protein-coding NCBI-supplied PMID: 16299333 phosphoribosylaminoimidazole synthetase purM Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3788879 BAB1_0730 20140405 359391 I protein-coding NCBI-supplied PMID: 16299333 MUTATION: B. abortus purN gene is essential for intracellular growth in HeLa cells as shown from transposon mutagenesis study [PMID:12761078]. 1738 phosphoribosylglycinamide formyltransferase purN Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3788880 BAB1_1791 20140405 359391 I protein-coding NCBI-supplied PMID: 16299333 MUTATION: pyc is one B. suis gene identified by signature-tagged mutagenesis. It is essential for survival and mulitplication in macrophages [PMID:10678941]. 1739 pyruvate carboxylase pyc Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3788883 BAB1_0341 20140405 359391 I protein-coding NCBI-supplied PMID: 16299333 MUTATION: B. suis pyrD mutation study indicated that pyrimidine synthesis pathway contributes to intracellular growth [PMID:12761078]. 1740 dihydroorotate dehydrogenase 2 pyrD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3788897 BAB1_1224 20140406 359391 I protein-coding NCBI-supplied PMID: 16299333 recombinase A recA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3788901 BAB1_0543 20130508 359391 I protein-coding NCBI-supplied PMID: 16299333 acriflavin ABC transporter rfbD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3788922 BAB1_1906 20130702 359391 I protein-coding NCBI-supplied PMID: 16299333 50S ribosomal protein L19 rplS Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3788935 BAB1_1231 20140405 359391 I protein-coding NCBI-supplied PMID: 16299333 DNA-directed RNA polymerase subunit alpha rpoA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3788939 BAB1_0025 20130508 359391 I protein-coding NCBI-supplied PMID: 16299333 MUTATION: rpsA is a B. suis gene identified by signature-tagged mutagenesis [PMID:10678941]. 1745 30S ribosomal protein S1 rpsA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3793454 SAB1216 20140406 273036 protein-coding NCBI-supplied PMID: 17971880 MUTATION: mprF mutant is attenuated in mice [PMID:11342591]. 4386 hypothetical protein mprF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3795442 SDY_2353 20140406 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: aroA deletion mutants are attenuated in HeLa cells [PMID:8757833]. 1523 3-phosphoshikimate 1-carboxyvinyltransferase aroA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3795635 SDY_2550 20140205 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: vacJ mutants are incapable of intercellular spread of epithelial cells [PMID:8145644]. 1524 lipoprotein vacJ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3795792 SDY_0161 20140222 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: dksA mutants are able to invade cultured cell monlayers but are incapable of cell to cell spread [PMID:11500451]. 1525 DnaK transcriptional regulator DksA dksA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3796555 SDY_1389 20140322 300267 protein-coding NCBI-supplied PMID: 16275786 Shiga toxin subunit A stxA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3796556 SDY_1390 20140322 300267 protein-coding NCBI-supplied PMID: 16275786 Shiga toxin subunit B stxB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3796726 SDY_3671 20140215 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: mutant of the ompB locus (both the envZ and ompR genes) showed attenuated virulence in HeLa cells, and a weak response to a Serany test [PMID:2121709]. 1528 sensor, EnvZ; outer membrane protein synthesis Other designations: osmolarity response regulator ompR Bin Zhao, Oliver He ompB WEB: http://www.ncbi.nlm.nih.gov/gene 3796727 SDY_3672 20140222 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: envZ insertion mutant is able to invade cells but has decreased virulence due to the inability to survive intracellularly [PMID:2121709]. 1529 modulates expression of ompF and ompC - Other designations: osmolarity sensor protein envZ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3796783 SDY_3554 20140215 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: shuA mutant was attenuated in HeLa cells subjected to an iron chelator, DIP to produce iron deficient conditions, suggesting that shuA plays a role in virulence in iron deficient conditions [PMID:16856494]. 1530 outer membrane heme/hemoglobin receptor shuA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3797002 SDY_3886 20140406 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: yihE mutant is unable to cause keratoconjunctivitis in guinea pigs [PMID:15073317]. 1531 serine/threonine protein kinase yihE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3797177 SDY_1022 20140406 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: iroN mutant was attenuated in HeLa cells subjected to an iron chelator, DIP to produce iron deficient conditions, suggesting that iroN plays a role in virulence in iron deficient conditions [PMID:16856494]. 1532 outer membrane receptor FepA iroN Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3797372 SDY_4410 20140406 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: vacB mutants had attenuated invasion of MK2 cells compared to the wild-type strain [PMID:1400189]. 1533 exoribonuclease R vacB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3797379 SDY_4417 20140406 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: hfq deletion mutants are attenuated in guinea pig eye infection model (Sereny test) [PMID:20080057]. 1534 a growth-related protein Other designations: RNA-binding protein Hfq hfq Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3797380 SDY_4418 20140406 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: miaA mutants had reduced ability to invade and spread in MK2 cell monolayers compared to the wildtype [PMID:9294434]. 1535 tRNA delta(2)-isopentenylpyrophosphate transferase miaA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3797994 SDY_1474 20140406 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: aroD deletion led to attenuation in HeLa cells and monkeys [PMID:8356844]. 1536 3-dehydroquinate dehydratase aroD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3798221 SDY_1882 20121017 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: sodB mutant is extremely sensitive to killing by phagocytes compared to the wild-type, and causes only mild damage in infection of rabbit ileal loops [PMID:2404874]. 1537 superoxide dismutase sodB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3798748 SDY_1316 20140406 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: tonB mutant is able to invade epithelial cells but is incapable of cell to cell spread [PMID:11035742]. 1538 energy transducer; uptake of iron, cyanocobalimin; sensitivity to phages, colicins Other designations: transporter tonB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3798805 SDY_2703 20140406 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: guaAguaB mutants are attenuated in HeLa cells [PMID:8757833]. 1539 GMP synthase guaA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3798806 SDY_2704 20140406 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: guaAguaB mutants are attenuated in HeLa cells [PMID:8757833]. 1540 inosine 5'-monophosphate dehydrogenase guaB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3798958 SDY_0078 20140406 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: surA mutant is able to infect epithelial cells but is incapable of cell to cell spread [PMID:20447864]. 1541 peptidyl-prolyl cis-trans isomerase SurA surA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3799410 SDY_1457 20140405 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: sitA mutant is attenuated in mice [PMID:19289511]. 1542 iron ABC transporter substrate-binding protein sitA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3799657 SDY_0861 20140405 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: ompC mutants were attenuated in their ability to spread cell to cell and kill epithelial cells, and had a negative Sereny test [PMID:8359885]. 1543 Ib;c Other designations: porin ompC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3799918 SDY_2022 20130406 300267 protein-coding NCBI-supplied PMID: 16275786 MUTATION: phoP mutants were resolved more quickly than wild type in animal models, and are more susceptible to killing by PMNs [PMID:11207599]. 1544 DNA-binding transcriptional regulator PhoP phoP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3827409 BAB2_1098 20140406 359391 II protein-coding NCBI-supplied PMID: 16299333 flagellar hook protein FlgE flgE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3827414 BAB2_1103 20140405 359391 II protein-coding NCBI-supplied PMID: 16299333 flagellar motor protein MotB motB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3827693 BAB2_0584 20130529 359391 II protein-coding NCBI-supplied PMID: 16299333 MUTATION: UgpA is one of the attenuated Signature-Tagged Mutagenesis mutants of Brucella melitensis identified during the acute phase of infection in mice [PMID:14638795]. 1748 binding-protein dependent transport system inner membrane protein ugpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3827694 BAB2_0585 20130529 359391 II protein-coding NCBI-supplied PMID: 16299333 MUTATION: B suis ugpB mutant does not contain SP41 protein. Mutants lacking SP41 production are less invasive, but proliferate in HeLa cells. An isogenic DeltaugpB mutant showed a significant inhibitory effect on Brucella adherence and invasion of human cultured epithelial cells and this effect could be reversed by restoration of the ugpB on a plasmid. [PMID:16817909]. 1749 solute-binding family 1 protein ugpB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3827700 BAB2_1079 20130702 359391 II protein-coding NCBI-supplied PMID: 16299333 MUTATION: Brucella abortus znuA mutant via mini-Tn5Km2 transposon mutagenesis has intracellular growth defect inside HeLa cells [PMID:12761078]. High-affinity zinc uptake system protein mutant (znuA mutant) showed reduced growth in zinc chelated medium, and failed to replicate in HeLa cells and mouse bone marrow-derived macrophages. Transformation of znuA mutant with a shuttle vector pBBR1MCS-4 containing znuA gene restored the growth in zinc chelated medium and intracellular replication in HeLa cells and macrophages to a level comparable to that of wild-type strain. Bacterial internalization into HeLa cells and macrophages and co-localization with either late endosomes or lysosomes of znuA mutant were not different from those of wild-type strain. These results suggest that znuA does not contribute to intracellular trafficking of B abortus, but contributes to utilization of zinc required for intracellular growth [PMID:12761078]. 1750 periplasmic solute binding protein znuA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3827702 BAB2_1080 20130702 359391 II protein-coding NCBI-supplied PMID: 16299333 ABC transporter ATPase znuC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3827703 BAB2_0891 20140222 359391 II protein-coding NCBI-supplied PMID: 16299333 glutaredoxin nrdH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3827823 BAB2_0641 20140405 359391 II protein-coding NCBI-supplied PMID: 16299333 aspartate carbamoyltransferase catalytic subunit pyrB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3827840 BAB2_0535 20140215 359391 II protein-coding NCBI-supplied PMID: 16299333 copper/Zinc superoxide dismutase sodC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3827898 BAB2_0061 20140222 359391 II protein-coding NCBI-supplied PMID: 16299333; 18469100 MUTATION: virB8 mutant was attenuated by a mini-Tn5 transposon mutagenesis [PMID:10678941]. Attenuated non-polar virB2, virB4, virB8, virB9 and virB10 Brucella mutants are capable of penetrating cells as the same rate as the virulent wild-type Brucella, transit through EEA1-positive early compartments and then localize in LAMP1-positive compartments at early times of infection [PMID:10678941]. 1755 virulence protein BAB2_0061 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3827916 BAB2_0475 20130529 359391 II protein-coding NCBI-supplied PMID: 16299333 exodeoxyribonuclease VII large subunit xseA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3827924 BAB2_0904 20140405 359391 II protein-coding NCBI-supplied PMID: 16299333 MUTATION: The narG gene encodes for an essential component of the dissimilatory nitrate reductase complex. This complex is encoded by the narGHIJ locus, which is present in the B suis genome together with the gene of the nitrite extrusion protein, narK. The narG mutant was unable to produce nitrite from nitrate [PMID:12438693]. A study with miniTn5 mutants of B. suis constitutively expressing gfp indicates that B. suis xx gene is required for intracellular multiplication in human macrophage THP-1 cells [PMID:12438693]. 1757 nitrate reductase subunit alpha narG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3827978 BAB2_0064 20130529 359391 II protein-coding NCBI-supplied PMID: 16299333; 18469100 MUTATION: A comparison of the VirB8 and VirB5 contents after induction of the B suis wild type and of virB5 and virB12 mutants further confirmed that the virB5 and virB12 genes belong to the same operon [PMID:12595417]. Smooth strains of Brucella unable to replicate (ie, killed B suis or the avirulent mutant B suis virB5) exhibit delayed phagosome-lysosome fusion [PMID:12595417]. Polar mutations in the operon upstream of virB5 exert a greater effect on the expression of virB5 than they do on the expression of the downstream gene virB12. It indicates that in B abortus , regulatory elements other than the virB promoter may influence VirB12 protein levels [PMID:12595417]. Four independent mutants in virB5, virB9 or virB10 were highly attenuated in an in vitro infection model with human macrophages [PMID:12595417]. 1758 type IV secretion system protein VirB5 BAB2_0064 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3827980 BAB2_0066 20130508 359391 II protein-coding NCBI-supplied PMID: 16299333 MUTATION: The B abortus virB3 gene is found to be essential for intracellular growth inside HeLa cells [PMID:12761078]. 1759 type IV secretion system protein VirB3-like protein BAB2_0066 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3827981 BAB2_0067 20140406 359391 II protein-coding NCBI-supplied PMID: 16299333 MUTATION: The Brucella abortus virB operon, encoding a type IV secretion system (T4SS), is required for intracellular replication and persistent infection in the mouse model. The products of the first two genes of the virB operon, virB1 and virB2, are predicted to be localized at the bacterial surface. Both mutants were shown to be nonpolar, as demonstrated by their ability to express the downstream gene virB5 during stationary phase of growth in vitro. Both VirB1 and VirB2 were essential for intracellular replication in J774 macrophages. The nonpolar virB2 mutant was unable to cause persistent infection in the mouse model, demonstrating the essential role of VirB2 in the function of the T4SS apparatus during infection [PMID:15322008]. Polar mutations in the virB1 to virB2 intergenic region or in virB2 reduced the detection of VirB5 to a greater extent than they did that of VirB12. A virB1 mutation also eliminates the transcription of virB12 in B suis [PMID:15322008]. 1760 type IV secretion system protein VirB2 BAB2_0067 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3828036 BAB2_0076 20121228 359391 II protein-coding NCBI-supplied PMID: 16299333 lipoprotein Omp10 omp10 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3828142 BAB2_0727 20140405 359391 II protein-coding NCBI-supplied PMID: 16299333; 22919638 MUTATION: cydB is a gene that is part of the cydAB operon encoding cytochrome bd oxidase , which catalyzes an alternate terminal electron transport step in bacterial respiration. Transposon (Tn5) mutagenesis of B abortus cydB was severely attenuated for intracellular survival. Unlike the virulent strain 2308, the Brucella cydB::Tn5 mutant was severely compromised for survival in the spleens of inoculated mice [PMID:11274104]. The cydB and cydD mutants are also defective for the intracellular growth of B abortus and B suis, suggesting that functional cytochrome bd oxidase is required for growth in an intracellular environment [PMID:11274104]. 1762 cytochrome bd ubiquinol oxidase subunit II cydB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3828149 BAB2_0628 20130702 359391 II protein-coding NCBI-supplied PMID: 16299333 response regulator receiver divK Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3828215 BAB2_0153 20120329 359391 II pseudo NCBI-supplied pseudo flgI Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3828216 BAB2_0154 20120329 359391 II pseudo NCBI-supplied pseudo flgI Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3828220 BAB2_1105 20140215 359391 II protein-coding NCBI-supplied PMID: 16299333 flagellar MS-ring protein fliF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3828233 BAB2_0515 20140405 359391 II protein-coding NCBI-supplied PMID: 16299333 glycine dehydrogenase gcvP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3828234 BAB2_0513 20140405 359391 II protein-coding NCBI-supplied PMID: 16299333 MUTATION: A study with miniTn5 mutants of B. suis constitutively expressing gfp indicates that B. suis gcvT gene is required for intracellular multiplication in human macrophage THP-1 cells [PMID:12438693]. 1768 glycine cleavage system aminomethyltransferase T gcvT Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3828238 BAB2_0796 20120329 359391 II pseudo NCBI-supplied pseudo glpK Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3828240 BAB2_0054 20140405 359391 II protein-coding NCBI-supplied PMID: 16299333 MUTATION: gltD encodes the small subunit of glutamate synthase. It is required for B. abortus growth as shown in signature-tagged transposon mutagenesis. It suggests that glutamate may serve as carbon and/or nitrogen sources during growth of B abortus [PMID:10858227]. 1770 glutamate synthase subunit beta gltD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3828241 BAB2_0109 20140405 359391 II protein-coding NCBI-supplied PMID: 16299333 MUTATION: gnd is involved in pentose phosphate pathway. It is essential for intracellular growth inside HeLa cells as shown by its Brucella suis miniTn5Km2 transposon mutation analysis. The mutant is attenuated in the mouse model [PMID:12761078]. 1771 6-phosphogluconate dehydrogenase gnd Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3828247 BAB2_0075 20140322 359391 II protein-coding NCBI-supplied PMID: 16299333 ferrochelatase hemH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3829299 pCoo056 20140410 562 protein-coding NCBI-supplied PMID: 16159784 MUTATION: interruption of the eatA gene retarded fluid accumulation in the rabbit ileal loop model, suggesting that this autotransporter contributes to the virulence of ETEC [PMID:14977988]. 6 secreted autotransporter serine protease EatA eatA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3830198 PY03011 20140222 352914 protein-coding NCBI-supplied PMID: 12368865; 18586738 MUTATION: Deletion of UIS3 in Plasmodium yoelii provided attenuation and full protection in mice [PMID:17624848]. 4991 early transcribed membrane protein PY03011 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3853397 O2ColV112 20140329 562 protein-coding NCBI-supplied PMID: 16954398 MUTATION: traT mutants have altered membrane permeability and are sensitive to hydrophobic antibiotics [PMID:3323837]. 7 surface exclusion protein; similar to GenBank Accession Number AAW58918 Other designations: conjugal transfer surface exclusion protein TraT traT Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3853505 O2ColV53 20140410 562 protein-coding NCBI-supplied PMID: 16954398 MUTATION: attenuated in chicks [PMID:18541653]. 8 iron-related glycotransferase; similar to NP_753168 Other designations: IroB iroB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3853506 O2ColV54 20140410 562 protein-coding NCBI-supplied PMID: 16954398 MUTATION: attenuated in chicks [PMID:18541653]. 9 iron-related ABC transporter protein; similar to GenBank Accession Number AAN76099 Other designations: IroC iroC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3853507 O2ColV55 20140410 562 protein-coding NCBI-supplied PMID: 16954398 MUTATION: attenuated in chicks [PMID:18541653]. 10 iron-related ferric enterochelin esterase; similar to GenBank Accession Number AAN76100 Other designations: IroD iroD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3853509 O2ColV57 20140410 562 protein-coding NCBI-supplied PMID: 16954398 MUTATION: iroA gene cluster mutants were unable to resist Lcn2 in mouse serum [PMID:17060628]. 11 iron-related siderophore receptor; similar to GenBank Accession Number AAN76093 Other designations: outer membrane receptor FepA iroN Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3853516 O2ColV11 20140329 562 protein-coding NCBI-supplied PMID: 16954398 MUTATION: attenuated in mice [PMID:2973985]. 12 aerobactin biosynthesis protein; similar to GenBank Accession Number CAA53707 Other designations: IucA iucA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3853517 O2ColV12 20140410 562 protein-coding NCBI-supplied PMID: 16954398 MUTATION: attenuated in mice [PMID:2973985]. 13 N-hydroxylysine acetylase; aerobactin biosynthesis protein; similar to GenBank Accession Number CAH64815 Other designations: IucB iucB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3853518 O2ColV13 20140410 562 protein-coding NCBI-supplied PMID: 16954398 MUTATION: attenuated in mice [PMID:2973985]. 14 aerobactin biosynthesis protein; similar to GenBank Accession Number CAH64814 Other designations: IucC iucC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3853519 O2ColV14 20140329 562 protein-coding NCBI-supplied PMID: 16954398 MUTATION: attenuated in mice [PMID:2973985]. 15 L-lysine 6-monooxigenase; similar to GenBank Accession Number CAE55773 Other designations: IucD iucD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3853520 O2ColV15 20140410 562 protein-coding NCBI-supplied PMID: 16954398 MUTATION: attenuated in mice [PMID:11553558]. 16 ferric aerobactin receptor; similar to GenBank Accession Number CAE55774 Other designations: IutA iutA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3885996 PFF1275c 20140329 36329 6 protein-coding NCBI-supplied GO_0004315 (EC: ISS, PMID: 12368867); GO_0020011 (EC: IDA, PMID: 11738814) PMID: 11738814; 12368867; 16467310; 19472174 MUTATION: A genetically attenuated parasite (GAP) with a mutation in the FabB/FabF gene is attenuated in mice by arresting in the late liver stage [PMID:21669394]. 4987 3-oxoacyl-acyl-carrier protein synthase I/II FabB/FabF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3897013 pCPF5603_44 20130608 1502 protein-coding NCBI-supplied PMID: 18078439 MUTATION: beta toxin null mutants are attenuated in rabbit ileal loop model of disease [PMID:18078439]. 1908 beta-2 toxin pCPF5603_44 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3919993 SAOUHSC_01262 20140406 93061 protein-coding NCBI-supplied MUTATION: recA mutant is attenuated in mice [PMID:9383163]. 4387 recombinase A recA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3920782 SAOUHSC_01373 20140322 93061 protein-coding NCBI-supplied PMID: 7590176; 8981974; 9393725; 14523106; 15228543; 23335411 MUTATION: femA mutant is attenuated in mice [PMID:9383163]. 4388 methicillin resistance factor FemA SAOUHSC_01373 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3926325 20140301 352914 other NCBI-supplied MUTATION: Targeted deletion of SAP1 in the rodent malaria parasite Plasmodium yoelii generated mutant parasites that traverse and invade hepatocytes normally but cannot initiate liver-stage development in vitro and in vivo [PMID:18466298]. 4465 Record to support submission of GeneRIFs for a gene not in Gene (Plasmodium yoelii yoelii str. 17XNL). NEWENTRY Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3950826 FTL_0837 20140406 376619 protein-coding NCBI-supplied MUTATION: a FTL_0837 mutant was attenuated for infection in a mouse lung [PMID:17420240] 403 D-methionine binding transport protein, ABC transporter, membrane and periplasmic protein FTL_0837 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3950835 FTL_0846 20140322 376619 protein-coding NCBI-supplied MUTATION: a FTL_0846 mutant was attenuated for infection in a mouse lung [PMID:17420240] 404 isochorismatase hydrolase family protein FTL_0846 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3950841 FTL_1528 20140406 376619 protein-coding NCBI-supplied MUTATION: a FTL_1528 mutant was attenuated for infection in a mouse lung [PMID:17420240] 405 major facilitator transporter FTL_1528 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3950886 FTL_1096 20140406 376619 protein-coding NCBI-supplied MUTATION: a FTL_1096 mutant was attenuated for infection in a mouse lung [PMID:17420240] 406 lipoprotein FTL_1096 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3950887 FTL_1097 20130330 376619 protein-coding NCBI-supplied MUTATION: a FTL_1097 mutant was attenuated for infection in a mouse lung [PMID:17420240] 407 hypothetical protein FTL_1097 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3950914 FTL_1867 20140406 376619 protein-coding NCBI-supplied MUTATION: a FTL_1867 mutant was attenuated for infection in a mouse lung [PMID:17420240] 408 protease yegQ FTL_1867 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3950922 FTL_1672 20140406 376619 protein-coding NCBI-supplied PMID: 18179581 MUTATION: a FTL_1672 mutant was attenuated for infection of a mouse lung [PMID:17420240] 409 AcrB/AcrD/AcrF family transporter FTL_1672 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3950928 FTL_1678 20140406 376619 protein-coding NCBI-supplied MUTATION: a FTL_1678 mutant was attenuated for infection in a mouse lung [PMID:17420240] 410 hypothetical protein FTL_1678 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3950940 FTL_0891 20140405 376619 protein-coding NCBI-supplied MUTATION: a tig mutant was attenuated for infection in a mouse lung [PMID:17420240] 411 trigger factor tig Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3950941 FTL_0892 20140322 376619 protein-coding NCBI-supplied MUTATION: a FTL_0892 mutant was attenuated for infection in a mouse lung [PMID:17420240] 412 ATP-dependent Clp protease proteolytic subunit clpP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3950942 FTL_0893 20140405 376619 protein-coding NCBI-supplied MUTATION: a clpX mutant was attenuated for infection in a mouse lung [PMID:17420240] 413 ATP-dependent protease ATP-binding subunit ClpX clpX Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3950943 FTL_0894 20140405 376619 protein-coding NCBI-supplied MUTATION: a FTL_0894 mutant was attenuated for infection in a mouse lung [PMID:17420240] 414 DNA-binding, ATP-dependent protease La FTL_0894 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3950948 FTL_0899 20140406 376619 protein-coding NCBI-supplied MUTATION: a FTL_0899 mutant was attenuated for infection in a mouse lung [PMID:17420240] 415 protease, GTP-binding subunit FTL_0899 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3950952 FTL_0903 20140406 376619 protein-coding NCBI-supplied MUTATION: a FTL_0903 mutant was attenuated for infection in a mouse lung [PMID:17420240] 416 hypothetical protein FTL_0903 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3950981 FTL_0483 20140406 376619 protein-coding NCBI-supplied MUTATION: a FTL_0483 mutant was attenuated for infection in a mouse lung [PMID:17420240] 417 glycogen branching protein FTL_0483 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3950983 FTL_0485 20140405 376619 protein-coding NCBI-supplied MUTATION: a FTL_0485 mutant was attenuated for infection in a mouse lung [PMID:17420240] 418 glucose-1-phosphate adenylyltransferase glgC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3951041 FTL_1134 20140406 376619 protein-coding NCBI-supplied MUTATION: a FTL_1134 mutant was attenuated for infection in a mouse lung [PMID:17420240] 419 hypothetical protein FTL_1134 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3951097 FTL_1030 20140406 376619 protein-coding NCBI-supplied MUTATION: a FTL_1030 mutant was attenuated for infection in a mouse lung [PMID:17420240] 420 ribosomal large subunit pseudouridine synthase B FTL_1030 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3951135 FTL_0768 20140406 376619 protein-coding NCBI-supplied MUTATION: a FTL_0768 mutant was attenuated for infection in a mouse lung [PMID:17420240] 421 GTP binding translational elongation factor Tu and G family protein FTL_0768 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3951196 FTL_0584 20140405 376619 protein-coding NCBI-supplied MUTATION: a FTL_0584 mutant was attenuated for infection in a mouse lung [PMID:17420240] 422 bifunctional 3-hydroxacyl-CoA dehydrogenase/acyl-CoA-binding protein FTL_0584 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3951237 FTL_0421 20130529 376619 protein-coding NCBI-supplied MUTATION: a FTL_0421 mutant was attenuated for infection in a mouse lung [PMID:17420240] 423 lipoprotein FTL_0421 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3951244 FTL_0428 20140322 376619 protein-coding NCBI-supplied MUTATION: a FTL_0428 mutant was attenuated for infection in a mouse lung [PMID:17420240] 424 chromosome partition protein B FTL_0428 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3951246 FTL_0430 20140322 376619 protein-coding NCBI-supplied MUTATION: a FTL_0430 mutant was attenuated for infection in a mouse lung [PMID:17420240] 425 hypothetical protein FTL_0430 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3951255 FTL_0439 20140406 376619 protein-coding NCBI-supplied PMID: 20696823 MUTATION: a FTL_0439 mutant was attenuated for infection in a mouse lung [PMID:17420240] 426 hypothetical protein FTL_0439 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3951256 FTL_0950 20140406 376619 protein-coding NCBI-supplied MUTATION: a FTL_0950 mutant was attenuated for infection in a mouse lung[PMID:17420240] 427 50S ribosomal protein L25 FTL_0950 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3951266 FTL_0960 20140406 376619 protein-coding NCBI-supplied MUTATION: a FTL_0960 mutant was attenuated for infection in a mouse lung [PMID:17420240] 428 soluble pyridine nucleotide transhydrogenase FTL_0960 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3951279 FTL_0257 20140322 376619 protein-coding NCBI-supplied MUTATION: a rpmJ mutant was attenuated for infection in a mouse lung [PMID:17420240] 429 50S ribosomal protein L36 rpmJ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3951342 FTL_0616 20140406 376619 protein-coding NCBI-supplied MUTATION: a FTL_0616 mutant was attenuated for infection in a mouse lung [PMID:17420240] 430 DNA-directed RNA polymerase subunit alpha FTL_0616 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3951343 FTL_0617 20140406 376619 protein-coding NCBI-supplied MUTATION: a FTL_0617 mutant was attenuated for infection in a mouse lung [PMID:17420240] 431 hypothetical protein FTL_0617 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3951375 FTL_0009 20140406 376619 protein-coding NCBI-supplied MUTATION: a FTL_0009 mutant was attenuated for infection in a mouse lung [PMID:17420240] 432 outer membrane protein FTL_0009 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3951376 FTL_0010 20140405 376619 protein-coding NCBI-supplied MUTATION: a FTL_0010 mutant was attenuated for infection in a mouse lung [PMID:17420240] 433 thiosulfate sulfurtransferase FTL_0010 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3951378 FTL_0012 20140322 376619 protein-coding NCBI-supplied MUTATION: a FTL_0012 mutant was attenuated for infection in a mouse lung [PMID:17420240] 434 recombinase A recA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3951407 FTL_1750 20140405 376619 protein-coding NCBI-supplied MUTATION: a secE mutant was attenuated for infection of a mouse lung [PMID:17420240] 435 preprotein translocase subunit SecE secE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3951501 FTL_0663 20121017 376619 protein-coding NCBI-supplied MUTATION: a FTL_0663 mutant was attenuated for infection in a mouse lung [PMID:17420240] 436 hypothetical protein FTL_0663 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3951508 FTL_1233 20140406 376619 protein-coding NCBI-supplied MUTATION: a FTL_1233 mutant was attenuated for infection in a mouse lung [PMID:17420240] 437 amino acid antiporter FTL_1233 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3951515 FTL_1240 20140406 376619 protein-coding NCBI-supplied MUTATION: a FTL_1240 mutant was attenuated for infection in a mouse lung [PMID:17420240] 438 phospho-2-dehydro-3-deoxyheptonate aldolase FTL_1240 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3951539 FTL_1225 20121017 376619 protein-coding NCBI-supplied MUTATION: a FTL_1225 mutant was attenuated for infection in a mouse lung [PMID:17420240] 439 hypothetical protein FTL_1225 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3951562 FTL_0645 20140322 376619 protein-coding NCBI-supplied PMID: 20006480 MUTATION: a FTL_0645 mutant was attenuated for infection in a mouse lung [PMID:17420240] 440 lipoprotein FTL_0645 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3951617 FTL_0723 20140405 376619 protein-coding NCBI-supplied MUTATION: a FTL_0723 mutant was attenuated for infection in a mouse lung [PMID:17420240] 441 hypothetical protein FTL_0723 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3951644 FTL_1419 20140322 376619 protein-coding NCBI-supplied MUTATION: a FTL_1419 mutant was attenuated for infection in a mouse lung [PMID:17420240] 442 cyanophycinase FTL_1419 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3951675 FTL_0803 20121017 376619 protein-coding NCBI-supplied MUTATION: a FTL_0803 mutant was attenuated for infection in a mouse lung [PMID:17420240] 443 hypothetical protein FTL_0803 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3951701 FTL_1071 20140405 376619 protein-coding NCBI-supplied MUTATION: A guaA mutant is highly attenuated in mice [PMID:19368784]. 4911 GMP synthase guaA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3951705 FTL_1075 20140322 376619 protein-coding NCBI-supplied MUTATION: a FTL_1075 mutant was attenuated for infection in a mouse lung [PMID:17420240] 444 hypothetical protein FTL_1075 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3951721 FTL_0111 20140406 376619 protein-coding NCBI-supplied MUTATION: a FTL_0111 mutant was attenuated for infection in a mouse lung [PMID:17420240] 445 intracellular growth locus, subunit A FTL_0111 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3951722 FTL_0112 20140406 376619 protein-coding NCBI-supplied MUTATION: a FTL_0112 mutant was attenuated for infection in a mouse lung [PMID:17420240] 446 intracellular growth locus, subunit B FTL_0112 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3951723 FTL_0113 20140222 376619 protein-coding NCBI-supplied MUTATION: a FTL_0113 mutant was attenuated for infection in a mouse lung [PMID:17420240] 447 intracellular growth locus, subunit C FTL_0113 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3951742 FTL_0133 20140405 376619 protein-coding NCBI-supplied MUTATION: a FTL_0133 mutant was attenuated for infection in a mouse lung [PMID:17420240] 448 ferrous iron transport protein FTL_0133 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3951776 FTL_1354 20140322 376619 protein-coding NCBI-supplied MUTATION: a FTL_1354 mutant was attenuated for infection in a mouse lung [PMID:17420240] 449 hypothetical protein FTL_1354 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3951826 FTL_1553 20140405 376619 protein-coding NCBI-supplied MUTATION: a sucC mutant was attenuated for infection in a mouse lung [PMID:17420240] 450 succinyl-CoA synthetase subunit beta sucC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3951827 FTL_1554 20140405 376619 protein-coding NCBI-supplied MUTATION: a FTL_1554 mutant was attenuated for infection in a mouse lung [PMID:17420240] 451 succinyl-CoA synthetase, alpha subunit FTL_1554 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3951917 FTL_0193 20140406 376619 protein-coding NCBI-supplied cytochrome O ubiquinol oxidase, subunit III FTL_0193 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3951951 FTL_1601 20140405 376619 protein-coding NCBI-supplied MUTATION: a FTL_1601 mutant was attenuated for infection in a mouse lung [PMID:17420240] 453 tRNA/rRNA methyltransferase FTL_1601 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3951957 FTL_1273 20140406 376619 protein-coding NCBI-supplied MUTATION: a FTL_1273 mutant was attenuated for infection in a mouse lung [PMID:17420240] 454 8-amino-7-oxononanoate synthase FTL_1273 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3951958 FTL_1274 20140406 376619 protein-coding NCBI-supplied MUTATION: a FTL_1274 mutant was attenuated for infection in a mouse lung [PMID:17420240] 455 biotin synthesis protein BioC FTL_1274 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3951959 FTL_1275 20140406 376619 protein-coding NCBI-supplied MUTATION: a FTL_1275 mutant was attenuated for infection in a mouse lung [PMID:17420240] 456 dethiobiotin synthetase FTL_1275 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3951994 FTL_1936 20140405 376619 protein-coding NCBI-supplied MUTATION: a FTL_1936 mutant was attenuated for infection in a mouse lung [PMID:17420240] 457 periplasmic solute binding family protein FTL_1936 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3952010 FTL_1622 20140406 376619 protein-coding NCBI-supplied MUTATION: a FTL_1622 mutant was attenuated for infection in a mouse lung [PMID:17420240] 458 multidrug transporter (tetracycline resistance protein) FTL_1622 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3952011 FTL_1623 20140406 376619 protein-coding NCBI-supplied MUTATION: a FTL_1623 mutant was attenuated for infection in a mouse lung [PMID:17420240] 459 hypothetical protein FTL_1623 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3952026 FTL_1452 20140406 376619 protein-coding NCBI-supplied MUTATION: a rpmA mutant was attenuated for infection in a mouse lung [PMID:17420240] 460 50S ribosomal protein L27 rpmA Bin Zhao, Oliver He azi div WEB: http://www.ncbi.nlm.nih.gov/gene 3952032 FTL_1458 20140405 376619 protein-coding NCBI-supplied MUTATION: a FTL_1458 mutant was attenuated for infection in a mouse lung [PMID:17420240] 461 preprotein translocase subunit SecA - FTL_1458 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3952047 FTL_R0003 20101218 376619 rRNA NCBI-supplied MUTATION: a FTL_R0003 mutant was attenuated for infection in a mouse lung [PMID:17420240] 462 16S ribosomal RNA FTL_R0003 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3952054 FTL_1504 20140406 376619 protein-coding NCBI-supplied MUTATION: a FTL_1504 mutant was attenuated for infection in a mouse lung [PMID:17420240] 463 peroxidase/catalase FTL_1504 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3952087 FTL_1266 20140322 376619 protein-coding NCBI-supplied MUTATION: a FTL_1266 mutant was attenuated for infection in a mouse lung [PMID:17420240] 464 lipase/esterase FTL_1266 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3952111 FTL_0928 20140322 376619 protein-coding NCBI-supplied MUTATION: a FTL_0928 mutant was attenuated for infection in a mouse lung [PMID:17420240] 465 isoprenoid biosynthesis protein with amidotransferase-like domain FTL_0928 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3952147 FTL_1912 20140406 376619 protein-coding NCBI-supplied MUTATION: a rpsA mutant was attenuated for infection in a mouse lung [PMID:17420240] 466 30S ribosomal protein S1 rpsA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3952178 FTL_1701 20140406 376619 protein-coding NCBI-supplied MUTATION: a glpX mutant was attenuated for infection in a mouse lung [PMID:17420240] 467 fructose 1,6-bisphosphatase II glpX Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3952219 FTL_0514 20140406 376619 protein-coding NCBI-supplied MUTATION: a FTL_0514 mutant was attenuated for infection in a mouse lung [PMID:17420240] 468 hypothetical protein FTL_0514 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3952224 FTL_0519 20140322 376619 protein-coding NCBI-supplied MUTATION: a FTL_0519 mutant was attenuated for infection in a mouse lung [PMID:17420240] 469 septum site-determining protein MinD FTL_0519 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3952225 FTL_0520 20140406 376619 protein-coding NCBI-supplied MUTATION: a FTL_0520 mutant was attenuated for infection in a mouse lung [PMID:17420240] 470 septum site-determining protein MinC FTL_0520 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3952271 FTL_0094 20140406 376619 protein-coding NCBI-supplied PMID: 18284578 MUTATION: a FTL_0094 mutant was attenuated for infection in a mouse lung [PMID:17420240] 471 ClpB protein FTL_0094 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3952320 FTL_0456 20140406 376619 protein-coding NCBI-supplied MUTATION: a rpsU mutant was attenuated for infection in a mouse lung [PMID:17420240] 472 30S ribosomal protein S21 rpsU Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3952390 FTL_1404 20140406 376619 protein-coding NCBI-supplied MUTATION: a rplT mutant was attenuated for infection in a mouse lung [PMID:17420240] 473 50S ribosomal protein L20 rplT Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3952400 FTL_1414 20140406 376619 protein-coding NCBI-supplied MUTATION: a FTL_1414 mutant was attenuated for infection in a mouse lung [PMID:17420240] 474 hypothetical protein FTL_1414 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3952401 FTL_1415 20140322 376619 protein-coding NCBI-supplied MUTATION: a FTL_1415 mutant was attenuated for infection in a mouse lung [PMID:17420240] 475 capsule biosynthesis protein CapC FTL_1415 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3952402 FTL_1416 20140406 376619 protein-coding NCBI-supplied MUTATION: a FTL_1416 mutant was attenuated for infection in a mouse lung [PMID:17420240] 476 capsule biosynthesis protein capB FTL_1416 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3952442 FTL_1832 20140406 376619 protein-coding NCBI-supplied MUTATION: a FTL_1832 mutant was attenuated for infection in a mouse lung [PMID:17420240] 477 hypothetical protein FTL_1832 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3952464 FTL_0440 20140406 376619 protein-coding NCBI-supplied MUTATION: a isftu1 mutant was attenuated for infection in a mouse lung [PMID:17420240] 478 transposase isftu1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3952483 FTL_1461 20140406 376619 protein-coding NCBI-supplied MUTATION: a FTL_1461 mutant was attenuated for infection in a mouse lung [PMID:17420240] 479 purine nucleoside phosphorylase FTL_1461 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3952491 FTL_1473 20140406 376619 protein-coding NCBI-supplied MUTATION: a FTL_1473 mutant was attenuated for infection in a mouse lung [PMID:17420240] 480 DNA excision repair protein subunit A FTL_1473 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3952492 FTL_1474 20130511 376619 protein-coding NCBI-supplied MUTATION: a FTL_1474 mutant was attenuated for infection in a mouse lung [PMID:17420240] 481 transcription elongation factor GreA greA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3952493 FTL_1475 20140406 376619 protein-coding NCBI-supplied MUTATION: a FTL_1475 mutant was attenuated for infection in a mouse lung [PMID:17420240] 482 Type IV pili fiber building block protein FTL_1475 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3952505 FTL_R0004 20111214 376619 tRNA NCBI-supplied MUTATION: a tRNA-Ile1 mutant was attenuated for infection in a mouse lung [PMID:17420240] 483 tRNA tRNA-Ile1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3952562 FTL_0382 20140406 376619 protein-coding NCBI-supplied MUTATION: a FTL_0382 mutant was attenuated for infection in a mouse lung [PMID:17420240] 484 amino acid permease FTL_0382 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3952567 FTL_0387 20140406 376619 protein-coding NCBI-supplied MUTATION: a FTL_0387 mutant was attenuated for infection in a mouse lung [PMID:17420240] 485 aspartate aminotransferase FTL_0387 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3952576 FTL_0396 20140406 376619 protein-coding NCBI-supplied MUTATION: A purMCD mutant in Francisela tularensis was attenuated in mice [PMID:16861631]. 4971 fusion protein PurC/PurD FTL_0396 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3952586 FTL_1947 20140406 376619 protein-coding NCBI-supplied MUTATION: a FTL_1947 mutant was attenuated for infection in a mouse lung [PMID:17420240] 486 putative ABC transporter ATP-binding protein FTL_1947 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3952608 FTL_1328 20140406 376619 protein-coding NCBI-supplied MUTATION: a FTL_1328 mutant was attenuated for infection in a mouse lung [PMID:17420240] 487 outer membrane associated protein FTL_1328 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3952648 FTL_0073 20121017 376619 protein-coding NCBI-supplied MUTATION: a FTL_0073 mutant was attenuated for infection in a mouse lung [PMID:17420240] 488 hypothetical protein FTL_0073 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3952665 FTL_0525 20140405 376619 protein-coding NCBI-supplied MUTATION: a FTL_0525 mutant was attenuated for infection in a mouse lung [PMID:17420240] 489 fumerate hydratase FTL_0525 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3952679 FTL_0540 20140322 376619 protein-coding NCBI-supplied MUTATION: a FTL_0540 mutant was attenuated for infection in a mouse lung [PMID:17420240] 490 lipid-A-disaccharide synthase lpxB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3952683 FTL_0337 20101002 376619 pseudo NCBI-supplied MUTATION: a FTL_0337 mutant was attenuated for infection in a mouse lung [PMID:17420240] 491 pseudo FTL_0337 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3952716 FTL_1392 20140406 376619 protein-coding NCBI-supplied MUTATION: a FTL_1392 mutant was attenuated for infection in a mouse lung [PMID:17420240] 492 cold-shock DEAD-box protein A FTL_1392 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3952717 FTL_1393 20140222 376619 protein-coding NCBI-supplied MUTATION: a FTL_1393 mutant was attenuated for infection in a mouse lung [PMID:17420240] 493 peptidyl-prolyl cis-trans isomerase FTL_1393 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3952730 FTL_0552 20140406 376619 protein-coding NCBI-supplied MUTATION: A FTL0552 mutant in Francisella tularensis was attenuated in mice [PMID:18613792]. 4972 two-component response regulator FTL_0552 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3952784 FTL_0589 20140406 376619 protein-coding NCBI-supplied MUTATION: a FTL_0589 mutant was attenuated for infection in a mouse lung [PMID:17420240] 494 hypothetical protein FTL_0589 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3952786 FTL_0592 20140406 376619 protein-coding NCBI-supplied MUTATION: a FTL_0592 mutant was attenuated for infection in a mouse lung [PMID:17420240] 495 dTDP-glucose 4,6-dehydratase FTL_0592 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3952791 FTL_0597 20140405 376619 protein-coding NCBI-supplied MUTATION: a FTL_0597 mutant was attenuated for infection in a mouse lung [PMID:17420240] 496 NAD dependent epimerase FTL_0597 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3952837 FTL_0789 20140406 376619 protein-coding NCBI-supplied MUTATION: a FTL_0789 mutant was attenuated for infection in a mouse lung [PMID:17420240] 497 aspartate aminotransferase FTL_0789 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3989640 UTI89_C4082 20140329 364106 protein-coding NCBI-supplied PMID: 16585510 MUTATION: dppA mutant was attenuated 10- to 50-fold compared to the wild type for colonization of the bladders and kidneys of mice [PMID:17074858]. 2069 periplasmic dipeptide transport protein dppA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3990770 UTI89_C4921 20140329 364106 protein-coding NCBI-supplied PMID: 16552031; 16585510; 16790748; 21291504; 21570972; 22020226; 23090961 MUTATION: attenuated in mice [PMID:11349064]. 2070 cytotoxic necrotizing factor 1 cnf1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3990775 UTI89_C4926 20140329 364106 protein-coding NCBI-supplied PMID: 16585510; 18553505 MUTATION: attenuated in zebra fish [PMID:20019794]. 2071 hemolysin A hlyA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3990776 UTI89_C4927 20140329 364106 protein-coding NCBI-supplied PMID: 16585510 MUTATION: hlyC is required for the acylation and therefore activation of the toxin hemolysin which has the ability to lyse several different types of cells [PMID:8793877]. 2072 hemolysin C hlyC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3991259 UTI89_C4028 20140329 364106 protein-coding NCBI-supplied PMID: 16585510 MUTATION: chuA mutant unable to grow on iron-depleted medium containing heme [PMID:9157252]. 2073 outer membrane hemin receptor ChuA chuA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3991364 UTI89_C1118 20140222 364106 protein-coding NCBI-supplied PMID: 16585510 MUTATION: iroA gene cluster mutants were unable to resist Lcn2 in mouse serum [PMID:17060628]. 2074 outer membrane receptor FepA iroN Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3991366 UTI89_C1120 20140329 364106 protein-coding NCBI-supplied PMID: 16585510 MUTATION: attenuated in chicks [PMID:18541653]. 2075 IroD protein iroD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3991367 UTI89_C1121 20140222 364106 protein-coding NCBI-supplied PMID: 16585510 MUTATION: attenuated in chicks [PMID:18541653]. 2076 IroC protein iroC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3991368 UTI89_C1122 20140329 364106 protein-coding NCBI-supplied PMID: 16585510 MUTATION: attenuated in chicks [PMID:18541653]. 2077 glucosyltransferase iroB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3991369 UTI89_C1451 20140406 364106 protein-coding NCBI-supplied PMID: 16585510 MUTATION: attenuated in mice [PMID:11553558]. 2078 transport protein TonB tonB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3992036 UTI89_C4887 20130126 364106 protein-coding NCBI-supplied PMID: 16585510; 23002225 MUTATION: attenuated to human neutrophils in vitro [PMID:7960108]. 2079 p pilus adhesin PapG protein papG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3992044 UTI89_C4895 20140329 364106 protein-coding NCBI-supplied PMID: 16585510 MUTATION: mutant papA in wild-type smooth strains do not mediate Gal-Gal adherence [PMID:1672263]. 2080 major pilin subunit PapA papA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3992235 UTI89_C5017 20140222 364106 protein-coding NCBI-supplied PMID: 16585510 MUTATION: attenuated in mice and humans [PMID:18482721]. 2081 type 1 fimbiral adhesin FimH fimH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3992253 UTI89_C5035 20140222 364106 protein-coding NCBI-supplied PMID: 16585510; 17083913; 21083634 MUTATION: deletion mutant was significantly less invasive in human brain microvascular endothelial cells (BMECs) than the parent strain (E. coli K1) [PMID:11237832]. 2082 invasion protein IbeA ibeA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3992515 UTI89_C4359 20140217 364106 protein-coding NCBI-supplied PMID: 16585510 MUTATION: disruption mutant was less invasive in an in vitro HBMEC invasion assay than the wild-type E. coli K1 [PMID:10948126]. 2083 arylsulfatase aslA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3992605 UTI89_C4447 20140405 364106 protein-coding NCBI-supplied PMID: 16585510 MUTATION: mutation of dsbA led to degradation of bundilin and an absence of localized adherence to host cells in EPEC [PMID:9224871]. 2084 periplasmic protein disulfide isomerase I dsbA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3993212 UTI89_C2124 20140329 364106 protein-coding NCBI-supplied PMID: 16585510 MUTATION: fliC deletion mutants had reduced adherence in bovine tissue compared to the wild type EHEC and EPEC strains [PMID:17693516]. 2085 flagellin fliC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3993833 UTI89_C4427 20140222 364106 protein-coding NCBI-supplied PMID: 16585510 MUTATION: attenuated in mice [PMID:12117951]. 2086 transcriptional activator RfaH rfaH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3994721 UTI89_C1022 20140329 364106 protein-coding NCBI-supplied PMID: 16585510; 19797074 MUTATION: OmpA− strains are unable to cause actin condensation needed for invasion of brain epithelial cells [PMID:10531228]. 2087 outer membrane protein OmpA ompA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3996471 UTI89_P104 20140329 364106 protein-coding NCBI-supplied PMID: 16585510 MUTATION: traJ mutants of E. coli K1 are attenuated in rat pups and macrophages [PMID:14688129]. 2290 functional relaxosome complex initiator traJ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 3996502 UTI89_P135 20140222 364106 protein-coding NCBI-supplied PMID: 16585510 MUTATION: traT mutants have altered membrane permeability and are sensitive to hydrophobic antibiotics [PMID:3323837]. 2291 conjugal transfer surface exclusion protein TraT traT Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4060566 MGAS9429_Spy0692 20140222 370551 protein-coding NCBI-supplied PMID: 16636287 MUTATION: lsp mutant is attenuated in a murine model of soft tissue infection [PMID:19398546]. 4389 lipoprotein signal peptidase lsp Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4061049 MGAS9429_Spy1720 20140406 370551 protein-coding NCBI-supplied PMID: 16636287 MUTATION: scpA mutant is attenuated in mouse pneumonia model [PMID:9119483]. 4390 C5A peptidase precursor scpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4063044 MGAS10270_Spy1782 20140315 370552 protein-coding NCBI-supplied PMID: 16636287 MUTATION: scpA mutant is attenuated in mouse pneumonia model [PMID:9119483]. 4391 C5A peptidase precursor scpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4063392 MGAS10270_Spy0693 20140315 370552 protein-coding NCBI-supplied PMID: 16636287 MUTATION: lsp mutant is attenuated in a murine model of soft tissue infection [PMID:19398546]. 4392 Lipoprotein signal peptidase lsp Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4064175 MGAS10270_Spy1676 20140405 370552 protein-coding NCBI-supplied PMID: 16636287 MUTATION: fba mutant showed diminished invasive capabilities to HEp-2 cells and low mortality in mice following skin infection [PMID:11679068]. 4393 Fructose-bisphosphate aldolase fba Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4064563 MGAS2096_Spy1744 20140406 370553 protein-coding NCBI-supplied PMID: 16636287 MUTATION: scpA mutant is attenuated in mouse pneumonia model [PMID:9119483]. 4394 C5A peptidase scpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4065311 MGAS2096_Spy0703 20140222 370553 protein-coding NCBI-supplied PMID: 16636287 MUTATION: lsp mutant is attenuated in a murine model of soft tissue infection [PMID:19398546]. 4395 lipoprotein signal peptidase lsp Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4066760 MGAS10750_Spy1663 20140405 370554 protein-coding NCBI-supplied PMID: 16636287 MUTATION: fba mutant showed diminished invasive capabilities to HEp-2 cells and low mortality in mice following skin infection [PMID:11679068]. 4396 fructose-bisphosphate aldolase fba Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4066822 MGAS10750_Spy1807 20140315 370554 protein-coding NCBI-supplied PMID: 16636287 MUTATION: scpA mutant is attenuated in mouse pneumonia model [PMID:9119483]. 4397 C5A peptidase precursor scpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4067861 MGAS10750_Spy0726 20140222 370554 protein-coding NCBI-supplied PMID: 16636287 MUTATION: lsp mutant is attenuated in a murine model of soft tissue infection [PMID:19398546]. 4398 lipoprotein signal peptidase lsp Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4118909 YPA_3601 20140406 360102 protein-coding NCBI-supplied PMID: 16740952 MUTATION: purH mutant is attenuated in mice [PMID:14742535]. 1773 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase purH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4120004 YPA_2877 20140406 360102 protein-coding NCBI-supplied PMID: 16740952 MUTATION: relA spoT deletion mutants are attenuated in mice [PMID:19701461]. 1774 GDP/GTP pyrophosphokinase relA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4121636 YPA_0055 20140222 360102 protein-coding NCBI-supplied PMID: 16740952 MUTATION: greA mutants are attenuated in mice [PMID:14742535]. 1775 transcription elongation factor GreA greA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4122242 YPA_2786 20140222 360102 protein-coding NCBI-supplied PMID: 16740952 MUTATION: pcm mutant is attenuated in mice [PMID:14742535]. 1776 protein-L-isoaspartate O-methyltransferase pcm Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4122330 YPA_r031 20111119 360102 miscRNA NCBI-supplied MUTATION: smpB ssrA mutant is attenuated in mice [PMID:20065026]. 1777 miscRNA ssrA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4122331 YPA_0579 20121017 360102 protein-coding NCBI-supplied PMID: 16740952 MUTATION: smpB ssrA mutant is attenuated in mice [PMID:20065026]. 1778 SsrA-binding protein smpB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4123391 YPN_2897 20121017 377628 protein-coding NCBI-supplied PMID: 16740952 MUTATION: smpB ssrA mutant is attenuated in mice [PMID:20065026]. 1813 SsrA-binding protein smpB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4123392 YPN_r084 20111119 377628 miscRNA NCBI-supplied MUTATION: smpB ssrA mutant is attenuated in mice [PMID:20065026]. 1814 miscRNA ssrA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4123547 YPN_0713 20140406 377628 protein-coding NCBI-supplied PMID: 16740952 MUTATION: relA spoT deletion mutants are attenuated in mice [PMID:19701461]. 1815 GDP/GTP pyrophosphokinase relA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4124166 YPN_0237 20140406 377628 protein-coding NCBI-supplied PMID: 16740952 MUTATION: purH mutant is attenuated in mice [PMID:14742535]. 1816 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase purH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4124797 YPN_0736 20140222 377628 protein-coding NCBI-supplied PMID: 16740952 MUTATION: pcm mutant is attenuated in mice [PMID:14742535]. 1817 protein-L-isoaspartate O-methyltransferase pcm Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4125180 YPN_2100 20130702 377628 protein-coding NCBI-supplied PMID: 16740952 MUTATION: ompX mutants are attenuated in their ability to attach to and invade HeLa cells [PMID:17768237]. 1818 outer membrane protein X ompX Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4125871 YPN_3249 20140222 377628 protein-coding NCBI-supplied PMID: 16740952 MUTATION: greA mutants are attenuated in mice [PMID:14742535]. 1819 transcription elongation factor GreA greA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4187921 ECP_4055 20140222 362663 protein-coding NCBI-supplied PMID: 16879640 MUTATION: attenuated in mice [PMID:12117951]. 2067 transcriptional activator RfaH rfaH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4190232 ECP_4655 20140322 362663 protein-coding NCBI-supplied PMID: 16879640 MUTATION: attenuated in mice and humans [PMID:18482721]. 2068 FimH protein ECP_4655 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4201274 CPF_0042 20140406 195103 protein-coding NCBI-supplied PMID: 16825665 MUTATION: plc mutant is attenuated in mice [PMID:7746141]. 1921 phospholipase C plc Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4203452 CPF_1751 20140322 195103 protein-coding NCBI-supplied PMID: 16825665 MUTATION: virS mutant is attenuated in mice [PMID:8052128]. 1922 sensor histidine kinase VirS virS Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4204801 CPR_0381 20140406 289380 protein-coding NCBI-supplied PMID: 16124435; 16825665 MUTATION: cpe knockout mutant is avirulent in rabbit ileal loop model [PMID:10476029]. 1923 enterotoxin Cpe cpe Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4204855 CPR_1481 20140322 289380 protein-coding NCBI-supplied PMID: 16825665 MUTATION: virS mutant is attenuated in mice [PMID:8052128]. 1924 sensor histidine kinase VirS virS Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4205371 CPR_0041 20140405 289380 protein-coding NCBI-supplied PMID: 16825665 MUTATION: plc mutant is attenuated in mice [PMID:7746141]. 1925 phospholipase C plc Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4207099 SFV_3854 20140405 373384 protein-coding NCBI-supplied PMID: 16822325 MUTATION: iuc mutants are attenuated in chicken embryos and rabbit ileal loops [PMID:19130265]. 1787 siderophore biosynthesis protein iucA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4207243 SFV_2414 20121017 373384 protein-coding NCBI-supplied PMID: 16822325 MUTATION: vacJ mutants are incapable of intercellular spread of epithelial cells [PMID:8145644]. 1788 lipoprotein vacJ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4207513 SFV_2554 20140329 373384 protein-coding NCBI-supplied PMID: 16822325 MUTATION: guaAguaB mutants are attenuated in HeLa cells [PMID:8757833]. 1789 GMP synthase guaA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4207514 SFV_2555 20140405 373384 protein-coding NCBI-supplied PMID: 16822325 MUTATION: guaAguaB mutants are attenuated in HeLa cells [PMID:8757833]. 1790 inosine 5'-monophosphate dehydrogenase guaB Bin Zhao, Oliver He ompB WEB: http://www.ncbi.nlm.nih.gov/gene 4207729 SFV_3409 20140222 373384 protein-coding NCBI-supplied PMID: 16822325 MUTATION: envZ insertion mutant is able to invade cells but has decreased virulence due to the inability to survive intracellularly [PMID:2121709]. 1791 osmolarity sensor protein - envZ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4207730 SFV_3410 20140215 373384 protein-coding NCBI-supplied PMID: 16822325 MUTATION: mutant of the ompB locus (both the envZ and ompR genes) showed attenuated virulence in HeLa cells, and a weak response to a Serany test [PMID:2121709]. 1792 osmolarity response regulator ompR Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4208207 SFV_0908 20140315 373384 protein-coding NCBI-supplied PMID: 16822325 MUTATION: aroA deletion mutants are attenuated in HeLa cells [PMID:8757833]. 1793 3-phosphoshikimate 1-carboxyvinyltransferase aroA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4208270 SFV_4329 20140329 373384 protein-coding NCBI-supplied PMID: 16822325 MUTATION: miaA mutants had reduced ability to invade and spread in MK2 cell monolayers compared to the wildtype [PMID:9294434]. 1794 tRNA delta(2)-isopentenylpyrophosphate transferase miaA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4208271 SFV_4330 20140222 373384 protein-coding NCBI-supplied PMID: 16822325 MUTATION: hfq deletion mutants are attenuated in guinea pig eye infection model (Sereny test) [PMID:20080057]. 1795 RNA-binding protein Hfq hfq Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4208278 SFV_4337 20130406 373384 protein-coding NCBI-supplied PMID: 16822325 MUTATION: vacB mutants had attenuated invasion of MK2 cells compared to the wild-type strain [PMID:1400189]. 1796 exoribonuclease R vacB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4208311 SFV_3526 20140222 373384 protein-coding NCBI-supplied PMID: 16822325 MUTATION: yhiE mutant is attenuated in causing keratoconjunctivitis in guinea pigs [PMID:15073317]. 1797 hypothetical protein yhiE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4208482 SFV_1719 20140406 373384 protein-coding NCBI-supplied PMID: 16822325 MUTATION: aroD deletion led to attenuation in HeLa cells and monkeys [PMID:8356844]. 1798 3-dehydroquinate dehydratase aroD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4208818 SFV_1678 20121017 373384 protein-coding NCBI-supplied PMID: 16822325 MUTATION: sodB mutant is extremely sensitive to killing by phagocytes compared to the wild-type, and causes only mild damage in infection of rabbit ileal loops [PMID:2404874]. 1799 superoxide dismutase sodB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4208998 SFV_3641 20140406 373384 protein-coding NCBI-supplied PMID: 16822325 MUTATION: dsbA mutants are less invasive to MK-2 cell monolayers compared to the wild-type [PMID:7761426]. 1800 periplasmic protein disulfide isomerase I dsbA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4208999 SFV_3642 20140322 373384 protein-coding NCBI-supplied PMID: 16822325 MUTATION: yihE mutant is unable to cause keratoconjunctivitis in guinea pigs [PMID:15073317]. 1801 serine/threonine protein kinase yihE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4209107 SFV_1165 20130406 373384 protein-coding NCBI-supplied PMID: 16822325 MUTATION: phoP mutants were resolved more quickly than wild type in animal models, and are more susceptible to killing by PMNs [PMID:11207599]. 1802 DNA-binding transcriptional regulator PhoP phoP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4209445 SFV_1198 20140322 373384 protein-coding NCBI-supplied PMID: 16822325 MUTATION: ipaH mutant is attenuated in mice [PMID:17214743]. 1803 possible fragment Other designations: invasion plasmid antigen ipaH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4209646 SFV_1379 20140406 373384 protein-coding NCBI-supplied PMID: 16822325 MUTATION: sitA mutant is attenuated in mice [PMID:19289511]. 1804 Iron transport protein sitA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4209759 SFV_1266 20140322 373384 protein-coding NCBI-supplied PMID: 16822325 MUTATION: tonB mutant is able to invade epithelial cells but is incapable of cell to cell spread [PMID:11035742]. 1805 transport protein TonB tonB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4210152 SFV_0130 20140222 373384 protein-coding NCBI-supplied PMID: 16822325 MUTATION: dksA mutants are able to invade cultured cell monlayers but are incapable of cell to cell spread [PMID:11500451]. 1806 RNA polymerase-binding transcription factor dksA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4210323 SFV_3850 20140322 373384 protein-coding NCBI-supplied PMID: 16822325 MUTATION: mutants of the iuc locus and the aerobactin receptor, iutA were attenuated in chicken embryos [PMID:3028962]. 1807 ferric siderophore receptor iutA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4210324 SFV_3851 20140329 373384 protein-coding NCBI-supplied PMID: 16822325 MUTATION: iuc mutants are attenuated in chicken embryos and rabbit ileal loops [PMID:19130265]. 1808 lysine:N6-hydroxylase iucD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4210325 SFV_3852 20140301 373384 protein-coding NCBI-supplied PMID: 16822325 MUTATION: iuc mutants are attenuated in chicken embryos and rabbit ileal loops [PMID:19130265]. 1809 siderophore biosynthesis protein iucC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4210326 SFV_3853 20140322 373384 protein-coding NCBI-supplied PMID: 16822325 MUTATION: iuc mutants are attenuated in chicken embryos and rabbit ileal loops [PMID:19130265]. 1810 siderophore biosynthesis protein iucB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4210380 SFV_0047 20140405 373384 protein-coding NCBI-supplied PMID: 16822325 MUTATION: surA mutant is able to infect epithelial cells but is incapable of cell to cell spread [PMID:20447864]. 1811 peptidyl-prolyl cis-trans isomerase SurA surA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4210775 SFV_2290 20140215 373384 protein-coding NCBI-supplied PMID: 16822325 MUTATION: ompC mutants were attenuated in their ability to spread cell to cell and kill epithelial cells, and had a negative Sereny test [PMID:8359885]. 1812 porin ompC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4362678 pCJ01p4 20130714 197 protein-coding NCBI-supplied PMID: 11322827 MUTATION: Mutation of plasmid gene ORF3 (comB3) reduced adherence/invasion of INT407 cells to approximately 1/3 of wild type strain 81-176 [PMID:10899834]. 1 ORF3 Other designations: hypothetical protein pCJ01p4 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4364265 pO86A1_p122 20140410 562 protein-coding NCBI-supplied MUTATION: traT mutants have altered membrane permeability and are sensitive to hydrophobic antibiotics [PMID:3323837]. 17 conjugal transfer surface exclusion protein TraT traT Bin Zhao, Oliver He pqsR# WEB: http://www.ncbi.nlm.nih.gov/gene 4379987 PA14_51340 20130831 208963 protein-coding NCBI-supplied PMID: 17038190; 23713667 MUTATION: mvfR (pho34B12) mutant is attenuated in burned mouse model [PMID:9371831]. 4399 transcriptional regulator MvfR - mvfR Bin Zhao, Oliver He pepA WEB: http://www.ncbi.nlm.nih.gov/gene 4380009 PA14_51530 20140222 208963 protein-coding NCBI-supplied PMID: 17038190; 23716613 MUTATION: exoU mutant is avirulent in Dictyostelium discoideum, a genetically tractable eukaryotic organism [PMID:11867744]. 4400 ExoU - exoU Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4380057 PA14_50290 20140405 208963 protein-coding NCBI-supplied PMID: 17038190 MUTATION: fliC mutant is attenuated in mice [PMID:9423837]. 4401 flagellin type B fliC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4380176 PA14_45720 20130526 208963 protein-coding NCBI-supplied PMID: 17038190 MUTATION: flhB mutant is attenuated in Drosophila melanogaster and in mice [PMID:18591226]. 4402 flagellar biosynthesis protein FlhB flhB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4380287 PA14_38610 20140215 208963 protein-coding NCBI-supplied PMID: 17038190 MUTATION: PA14_38610 mutant is attenuated in Drosophila melanogaster and in mice [PMID:18591226]. 4403 hypothetical protein PA14_38610 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4380319 PA14_37650 20130526 208963 protein-coding NCBI-supplied PMID: 17038190 MUTATION: PA14_37650 mutant is attenuated in Drosophila melanogaster and in mice [PMID:18591226]. 4404 hypothetical protein PA14_37650 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4380359 PA14_42270 20140222 208963 protein-coding NCBI-supplied PMID: 17038190 MUTATION: pscJ mutant is attenuated in Dictyostelium discoideum, a genetically tractable eukaryotic organism [PMID:11867744]. 4405 pscJ type III export protein pscJ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4380463 PA14_33610 20130518 208963 protein-coding NCBI-supplied PMID: 17038190 MUTATION: PA14_33610 (pvdI) mutant is attenuated in Drosophila melanogaster and in mice [PMID:18591226]. 4406 peptide synthase PA14_33610 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4380617 PA14_30650 20140406 208963 protein-coding NCBI-supplied PMID: 17038190 MUTATION: gacA mutant is attenuated in burned mouse model [PMID:9371831]. 4407 response regulator GacA gacA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4381036 PA14_41070 20140215 208963 protein-coding NCBI-supplied PMID: 17038190 MUTATION: kerV (PA14_41070) mutant is attenuated in mice [PMID:19779606]. 4408 hypothetical protein PA14_41070 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4381387 PA14_36000 20130518 208963 protein-coding NCBI-supplied PMID: 17038190 MUTATION: prpR mutant is attenuated in mice and Drosophila melanogaster [PMID:18591226]. 4409 propionate catabolism operon regulator prpR Bin Zhao, Oliver He eta WEB: http://www.ncbi.nlm.nih.gov/gene 4381678 PA14_49560 20140329 208963 protein-coding NCBI-supplied PMID: 17038190 MUTATION: toxA mutant is attenuated in burned mouse model [PMID:7604262]. 4410 exotoxin A - toxA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4381738 PA14_00560 20130511 208963 protein-coding NCBI-supplied PMID: 17038190 exoenzyme T exoT Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4381875 PA14_14850 20140301 208963 protein-coding NCBI-supplied PMID: 17038190 MUTATION: pilF mutant is attenuated in Drosophila melanogaster and in mice [PMID:18591226]. 4412 type 4 fimbrial biogenesis protein PilF pilF Bin Zhao, Oliver He tpnA WEB: http://www.ncbi.nlm.nih.gov/gene 4382109 PA14_35740 20130420 208963 protein-coding NCBI-supplied PMID: 17038190 MUTATION: tpnA mutant is attenuated in Drosophila melanogaster and in mice [PMID:18591226]. 4413 transposase - PA14_35740 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4382190 PA14_09900 20120929 208963 protein-coding NCBI-supplied PMID: 17038190 MUTATION: prpL mutant is attenuated in rats [PMID:11500408]. 4414 Pvds-regulated endoprotease, lysyl class prpL Bin Zhao, Oliver He xcpA WEB: http://www.ncbi.nlm.nih.gov/gene 4382650 PA14_58770 20140222 208963 protein-coding NCBI-supplied PMID: 17038190 MUTATION: pilD mutant is attenuated in rats [PMID:14641575]. 4415 type 4 prepilin peptidase PilD - pilD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4382864 PA14_45960 20140217 208963 protein-coding NCBI-supplied PMID: 17038190 MUTATION: lasR mutant is avirulent in Dictyostelium discoideum [PMID:11867744]. 4416 transcriptional regulator LasR lasR Bin Zhao, Oliver He catA WEB: http://www.ncbi.nlm.nih.gov/gene 4382943 PA14_09150 20140405 208963 protein-coding NCBI-supplied PMID: 17038190; 18165301; 19933365; 20075613 MUTATION: katA mutant is attenuated in Drosophila melanogaster and in mice [PMID:15972537]. 4417 catalase - katA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4383664 PA14_03120 20130511 208963 protein-coding NCBI-supplied PMID: 17038190 MUTATION: PA14_03120 (hudR) mutant is attenuated in Drosophila melanogaster and in mice [PMID:18591226]. 4418 transcriptional regulator PA14_03120 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4383677 PA14_03530 20140329 208963 protein-coding NCBI-supplied PMID: 17038190 MUTATION: PA14_03530 mutant is attenuated in Drosophila melanogaster and in mice [PMID:18591226]. 4419 transcriptional regulator PA14_03530 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4383758 PA14_04850 20120929 208963 protein-coding NCBI-supplied PMID: 17038190 MUTATION: PA14_04850 mutant is attenuated in Drosophila melanogaster and in mice [PMID:18591226]. 4420 hypothetical protein PA14_04850 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4383800 PA14_05340 20140215 208963 protein-coding NCBI-supplied PMID: 17038190 MUTATION: pilI mutant is attenuated in rats [PMID:14641575]. 4421 twitching motility protein PilI pilI Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4384258 PA14_36345 20130518 208963 protein-coding NCBI-supplied PMID: 17038190 adenylate cyclase exoY Bin Zhao, Oliver He fabF WEB: http://www.ncbi.nlm.nih.gov/gene 4384346 PA14_25690 20140405 208963 protein-coding NCBI-supplied PMID: 17038190 MUTATION: fabF1 mutant is attenuated in Drosophila melanogaster and in mice [PMID:18591226]. 4423 3-oxoacyl-ACP synthase - fabF1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4384652 PA14_16480 20130420 208963 protein-coding NCBI-supplied PMID: 17038190; 18667850 MUTATION: wspF mutant is attenuated in Drosophila melanogaster [PMID:18591226]. 4424 chemotaxis-specific methylesterase wspF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4385158 PA14_72450 20140222 208963 protein-coding NCBI-supplied PMID: 17038190 MUTATION: dsbA mutant is attenuated in Drosophila melanogaster and in mice [PMID:18591226]. 4425 thiol:disulfide interchange protein DsbA dsbA Bin Zhao, Oliver He phlC plcS WEB: http://www.ncbi.nlm.nih.gov/gene 4385302 PA14_53360 20140405 208963 protein-coding NCBI-supplied PMID: 17038190 MUTATION: plcH mutant is attenuated in burned mouse model [PMID:7604262]. 4426 hemolytic phospholipase C - plcH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4385727 PA14_60310 20130511 208963 protein-coding NCBI-supplied PMID: 17038190; 19054330 MUTATION: pilY1 mutant is attenuated in rats [PMID:14641575]. 4427 type 4 fimbrial biogenesis protein PilY1 pilY1 Bin Zhao, Oliver He opdO WEB: http://www.ncbi.nlm.nih.gov/gene 4385800 PA14_37260 20140329 208963 protein-coding NCBI-supplied PMID: 17038190 MUTATION: opdO mutant is attenuated in Drosophila melanogaster and in mice [PMID:18591226]. 4428 porin - PA14_37260 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4441159 SPD_2017 20140217 373153 protein-coding NCBI-supplied PMID: 17041037; 17220227; 17261599; 17526693 MUTATION: cbpA mutant is attenuated in rat pups [PMID:9364908]. 3062 choline binding protein A cbpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4441190 SPD_0701 20130420 373153 protein-coding NCBI-supplied PMID: 17041037 MUTATION: ciaR mutant is attenuated in mice [PMID:15292127]. 3063 DNA-binding response regulator CiaR ciaR Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4441251 SPD_1031 20140405 373153 protein-coding NCBI-supplied PMID: 17041037 MUTATION: mutX mutant is attenuated in mice [PMID:9826334]. 3064 Mutator mutT protein (7,8-dihydro-8-oxoguanine-triphosphatase) (8-oxo-dGTPase) mutX Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4441316 SPD_0417 20140222 373153 protein-coding NCBI-supplied PMID: 17041037 MUTATION: a bacA mutant was attenuated in a murine model [PMID:11359563] 3065 undecaprenyl pyrophosphate phosphatase bacA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4441373 SPD_0126 20140406 373153 protein-coding NCBI-supplied PMID: 17041037; 17261599; 17526693 MUTATION: pspA mutant is attenuated in mice [PMID:10603379]. 3066 surface protein A pspA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4441432 SPD_0301 20130508 373153 protein-coding NCBI-supplied PMID: 17041037 MUTATION: regR mutant is attenuated in mice [PMID:12704136]. 3067 sugar binding transcriptional regulator RegR regR Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4441459 SPD_0309 20140405 373153 protein-coding NCBI-supplied PMID: 17041037; 21825061; 23403556 MUTATION: luxS mutant has defective ability to persist in the nasopharyngeal tissues of mice [PMID:15102809]. 3068 S-ribosylhomocysteinase luxS Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4441476 SPD_0650 20140222 373153 protein-coding NCBI-supplied PMID: 17041037; 20437156; 22198546 MUTATION: clpP mutant is attenuated in mice [PMID:15664911]. 3069 ATP-dependent Clp protease proteolytic subunit clpP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4441485 SPD_0821 20130508 373153 protein-coding NCBI-supplied PMID: 17041037 MUTATION: cbpE has reduced colonization of nasopharynx of rats and reduced adherence to human epithelial cells [PMID:10992472]. 3070 choline binding protein E cbpE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4441545 SPD_1403 20130508 373153 protein-coding NCBI-supplied PMID: 17041037; 21886805 MUTATION: lytC mutant have reduced colonization of rat nasopharynx compared to wild type [PMID:10992472]. 3071 1,4-beta-N-acetylmuramidase lytC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4441553 SPD_1309 20130508 373153 protein-coding NCBI-supplied PMID: 17041037 MUTATION: pgdA mutant is attenuated in mice [PMID:12438406]. 3072 peptidoglycan GlcNAc deacetylase pgdA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4441567 SPD_0055 20140405 373153 protein-coding NCBI-supplied PMID: 17041037 MUTATION: a purN mutant was attenuated in a murine model [PMID:11359563] 3073 phosphoribosylglycinamide formyltransferase purN Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4441611 SPD_1726 20140222 373153 protein-coding NCBI-supplied PMID: 17041037; 17237423; 17261599; 17562768; 17711480; 18195026; 18559434; 19040644; 19168620; 20483738; 20868379; 21825061; 23625220; 23785278 MUTATION: ply mutant is attenuated in mice [PMID:10603379]. 3074 pneumolysin ply Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4441644 SPD_0636 20140405 373153 protein-coding NCBI-supplied PMID: 17041037; 18179423 MUTATION: spxB mutant has a loss in the ability to attach eukayrotic cells and is attenuated in rabbits [PMID:8820650]. 3075 pyruvate oxidase spxB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4441680 SPD_0577 20140222 373153 protein-coding NCBI-supplied PMID: 17041037 MUTATION: zmpB mutant is attenuated in mice [PMID:12841855]. 3076 zinc metalloprotease ZmpB zmpB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4441881 SPD_1797 20130131 373153 protein-coding NCBI-supplied PMID: 17041037; 17496092 MUTATION: ccpA mutant is attenuated in mice [PMID:16321938]. 3077 catabolite control protein A ccpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4441884 SPD_0853 20130508 373153 protein-coding NCBI-supplied PMID: 17041037; 21886805 MUTATION: lytB has reduced colonization of nasopharynx of rats compared to wild type [PMID:10992472]. 3078 endo-beta-N-acetylglucosaminidase lytB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4442061 SPD_0261 20140406 373153 protein-coding NCBI-supplied PMID: 17041037 MUTATION: a pepC mutant was attenuated in a murine model [PMID:11359563] 3079 aminopeptidase C pepC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4442230 SPD_1737 20140215 373153 protein-coding NCBI-supplied PMID: 17041037 MUTATION: lytA mutant is attenuated in mice [PMID:10603379]. 3080 autolysin/N-acetylmuramoyl-L-alanine amidase lytA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4442282 SPD_1462 20130330 373153 protein-coding NCBI-supplied PMID: 17041037 MUTATION: psaC mutant is attenuated in mice [PMID:11988523]. 3081 manganese ABC transporter permease psaC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4442379 SPD_1504 20140405 373153 protein-coding NCBI-supplied PMID: 17041037; 19284989; 19687228; 20557315; 22215570 MUTATION: nanA mutant is attenuated in mice [PMID:9826334]. 3082 sialidase A nanA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4442401 SPD_0062 20140405 373153 protein-coding NCBI-supplied PMID: 17041037 MUTATION: a purB mutant was attenuated in a murine model [PMID:11359563] 3083 adenylosuccinate lyase purB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4442404 SPD_1412 20140215 373153 protein-coding NCBI-supplied PMID: 17041037; 18024519; 20979332 MUTATION: codY mutant has lower bacterial loads during infection in mice compared to the wild type and have a diminished ability to adhere to nasopharangeal cells in vitro [PMID:18024519]. 3084 transcriptional repressor CodY codY Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4442443 SPD_2028 20130508 373153 protein-coding NCBI-supplied PMID: 17041037 MUTATION: cbpD has reduced colonization of nasopharynx of rats compared to the wild type [PMID:10992472]. 3085 choline binding protein D cbpD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4442449 SPD_1298 20140222 373153 protein-coding NCBI-supplied PMID: 17041037; 23577197 MUTATION: nox mutant is attenuated in mice [PMID:11158360]. 3086 NADH oxidase nox Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4442466 SPD_1678 20140405 373153 protein-coding NCBI-supplied PMID: 17041037 MUTATION: an aga mutant was attenuated in a murine model [PMID:11359563] 3087 alpha-galactosidase AgaN aga Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4442604 SPD_1218 20140222 373153 protein-coding NCBI-supplied PMID: 17041037; 18572376 MUTATION: potD mutant is attenuated in pulmonary and systemic models of infection in mice [PMID:16368990]. 3088 spermidine/putrescine ABC transporter spermidine/putrescine-binding protein potD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4442613 SPD_0854 20130508 373153 protein-coding NCBI-supplied PMID: 17041037; 19570831; 20331793 MUTATION: pavA mutant is attenuated in mice [PMID:11580843]. 3089 adherence and virulence protein A pavA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4442684 SPD_0448 20140405 373153 protein-coding NCBI-supplied PMID: 17041037 MUTATION: glnA mutant had significantly reduced adhesion to Detroit 562 human pharyngeal epithelial cells [PMID:16787930]. 3090 glutamine synthetase, type I glnA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4442721 SPD_0667 20140222 373153 protein-coding NCBI-supplied PMID: 17041037 MUTATION: sodA mutant is attenuated in mice [PMID:10768978]. 3091 superoxide dismutase, manganese-dependent sodA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4442774 SPD_1461 20140222 373153 protein-coding NCBI-supplied PMID: 17041037 MUTATION: psaB mutant is attenuated in mice [PMID:11988523]. 3092 manganese ABC transporter ATP-binding protein psaB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4442813 SPD_0336 20140329 373153 protein-coding NCBI-supplied PMID: 17041037; 18394970 MUTATION: a pbp1A mutant was attenuated in a murine model [PMID:11359563] 3093 penicillin-binding protein 1A pbp1A Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4442828 SPD_1018 20140215 373153 protein-coding NCBI-supplied PMID: 17041037 MUTATION: iga mutant is attenuated in mice [PMID:12841855]. 3094 immunoglobulin A1 protease iga Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4442999 SPD_1076 20140217 373153 protein-coding NCBI-supplied PMID: 17041037 MUTATION: The srtA mutant colonized the nasopharynx of chinchillas at a significantly lower level than the wild type [PMID:16246506]. 3095 sortase srtA MUTATION: An A. hydrophila aroA mutant is highly attenuated in trout [PMID:9573055]. 4945 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4491551 APECO1_483 20140329 405955 protein-coding NCBI-supplied PMID: 17293413 MUTATION: mppA mutant is attenuated in chickens [PMID:15845486]. 2044 periplasmic murein peptide-binding protein mppA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4491947 APECO1_1631 20140406 405955 protein-coding NCBI-supplied PMID: 17293413 MUTATION: sbmA mutant is attenuated in chickens [PMID:15845486]. 2045 transporter sbmA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4492146 APECO1_2110 20140322 405955 protein-coding NCBI-supplied PMID: 17293413 MUTATION: attenuated in mice and humans [PMID:18482721]. 2046 type 1 fimbiral adhesin FimH fimH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4492443 APECO1_319 20140222 405955 protein-coding NCBI-supplied PMID: 17293413 MUTATION: ychF mutant is attenuated in chickens [PMID:15845486]. 2047 GTP-dependent nucleic acid-binding protein EngD ychF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4492586 APECO1_2834 20140405 405955 protein-coding NCBI-supplied PMID: 17293413 MUTATION: waaL mutant is attenuated in chickens [PMID:15845486]. 2048 lipid A-core, surface polymer ligase waaL Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4492758 APECO1_2904 20140405 405955 protein-coding NCBI-supplied PMID: 17293413 MUTATION: dppA mutant was attenuated 10- to 50-fold compared to the wild type for colonization of the bladders and kidneys of mice [PMID:17074858]. 2049 dipeptide transporter protein DppA dppA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4492849 APECO1_2601 20140406 405955 protein-coding NCBI-supplied PMID: 17019443; 17293413 MUTATION: mutation of dsbA led to degradation of bundilin and an absence of localized adherence to host cells in EPEC [PMID:9224871]. 2050 protein disulfide isomerase I dsbA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4493341 APECO1_2093 20140222 405955 protein-coding NCBI-supplied PMID: 17293413 MUTATION: deletion mutant was significantly less invasive in human brain microvascular endothelial cells (BMECs) than the parent strain (E. coli K1) [PMID:11237832]. 2051 invasion protein IbeA ibeA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4493551 APECO1_3519 20140315 405955 protein-coding NCBI-supplied PMID: 17293413 MUTATION: mutant papA in wild-type smooth strains do not mediate Gal-Gal adherence [PMID:1672263]. 2052 major fibrial protein papA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4493636 APECO1_273 20140324 405955 protein-coding NCBI-supplied PMID: 17293413 MUTATION: sitB mutant is attenuated in chickens [PMID:15845486]. 2053 Mn+2/Fe+2 ABC transporter ATPase SitB sitB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4493654 APECO1_704 20140405 405955 protein-coding NCBI-supplied PMID: 17293413 MUTATION: malX mutant is attenuated in chickens [PMID:15845486]. 2054 bifunctional PTS system maltose and glucose-specific transporter subunits IICB malX Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4493784 APECO1_62 20130518 405955 protein-coding NCBI-supplied PMID: 17293413 MUTATION: OmpA− strains are unable to cause actin condensation needed for invasion of brain epithelial cells [PMID:10531228]. 2055 outer membrane protein A ompA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4493822 APECO1_3530 20140315 405955 protein-coding NCBI-supplied PMID: 17293413 MUTATION: tia deletion strains were noninvasive and lacked the ability to adhere to human ileocecal cells [PMID:8675335]. 2056 tia invasion determinant tia Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4493827 APECO1_3527 20140217 405955 protein-coding NCBI-supplied PMID: 17293413 MUTATION: attenuated to human neutrophils in vitro [PMID:7960108]. 2057 allele II Other designations: protein PapG papG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4494179 APECO1_2615 20140222 405955 protein-coding NCBI-supplied PMID: 17293413 MUTATION: attenuated in mice [PMID:12117951]. 2058 transcriptional activator RfaH rfaH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4494206 APECO1_3477 20140315 405955 protein-coding NCBI-supplied PMID: 17293413 MUTATION: kpsS mutant is attenuated in chickens [PMID:15845486]. 2059 polysialic acid capsule synthesis protein KpsS kpsS Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4494493 APECO1_1145 20130508 405955 protein-coding NCBI-supplied PMID: 17293413 MUTATION: wcaE mutant is attenuated in chickens [PMID:15845486]. 2060 glycosyl transferase family protein wcaE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4494532 APECO1_3367 20140329 405955 protein-coding NCBI-supplied PMID: 17293413 MUTATION: yqi mutant is attenuated in chickens [PMID:19907658]. 2061 Yqi fimbrial adhesin APECO1_3367 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4494642 APECO1_964 20140405 405955 protein-coding NCBI-supplied PMID: 17293413 MUTATION: fliC deletion mutants had reduced adherence in bovine tissue compared to the wild type EHEC and EPEC strains [PMID:17693516]. 2062 flagellin fliC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4494948 APECO1_2059 20130508 405955 protein-coding NCBI-supplied PMID: 17293413 MUTATION: yjjQ mutant is attenuated in chickens [PMID:18375801]. 2063 global regulator Other designations: hypothetical protein yjjQ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4495129 APECO1_2948 20140329 405955 protein-coding NCBI-supplied PMID: 17293413 MUTATION: chuA mutant unable to grow on iron-depleted medium containing heme [PMID:9157252]. 2064 outer membrane heme/hemoglobin receptor ChuA chuA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4495170 APECO1_3594 20140405 405955 protein-coding NCBI-supplied PMID: 17293413 MUTATION: tktA mutant is attenuated in chickens [PMID:15845486]. 2065 transketolase tktA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4495352 APECO1_368 20140406 405955 protein-coding NCBI-supplied PMID: 17293413 MUTATION: attenuated in mice [PMID:11553558]. 2066 transporter tonB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4557754 VACWR053.5 20121122 10245 protein-coding NCBI-supplied hypothetical protein F14.5L Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4674848 NMC0406 20140405 272831 protein-coding NCBI-supplied PMID: 17305430 MUTATION: aroB mutant is attenuated in rats [PMID:11062540]. 2919 3-dehydroquinate synthase aroB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4674894 NMC0350 20140405 272831 protein-coding NCBI-supplied PMID: 17305430 MUTATION: fba mutant is attenuated in rats [PMID:11062540]. 2920 fructose-1,6-bisphosphate aldolase fba Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4675030 NMC1456 20140322 272831 protein-coding NCBI-supplied PMID: 17305430 MUTATION: rfaF mutant is attenuated in rats [PMID:11062540]. 2921 ADP-heptose--LPS heptosyltransferase rfaF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4675118 NMC0007 20140315 272831 protein-coding NCBI-supplied PMID: 17305430 MUTATION: metG mutant is attenuated in rats [PMID:11062540]. 2922 methionyl-tRNA synthetase metG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4675192 NMC1598 20140405 272831 protein-coding NCBI-supplied PMID: 17305430 MUTATION: aroC mutant is attenuated in rats [PMID:11062540]. 2923 chorismate synthase aroC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4675196 NMC1625 20140405 272831 protein-coding NCBI-supplied PMID: 17305430 MUTATION: gdhA mutant is attenuated in rats [PMID:11062540]. 2924 glutamate dehydrogenase gdhA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4675430 NMC0921 20140405 272831 protein-coding NCBI-supplied PMID: 17305430 MUTATION: metF mutant is attenuated in rats [PMID:11062540]. 2925 5,10-methylenetetrahydrofolate reductase metF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4675580 NMC0617 20140315 272831 protein-coding NCBI-supplied PMID: 17305430 MUTATION: ampD mutant is attenuated in rats [PMID:11062540]. 2926 N-acetyl-anhydromuranmyl-L-alanine amidase ampD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4675618 NMC0637 20140315 272831 protein-coding NCBI-supplied PMID: 17305430 MUTATION: rnc mutant is attenuated in rats [PMID:11062540]. 2927 ribonuclease III rnc Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4675619 NMC0408 20140315 272831 protein-coding NCBI-supplied PMID: 17305430 MUTATION: pilQ mutant were unable to colonize human nasopharyngeal tissue in an organ culture model [PMID:18936183]. 2928 pilus secretin pilQ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4675764 NMC1383 20140405 272831 protein-coding NCBI-supplied PMID: 17305430 MUTATION: aroD mutant is attenuated in rats [PMID:11062540]. 2929 3-dehydroquinate dehydratase aroD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4675875 NMC1649 20130508 272831 protein-coding NCBI-supplied PMID: 17305430 MUTATION: exbB mutant is attenuated in rats [PMID:11062540]. 2930 biopolymer transport protein exbB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4675898 NMC1650 20140315 272831 protein-coding NCBI-supplied PMID: 17305430 MUTATION: tonB mutant is unable to replicate within human epithelial cells [PMID:11854233]. 2931 TonB protein tonB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4675932 NMC1090 20140405 272831 protein-coding NCBI-supplied PMID: 17305430 MUTATION: ilvD mutant is attenuated in rats [PMID:11062540]. 2932 dihydroxy-acid dehydratase ilvD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4675978 NMC1902 20140222 272831 protein-coding NCBI-supplied PMID: 17305430 MUTATION: lgtA mutant is attenuated in rats [PMID:11062540]. 2933 lacto-N-neotetraose biosynthesis glycosyl transferase lgtA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4676011 NMC2025 20130508 272831 protein-coding NCBI-supplied PMID: 17305430 MUTATION: ptsH mutant is attenuated in rats [PMID:11062540]. 2934 sugar transport PTS system phosphocarrier protein HPr ptsH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4676178 NMC1844 20140222 272831 protein-coding NCBI-supplied PMID: 17305430 MUTATION: pilF mutant were unable to colonize human nasopharyngeal tissue in an organ culture model [PMID:18936183]. 2935 type IV pilus assembly protein pilF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4676301 NMC1016 20130508 272831 protein-coding NCBI-supplied PMID: 17305430 MUTATION: dedA mutant is attenuated in rats [PMID:11062540]. 2936 DedA protein ortholog dedA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4676346 NMC1772 20140329 272831 protein-coding NCBI-supplied PMID: 17305430 MUTATION: NadA mutation decreases epithelial adhesion of capsulate N. meningitidis and invasion by acapsulate N. meningitidis [PMID:19481311]. 2937 quinolinate synthetase nadA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4676380 NMC1619 20130508 272831 protein-coding NCBI-supplied PMID: 17305430 MUTATION: rfaK mutant is attenuated in rats [PMID:11062540]. 2938 alpha 1,2 N-acetylglucosamine transferase rfaK Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4676394 NMC0067 20140315 272831 protein-coding NCBI-supplied PMID: 17305430 MUTATION: lipB mutant is attenuated in rats [PMID:11062540]. 2939 capsule polysaccharide modification protein lipB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4676427 NMC1497 20140405 272831 protein-coding NCBI-supplied PMID: 17305430 MUTATION: ilvI mutant is attenuated in rats [PMID:11062540]. 2940 acetolactate synthase isozyme III large subunit ilvI Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4676530 NMC2024 20140315 272831 protein-coding NCBI-supplied PMID: 17305430 MUTATION: ptsI mutant is attenuated in rats [PMID:11062540]. 2941 phosphoenolpyruvate-protein phosphotransferase ptsI Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4676581 NMC1810 20140405 272831 protein-coding NCBI-supplied PMID: 17305430 MUTATION: aroE mutant is attenuated in rats [PMID:11062540]. 2942 shikimate dehydrogenase aroE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4676582 NMC1972 20140405 272831 protein-coding NCBI-supplied PMID: 17305430 MUTATION: purL mutant is attenuated in rats [PMID:11062540]. 2943 phosphoribosylformylglycinamidine synthase purL Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4676597 NMC1212 20140315 272831 protein-coding NCBI-supplied PMID: 17305430 MUTATION: mltB mutant is attenuated in rats [PMID:11062540]. 2944 murein hydrolase mltB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4676643 NMC1648 20140222 272831 protein-coding NCBI-supplied PMID: 17305430 MUTATION: exbD mutant is attenuated in rats [PMID:11062540]. 2945 biopolymer transport protein exbD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4676702 NMC1874 20140405 272831 protein-coding NCBI-supplied PMID: 17305430 MUTATION: aroG mutant is attenuated in rats [PMID:11062540]. 2946 phospho-2-dehydro-3-deoxyheptonate aldolase aroG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4677485 BMASAVP1_0602 20140329 320388 II protein-coding NCBI-supplied MUTATION: virG mutant is avirulent in hamsters [PMID:15377793]. 1976 DNA-binding response regulator virG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4682094 CJJ81176_0929 20140322 354242 protein-coding NCBI-supplied MUTATION: PEB1 mutants had a significantly reduced in vivo colonization of broiler chickens [PMID:19349427] 1688 amino acid ABC transporter, ATP-binding protein PEB1 pebC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4682104 CJJ81176_0358 20140322 354242 protein-coding NCBI-supplied MUTATION: A motB insertion-deletion mutant failed to establish colonization in LF mice [PMID:16926420] 1689 flagellar motor protein MotB motB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4682456 CJJ81176_1136 20140329 354242 protein-coding NCBI-supplied MUTATION: Insertional inactivation of the cheY gene in 81-176 resulted in an approx. threefold increase in adherence and invasion in vitro, but this strain was unable to colonize or cause disease in animals [PMID:9076738] 1690 chemotaxis protein CheY cheY Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4682610 CJJ81176_0310 20140329 354242 protein-coding NCBI-supplied MUTATION: A cheA insertion-deletion mutant failed to establish colonization in LF mice [PMID:16926420] 1691 chemotaxis protein CheA cheA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4682683 CJJ81176_1002 20130529 354242 protein-coding NCBI-supplied PMID: 22245776 MUTATION: adherence of deletion mutants of jlpA to HEp-2 epithelial cells was reduced compared with that of parental C. jejuni [PMID:11251839] 1692 surface-exposed lipoprotein jlpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4682759 CJJ81176_0921 20130529 354242 protein-coding NCBI-supplied invasion antigen B ciaB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4682880 CJJ81176_1143 20140215 354242 protein-coding NCBI-supplied MUTATION: pglB impaired in glycosylation showed reduced ability to adhere to INT407 cells and colonize in mice [PMID:11895996]. 1694 general glycosylation pathway protein pglB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4683249 CJJ81176_0927 20140217 354242 protein-coding NCBI-supplied MUTATION: PEB1 mutants had a significantly reduced in vivo colonization of broiler chickens [PMID:19349427] 1695 amino acid ABC transporter, permease protein PEB1 CJJ81176_0927 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4683284 CJJ81176_1413 20140322 354242 protein-coding NCBI-supplied MUTATION: kpsC mutants were defective in colonization and virulence [PMID:16332783] 1696 capsule polysaccharide export protein KpsC kpsC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4683357 CJJ81176_1165 20130529 354242 protein-coding NCBI-supplied MUTATION: knockout strains showed reduced ability to invade epithelial cells [PMID:18644887]. 1697 LPS glycosyltransferase subfamily protein CJJ81176_1165 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4683388 CJJ81176_0226 20140322 354242 protein-coding NCBI-supplied MUTATION: A flil insertion-deletion mutant failed to establish colonization in LF mice [PMID:16926420] 1698 flagellum-specific ATP synthase fliI Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4683465 CJJ81176_0067 20140405 354242 protein-coding NCBI-supplied MUTATION: mutations in ggt showed it to be required for persistent colonization of the avian gut [PMID:17600669] 1699 gamma-glutamyltransferase ggt Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4683585 CJJ81176_1471 20140322 354242 protein-coding NCBI-supplied MUTATION: cadF mutants had reduced binding to immobilized Fn as compared to wt strains [PMID:12576589] 1700 fibronectin-binding protein cadF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4683595 CJJ81176_1146 20140315 354242 protein-coding NCBI-supplied MUTATION: reduce ability to adhere to human epithelial Caco-2 cells [PMID:15184581]. 1701 general glycosylation pathway protein pglH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4683648 CJJ81176_0926 20140222 354242 protein-coding NCBI-supplied MUTATION: PEB1 mutants had a significantly reduced in vivo colonization of broiler chickens [PMID:19349427] 1702 amino acid ABC transporter, permease protein PEB1 CJJ81176_0926 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4683652 CJJ81176_1139 20130529 354242 protein-coding NCBI-supplied MUTATION: knockout mutant impaired for flagella-mediated motility and invasion of intestinal epithelial cells [PMID:16690622]. 1703 general glycosylation pathway protein pglE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4683743 CJJ81176_1441 20140222 354242 protein-coding NCBI-supplied MUTATION: kpsM mutant is significantly reduced in invasion of INT407 cells and reduced in virulence in a ferret diarrhoeal disease model [PMID:11359581]. 4874 capsular polysaccharide ABC transporter, permease protein kpsM Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4683978 BARBAKC583_1172 20140222 360095 protein-coding NCBI-supplied MUTATION: LSS100, a strain that synthesizes markedly greater quantities of GroEL relative to others, significantly accelerates apoptosis of the cocultured HUVECs relative to other strains [PMID:16481529]. 4569 chaperonin GroEL groEL Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4684760 BARBAKC583_0326 20140217 360095 protein-coding NCBI-supplied MUTATION: mutagenesis of ialB decreased bacterial association and invasion of human erythrocytes by 47 to 53% relative to controls [PMID:11401976]. 4570 invasion protein B ialB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4711837 YEP0015 20140215 393305 protein-coding NCBI-supplied PMID: 17173484 MUTATION: lcrV mutant is attenuated in mice [PMID:10216859]. 4006 virulence-associated V antigen lcrV Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4711865 YEP0038 20140222 393305 protein-coding NCBI-supplied PMID: 17173484 MUTATION: yscC mutant is attenuated in mice [PMID:10216859]. 4007 putative type III secretion protein yscC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4711885 YEP0047 20140217 393305 protein-coding NCBI-supplied PMID: 17173484 MUTATION: yscL mutant is attenuated in mice [PMID:10216859]. 4008 type III secretion system protein yscL Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4711894 YEP0033 20140217 393305 protein-coding NCBI-supplied PMID: 17173484 MUTATION: virG mutant is attenuated in mice [PMID:10216859]. 4009 putative type III secretion effector targeting lipoprotein virG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4711903 YEP0031 20140406 393305 protein-coding NCBI-supplied PMID: 17173484 MUTATION: yscU mutant is attenuated in mice [PMID:10216859]. 4010 putative type III secretion protein yscU Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4711911 YEP0028 20140222 393305 protein-coding NCBI-supplied PMID: 17173484 MUTATION: yscR mutant is attenuated in mice [PMID:10216859]. 4011 type III secretion system protein yscR Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4711913 YEP0035 20140406 393305 protein-coding NCBI-supplied PMID: 17173484 MUTATION: virF mutant is attenuated in mice [PMID:10216859]. 4012 virulence regulon transcriptional activator virF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4712699 YE4200 20140329 393305 protein-coding NCBI-supplied PMID: 12834539; 17173484 MUTATION: pstC mutant is attenuated in mice [PMID:10216859]. 4013 phosphate transporter permease subunit PstC pstC Bin Zhao, Oliver He groP WEB: http://www.ncbi.nlm.nih.gov/gene 4712915 YE0610 20140329 393305 protein-coding NCBI-supplied PMID: 12834539; 17173484 MUTATION: dnaJ mutant is attenuated in mice [PMID:10216859]. 4014 chaperone protein DnaJ - dnaJ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4713234 YE1538 20140405 393305 protein-coding NCBI-supplied PMID: 12834539; 17173484 MUTATION: An aroA mutant is highly attenuated in mice [PMID:2777382]. 4938 3-phosphoshikimate 1-carboxyvinyltransferase aroA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4713518 YE2119 20140329 393305 protein-coding NCBI-supplied PMID: 12834539; 17173484; 19775245 MUTATION: pspC mutant is attenuated in mice [PMID:10216859]. 4015 DNA-binding transcriptional activator PspC pspC Bin Zhao, Oliver He rovA slyA WEB: http://www.ncbi.nlm.nih.gov/gene 4713544 YE2144 20140222 393305 protein-coding NCBI-supplied PMID: 12834539; 17173484; 22505678 MUTATION: rovA mutant is attenuated when delivered orally in mice [PMID:12761136]. 4016 transcriptional regulator SlyA - horYe Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4714264 YE2618 20140329 393305 protein-coding NCBI-supplied PMID: 12834539; 17173484 MUTATION: irp1 mutant is attenuated in mice [PMID:10216859]. 4017 yersiniabactin biosynthetic protein irp1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4714558 YE3071 20140405 393305 protein-coding NCBI-supplied PMID: 12834539; 17173484 MUTATION: galE mutant is attenuated in mice [PMID:10216859]. 4018 UDP-glucose 4-epimerase galE Bin Zhao, Oliver He rfbK WEB: http://www.ncbi.nlm.nih.gov/gene 4714559 YE3072 20140405 393305 protein-coding NCBI-supplied PMID: 12834539; 17173484 MUTATION: manB mutant is attenuated in mice [PMID:10216859]. 4019 phosphomannomutase - manB Bin Zhao, Oliver He rfbM WEB: http://www.ncbi.nlm.nih.gov/gene 4714560 YE3073 20140405 393305 protein-coding NCBI-supplied PMID: 12834539; 17173484 MUTATION: manC mutant is attenuated in mice [PMID:10216859]. 4020 mannose-1-phosphate guanylyltransferase - manC Bin Zhao, Oliver He rfpP wbcI WEB: http://www.ncbi.nlm.nih.gov/gene 4714563 YE3076 20140215 393305 protein-coding NCBI-supplied PMID: 12834539; 17173484 MUTATION: wcbI mutant is attenuated in mice [PMID:10216859]. 4021 galactosyltransferase - rfpB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4714564 YE3077 20140329 393305 protein-coding NCBI-supplied PMID: 12834539; 17173484 MUTATION: wbcH mutant is attenuated in mice [PMID:10216859]. 4022 glycosyl transferase wbcH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4714566 YE3079 20140329 393305 protein-coding NCBI-supplied PMID: 12834539; 17173484 MUTATION: wbcF mutant is attenuated in mice [PMID:10216859]. 4023 hypothetical protein wbcF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4714570 YE3083 20140329 393305 protein-coding NCBI-supplied PMID: 12834539; 17173484 MUTATION: wbcC mutant is attenuated in mice [PMID:10216859]. 4024 glycosyltransferase wbcC Bin Zhao, Oliver He rfbG WEB: http://www.ncbi.nlm.nih.gov/gene 4714573 YE3086 20140405 393305 protein-coding NCBI-supplied PMID: 12834539; 17173484 MUTATION: ddhB mutant is attenuated in mice [PMID:10216859]. 4025 CDP-glucose 4,6-dehydratase - ddhB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4714987 YE1612 20140329 393305 protein-coding NCBI-supplied PMID: 12834539; 17173484 MUTATION: htrB mutant has diminished invasion of HeLa cells and is attenuated in vivo [PMID:20385763]. 4026 lipid A biosynthesis lauroyl acyltransferase htrB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4715094 YE2386 20140329 393305 protein-coding NCBI-supplied PMID: 12834539; 17173484 MUTATION: msbB mutant has diminished invasion of HeLa cells [PMID:20385763]. 4027 lipid A biosynthesis (KDO)2-(lauroyl)-lipid IVA acyltransferase msbB Bin Zhao, Oliver He rfbF WEB: http://www.ncbi.nlm.nih.gov/gene 4715407 YE3087 20140405 393305 protein-coding NCBI-supplied PMID: 12834539; 17173484 MUTATION: ddhA mutant is attenuated in mice [PMID:10216859]. 4028 glucose-1-phosphate cytidylyltransferase - ddhA Bin Zhao, Oliver He topA WEB: http://www.ncbi.nlm.nih.gov/gene 4715471 YE2199 20140329 393305 protein-coding NCBI-supplied PMID: 12834539; 17173484 MUTATION: topA mutant is attenuated in mice [PMID:10216859]. 4029 DNA topoisomerase I - supX Bin Zhao, Oliver He gsrA htrA ptd WEB: http://www.ncbi.nlm.nih.gov/gene 4715899 YE0741 20140222 393305 protein-coding NCBI-supplied PMID: 12834539; 17173484 MUTATION: htrA mutant is avirulent in mice [PMID:8675311]. 4030 serine endoprotease - degP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4716124 YE0774 20140329 393305 protein-coding NCBI-supplied PMID: 12834539; 17173484 MUTATION: nlpD mutant is attenuated in mice [PMID:10216859]. 4031 lipoprotein NlpD nlpD Bin Zhao, Oliver He ompB WEB: http://www.ncbi.nlm.nih.gov/gene 4716266 YE4004 20140405 393305 protein-coding NCBI-supplied PMID: 12834539; 17173484 MUTATION: ompR mutant is unable to invade HeLa cells [PMID:15330261]. 4032 osmolarity response regulator - ompR Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4716532 YE4138 20140329 393305 protein-coding NCBI-supplied PMID: 12834539; 17173484 MUTATION: A sodA mutant in Yersinia enterocolitica was highly attenuated in mice [PMID:10496939]. 5015 Mn Other designations: superoxide dismutase sodA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4789543 BMA10229_0713 20140329 412022 II protein-coding NCBI-supplied MUTATION: virG mutant is avirulent in hamsters [PMID:15377793]. 1964 DNA-binding response regulator virG Bin Zhao, Oliver He GaHV2Md5_gp076 WEB: http://www.ncbi.nlm.nih.gov/gene 4811549 MD5V_076 20131019 10390 protein-coding NCBI-supplied PMID: 10933706; 17516161; 18971275; 19189855; 19494050; 19692466; 20137800; 21205328; 21503681; 21789633; 23055556; 23740999 related to bZIP proteins; binds to CtBP - Other designations: oncoprotein MEQ MDV076 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4848512 APL_0061 20140301 416269 protein-coding NCBI-supplied PMID: 18065534 MUTATION: yibK mutant is attenuated in pigs [PMID:12819083]. 4033 tRNA/rRNA methyltransferase yibK Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4848587 APL_1906 20140222 416269 protein-coding NCBI-supplied PMID: 18065534 MUTATION: dnaK mutant is attenuated in porcine model of infection [PMID:10873489]. 4034 molecular chaperone DnaK dnaK Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4848604 APL_0150 20140222 416269 protein-coding NCBI-supplied PMID: 18065534 MUTATION: ngrA mutant is attenuated in pigs [PMID:12819083]. 4035 Na(+)-translocating NADH-quinone reductase subunit A nqrA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4848647 APL_0699 20140405 416269 protein-coding NCBI-supplied PMID: 18065534 MUTATION: aroA mutant is attenuated in pigs [PMID:12027598]. 4036 3-phosphoshikimate 1-carboxyvinyltransferase aroA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4848648 APL_1218 20130511 416269 protein-coding NCBI-supplied PMID: 18065534 MUTATION: fur mutant is attenuated in pigs [PMID:12819083]. 4037 ferric uptake regulation protein fur Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4848653 APL_0690 20140405 416269 protein-coding NCBI-supplied PMID: 18065534 MUTATION: moaA mutant is attenuated in pigs [PMID:12819083]. 4038 molybdenum cofactor biosynthesis protein A moaA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4848714 APL_0841 20140315 416269 protein-coding NCBI-supplied PMID: 18065534 MUTATION: pntB mutant is attenuated in pigs [PMID:12819083]. 4039 pyridine nucleotide transhydrogenase pntB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4848733 APL_0175 20140329 416269 protein-coding NCBI-supplied PMID: 18065534 MUTATION: dksA mutant is attenuated in porcine model of infection [PMID:10873489]. 4040 DnaK suppressor protein dksA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4848738 APL_0956 20130518 416269 protein-coding NCBI-supplied PMID: 18065534 MUTATION: A ΔapxIIA is attenuated in pigs [PMID:12438394]. MUTATION: ureC/apxIIA deletion mutant is attenuated in pigs [PMID:12438394]. 4939 RTX-II toxin determinant A apxIIA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4848740 APL_1426 20140405 416269 protein-coding NCBI-supplied PMID: 18065534 MUTATION: napB mutant is attenuated in pigs [PMID:12819083]. 4041 nitrate reductase cytochrome c-type subunit napB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4848759 APL_0727 20140405 416269 protein-coding NCBI-supplied PMID: 18065534 MUTATION: ilvl mutant is attenuated in pigs [PMID:19703979]. 4042 acetolactate synthase 3 catalytic subunit ilvI Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4848795 APL_1000 20140222 416269 protein-coding NCBI-supplied PMID: 18065534 MUTATION: mrp mutant is attenuated in pigs [PMID:12819083]. 4043 ATPase mrp Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4848844 APL_0987 20140222 416269 protein-coding NCBI-supplied PMID: 18065534 MUTATION: htpG mutant is attenuated in pigs [PMID:12819083]. 4044 heat shock protein 90 htpG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4848887 APL_1499 20140405 416269 protein-coding NCBI-supplied PMID: 18065534 MUTATION: thrC mutant is attenuated in pigs [PMID:12819083]. 4045 threonine synthase thrC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4848935 APL_0074 20140301 416269 protein-coding NCBI-supplied PMID: 18065534 MUTATION: recR mutant is attenuated in pigs [PMID:12819083]. 4046 recombination protein RecR recR Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4848963 APL_0276 20140301 416269 protein-coding NCBI-supplied PMID: 18065534 MUTATION: frpB mutant is avirulent in pigs [PMID:19343711]. 4047 iron-regulated outer membrane protein B frpB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4849025 APL_1582 20140222 416269 protein-coding NCBI-supplied PMID: 18065534 MUTATION: cpxD mutant is attenuated in pigs [PMID:12819083]. 4048 capsule polysaccharide export protein cpxD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4849026 APL_1583 20140215 416269 protein-coding NCBI-supplied PMID: 18065534 MUTATION: cpxC mutant is attenuated in pigs [PMID:12819083]. 4049 capsule polysaccharide export inner-membrane protein cpxC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4849054 APL_0577 20140405 416269 protein-coding NCBI-supplied PMID: 18065534 MUTATION: pnp mutant is attenuated in porcine model of infection [PMID:10873489]. 4050 polynucleotide phosphorylase/polyadenylase pnp Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4849145 APL_0919 20130518 416269 protein-coding NCBI-supplied PMID: 18065534 MUTATION: irp mutant is attenuated in competitive index experiment in pig infection model [PMID:19703979]. 4051 iron-regulated outer membrane protein irp Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4849158 APL_1640 20140222 416269 protein-coding NCBI-supplied PMID: 18065534 MUTATION: fkpA mutant is attenuated in porcine model of infection [PMID:10873489]. 4052 FKBP-type peptidyl-prolyl cis-trans isomerase fkpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4849166 APL_0422 20140405 416269 protein-coding NCBI-supplied PMID: 18065534 MUTATION: argG mutant is attenuated in pigs [PMID:12819083]. 4053 argininosuccinate synthase argG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4849184 APL_1674 20130831 416269 protein-coding NCBI-supplied PMID: 18065534 MUTATION: dmsA mutant is attenuated in pigs [PMID:14638764]. 4054 anaerobic dimethyl sulfoxide reductase subunit A dmsA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4849211 APL_0372 20130511 416269 protein-coding NCBI-supplied PMID: 18065534 MUTATION: corC mutant is attenuated in pigs [PMID:12819083]. 4055 magnesium and cobalt efflux protein corC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4849247 APL_1419 20130518 416269 protein-coding NCBI-supplied PMID: 18065534 MUTATION: mglA mutant is attenuated in pigs [PMID:12819083]. 4056 galactose/methyl galaxtoside transporter ATP-binding protein mglA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4849278 APL_1567 20140329 416269 protein-coding NCBI-supplied PMID: 18065534 MUTATION: tbpA mutant is attenuated in pigs [PMID:12007819]. 4057 transferrin-binding protein 1 Tbp1 tbpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4849429 APL_1905 20140222 416269 protein-coding NCBI-supplied PMID: 18065534 MUTATION: dnaJ mutant is attenuated in pigs [PMID:12819083]. 4058 chaperone protein DnaJ dnaJ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4849515 APL_0651 20140405 416269 protein-coding NCBI-supplied PMID: 18065534 MUTATION: galU mutant is attenuated in pigs [PMID:12819083]. 4059 UTP--glucose-1-phosphate uridylyltransferase galU Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4849643 APL_1862 20140405 416269 protein-coding NCBI-supplied PMID: 18065534 MUTATION: aroQ mutant is attenuated in pigs [PMID:11731178]. 4060 3-dehydroquinate dehydratase aroQ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4849723 APL_1507 20140222 416269 protein-coding NCBI-supplied PMID: 18065534 MUTATION: tig mutant is attenuated in porcine model of infection [PMID:10873489]. 4061 trigger factor tig Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4849746 APL_0771 20140405 416269 protein-coding NCBI-supplied PMID: 18065534 MUTATION: lpdA mutant is attenuated in porcine model of infection [PMID:10873489]. 4062 dihydrolipoamide dehydrogenase lpdA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4849777 APL_1047 20130511 416269 protein-coding NCBI-supplied PMID: 18065534 MUTATION: hgbA mutant is attenuated in pigs [PMID:16699590]. 4063 hemoglobin-binding protein A hgbA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4849793 APL_1570 20130511 416269 protein-coding NCBI-supplied PMID: 18065534 MUTATION: exbB mutant is attenuated in porcine model of infection [PMID:10873489]. 4064 biopolymer transport ExbB protein exbB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4849853 APL_0404 20140405 416269 protein-coding NCBI-supplied PMID: 18065534 MUTATION: hemA mutant is attenuated in pigs [PMID:12819083]. 4065 glutamyl-tRNA reductase hemA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4849898 APL_1445 20140217 416269 protein-coding NCBI-supplied PMID: 18065534 MUTATION: apxlC mutant is attenuated in mice [PMID:18062275]. 4066 RTX-I toxin-activating lysine-acyltransferase ApxIC apxIC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4849920 APL_0592 20140329 416269 protein-coding NCBI-supplied PMID: 18065534 MUTATION: guaA mutant is attenuated in pigs [PMID:12819083]. 4067 GMP synthase guaA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4849922 APL_0120 20130511 416269 protein-coding NCBI-supplied PMID: 18065534 MUTATION: prc mutant is attenuated in pigs [PMID:12819083]. 4068 carboxy-terminal protease prc Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4849930 APL_0376 20130511 416269 protein-coding NCBI-supplied PMID: 18065534 MUTATION: lon mutant is attenuated in pigs [PMID:12819083]. 4069 ATP-dependent protease La lon Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4849940 APL_0112 20140329 416269 protein-coding NCBI-supplied PMID: 18065534 MUTATION: hemE mutant is attenuated in pigs [PMID:12819083]. 4070 uroporphyrinogen decarboxylase hemE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4849992 APL_1868 20140301 416269 protein-coding NCBI-supplied PMID: 18065534 MUTATION: dsbA mutant is attenuated in pigs [PMID:12819083]. 4071 Thiol:disulfide interchange protein dsbA precursor dsbA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4850001 APL_0114 20140222 416269 protein-coding NCBI-supplied PMID: 18065534 MUTATION: hupA mutant is attenuated in porcine model of infection [PMID:10873489]. 4072 DNA-binding protein HU hupA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4850085 APL_1647 20140405 416269 protein-coding NCBI-supplied PMID: 18065534 MUTATION: atpG mutant is attenuated in porcine model of infection [PMID:10873489]. 4073 F0F1 ATP synthase subunit gamma atpG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4850127 APL_1386 20140222 416269 protein-coding NCBI-supplied PMID: 18065534 MUTATION: rpmF mutant is attenuated in porcine model of infection [PMID:10873489]. 4074 50S ribosomal protein L32 rpmF Bin Zhao, Oliver He yebL WEB: http://www.ncbi.nlm.nih.gov/gene 4850149 APL_1440 20140301 416269 protein-coding NCBI-supplied PMID: 18065534 MUTATION: znuA mutant is attenuated in pigs [PMID:12819083]. 4075 high-affinity zinc transporter periplasmic protein - znuA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4850203 APL_1648 20140405 416269 protein-coding NCBI-supplied PMID: 18065534 MUTATION: atpA mutant is attenuated in pigs [PMID:12819083]. 4076 F0F1 ATP synthase subunit alpha atpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4850217 APL_1584 20140222 416269 protein-coding NCBI-supplied PMID: 18065534 MUTATION: cpxB mutant is attenuated in pigs [PMID:12819083]. 4077 capsule polysaccharide export inner-membrane protein cpxB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4850247 APL_1444 20140301 416269 protein-coding NCBI-supplied PMID: 18065534 MUTATION: apxIA mutant is attenuated in mice [PMID:16930871]. 4078 RTX-I toxin determinant A apxIA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4850274 APL_0333 20130518 416269 protein-coding NCBI-supplied PMID: 18065534 MUTATION: visC mutant is attenuated in pigs [PMID:12819083]. 4079 monooxygenase family protein visC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4850318 APL_0656 20140222 416269 protein-coding NCBI-supplied PMID: 18065534 MUTATION: hlyX mutant is attenuated in pigs [PMID:16040973]. 4080 fumarate/nitrate reduction transcriptional regulator hlyX Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4850335 APL_1568 20140215 416269 protein-coding NCBI-supplied PMID: 18065534; 21297163; 22369045 MUTATION: tbpB mutant is attenuated in pigs [PMID:12007819]. 4081 transferrin-binding protein tbpB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4850346 APL_1649 20140405 416269 protein-coding NCBI-supplied PMID: 18065534 MUTATION: atpH mutant is attenuated in porcine model of infection [PMID:10873489]. 4082 F0F1 ATP synthase subunit delta atpH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4850390 APL_1216 20140329 416269 protein-coding NCBI-supplied PMID: 18065534 MUTATION: luxS mutant is attenuated in mice [PMID:18585450]. 4083 S-ribosylhomocysteinase luxS Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4850431 APL_0048 20130511 416269 protein-coding NCBI-supplied PMID: 18065534 MUTATION: arcA mutant is attenuated in pigs [PMID:17881160]. 4084 two-component response regulator arcA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4850464 APL_0394 20130518 416269 protein-coding NCBI-supplied PMID: 18065534 MUTATION: rpoE mutant is attenuated in pigs [PMID:12819083]. 4085 RNA polymerase sigma factor RpoE rpoE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4850473 APL_0030 20140222 416269 protein-coding NCBI-supplied PMID: 18065534 MUTATION: prfC mutant is attenuated in pigs [PMID:12819083]. 4086 peptide chain release factor 3 prfC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4882076 BURPS668_3556 20140405 320373 I protein-coding NCBI-supplied MUTATION: pabB mutant is attenuated in mice [PMID:19121696]. 1966 anthranilate synthase component I pabB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4882105 BURPS668_3275 20140329 320373 I protein-coding NCBI-supplied MUTATION: pabB mutant is avirulent in mice [PMID:19121696]. 1967 para-aminobenzoate synthase, component I pabB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4883825 BURPS668_3267 20140405 320373 I protein-coding NCBI-supplied MUTATION: purM mutant is attenuated in mice [PMID:16714590]. 1968 phosphoribosylaminoimidazole synthetase purM Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4884302 BURPS668_1689 20140405 320373 I protein-coding NCBI-supplied MUTATION: aroC mutant is highly attenuated in mice [PMID:19323044]. 1969 chorismate synthase aroC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4887799 BURPS668_A2153 20130610 320373 II protein-coding NCBI-supplied MUTATION: BopA mutant is attenuated in mice [PMID:16714590]. 1965 BopA protein BURPS668_A2153 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4890091 BMA10247_A1669 20140329 320389 II protein-coding NCBI-supplied MUTATION: virG mutant is avirulent in hamsters [PMID:15377793]. 1975 DNA-binding response regulator virG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4899749 BURPS1106A_1713 20140405 357348 I protein-coding NCBI-supplied MUTATION: aroC mutant is highly attenuated in mice [PMID:19323044]. 1961 chorismate synthase aroC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4900497 BURPS1106A_3583 20140329 357348 I protein-coding NCBI-supplied MUTATION: pabB mutant is attenuated in mice [PMID:19121696]. 1962 anthranilate synthase component I pabB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4902449 BURPS1106A_3308 20140406 357348 I protein-coding NCBI-supplied MUTATION: pabB mutant is attenuated in mice [PMID:19121696]. 1963 para-aminobenzoate synthase, component I pabB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4914074 CD630_06600 20140329 272563 protein-coding NCBI-supplied PMID: 16804543; 17901056; 18509107; 19324080; 19781061; 20070948; 20620216; 20675495; 20808849; 20844489; 21349987; 22107906; 23484044; 23935501; 24167244; 24311789 toxin B tcdB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4914076 CD630_06630 20140329 272563 protein-coding NCBI-supplied PMID: 16804543; 18385352; 18509107; 19324080; 20675495; 20844489; 21349987; 21595735; 22107906; 22571633; 22747490; 24311789 toxin A tcdA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4915973 CD630_26040 20121222 272563 pseudo NCBI-supplied PMID: 18385352 pseudo CD630_26040 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4933995 CNBA7290 20140405 283643 1 protein-coding NCBI-supplied MUTATION: pbs2 mutant is attenuated in mice [PMID:15728721]. 4858 hypothetical protein CNBA7290 MUTATION: It serves as an important link between sterol biosynthesis, oxygen sensing, CoCl2 sensitivity. The mutation showed no virulence in a mouse infection model [PMID:19749173]. 5315 MUTATION: MPD is required for mannitol biosynthesis and the ability to synthesize mannitol is essential for wild-type stress tolerance and virulence [PMID:11021946]. 5334 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4939624 CNBN0070 20140406 283643 14 protein-coding NCBI-supplied MUTATION: nmt mutant is attenuated in immunosuppressed rabbits [PMID:7991574]. 4738 hypothetical protein CNBN0070 Bin Zhao, Oliver He lspA WEB: http://www.ncbi.nlm.nih.gov/gene 4963525 SpyM51170 20140222 160491 protein-coding NCBI-supplied PMID: 17012393 MUTATION: lsp mutant is attenuated in a murine model of soft tissue infection [PMID:19398546]. 4429 lipoprotein signal peptidase - lsp Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4964259 SpyM51681 20140329 160491 protein-coding NCBI-supplied PMID: 17012393 MUTATION: scpA mutant is attenuated in mouse pneumonia model [PMID:9119483]. 4430 C5A peptidase precursor scpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4994878 ASA_3762 20140217 382245 protein-coding NCBI-supplied PMID: 18801193 MUTATION: asaI mutant is attenuated in fish [PMID:20708354]. 4087 N-acyl homoserine lactone synthase asaI Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4995831 ASA_0414 20140215 382245 protein-coding NCBI-supplied PMID: 18801193 MUTATION: tapA mutant is attenuated in rainbow trout [PMID:12240967]. 4088 type IV prepilin TapA tapA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4996672 ASA_3136 20140322 382245 protein-coding NCBI-supplied PMID: 18801193 MUTATION: asoB mutant was avirulent via immersion bath in rainbow trout [PMID:8917088]. 4089 inner membrane protein YjeH asoB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4997369 ASA_1859 20140405 382245 protein-coding NCBI-supplied PMID: 18801193 MUTATION: aroA mutant is attenuated in salmon [PMID:8478107]. 4090 3-phosphoshikimate 1-carboxyvinyltransferase aroA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4998373 ASA_4266 20140222 382245 protein-coding NCBI-supplied PMID: 18801193 TTSS effector protein AexT aexT Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4998702 ASA_1660 20111201 382245 pseudo NCBI-supplied MUTATION: asaP1 mutant was attenuated in charr and salmon [PMID:18952802]. 4092 toxic extracellular endopeptidase asaP1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4999240 ASA_P5G070 20140406 382245 protein-coding NCBI-supplied MUTATION: ascV mutant is attenuated in rainbow trout model [PMID:15942017]. 4093 AscV protein ascV Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4999280 ASA_P5G009 20140329 382245 protein-coding NCBI-supplied MUTATION: aopH mutant is attenuated in salmon [PMID:16735747]. 4094 putative protein-tyrosine phosphatase Aop effector AopH aopH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 4999328 ASA_P5G057 20130703 382245 protein-coding NCBI-supplied MUTATION: ascC mutant was less invasive of Atlantic salmon anterior head kidney leucocytes (AHKL) and had less survival than the wild type strain [PMID:19751835]. 4095 AscC protein ascC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5062094 YPDSF_3554 20140222 386656 protein-coding NCBI-supplied MUTATION: greA mutants are attenuated in mice [PMID:14742535]. 1820 transcription elongation factor GreA greA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5062871 YPDSF_2980 20140406 386656 protein-coding NCBI-supplied MUTATION: relA spoT deletion mutants are attenuated in mice [PMID:19701461]. 1821 GDP/GTP pyrophosphokinase relA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5062894 YPDSF_3003 20140222 386656 protein-coding NCBI-supplied MUTATION: pcm mutant is attenuated in mice [PMID:14742535]. 1822 protein-L-isoaspartate O-methyltransferase pcm Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5063065 YPDSF_3726 20140406 386656 protein-coding NCBI-supplied MUTATION: purH mutant is attenuated in mice [PMID:14742535]. 1823 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase purH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5063531 YPDSF_2596 20121017 386656 protein-coding NCBI-supplied MUTATION: smpB ssrA mutant is attenuated in mice [PMID:20065026]. 1824 SsrA-binding protein smpB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5063532 YPDSF_R0054 20111021 386656 miscRNA NCBI-supplied MUTATION: smpB ssrA mutant is attenuated in mice [PMID:20065026]. 1825 miscRNA ssrA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5064369 YPDSF_1918 20121017 386656 protein-coding NCBI-supplied MUTATION: ompX mutants are attenuated in their ability to attach to and invade HeLa cells [PMID:17768237]. 1826 outer membrane protein X ompX Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5133978 VC0395_0341 20140405 345073 1 protein-coding NCBI-supplied PMID: 19115014 MUTATION: zwf mutant is attenuated in mice [PMID:11952899]. 2377 glucose-6-phosphate 1-dehydrogenase zwf Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5133989 VC0395_0463 20140405 345073 1 protein-coding NCBI-supplied PMID: 19115014 MUTATION: ydbK mutant is attenuated in mice [PMID:11952899]. 2378 pyruvate-flavoredoxin oxidoreductase ydbK Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5134229 VC0395_0510 20140322 345073 1 protein-coding NCBI-supplied PMID: 19115014; 21366345 accessory enterotoxin ace Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5134487 VC0395_0511 20140322 345073 1 protein-coding NCBI-supplied PMID: 17553496; 19115014 zona occludens toxin zot Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5134754 VC0395_0628 20140329 345073 1 protein-coding NCBI-supplied PMID: 19115014 MUTATION: phaC mutant is attenuated in mice [PMID:11952899]. 2381 polyhydroxyalkanoic acid synthase phaC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5134988 VC0395_0512 20140322 345073 1 protein-coding NCBI-supplied PMID: 19115014 cholera enterotoxin, A subunit ctxA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5135110 VC0395_A0037 20140405 345073 2 protein-coding NCBI-supplied PMID: 19115014 MUTATION: pykF mutant is attenuated in mice [PMID:11952899]. 2329 pyruvate kinase pykF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5135123 VC0395_A2122 20140405 345073 2 protein-coding NCBI-supplied PMID: 19115014 MUTATION: fbp mutant is attenuated in mice [PMID:11952899]. 2330 fructose-1,6-bisphosphatase fbp Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5135225 VC0395_A2397 20140406 345073 2 protein-coding NCBI-supplied PMID: 19115014 MUTATION: cyaA mutant is attenuated in mice [PMID:11952899]. 2331 adenylate cyclase cyaA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5135247 VC0395_A1690 20140222 345073 2 protein-coding NCBI-supplied PMID: 19115014; 21965571 MUTATION: fur mutant is attenuated in mice [PMID:11952899]. 2332 ferric uptake regulator fur Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5135251 VC0395_A1317 20140329 345073 2 protein-coding NCBI-supplied PMID: 19115014 MUTATION: mukB mutant is attenuated in mice [PMID:11952899]. 2333 cell division protein MukB mukB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5135279 VC0395_A1062 20140322 345073 2 protein-coding NCBI-supplied PMID: 19115014; 21366345 accessory enterotoxin ace Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5135353 VC0395_A2232 20140405 345073 2 protein-coding NCBI-supplied PMID: 19115014 MUTATION: frdC mutant is attenuated in mice [PMID:11952899]. 2335 fumarate reductase subunit C frdC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5135444 VC0395_A2622 20140406 345073 2 protein-coding NCBI-supplied PMID: 19115014 MUTATION: rfbB mutant is attenuated in mice [PMID:9515705]. 2336 phosphomannomutase rfbB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5135591 VC0395_A2420 20140315 345073 2 protein-coding NCBI-supplied PMID: 19115014 MUTATION: ubiC mutant is attenuated in mice [PMID:11952899]. 2337 chorismate--pyruvate lyase ubiC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5135619 VC0395_A1429 20140322 345073 2 protein-coding NCBI-supplied PMID: 19115014 MUTATION: tolB mutant is attenuated in mice [PMID:11952899]. 2338 translocation protein TolB tolB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5135659 VC0395_A2035 20140329 345073 2 protein-coding NCBI-supplied PMID: 19115014 MUTATION: acpS mutant is attenuated in mice [PMID:11952899]. 2339 4'-phosphopantetheinyl transferase acpS Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5135811 VC0395_A1640 20140322 345073 2 protein-coding NCBI-supplied PMID: 19115014 cytochrome c-type biogenesis protein CcmF ccmF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5135974 VC0395_A0360 20140215 345073 2 protein-coding NCBI-supplied PMID: 17434972; 19115014 MUTATION: tcpT mutant is attenuated in mice [PMID:9515705]. 2341 toxin co-regulated pilus biosynthesis protein T tcpT Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5136021 VC0395_A0505 20140322 345073 2 protein-coding NCBI-supplied PMID: 17890167; 17898856; 19115014; 21542860 MUTATION: toxR mutant is attenuated in mice [PMID:2883655]. 2342 cholera toxin transcriptional activator toxR Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5136023 VC0395_A1060 20140405 345073 2 protein-coding NCBI-supplied PMID: 19115014 cholera enterotoxin, A subunit ctxA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5136051 VC0395_A1967 20140405 345073 2 protein-coding NCBI-supplied PMID: 19115014 MUTATION: carB mutant is attenuated in mice [PMID:11952899]. 2344 carbamoyl phosphate synthase large subunit carB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5136175 VC0395_A1061 20140322 345073 2 protein-coding NCBI-supplied PMID: 19115014 zona occludens toxin zot Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5136329 VC0395_A0020 20140329 345073 2 protein-coding NCBI-supplied PMID: 19115014 MUTATION: gshB mutant is attenuated in mice [PMID:11952899]. 2346 glutathione synthetase gshB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5136378 VC0395_A1880 20140322 345073 2 protein-coding NCBI-supplied PMID: 19115014 MUTATION: nqrE mutant is attenuated in mice [PMID:11952899]. 2347 Na(+)-translocating NADH-quinone reductase subunit E nqrE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5136416 VC0395_A1607 20140405 345073 2 protein-coding NCBI-supplied PMID: 19115014 MUTATION: fabG mutant is attenuated in mice [PMID:11952899]. 2348 3-ketoacyl-ACP reductase fabG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5136424 VC0395_A0363 20140322 345073 2 protein-coding NCBI-supplied PMID: 18849430; 19115014; 21330435; 21542860; 21778208; 21856848; 21883522 MUTATION: toxT mutant is attenuated in mice [PMID:9515705]. 2349 TCP pilus virulence regulatory protein tcpN/toxT Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5136447 VC0395_A2652 20140405 345073 2 protein-coding NCBI-supplied PMID: 19115014 MUTATION: purD mutant is attenuated in mice [PMID:9515705]. 2350 phosphoribosylamine--glycine ligase purD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5136575 VC0395_A0062 20140329 345073 2 protein-coding NCBI-supplied PMID: 19115014 MUTATION: rpoS mutants had defective colonization ability of mice intestines compared to the wild type [PMID:11083783]. 2351 RNA polymerase sigma factor RpoS rpoS Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5136631 VC0395_A0795 20140405 345073 2 protein-coding NCBI-supplied PMID: 19115014 MUTATION: trpG mutant is attenuated in mice [PMID:11952899]. 2352 anthranilate synthase component II trpG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5136658 VC0395_A0525 20140405 345073 2 protein-coding NCBI-supplied PMID: 19115014 MUTATION: purF mutant is attenuated in mice [PMID:11952899]. 2353 amidophosphoribosyltransferase purF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5136680 VC0395_A0395 20140329 345073 2 protein-coding NCBI-supplied PMID: 19115014 MUTATION: purL mutant is attenuated in mice [PMID:11952899]. 2354 phosphoribosylformylglycinamidine synthase purL Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5136709 VC0395_A2045 20140222 345073 2 protein-coding NCBI-supplied PMID: 19115014 MUTATION: rpoE mutant is attenuated in mice [PMID:12228259]. 2355 RNA polymerase sigma factor RpoE rpoE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5136723 VC0395_A2029 20140217 345073 2 protein-coding NCBI-supplied PMID: 19115014 MUTATION: relA mutant is attenuated in mice [PMID:12896985]. 2356 GTP pyrophosphokinase relA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5136731 VC0395_A2394 20140405 345073 2 protein-coding NCBI-supplied PMID: 19115014 MUTATION: lysA mutant is attenuated in mice [PMID:11952899]. 2357 diaminopimelate decarboxylase lysA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5136758 VC0395_A1989 20140405 345073 2 protein-coding NCBI-supplied PMID: 19115014 MUTATION: aceF mutant is attenuated in mice [PMID:11952899]. 2358 dihydrolipoamide acetyltransferase aceF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5136800 VC0395_A0353 20140405 345073 2 protein-coding NCBI-supplied PMID: 19054108; 19115014; 20545841 MUTATION: tcpA mutant has defect in colonization of infant mice [PMID:8698524]. 2359 toxin co-regulated pilin tcpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5136801 VC0395_A0366 20140222 345073 2 protein-coding NCBI-supplied PMID: 19115014 MUTATION: acfC mutant had a defect in colonization of mice, and had a ten-fold increase in the 50% lethal dose in mice [PMID:2902009]. 2360 accessory colonization factor AcfC acfC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5136823 VC0395_A2629 20140322 345073 2 protein-coding NCBI-supplied PMID: 19115014 MUTATION: rfbL mutant is attenuated in mice [PMID:9515705]. 2361 rfbL protein rfbL Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5136909 VC0395_A1879 20140322 345073 2 protein-coding NCBI-supplied PMID: 19115014 MUTATION: nqrF mutant is attenuated in mice [PMID:11952899]. 2362 Na(+)-translocating NADH-quinone reductase subunit F nqrF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5136975 VC0395_A1196 20140405 345073 2 protein-coding NCBI-supplied PMID: 19115014 MUTATION: galM mutant is attenuated in mice [PMID:11952899]. 2363 aldose 1-epimerase galM Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5137028 VC0395_A2037 20140322 345073 2 protein-coding NCBI-supplied PMID: 19115014 MUTATION: recO mutant is attenuated in mice [PMID:11952899]. 2364 DNA repair protein RecO recO Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5137059 VC0395_A2491 20140405 345073 2 protein-coding NCBI-supplied PMID: 19115014 MUTATION: ilvD mutant is attenuated in mice [PMID:11952899]. 2365 dihydroxy-acid dehydratase ilvD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5137095 VC0395_A1929 20140322 345073 2 protein-coding NCBI-supplied PMID: 19115014 MUTATION: deoC mutant is attenuated in mice [PMID:11952899]. 2366 deoxyribose-phosphate aldolase deoC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5137124 VC0395_A0365 20140222 345073 2 protein-coding NCBI-supplied PMID: 19115014; 19929967 MUTATION: acfB mutant had a defect in colonization of mice, and had a ten-fold increase in the 50% lethal dose in mice [PMID:2902009]. 2367 accessory colonization factor AcfB acfB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5137360 VC0395_A2468 20140405 345073 2 protein-coding NCBI-supplied PMID: 19115014 MUTATION: purK mutant is attenuated in mice [PMID:9515705]. 2368 phosphoribosylaminoimidazole carboxylase ATPase subunit purK Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5137512 VC0395_A0615 20140406 345073 2 protein-coding NCBI-supplied PMID: 19115014 MUTATION: pta mutant is attenuated in mice [PMID:9515705]. 2369 phosphate acetyltransferase pta Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5137546 VC0395_A0368 20140322 345073 2 protein-coding NCBI-supplied PMID: 19115014 MUTATION: acfA mutant had a defect in colonization of mice, and had a ten-fold increase in the 50% lethal dose in mice [PMID:2902009]. 2370 accessory colonization factor AcfA acfA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5137652 VC0395_A1197 20140405 345073 2 protein-coding NCBI-supplied PMID: 19115014 MUTATION: galK mutant is attenuated in mice [PMID:11952899]. 2371 galactokinase galK Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5137723 VC0395_A1968 20140405 345073 2 protein-coding NCBI-supplied PMID: 19115014 MUTATION: carA mutant is attenuated in mice [PMID:11952899]. 2372 carbamoyl phosphate synthase small subunit carA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5137829 VC0395_A0108 20140322 345073 2 protein-coding NCBI-supplied PMID: 19115014 MUTATION: sspA mutant is attenuated in mice [PMID:11952899]. 2373 stringent starvation protein A sspA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5137832 VC0395_A0630 20140405 345073 2 protein-coding NCBI-supplied PMID: 19115014 MUTATION: bioB mutant is attenuated in mice [PMID:9515705]. 2374 biotin synthase bioB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5137888 VC0395_A0028 20140322 345073 2 protein-coding NCBI-supplied PMID: 12065481; 19115014 MUTATION: irgA mutant is attenuated in mice [PMID:2152889]. 2375 enterobactin receptor protein irgA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5137918 VC0395_A0361 20140406 345073 2 protein-coding NCBI-supplied PMID: 19115014; 23519659 MUTATION: tcpE mutant is attenuated in mice [PMID:9515705]. 2376 toxin co-regulated pilus biosynthesis protein E tcpE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5180329 LPC_2500 20130704 400673 protein-coding NCBI-supplied PMID: 17888731 MUTATION: mip mutants are approximately 50- to 100-fold less infective for A. castellanii and for human mononuclear phagocytes in vitro compared with their isogenic Mip-positive parental strains [PMID:7591108]. 1827 macrophage infectivity potentiator mip Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5180371 LPC_2545 20140222 400673 protein-coding NCBI-supplied PMID: 17888731 MUTATION: iraA mutant is attenuated in guinea pigs [PMID:10678909]. 1828 small-molecule methyltransferase IraA iraA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5180541 LPC_0709 20140406 400673 protein-coding NCBI-supplied PMID: 17888731 MUTATION: rpoS mutant has defective intracellular replication in its protozoan host [PMID:19218380]. 1829 stationary phase specific sigma factor RpoS rpoS Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5180685 LPC_0854 20140329 400673 protein-coding NCBI-supplied PMID: 17888731 MUTATION: cpxR mutant is attenuated in mouse macrophages [PMID:16997951]. 1830 transcriptional regulator CpxR cpxR Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5180855 LPC_1029 20121017 400673 protein-coding NCBI-supplied PMID: 17888731; 20153694 MUTATION: plaB mutant is attenuated in guinea pigs [PMID:20153694]. 1831 phospholipase plaB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5181617 LPC_1809 20140406 400673 protein-coding NCBI-supplied PMID: 17888731 MUTATION: djlA mutant is attenuated in mouse macrophages [PMID:16997951]. 1832 Dna-J like membrane chaperone protein djlA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5182246 LPC_0447 20121017 400673 protein-coding NCBI-supplied PMID: 17888731 MUTATION: icmX mutant is attenuated in guinea pigs [PMID:10393970]. 1833 intracellular multiplication protein IcmX icmX Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5182249 LPC_0450 20140406 400673 protein-coding NCBI-supplied PMID: 17888731 MUTATION: dotA mutant is unable to replicate in mouse macrophages [PMID:16997951]. 1834 organelle trafficking lipoprotein defect DotA dotA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5182260 LPC_0461 20140405 400673 protein-coding NCBI-supplied PMID: 17888731 MUTATION: dotB mutant is attenuated in guinea pigs [PMID:10393970]. 1835 organelle trafficking lipoprotein defect DotB dotB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5182279 LPC_0482 20140406 400673 protein-coding NCBI-supplied PMID: 17888731 MUTATION: feoB mutant is attenuated in human macrophages [PMID:12228295]. 1836 ferrous iron transporter B feoB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5182556 LPC_2777 20121017 400673 protein-coding NCBI-supplied PMID: 17888731 MUTATION: lvgA mutant is attenuated in guinea pigs [PMID:12704109]. 1837 hypothetical protein lvgA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5182665 LPC_2887 20140406 400673 protein-coding NCBI-supplied PMID: 17888731 MUTATION: icmB mutant is attenuated in guinea pigs [PMID:10393970]. 1838 hypothetical protein icmB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5182669 LPC_2891 20140406 400673 protein-coding NCBI-supplied PMID: 17888731 MUTATION: icmG mutant is attenuated in mice [PMID:10393970]. 1839 hypothetical protein icmG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5182750 LPC_2972 20140406 400673 protein-coding NCBI-supplied PMID: 17888731 MUTATION: fur mutant is attenuated in growth within U937 cell monolayers [PMID:8975903]. 1840 ferric uptake regulation protein fur Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5182932 LPC_3157 20140405 400673 protein-coding NCBI-supplied PMID: 17888731 MUTATION: ptsP mutant is attenuated in guinea pigs [PMID:11447151]. 1841 phosphoenolpyruvate protein phosphotransferase PtsP ptsP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5211668 MRA_1823 20140406 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: mgtC mutant is attenuated in human macrophages and mice [PMID:10760138]. 1845 Mg2+ transport P-type ATPase C mgtC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5211729 MRA_0362 20140217 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: hspR mutant is attenuated in mice [PMID:11385512]. 1846 heat shock protein transcriptional repressor HspR hspR Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5211733 MRA_3454 20140217 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: sigD mutant is attenuated in human macrophages and mice [PMID:15659067]. 1847 RNA polymerase sigma factor SigD sigD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5211735 MRA_3456 20140217 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: whiB3 mutant is attenuated in mice [PMID:11880648]. 1848 transcriptional regulatory protein whib-like WhiB3 whiB3 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5211750 MRA_0596 20140222 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: mce2A mutant is attenuated in mice [PMID:15804490]. 1849 MCE-family protein Mce2A mce2A Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5211814 MRA_0482 20130704 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: hbhA mutant is attenuated in attachment and invasion of pneumocytes [PMID:11449276]. 1850 iron-regulated heparin binding hemagglutinin Hbha hbhA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5211927 MRA_2063 20140406 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: pks12 mutant is attenuated in mice [PMID:12819062]. 1851 polyketide synthase pks12 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5211946 MRA_1977 20140222 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: mce3A mutant is attenuated in mice [PMID:15804490]. 1852 MCE-family protein Mce3A mce3A Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5212238 MRA_0174 20140406 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: fadD5 mutant is attenuated in mice [PMID:20214478]. 1853 long-chain-fatty-acid--CoA ligase fadD5 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5212242 MRA_0743 20130704 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: sigL mutant is attenuated in mice [PMID:16199577]. 1854 RNA polymerase sigma factor SigL sigL Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5212263 MRA_0210 20140222 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: mmpL11 mutant is attenuated in mice [PMID:15908378]. 1855 membrane protein MmpL11 mmpL11 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5212269 MRA_0497 20140222 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: senX3-regX3 deletion mutant is attenuated in mice [PMID:12777483]. 1856 two component sensor histidine kinase SenX3 senX3 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5212270 MRA_0498 20140222 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: senX3-regX3 deletion mutant is attenuated in mice [PMID:12777483]. 1857 two component sensory transduction protein RegX3 regX3 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5212285 MRA_2369 20140405 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: plcABC triple mutants are attenuated in mice [PMID:12100560]. 1858 phospholipase C 3 PlcC plcC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5212286 MRA_2370 20140406 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: plcABC triple mutants are attenuated in mice [PMID:12100560]. 1859 membrane-associated phospholipase C 2 plcB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5212287 MRA_2371 20140405 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: plcABC triple mutants are attenuated in mice [PMID:12100560]. 1860 membrane-associated phospholipase C 1 plcA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5212298 MRA_3165 20140222 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: devR mutant is attenuated in guinea pigs [PMID:14987770]. 1861 two component transcriptional regulatory protein DevR devR Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5212340 MRA_2046 20140222 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: hspX mutant is attenuated in murine macrophages and THP-1 cells [PMID:9689123]. 1862 antigen Hsp20 hspX Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5212516 MRA_2956 20140222 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: fadD26 mutant is attenuated in mice [PMID:15958066]. 1863 acyl-CoA synthetase fadD26 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5212564 MRA_2083 20140222 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: sigC mutant is attenuated in mice [PMID:15049808]. 1864 RNA polymerase sigma factor SigC sigC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5212587 MRA_0988 20140222 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: mprA mutant is attenuated in mice [PMID:11675502]. 1865 two component response transcriptional regulatory protein MprA mprA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5212589 MRA_0990 20140215 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: pepD mutant has altered virulence in mouse model of infection [PMID:20061478]. 1866 serine protease PepD pepD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5212676 MRA_0049 20140405 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: ino1 mutant is attenuated in resting macrophages and guinea pigs [PMID:14763976]. 1867 1L-myo-inositol-1-phosphate synthase ino1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5212696 MRA_2208 20140405 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: trpD mutant is attenuated in mice [PMID:11160012]. 1868 anthranilate phosphoribosyltransferase trpD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5212740 MRA_3527 20140222 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: lipF mutant is attenuated in mice lungs [PMID:10564470]. 1869 esterase lipF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5212915 MRA_2973 20140215 419947 protein-coding NCBI-supplied PMID: 18584054; 22123254 MUTATION: pks1 mutant is attenuated in mice [PMID:12730158]. 1870 polyketide synthase Pks1 pks1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5212916 MRA_2974 20140215 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: pks15 mutant is attenuated in mice [PMID:12730158]. 1871 polyketide synthase pks15 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5213172 MRA_2416 20140329 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: cysH mutant is attenuated in mice [PMID:16553880]. 1872 phosphoadenosine phosphosulfate reductase cysH Bin Zhao, Oliver He azi div WEB: http://www.ncbi.nlm.nih.gov/gene 5213460 MRA_1833 20140405 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: secA2 mutant is attenuated in mice [PMID:12675804]. 1873 preprotein translocase subunit SecA - secA2 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5213487 MRA_2612 20140222 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: Long-term survival of the relA mutant during in vitro starvation or nutrient run out in normal media was significantly impaired compared to that in the wild type. In addition, the mutant was significantly less able to survive extended anaerobic incubation than the wild-type virulent organism [PMID:10940033]. 1874 GTP pyrophosphokinase relA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5213524 MRA_2964 20140215 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: drrC mutant is attenuated in mice [PMID:10564470]. 1875 daunorubicin-dim ABC transporter permease DrrC drrC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5213527 MRA_2967 20130704 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: fadD28 mutant is attenuated in mice [PMID:10573420]. 1876 acyl-CoA synthetase fadD28 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5213528 MRA_2968 20140215 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: mmpL7 mutant is attenuated in mice [PMID:10573420]. 1877 transmembrane transport protein MmpL7 mmpL7 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5213568 MRA_0437 20140406 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: sodC mutant is more susceptible to killing by activated murine macrophages than the wild type [PMID:11447176]. 1878 superoxide dismutase sodC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5213745 MRA_1539 20140222 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: pks5 mutant is attenuated in mice [PMID:12855735]. 1879 polyketide synthase pks5 pks5 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5213873 MRA_3886 20140222 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: sodA mutant is attenuated in mice [PMID:11751190]. 1880 superoxide dismutase sodA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5214000 MRA_2406 20140217 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: mbtB mutant is attenuated in macrophage like THP-1 cells [PMID:10655517]. 1881 dihydroaeruginoic acid synthetase mbtB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5214120 MRA_3016 20140405 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: leuD mutant is attenuated in mice [PMID:10768986]. 1882 isopropylmalate isomerase small subunit leuD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5214150 MRA_3263 20140222 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: sigH mutant has diminished immunopathology and is nonlethal in mice [PMID:12060776]. 1883 RNA polymerase sigma factor RpoE sigH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5214181 MRA_0507 20140329 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: proC mutant is attenuated in mice [PMID:11160012]. 1884 pyrroline-5-carboxylate reductase proC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5214250 MRA_0416 20140222 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: pknG mutant is attenuated in mice [PMID:15186418]. 1885 serine/threonine protein kinase pknG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5214363 MRA_0910 20140215 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: prrA mutant is attenuated in murine macrophages [PMID:11953357]. 1886 two component response transcriptional regulatory protein PrrA prrA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5214412 MRA_1919 20140405 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: katG mutant is attenuated in mice and guinea pigs [PMID:9534978]. 1887 catalase-peroxidase katG from M. tuberculosis H37Ra Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5214548 MRA_3913 20140217 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: esxB (CFP-10) mutant is attenuated in mice [PMID:16030141]. 1888 antigen EsxB esxB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5214549 MRA_3914 20140222 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: esxA (ESAT-6) mutant is attenuated in mice [PMID:16030141]. 1889 early secretory antigenic target EsxA esxA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5214557 MRA_3922 20140222 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: mycP1 is attenuated in chronic infection of mice [PMID:20227664]. 1890 membrane-anchored mycosin Mycp1 mycP1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5214567 MRA_3844 20140406 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: fbpA mutant is attenuated in mice [PMID:15557632]. 1891 secreted antigen 85-A FbpA fbpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5214581 MRA_2455 20140222 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: ahpC mutant has decreased survival in unactivated macrophages compared to the wild type [PMID:12368447]. 1892 hypothetical protein ahpC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5214616 MRA_3640 20140405 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: panCD mutant is attenuated in mice [PMID:12219086]. 1893 aspartate alpha-decarboxylase panD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5214617 MRA_3641 20140405 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: panCD mutant is attenuated in mice [PMID:12219086]. 1894 pantoate--beta-alanine ligase panC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5214708 MRA_0906 20140217 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: ompA mutant is impaired in its ability to grow in macrophages and in normal mice, although it was as virulent as the wild type in mice that lack T cells [PMID:12366842]. 1895 outer membrane protein A ompA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5214891 MRA_1551 20140405 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: lspA mutant is attenuated in mice [PMID:18832305]. 1896 lipoprotein signal peptidase lspA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5214944 MRA_3863 20140215 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: mmpL8 mutant is attenuated in mice [PMID:12724526]. 1897 transmembrane transport protein MmpL8 mmpL8 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5215107 MRA_0176 20140406 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: yrbE1B mutant is attenuated in mice [PMID:15804490]. 1898 hypothetical protein yrbE1B Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5215306 MRA_0767 20140406 419947 protein-coding NCBI-supplied PMID: 18065542; 18584054; 18757548 MUTATION: phoP mutant is attenuated in mice [PMID:11454210]. 1899 two component system response transcriptional positive regulator PhoP phoP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5215324 MRA_3033 20140405 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: ilvB1 mutant is attenuated in mice [PMID:19542000]. 1900 acetolactate synthase 1 catalytic subunit ilvB1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5215382 MRA_1230 20140406 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: sigE mutant is unable to grow in unactivated human and murine macrophages and is more susceptible to killing by activated macrophages than the wild type [PMID:11489128]. 1901 RNA polymerase sigma factor SigE sigE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5215526 MRA_1671 20140215 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: pks10 mutant is attenuated in mice [PMID:12730158]. 1902 chalcone synthase Pks10 pks10 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5215527 MRA_1672 20130704 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: pks7 mutant is attenuated in mice [PMID:12855735]. 1903 polyketide synthase Pks7 pks7 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5215558 MRA_3244 20140222 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: moeB1 mutant is attenuated in mice [PMID:17353284]. 1904 molybdopterin biosynthesis-like protein MoeZ moeB1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5215578 MRA_0473 20140405 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: icl mutant is attenuated in activated macrophages [PMID:10963599]. 1905 isocitrate lyase Icl icl Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5215613 MRA_0476 20140215 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: pcaA mutant is attenuated in mice [PMID:10882107]. 1906 mycolic acid synthase PcaA pcaA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5215636 MRA_1353 20140222 419947 protein-coding NCBI-supplied PMID: 18584054 MUTATION: fadD33 mutant is attenuated in mice [PMID:12480891]. 1907 long-chain-fatty-acid--[acyl-carrier-protein] ligase fadD33 Bin Zhao, Oliver He TBFG_01546 WEB: http://www.ncbi.nlm.nih.gov/gene 5222252 TBFG_11572 20130630 336982 protein-coding NCBI-supplied MUTATION: lspA mutant is attenuated in mice [PMID:18832305]. 1648 lipoprotein signal peptidase - lspA Bin Zhao, Oliver He TBFG_02179 WEB: http://www.ncbi.nlm.nih.gov/gene 5222896 TBFG_12220 20140405 336982 protein-coding NCBI-supplied MUTATION: trpD mutant is attenuated in mice [PMID:11160012]. 1649 anthranilate phosphoribosyltransferase - trpD Bin Zhao, Oliver He TBFG_02964 WEB: http://www.ncbi.nlm.nih.gov/gene 5223688 TBFG_13002 20140405 336982 protein-coding NCBI-supplied MUTATION: leuD mutant is attenuated in mice [PMID:10768986]. 1650 isopropylmalate isomerase small subunit - leuD Bin Zhao, Oliver He TBFG_03591 WEB: http://www.ncbi.nlm.nih.gov/gene 5224323 TBFG_13634 20140405 336982 protein-coding NCBI-supplied MUTATION: pan CD mutant is attenuated in mice [PMID:12219086]. 1651 pantoate--beta-alanine ligase - panC Bin Zhao, Oliver He yopQ WEB: http://www.ncbi.nlm.nih.gov/gene 5236061 YPE_4233 20121127 412420 protein-coding NCBI-supplied MUTATION: yopK mutant has an increased LD50 dose in mice, and infected mice died after 5 days as compared to mice infected with the wild type died after just 3 days [PMID:3002984]. 2479 secreted targeting protein, regulator, Type III system - yopK Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5236062 YPE_4232 20140406 412420 protein-coding NCBI-supplied translocated cysteine protease/Rho GTPase toxin yopT Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5236067 YPE_4227 20140222 412420 protein-coding NCBI-supplied MUTATION: yopM mutant is attenuated in mice compared to the wild type [PMID:2401564]. 2481 leucine-rich repeat-containing translocated effector protein yopM Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5236068 YPE_4226 20140406 412420 protein-coding NCBI-supplied MUTATION: yopD mutants are unable to induce cytotoxicity in HeLa cells [PMID:1937815]. 2482 putative secreted pore/translocation protein yopD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5236069 YPE_4225 20130508 412420 protein-coding NCBI-supplied MUTATION: yopB mutant is avirulent in mouse model, fails to elicit a cytotoxic response in cultured HeLa cells and is unable to inhibit phagocytosis by macrophage-like J774 cells [PMID:8918459]. 2483 putative secreted pore/translocation protein yopB Bin Zhao, Oliver He sycD WEB: http://www.ncbi.nlm.nih.gov/gene 5236070 YPE_4224 20140406 412420 protein-coding NCBI-supplied MUTATION: lcrH mutant is avirulent in mice [PMID:2707857]. 2484 putative yopB/yopD chaperone - lcrH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5236071 YPE_4223 20121127 412420 protein-coding NCBI-supplied MUTATION: lcrV mutants are avirulent in mice [PMID:7730287]. 2485 V antigen lcrV Bin Zhao, Oliver He virF WEB: http://www.ncbi.nlm.nih.gov/gene 5236089 YPE_4205 20130508 412420 protein-coding NCBI-supplied MUTATION: lcrF mutant is attenuated in mice [PMID:14742535]. 2486 putative thermoregulatory protein - lcrF Bin Zhao, Oliver He lcrP yopR WEB: http://www.ncbi.nlm.nih.gov/gene 5236097 YPE_4197 20140406 412420 protein-coding NCBI-supplied MUTATION: The LD50 for the mouse of the yscH mutant was 10-fold higher than that of the parental strain indicating that YopR is involved in pathogenesis [PMID:8709853]. 2487 type III secreted virulence protein - yscH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5236107 YPE_4187 20140222 412420 protein-coding NCBI-supplied MUTATION: yopH mutants are unable to resist phagocytosis by J774 cells, while wild type Yersinia is able to resist phagocytosis [PMID:8809758]. 2488 translocated protein-tyrosine kinase, inhibitor of phagocytosis yopH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5236112 YPE_4182 20140215 412420 protein-coding NCBI-supplied MUTATION: ypkA mutants of Y. pseudotuberculosis are attenuated in mice [PMID:8441468]. 2489 protein kinase, host Rho GTPase toxin ypkA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5236139 YPE_4152 20140217 412420 protein-coding NCBI-supplied MUTATION: yopE mutants are attenuated after oral or intraperitoneal infection in mice, but are not attenuated after intravenous infection in mice [PMID:2191183]. 2490 translocated host-GTPase-activating protein yopE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5236150 YPE_4333 20140406 412420 protein-coding NCBI-supplied MUTATION: ymt mutants are unable to block X. cheopsis fleas and have low survival rates in the flea gut [PMID:11976454]. 1958 toxin ymt Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5236158 YPE_4324 20140215 412420 protein-coding NCBI-supplied MUTATION: caf1M mutants are attenuated in mice [PMID:14711524]. 1959 putative F1 chaperone protein caf1M Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5236159 YPE_4323 20140215 412420 protein-coding NCBI-supplied MUTATION: caf1A mutants are attenuated in mice [PMID:14711524]. 1960 putative F1 capsule anchoring protein caf1A Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5330252 NWMN_0471 20130704 426430 protein-coding NCBI-supplied PMID: 17951380 MUTATION: mutant attenuated in a C. elegans-killing model [PMID:15664928]. 4431 hypothetical protein tilS Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5330660 NWMN_1073 20130704 426430 protein-coding NCBI-supplied PMID: 17951380; 22802349 alpha-hemolysin precursor hla Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5331488 NWMN_2414 20140405 426430 protein-coding NCBI-supplied PMID: 17951380 MUTATION: mutant attenuated in a C. elegans-killing model [PMID:15664928]. 4432 fructose-1,6-bisphosphatase fbp Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5331715 NWMN_1629 20140215 426430 protein-coding NCBI-supplied PMID: 17951380; 18710862; 19450265; 20525824; 22905199; 23342123 MUTATION: mutant displayed reduced replication and infection in murine model [PMID:20525824]. 4433 catabolite control protein A ccpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5332074 NWMN_0055 20140322 426430 protein-coding NCBI-supplied PMID: 17951380; 23154968; 24002060 immunoglobulin G binding protein A precursor (protein A) spa Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5332320 NWMN_1113 20140405 426430 protein-coding NCBI-supplied PMID: 17951380 MUTATION: mutant attenuated in a Caenorhabditis elegans-killing model [PMID:15664928]. 4434 carbamoyl phosphate synthase small subunit pyrAA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5385392 YpsIP31758_3041 20140405 349747 protein-coding NCBI-supplied PMID: 17784789 MUTATION: gmd mutant is attenuated in mice [PMID:11292689]. 4096 GDP-mannose 4,6-dehydratase gmd Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5385452 YpsIP31758_3820 20140406 349747 protein-coding NCBI-supplied PMID: 17784789 MUTATION: yscL mutant is attenuated in mice [PMID:11292689]. 4097 HrpE/YscL family type III secretion apparatus protein YpsIP31758_3820 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5385453 YpsIP31758_3046 20121017 349747 protein-coding NCBI-supplied PMID: 17784789 MUTATION: wzx mutant is attenuated in mice [PMID:11292689]. 4098 O-unit flippase protein Wzx YpsIP31758_3046 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5386024 YpsIP31758_0676 20140322 349747 protein-coding NCBI-supplied PMID: 17784789 MUTATION: yopM mutant is attenuated in invasion of mouse host tissues [PMID:20368345]. 4099 outer membrane protein YopM yopM Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5386943 YpsIP31758_3444 20130827 349747 protein-coding NCBI-supplied PMID: 17784789 MUTATION: ksgA mutant is attenuated in mice [PMID:11292689]. 4100 dimethyladenosine transferase ksgA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5387169 YpsIP31758_3653 20130701 349747 protein-coding NCBI-supplied PMID: 17784789 MUTATION: hfq mutant is attenuated in mice [PMID:20231416]. 4101 RNA-binding protein Hfq hfq Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5387564 YpsIP31758_3049 20140406 349747 protein-coding NCBI-supplied PMID: 17784789; 18491919 MUTATION: ddhC mutant is attenuated in mice [PMID:11292689]. 4102 CDP-4-keto-6-deoxy-D-glucose-3-dehydrase ddhC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5387764 YpsIP31758_1953 20140215 349747 protein-coding NCBI-supplied PMID: 17784789 MUTATION: cls mutant is attenuated in mice [PMID:11292689]. 4103 cardiolipin synthetase cls Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5388635 JJD26997_0895 20130702 360109 protein-coding NCBI-supplied MUTATION: PEB1 mutants had a significantly reduced in vivo colonization of broiler chickens [PMID:19349427] 1779 amino acid ABC transporter permease JJD26997_0895 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5388922 JJD26997_0805 20130702 360109 protein-coding NCBI-supplied MUTATION: adherence of deletion mutants of jlpA to HEp-2 epithelial cells was reduced compared with that of parental C. jejuni [PMID:11251839] 1780 surface-exposed lipoprotein jlpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5389528 JJD26997_0892 20140322 360109 protein-coding NCBI-supplied MUTATION: PEB1 mutants had a significantly reduced in vivo colonization of broiler chickens [PMID:19349427] 1781 amino acid ABC transporter ATP-binding protein PEB1 pebC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5389725 JJD26997_0893 20130702 360109 protein-coding NCBI-supplied MUTATION: PEB1 mutants had a significantly reduced in vivo colonization of broiler chickens [PMID:19349427] 1782 bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein pebA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5390001 JJD26997_0900 20130702 360109 protein-coding NCBI-supplied invasion antigen B ciaB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5390171 JJD26997_0894 20130702 360109 protein-coding NCBI-supplied MUTATION: PEB1 mutants had a significantly reduced in vivo colonization of broiler chickens [PMID:19349427] 1784 amino acid ABC transporter permease JJD26997_0894 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5390397 JJD26997_0042 20140405 360109 protein-coding NCBI-supplied gamma-glutamyltransferase ggt Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5390593 JJD26997_0592 20140322 360109 protein-coding NCBI-supplied MUTATION: reduce ability to adhere to human epithelial Caco-2 cells [PMID:15184581]. 1786 general glycosylation pathway protein pglH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5397793 CLB_0848 20140222 441770 protein-coding NCBI-supplied PMID: 18060065 MUTATION: inserting a group II intron into the botulinum neurotoxin type A gene (bont/A) rendered mutant clones nontoxigenic [PMID:19933346] 2562 botulinum neurotoxin type A1 boNT/A1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5398487 CLC_0862 20140222 441771 protein-coding NCBI-supplied PMID: 18060065; 22146011; 24096023 MUTATION: a BoNT/A mutant was rendered nontoxigenic [PMID:19933346] 2563 botulinum neurotoxin type A1 boNT/A1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5522688 FTA_0635 20140301 458234 protein-coding NCBI-supplied PMID: 19756146 MUTATION: A wbtI mutant is attenuated in mice [PMID:17768257]. 4913 DegT/DnrJ/EryC1/StrS family sugar aminotransferase wbtI Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5522867 FTA_0403 20140222 458234 protein-coding NCBI-supplied PMID: 19756146 MUTATION: A sodC mutant in Francisella tularensis subspecies holarctica was attenuated in mice [PMID:19684141]. 4970 copper/zinc superoxide dismutase sodC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5523917 FTA_1563 20140406 458234 protein-coding NCBI-supplied PMID: 19756146 MUTATION: A guaB mutant is attenuated in mice [PMID:19368784]. 4912 inosine-5'-monophosphate dehydrogenase guaB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5560751 SAHV_1395 20140406 418127 protein-coding NCBI-supplied PMID: 9400512; 17954695 MUTATION: mutant attenuated in murine infection model [PMID:15664928]. 4435 branched-chain amino acid carrier protein braB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5560784 SAHV_0924 20130330 418127 protein-coding NCBI-supplied PMID: 9400512; 17954695 MUTATION: NagD mutant attenuated in C. Elegans-killing model [PMID:15664928]. 4436 hypothetical protein SAHV_0924 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5561057 SAHV_0683 20140406 418127 protein-coding NCBI-supplied PMID: 9400512; 17954695; 18304359; 18805983; 18852246; 20233929 MUTATION: mutant showed less bacterial persistence in kidneys and attenuated virulence in mice [PMID:18692591]. 4437 MarR family transcriptional regulator mgrA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5563318 CP0048 20130611 198214 protein-coding NCBI-supplied PMID: 12384590 MUTATION: ospE mutants had attenuated adhesion to HeLa cells than the wild-type [PMID:19489119]. 926 OspE2 ospE2 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5563319 CP0265a 20130611 198214 protein-coding NCBI-supplied PMID: 12384590 MUTATION: ospE mutants had attenuated adhesion to HeLa cells than the wild-type [PMID:19489119]. 927 OspE1 ospE1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5563327 SBO_P094a 20121017 300268 protein-coding NCBI-supplied PMID: 16275786 MUTATION: ospE mutants had attenuated adhesion to HeLa cells than the wild-type [PMID:19489119]. 1577 OspE2 ospE2 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5585630 EcE24377A_F0020 20140406 331111 protein-coding NCBI-supplied PMID: 18676672 MUTATION: Deletion mutants of eltA and eltB had decreased levels of inducing cAMP secretion in an in vitro culture system, and had less adherence to IPEC-J2 and Caco-2 cells than the wild-type ETEC [PMID:18978047]. 2300 heat-labile enterotoxin A eltA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5585733 EcE24377A_C0002 20140406 331111 protein-coding NCBI-supplied PMID: 18676672 MUTATION: traT mutants have altered membrane permeability and are sensitive to hydrophobic antibiotics [PMID:3323837]. 2299 TraT complement resistance protein traT Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5585855 EcE24377A_E0051 20140406 331111 protein-coding NCBI-supplied PMID: 18676672 MUTATION: interruption of the eatA gene retarded fluid accumulation in the rabbit ileal loop model, suggesting that this autotransporter contributes to the virulence of ETEC [PMID:14977988]. 2289 secreted serine peptidase EatA eatA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5586647 EcE24377A_4360 20140215 331111 protein-coding NCBI-supplied PMID: 18676672 MUTATION: attenuated in mice [PMID:12117951]. 2032 transcriptional activator RfaH rfaH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5586739 EcE24377A_4037 20140405 331111 protein-coding NCBI-supplied PMID: 18676672 MUTATION: dppA mutant was attenuated 10- to 50-fold compared to the wild type for colonization of the bladders and kidneys of mice [PMID:17074858]. 2033 dipeptide ABC transporter periplasmic dipeptide-binding protein dppA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5586916 EcE24377A_2158 20140405 331111 protein-coding NCBI-supplied PMID: 18676672 MUTATION: fliC deletion mutants had reduced adherence in bovine tissue compared to the wild type EHEC and EPEC strains [PMID:17693516]. 2034 flagellin fliC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5589214 EcE24377A_1071 20130630 331111 protein-coding NCBI-supplied PMID: 18676672 MUTATION: OmpA− strains are unable to cause actin condensation needed for invasion of brain epithelial cells [PMID:10531228]. 2035 outer membrane protein A ompA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5589412 EcE24377A_4917 20140406 331111 protein-coding NCBI-supplied PMID: 18676672; 18981086 MUTATION: attenuated in mice and humans [PMID:18482721]. 2036 protein FimH fimH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5590815 EcE24377A_4378 20140406 331111 protein-coding NCBI-supplied PMID: 18676672 MUTATION: mutation of dsbA led to degradation of bundilin and an absence of localized adherence to host cells in EPEC [PMID:9224871]. 2037 protein disulfide isomerase I dsbA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5591486 EcHS_A4083 20140406 331112 protein-coding NCBI-supplied PMID: 18325532; 18676672 MUTATION: mutation of dsbA led to degradation of bundilin and an absence of localized adherence to host cells in EPEC [PMID:9224871]. 2038 periplasmic protein disulfide isomerase I dsbA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5591791 EcHS_A4546 20140222 331112 protein-coding NCBI-supplied PMID: 18676672 MUTATION: attenuated in mice and humans [PMID:18482721]. 2039 protein FimH fimH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5591810 EcHS_A1066 20140406 331112 protein-coding NCBI-supplied PMID: 18676672 MUTATION: OmpA− strains are unable to cause actin condensation needed for invasion of brain epithelial cells [PMID:10531228]. 2040 outer membrane protein A ompA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5593249 EcHS_A1361 20130630 331112 protein-coding NCBI-supplied PMID: 18676672 MUTATION: attenuated in mice [PMID:11553558]. 2041 transport protein TonB tonB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5593889 EcHS_A3744 20140405 331112 protein-coding NCBI-supplied PMID: 18676672 MUTATION: dppA mutant was attenuated 10- to 50-fold compared to the wild type for colonization of the bladders and kidneys of mice [PMID:17074858]. 2042 dipeptide ABC transporter periplasmic dipeptide-binding protein dppA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5594372 EcHS_A4064 20140215 331112 protein-coding NCBI-supplied PMID: 18676672 MUTATION: attenuated in mice [PMID:12117951]. 2043 transcriptional activator RfaH rfaH Bin Zhao, Oliver He O1_ColBM_27 WEB: http://www.ncbi.nlm.nih.gov/gene 5616535 APECO1_O1CoBM27 20130508 405955 protein-coding NCBI-supplied PMID: 16885466 MUTATION: traJ mutants of E. coli K1 are attenuated in rat pups and macrophages [PMID:14688129]. 2278 positive regulator of conjugative transfer; similar to AAO49515 - Other designations: conjugal transfer transcriptional regulator TraJ traJ Bin Zhao, Oliver He O1_ColBM_55 WEB: http://www.ncbi.nlm.nih.gov/gene 5616563 APECO1_O1CoBM55 20140406 405955 protein-coding NCBI-supplied PMID: 16885466 MUTATION: traT mutants have altered membrane permeability and are sensitive to hydrophobic antibiotics [PMID:3323837]. 2279 surface exclusion and complement resistance protein; similar to AAT85681; identified by match to protein family HMM PF05818 - Other designations: conjugal transfer surface exclusion protein TraT traT Bin Zhao, Oliver He O1_ColBM_73 WEB: http://www.ncbi.nlm.nih.gov/gene 5616581 APECO1_O1CoBM73 20140329 405955 protein-coding NCBI-supplied PMID: 16885466 MUTATION: tsh mutant is attenuated in chickens [PMID:18589815]. 2280 temperature sensitive hemagglutinin; similar to AAA24698; identified by match to protein family HMM PF02395 - Other designations: Tsh tsh Bin Zhao, Oliver He O1_ColBM_137 WEB: http://www.ncbi.nlm.nih.gov/gene 5616645 APECO1_O1CoBM137 20140222 405955 protein-coding NCBI-supplied PMID: 16885466 MUTATION: iroA gene cluster mutants were unable to resist Lcn2 in mouse serum [PMID:17060628]. 2281 salmochelin siderophore system, salmochelin receptor; similar to AAS80269; identified by match to protein family HMM PF00593 - Other designations: outer membrane receptor FepA iroN Bin Zhao, Oliver He O1_ColBM_139 WEB: http://www.ncbi.nlm.nih.gov/gene 5616647 APECO1_O1CoBM139 20130508 405955 protein-coding NCBI-supplied PMID: 16885466 MUTATION: attenuated in chicks [PMID:18541653]. 2282 salmochelin siderophore system, ferric enterochelin esterase; similar to AAS80267; identified by match to protein family HMM PF - Other designations: IroD iroD Bin Zhao, Oliver He O1_ColBM_140 WEB: http://www.ncbi.nlm.nih.gov/gene 5616648 APECO1_O1CoBM140 20140222 405955 protein-coding NCBI-supplied PMID: 16885466 MUTATION: attenuated in chicks [PMID:18541653]. 2283 salmochelin siderophore system, ATP-binding cassette; similar to AAP41471; identified by match to protein family HMM PF00005 - Other designations: IroC iroC Bin Zhao, Oliver He O1_ColBM_141 WEB: http://www.ncbi.nlm.nih.gov/gene 5616649 APECO1_O1CoBM141 20140329 405955 protein-coding NCBI-supplied PMID: 16885466 MUTATION: attenuated in chicks [PMID:18541653]. 2284 salmochelin siderophore system, glycosyltransferase; similar to AAS80265; identified by match to protein family HMM PF06722 - Other designations: IroB iroB Bin Zhao, Oliver He O1_ColBM_168 WEB: http://www.ncbi.nlm.nih.gov/gene 5616676 APECO1_O1CoBM168 20140329 405955 protein-coding NCBI-supplied PMID: 16885466 MUTATION: attenuated in mice [PMID:11553558]. 2285 aerobactin siderophore system, ferric aerobactin receptor protein; similar to ABA54744; identified by match to protein family HMM PF00593 - Other designations: IutA iutA Bin Zhao, Oliver He O1_ColBM_169 WEB: http://www.ncbi.nlm.nih.gov/gene 5616677 APECO1_O1CoBM169 20140405 405955 protein-coding NCBI-supplied PMID: 16885466 MUTATION: attenuated in mice [PMID:2973985]. 2286 aerobactin siderophore system, L-lysine 6-monooxygenase; similar to CAE55774 - Other designations: IucD iucD Bin Zhao, Oliver He O1_ColBM_170 WEB: http://www.ncbi.nlm.nih.gov/gene 5616678 APECO1_O1CoBM170 20140329 405955 protein-coding NCBI-supplied PMID: 16885466 MUTATION: attenuated in mice [PMID:2973985]. 2287 aerobactin siderophore system, aerobactin biosynthesis protein; similar to ABA54742; identified by match to protein family HMMPFO4183 - Other designations: IucC iucC Bin Zhao, Oliver He O1_ColBM_172 WEB: http://www.ncbi.nlm.nih.gov/gene 5616680 APECO1_O1CoBM172 20140329 405955 protein-coding NCBI-supplied PMID: 16885466 MUTATION: attenuated in mice [PMID:2973985]. 2288 aerobactin siderophore system, aerobactin synthetase; similar to ABA54740; identified by match to protein family HMM PF04183 - Other designations: IucA iucA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5617154 C8J_1205 20140329 407148 protein-coding NCBI-supplied PMID: 17873037 MUTATION: A mutation of the response regulator gene racR reduced the organism's ability to colonize the chicken intestinal tract [PMID:10322038] 1842 DNA-binding response regulator racR Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5617759 C8J_1352 20140222 407148 protein-coding NCBI-supplied PMID: 17873037 MUTATION: the capacity of a kpsE mutant to adhere to the INT-407 cells was reduced 20-fold, and the invasion capability of the kpsE mutant was two-fold lower than that of the wild type [PMID:17266722]. 4875 capsular polysaccharide ABC transporter kpsE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5617830 C8J_0850 20121127 407148 protein-coding NCBI-supplied PMID: 17873037 invasion antigen B C8J_0850 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5618176 C8J_0858 20140322 407148 protein-coding NCBI-supplied PMID: 17873037 MUTATION: PEB1 mutants had a significantly reduced in vivo colonization of broiler chickens [PMID:19349427] 1844 bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein pebA Bin Zhao, Oliver He Clan MA(M) Family M8 metallo-peptidase WEB: http://www.ncbi.nlm.nih.gov/gene 5649648 LMJF_10_0480 20140315 347515 10 protein-coding NCBI-supplied PMID: 16020728; 20976196; 22038252 MUTATION: gp63 mutant is attenuated for survival in murine macrophages [PMID:7808483]. 4484 GP63, leishmanolysin - GP63-4 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5654245 LMJF_31_3060 20140322 347515 31 protein-coding NCBI-supplied PMID: 16020728; 22038252 MUTATION: Inactivation of LIT1 gene results in attenuated virulence in murine footpad model of infection and reduced viability and replication in bone marrow macrophages [PMID:17257847]. 4481 iron/zinc transporter protein-like protein LMJF_31_3060 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5794959 NMCC_1783 20140406 374833 protein-coding NCBI-supplied PMID: 18031983 MUTATION: aroE mutant is attenuated in rats [PMID:11062540]. 2878 shikimate dehydrogenase aroE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5794989 NMCC_1616 20140406 374833 protein-coding NCBI-supplied PMID: 18031983 MUTATION: rfaK mutant is attenuated in rats [PMID:11062540]. 2879 alpha 1,2 N-acetylglucosamine transferase rfaK Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5795024 NMCC_0886 20140406 374833 protein-coding NCBI-supplied PMID: 18031983 MUTATION: metF mutant is attenuated in rats [PMID:11062540]. 2880 5,10-methylenetetrahydrofolate reductase metF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5795078 NMCC_0642 20140406 374833 protein-coding NCBI-supplied PMID: 18031983 MUTATION: rnc mutant is attenuated in rats [PMID:11062540]. 2881 ribonuclease III rnc Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5795151 NMCC_0383 20140406 374833 protein-coding NCBI-supplied PMID: 18031983 MUTATION: fhs mutant is attenuated in rats [PMID:11062540]. 2882 formate--tetrahydrofolate ligase fhs Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5795172 NMCC_0851 20140406 374833 protein-coding NCBI-supplied PMID: 18031983 MUTATION: pilX mutant has reduced adherence to human epithelial cells [PMID:15612917]. 2883 type IV pilus assembly protein PilX pilX Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5795290 NMCC_1621 20140405 374833 protein-coding NCBI-supplied PMID: 18031983 MUTATION: gdhA mutant is attenuated in rats [PMID:11062540]. 2884 glutamate dehydrogenase gdhA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5795358 NMCC_1433 20140406 374833 protein-coding NCBI-supplied PMID: 18031983 MUTATION: rfaF mutant is attenuated in rats [PMID:11062540]. 2885 ADP-heptose--LPS heptosyltransferase rfaF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5795400 NMCC_0352 20140406 374833 protein-coding NCBI-supplied PMID: 18031983 MUTATION: fba mutant is attenuated in rats [PMID:11062540]. 2886 fructose-1,6-bisphosphate aldolase fba Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5795401 NMCC_0142 20140406 374833 protein-coding NCBI-supplied PMID: 18031983 MUTATION: ptsI mutant is attenuated in rats [PMID:11062540]. 2887 phosphoenolpyruvate-protein phosphotransferase ptsI Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5795405 NMCC_0436 20140315 374833 protein-coding NCBI-supplied PMID: 18031983 MUTATION: grxC mutant is attenuated in rats [PMID:11062540]. 2888 glutaredoxin 3 grxC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5795455 NMCC_2036 20140405 374833 protein-coding NCBI-supplied PMID: 18031983 MUTATION: rsmB mutant is attenuated in rats [PMID:11062540]. 2889 16S RNA methyltransferase rsmB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5795502 NMCC_0431 20140406 374833 protein-coding NCBI-supplied PMID: 18031983 MUTATION: pbp3 mutant is attenuated in rats [PMID:11062540]. 2890 penicillin-binding protein 3 pbp3 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5795606 NMCC_1480 20140406 374833 protein-coding NCBI-supplied PMID: 18031983 MUTATION: ilvI mutant is attenuated in rats [PMID:11062540]. 2891 acetolactate synthase isozyme III large subunit ilvI Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5795648 NMCC_0414 20140406 374833 protein-coding NCBI-supplied PMID: 18031983 MUTATION: aroB mutant is attenuated in rats [PMID:11062540]. 2892 3-dehydroquinate synthase aroB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5795650 NMCC_0091 20140406 374833 protein-coding NCBI-supplied PMID: 18031983 MUTATION: lipB mutant is attenuated in rats [PMID:11062540]. 2893 capsule polysaccharide modification protein lipB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5795721 NMCC_0722 20140406 374833 protein-coding NCBI-supplied PMID: 18031983 MUTATION: pnp mutant is attenuated in rats [PMID:11062540]. 2894 polynucleotide phosphorylase/polyadenylase pnp Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5795870 NMCC_0416 20140222 374833 protein-coding NCBI-supplied PMID: 18031983 MUTATION: pilQ mutant were unable to colonize human nasopharyngeal tissue in an organ culture model [PMID:18936183]. 2895 type IV pilus assembly protein PilQ pilQ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5795881 NMCC_1593 20140405 374833 protein-coding NCBI-supplied PMID: 18031983 MUTATION: aroC mutant is attenuated in rats [PMID:11062540]. 2896 chorismate synthase aroC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5795982 NMCC_0209 20140406 374833 protein-coding NCBI-supplied PMID: 18031983 MUTATION: purL mutant is attenuated in rats [PMID:11062540]. 2897 phosphoribosylformylglycinamidine synthase purL Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5796004 NMCC_1068 20140406 374833 protein-coding NCBI-supplied PMID: 18031983 MUTATION: ilvD mutant is attenuated in rats [PMID:11062540]. 2898 dihydroxy-acid dehydratase ilvD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5796129 NMCC_1643 20140222 374833 protein-coding NCBI-supplied PMID: 18031983 MUTATION: tonB mutant is unable to replicate within human epithelial cells [PMID:11854233]. 2899 TonB protein tonB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5796140 NMCC_0621 20140406 374833 protein-coding NCBI-supplied PMID: 18031983 MUTATION: ampD mutant is attenuated in rats [PMID:11062540]. 2900 N-acetyl-anhydromuranmyl-L-alanine amidase ampD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5796145 NMCC_0786 20140406 374833 protein-coding NCBI-supplied PMID: 18031983 MUTATION: rfaE mutant is attenuated in rats [PMID:11062540]. 2901 ADP-heptose synthetase rfaE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5796169 NMCC_1814 20140222 374833 protein-coding NCBI-supplied PMID: 18031983 MUTATION: pilF mutant were unable to colonize human nasopharyngeal tissue in an organ culture model [PMID:18936183]. 2902 type IV pilus assembly protein pilF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5796183 NMCC_0031 20140406 374833 protein-coding NCBI-supplied PMID: 18031983 MUTATION: metG mutant is attenuated in rats [PMID:11062540]. 2903 methionyl-tRNA synthetase metG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5796187 NMCC_0141 20140406 374833 protein-coding NCBI-supplied PMID: 18031983 MUTATION: ptsH mutant is attenuated in rats [PMID:11062540]. 2904 sugar transport PTS system phosphocarrier protein HPr ptsH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5796233 NMCC_2032 20140406 374833 protein-coding NCBI-supplied PMID: 18031983 MUTATION: dprA mutant is attenuated in rats [PMID:11062540]. 2905 DNA processing protein DprA dprA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5796235 NMCC_2034 20140406 374833 protein-coding NCBI-supplied PMID: 18031983 MUTATION: ntrY mutant is attenuated in rats [PMID:11062540]. 2906 nitrogen regulation protein NtrY, putative ntrY Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5796331 NMCC_1357 20140405 374833 protein-coding NCBI-supplied PMID: 18031983 MUTATION: aroD mutant is attenuated in rats [PMID:11062540]. 2907 3-dehydroquinate dehydratase aroD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5796357 NMCC_0289 20140406 374833 protein-coding NCBI-supplied PMID: 18031983 MUTATION: lgtA mutant is attenuated in rats [PMID:11062540]. 2908 lacto-N-neotetraose biosynthesis glycosyl transferase lgtA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5796649 NMCC_1602 20140406 374833 protein-coding NCBI-supplied PMID: 18031983 putative DedA protein dedA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5796685 NMCC_1641 20140406 374833 protein-coding NCBI-supplied PMID: 18031983 MUTATION: exbD mutant is attenuated in rats [PMID:11062540]. 2910 biopolymer transport protein exbD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5796686 NMCC_1642 20140406 374833 protein-coding NCBI-supplied PMID: 18031983 MUTATION: exbB mutant is attenuated in rats [PMID:11062540]. 2911 biopolymer transport protein exbB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5796698 NMCC_0967 20130508 374833 protein-coding NCBI-supplied PMID: 18031983 MUTATION: dedA mutant is attenuated in rats [PMID:11062540]. 2912 putative DedA protein dedA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5796699 NMCC_0968 20140406 374833 protein-coding NCBI-supplied PMID: 18031983 outer membrane protein opcA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5796721 NMCC_1579 20111206 374833 pseudo NCBI-supplied MUTATION: hmbR mutant was attenuated in an infant rat model [PMID:7783623]. 2914 hemoglobin receptor hmbR Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5796762 NMCC_0075 20140406 374833 protein-coding NCBI-supplied PMID: 18031983 MUTATION: siaD mutant is attenuated in rats [PMID:11062540]. 2915 alpha-2,8 polysialyltransferase siaD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5796858 NMCC_1750 20140406 374833 protein-coding NCBI-supplied PMID: 18031983 MUTATION: NadA mutation decreases epithelial adhesion of capsulate N. meningitidis and invasion by acapsulate N. meningitidis [PMID:19481311]. 2916 quinolinate synthetase nadA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5796882 NMCC_0586 20140405 374833 protein-coding NCBI-supplied PMID: 18031983 MUTATION: galU mutant is attenuated in rats [PMID:11062540]. 2917 UTP--glucose-1-phosphate uridylyltransferase galU Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5796971 NMCC_0194 20140406 374833 protein-coding NCBI-supplied PMID: 18031983 MUTATION: hrpA mutants are deficient in the ability to live/grow in HeLa cells [PMID:18680551]. 2918 ATP-dependent RNA helicase HrpA hrpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5798229 YpAngola_B0059 20140405 349746 protein-coding NCBI-supplied PMID: 20061468 MUTATION: The LD50 for the mouse of the yscH mutant was 10-fold higher than that of the parental strain indicating that YopR is involved in pathogenesis [PMID:8709853]. 1926 type III secretion protein YopR yscH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5798230 YpAngola_B0015 20121017 349746 protein-coding NCBI-supplied PMID: 20061468 MUTATION: yopK mutant has an increased LD50 dose in mice, and infected mice died after 5 days as compared to mice infected with the wild type died after just 3 days [PMID:3002984]. 1927 YopK protein yopK Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5798234 YpAngola_B0031 20140406 349746 protein-coding NCBI-supplied PMID: 20061468 MUTATION: lcrH mutant is avirulent in mice [PMID:2707857]. 1928 type III secretion low calcium response chaperone LcrH lcrH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5798258 YpAngola_B0050 20130508 349746 protein-coding NCBI-supplied PMID: 20061468; 22359501 MUTATION: lcrF mutant is attenuated in mice [PMID:14742535]. 1929 thermoregulatory protein LcrF lcrF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5798272 YpAngola_B0003 20140215 349746 protein-coding NCBI-supplied PMID: 20061468 MUTATION: yopE mutants are attenuated after oral or intraperitoneal infection in mice, but are not attenuated after intravenous infection in mice [PMID:2191183]. 1930 outer membrane virulence protein YopE yopE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5798273 YpAngola_B0067 20140222 349746 protein-coding NCBI-supplied PMID: 20061468 MUTATION: yopH mutants are unable to resist phagocytosis by J774 cells, while wild type Yersinia is able to resist phagocytosis [PMID:8809758]. 1931 protein-tyrosine-phosphatase YopH yopH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5798275 YpAngola_B0030 20130508 349746 protein-coding NCBI-supplied PMID: 20061468 MUTATION: yopB mutant is avirulent in mouse model, fails to elicit a cytotoxic response in cultured HeLa cells and is unable to inhibit phagocytosis by macrophage-like J774 cells [PMID:8918459]. 1932 translocator protein YopB yopB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5798276 YpAngola_B0025 20140406 349746 protein-coding NCBI-supplied PMID: 20061468 MUTATION: yopM mutant is attenuated in mice compared to the wild type [PMID:2401564]. 1933 effector protein YopM yopM Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5798299 YpAngola_B0016 20140406 349746 protein-coding NCBI-supplied PMID: 20061468 cysteine protease YopT yopT Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5798303 YpAngola_B0029 20140406 349746 protein-coding NCBI-supplied PMID: 20061468 MUTATION: yopD mutants are unable to induce cytotoxicity in HeLa cells [PMID:1937815]. 1935 translocator protein YopD yopD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5798320 YpAngola_B0032 20140406 349746 protein-coding NCBI-supplied PMID: 20061468 MUTATION: lcrV mutants are avirulent in mice [PMID:7730287]. 1936 virulence-associated V antigen LcrV lcrV Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5798447 YpAngola_0009 20140301 349746 protein-coding NCBI-supplied PMID: 20061468 MUTATION: pla mutant is attenuated in mice [PMID:1439793]. 1937 outer membrane protease pla Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5798450 YpAngola_0023 20140301 349746 protein-coding NCBI-supplied PMID: 20061468 MUTATION: pla mutant is attenuated in mice [PMID:1439793]. 1938 outer membrane protease pla Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5798508 YpAngola_A0043 20130701 349746 protein-coding NCBI-supplied PMID: 20061468 MUTATION: relA spoT deletion mutants are attenuated in mice [PMID:19701461]. 1939 bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase spoT Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5798908 YpAngola_A0444 20140406 349746 protein-coding NCBI-supplied PMID: 20061468 MUTATION: a Y. pestis ail deletion mutant was rapidly killed by sera from all mammals tested except mice [PMID:18025094]. 1940 attachment invasion locus protein ail Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5798929 YpAngola_A0465 20140406 349746 protein-coding NCBI-supplied PMID: 20061468 MUTATION: purH mutant is attenuated in mice [PMID:14742535]. 1941 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase purH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5799423 YpAngola_A0960 20140222 349746 protein-coding NCBI-supplied PMID: 20061468 MUTATION: pcm mutant is attenuated in mice [PMID:14742535]. 1942 protein-L-isoaspartate O-methyltransferase pcm Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5799446 YpAngola_A0983 20140406 349746 protein-coding NCBI-supplied PMID: 20061468 MUTATION: relA spoT deletion mutants are attenuated in mice [PMID:19701461]. 1943 GDP/GTP pyrophosphokinase relA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5799740 YpAngola_A1274 20140406 349746 protein-coding NCBI-supplied PMID: 20061468 MUTATION: purK mutant is attenuated in mice [PMID:14742535]. 1944 phosphoribosylaminoimidazole carboxylase ATPase subunit purK Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5799838 YpAngola_A4223 20111130 349746 miscRNA NCBI-supplied MUTATION: smpB ssrA mutant is attenuated in mice [PMID:20065026]. 1945 miscRNA ssrA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5799839 YpAngola_A1372 20130701 349746 protein-coding NCBI-supplied PMID: 20061468 MUTATION: smpB ssrA mutant is attenuated in mice [PMID:20065026]. 1946 SsrA-binding protein smpB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5800238 YpAngola_A1767 20130701 349746 protein-coding NCBI-supplied PMID: 20061468 MUTATION: ompX mutants are attenuated in their ability to attach to and invade HeLa cells [PMID:17768237]. 1947 outer membrane protein X ompX Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5800563 YpAngola_A2093 20140215 349746 protein-coding NCBI-supplied PMID: 20061468 MUTATION: psn (fyuA) mutant is unable to grow on iron-deficient media at 37 degrees C [PMID:7896707]. 1948 yersiniabactin/pesticin receptor FyuA fyuA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5800568 YpAngola_A2098 20140406 349746 protein-coding NCBI-supplied PMID: 20061468 MUTATION: irp2 mutants are unable to grow at 37 degrees in iron deficient media [PMID:7896707]. 1949 yersiniabactin synthetase, HMWP2 component irp2 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5800570 YpAngola_A2100 20140217 349746 protein-coding NCBI-supplied PMID: 20061468 MUTATION: ybtP mutant is avirulent in mouse bubonic plague model [PMID:10231486]. 1950 yersiniabactin ABC transporter ATP-binding protein/permease ybtP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5801054 YpAngola_A2583 20140301 349746 protein-coding NCBI-supplied PMID: 20061468 MUTATION: lpp deletion mutant is attenuated in mice [PMID:19737605]. 1951 major outer membrane lipoprotein lpp Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5801102 YpAngola_A2630 20140222 349746 protein-coding NCBI-supplied PMID: 20061468 MUTATION: yfeAB mutant is attenuated when given subcutaneously to mice and is avirulent when given to mice intravenously [PMID:10231495]. 1952 periplasmic-binding protein yfeA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5801103 YpAngola_A2631 20140222 349746 protein-coding NCBI-supplied PMID: 20061468 MUTATION: yfeAB mutant is attenuated when given subcutaneously to mice and is avirulent when given to mice intravenously [PMID:10231495]. 1953 ATP-binding transport protein yfeB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5801327 YpAngola_A2855 20140222 349746 protein-coding NCBI-supplied PMID: 20061468 MUTATION: phoP mutants have a reduced ability to survive in J774 macrophage cell cultures and under conditions of low pH and oxidative stress in vitro. The mean lethal dose of the phoP mutant in mice was increased 75-fold in comparison with that of the wild-type strain [PMID:10816493]. 1954 DNA-binding transcriptional regulator PhoP phoP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5802050 YpAngola_A3574 20140406 349746 protein-coding NCBI-supplied PMID: 20061468 MUTATION: pgm mutant of Y. pestis is attenuated in mice [PMID:12009274]. 1955 phosphoglucomutase pgm Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5802179 YpAngola_A3702 20140222 349746 protein-coding NCBI-supplied PMID: 20061468 MUTATION: crp mutant is attenuated in mice [PMID:20086087]. 1956 cAMP-regulatory protein crp Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5802460 YpAngola_A3982 20140222 349746 protein-coding NCBI-supplied PMID: 20061468 MUTATION: greA mutants are attenuated in mice [PMID:14742535]. 1957 transcription elongation factor GreA greA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5829850 Btr_1701 20140217 382640 protein-coding NCBI-supplied PMID: 18037886 MUTATION: virD4 mutant is attenuated in rats [PMID:15049812]. 4582 conjugal transfer coupling protein TraG virD4 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5850734 APJL_1404 20140222 434271 protein-coding NCBI-supplied PMID: 18197260 MUTATION: rpmF mutant is attenuated in porcine model of infection [PMID:10873489]. 4104 50S ribosomal protein L32 rpmF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5850813 APJL_1524 20140405 434271 protein-coding NCBI-supplied PMID: 18197260 MUTATION: thrC mutant is attenuated in pigs [PMID:12819083]. 4105 threonine synthase thrC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5850850 APJL_1472 20140406 434271 protein-coding NCBI-supplied PMID: 18197260 MUTATION: znuA mutant is attenuated in pigs [PMID:12819083]. 4106 high-affinity zinc transporter periplasmic protein znuA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5850858 APJL_0349 20140406 434271 protein-coding NCBI-supplied PMID: 18197260 MUTATION: visC mutant is attenuated in pigs [PMID:12819083]. 4107 monoxygenase visC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5850859 APJL_0415 20140301 434271 protein-coding NCBI-supplied PMID: 18197260 MUTATION: rpoE mutant is attenuated in pigs [PMID:12819083]. 4108 RNA polymerase sigma factor RpoE rpoE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5850894 APJL_1681 20140405 434271 protein-coding NCBI-supplied PMID: 18197260 MUTATION: atpA mutant is attenuated in pigs [PMID:12819083]. 4109 F0F1 ATP synthase subunit alpha atpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5850906 APJL_1682 20140329 434271 protein-coding NCBI-supplied PMID: 18197260 MUTATION: atpH mutant is attenuated in porcine model of infection [PMID:10873489]. 4110 F0F1 ATP synthase subunit delta atpH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5850919 APJL_0115 20140222 434271 protein-coding NCBI-supplied PMID: 18197260 MUTATION: hupA mutant is attenuated in porcine model of infection [PMID:10873489]. 4111 DNA-binding protein HU hupA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5850978 APJL_0121 20130511 434271 protein-coding NCBI-supplied PMID: 18197260 MUTATION: prc mutant is attenuated in pigs [PMID:12819083]. 4112 carboxy-terminal protease prc Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5851075 APJL_1458 20140405 434271 protein-coding NCBI-supplied PMID: 18197260 MUTATION: napB mutant is attenuated in pigs [PMID:12819083]. 4113 nitrate reductase cytochrome c-type subunit napB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5851167 APJL_1451 20140406 434271 protein-coding NCBI-supplied PMID: 18197260 MUTATION: mglA mutant is attenuated in pigs [PMID:12819083]. 4114 galactose/methyl galaxtoside transporter ATP-binding protein mglA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5851169 APJL_0176 20140329 434271 protein-coding NCBI-supplied PMID: 18197260 MUTATION: dksA mutant is attenuated in porcine model of infection [PMID:10873489]. 4115 dosage-dependent DnaK suppressor protein dksA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5851276 APJL_1705 20140406 434271 protein-coding NCBI-supplied PMID: 18197260 MUTATION: dmsA mutant is attenuated in pigs [PMID:14638764]. 4116 anaerobic dimethyl sulfoxide reductase subunit A dmsA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5851335 APJL_0286 20140301 434271 protein-coding NCBI-supplied PMID: 18197260 MUTATION: frpB mutant is avirulent in pigs [PMID:19343711]. 4117 iron-regulated outer membrane protein frpB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5851399 APJL_0280 20130511 434271 protein-coding NCBI-supplied PMID: 18197260 MUTATION: yfeB mutant is attenuated in pigs [PMID:12819083]. 4118 iron (chelated) transporter, ATP-binding protein yfeB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5851473 APJL_1978 20140406 434271 protein-coding NCBI-supplied PMID: 18197260 MUTATION: lppB mutant is attenuated in pigs [PMID:12819083]. 4119 outer membrane antigenic lipoprotein B lppB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5851529 APJL_0031 20140406 434271 protein-coding NCBI-supplied PMID: 18197260 MUTATION: prfC mutant is attenuated in pigs [PMID:12819083]. 4120 peptide chain release factor 3 prfC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5851531 APJL_0113 20140406 434271 protein-coding NCBI-supplied PMID: 18197260 MUTATION: hemE mutant is attenuated in pigs [PMID:12819083]. 4121 uroporphyrinogen decarboxylase hemE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5851670 APJL_0151 20140406 434271 protein-coding NCBI-supplied PMID: 18197260 MUTATION: nqrA mutant is attenuated in pigs [PMID:12819083]. 4122 Na(+)-translocating NADH-quinone reductase subunit A nqrA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5851696 APJL_0447 20140406 434271 protein-coding NCBI-supplied PMID: 18197260 MUTATION: argG mutant is attenuated in pigs [PMID:12819083]. 4123 argininosuccinate synthase argG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5851732 APJL_1533 20130511 434271 protein-coding NCBI-supplied PMID: 18197260 MUTATION: tig mutant is attenuated in porcine model of infection [PMID:10873489]. 4124 trigger factor tig Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5851786 APJL_1231 20140406 434271 protein-coding NCBI-supplied PMID: 18197260 MUTATION: fur mutant is attenuated in pigs [PMID:12819083]. 4125 ferric uptake regulation protein fur Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5851794 APJL_1229 20140405 434271 protein-coding NCBI-supplied PMID: 18197260 MUTATION: luxS mutant is attenuated in mice [PMID:18585450]. 4126 S-ribosylhomocysteinase luxS Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5851863 APJL_1615 20140405 434271 protein-coding NCBI-supplied PMID: 18197260 MUTATION: cpxD mutant is attenuated in pigs [PMID:12819083]. 4127 HexD, capsule biosynthetic locus protein cpxD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5851868 APJL_0390 20130511 434271 protein-coding NCBI-supplied PMID: 18197260 MUTATION: corC mutant is attenuated in pigs [PMID:12819083]. 4128 magnesium and cobalt efflux protein corC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5851869 APJL_1617 20140406 434271 protein-coding NCBI-supplied PMID: 18197260 MUTATION: cpxB mutant is attenuated in pigs [PMID:12819083]. 4129 capsule polysaccharide export transport system permease cpxB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5851945 APJL_0570 20140405 434271 protein-coding NCBI-supplied PMID: 18197260 MUTATION: pnp mutant is attenuated in porcine model of infection [PMID:10873489]. 4130 polynucleotide phosphorylase/polyadenylase pnp Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5851954 APJL_1616 20140406 434271 protein-coding NCBI-supplied PMID: 18197260 MUTATION: cpxC mutant is attenuated in pigs [PMID:12819083]. 4131 capsule polysaccharide export transport system permease cpxC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5851973 APJL_0585 20140406 434271 protein-coding NCBI-supplied PMID: 18197260 MUTATION: guaA mutant is attenuated in pigs [PMID:12819083]. 4132 GMP synthase guaA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5852036 APJL_1905 20140405 434271 protein-coding NCBI-supplied PMID: 18197260 MUTATION: aroQ mutant is attenuated in pigs [PMID:11731178]. 4133 3-dehydroquinate dehydratase aroQ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5852041 APJL_0425 20140406 434271 protein-coding NCBI-supplied PMID: 18197260 MUTATION: hemA mutant is attenuated in pigs [PMID:12819083]. 4134 glutamyl-tRNA reductase hemA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5852086 APJL_1911 20140406 434271 protein-coding NCBI-supplied PMID: 18197260 MUTATION: dsbA mutant is attenuated in pigs [PMID:12819083]. 4135 thiol:disulfide interchange protein dsbA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5852221 APJL_1065 20140215 434271 protein-coding NCBI-supplied PMID: 18197260 MUTATION: hgbA mutant is attenuated in pigs [PMID:16699590]. 4136 hemoglobin and hemoglobin-haptoglobin-binding protein 4 hgbA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5852278 APJL_1018 20140406 434271 protein-coding NCBI-supplied PMID: 18197260 MUTATION: mrp mutant is attenuated in pigs [PMID:12819083]. 4137 putative ATPase mrp Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5852294 APJL_1004 20140406 434271 protein-coding NCBI-supplied PMID: 18197260 MUTATION: htpG mutant is attenuated in pigs [PMID:12819083]. 4138 heat shock protein 90 htpG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5852390 APJL_0930 20140406 434271 protein-coding NCBI-supplied PMID: 18197260 MUTATION: irp mutant is attenuated in competitive index experiment in pig infection model [PMID:19703979]. 4139 iron-regulated outer membrane protein irp Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5852493 APJL_0849 20140405 434271 protein-coding NCBI-supplied PMID: 18197260 MUTATION: pntB mutant is attenuated in pigs [PMID:12819083]. 4140 pyridine nucleotide transhydrogenase pntB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5852506 APJL_0074 20140406 434271 protein-coding NCBI-supplied PMID: 18197260 MUTATION: recR mutant is attenuated in pigs [PMID:12819083]. 4141 recombination protein RecR recR Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5852591 APJL_0774 20140406 434271 protein-coding NCBI-supplied PMID: 18197260 MUTATION: lpdA mutant is attenuated in porcine model of infection [PMID:10873489]. 4142 dihydrolipoamide dehydrogenase lpdA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5852606 APJL_1953 20140406 434271 protein-coding NCBI-supplied PMID: 18197260 MUTATION: dnaK mutant is attenuated in porcine model of infection [PMID:10873489]. 4143 molecular chaperone DnaK dnaK Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5852660 APJL_0729 20140406 434271 protein-coding NCBI-supplied PMID: 18197260; 19703979 MUTATION: ilvI mutant is attenuated in pigs [PMID:19703979]. 4144 acetolactate synthase 3 catalytic subunit ilvI Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5852699 APJL_0697 20140406 434271 protein-coding NCBI-supplied PMID: 18197260 MUTATION: aroA mutant is attenuated in pigs [PMID:12027598]. 4145 3-phosphoshikimate 1-carboxyvinyltransferase aroA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5852711 APJL_0688 20140406 434271 protein-coding NCBI-supplied PMID: 18197260 MUTATION: moaA mutant is attenuated in pigs [PMID:12819083]. 4146 molybdenum cofactor biosynthesis protein A moaA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5852738 APJL_1952 20140406 434271 protein-coding NCBI-supplied PMID: 18197260 MUTATION: dnaJ mutant is attenuated in pigs [PMID:12819083]. 4147 chaperone protein DnaJ dnaJ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5852761 APJL_0646 20140406 434271 protein-coding NCBI-supplied PMID: 18197260 MUTATION: hlyX mutant is attenuated in pigs [PMID:16040973]. 4148 fumarate/nitrate reduction transcriptional regulator hlyX Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5852767 APJL_0641 20140406 434271 protein-coding NCBI-supplied PMID: 18197260; 18713318 MUTATION: galU mutant is attenuated in pigs [PMID:12819083]. 4149 UTP-glucose-1-phosphate uridylyltransferase galU Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5852795 APJL_0049 20130511 434271 protein-coding NCBI-supplied PMID: 17881160; 18197260 MUTATION: arcA mutant is attenuated in pigs [PMID:17881160]. 4150 two-component response regulator arcA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5852826 APJL_1680 20140405 434271 protein-coding NCBI-supplied PMID: 18197260 MUTATION: atpG mutant is attenuated in porcine model of infection [PMID:10873489]. 4151 F0F1 ATP synthase subunit gamma atpG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 5852841 APJL_0394 20140406 434271 protein-coding NCBI-supplied PMID: 18197260 MUTATION: lon mutant is attenuated in pigs [PMID:12819083]. 4152 ATP-dependent protease LA lon Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6028624 SPH_0848 20140222 487214 protein-coding NCBI-supplied MUTATION: clpP mutant is attenuated in mice [PMID:15664911]. 3055 ATP-dependent Clp protease proteolytic subunit clpP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6028647 SPH_0817 20140405 487214 protein-coding NCBI-supplied MUTATION: spxB mutant has a loss in the ability to attach eukayrotic cells and is attenuated in rabbits [PMID:8820650]. 3056 pyruvate oxidase spxB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6028818 SPH_1697 20140329 487214 protein-coding NCBI-supplied MUTATION: codY mutant has lower bacterial loads during infection in mice compared to the wild type and have a diminished ability to adhere to nasopharangeal cells in vitro [PMID:18024519]. 3057 transcriptional repressor CodY codY Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6028839 SPH_0759 20140406 487214 protein-coding NCBI-supplied MUTATION: zmpB mutant is attenuated in mice [PMID:12841855]. 3058 zinc metalloprotease ZmpB zmpB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6029035 SPH_0450 20140405 487214 protein-coding NCBI-supplied MUTATION: luxS mutant has defective ability to persist in the nasopharyngeal tissues of mice [PMID:15102809]. 3059 S-ribosylhomocysteinase luxS Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6029135 SPH_0611 20140405 487214 protein-coding NCBI-supplied MUTATION: glnA mutant had significantly reduced adhesion to Detroit 562 human pharyngeal epithelial cells [PMID:16787930]. 3060 glutamine synthetase, type I glnA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6029776 SPH_2142 20140329 487214 protein-coding NCBI-supplied MUTATION: ccpA mutant is attenuated in mice [PMID:16321938]. 3061 catabolite control protein A ccpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6030102 CLD_A0068 20130705 498213 protein-coding NCBI-supplied PMID: 18060065; 18571196; 22146011 MUTATION: BoNT/B toxoid without non-toxic components, which are generally associated with the toxin was used attenuated and used as a vaccine candidate [PMID:15225558] 2564 botulinum neurotoxin type B boNT/B Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6030483 CLK_A0076 20140406 498214 protein-coding NCBI-supplied PMID: 18060065 botulinum neurotoxin type A3 boNT/A3 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6058256 ECDH10B_4049 20140406 316385 protein-coding NCBI-supplied PMID: 18245285 MUTATION: mutation of dsbA led to degradation of bundilin and an absence of localized adherence to host cells in EPEC [PMID:9224871]. 2268 protein disulfide isomerase I dsbA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6058282 ECDH10B_1367 20130330 316385 protein-coding NCBI-supplied PMID: 18245285; 18390658; 21840979; 22497281 MUTATION: attenuated in mice [PMID:11553558]. 2269 transporter tonB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6058698 ECDH10B_3723 20140405 316385 protein-coding NCBI-supplied PMID: 18245285 MUTATION: dppA mutant was attenuated 10- to 50-fold compared to the wild type for colonization of the bladders and kidneys of mice [PMID:17074858]. 2270 peptide ABC transporter periplasmic substrate-binding protein dppA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6058984 ECDH10B_4031 20140215 316385 protein-coding NCBI-supplied PMID: 18245285; 19096362 MUTATION: attenuated in mice [PMID:12117951]. 2271 transcriptional activator RfaH rfaH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6060328 ECDH10B_1027 20140406 316385 protein-coding NCBI-supplied PMID: 18245285 MUTATION: OmpA− strains are unable to cause actin condensation needed for invasion of brain epithelial cells [PMID:10531228]. 2272 outer membrane protein A ompA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6061059 ECDH10B_3991 20140406 316385 protein-coding NCBI-supplied PMID: 18245285 MUTATION: disruption mutant was less invasive in an in vitro HBMEC invasion assay than the wild-type E. coli K1 [PMID:10948126]. 2273 acrylsulfatase-like protein aslA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6087380 YPK_2063 20140406 502800 protein-coding NCBI-supplied MUTATION: cls mutant is attenuated in mice [PMID:11292689]. 4153 cardiolipin synthetase cls Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6087427 YPK_3908 20140406 502800 protein-coding NCBI-supplied MUTATION: yscL mutant is attenuated in mice [PMID:11292689]. 4154 HrpE/YscL family type III secretion apparatus protein YPK_3908 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6088309 YPK_3573 20130705 502800 protein-coding NCBI-supplied MUTATION: ksgA mutant is attenuated in mice [PMID:11292689]. 4155 dimethyladenosine transferase ksgA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6090945 YPK_3799 20121017 502800 protein-coding NCBI-supplied MUTATION: hfq mutant is attenuated in mice [PMID:20231416]. 4156 RNA-binding protein Hfq hfq Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6106483 EcSMS35_A0041 20140315 439855 protein-coding NCBI-supplied PMID: 18708504 MUTATION: traJ mutants of E. coli K1 are attenuated in rat pups and macrophages [PMID:14688129]. 2254 type IV secretion-like conjugative transfer system regulator TraJ traJ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6106527 EcSMS35_A0012 20140406 439855 protein-coding NCBI-supplied PMID: 18708504 MUTATION: traT mutants have altered membrane permeability and are sensitive to hydrophobic antibiotics [PMID:3323837]. 2255 conjugal transfer surface exclusion protein TraT traT Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6143094 EcSMS35_3178 20140315 439855 protein-coding NCBI-supplied PMID: 18708504 MUTATION: attenuated in mice [PMID:11553558]. 2239 ferric aerobactin receptor IutA iutA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6143458 EcSMS35_4222 20140315 439855 protein-coding NCBI-supplied PMID: 18708504 MUTATION: attenuated in mice [PMID:12117951]. 2240 transcriptional activator RfaH rfaH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6144084 EcSMS35_3181 20140315 439855 protein-coding NCBI-supplied PMID: 18708504 MUTATION: attenuated in mice [PMID:2973985]. 2241 aerobactin siderophore biosynthesis protein IucB iucB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6144184 EcSMS35_4241 20140315 439855 protein-coding NCBI-supplied PMID: 18708504 MUTATION: mutation of dsbA led to degradation of bundilin and an absence of localized adherence to host cells in EPEC [PMID:9224871]. 2242 periplasmic protein disulfide isomerase I dsbA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6144283 EcSMS35_3863 20140301 439855 protein-coding NCBI-supplied PMID: 18708504 MUTATION: dppA mutant was attenuated 10- to 50-fold compared to the wild type for colonization of the bladders and kidneys of mice [PMID:17074858]. 2243 dipeptide ABC transporter periplasmic dipeptide-binding protein dppA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6144795 EcSMS35_1258 20140405 439855 protein-coding NCBI-supplied PMID: 18708504 MUTATION: fliC deletion mutants had reduced adherence in bovine tissue compared to the wild type EHEC and EPEC strains [PMID:17693516]. 2244 flagellin fliC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6145010 EcSMS35_1880 20140329 439855 protein-coding NCBI-supplied PMID: 18708504 MUTATION: attenuated in mice [PMID:11553558]. 2245 transport protein TonB tonB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6145117 EcSMS35_3179 20140322 439855 protein-coding NCBI-supplied PMID: 18708504 MUTATION: attenuated in mice [PMID:2973985]. 2246 L-lysine 6-monooxygenase IucD iucD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6145732 EcSMS35_4847 20140222 439855 protein-coding NCBI-supplied PMID: 18708504 MUTATION: attenuated in mice and humans [PMID:18482721]. 2247 protein FimH fimH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6145998 EcSMS35_3182 20140329 439855 protein-coding NCBI-supplied PMID: 18708504 MUTATION: attenuated in mice [PMID:2973985]. 2248 aerobactin siderophore biosynthesis protein IucA iucA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6146022 EcSMS35_4166 20140315 439855 protein-coding NCBI-supplied PMID: 18708504 MUTATION: disruption mutant was less invasive in an in vitro HBMEC invasion assay than the wild-type E. coli K1 [PMID:10948126]. 2249 arylsulfatase aslA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6146246 EcSMS35_2163 20140329 439855 protein-coding NCBI-supplied PMID: 18708504 MUTATION: OmpA− strains are unable to cause actin condensation needed for invasion of brain epithelial cells [PMID:10531228]. 2250 outer membrane protein A ompA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6146360 EcSMS35_4868 20140315 439855 protein-coding NCBI-supplied PMID: 18708504 MUTATION: deletion mutant was significantly less invasive in human brain microvascular endothelial cells (BMECs) than the parent strain (E. coli K1) [PMID:11237832]. 2251 invasion protein IbeA ibeA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6146648 EcSMS35_3802 20140315 439855 protein-coding NCBI-supplied PMID: 18708504 MUTATION: chuA mutant unable to grow on iron-depleted medium containing heme [PMID:9157252]. 2252 outer membrane heme/hemoglobin receptor ChuA chuA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6147083 EcSMS35_3180 20140405 439855 protein-coding NCBI-supplied PMID: 18708504 MUTATION: attenuated in mice [PMID:2973985]. 2253 aerobactin siderophore biosynthesis protein IucC iucC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6216375 SPCG_1143 20140217 516950 protein-coding NCBI-supplied PMID: 19361343 MUTATION: iga mutant is attenuated in mice [PMID:12841855]. 3033 immunoglobulin A1 protease iga Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6216376 SPCG_0334 20140217 516950 protein-coding NCBI-supplied PMID: 19361343 MUTATION: regR mutant is attenuated in mice [PMID:12704136]. 3034 sugar binding transcriptional regulator RegR regR Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6216487 SPCG_0679 20140329 516950 protein-coding NCBI-supplied PMID: 19361343 MUTATION: spxB mutant has a loss in the ability to attach eukayrotic cells and is attenuated in rabbits [PMID:8820650]. 3035 pyruvate oxidase spxB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6216649 SPCG_1458 20140222 516950 protein-coding NCBI-supplied PMID: 19361343 MUTATION: nox mutant is attenuated in mice [PMID:11158360]. 3036 NADH oxidase nox Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6216676 SPCG_1964 20130705 516950 protein-coding NCBI-supplied PMID: 19361343 MUTATION: ccpA mutant is attenuated in mice [PMID:16321938]. 3037 catabolite control protein A ccpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6216707 SPCG_1559 20140217 516950 protein-coding NCBI-supplied PMID: 19361343 MUTATION: lytC mutant have reduced colonization of rat nasopharynx compared to wild type [PMID:10992472]. 3038 lysozyme lytC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6217141 SPCG_0343 20140405 516950 protein-coding NCBI-supplied PMID: 19361343 MUTATION: luxS mutant has defective ability to persist in the nasopharyngeal tissues of mice [PMID:15102809]. 3039 S-ribosylhomocysteinase luxS Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6217360 SPCG_1898 20130705 516950 protein-coding NCBI-supplied PMID: 19361343 MUTATION: ply mutant is attenuated in mice [PMID:10603379]. 3040 pneumolysin ply Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6217389 SPCG_0620 20140215 516950 protein-coding NCBI-supplied PMID: 19361343 MUTATION: zmpB mutant is attenuated in mice [PMID:12841855]. 3041 zinc metalloprotease ZmpB zmpB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6217403 SPCG_2158 20140215 516950 protein-coding NCBI-supplied PMID: 19361343 MUTATION: pspC mutant is has reduced ability to colonize nasopharynx of mice compared to the wild type [PMID:17261599]. 3042 choline binding protein A pspC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6217428 SPCG_0387 20140215 516950 protein-coding NCBI-supplied PMID: 19361343 MUTATION: cbpG has reduced colonization of nasopharynx of rats and reduced adherence to human epithelial cells [PMID:10992472]. 3043 choline binding protein G cbpG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6217546 SPCG_2168 20140406 516950 protein-coding NCBI-supplied PMID: 19361343 MUTATION: cbpD has reduced colonization of nasopharynx of rats compared to the wild type [PMID:10992472]. 3044 choline binding protein D cbpD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6217600 SPCG_1665 20140405 516950 protein-coding NCBI-supplied PMID: 19361343 MUTATION: nanA mutant is attenuated in mice [PMID:9826334]. 3045 sialidase A (neuraminidase A) nanA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6217646 SPCG_0715 20140222 516950 protein-coding NCBI-supplied PMID: 19361343 MUTATION: sodA mutant is attenuated in mice [PMID:10768978]. 3046 superoxide dismutase, manganese-dependent sodA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6217682 SPCG_0120 20140215 516950 protein-coding NCBI-supplied PMID: 19361343 MUTATION: pspA mutant is attenuated in mice [PMID:10603379]. 3047 surface protein A pspA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6217943 SPCG_1467 20140406 516950 protein-coding NCBI-supplied PMID: 19361343 MUTATION: pgdA mutant is attenuated in mice [PMID:12438406]. 3048 peptidoglycan N-acetylglucosamine deacetylase A pgdA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6217991 SPCG_1911 20140406 516950 protein-coding NCBI-supplied PMID: 19361343 MUTATION: lytA mutant is attenuated in mice [PMID:10603379]. 3049 autolysin lytA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6218247 SPCG_0747 20130705 516950 protein-coding NCBI-supplied PMID: 19361343 MUTATION: ciaR mutant is attenuated in mice [PMID:15292127]. 3050 DNA-binding response regulator CiaR ciaR Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6218274 SPCG_0941 20140329 516950 protein-coding NCBI-supplied PMID: 19361343 MUTATION: lytB has reduced colonization of nasopharynx of rats compared to wild type [PMID:10992472]. 3051 endo-beta-N-acetylglucosaminidase lytB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6218347 SPCG_0480 20140405 516950 protein-coding NCBI-supplied PMID: 19361343 MUTATION: glnA mutant had significantly reduced adhesion to Detroit 562 human pharyngeal epithelial cells [PMID:16787930]. 3052 glutamine synthetase, type I glnA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6218441 SPCG_1567 20140329 516950 protein-coding NCBI-supplied PMID: 19361343 MUTATION: codY mutant has lower bacterial loads during infection in mice compared to the wild type and have a diminished ability to adhere to nasopharangeal cells in vitro [PMID:18024519]. 3053 transcriptional repressor CodY codY Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6218513 SPCG_1129 20140217 516950 protein-coding NCBI-supplied PMID: 19361343 MUTATION: mutX mutant is attenuated in mice [PMID:9826334]. 3054 mutator MutT protein mutX Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6259537 YPTS_2180 20140405 502801 protein-coding NCBI-supplied MUTATION: cls mutant is attenuated in mice [PMID:11292689]. 4157 cardiolipin synthetase cls Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6260861 YPTS_0345 20140215 502801 protein-coding NCBI-supplied MUTATION: yscL mutant is attenuated in mice [PMID:11292689]. 4158 HrpE/YscL family type III secretion apparatus protein YPTS_0345 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6260970 YPTS_0453 20130705 502801 protein-coding NCBI-supplied MUTATION: hfq mutant is attenuated in mice [PMID:20231416]. 4159 RNA-binding protein Hfq hfq Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6261178 YPTS_0656 20130518 502801 protein-coding NCBI-supplied MUTATION: ksgA mutant is attenuated in mice [PMID:11292689]. 4160 dimethyladenosine transferase ksgA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6261827 YPTS_4218 20140215 502801 protein-coding NCBI-supplied MUTATION: yopH mutant is attenuated in mice [PMID:12542470]. 4161 protein-tyrosine phosphatase YopH YPTS_4218 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6261883 YPTS_4278 20140222 502801 protein-coding NCBI-supplied MUTATION: lcrR mutant is attenuated in mice [PMID:11292689]. 4162 type III secretion system regulator LcrR YPTS_4278 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6261897 YPTS_4292 20140217 502801 protein-coding NCBI-supplied MUTATION: yscU mutant is attenuated in mice [PMID:11292689]. 4163 YscU/HrpY family type III secretion protein YPTS_4292 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6261899 YPTS_4207 20140222 502801 protein-coding NCBI-supplied MUTATION: yscB mutant is attenuated in mice [PMID:11292689]. 4164 YscB family type III secretion system chaperone YPTS_4207 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6261902 YPTS_4221 20140222 502801 protein-coding NCBI-supplied PMID: 23519663 MUTATION: yopH mutant is attenuated in mice [PMID:12542470]. 4165 protein-tyrosine phosphatase YopH YPTS_4221 Bin Zhao, Oliver He wlbL WEB: http://www.ncbi.nlm.nih.gov/gene 6264488 BAV0090 20140406 360910 protein-coding NCBI-supplied PMID: 16885469 MUTATION: mutant attenuated in turkey tracheal colonization [PMID:10931292]. 4166 sugar epimerase/dehydratase - bplL Bin Zhao, Oliver He wlbA WEB: http://www.ncbi.nlm.nih.gov/gene 6266731 BAV0098 20140406 360910 protein-coding NCBI-supplied PMID: 16885469 MUTATION: mutant attenuated in turkey tracheal colonization [PMID:10931292]. 4167 oxidoreductase - bplA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6266746 BAV1876 20140405 360910 protein-coding NCBI-supplied PMID: 16885469 MUTATION: bvgS mutant is avirulent in turkeys [PMID:12704133]. 4168 virulence sensor protein bvgS Bin Zhao, Oliver He fimC WEB: http://www.ncbi.nlm.nih.gov/gene 6266977 BAV1963 20130518 360910 protein-coding NCBI-supplied PMID: 16885469 MUTATION: fhaA (fimC) mutant is avirulent in turkeys [PMID:12704133]. 4169 outer membrane fimbrial usher protein - fhaA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6266978 BAV1966 20130518 360910 protein-coding NCBI-supplied PMID: 16885469 MUTATION: fhaB mutant is avirulent in turkeys [PMID:12704133]. 4170 Filamentous hemagglutinin/adhesin fhaB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6267085 BAV1961 20130518 360910 protein-coding NCBI-supplied PMID: 16885469 hemolysin activator protein fhaC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6268332 SbBS512_0046 20140215 344609 protein-coding NCBI-supplied MUTATION: virB mutants have an avirulent phenotype and do not invade host cells [PMID:8385666]. 1652 P-type DNA transfer ATPase VirB11 virB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6268351 SbBS512_0044 20140215 344609 protein-coding NCBI-supplied MUTATION: virB mutants have an avirulent phenotype and do not invade host cells [PMID:8385666]. 1653 P-type conjugative transfer protein VirB9 virB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6268448 SbBS512_E4630 20130701 344609 protein-coding NCBI-supplied MUTATION: mutants of the iuc locus and the aerobactin receptor, iutA were attenuated in chicken embryos [PMID:3028962]. 1654 ferric aerobactin receptor IutA iutA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6268800 SbBS512_E0154 20140222 344609 protein-coding NCBI-supplied MUTATION: degP mutant is unable to form plaques on Henle cell monolayers [PMID:17526712]. 1655 serine endoprotease degP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6268872 SbBS512_E4633 20140405 344609 protein-coding NCBI-supplied MUTATION: iuc mutants are attenuated in chicken embryos and rabbit ileal loops [PMID:19130265]. 1656 N(6)-hydroxylysine O-acetyltransferase, aerobactin biosynthetic iucB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6268971 SbBS512_E0136 20140222 344609 protein-coding NCBI-supplied MUTATION: dksA mutants are able to invade cultured cell monlayers but are incapable of cell to cell spread [PMID:11500451]. 1657 RNA polymerase-binding transcription factor dksA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6269094 SbBS512_E4702 20140405 344609 protein-coding NCBI-supplied MUTATION: miaA mutants had reduced ability to invade and spread in MK2 cell monolayers compared to the wildtype [PMID:9294434]. 1658 tRNA delta(2)-isopentenylpyrophosphate transferase miaA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6269245 SbBS512_E1308 20130701 344609 protein-coding NCBI-supplied MUTATION: phoP mutants were resolved more quickly than wild type in animal models, and are more susceptible to killing by PMNs [PMID:11207599]. 1659 DNA-binding transcriptional regulator PhoP phoP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6269334 SbBS512_E3783 20130701 344609 protein-coding NCBI-supplied MUTATION: envZ insertion mutant is able to invade cells but has decreased virulence due to the inability to survive intracellularly [PMID:2121709]. 1660 osmolarity sensor protein envZ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6269369 SbBS512_E4632 20140405 344609 protein-coding NCBI-supplied MUTATION: iuc mutants are attenuated in chicken embryos and rabbit ileal loops [PMID:19130265]. 1661 aerobactin synthase subunit IucC iucC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6269390 SbBS512_E4634 20140405 344609 protein-coding NCBI-supplied MUTATION: iuc mutants are attenuated in chicken embryos and rabbit ileal loops [PMID:19130265]. 1662 aerobactin synthase subunit IucA iucA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6269502 SbBS512_E1421 20130701 344609 protein-coding NCBI-supplied MUTATION: tonB mutant is able to invade epithelial cells but is incapable of cell to cell spread [PMID:11035742]. 1663 transporter tonB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6269616 SbBS512_E0171 20140406 344609 protein-coding NCBI-supplied MUTATION: skp mutants are capable of infecting Henle cells but are incapable of cell to cell spread [PMID:17526712]. 1664 periplasmic chaperone skp Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6269720 SbBS512_E2882 20140322 344609 protein-coding NCBI-supplied MUTATION: guaAguaB mutants are attenuated in HeLa cells [PMID:8757833]. 1665 GMP synthase guaA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6269855 SbBS512_E0047 20130701 344609 protein-coding NCBI-supplied MUTATION: surA mutant is able to infect epithelial cells but is incapable of cell to cell spread [PMID:20447864]. 1666 peptidyl-prolyl cis-trans isomerase SurA surA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6269919 SbBS512_E4703 20130701 344609 protein-coding NCBI-supplied MUTATION: hfq deletion mutants are attenuated in guinea pig eye infection model (Sereny test) [PMID:20080057]. 1667 RNA-binding protein Hfq hfq Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6269987 SbBS512_E1853 20130701 344609 protein-coding NCBI-supplied MUTATION: sodB mutant is extremely sensitive to killing by phagocytes compared to the wild-type, and causes only mild damage in infection of rabbit ileal loops [PMID:2404874]. 1668 superoxide dismutase sodB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6270232 SbBS512_E0724 20130701 344609 protein-coding NCBI-supplied MUTATION: ompC mutants were attenuated in their ability to spread cell to cell and kill epithelial cells, and had a negative Sereny test [PMID:8359885]. 1669 outer membrane porin protein C ompC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6271178 SbBS512_E2420 20140329 344609 protein-coding NCBI-supplied MUTATION: aroA deletion mutants are attenuated in HeLa cells [PMID:8757833]. 1670 3-phosphoshikimate 1-carboxyvinyltransferase aroA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6271528 SbBS512_E2883 20140406 344609 protein-coding NCBI-supplied MUTATION: guaAguaB mutants are attenuated in HeLa cells [PMID:8757833]. 1671 inosine 5'-monophosphate dehydrogenase guaB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6272178 SbBS512_E3784 20140215 344609 protein-coding NCBI-supplied MUTATION: mutant of the ompB locus (both the envZ and ompR genes) showed attenuated virulence in HeLa cells, and a weak response to a Serany test [PMID:2121709]. 1672 osmolarity response regulator ompR Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6272400 SbBS512_E4332 20140406 344609 protein-coding NCBI-supplied MUTATION: dsbA mutants are less invasive to MK-2 cell monolayers compared to the wild-type [PMID:7761426]. 1673 protein disulfide isomerase I dsbA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6272464 SbBS512_E1896 20140405 344609 protein-coding NCBI-supplied MUTATION: aroD deletion led to attenuation in HeLa cells and monkeys [PMID:8356844]. 1674 3-dehydroquinate dehydratase aroD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6272715 SbBS512_E4631 20140405 344609 protein-coding NCBI-supplied MUTATION: iuc mutants are attenuated in chicken embryos and rabbit ileal loops [PMID:19130265]. 1675 L-lysine 6-monooxygenase iucD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6273328 SbBS512_A0178 20140222 344609 protein-coding NCBI-supplied MUTATION: mxiE deletion mutants are unable to block apoptosis of host epithelial cells [PMID:17339354]. 1676 transcriptional regulator MxiE mxiE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6273360 SbBS512_A0164 20121017 344609 protein-coding NCBI-supplied MUTATION: icsB mutants are attenuated in guinea pig eyes [PMID:12753186]. 1677 virulence protein IcsB icsB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6273424 SbBS512_A0159 20140322 344609 protein-coding NCBI-supplied MUTATION: ipaC mutants cannot invade cultured cells or lyse red blood cells [PMID:18656530]. 1678 invasin protein IpaC ipaC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6273427 SbBS512_A0166 20140405 344609 protein-coding NCBI-supplied MUTATION: ipgD mutant is unable to dephosphorylate phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P2] and induces shorter filapodia in host cells [PMID:12356723]. 1679 inositol phosphate phosphatase IpgD ipgD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6273497 SbBS512_A0158 20140322 344609 protein-coding NCBI-supplied MUTATION: ipaD mutants are completely unable to invade cultured cells or lyse RBCs [PMID:15731041]. 1680 invasin protein IpaD ipaD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6273518 SbBS512_A0157 20140405 344609 protein-coding NCBI-supplied MUTATION: ipaA mutants are attenuated in invasion of HeLa cells [PMID:9184218]. 1681 invasin protein IpaA ipaA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6273536 SbBS512_A0163 20130518 344609 protein-coding NCBI-supplied MUTATION: transposon mutants of ipgA cannot invade epithelial cells and cannot induce keratoconjunctivitis in mice [PMID:8376337]. 1682 chaperone protein IpgA ipgA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6273557 SbBS512_A0179 20140215 344609 protein-coding NCBI-supplied MUTATION: mxiD mutant is unable to invade HeLa cells or to provoke keratoconjunctivitis in guinea-pigs [PMID:8437520]. 1683 type III secretion outer membrane protein MxiD mxiD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6273571 SbBS512_A0173 20140217 344609 protein-coding NCBI-supplied MUTATION: mxiK mutants are unable to invade HeLa cells [PMID:12864857]. 1684 type III secretion apparatus protein MxiK mxiK Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6273598 SbBS512_A0161 20140222 344609 protein-coding NCBI-supplied MUTATION: ipgC mutant attenuated in infecting Caco-2 cells monolayer [PMID:11207551]. 1685 chaperone protein IpgC ipgC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6273614 SbBS512_A0170 20140217 344609 protein-coding NCBI-supplied MUTATION: mxiH mutants are unable to invade HeLa cells [PMID:11169106]. 1686 type III secretion apparatus needle protein mxiH mxiH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6273621 SbBS512_A0162 20140322 344609 protein-coding NCBI-supplied MUTATION: transposon mutants of ipgB cannot invade epithelial cells and cannot induce keratoconjunctivitis in mice [PMID:8376337] 1687 IpgB1 ipgB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6319260 CLH_1110 20140329 508767 protein-coding NCBI-supplied MUTATION: BoNT/E mutants were nontoxigenic as opposed to the toxigenic wild type strain [PMID:4633199] 2566 botulinum neurotoxin, type E3, BoNT/E3 boNT/E3 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6382168 MAR003 20140410 562 protein-coding NCBI-supplied PMID: 16926437; 19797469 MUTATION: bfpA deletion mutant of EPEC was less virulent in humans than the wild-type EPEC [PMID:9641917]. 18 Major pilin structural unit bundlin bfpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6382170 MAR005 20140406 562 protein-coding NCBI-supplied PMID: 16926437 MUTATION: bfpB mutant EPEC is unable to form BFP which is a major virulence factor of EPEC [PMID:8932312]. 19 Lipoprotein bfpB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6382174 MAR009 20140410 562 protein-coding NCBI-supplied PMID: 16926437 MUTATION: bfpE mutant strain of EPEC fails to form detectable BFP and fails to carry out autoaggregation and localized adherence to HEp-2 epithelial cells in tissue culture [PMID:11443077]. 20 Transmembrane protein bfpE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6382175 MAR010 20130913 562 protein-coding NCBI-supplied PMID: 16926437 MUTATION: bfpF mutant colonized the human intestine but was about 200-fold less virulent than the wild-type EPEC [PMID:9641917]. 21 Nucleotide binding protein bfpF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6382176 MAR011 20140410 562 protein-coding NCBI-supplied PMID: 16926437 MUTATION: mutation in bfpP blocks BFP biogenesis and localized adherence to host cells by EPEC [PMID:10762251]. 22 Prepilin peptidase bfpP Bin Zhao, Oliver He bfpT WEB: http://www.ncbi.nlm.nih.gov/gene 6382186 MAR020 20140410 562 protein-coding NCBI-supplied PMID: 16926437; 19797469 MUTATION: bfpT (perA) disruption mutant of EPEC was less virulent in humans than the wild-type EPEC [PMID:9641917]. 23 Transcriptional activator, bfp operon - perA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6395887 APP7_0898 20140329 537457 protein-coding NCBI-supplied MUTATION: pntB mutant is attenuated in pigs [PMID:12819083]. 4172 NAD(P) transhydrogenase subunit beta APP7_0898 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6396208 APP7_0732 20140405 537457 protein-coding NCBI-supplied MUTATION: moaA mutant is attenuated in pigs [PMID:12819083]. 4173 molybdenum cofactor biosynthesis protein A APP7_0732 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6396394 APP7_0637 20140315 537457 protein-coding NCBI-supplied MUTATION: guaA mutant is attenuated in pigs [PMID:12819083]. 4174 GMP synthase APP7_0637 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6396804 APP7_0428 20140406 537457 protein-coding NCBI-supplied MUTATION: hemA mutant is attenuated in pigs [PMID:12819083]. 4175 glutamyl-tRNA reductase APP7_0428 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6397101 APP7_1995 20140217 537457 protein-coding NCBI-supplied MUTATION: dnaK mutant is attenuated in porcine model of infection [PMID:10873489]. 4176 chaperone protein DnaK APP7_1995 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6397393 APP7_0112 20140405 537457 protein-coding NCBI-supplied MUTATION: hemE mutant is attenuated in pigs [PMID:12819083]. 4177 uroporphyrinogen decarboxylase APP7_0112 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6397642 APP7_0030 20140217 537457 protein-coding NCBI-supplied MUTATION: prfC mutant is attenuated in pigs [PMID:12819083]. 4178 peptide chain release factor 3 APP7_0030 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6397685 APP7_1492 20140301 537457 protein-coding NCBI-supplied MUTATION: znuA mutant is attenuated in pigs [PMID:12819083]. 4179 high-affinity zinc uptake system protein ZnuA precursor APP7_1492 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6397705 APP7_0074 20140215 537457 protein-coding NCBI-supplied MUTATION: recR mutant is attenuated in pigs [PMID:12819083]. 4180 recombination protein RecR APP7_0074 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6397772 APP7_1567 20130511 537457 protein-coding NCBI-supplied MUTATION: tig mutant is attenuated in porcine model of infection [PMID:10873489]. 4181 trigger factor APP7_1567 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6397986 APP7_1437 20140215 537457 protein-coding NCBI-supplied MUTATION: rpmF mutant is attenuated in porcine model of infection [PMID:10873489]. 4182 50S ribosomal protein L32 APP7_1437 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6478692 SPG_2147 20140215 512566 protein-coding NCBI-supplied PMID: 11442348 MUTATION: cbpD has reduced colonization of nasopharynx of rats compared to the wild type [PMID:10992472]. 3431 choline binding protein D cbpD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6478755 SPG_0956 20140215 512566 protein-coding NCBI-supplied PMID: 11442348 MUTATION: piaA piuB double mutant is attenuated in systemic infection of mice [PMID:12117949]. 3432 iron ABC transporter iron-binding protein piaA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6478858 SPG_1558 20140222 512566 protein-coding NCBI-supplied PMID: 11442348 MUTATION: psaB mutant is attenuated in mice [PMID:11988523]. 3433 manganese ABC transporter ATP-binding protein psaB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6478869 SPG_0458 20140405 512566 protein-coding NCBI-supplied PMID: 11442348 MUTATION: glnA mutant had significantly reduced adhesion to Detroit 562 human pharyngeal epithelial cells [PMID:16787930]. 3434 type I glutamine synthetase glnA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6478876 SPG_1053 20140217 512566 protein-coding NCBI-supplied PMID: 11442348 MUTATION: iga mutant is attenuated in mice [PMID:12841855]. 3435 immunoglobulin A1 protease igA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6478888 SPG_0316 20140215 512566 protein-coding NCBI-supplied PMID: 11442348 MUTATION: cpsC mutant is avirulent in mice [PMID:15122528]. 3436 capsular polysaccharide biosynthesis protein Wzh cpsC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6478940 SPG_0697 20140222 512566 protein-coding NCBI-supplied PMID: 11442348 MUTATION: sodA mutant is attenuated in mice [PMID:10768978]. 3437 manganese-dependent superoxide dismutase sodA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6478968 SPG_0856 20140215 512566 protein-coding NCBI-supplied PMID: 11442348 MUTATION: cbpE has reduced colonization of nasopharynx of rats and reduced adherence to human epithelial cells [PMID:10992472]. 3438 choline binding protein E cbpE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6478994 SPG_1509 20140217 512566 protein-coding NCBI-supplied PMID: 11442348 MUTATION: codY mutant has lower bacterial loads during infection in mice compared to the wild type and have a diminished ability to adhere to nasopharangeal cells in vitro [PMID:18024519]. 3439 transcriptional repressor CodY codY Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6479000 SPG_0889 20140217 512566 protein-coding NCBI-supplied PMID: 11442348 MUTATION: lytB has reduced colonization of nasopharynx of rats compared to the wild type [PMID:10992472]. 3440 endo-beta-N-acetylglucosaminidase lytB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6479105 SPG_0605 20140215 512566 protein-coding NCBI-supplied PMID: 11442348 MUTATION: zmpB mutant is attenuated in mice [PMID:12841855]. 3441 zinc metalloprotease ZmpB zmpB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6479228 SPG_0356 20140215 512566 protein-coding NCBI-supplied PMID: 11442348 MUTATION: cbpG has reduced colonization of nasopharynx of rats and reduced adherence to human epithelial cells [PMID:10992472]. 3442 choline binding protein G cbpG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6479310 SPG_0051 20140322 512566 protein-coding NCBI-supplied PMID: 11442348 MUTATION: a purL mutant was attenuated in a murine model [PMID:11359563] 3443 phosphoribosylformylglycinamide synthetase purL Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6479320 SPG_0663 20140405 512566 protein-coding NCBI-supplied PMID: 11442348 MUTATION: spxB mutant has a loss in the ability to attach eukayrotic cells and is attenuated in rabbits [PMID:8820650]. 3444 pyruvate oxidase spxB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6479325 SPG_1406 20140217 512566 protein-coding NCBI-supplied PMID: 11442348 MUTATION: pgdA mutant is attenuated in mice [PMID:12438406]. 3445 peptidoglycan GlcNAc deacetylase PgdA pgdA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6479425 SPG_0315 20140215 512566 protein-coding NCBI-supplied PMID: 11442348 MUTATION: cpsB mutant is avirulent in mice [PMID:15122528]. 3446 tyrosine-protein phosphatase wzh cpsB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6479482 SPG_0074 20140329 512566 protein-coding NCBI-supplied PMID: 11442348 MUTATION: zmpC mutant is attenuated in mice [PMID:12864860]. 3447 zinc metalloprotease ZmpC zmpC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6479630 SPG_0728 20140406 512566 protein-coding NCBI-supplied PMID: 11442348 MUTATION: ciaR mutant is attenuated in mice [PMID:15292127]. 3448 CiaR response regulator TCS05 ciaR Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6479683 SPG_1836 20130705 512566 protein-coding NCBI-supplied PMID: 11442348 MUTATION: ply mutant is attenuated in mice [PMID:10603379]. 3449 pneumolysin ply Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6479746 SPG_1600 20140405 512566 protein-coding NCBI-supplied PMID: 11442348 MUTATION: nanA mutant is attenuated in mice [PMID:9826334]. 3450 neuraminidase A nanA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6479772 SPG_0342 20130705 512566 protein-coding NCBI-supplied PMID: 11442348; 23184523 MUTATION: ritR mutant is attenuated in lung infection model of mice [PMID:15547286]. 3451 RitR response regulator ritR Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6479830 SPG_1131 20140217 512566 protein-coding NCBI-supplied PMID: 11442348 MUTATION: glnP mutant is attenuated in mice [PMID:18174343]. 3452 ABC transporter amino acid-binding protein/permease glnP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6480061 SPG_1068 20140215 512566 protein-coding NCBI-supplied PMID: 11442348 MUTATION: mutX is attenuated in mice [PMID:9826334]. 3453 mutator mutT protein mutX Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6480079 SPG_0309 20140315 512566 protein-coding NCBI-supplied PMID: 11442348 MUTATION: luxS mutant has defective ability to persist in the nasopharyngeal tissues of mice [PMID:15102809]. 3454 S-ribosylhomocysteinase luxS Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6480115 SPG_2135 20140215 512566 protein-coding NCBI-supplied PMID: 11442348 MUTATION: pspC mutant has reduced ability to colonize the nasopharynx of mice compared to t he wild type [PMID:17261599]. 3455 surface protein PspC pspC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6480167 SPG_0121 20140217 512566 protein-coding NCBI-supplied PMID: 11442348 MUTATION: pspA mutant is attenuated in mice [PMID:10603379]. 3456 surface protein A pspA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6480263 SPG_0298 20140222 512566 protein-coding NCBI-supplied PMID: 11442348 MUTATION: regR mutant is attenuated in mice [PMID:12704136]. 3457 sugar binding transcriptional regulator RegR regR Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6480363 SPG_1847 20140406 512566 protein-coding NCBI-supplied PMID: 11442348; 21825061 MUTATION: lytA mutant is attenuated in mice [PMID:10603379]. 3458 autolysin lytA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6480374 SPG_1325 20140222 512566 protein-coding NCBI-supplied PMID: 11442348 MUTATION: potD mutant is attenuated in pulmonary and systemic models of infection in mice [PMID:16368990]. 3459 spermidine/putrescine ABC transporter spermidine/putrescine-binding protein potD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6480618 SPG_1499 20140215 512566 protein-coding NCBI-supplied PMID: 11442348 MUTATION: lytC mutant have reduced colonization of rat nasopharynx compared to wild type [PMID:10992472]. 3460 endo-beta-N-acetylglucosaminidase lytC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6480660 SPG_1560 20140215 512566 protein-coding NCBI-supplied PMID: 11442348; 23683724 MUTATION: psaA mutant is attenuated in mice [PMID:8945574]. 3461 manganese ABC transporter substrate-binding lipoprotein psaA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6480715 SPG_1559 20130705 512566 protein-coding NCBI-supplied PMID: 11442348 MUTATION: psaC mutant is attenuated in mice [PMID:11988523]. 3462 manganese ABC transporter permease psaC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6760966 Sez_1395 20140215 552526 protein-coding NCBI-supplied PMID: 18716664 MUTATION: vicK mutant was attenuated in mice [PMID:19088917]. 4183 TCS sensor kinase VicK vicK Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6761408 Sez_0809 20140222 552526 protein-coding NCBI-supplied PMID: 18716664; 22384152 MUTATION: szp mutant is attenuated in mice [PMID:18983882]. 4184 M-like proptein Szp szp Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6761983 Sez_1357 20140217 552526 protein-coding NCBI-supplied PMID: 18716664 MUTATION: lgt mutant is attenuated in mice [PMID:17015455]. 4185 prolipoprotein diacylglyceryl transferase lgt MUTATION: sopE2 mutant has reduced ability to invade HeLa cells compared to wild-type [PMID:10735884]. 3427 MUTATION: A cbiA mutant, in combination with a cobS mutation, is attenuated in chickens [PMID:20153354]. 4920 MUTATION: A lon mutant is attenuated in mice [PMID:20487719]. MUTATION: ion mutant is attenuated in chickens [PMID:20487719]. 4923 5004 MUTATION: A cobS mutant, in combination with a cbiA mutation, is attenuated in chickens [PMID:20153354]. 4921 MUTATION: A cpxR mutant is attenuated in mice [PMID:20487719]. 4925 MUTATION: A nuoG mutant is attenuated in chickens [PMID:9682335]. 4930 MUTATION: slyA mutant is attenuated in mice [PMID:8290552]. 3428 MUTATION: ssaV and aroC double mutants are attenuated in humans [PMID:19745519]. 3429 MUTATION: fur mutants are attenuated in mice [PMID:19577637]. 3400 MUTATION: sodC mutant is attenuated in mice [PMID:19577637]. 3401 MUTATION: sopE2 mutant has reduced ability to invade HeLa cells compared to wild-type [PMID:10735884]. 3402 MUTATION: sodC mutant is attenuated in mice [PMID:19577637]. 3403 MUTATION: rpoS mutants are attenuated in mice [PMID:19577637]. 3404 MUTATION: relA mutant is attenuated in mice [PMID:19577637]. 3405 MUTATION: htrA mutant is attenuated in mice [PMID:19577637]. 3406 MUTATION: ompR mutants are attenuated in mice [PMID:19577637]. 3407 MUTATION: galE mutants are attenuated in mice [PMID:19577637]. 3408 MUTATION: guaB mutant is attenuated in BALB/c mice [PMID:17261603]. 4922 MUTATION: invA mutants are attenuated in chicks infected orally but not intraperitoneally [PMID:9087319]. 3409 MUTATION: invC mutants are attenuated in chicks infected orally but not intraperitoneally [PMID:9087319]. 3410 MUTATION: hfq mutant is attenuated in mice [PMID:19577637]. 3411 MUTATION: phoP mutants are attenuated in mice [PMID:19577637]. 3412 MUTATION: rfaL mutants are attenuated in mice [PMID:19577637]. 3413 MUTATION: rfaG mutants are attenuated in mice [PMID:19577637]. 3414 MUTATION: misL mutant is attenuated in mice [PMID:19577637]. 3415 MUTATION: spoT mutants are attenuated in mice [PMID:19577637]. 3416 MUTATION: aroA mutants are attenuated in mice [PMID:19577637]. 3417 MUTATION: iacP mutants were noninvasive in chicks [PMID:11731137]. 3418 MUTATION: sipD mutants were noninvasive in chicks [PMID:11731137]. 3419 MUTATION: sipB mutants were significantly less invasive in chickens than the wild-type [PMID:19322708]. 3420 MUTATION: slyA mutant is attenuated in mice [PMID:8290552]. 3421 MUTATION: ssrA mutant is attenuated in mice [PMID:19577637]. 3422 MUTATION: ssaV and aroC double mutants are attenuated in humans [PMID:19745519]. 3423 MUTATION: sseA mutant is attenuated in mice [PMID:19577637]. 3424 MUTATION: clpP mutant is attenuated in mice [PMID:19577637]. 3425 MUTATION: aroD mutants are attenuated in mice [PMID:19577637]. 3426 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6962890 HPG27_8 20140215 563041 protein-coding NCBI-supplied PMID: 18952803 MUTATION: knockout strain reduced adherence to human gastric epithelial cells [PMID:10454640]. 3390 outer membrane protein hopZ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6962945 HPG27_63 20140406 563041 protein-coding NCBI-supplied PMID: 18767150; 18952803; 22698670 MUTATION: urease-negative strain showed reduced colonization in gnotobiotic piglets [PMID:8063376]. 3391 urease accessory protein ureG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6962991 HPG27_107 20140315 563041 protein-coding NCBI-supplied PMID: 18952803 MUTATION: mutant strains showed reduced motility and colonization in piglets [PMID:8698465]. 3392 flagellin B flaB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6963000 HPG27_116 20130508 563041 protein-coding NCBI-supplied PMID: 18952803 MUTATION: knockout strain showed reduced adhesion and colonization in mice [PMID:17492999]. 3393 outer membrane protein horB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6963184 HPG27_298 20140215 563041 protein-coding NCBI-supplied PMID: 18952803 MUTATION: strains lacking BabA cannot adhere to Leb, expressed on gastric epithelium [PMID:14762173]. 3394 outer membrane protein babA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6963392 HPG27_503 20140215 563041 protein-coding NCBI-supplied PMID: 18952803 MUTATION: knock out deprived wild-type of the pathogenicity for gastritis and gastric ulcer in Mongolian gerbils [PMID:11104802]. 3395 cag pathogenicity island protein E cagE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6963451 HPG27_562 20140329 563041 protein-coding NCBI-supplied PMID: 18952803 MUTATION: mutant strains showed reduced colonization in piglets [PMID:8698465]. 3396 flagellin A flaA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6963488 HPG27_599 20140215 563041 protein-coding NCBI-supplied PMID: 18952803 MUTATION: mutant strain showed reduction in bacterial adherence to gastric epithelia in vitro [PMID:17054063]. 3397 outer membrane protein hopH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6963569 HPG27_680 20140215 563041 protein-coding NCBI-supplied PMID: 18705343; 18952803 MUTATION: deletion mutant lost ability to bind to sialyl-Lewis antigens [PMID:17121461], and had no neutrophil-activating capacity [PMID:17121461]. 3398 outer membrane protein sabA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6963731 HPG27_840 20140405 563041 protein-coding NCBI-supplied PMID: 18952803 MUTATION: knockout did not cause gastric ulcers in mice compared to wild type [PMID:20046046]. 3399 vacuolating cytotoxin A vacA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6967035 ECH74115_1739 20140222 444450 protein-coding NCBI-supplied PMID: 22135463 MUTATION: attenuated in mice [PMID:11553558] 3369 transporter tonB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6967123 ECH74115_5300 20140406 444450 protein-coding NCBI-supplied PMID: 22135463 MUTATION: mutation of dsbA led to degradation of bundilin and an absence of localized adherence to host cells in EPEC [PMID:9224871]. 3370 protein disulfide isomerase I dsbA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6967851 ECH74115_4912 20140406 444450 protein-coding NCBI-supplied PMID: 22135463 MUTATION: dppA mutant was attenuated 10- to 50-fold compared to the wild type for colonization of the bladders and kidneys of mice [PMID:17074858]. 3371 dipeptide ABC transporter substrate-binding protein dppA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6967853 ECH74115_4857 20140406 444450 protein-coding NCBI-supplied PMID: 22135463 MUTATION: chuA mutant unable to grow on iron-depleted medium containing heme [PMID:9157252]. 3372 outer membrane heme/hemoglobin receptor ChuA chuA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6968671 ECH74115_5280 20140217 444450 protein-coding NCBI-supplied PMID: 22135463 MUTATION: attenuated in mice [PMID:12117951]. 3373 transcriptional activator RfaH rfaH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6969157 ECH74115_1121 20140215 444450 protein-coding NCBI-supplied PMID: 22135463 MUTATION: OmpA− strains are unable to cause actin condensation needed for invasion of brain epithelial cells [PMID:10531228]. 3374 outer membrane protein A ompA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6969617 ECH74115_5826 20140222 444450 protein-coding NCBI-supplied PMID: 22135463 MUTATION: attenuated in mice and humans [PMID:18482721]. 3375 protein FimH fimH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6985084 Spy49_1559c 20140405 471876 protein-coding NCBI-supplied PMID: 18820018 MUTATION: fba mutant showed diminished invasive capabilities to HEp-2 cells and low mortality in mice following skin infection [PMID:11679068]. 4438 fructose-bisphosphate aldolase fba Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6985239 Spy49_1630 20140406 471876 protein-coding NCBI-supplied PMID: 18820018; 23106864 MUTATION: ska mutant was attenuated in mouse acute poststreptococcal glomerulonephritis model [PMID:10678902]. 4439 streptokinase ska Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6985276 Spy49_1669c 20140329 471876 protein-coding NCBI-supplied PMID: 18820018 MUTATION: scpA mutant is attenuated in mouse pneumonia model [PMID:9119483]. 4440 C5a peptidase scpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6985280 Spy49_1673c 20140322 471876 protein-coding NCBI-supplied PMID: 18820018 MUTATION: mga mutant is attenuated in a humanized mouse model for superficial skin infection [PMID:18588968]. 4441 M protein trans-acting positive regulator (Mga) mga Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6985296 Spy49_1690c 20140217 471876 protein-coding NCBI-supplied PMID: 18820018; 22267517; 22610375 MUTATION: Mice infected by M1, M3 and M49 speB mutants, through air pouch or intraperitoneal challenge, showed less mortality compared with that of the wild-type strains [PMID:18796357]. 4442 strepotococcal cysteine protease (streptopain) / streptococcal pyrogenic exotoxin B (SpeB) speB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6985582 Spy49_0568 20130704 471876 protein-coding NCBI-supplied PMID: 18820018 MUTATION: sagA mutant is attenuated in mice [PMID:11801184]. 4443 streptolysin S associated protein (SagA) Other designations: streptolysin S associated protein SagA sagA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 6985658 Spy49_0647 20140315 471876 protein-coding NCBI-supplied PMID: 18820018 MUTATION: lsp mutant is attenuated in a murine model of soft tissue infection [PMID:19398546]. 4444 lipoprotein signal peptidase lsp Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7002513 ECSE_4128 20140217 409438 protein-coding NCBI-supplied PMID: 18931093 MUTATION: attenuated in mice [PMID:12117951]. 3368 transcriptional activator RfaH rfaH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7003474 pCP8533etx_p28 20140406 1502 protein-coding NCBI-supplied PMID: 18776010; 21781280; 23056496; 23630957 epsilon toxin pCP8533etx_p28 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7009743 HPP12_0609 20140308 570508 protein-coding NCBI-supplied PMID: 20478826 MUTATION: mutant strains showed reduced colonization in piglets [PMID:8698465]. 3376 flagellin A flaA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7009784 HPP12_0650 20140217 570508 protein-coding NCBI-supplied PMID: 20478826 MUTATION: mutant strain showed reduction in bacterial adherence to gastric epithelia in vitro [PMID:17054063]. 3377 outer membrane protein HopH hopH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7009855 HPP12_0721 20140215 570508 protein-coding NCBI-supplied PMID: 20478826 MUTATION: knockout strains reduced damage and adherence to human gastric epithelial cells [PMID:18811585]. 3378 outer membrane protein HomB homB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7010020 HPP12_0884 20140301 570508 protein-coding NCBI-supplied PMID: 20478826 MUTATION: knockout did not cause gastric ulcers in mice compared to wild type [PMID:20046046]. 3379 vacuolating cytotoxin VacA vacA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7010027 HPP12_0891 20140215 570508 protein-coding NCBI-supplied PMID: 20478826 MUTATION: strains slacking BabA cannot adhere to Leb, expressed on gastric epithelium [PMID:14762173]. 3380 outer membrane protein BabA babA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7010048 HPP12_0910 20140217 570508 protein-coding NCBI-supplied PMID: 20478826 MUTATION: mutant showed severe reduction in ability to bind to gastric cell line [PMID:10200971]. 3381 outer membrane protein HopC/AlpA alpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7010049 HPP12_0911 20140217 570508 protein-coding NCBI-supplied PMID: 20478826 MUTATION: mutant showed severe reduction in ability to bind to gastric cell line [PMID:10200971]. 3382 outer membrane protein HopB/AlpB alpB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7010375 HPP12_0007 20140217 570508 protein-coding NCBI-supplied PMID: 20478826 MUTATION: knockout strain reduced adherence to human gastric epithelial cells [PMID:10454640]. 3383 outer membrane protein HopZ hopZ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7010440 HPP12_0072 20140215 570508 protein-coding NCBI-supplied PMID: 20478826 MUTATION: urease-negative strain showed reduced colonization in gnotobiotic piglets [PMID:8063376]. 3384 urease accessory protein UreG ureG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7010487 HPP12_0117 20140405 570508 protein-coding NCBI-supplied PMID: 20478826 MUTATION: mutant strains showed reduced motility and colonization in piglets [PMID:8698465]. 3385 flagellin B flaB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7010497 HPP12_0127 20140217 570508 protein-coding NCBI-supplied PMID: 20478826 MUTATION: knockout strain showed reduced adhesion and colonization in mice [PMID:17492999]. 3386 outer membrane protein HorB horB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7010614 HPP12_0243 20140215 570508 protein-coding NCBI-supplied PMID: 20478826 MUTATION: deletion impaired adherence to host cells [PMID:16758245]. 3387 neutrophil-activating protein A napA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7010918 HPP12_0543 20121127 570508 protein-coding NCBI-supplied PMID: 20478826 MUTATION: mutant strain adhered less to AGS cells than wild-type strain [PMID:12018657]. 3388 cag pathogenicity island protein P cagP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7010926 HPP12_0551 20140217 570508 protein-coding NCBI-supplied PMID: 20478826 MUTATION: knock out deprived wild-type of the pathogenicity for gastritis and gastric ulcer in Mongolian gerbils [PMID:11104802]. 3389 cag pathogenicity island protein E VirB4-like protein cagE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7011361 RVA_s10_gp1 20140406 28875 protein-coding NCBI-supplied PMID: 17059839; 18787006; 21151776; 22036730; 22406141; 24109210 MUTATION: NSP4 mutants that fail to bind or signal through integrin alpha2 were attenuated in diarrhea induction in neonatal mice [PMID:18587047]. 3430 NSP4 RVA_s10_gp1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7056322 E2348_P1_009 20140222 574521 protein-coding NCBI-supplied PMID: 18952797 MUTATION: bfpE mutant strain of EPEC fails to form detectable BFP and fails to carry out autoaggregation and localized adherence to HEp-2 epithelial cells in tissue culture [PMID:11443077]. 3593 transmembrane protein bfpE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7056323 E2348_P1_010 20130508 574521 protein-coding NCBI-supplied PMID: 18952797 MUTATION: bfpF mutant colonized the human intestine but was about 200-fold less virulent than the wild-type EPEC [PMID:9641917]. 3594 nucleotide binding protein bfpF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7056324 E2348_P1_011 20130508 574521 protein-coding NCBI-supplied PMID: 18952797 MUTATION: mutation in bfpP blocks BFP biogenesis and localized adherence to host cells by EPEC [PMID:10762251]. 3595 prepilin peptidase bfpP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7056325 E2348_P1_005 20140406 574521 protein-coding NCBI-supplied PMID: 18952797; 22247509 MUTATION: bfpB mutant EPEC is unable to form BFP which is a major virulence factor of EPEC [PMID:8932312]. 3596 lipoprotein bfpB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7056343 E2348_P1_003 20140215 574521 protein-coding NCBI-supplied PMID: 18952797 MUTATION: bfpA deletion mutant of EPEC was less virulent in humans than the wild-type EPEC [PMID:9641917]. 3597 major pilin structural unit bundlin bfpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7056350 E2348_P1_046 20130508 574521 protein-coding NCBI-supplied PMID: 18952797 MUTATION: traT mutants have altered membrane permeability and are sensitive to hydrophobic antibiotics [PMID:3323837]. 3598 conjugal transfer surface exclusion protein TraT traT Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7056370 E2348_P1_075 20130508 574521 protein-coding NCBI-supplied PMID: 18952797 MUTATION: traJ mutants of E. coli K1 are attenuated in rat pups and macrophages [PMID:14688129]. 3599 transcriptional activator traJ Bin Zhao, Oliver He E2348_C_3930 WEB: http://www.ncbi.nlm.nih.gov/gene 7061130 E2348C_3930 20121017 574521 protein-coding NCBI-supplied PMID: 18952797 MUTATION: espF mutant of EPEC is deficient in its ability to disrupt electrical resistance across a polarized monolayer of intestinal epithelial cells, suggesting that EspF is an effector molecule required for disrupting intestinal epithelial barrier function [PMID:11238563]. 3480 LEE-encoded effector EspF - espF Bin Zhao, Oliver He E2348_C_1379 WEB: http://www.ncbi.nlm.nih.gov/gene 7061491 E2348C_1379 20140217 574521 protein-coding NCBI-supplied PMID: 18952797 MUTATION: attenuated in mice [PMID:11553558]. 3481 transporter - tonB Bin Zhao, Oliver He E2348_C_4154 WEB: http://www.ncbi.nlm.nih.gov/gene 7061758 E2348C_4154 20140222 574521 protein-coding NCBI-supplied PMID: 18952797 MUTATION: attenuated in mice [PMID:12117951]. 3482 transcriptional activator RfaH - rfaH Bin Zhao, Oliver He E2348_C_3942 WEB: http://www.ncbi.nlm.nih.gov/gene 7061805 E2348C_3942 20140215 574521 protein-coding NCBI-supplied PMID: 18952797; 20618342 MUTATION: map EPEC mutants have significantly reduced levels of invasion of HeLa cells [PMID:14531893]. 3483 LEE-encoded effector Map - map Bin Zhao, Oliver He E2348_C_2041 WEB: http://www.ncbi.nlm.nih.gov/gene 7061913 E2348C_2041 20140315 574521 protein-coding NCBI-supplied PMID: 18952797 MUTATION: fliC deletion mutants had reduced adherence in bovine tissue compared to the wild type EHEC and EPEC strains [PMID:17693516]. 3484 flagellin - fliC Bin Zhao, Oliver He E2348_C_4627 WEB: http://www.ncbi.nlm.nih.gov/gene 7062125 E2348C_4627 20140217 574521 protein-coding NCBI-supplied PMID: 18952797 MUTATION: attenuated in mice and humans [PMID:18482721]. 3485 minor component of type 1 fimbriae - fimH Bin Zhao, Oliver He E2348_C_3948 WEB: http://www.ncbi.nlm.nih.gov/gene 7062686 E2348C_3948 20140215 574521 protein-coding NCBI-supplied PMID: 18952797; 21804003 MUTATION: deletion of escN abolished pathogenicity in infant rabbits compared to wild-type EHEC [PMID:15731044]. 3486 translocator EscN - escN Bin Zhao, Oliver He E2348_C_3968 WEB: http://www.ncbi.nlm.nih.gov/gene 7062691 E2348C_3968 20130508 574521 protein-coding NCBI-supplied PMID: 18835988; 18952797 MUTATION: ler mutants had less adhesion to HeLa cells, ler is a regulator of many virulence genes in the LEE PAI which are needed for adherence [PMID:18794291]. 3487 transcriptional regulator Ler - ler Bin Zhao, Oliver He E2348_C_3970 WEB: http://www.ncbi.nlm.nih.gov/gene 7062692 E2348C_3970 20140222 574521 protein-coding NCBI-supplied PMID: 18952797 MUTATION: the inhibitory effect of the espG mutant on Cl– uptake in Caco-2 monolayers was significantly attenuated as compared with wild-type EPEC [PMID:17256057]. 3488 LEE-encoded effector EspG - espG Bin Zhao, Oliver He E2348_C_3743 WEB: http://www.ncbi.nlm.nih.gov/gene 7062790 E2348C_3743 20140217 574521 protein-coding NCBI-supplied PMID: 18952797 MUTATION: chuA mutant unable to grow on iron-depleted medium containing heme [PMID:9157252]. 3489 outer membrane heme/hemoglobin receptor - chuA Bin Zhao, Oliver He E2348_C_0943 WEB: http://www.ncbi.nlm.nih.gov/gene 7063342 E2348C_0943 20140217 574521 protein-coding NCBI-supplied PMID: 18952797 MUTATION: OmpA− strains are unable to cause actin condensation needed for invasion of brain epithelial cells [PMID:10531228]. 3490 outer membrane protein A - ompA Bin Zhao, Oliver He E2348_C_0249 WEB: http://www.ncbi.nlm.nih.gov/gene 7063831 E2348C_0249 20121017 574521 protein-coding NCBI-supplied PMID: 18952797 MUTATION: ecpA mutant had attenuated adherence to HEp-2 cells compared to the parental EHEC strain [PMID:17563352]. 3491 fimbrillin precursor - ecpA Bin Zhao, Oliver He E2348_C_3939 WEB: http://www.ncbi.nlm.nih.gov/gene 7063868 E2348C_3939 20140215 574521 protein-coding NCBI-supplied PMID: 18952797 MUTATION: attenuated in humans [PMID:8376594]. 3492 intimin EaeA - eaeA Bin Zhao, Oliver He E2348_C_3935 WEB: http://www.ncbi.nlm.nih.gov/gene 7063878 E2348C_3935 20140217 574521 protein-coding NCBI-supplied PMID: 18952797; 20400543 MUTATION: espD deletion mutant of the enterohemorrhagic E. coli (EHEC) strain EDL933 had impaired attachment to HeLa cells [PMID:10456938]. 3493 translocon EspD - espD Bin Zhao, Oliver He E2348_C_3936 WEB: http://www.ncbi.nlm.nih.gov/gene 7063880 E2348C_3936 20140406 574521 protein-coding NCBI-supplied PMID: 18952797; 19218393; 20400543 MUTATION: deletion of espA in STEC abolished ability to attach to HeLa cells and induce actin rearrangements [PMID:9786192]. 3494 translocon EspA - espA Bin Zhao, Oliver He E2348_C_4167 WEB: http://www.ncbi.nlm.nih.gov/gene 7063974 E2348C_4167 20140406 574521 protein-coding NCBI-supplied PMID: 18952797; 19525348 MUTATION: mutation of dsbA led to degradation of bundilin and an absence of localized adherence to host cells in EPEC [PMID:9224871]. 3495 protein disulfide isomerase I - dsbA Bin Zhao, Oliver He E2348_C_3934 WEB: http://www.ncbi.nlm.nih.gov/gene 7064346 E2348C_3934 20121017 574521 protein-coding NCBI-supplied PMID: 18952797; 20400543 MUTATION: deletion mutant attenuated in humans compared to wild-type EPEC [PMID:10816529]. 3496 translocon EspB - espB Bin Zhao, Oliver He E2348_C_3944 WEB: http://www.ncbi.nlm.nih.gov/gene 7064347 E2348C_3944 20121017 574521 protein-coding NCBI-supplied PMID: 18952797; 22251971 MUTATION: deletion mutant is attenuated in infant rabbits [PMID:15731044]. 3497 LEE-encoded effector EspH - espH Bin Zhao, Oliver He E2348_C_3941 WEB: http://www.ncbi.nlm.nih.gov/gene 7064348 E2348C_3941 20140222 574521 protein-coding NCBI-supplied PMID: 18952797; 20345487; 21179574 MUTATION: tir deletion strains are unable to adhere to tissue in an in vitro organ culture [PMID:17474908]. 3498 translocated intimin receptor Tir - tir Bin Zhao, Oliver He E2348_C_3792 WEB: http://www.ncbi.nlm.nih.gov/gene 7065057 E2348C_3792 20140405 574521 protein-coding NCBI-supplied PMID: 18952797 MUTATION: dppA mutant was attenuated 10- to 50-fold compared to the wild type for colonization of the bladders and kidneys of mice [PMID:17074858]. 3499 dipeptide transporter - dppA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7078568 LMHCC_1513 20140406 552536 protein-coding NCBI-supplied PMID: 21602330 MUTATION: mutant strain showed reduced bacterial escape from phagosomes of macrophages and virulence in mice [PMID:10760131]. 3600 ATP-dependent Clp protease proteolytic subunit clpP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7078927 LMHCC_0048 20140217 552536 protein-coding NCBI-supplied PMID: 21602330 MUTATION: a gtcA mutant was attenuated in mice [PMID:11254558] 3601 cell wall teichoic acid glycosylation protein GtcA LMHCC_0048 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7078992 LMHCC_0614 20140215 552536 protein-coding NCBI-supplied PMID: 21602330 MUTATION: a recQ mutant was attenuated in mice [PMID:11254558] 3602 ATP-dependent DNA helicase, recQ LMHCC_0614 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7079328 LMHCC_0131 20140406 552536 protein-coding NCBI-supplied PMID: 21602330 MUTATION: mutant strain showed reduced bacterial escape from phagosomes of macrophages and virulence in mice [PMID:10760131]. 3603 ATP-dependent Clp protease proteolytic subunit clpP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7079719 LMHCC_0362 20140217 552536 protein-coding NCBI-supplied PMID: 21602330 MUTATION: mutant showed attenuated virulence in mice [PMID:15028680]. 3604 sortase srtB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7080110 LMHCC_2768 20140215 552536 protein-coding NCBI-supplied PMID: 21602330 MUTATION: a recQ mutant was attenuated in mice [PMID:11254558] 3605 ATP-dependent DNA helicase RecQ LMHCC_2768 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7080876 LMHCC_2601 20140215 552536 protein-coding NCBI-supplied PMID: 21602330 MUTATION: attenuated in mice [PMID:14638794]. 3606 pentapeptide repeats domain protein LMHCC_2601 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7081139 LMHCC_1438 20140217 552536 protein-coding NCBI-supplied PMID: 21602330 MUTATION: mutant strain severely attenuated in cell culture, impaired for adhesion to certain eukaryotic cells [PMID:18599819]. 3607 exo-glucosaminidase LytG LMHCC_1438 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7106930 BbuZS7_0667 20140222 445985 protein-coding NCBI-supplied PMID: 20935092; 21347346 MUTATION: BosR mutant attenuated in mice [PMID:19906179]. 4445 oxidative stress regulator protein BosR bosR Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7119366 pECS88_0009 20140329 585035 protein-coding NCBI-supplied PMID: 19165319; 19307211 MUTATION: attenuated in mice [PMID:11553558]. 3561 Ferric aerobactin receptor precusor IutA iutA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7119392 pECS88_0124 20140215 585035 protein-coding NCBI-supplied PMID: 19165319; 19307211 MUTATION: iroA gene cluster mutants were unable to resist Lcn2 in mouse serum [PMID:17060628]. 3562 outer membrane receptor FepA iroN Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7119430 pECS88_0128 20140215 585035 protein-coding NCBI-supplied PMID: 19165319; 19307211 MUTATION: attenuated in chicks [PMID:18541653]. 3563 IroB, putative glucosyltransferase iroB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7119431 pECS88_0127 20140215 585035 protein-coding NCBI-supplied PMID: 19165319; 19307211 MUTATION: attenuated in chicks [PMID:18541653]. 3564 IroC, ATP binding cassette (ABC) transporter homolog iroC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7119432 pECS88_0126 20140329 585035 protein-coding NCBI-supplied PMID: 19165319; 19307211 MUTATION: attenuated in chicks [PMID:18541653]. 3565 IroD, putative ferric enterochelin esterase iroD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7119436 pECS88_0013 20140329 585035 protein-coding NCBI-supplied PMID: 19165319; 19307211 MUTATION: attenuated in mice [PMID:2973985]. 3566 Aerobactin siderophore biosynthesis protein IucA iucA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7119437 pECS88_0012 20140405 585035 protein-coding NCBI-supplied PMID: 19165319; 19307211 MUTATION: attenuated in mice [PMID:2973985]. 3567 N(6)-hydroxylysine acetylase IucB iucB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7119438 pECS88_0011 20140405 585035 protein-coding NCBI-supplied PMID: 19165319; 19307211 MUTATION: attenuated in mice [PMID:2973985]. 3568 Aerobactin siderophore biosynthesis protein IucC iucC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7119439 pECS88_0010 20140405 585035 protein-coding NCBI-supplied PMID: 19165319; 19307211 MUTATION: attenuated in mice [PMID:2973985]. 3569 L-lysine 6-monooxigenase IucD iucD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7119465 pECS88_0064 20140215 585035 protein-coding NCBI-supplied PMID: 19165319; 19307211 MUTATION: traJ mutants of E. coli K1 are attenuated in rat pups and macrophages [PMID:14688129]. 3570 conjugal transfer transcriptional regulator TraJ traJ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7119470 pECS88_0092 20140215 585035 protein-coding NCBI-supplied PMID: 19165319; 19307211 MUTATION: traT mutants have altered membrane permeability and are sensitive to hydrophobic antibiotics [PMID:3323837]. 3571 conjugal transfer surface exclusion protein TraT traT Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7124740 ECIAI1_0998 20140217 585034 protein-coding NCBI-supplied PMID: 19165319 MUTATION: OmpA− strains are unable to cause actin condensation needed for invasion of brain epithelial cells [PMID:10531228]. 3585 outer membrane protein A ompA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7125629 ECIAI1_3703 20140405 585034 protein-coding NCBI-supplied PMID: 19165319 MUTATION: dppA mutant was attenuated 10- to 50-fold compared to the wild type for colonization of the bladders and kidneys of mice [PMID:17074858]. 3586 dipeptide ABC transporter periplasmic-binding protein dppA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7126217 ECIAI1_4035 20140217 585034 protein-coding NCBI-supplied PMID: 19165319 MUTATION: attenuated in mice [PMID:12117951]. 3587 transcriptional activator RfaH rfaH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7126700 ECIAI1_0294 20121127 585034 protein-coding NCBI-supplied PMID: 19165319 MUTATION: ecpA mutant had attenuated adherence to HEp-2 cells compared to the parental EHEC strain [PMID:17563352]. 3588 common pilus ECP ecpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7126825 ECIAI1_2009 20140405 585034 protein-coding NCBI-supplied PMID: 19165319 MUTATION: fliC deletion mutants had reduced adherence in bovine tissue compared to the wild type EHEC and EPEC strains [PMID:17693516]. 3589 flagellin fliC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7127116 ECIAI1_4536 20140222 585034 protein-coding NCBI-supplied PMID: 19165319 MUTATION: attenuated in mice and humans [PMID:18482721]. 3590 minor component of type 1 fimbriae fimH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7127821 ECIAI1_1272 20130420 585034 protein-coding NCBI-supplied PMID: 19165319 MUTATION: attenuated in mice [PMID:11553558]. 3591 transport protein TonB tonB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7128194 ECIAI1_4059 20140406 585034 protein-coding NCBI-supplied PMID: 19165319 periplasmic protein disulfide isomerase I dsbA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7129499 ECS88_4938 20140217 585035 protein-coding NCBI-supplied PMID: 19165319 MUTATION: attenuated in mice and humans [PMID:18482721]. 3572 minor component of type 1 fimbriae fimH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7129944 ECS88_4222 20140217 585035 protein-coding NCBI-supplied PMID: 19165319 MUTATION: disruption mutant was less invasive in an in vitro HBMEC invasion assay than the wild-type E. coli K1 [PMID:10948126]. 3573 arylsulfatase-like enzyme aslA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7130155 ECS88_0978 20130508 585035 protein-coding NCBI-supplied PMID: 19165319 MUTATION: OmpA− strains are unable to cause actin condensation needed for invasion of brain epithelial cells [PMID:10531228]. 3574 outer membrane protein A ompA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7130233 ECS88_3964 20140405 585035 protein-coding NCBI-supplied PMID: 19165319 MUTATION: dppA mutant was attenuated 10- to 50-fold compared to the wild type for colonization of the bladders and kidneys of mice [PMID:17074858]. 3575 dipeptide transporter ; periplasmic-binding component of ABC superfamily dppA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7130299 ECS88_0290 20121017 585035 protein-coding NCBI-supplied PMID: 19165319 MUTATION: ecpA mutant had attenuated adherence to HEp-2 cells compared to the parental EHEC strain [PMID:17563352]. 3576 common pilus ECP ecpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7130870 ECS88_4310 20140406 585035 protein-coding NCBI-supplied PMID: 19165319 MUTATION: mutation of dsbA led to degradation of bundilin and an absence of localized adherence to host cells in EPEC [PMID:9224871]. 3577 protein disulfide isomerase I dsbA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7131265 ECS88_4290 20140222 585035 protein-coding NCBI-supplied PMID: 19165319 MUTATION: attenuated in mice [PMID:12117951]. 3578 transcriptional activator RfaH rfaH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7131480 ECS88_1322 20140329 585035 protein-coding NCBI-supplied PMID: 19165319 MUTATION: attenuated in mice [PMID:11553558]. 3579 transporter tonB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7131907 ECS88_3913 20140329 585035 protein-coding NCBI-supplied PMID: 19165319 MUTATION: chuA mutant unable to grow on iron-depleted medium containing heme [PMID:9157252]. 3580 outer membrane hemin receptor chuA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7132788 ECS88_1977 20140329 585035 protein-coding NCBI-supplied PMID: 19165319 MUTATION: fliC deletion mutants had reduced adherence in bovine tissue compared to the wild type EHEC and EPEC strains [PMID:17693516]. 3581 flagellin FliC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7133169 ECS88_3265 20140215 585035 protein-coding NCBI-supplied PMID: 19165319 MUTATION: mutant papA in wild-type smooth strains do not mediate Gal-Gal adherence [PMID:1672263]. 3582 major pilin protein PapA papA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7133342 ECS88_3256 20140315 585035 protein-coding NCBI-supplied PMID: 19165319 MUTATION: tia deletion strains were noninvasive and lacked the ability to adhere to human ileocecal cells [PMID:8675335]. 3583 Tia invasion determinant tia Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7133471 ECS88_3257 20140301 585035 protein-coding NCBI-supplied PMID: 19165319 MUTATION: attenuated to human neutrophils in vitro [PMID:7960108]. 3584 Fimbrial PapG protein (P pilus class II adhesin) (PapGII) papG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7140515 ECED1_4223 20140322 585397 protein-coding NCBI-supplied PMID: 19165319 MUTATION: dppA mutant was attenuated 10- to 50-fold compared to the wild type for colonization of the bladders and kidneys of mice [PMID:17074858]. 3549 dipeptide ABC transporter periplasmic-binding dppA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7141136 ECED1_0335 20130827 585397 protein-coding NCBI-supplied PMID: 19165319 MUTATION: ecpA mutant had attenuated adherence to HEp-2 cells compared to the parental EHEC strain [PMID:17563352]. 3550 common pilus ECP ecpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7141515 ECED1_4544 20140222 585397 protein-coding NCBI-supplied PMID: 19165319 MUTATION: attenuated in mice [PMID:12117951]. 3551 transcriptional activator RfaH rfaH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7141983 ECED1_1406 20140406 585397 protein-coding NCBI-supplied PMID: 19165319 MUTATION: attenuated in mice [PMID:11553558]. 3552 transport protein TonB tonB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7142129 ECED1_2188 20140405 585397 protein-coding NCBI-supplied PMID: 19165319 MUTATION: fliC deletion mutants had reduced adherence in bovine tissue compared to the wild type EHEC and EPEC strains [PMID:17693516]. 3553 Flagellin (Phase 1-C flagellin) fliC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7142472 ECED1_4905 20140405 585397 protein-coding NCBI-supplied PMID: 19165319 MUTATION: attenuated in mice [PMID:2973985]. 3554 aerobactin siderophore biosynthesis protein iucA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7142473 ECED1_4904 20140405 585397 protein-coding NCBI-supplied PMID: 19165319 MUTATION: attenuated in mice [PMID:2973985]. 3555 aerobactin siderophore biosynthesis N(6)-hydroxylysine acetylase iucB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7142474 ECED1_4903 20140329 585397 protein-coding NCBI-supplied PMID: 19165319 MUTATION: attenuated in mice [PMID:2973985]. 3556 Aerobactin siderophore biosynthesis protein iucC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7142475 ECED1_4902 20140322 585397 protein-coding NCBI-supplied PMID: 19165319 MUTATION: attenuated in mice [PMID:2973985]. 3557 L-lysine 6-monooxygenase iucD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7142711 ECED1_0980 20140217 585397 protein-coding NCBI-supplied PMID: 19165319 MUTATION: OmpA− strains are unable to cause actin condensation needed for invasion of brain epithelial cells [PMID:10531228]. 3558 outer membrane protein A ompA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7142882 ECED1_4561 20140406 585397 protein-coding NCBI-supplied PMID: 19165319 MUTATION: mutation of dsbA led to degradation of bundilin and an absence of localized adherence to host cells in EPEC [PMID:9224871]. 3559 periplasmic protein disulfide isomerase I dsbA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7143612 ECED1_4901 20140215 585397 protein-coding NCBI-supplied PMID: 19165319 MUTATION: attenuated in mice. [PMID:11553558]. 3560 Ferric aerobactin receptor iutA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7144273 p1ECUMN_0115 20140329 585056 protein-coding NCBI-supplied PMID: 19165319 MUTATION: traJ mutants of E. coli K1 are attenuated in rat pups and macrophages [PMID:14688129]. 3536 conjugation transfer regulator traJ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7144350 p1ECUMN_0081 20140217 585056 protein-coding NCBI-supplied PMID: 19165319 MUTATION: traT mutants have altered membrane permeability and are sensitive to hydrophobic antibiotics [PMID:3323837]. 3537 conjugal transfer protein TraT traT Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7145054 EC55989_3996 20140405 585055 protein-coding NCBI-supplied PMID: 19165319 MUTATION: dppA mutant was attenuated 10- to 50-fold compared to the wild type for colonization of the bladders and kidneys of mice [PMID:17074858]. 3538 dipeptide transporter ; periplasmic-binding component of ABC superfamily dppA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7145114 EC55989_4641 20140217 585055 protein-coding NCBI-supplied PMID: 19165319 MUTATION: attenuated in mice [PMID:11553558]. 3539 Ferric aerobactin receptor precursor iutA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7146638 EC55989_4645 20140405 585055 protein-coding NCBI-supplied PMID: 19165319 MUTATION: attenuated in mice [PMID:2973985]. 3540 aerobactin siderophore biosynthesis protein iucA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7146639 EC55989_4644 20140329 585055 protein-coding NCBI-supplied PMID: 19165319 MUTATION: attenuated in mice [PMID:2973985]. 3541 aerobactin siderophore biosynthesis protein, N(6)-hydroxylysine acetylase iucB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7146640 EC55989_4643 20140329 585055 protein-coding NCBI-supplied PMID: 19165319 MUTATION: attenuated in mice [PMID:2973985]. 3542 Aerobactin siderophore biosynthesis protein iucC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7146641 EC55989_4642 20140315 585055 protein-coding NCBI-supplied PMID: 19165319 MUTATION: attenuated in mice [PMID:2973985]. 3543 L-lysine 6-monooxygenase (Lysine N(6)-hydroxylase) iucD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7147756 EC55989_4317 20140217 585055 protein-coding NCBI-supplied PMID: 19165319 MUTATION: attenuated in mice [PMID:12117951]. 3544 transcriptional activator RfaH rfaH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7148058 EC55989_0297 20121017 585055 protein-coding NCBI-supplied PMID: 19165319 MUTATION: ecpA mutant had attenuated adherence to HEp-2 cells compared to the parental EHEC strain [PMID:17563352]. 3545 common pilus ECP ecpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7148255 EC55989_1006 20140406 585055 protein-coding NCBI-supplied PMID: 19165319 MUTATION: OmpA− strains are unable to cause actin condensation needed for invasion of brain epithelial cells [PMID:10531228]. 3546 outer membrane protein A ompA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7148346 EC55989_1350 20130420 585055 protein-coding NCBI-supplied PMID: 19165319 MUTATION: attenuated in mice [PMID:11553558]. 3547 transporter tonB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7149102 EC55989_4336 20140406 585055 protein-coding NCBI-supplied PMID: 19165319 MUTATION: mutation of dsbA led to degradation of bundilin and an absence of localized adherence to host cells in EPEC [PMID:9224871]. 3548 protein disulfide isomerase I dsbA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7149956 ECIAI39_2190 20140215 585057 protein-coding NCBI-supplied PMID: 19165319 MUTATION: OmpA− strains are unable to cause actin condensation needed for invasion of brain epithelial cells [PMID:10531228]. 3517 outer membrane protein A ompA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7150281 ECIAI39_4192 20140323 585057 protein-coding NCBI-supplied PMID: 19165319 MUTATION: tia deletion strains were noninvasive and lacked the ability to adhere to human ileocecal cells [PMID:8675335]. 3518 Tia invasion determinant tia Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7150945 ECIAI39_4002 20140217 585057 protein-coding NCBI-supplied PMID: 19165319 MUTATION: chuA mutant unable to grow on iron-depleted medium containing heme [PMID:9157252]. 3519 outer membrane hemin receptor chuA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7151167 ECIAI39_4053 20140329 585057 protein-coding NCBI-supplied PMID: 19165319 MUTATION: dppA mutant was attenuated 10- to 50-fold compared to the wild type for colonization of the bladders and kidneys of mice [PMID:17074858]. 3520 dipeptide ABC transporter periplasmic-binding protein dppA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7151334 ECIAI39_4793 20140217 585057 protein-coding NCBI-supplied PMID: 19165319 MUTATION: attenuated in mice and humans [PMID:18482721]. 3521 minor component of type 1 fimbriae fimH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7151372 ECIAI39_1132 20140315 585057 protein-coding NCBI-supplied PMID: 19165319 MUTATION: fliC deletion mutants had reduced adherence in bovine tissue compared to the wild type EHEC and EPEC strains [PMID:17693516]. 3522 flagellin fliC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7151788 ECIAI39_3404 20121127 585057 pseudo NCBI-supplied MUTATION: mutant papA in wild-type smooth strains do not mediate Gal-Gal adherence [PMID:1672263]. 3523 pseudo papA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7151862 ECIAI39_3424 20140405 585057 protein-coding NCBI-supplied PMID: 19165319 MUTATION: attenuated in mice [PMID:2973985]. 3524 aerobactin siderophore biosynthesis N(6)-hydroxylysine acetylase iucB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7151863 ECIAI39_3425 20140406 585057 protein-coding NCBI-supplied PMID: 19165319 MUTATION: attenuated in mice [PMID:2973985]. 3525 Aerobactin siderophore biosynthesis protein iucC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7151864 ECIAI39_3426 20140405 585057 protein-coding NCBI-supplied PMID: 19165319 MUTATION: attenuated in mice [PMID:2973985]. 3526 L-lysine 6-monooxygenase iucD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7151865 ECIAI39_3427 20130508 585057 protein-coding NCBI-supplied PMID: 19165319 MUTATION: attenuated in mice [PMID:11553558]. 3527 Ferric aerobactin receptor iutA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7152332 ECIAI39_4587 20140217 585057 protein-coding NCBI-supplied PMID: 19165319 MUTATION: mutant papA in wild-type smooth strains do not mediate Gal-Gal adherence [PMID:1672263]. 3528 major pilin protein PapA papA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7152338 ECIAI39_4595 20140217 585057 protein-coding NCBI-supplied PMID: 19165319 MUTATION: attenuated to human neutrophils in vitro [PMID:7960108]. 3529 fimbrial PapG protein papG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7152341 ECIAI39_4596 20140323 585057 protein-coding NCBI-supplied PMID: 19165319 MUTATION: tia deletion strains were noninvasive and lacked the ability to adhere to human ileocecal cells [PMID:8675335]. 3530 Tia invasion determinant tia Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7152793 ECIAI39_2989 20140315 585057 protein-coding NCBI-supplied PMID: 19165319 MUTATION: disruption mutant was less invasive in an in vitro HBMEC invasion assay than the wild-type E. coli K1 [PMID:10948126]. 3531 arylsulfatase-like enzyme aslA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7152851 ECIAI39_3423 20140405 585057 protein-coding NCBI-supplied PMID: 19165319 MUTATION: attenuated in mice [PMID:2973985]. 3532 aerobactin siderophore biosynthesis protein iucA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7153071 ECIAI39_3155 20140215 585057 protein-coding NCBI-supplied PMID: 19165319 MUTATION: attenuated in mice [PMID:12117951]. 3533 transcriptional activator RfaH rfaH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7153490 ECIAI39_1589 20140406 585057 protein-coding NCBI-supplied PMID: 19165319 MUTATION: attenuated in mice [PMID:11553558]. 3534 transport protein TonB tonB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7154218 ECIAI39_3140 20140406 585057 protein-coding NCBI-supplied PMID: 19165319 MUTATION: mutation of dsbA led to degradation of bundilin and an absence of localized adherence to host cells in EPEC [PMID:9224871]. 3535 periplasmic protein disulfide isomerase I dsbA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7155270 ECUMN_3331 20140217 585056 protein-coding NCBI-supplied PMID: 19165319 MUTATION: attenuated to human neutrophils in vitro [PMID:7960108]. 3500 Fimbrial PapG protein papG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7155292 ECUMN_3367 20140222 585056 protein-coding NCBI-supplied PMID: 19165319 MUTATION: Sat elicits cytopathic activity that damages host tissue and may increase the ability of E. coli to propagate [PMID:12117966]. 3501 Serine protease sat Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7155293 ECUMN_3371 20130508 585056 protein-coding NCBI-supplied PMID: 19165319 MUTATION: attenuated in mice [PMID:11553558]. 3502 Ferric aerobactin receptor iutA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7155420 ECUMN_4055 20140215 585056 protein-coding NCBI-supplied PMID: 19165319 MUTATION: dppA mutant was attenuated 10- to 50-fold compared to the wild type for colonization of the bladders and kidneys of mice [PMID:17074858]. 3503 dipeptide ABC transporter periplasmic-binding protein dppA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7155811 ECUMN_4324 20140315 585056 protein-coding NCBI-supplied PMID: 19165319 MUTATION: disruption mutant was less invasive in an in vitro HBMEC invasion assay than the wild-type E. coli K1 [PMID:10948126]. 3504 arylsulfatase-like enzyme aslA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7155958 ECUMN_4000 20140217 585056 protein-coding NCBI-supplied PMID: 19165319 MUTATION: chuA mutant unable to grow on iron-depleted medium containing heme [PMID:9157252]. 3505 outer membrane hemin receptor chuA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7156362 ECUMN_4927 20140406 585056 protein-coding NCBI-supplied PMID: 19165319 MUTATION: attenuated in mice in humans [PMID:18482721]. 3506 minor component of type 1 fimbriae fimH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7156875 ECUMN_3375 20140406 585056 protein-coding NCBI-supplied PMID: 19165319 MUTATION: attenuated in mice [PMID:2973985]. 3507 aerobactin siderophore biosynthesis protein iucA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7156876 ECUMN_3374 20140308 585056 protein-coding NCBI-supplied PMID: 19165319 MUTATION: attenuated in mice [PMID:2973985]. 3508 aerobactin siderophore biosynthesis protein, N(6)-hydroxylysine acetylase iucB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7156877 ECUMN_3373 20140329 585056 protein-coding NCBI-supplied PMID: 19165319 MUTATION: attenuated in mice [PMID:2973985]. 3509 Aerobactin siderophore biosynthesis protein iucC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7156878 ECUMN_3372 20140322 585056 protein-coding NCBI-supplied PMID: 19165319 MUTATION: attenuated in mice [PMID:2973985]. 3510 L-lysine 6-monooxygenase iucD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7157388 ECUMN_3339 20140215 585056 protein-coding NCBI-supplied PMID: 19165319 MUTATION: mutant papA in wild-type smooth strains do not mediate Gal-Gal adherence [PMID:1672263]. 3511 P-fimbriae major subunit papA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7158028 ECUMN_4366 20140215 585056 protein-coding NCBI-supplied PMID: 19165319 transcriptional activator RfaH rfaH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7158311 ECUMN_0327 20121017 585056 protein-coding NCBI-supplied PMID: 19165319 MUTATION: ecpA mutant had attenuated adherence to HEp-2 cells compared to the parental EHEC strain [PMID:17563352]. 3513 common pilus ECP ecpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7158500 ECUMN_1146 20130508 585056 protein-coding NCBI-supplied PMID: 19165319 MUTATION: OmpA− strains are unable to cause actin condensation needed for invasion of brain epithelial cells [PMID:10531228]. 3514 outer membrane protein A ompA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7158576 ECUMN_1551 20130420 585056 protein-coding NCBI-supplied PMID: 19165319 MUTATION: attenuated in mice [PMID:11553558]. 3515 transport protein TonB tonB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7159290 ECUMN_4384 20140406 585056 protein-coding NCBI-supplied PMID: 19165319 MUTATION: mutation of dsbA led to degradation of bundilin and an absence of localized adherence to host cells in EPEC [PMID:9224871]. 3516 periplasmic protein disulfide isomerase I dsbA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7175181 PLES_00451 20140217 557722 protein-coding NCBI-supplied PMID: 19047519 exoenzyme T exoT Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7177486 PLES_31341 20140222 557722 protein-coding NCBI-supplied PMID: 19047519 adenylate cyclase ExoY exoY Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7178280 PLES_41711 20140215 557722 protein-coding NCBI-supplied PMID: 19047519 exotoxin A toxA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7178326 PLES_42291 20140405 557722 protein-coding NCBI-supplied PMID: 19047519 MUTATION: fliC mutant is attenuated in mice [PMID:9423837]. 4449 flagellin type B fliC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7205433 BbuZS7_A59 20140315 445985 protein-coding NCBI-supplied PMID: 20935092 MUTATION: mutant showed reduced ability to adhere to human PH cells [PMID:19451251]. 4450 complement regulator-acquiring surface protein 1 (CRASP-1) cspA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7205446 BbuZS7_A21 20140329 445985 protein-coding NCBI-supplied PMID: 20935092 MUTATION: dbpA deletion mutant was unable to colonize heart tissue of mice [PMID:18195034]. 4451 decorin-binding protein A dbpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7256873 pO26I_p078 20140410 562 protein-coding NCBI-supplied PMID: 21212019 MUTATION: traT mutants have altered membrane permeability and are sensitive to hydrophobic antibiotics [PMID:3323837]. 3479 conjugal transfer surface exclusion protein TraT traT Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7265888 Bbu156a_A60 20140315 445983 protein-coding NCBI-supplied PMID: 20935092 MUTATION: mutant showed reduced ability to adhere to human PH cells [PMID:19451251]. 4453 complement regulator-acquiring surface protein 1 (CRASP-1) cspA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7279517 Bbu156a_K19 20130704 445983 protein-coding NCBI-supplied PMID: 20935092 MUTATION: bbk32 knockout was significantly attenuated in murine model [PMID:16468997]. 4452 fibronectin-binding protein hypothetical protein bbk32 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7324506 pO103_24 20140329 562 protein-coding NCBI-supplied PMID: 20160015 MUTATION: attenuated in mice [PMID:2973985]. 3469 Aerobactin siderophore biosynthesis protein IucA iucA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7324507 pO103_25 20140410 562 protein-coding NCBI-supplied PMID: 20160015 MUTATION: attenuated in mice [PMID:2973985]. 3470 Aerobactin siderophore biosynthesis protein IucB iucB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7324508 pO103_26 20140410 562 protein-coding NCBI-supplied PMID: 20160015 MUTATION: attenuated in mice [PMID:2973985]. 3471 Aerobactin siderophore biosynthesis protein IucC iucC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7324509 pO103_27 20140410 562 protein-coding NCBI-supplied PMID: 20160015 MUTATION: attenuated in mice [PMID:2973985]. 3472 Aerobactin siderophore L-lysine 6-monooxygenase IucD iucD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7324510 pO103_28 20140410 562 protein-coding NCBI-supplied PMID: 20160015 MUTATION: attenuated in mice [PMID:11553558]. 3473 Aerobactin siderophore ferric receptor protein IutA iutA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7324522 pO103_42 20140410 562 protein-coding NCBI-supplied PMID: 20160015 MUTATION: attenuated in chicks [PMID:18541653]. 3474 Salmochelin siderophore glycosyltransferase IroB iroB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7324523 pO103_43 20140222 562 protein-coding NCBI-supplied PMID: 20160015 MUTATION: attenuated in chicks [PMID:18541653]. 3475 Salmochelin siderophore ATP-binding cassette IroC iroC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7324524 pO103_44 20140410 562 protein-coding NCBI-supplied PMID: 20160015 MUTATION: attenuated in chicks [PMID:18541653]. 3476 Salmochelin siderophore ferric enterochelin esterase IroD iroD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7324526 pO103_46 20140410 562 protein-coding NCBI-supplied PMID: 20160015 MUTATION: iroA gene cluster mutants were unable to resist Lcn2 in mouse serum [PMID:17060628]. 3477 outer membrane receptor FepA iroN Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7324607 pO103_127 20140410 562 protein-coding NCBI-supplied PMID: 20160015 MUTATION: traT mutants have altered membrane permeability and are sensitive to hydrophobic antibiotics [PMID:3323837]. 3478 conjugal transfer surface exclusion protein TraT traT Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7327429 SPN23F_10710 20140406 561276 protein-coding NCBI-supplied PMID: 19114491 MUTATION: mutX mutant is attenuated in mice [PMID:9826334]. 3608 mutator MutX protein (7,8-dihydro-8-oxoguanine-triphosphatase) mutX Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7327431 SPN23F_08900 20130508 561276 protein-coding NCBI-supplied PMID: 19114491 MUTATION: lytB has reduced colonization of nasopharynx of rats compared to the wild type [PMID:10992472]. 3609 endo-beta-N-acetylglucosaminidase lytB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7327530 SPN23F_03640 20140215 561276 protein-coding NCBI-supplied PMID: 19114491 MUTATION: cbpG has reduced colonization of nasopharynx of rats and reduced adherence to human epithelial cells [PMID:10992472]. 3610 choline binding protein G cbpG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7327675 SPN23F_11150 20140215 561276 protein-coding NCBI-supplied PMID: 19114491 MUTATION: The srtA mutant colonized the nasopharynx of chinchillas at a significantly lower level than the wild type [PMID:16246506]. 3611 sortase SrtA srtA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7327738 SPN23F_12210 20140217 561276 protein-coding NCBI-supplied PMID: 19114491 MUTATION: nanA mutant is attenuated in mice [PMID:9826334]. 3612 N-acetylneuraminate lyase nanA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7327765 SPN23F_07270 20140217 561276 protein-coding NCBI-supplied PMID: 19114491 MUTATION: ciaR mutant is attenuated in mice [PMID:15292127]. 3613 response regulator protein ciaR Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7328238 SPN23F_05990 20140406 561276 protein-coding NCBI-supplied PMID: 19114491 MUTATION: zmpB mutant is attenuated in mice [PMID:12841855]. 3614 zinc metalloproteinase ZmpB zmpB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7328274 SPN23F_06550 20140322 561276 protein-coding NCBI-supplied PMID: 19114491 MUTATION: spxB mutant has a loss in the ability to attach eukayrotic cells and is attenuated in rabbits [PMID:8820650]. 3615 pyruvate oxidase spxB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7328296 SPN23F_06880 20140222 561276 protein-coding NCBI-supplied PMID: 19114491 MUTATION: sodA mutant is attenuated in mice [PMID:10768978]. 3616 superoxide dismutase sodA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7328330 SPN23F_19470 20140222 561276 protein-coding NCBI-supplied PMID: 19114491 MUTATION: ply mutant is attenuated in mice [PMID:10603379]. 3617 pneumolysin (thiol-activated cytolysin) ply Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7328513 SPN23F_22240 20140215 561276 protein-coding NCBI-supplied PMID: 19114491 MUTATION: cbpA mutant is attenuated in rat pups [PMID:9364908]. 3618 choline-binding surface protein A cbpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7328606 SPN23F_04560 20140405 561276 protein-coding NCBI-supplied PMID: 19114491 MUTATION: glnA mutant had significantly reduced adhesion to Detroit 562 human pharyngeal epithelial cells [PMID:16787930]. 3619 glutamine synthetase glnA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7328624 SPN23F_22720 20140329 561276 protein-coding NCBI-supplied PMID: 19114491 MUTATION: htrA mutant is attenuated in mice [PMID:15292127]. 3620 serine protease htrA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7328668 SPN23F_20200 20140215 561276 protein-coding NCBI-supplied PMID: 19114491 MUTATION: ccpA mutant is attenuated in mice [PMID:16321938]. 3621 catabolite control protein A ccpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7328731 SPN23F_15100 20140406 561276 protein-coding NCBI-supplied PMID: 19114491 MUTATION: pclA mutant was defective in adherence and invasion of host cells in vitro [PMID:18557785]. 3622 NADPH-dependent FMN reductase pclA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7328802 SPN23F_16000 20140329 561276 protein-coding NCBI-supplied PMID: 19114491 MUTATION: codY mutant has lower bacterial loads during infection in mice compared to the wild type and have a diminished ability to adhere to nasopharangeal cells in vitro [PMID:18024519]. 3623 transcriptional repressor CodY codY Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7328890 SPN23F_08530 20140329 561276 protein-coding NCBI-supplied PMID: 19114491 MUTATION: cbpE has reduced colonization of nasopharynx of rats and reduced adherence to human epithelial cells [PMID:10992472]. 3624 choline binding protein E cbpE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7329269 SPN23F_13500 20140222 561276 protein-coding NCBI-supplied PMID: 19114491 MUTATION: potD mutant is attenuated in pulmonary and systemic models of infection in mice [PMID:16368990]. 3625 spermidine/putrescine extracellular binding protein potD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7329323 SPN23F_14330 20140222 561276 protein-coding NCBI-supplied PMID: 19114491 MUTATION: nox mutant is attenuated in mice [PMID:11158360]. 3626 NADH oxidase nox Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7329421 SPN23F_06700 20140222 561276 protein-coding NCBI-supplied PMID: 19114491 MUTATION: clpP mutant is attenuated in mice [PMID:15664911]. 3627 ATP-dependent Clp protease proteolytic subunit clpP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7329460 SPN23F_03130 20140405 561276 protein-coding NCBI-supplied PMID: 19114491 MUTATION: luxS mutant has defective ability to persist in the nasopharyngeal tissues of mice [PMID:15102809]. 3628 S-ribosylhomocysteinase luxS Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7329486 SPN23F_22340 20140406 561276 protein-coding NCBI-supplied PMID: 19114491 MUTATION: cbpD has reduced colonization of nasopharynx of rats compared to the wild type [PMID:1099247]. 3629 choline binding protein D cbpD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7329489 SPN23F_16920 20140405 561276 protein-coding NCBI-supplied PMID: 19114491 MUTATION: nanA mutant is attenuated in mice [PMID:9826334]. 3630 sialidase A (neuraminidase A) nanA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7329552 SPN23F_17820 20140215 561276 protein-coding NCBI-supplied PMID: 19114491; 19627498; 20714350 MUTATION: psrP mutants failed to bind to A549 and LA-4 lung cells, yet adhered normally to human nasopharyngeal epithelial cells and to cells from human and rodent capillary endothelial cell lines. psrP mutants were also unable to persist in the lungs of mice [PMID:18507531]. 3631 cell wall surface anchored protein psrP MUTATION: iroA gene cluster mutants were unable to resist Lcn2 in mouse serum [PMID:17060628]. 3463 MUTATION: attenuated in chicks [PMID:18541653]. 3464 MUTATION: attenuated in mice [PMID:11553558]. 3465 MUTATION: attenuated in mice [PMID:2973985]. 3466 MUTATION: attenuated in mice [PMID:2973985]. 3467 MUTATION: attenuated in mice [PMID:2973985]. 3468 MUTATION: spvB mutants are attenuated in mice [PMID:11260464]. TOXIN: spvB encodes an ADP-ribosylating enzyme that uses actin as a substrate and depolymerizes actin filaments when expressed in CHO cells [PMID:11260464]. 3839 MUTATION: The spvBC-bearing plasmid was capable of replacing all of the spv genes, as well as the entire virulence plasmid, of serovar Typhimurium for causing systemic infection in BALB/c mice after subcutaneous, but not oral, inoculation. A point mutation in the spvBC plasmid preventing translation but not transcription of spvC eliminated the ability of the plasmid to confer virulence [PMID:11443102]. 3840 MUTATION: slyA mutant is attenuated in mice [PMID:8290552]. 3827 MUTATION: ssaV and aroC double mutants are attenuated in humans [PMID:19745519]. 3828 MUTATION: spiC mutant cannot survive within macrophages and is attenuated in mice [PMID:10406797]. 3829 MUTATION: sigD mutant is less invasive than the wild type in both HEp-2 and CHO cell lines [PMID:9537377]. 3830 MUTATION: sigE mutant is less invasive than the wild type in both HEp-2 and CHO cell lines [PMID:9537377]. 3831 MUTATION: invJ mutants are defective for entry into cultured epithelial cells [PMID:7752894]. 3832 MUTATION: invI mutants are defective for entry into cultured epithelial cells [PMID:7752894]. 3833 MUTATION: slyA mutant is attenuated in mice [PMID:8290552]. 3834 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7636529 pC2C203U28_p056 20140215 1491 protein-coding NCBI-supplied PMID: 19270093 C2 toxin,component I pC2C203U28_p056 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7636534 pC2C203U28_p057 20140215 1491 protein-coding NCBI-supplied PMID: 19270093 C2 toxin,component II pC2C203U28_p057 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7678909 SPJ_0332 20140405 488222 protein-coding NCBI-supplied MUTATION: luxS mutant has defective ability to persist in the nasopharyngeal tissues of mice [PMID:15102809]. 3931 S-ribosylhomocysteinase luxS Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7679297 SPJ_0471 20140405 488222 protein-coding NCBI-supplied MUTATION: glnA mutant had significantly reduced adhesion to Detroit 562 human pharyngeal epithelial cells [PMID:16787930]. 3932 glutamine synthetase, type I glnA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7679394 SPJ_1490 20140329 488222 protein-coding NCBI-supplied MUTATION: codY mutant has lower bacterial loads during infection in mice compared to the wild type and have a diminished ability to adhere to nasopharangeal cells in vitro [PMID:18024519]. 3933 transcriptional repressor CodY codY Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7679761 SPJ_1993 20140215 488222 protein-coding NCBI-supplied MUTATION: ccpA mutant is attenuated in mice [PMID:16321938]. 3934 catabolite control protein A ccpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7680032 SPJ_0670 20140308 488222 protein-coding NCBI-supplied MUTATION: spxB mutant has a loss in the ability to attach eukayrotic cells and is attenuated in rabbits [PMID:8820650]. 3935 pyruvate oxidase spxB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7680127 SPJ_0685 20140222 488222 protein-coding NCBI-supplied MUTATION: clpP mutant is attenuated in mice [PMID:15664911]. 3936 ATP-dependent Clp protease proteolytic subunit clpP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7680711 SPP_0375 20140405 488223 protein-coding NCBI-supplied MUTATION: luxS mutant has defective ability to persist in the nasopharyngeal tissues of mice [PMID:15102809]. 3925 S-ribosylhomocysteinase luxS Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7681180 SPP_0741 20140201 488223 protein-coding NCBI-supplied MUTATION: spxB mutant has a loss in the ability to attach eukayrotic cells and is attenuated in rabbits [PMID:8820650]. 3926 pyruvate oxidase spxB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7681757 SPP_1606 20140329 488223 protein-coding NCBI-supplied MUTATION: codY mutant has lower bacterial loads during infection in mice compared to the wild type and have a diminished ability to adhere to nasopharangeal cells in vitro [PMID:18024519]. 3927 transcriptional repressor CodY codY Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7682073 SPP_2023 20140217 488223 protein-coding NCBI-supplied MUTATION: ccpA mutant is attenuated in mice [PMID:16321938]. 3928 catabolite control protein A ccpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7682623 SPP_0524 20140405 488223 protein-coding NCBI-supplied MUTATION: glnA mutant had significantly reduced adhesion to Detroit 562 human pharyngeal epithelial cells [PMID:16787930]. 3929 glutamine synthetase, type I glnA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7682798 SPP_0757 20140217 488223 protein-coding NCBI-supplied MUTATION: clpP mutant is attenuated in mice [PMID:15664911]. 3930 ATP-dependent Clp protease proteolytic subunit clpP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7683145 SP70585_0777 20140329 488221 protein-coding NCBI-supplied MUTATION: spxB mutant has a loss in the ability to attach eukayrotic cells and is attenuated in rabbits [PMID:8820650]. 3918 pyruvate oxidase spxB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7683357 SP70585_2072 20140215 488221 protein-coding NCBI-supplied MUTATION: ccpA mutant is attenuated in mice [PMID:16321938]. 3919 catabolite control protein A ccpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7683683 SP70585_1624 20140329 488221 protein-coding NCBI-supplied MUTATION: codY mutant has lower bacterial loads during infection in mice compared to the wild type and have a diminished ability to adhere to nasopharangeal cells in vitro [PMID:18024519]. 3920 transcriptional repressor CodY codY Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7684294 SP70585_0404 20140315 488221 protein-coding NCBI-supplied MUTATION: luxS mutant has defective ability to persist in the nasopharyngeal tissues of mice [PMID:15102809]. 3921 S-ribosylhomocysteinase luxS Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7684741 SP70585_0562 20140405 488221 protein-coding NCBI-supplied MUTATION: glnA mutant had significantly reduced adhesion to Detroit 562 human pharyngeal epithelial cells [PMID:16787930]. 3922 glutamine synthetase, type I glnA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7684951 SP70585_0723 20140215 488221 protein-coding NCBI-supplied MUTATION: zmpB mutant is attenuated in mice [PMID:12841855]. 3923 zinc metalloprotease ZmpB zmpB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7685058 SP70585_0792 20140217 488221 protein-coding NCBI-supplied MUTATION: clpP mutant is attenuated in mice [PMID:15664911]. 3924 ATP-dependent Clp protease proteolytic subunit clpP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7685361 SPT_1980 20140329 487213 protein-coding NCBI-supplied MUTATION: ccpA mutant is attenuated in mice [PMID:16321938]. 3911 catabolite control protein A ccpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7685557 SPT_0389 20140405 487213 protein-coding NCBI-supplied MUTATION: luxS mutant has defective ability to persist in the nasopharyngeal tissues of mice [PMID:15102809]. 3912 S-ribosylhomocysteinase luxS Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7686158 SPT_1523 20140329 487213 protein-coding NCBI-supplied MUTATION: codY mutant has lower bacterial loads during infection in mice compared to the wild type and have a diminished ability to adhere to nasopharangeal cells in vitro [PMID:18024519]. 3913 transcriptional repressor CodY codY Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7686335 SPT_0688 20140217 487213 protein-coding NCBI-supplied MUTATION: zmpB mutant is attenuated in mice [PMID:12841855]. 3914 zinc metalloprotease ZmpB zmpB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7686610 SPT_0539 20140405 487213 protein-coding NCBI-supplied MUTATION: glnA mutant had significantly reduced adhesion to Detroit 562 human pharyngeal epithelial cells [PMID:16787930]. 3915 glutamine synthetase, type I glnA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7686613 SPT_0761 20140222 487213 protein-coding NCBI-supplied MUTATION: clpP mutant is attenuated in mice [PMID:15664911]. 3916 ATP-dependent Clp protease proteolytic subunit clpP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7687021 SPT_0746 20140405 487213 protein-coding NCBI-supplied MUTATION: spxB mutant has a loss in the ability to attach eukayrotic cells and is attenuated in rabbits [PMID:8820650]. 3917 pyruvate oxidase spxB MUTATION: sopA mutants induce significantly less fluid accumulation in bovine ligated ileal loops than the wild-type [PMID:12065528]. 2577 MUTATION: ydjA mutant is attenuated in pigs [PMID:17526851]. 2579 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7702134 Lm4b_00433 20140322 568819 protein-coding NCBI-supplied MUTATION: deletion mutant avirulent in mice [PMID:9791184]. 3809 internalin, peptidoglycan bound protein (LPXTG motif) inlF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7702161 Lm4b_00461 20140315 568819 protein-coding NCBI-supplied MUTATION: attenuated in mice [PMID:7558297]. 3810 Internalin A inlA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7702259 Lm4b_01088 20140405 568819 protein-coding NCBI-supplied MUTATION: pycA mutant unable to replicate in mammalian cells, attenuated in mice [PMID:20097852]. 3811 pyruvate carboxylase pycA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7702376 Lm4b_01533 20130511 568819 protein-coding NCBI-supplied MUTATION: impaired growth, avirulent in murine model [PMID:11790730]. 3812 (p)ppGpp synthetase relA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7702426 Lm4b_02518 20140215 568819 protein-coding NCBI-supplied MUTATION: a gtcA mutant was attenuated in mice [PMID:11254558] 3813 cell wall teichoic acid glycosylation protein GtcA gtcA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7702498 Lm4b_00201 20140301 568819 protein-coding NCBI-supplied PMID: 19346305 MUTATION: attenuated in mice [PMID:1311708]. 3814 Zinc metalloproteinase precursor mpl Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7702512 Lm4b_00462 20140215 568819 protein-coding NCBI-supplied MUTATION: attenuated in mice [PMID:7558297]. 3815 Internalin B inlB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7702587 Lm4b_01378 20140315 568819 protein-coding NCBI-supplied MUTATION: ptb mutant is attenuated in mice [PMID:11254558]. 4847 phosphotransbutyrylase Lm4b_01378 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7702964 Lm4b_01860 20130705 568819 protein-coding NCBI-supplied PMID: 22530965 MUTATION: mutant strain showed a reduced efficiency of phagosomal escape in eucaryotic cells and an attenuated virulence [PMID:12975369]. 3816 lipoprotein signal peptidase lspA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7702988 Lm4b_01887 20130511 568819 protein-coding NCBI-supplied MUTATION: attenuated in mice [PMID:14638794]. 3817 hypothetical protein Lm4b_01887 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7703080 Lm4b_01017 20140217 568819 protein-coding NCBI-supplied MUTATION: mutant strain was avirulent in mice, eliminated in the liver, affected cell division [PMID:9987121]. 3818 ATP-dependent protease clpE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7703657 Lm4b_00252 20130511 568819 protein-coding NCBI-supplied MUTATION: mutant strain showed a restricted capacity to grow in bone-marrow-derived macrophages, and an attenuated virulence in mice [PMID:8885268]. 3819 endopeptidase Clp ATP-binding chain C clpC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7703714 Lm4b_00320 20130511 568819 protein-coding NCBI-supplied MUTATION: attenuated in mice [PMID:16369036]. 3820 heat-shock protein htrA serine protease Lm4b_00320 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7703775 Lm4b_00718 20140322 568819 protein-coding NCBI-supplied MUTATION: mutant strain impaired colonization in plant tissue [PMID:19295651], reduced adhesion [PMID:19295651]. 3821 flagellin flaA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7704059 Lm4b_00200 20140301 568819 protein-coding NCBI-supplied PMID: 22530965 MUTATION: mutant strain resulted in a 100-fold virulence defect in mice, prematurely killed host cell [PMID:11901168]. 3822 listeriolysin O precursor hly Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7704069 Lm4b_01841 20140405 568819 protein-coding NCBI-supplied MUTATION: dfp mutant is attenuated in mice [PMID:11254558]. 4840 pantothenate metabolism flavoprotein Lm4b_01841 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7704073 Lm4b_00197 20140222 568819 protein-coding NCBI-supplied PMID: 19255187 MUTATION: attenuated in mice [PMID:1729245]. 3823 listeriolysin positive regulatory protein prfA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7704098 Lm4b_02437 20140217 568819 protein-coding NCBI-supplied MUTATION: mutant strain showed reduced bacterial escape from phagosomes of macrophages and virulence in mice [PMID:10760131]. 3824 ATP-dependent Clp protease proteolytic subunit clpP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7704359 Lm4b_00203 20140405 568819 protein-coding NCBI-supplied MUTATION: deletion mutants showed reduced virulence in mice, escape from vacuole and cell-to-cell spread [PMID:7591052]. 3825 phospholipase C plcB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7704527 Lm4b_00948 20121126 568819 protein-coding NCBI-supplied MUTATION: attenuated in mice [PMID:16177371]. 3826 Sortase srtA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7771326 VCM66_0028 20140405 579112 I protein-coding NCBI-supplied PMID: 19115014 MUTATION: ilvD mutant is attenuated in mice [PMID:11952899]. 3841 dihydroxy-acid dehydratase ilvD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7771349 VCM66_0051 20140405 579112 I protein-coding NCBI-supplied PMID: 19115014 MUTATION: purK mutant is attenuated in mice [PMID:9515705]. 3842 phosphoribosylaminoimidazole carboxylase ATPase subunit purK Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7771392 VCM66_0095 20140405 579112 I protein-coding NCBI-supplied PMID: 19115014 MUTATION: ubiC mutant is attenuated in mice [PMID:11952899]. 3843 chorismate-pyruvate lyase ubiC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7771419 VCM66_0122 20140406 579112 I protein-coding NCBI-supplied PMID: 19115014 MUTATION: cyaA mutant is attenuated in mice [PMID:11952899]. 3844 adenylate cyclase cyaA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7771422 VCM66_0125 20140406 579112 I protein-coding NCBI-supplied PMID: 19115014 MUTATION: lysA mutant is attenuated in mice [PMID:11952899]. 3845 diaminopimelate decarboxylase lysA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7771522 VCM66_0230 20140406 579112 I protein-coding NCBI-supplied PMID: 19115014 MUTATION: rfbB mutant is attenuated in mice [PMID:9515705]. 3846 phosphomannomutase rfbB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7771529 VCM66_0237 20140215 579112 I protein-coding NCBI-supplied PMID: 19115014 MUTATION: rfbL mutant is attenuated in mice [PMID:9515705]. 3847 rfbL protein rfbL Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7771550 VCM66_0260 20140405 579112 I protein-coding NCBI-supplied PMID: 19115014 MUTATION: purD mutant is attenuated in mice [PMID:9515705]. 3848 phosphoribosylamine--glycine ligase purD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7771739 VCM66_0453 20140405 579112 I protein-coding NCBI-supplied PMID: 19115014 MUTATION: gshB mutant is attenuated in mice [PMID:11952899]. 3849 glutathione synthetase gshB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7771756 VCM66_0470 20140405 579112 I protein-coding NCBI-supplied PMID: 19115014 MUTATION: pykF mutant is attenuated in mice [PMID:11952899]. 3850 pyruvate kinase pykF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7771778 VCM66_0492 20140215 579112 I protein-coding NCBI-supplied PMID: 19115014 MUTATION: rpoS mutants are defective in colonization of mouse intestines compared to the wild type [PMID:11083783]. 3851 RNA polymerase sigma factor RpoS rpoS Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7771820 VCM66_0534 20130330 579112 I protein-coding NCBI-supplied PMID: 19115014 MUTATION: sspA mutant is attenuated in mice [PMID:11952899]. 3852 stringent starvation protein A sspA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7772066 VCM66_0785 20140215 579112 I protein-coding NCBI-supplied PMID: 19115014 MUTATION: tcpA mutant is defective at colonizing infant mice [PMID:8698524]. 3853 toxin co-regulated pilin tcpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7772073 VCM66_0792 20140215 579112 I protein-coding NCBI-supplied PMID: 19115014 MUTATION: tcpT mutant is attenuated in mice [PMID:9515705]. 3854 toxin co-regulated pilus biosynthesis protein T tcpT Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7772074 VCM66_0793 20140406 579112 I protein-coding NCBI-supplied PMID: 19115014 MUTATION: tcpE mutant is attenuated in mice [PMID:9515705]. 3855 toxin co-regulated pilus biosynthesis protein E tcpE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7772078 VCM66_0797 20140315 579112 I protein-coding NCBI-supplied PMID: 19115014 MUTATION: acfB mutant had a defect in colonization of mice, and had a ten-fold increase in the 50% lethal dose in mice [PMID:2902009]. 3856 accessory colonization factor AcfB acfB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7772079 VCM66_0798 20140222 579112 I protein-coding NCBI-supplied PMID: 19115014 MUTATION: acfC mutant had a defect in colonization of mice, and had a ten-fold increase in the 50% lethal dose in mice [PMID:2902009]. 3857 accessory colonization factor AcfC acfC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7772082 VCM66_0801 20140222 579112 I protein-coding NCBI-supplied PMID: 19115014 MUTATION: acfA mutant had a defect in colonization of mice, and had a ten-fold increase in the 50% lethal dose in mice [PMID:2902009]. 3858 accessory colonization factor AcfA acfA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7772106 VCM66_0826 20140405 579112 I protein-coding NCBI-supplied PMID: 19115014 MUTATION: purL mutant is attenuated in mice [PMID:11952899]. 3859 phosphoribosylformylglycinamidine synthase purL Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7772176 VCM66_0897 20140405 579112 I protein-coding NCBI-supplied PMID: 19115014 MUTATION: glyA-1 mutant is attenuated in mice [PMID:11952899]. 3860 serine hydroxymethyltransferase glyA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7772239 VCM66_0960 20140405 579112 I protein-coding NCBI-supplied PMID: 19115014 MUTATION: purF mutant is attenuated in mice [PMID:11952899]. 3861 amidophosphoribosyltransferase purF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7772331 VCM66_1053 20140406 579112 I protein-coding NCBI-supplied PMID: 19115014 MUTATION: pta mutant is attenuated in mice [PMID:9515705]. 3862 phosphate acetyltransferase pta Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7772346 VCM66_1068 20140405 579112 I protein-coding NCBI-supplied PMID: 19115014 MUTATION: bioB mutant is attenuated in mice [PMID:9515705]. 3863 biotin synthase bioB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7772406 VCM66_1128 20140405 579112 I protein-coding NCBI-supplied PMID: 19115014 MUTATION: trpG mutant is attenuated in mice [PMID:11952899]. 3864 anthranilate synthase component II trpG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7772684 VCM66_1407 20140222 579112 I protein-coding NCBI-supplied PMID: 19115014 RTX toxin RtxA rtxA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7772808 VCM66_1534 20140405 579112 I protein-coding NCBI-supplied PMID: 19115014 MUTATION: galM mutant is attenuated in mice [PMID:11952899]. 3866 aldose 1-epimerase galM Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7772809 VCM66_1535 20140405 579112 I protein-coding NCBI-supplied PMID: 19115014 MUTATION: galK mutant is attenuated in mice [PMID:11952899]. 3867 galactokinase galK Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7772924 VCM66_1654 20140217 579112 I protein-coding NCBI-supplied PMID: 19115014 MUTATION: mukB mutant is attenuated in mice [PMID:11952899]. 3868 cell division protein MukB mukB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7773026 VCM66_1759 20130706 579112 I protein-coding NCBI-supplied PMID: 19115014 MUTATION: tolB mutant is attenuated in mice [PMID:11952899]. 3869 translocation protein TolB tolB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7773209 VCM66_1945 20140405 579112 I protein-coding NCBI-supplied PMID: 19115014 MUTATION: fabG mutant is attenuated in mice [PMID:11952899]. 3870 3-ketoacyl-ACP reductase fabG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7773240 VCM66_1976 20140222 579112 I protein-coding NCBI-supplied PMID: 19115014 MUTATION: ccmF mutant is attenuated in mice [PMID:11952899]. 3871 cytochrome c-type biogenesis protein CcmF ccmF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7773274 VCM66_2011 20140405 579112 I protein-coding NCBI-supplied PMID: 19115014 MUTATION: sucA mutant is attenuated in mice [PMID:11952899]. 3872 2-oxoglutarate dehydrogenase E1 component sucA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7773292 VCM66_2029 20140406 579112 I protein-coding NCBI-supplied PMID: 19115014 MUTATION: fur mutant is attenuated in mice [PMID:11952899]. 3873 ferric uptake regulator fur Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7773475 VCM66_2213 20140222 579112 I protein-coding NCBI-supplied PMID: 19115014 MUTATION: nqrF mutant is attenuated in mice [PMID:11952899]. 3874 Na(+)-translocating NADH-quinone reductase subunit F nqrF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7773476 VCM66_2214 20130706 579112 I protein-coding NCBI-supplied PMID: 19115014 MUTATION: nqrE mutant is attenuated in mice [PMID:11952899]. 3875 Na(+)-translocating NADH-quinone reductase subunit E nqrE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7773535 VCM66_2273 20140215 579112 I protein-coding NCBI-supplied PMID: 19115014 MUTATION: deoC mutant is attenuated in mice [PMID:11952899]. 3876 deoxyribose-phosphate aldolase deoC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7773573 VCM66_2312 20140405 579112 I protein-coding NCBI-supplied PMID: 19115014 MUTATION: carB mutant is attenuated in mice [PMID:11952899]. 3877 carbamoyl phosphate synthase large subunit carB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7773574 VCM66_2313 20140405 579112 I protein-coding NCBI-supplied PMID: 19115014 MUTATION: carA mutant is attenuated in mice [PMID:11952899]. 3878 carbamoyl phosphate synthase small subunit carA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7773595 VCM66_2336 20140405 579112 I protein-coding NCBI-supplied PMID: 19115014 MUTATION: aceF mutant is attenuated in mice [PMID:11952899]. 3879 dihydrolipoamide acetyltransferase aceF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7773639 VCM66_2380 20140222 579112 I protein-coding NCBI-supplied PMID: 19115014 MUTATION: acpS mutant is attenuated in mice [PMID:11952899]. 3880 4'-phosphopantetheinyl transferase acpS Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7773641 VCM66_2382 20130330 579112 I protein-coding NCBI-supplied PMID: 19115014 MUTATION: recO mutant is attenuated in mice [PMID:11952899]. 3881 DNA repair protein RecO recO Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7773649 VCM66_2390 20140222 579112 I protein-coding NCBI-supplied PMID: 19115014 MUTATION: rpoE mutant is attenuated in mice [PMID:12228259]. 3882 RNA polymerase sigma factor RpoE rpoE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7773723 VCM66_2465 20140405 579112 I protein-coding NCBI-supplied PMID: 19115014 MUTATION: fbp mutant is attenuated in mice [PMID:11952899]. 3883 fructose-1,6-bisphosphatase fbp Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7773835 VCM66_2578 20140405 579112 I protein-coding NCBI-supplied PMID: 19115014 MUTATION: frdC mutant is attenuated in mice [PMID:11952899]. 3884 fumarate reductase subunit C frdC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7780535 BAMEG_B0065 20140406 568206 protein-coding NCBI-supplied MUTATION: acpB mutant is attenuated in mice [PMID:15616593]. 3663 capsule synthesis trans-acting positive regulator AcpB acpB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7780538 BAMEG_B0067 20130705 568206 protein-coding NCBI-supplied MUTATION: capE mutant is avirulent in mice [PMID:16267300]. 3664 polyglutamate capsule biosynthesis protein CapE capE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7780572 BAMEG_B0068 20140405 568206 protein-coding NCBI-supplied MUTATION: capD mutant is attenuated in mice [PMID:16045616]. 3665 capsule anchoring protein CapD capD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7780695 BAMEG_A0160 20140406 568206 protein-coding NCBI-supplied MUTATION: pagA mutant is non-lethal in mice [PMID:1910002]. 3659 protective antigen pagA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7780712 BAMEG_A0137 20140222 568206 protein-coding NCBI-supplied calmodulin-sensitive adenylate cyclase cya Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7780718 BAMEG_A0165 20140215 568206 protein-coding NCBI-supplied PMID: 19922472 MUTATION: lef mutant is non-lethal in mice [PMID:1910002]. 3661 anthrax lethal factor endopeptidase lef Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7780750 BAMEG_A0144 20140406 568206 protein-coding NCBI-supplied MUTATION: atxA mutant is avirulent in mice [PMID:12224521]. 3662 anthrax toxin expression trans-acting positive regulator atxA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7780871 VCM66_A0646 20140222 579112 II protein-coding NCBI-supplied PMID: 19115014 MUTATION: phaC mutant is attenuated in mice [PMID:11952899]. 3885 polyhydroxyalkanoic acid synthase phaC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7781079 VCM66_A0856 20140405 579112 II protein-coding NCBI-supplied PMID: 19115014 MUTATION: zwf mutant is attenuated in mice [PMID:11952899]. 3886 glucose-6-phosphate 1-dehydrogenase zwf Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7781770 VCM66_A0489 20140405 579112 II protein-coding NCBI-supplied PMID: 19115014 MUTATION: ydbK mutant is attenuated in mice [PMID:11952899]. 3887 pyruvate-flavoredoxin oxidoreductase ydbK Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7782491 BAMEG_1271 20140406 568206 protein-coding NCBI-supplied MUTATION: alo mutant has diminished ability to grow in association of macrophages [PMID:17419764]. 3649 anthrolysin O alo Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7782752 BAMEG_0666 20140222 568206 protein-coding NCBI-supplied MUTATION: codY mutant is attenuated in mice [PMID:19651859]. 3650 transcriptional repressor CodY codY Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7782926 BAMEG_2610 20140222 568206 protein-coding NCBI-supplied MUTATION: asbA mutant is attenuated in macrophages and mice [PMID:14756782]. 3651 petrobactin biosynthesis protein AsbA asbA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7782979 BAMEG_3579 20140215 568206 protein-coding NCBI-supplied MUTATION: sigB mutant is less virulent in mice than the parent strain [PMID:10960085]. 3652 RNA polymerase sigma factor SigB sigB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7783063 BAMEG_5196 20140222 568206 protein-coding NCBI-supplied MUTATION: A quadruple-knockout strain (Delta sod15 Delta sodA1 Delta sodC Delta sodA2) was attenuated more than 40-fold upon intranasal challenge of mice compared to the wild type [PMID:18955476]. 3653 superoxide dismutase, Cu-Zn sodC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7783280 BAMEG_1423 20140222 568206 protein-coding NCBI-supplied MUTATION: mntA mutant is attenuated in guinea pigs [PMID:16194238]. 3654 manganese ABC transporter, manganese-binding protein mntA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7783761 BAMEG_5743 20140405 568206 protein-coding NCBI-supplied MUTATION: nos mutant is attenuated in mice [PMID:18215992]. 3655 nitric-oxide synthase, oxygenase subunit nos Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7784922 BAMEG_4740 20140215 568206 protein-coding NCBI-supplied MUTATION: clpX deletion mutant is attenuated in mice [PMID:20375606]. 3656 ATP-dependent protease ATP-binding subunit ClpX clpX Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7786419 BAMEG_4536 20140222 568206 protein-coding NCBI-supplied MUTATION: A quadruple-knockout strain (Delta sod15 Delta sodA1 Delta sodC Delta sodA2) was attenuated more than 40-fold upon intranasal challenge of mice compared to the wild type [PMID:18955476]. 3657 superoxide dismutase sodA1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7787415 BAMEG_5744 20140217 568206 protein-coding NCBI-supplied MUTATION: A quadruple-knockout strain (Delta sod15 Delta sodA1 Delta sodC Delta sodA2) was attenuated more than 40-fold upon intranasal challenge of mice compared to the wild type [PMID:18955476]. 3658 superoxide dismutase sodA2 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7847529 BAA_B0065 20140222 592021 protein-coding NCBI-supplied MUTATION: acpB mutant is attenuated in mice [PMID:15616593]. 3646 capsule synthesis trans-acting positive regulator AcpB acpB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7847571 BAA_B0068 20140405 592021 protein-coding NCBI-supplied MUTATION: capD mutant is attenuated in mice [PMID:16045616]. 3647 capsule anchoring protein CapD capD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7847606 BAA_B0067 20121127 592021 protein-coding NCBI-supplied MUTATION: capE mutant is avirulent in mice [PMID:16267300]. 3648 polyglutamate capsule biosynthesis protein CapE capE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7847664 BAA_A0173 20140215 592021 protein-coding NCBI-supplied MUTATION: lef mutant is non-lethal in mice [PMID:1910002]. 3642 anthrax lethal factor endopeptidase lef Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7847735 BAA_A0144 20140222 592021 protein-coding NCBI-supplied calmodulin-sensitive adenylate cyclase cya Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7847827 BAA_A0168 20140222 592021 protein-coding NCBI-supplied MUTATION: pagA mutant is non-lethal in mice [PMID:1910002]. 3644 protective antigen pagA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7847839 BAA_A0151 20140406 592021 protein-coding NCBI-supplied MUTATION: atxA mutant is avirulent in mice [PMID:12224521]. 3645 anthrax toxin expression trans-acting positive regulator atxA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7847881 BAA_5726 20140405 592021 protein-coding NCBI-supplied MUTATION: nos mutant is attenuated in mice [PMID:18215992]. 3632 nitric-oxide synthase, oxygenase subunit nos Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7848141 BAA_3238 20140222 592021 protein-coding NCBI-supplied MUTATION: mntA mutant is attenuated in guinea pigs [PMID:16194238]. 3633 manganese ABC transporter, manganese-binding protein mntA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7848168 BAA_2049 20140222 592021 protein-coding NCBI-supplied MUTATION: asbA mutant is attenuated in macrophages and mice [PMID:14756782]. 3634 petrobactin biosynthesis protein AsbA asbA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7848233 BAA_5727 20140217 592021 protein-coding NCBI-supplied MUTATION: A quadruple-knockout strain (Delta sod15 Delta sodA1 Delta sodC Delta sodA2) was attenuated more than 40-fold upon intranasal challenge of mice compared to the wild type [PMID:18955476]. 3635 superoxide dismutase, Mn sodA2 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7848783 BAA_3989 20140222 592021 protein-coding NCBI-supplied MUTATION: codY mutant is attenuated in mice [PMID:19651859]. 3636 transcriptional repressor CodY codY Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7848794 BAA_1086 20140215 592021 protein-coding NCBI-supplied MUTATION: sigB mutant is less virulent in mice than the parental strain [PMID:10960085]. 3637 RNA polymerase sigma factor SigB sigB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7850123 BAA_4518 20140222 592021 protein-coding NCBI-supplied MUTATION: A quadruple-knockout strain (Delta sod15 Delta sodA1 Delta sodC Delta sodA2) was attenuated more than 40-fold upon intranasal challenge of mice compared to the wild type [PMID:18955476]. 3638 superoxide dismutase, Mn sodA1 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7851138 BAA_4722 20140217 592021 protein-coding NCBI-supplied MUTATION: clpX deletion mutant is attenuated in mice [PMID:20375606]. 3639 ATP-dependent protease ATP-binding subunit ClpX clpX Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7851421 BAA_3389 20140222 592021 protein-coding NCBI-supplied MUTATION: alo mutant had diminished ability to grow in association with macrophages [PMID:17419764]. 3640 anthrolysin O alo Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7853218 BAA_5175 20140222 592021 protein-coding NCBI-supplied MUTATION: A quadruple-knockout strain (Delta sod15 Delta sodA1 Delta sodC Delta sodA2) was attenuated more than 40-fold upon intranasal challenge of mice compared to the wild type [PMID:18955476]. 3641 superoxide dismutase, Cu-Zn sodC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7887507 GBP346_A0742 20130511 536230 I protein-coding NCBI-supplied MUTATION: pilA mutant is attenuated in mice [PMID:15664977]. 3666 putative type IV pilin protein PilA GBP346_A0742 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7888150 GBP346_A0847 20140222 536230 I protein-coding NCBI-supplied MUTATION: mviN mutant displayed an increased LD50 value in the hamster infection model and a loss of the ability to invade human lung epithelial cells [PMID:17110975]. 3667 integral membrane protein MviN mviN Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7888461 GBP346_A3446 20140405 536230 I protein-coding NCBI-supplied MUTATION: purM mutant is attenuated in mice [PMID:16714590]. 3668 phosphoribosylaminoimidazole synthetase purM Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7889124 GBP346_A1203 20130330 536230 I protein-coding NCBI-supplied MUTATION: nth mutant is attenuated in mice [PMID:17189432]. 3669 endonuclease III nth Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7889272 GBP346_A2540 20140405 536230 I protein-coding NCBI-supplied MUTATION: ppsA mutant is attenuated in mice [PMID:17189432]. 3670 phosphoenolpyruvate synthase ppsA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7889294 GBP346_A3845 20140405 536230 I protein-coding NCBI-supplied MUTATION: hisF mutant is attenuated in mice [PMID:16714590]. 3671 imidazole glycerol phosphate synthase subunit HisF hisF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7889759 GBP346_A0898 20140405 536230 I protein-coding NCBI-supplied MUTATION: purN mutant is attenuated in mice [PMID:16714590]. 3672 phosphoribosylglycinamide formyltransferase purN Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7889774 GBP346_A2967 20130330 536230 I protein-coding NCBI-supplied MUTATION: rpoE mutant is attenuated in mice [PMID:17346071]. 3673 RNA polymerase sigma factor RpoE rpoE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7890481 GBP346_A0371 20140329 536230 I protein-coding NCBI-supplied MUTATION: lipB mutant is attenuated in mice [PMID:16714590]. 3674 lipoate-protein ligase B lipB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7890564 GBP346_A3066 20140405 536230 I protein-coding NCBI-supplied MUTATION: serC mutant is attenuated in mice [PMID:16997946]. 3675 phosphoserine aminotransferase serC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7894256 TGME49_052360 20140215 508771 protein-coding NCBI-supplied PMID: 22286708 MUTATION: Transfection of the virulent ROP18 allele into a nonpathogenic type III strain increased growth and enhanced mortality by 4 to 5 logs [PMID:17170305]. 4476 rhoptry protein, putative TGME49_052360 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7899615 TGME49_059690 20140215 508771 protein-coding NCBI-supplied MUTATION: An OMPDC mutant, alone or in combination with an UP mutation, is attenuated in mice [PMID:20605980]. 4935 orotidine-monophosphate-decarboxylase, putative TGME49_059690 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7900172 TGME49_034370 20140215 508771 protein-coding NCBI-supplied MUTATION: a SAG1 mutant is attenuated in mice in an oral model of infection [PMID:15294991]. 4478 surface antigen, putative TGME49_034370 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7900273 TGME49_110640 20140405 508771 protein-coding NCBI-supplied MUTATION: A UP mutant, in combination with an OMPDC mutation, is attenuated in mice [PMID:20605980]. 4936 uridine phosphorylase, putative TGME49_110640 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7900755 TGME49_014940 20131108 508771 protein-coding NCBI-supplied MUTATION: M2AP mutant is attenuated for cell invasion and virulence in mice [PMID:16385407]. 4473 MIC2-associated protein M2AP TGME49_014940 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7952946 BWG_0809 20140406 595496 protein-coding NCBI-supplied PMID: 19376874 MUTATION: OmpA− strains are unable to cause actin condensation needed for invasion of brain epithelial cells [PMID:10531228]. 3794 outer membrane protein A ompA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7953267 BWG_3233 20140405 595496 protein-coding NCBI-supplied PMID: 19376874 MUTATION: dppA mutant was attenuated 10- to 50-fold compared to the wild type for colonization of the bladders and kidneys of mice [PMID:17074858]. 3795 dipeptide transporter dppA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7953491 BWG_3518 20140217 595496 protein-coding NCBI-supplied PMID: 19376874 MUTATION: attenuated in mice [PMID:12117951]. 3796 transcriptional activator RfaH rfaH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7954265 BWG_4018 20140406 595496 protein-coding NCBI-supplied PMID: 19376874 MUTATION: attenuated in mice and humans [PMID:18482721]. 3797 minor component of type 1 fimbriae fimH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7954839 BWG_1081 20130330 595496 protein-coding NCBI-supplied PMID: 19376874 MUTATION: attenuated in mice [PMID:11553558]. 3798 transporter tonB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7955988 BWG_1732 20140329 595496 protein-coding NCBI-supplied PMID: 19376874 MUTATION: fliC deletion mutants had reduced adherence in bovine tissue compared to the wild type EHEC and EPEC strains [PMID:17693516]. 3799 flagellin fliC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 7956141 BWG_3531 20140406 595496 protein-coding NCBI-supplied PMID: 19376874 MUTATION: mutation of dsbA led to degradation of bundilin and an absence of localized adherence to host cells in EPEC [PMID:9224871]. 3800 protein disulfide isomerase I dsbA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8164705 pVir_80 20140217 563770 protein-coding NCBI-supplied PMID: 20060660 MUTATION: traT mutants have altered membrane permeability and are sensitive to hydrophobic antibiotics [PMID:3323837]. 3792 conjugal transfer surface exclusion protein TraT traT Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8164736 pVir_111 20140222 563770 protein-coding NCBI-supplied PMID: 20060660 MUTATION: hlyC is required for the acylation and therefore activation of the toxin hemolysin which has the ability to lyse several different types of cells [PMID:8793877]. 3793 hemolysin activating protein HlyC hlyC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8175755 ECB_00961 20140406 413997 protein-coding NCBI-supplied PMID: 19786035 MUTATION: OmpA− strains are unable to cause actin condensation needed for invasion of brain epithelial cells [PMID:10531228]. 3681 outer membrane protein A ompA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8177616 ECB_03395 20140405 413997 protein-coding NCBI-supplied PMID: 19786035 MUTATION: dppA mutant was attenuated 10- to 50-fold compared to the wild type for colonization of the bladders and kidneys of mice [PMID:17074858]. 3682 dipeptide transporter dppA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8177876 ECB_03733 20140215 413997 protein-coding NCBI-supplied PMID: 19786035 MUTATION: attenuated in mice [PMID:12117951]. 3683 transcriptional activator RfaH rfaH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8177889 ECB_03746 20140406 413997 protein-coding NCBI-supplied PMID: 19786035 MUTATION: mutation of dsbA led to degradation of bundilin and an absence of localized adherence to host cells in EPEC [PMID:9224871]. 3684 periplasmic protein disulfide isomerase I dsbA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8178231 ECB_04189 20140222 413997 protein-coding NCBI-supplied PMID: 19786035 MUTATION: attenuated in mice and humans [PMID:18482721]. 3685 minor component of type 1 fimbriae fimH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8178456 ECB_01226 20130420 413997 protein-coding NCBI-supplied PMID: 19786035 MUTATION: attenuated in mice [PMID:11553558]. 3686 transport protein TonB tonB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8206889 ECSP_6017 20140215 544404 protein-coding NCBI-supplied PMID: 19564389 MUTATION: hlyC is required for the acylation and therefore activation of the toxin hemolysin which has the ability to lyse several different types of cells [PMID:8793877]. 3789 hemolysin transport protein hlyC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8206890 ECSP_6018 20140329 544404 protein-coding NCBI-supplied PMID: 19564389 MUTATION: attenuated in zebra fish [PMID:20019794]. 3790 hemolysin toxin protein hlyA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8206968 ECSP_6096 20140222 544404 protein-coding NCBI-supplied PMID: 19564389 MUTATION: espP mutant is attenuated in calves [PMID:17451446]. 3791 putative exoprotein-precursor espP Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8207576 HELPY_0115 20140322 592205 protein-coding NCBI-supplied PMID: 20537153 MUTATION: mutant strains showed reduced motility and colonization in piglets [PMID:8698465]. 3801 flagellin B flaB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8207634 HELPY_0248 20140217 592205 protein-coding NCBI-supplied PMID: 20537153 MUTATION: deletion impaired adherence to host cells [PMID:16758245]. 3802 Neutrophil activating protein NapA (bacterioferritin) napA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8207891 HELPY_0733 20140222 592205 protein-coding NCBI-supplied PMID: 20537153 MUTATION: mutant strain showed reduction in bacterial adherence to gastric epithelia in vitro [PMID:17054063]. 3803 outer membrane protein HopH hopH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8208349 HELPY_0007 20140222 592205 protein-coding NCBI-supplied PMID: 20537153 MUTATION: knockout strain reduced adherence to human gastric epithelial cells [PMID:10454640]. 3804 outer membrane protein HopZ hopZ Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8208748 HELPY_0771 20140406 592205 protein-coding NCBI-supplied PMID: 20537153 MUTATION: mutant strains showed reduced colonization in piglets [PMID:8698465]. 3805 flagellin A flaA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8208922 HELPY_0367 20140222 592205 protein-coding NCBI-supplied PMID: 20537153 MUTATION: mutated strain showed a reduction in adherence ability [PMID:12018657]. 3806 Pore-forming cytolysin tlyA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8208956 HELPY_0126 20140222 592205 protein-coding NCBI-supplied PMID: 20537153 MUTATION: knockout strain showed reduced adhesion and colonization in mice [PMID:17492999]. 3807 outer membrane protein HorB horB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8209081 HELPY_0064 20140406 592205 protein-coding NCBI-supplied PMID: 20537153 MUTATION: urease-negative strain showed reduced colonization in gnotobiotic piglets [PMID:8063376]. 3808 urease accessory protein UreG ureG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8214675 ECSP_0109 20140222 544404 protein-coding NCBI-supplied PMID: 19564389 MUTATION: hcpA deletion mutant had attenuated invasion of cultured epithelial cells compared to wild-type EHEC [PMID:18952791]. 3692 major pilin subunit hcpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8214896 ECSP_0330 20121017 544404 protein-coding NCBI-supplied PMID: 19564389 MUTATION: ecpA mutant had attenuated adherence to HEp-2 cells compared to the parental EHEC strain [PMID:17563352]. 3693 Mat fimbrillin ecpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8215629 ECSP_1063 20140406 544404 protein-coding NCBI-supplied PMID: 19564389 MUTATION: OmpA− strains are unable to cause actin condensation needed for invasion of brain epithelial cells [PMID:10531228]. 3694 outer membrane protein A ompA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8216050 ECSP_1484 20140215 544404 protein-coding NCBI-supplied PMID: 19564389 MUTATION: espK mutant attenuated in calves [PMID:16958848]. 3695 non-LEE-encoded type III effector espK Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8216210 ECSP_1644 20140222 544404 protein-coding NCBI-supplied PMID: 19564389 MUTATION: attenuated in mice [PMID:11553558]. 3696 transport protein TonB tonB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8216268 ECSP_1702 20121017 544404 protein-coding NCBI-supplied PMID: 19564389 MUTATION: nelA deletion mutant attenuated in mice [PMID:14982621]. 3697 non-LEE-encoded type III effector nleA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8217094 ECSP_2528 20140405 544404 protein-coding NCBI-supplied PMID: 19564389 MUTATION: fliC deletion mutants had reduced adherence in bovine tissue compared to the wild type EHEC and EPEC strains [PMID:17693516]. 3698 flagellin fliC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8217818 ECSP_3252 20140406 544404 protein-coding NCBI-supplied PMID: 19564389; 21203383 shiga toxin II subunit B stx2B Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8219055 ECSP_4489 20140406 544404 protein-coding NCBI-supplied PMID: 19564389 MUTATION: chuA mutant unable to grow on iron-depleted medium containing heme [PMID:9157252]. 3700 outer membrane heme/hemoglobin receptor chuA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8219101 ECSP_4535 20140406 544404 protein-coding NCBI-supplied PMID: 19564389 MUTATION: dppA mutant was attenuated 10- to 50-fold compared to the wild type for colonization of the bladders and kidneys of mice [PMID:17074858]. 3701 dipeptide ABC transporter periplasmic-binding protein dppA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8219231 ECSP_4665 20140406 544404 protein-coding NCBI-supplied PMID: 19564389 MUTATION: espF mutant of EPEC is deficient in its ability to disrupt electrical resistance across a polarized monolayer of intestinal epithelial cells, suggesting that EspF is an effector molecule required for disrupting intestinal epithelial barrier function [PMID:11238563]. 3702 LEE-encoded type III effector espF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8219235 ECSP_4669 20140405 544404 protein-coding NCBI-supplied PMID: 19564389 MUTATION: deletion mutant attenuated in humans compared to wild-type EPEC [PMID:10816529]. 3703 hypothetical protein EspB espB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8219236 ECSP_4670 20140406 544404 protein-coding NCBI-supplied PMID: 19564389 MUTATION: espD deletion mutant of the enterohemorrhagic E. coli (EHEC) strain EDL933 had impaired attachment to HeLa cells [PMID:10456938]. 3704 hypothetical protein EspD espD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8219237 ECSP_4671 20140215 544404 protein-coding NCBI-supplied PMID: 19564389 MUTATION: deletion of espA in STEC abolished ability to attach to HeLa cells and induce actin rearrangements [PMID:9786192]. 3705 hypothetical protein EspA espA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8219240 ECSP_4674 20140222 544404 protein-coding NCBI-supplied PMID: 19564389 MUTATION: attenuated in humans [PMID:8376594]. 3706 intimin adherence protein eae Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8219242 ECSP_4676 20140222 544404 protein-coding NCBI-supplied PMID: 19564389; 21893288 MUTATION: tir deletion strains are unable to adhere to tissue in an in vitro organ culture [PMID:17474908]. 3707 translocated intimin receptor protein tir Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8219245 ECSP_4679 20121017 544404 protein-coding NCBI-supplied PMID: 19564389 MUTATION: deletion mutant is attenuated in infant rabbits [PMID:15731044]. 3708 LEE-encoded type III effector espH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8219249 ECSP_4683 20140222 544404 protein-coding NCBI-supplied PMID: 19564389 MUTATION: deletion of escN abolished pathogenicity in infant rabbits compared to wild-type EHEC [PMID:15731044]. 3709 LEE-encoded type III secretion system factor escN Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8219269 ECSP_4703 20140406 544404 protein-coding NCBI-supplied PMID: 19564389; 19942657 MUTATION: ler mutants had less adhesion to HeLa cells, ler is a regulator of many virulence genes in the LEE PAI which are needed for adherence [PMID:18794291]. 3710 enterocyte effacement (LEE)-encoded regulator ler Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8219270 ECSP_4704 20121017 544404 protein-coding NCBI-supplied PMID: 19564389 MUTATION: the inhibitory effect of the espG mutant on Cl– uptake in Caco-2 monolayers was significantly attenuated as compared with wild-type EPEC [PMID:17256057]. 3711 LEE-encoded type III effector espG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8219461 ECSP_4895 20140215 544404 protein-coding NCBI-supplied PMID: 19564389 MUTATION: attenuated in mice [PMID:12117951]. 3712 transcriptional activator RfaH rfaH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8219479 ECSP_4913 20140406 544404 protein-coding NCBI-supplied PMID: 19564389 MUTATION: mutation of dsbA led to degradation of bundilin and an absence of localized adherence to host cells in EPEC [PMID:9224871]. 3713 periplasmic protein disulfide isomerase I dsbA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8219970 ECSP_5404 20140222 544404 protein-coding NCBI-supplied PMID: 19564389 MUTATION: attenuated in mice and humans [PMID:18482721]. 3714 minor fimbrial subunit, D-mannose specific adhesin fimH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8221101 NMO_0123 20130508 662598 protein-coding NCBI-supplied PMID: 18305155 MUTATION: ptsH mutant is attenuated in rats [PMID:11062540]. 3888 phosphocarrier protein HPr ptsH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8221120 NMO_0159 20140222 662598 protein-coding NCBI-supplied PMID: 18305155 MUTATION: hrpA mutant was deficient in the ability to grow/live in HeLa cells [PMID:18680551]. 3889 ATP-dependent helicase hrpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8221129 NMO_0171 20140405 662598 protein-coding NCBI-supplied PMID: 18305155 MUTATION: purL mutant is attenuated in rats [PMID:11062540]. 3890 phosphoribosylformylglycinamidine synthase purL Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8221210 NMO_0323 20140405 662598 protein-coding NCBI-supplied PMID: 18305155 MUTATION: fhs mutant is attenuated in rats [PMID:11062540]. 3891 formate--tetrahydrofolate ligase fhs Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8221238 NMO_0364 20140405 662598 protein-coding NCBI-supplied PMID: 18305155 MUTATION: aroB mutant is attenuated in rats [PMID:11062540]. 3892 3-dehydroquinate synthase aroB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8221600 NMO_1006 20140405 662598 protein-coding NCBI-supplied PMID: 18305155 MUTATION: ilvD mutant is attenuated in rats [PMID:11062540]. 3893 dihydroxy-acid dehydratase ilvD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8221908 NMO_1544 20140222 662598 protein-coding NCBI-supplied PMID: 18305155 MUTATION: exbD mutant is attenuated in rats [PMID:11062540]. 3894 biopolymer transport protein ExbD/TolR exbD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8221962 NMO_1648 20140329 662598 protein-coding NCBI-supplied PMID: 18305155 MUTATION: NadA mutation decreases epithelial adhesion of capsulate N. meningitidis and invasion by acapsulate N. meningitidis [PMID:19481311]. 3895 quinolinate synthetase nadA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8222190 NMO_0955 20140222 662598 protein-coding NCBI-supplied PMID: 18305155 MUTATION: dedA mutant is attenuated in rats [PMID:11062540]. 3896 DedA protein dedA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8222370 NMO_1733 20140405 662598 protein-coding NCBI-supplied PMID: 18305155 MUTATION: aroG mutant is attenuated in rats [PMID:11062540]. 3897 phospho-2-dehydro-3-deoxyheptonate aldolase aroG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8222414 NMO_1976 20140322 662598 protein-coding NCBI-supplied PMID: 18305155 MUTATION: metG mutant is attenuated in rats [PMID:11062540]. 3898 methionyl-tRNA synthetase metG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8222416 NMO_1682 20140405 662598 protein-coding NCBI-supplied PMID: 18305155 MUTATION: aroE mutant is attenuated in rats [PMID:11062540]. 3899 shikimate 5-dehydrogenase aroE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8222431 NMO_0241 20140222 662598 protein-coding NCBI-supplied PMID: 18305155 MUTATION: lgtA mutant is attenuated in rats [PMID:11062540]. 3900 lacto-N-neotetraose biosynthesis glycosyl transferase lgtA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8222500 NMO_1388 20140405 662598 protein-coding NCBI-supplied PMID: 18305155 MUTATION: ilvI mutant is attenuated in rats [PMID:11062540]. 3901 acetolactate synthase large subunit ilvI Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8222536 NMO_1520 20130508 662598 protein-coding NCBI-supplied PMID: 18305155 MUTATION: rfaK mutant is attenuated in rats [PMID:11062540]. 3902 alpha 1,2 N-acetylglucosamine transferase rfaK Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8222730 NMO_0766 20140222 662598 protein-coding NCBI-supplied PMID: 18305155 MUTATION: pilX mutant had reduced adherence to human epithelial cells [PMID:15612917]. 3903 type IV pilus assembly protein pilX Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8222774 NMO_0124 20140222 662598 protein-coding NCBI-supplied PMID: 18305155 MUTATION: ptsI mutant is attenuated in rats [PMID:11062540]. 3904 phosphoenolpyruvate-protein phosphotransferase ptsI Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8222779 NMO_0647 20140405 662598 protein-coding NCBI-supplied PMID: 18305155 MUTATION: pnp mutant is attenuated in rats [PMID:11062540]. 3905 polynucleotide phosphorylase/polyadenylase pnp Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8222793 NMO_0711 20140222 662598 protein-coding NCBI-supplied PMID: 18305155 MUTATION: rfaE mutant is attenuated in rats [PMID:11062540]. 3906 ADP-heptose synthase rfaE Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8222803 NMO_1279 20140405 662598 protein-coding NCBI-supplied PMID: 18305155 MUTATION: aroD mutant is attenuated in rats [PMID:11062540]. 3907 3-dehydroquinate dehydratase aroD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8222872 NMO_0840 20140405 662598 protein-coding NCBI-supplied PMID: 18305155 MUTATION: metF mutant is attenuated in rats [PMID:11062540]. 3908 5,10-methylenetetrahydrofolate reductase metF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8222929 NMO_1348 20140405 662598 protein-coding NCBI-supplied PMID: 18305155 MUTATION: rfaF mutant is attenuated in rats [PMID:11062540]. 3909 ADP-heptose--LPS heptosyltransferase II rfaF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8222977 NMO_1499 20140405 662598 protein-coding NCBI-supplied PMID: 18305155 MUTATION: aroC mutant is attenuated in rats [PMID:11062540]. 3910 chorismate synthase aroC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8319157 pEK516_p77 20140222 562 protein-coding NCBI-supplied PMID: 19687243 MUTATION: tir deletion strains are unable to adhere to tissue in an in vitro organ culture [PMID:17474908]. 3689 Tir tir Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8319255 pEK499_p062 20140410 562 protein-coding NCBI-supplied PMID: 19687243 MUTATION: tir deletion strains are unable to adhere to tissue in an in vitro organ culture [PMID:17474908]. 3688 inner membrane protein tir Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8319341 Bbu297_A24 20140406 521009 protein-coding NCBI-supplied PMID: 19505540; 20118265; 21708995; 22985470 decorin binding protein A dbpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8319504 BbuN40_A68 20140215 521007 protein-coding NCBI-supplied PMID: 19505540 MUTATION: mutant showed reduced ability to adhere to human PH cells [PMID:19451251]. 4455 complement regulator acquiring protein 1; putative lipoprotein cspA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8381950 pEC14_110 20140410 562 protein-coding NCBI-supplied PMID: 19887083 MUTATION: traT mutants have altered membrane permeability and are sensitive to hydrophobic antibiotics [PMID:3323837]. 3687 conjugal transfer surface exclusion protein TraT traT Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8470589 ECO103_p32 20140217 585395 protein-coding NCBI-supplied PMID: 19815525 MUTATION: hlyC is required for the acylation and therefore activation of the toxin hemolysin which has the ability to lyse several different types of cells [PMID:8793877]. 3788 hemolysin C hylC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8470732 ECO111_p3-02 20140222 585396 protein-coding NCBI-supplied PMID: 19815525 MUTATION: attenuated in zebra fish [PMID:20019794]. 3786 hemolysin A hlyA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8470734 ECO111_p3-01 20140215 585396 protein-coding NCBI-supplied PMID: 19815525 MUTATION: hlyC is required for the acylation and therefore activation of the toxin hemolysin which has the ability to lyse several different types of cells [PMID:8793877]. 3787 hemolysin C hlyC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8473051 ECO26_p1-02 20140329 573235 protein-coding NCBI-supplied PMID: 19815525 MUTATION: attenuated in zebra fish [PMID:20019794]. 3784 hemolysin A hlyA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8473053 ECO26_p1-01 20140215 573235 protein-coding NCBI-supplied PMID: 19815525 MUTATION: hlyC is required for the acylation and therefore activation of the toxin hemolysin which has the ability to lyse several different types of cells [PMID:8793877]. 3785 hemolysin C hlyC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8474155 ECO103_3564 20140222 585395 protein-coding NCBI-supplied PMID: 19815525 MUTATION: deletion mutant lacks the ability to inhibit lymphokine production and lymphocyte proliferation compared to wild type EPEC [PMID:10722613]. 3764 Efa1/LifA-like protein efa1/lifA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8474190 ECO103_3600 20121017 585395 protein-coding NCBI-supplied PMID: 19815525 MUTATION: espF mutant of EPEC is deficient in its ability to disrupt electrical resistance across a polarized monolayer of intestinal epithelial cells, suggesting that EspF is an effector molecule required for disrupting intestinal epithelial barrier function [PMID:11238563]. 3765 T3SS effector EspF espF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8474193 ECO103_3618 20130508 585395 protein-coding NCBI-supplied PMID: 19815525 MUTATION: deletion of escN abolished pathogenicity in infant rabbits compared to wild-type EHEC [PMID:15731044]. 3766 translocator EscN escN Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8474199 ECO103_3638 20140222 585395 protein-coding NCBI-supplied PMID: 19815525 MUTATION: ler mutants had less adhesion to HeLa cells, ler is a regulator of many virulence genes in the LEE PAI which are needed for adherence [PMID:18794291]. 3767 transcription regulator Ler ler Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8474872 ECO103_3604 20140222 585395 protein-coding NCBI-supplied PMID: 19815525; 20633933 MUTATION: deletion mutant attenuated in humans compared to wild-type EPEC [PMID:10816529]. 3768 translocon EspB espB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8474873 ECO103_3614 20121017 585395 protein-coding NCBI-supplied PMID: 19815525 MUTATION: deletion mutant is attenuated in infant rabbits [PMID:15731044]. 3769 T3SS effector EspH espH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8474874 ECO103_3611 20130508 585395 protein-coding NCBI-supplied PMID: 19815525; 20633933 MUTATION: tir deletion strains are unable to adhere to tissue in an in vitro organ culture [PMID:17474908]. 3770 translocated intimin receptor Tir tir Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8475113 ECO103_4276 20140329 585395 protein-coding NCBI-supplied PMID: 19815525 MUTATION: dppA mutant was attenuated 10- to 50-fold compared to the wild type for colonization of the bladders and kidneys of mice [PMID:17074858]. 3771 dipeptide transport protein dppA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8475139 ECO103_0270 20121017 585395 protein-coding NCBI-supplied PMID: 19815525 MUTATION: ecpA mutant had attenuated adherence to HEp-2 cells compared to the parental EHEC strain [PMID:17563352]. 3772 fimbrillin precursor matB/ecpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8475178 ECO103_3609 20140217 585395 protein-coding NCBI-supplied PMID: 19815525 MUTATION: attenuated in humans [PMID:8376594]. 3773 intimin epsilon eae Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8475188 ECO103_3605 20140222 585395 protein-coding NCBI-supplied PMID: 19815525 MUTATION: espD deletion mutant of the enterohemorrhagic E. coli (EHEC) strain EDL933 had impaired attachment to HeLa cells [PMID:10456938]. 3774 translocon EspD espD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8475189 ECO103_3606 20130508 585395 protein-coding NCBI-supplied PMID: 19815525 MUTATION: deletion of espA in STEC abolished ability to attach to HeLa cells and induce actin rearrangements [PMID:9786192]. 3775 translocon EspA espA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8475277 ECO103_5101 20140222 585395 protein-coding NCBI-supplied PMID: 19815525 MUTATION: attenuated in mice and humans [PMID:18482721]. 3776 minor component FimH of type 1 fimbriae fimH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8475311 ECO103_2179 20140405 585395 protein-coding NCBI-supplied PMID: 19815525 MUTATION: fliC deletion mutants had reduced adherence in bovine tissue compared to the wild type EHEC and EPEC strains [PMID:17693516]. 3777 flagellin fliC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8475820 ECO103_3639 20121017 585395 protein-coding NCBI-supplied PMID: 19815525 MUTATION: the inhibitory effect of the espG mutant on Cl– uptake in Caco-2 monolayers was significantly attenuated as compared with wild-type EPEC [PMID:17256057]. 3778 T3SS effector EspG espG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8476939 ECO103_3612 20130508 585395 protein-coding NCBI-supplied PMID: 19815525 MUTATION: map EPEC mutants have significantly reduced levels of invasion of HeLa cells [PMID:14531893]. 3779 T3SS effector Map map Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8477018 ECO103_4323 20140217 585395 protein-coding NCBI-supplied PMID: 19815525 MUTATION: attenuated in mice [PMID:12117951]. 3780 DNA-binding transcriptional antiterminator RfaH rfaH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8477375 ECO103_1003 20140406 585395 protein-coding NCBI-supplied PMID: 19815525 MUTATION: OmpA− strains are unable to cause actin condensation needed for invasion of brain epithelial cells [PMID:10531228]. 3781 outer membrane protein A ompA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8477474 ECO103_1353 20130420 585395 protein-coding NCBI-supplied PMID: 19815525 MUTATION: attenuated in mice [PMID:11553558]. 3782 membrane spanning protein TonB tonB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8478162 ECO103_4310 20140405 585395 protein-coding NCBI-supplied PMID: 19815525 MUTATION: mutation of dsbA led to degradation of bundilin and an absence of localized adherence to host cells in EPEC [PMID:9224871]. 3783 periplasmic protein disulfide isomerase I dsbA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8479008 ECO26_1345 20140322 573235 protein-coding NCBI-supplied PMID: 19815525 MUTATION: attenuated in mice [PMID:2973985]. 3739 siderophore biosynthesis protein iucA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8480236 ECO26_5250 20140215 573235 protein-coding NCBI-supplied PMID: 19815525 MUTATION: the inhibitory effect of the espG mutant on Cl– uptake in Caco-2 monolayers was significantly attenuated as compared with wild-type EPEC [PMID:17256057]. 3740 T3SS effector EspG espG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8480244 ECO26_5289 20121017 573235 protein-coding NCBI-supplied PMID: 19815525 MUTATION: espF mutant of EPEC is deficient in its ability to disrupt electrical resistance across a polarized monolayer of intestinal epithelial cells, suggesting that EspF is an effector molecule required for disrupting intestinal epithelial barrier function [PMID:11238563]. 3741 T3SS effector EspF espF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8480245 ECO26_5291 20140406 573235 protein-coding NCBI-supplied PMID: 19815525 MUTATION: deletion mutant lacks the ability to inhibit lymphokine production and lymphocyte proliferation compared to wild type EPEC [PMID:10722613]. 3742 Efa1/LifA efa1/lifA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8480654 ECO26_5277 20140406 573235 protein-coding NCBI-supplied PMID: 19815525 MUTATION: map EPEC mutants have significantly reduced levels of invasion of HeLa cells [PMID:14531893]. 3743 T3SS effector Map map Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8480655 ECO26_5280 20130508 573235 protein-coding NCBI-supplied PMID: 19815525 MUTATION: attenuated in humans [PMID:8376594]. 3744 intimin eae Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8480894 ECO26_4638 20140329 573235 protein-coding NCBI-supplied PMID: 19815525 MUTATION: dppA mutant was attenuated 10- to 50-fold compared to the wild type for colonization of the bladders and kidneys of mice [PMID:17074858]. 3745 dipeptide transport protein dppA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8480920 ECO26_0328 20121017 573235 protein-coding NCBI-supplied PMID: 19815525 MUTATION: ecpA mutant had attenuated adherence to HEp-2 cells compared to the parental EHEC strain [PMID:17563352]. 3746 fimbrillin precursor matB/ecpA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8480968 ECO26_5271 20140222 573235 protein-coding NCBI-supplied PMID: 19815525 MUTATION: deletion of escN abolished pathogenicity in infant rabbits compared to wild-type EHEC [PMID:15731044]. 3747 T3SS structure protein EscN escN Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8480969 ECO26_5284 20140217 573235 protein-coding NCBI-supplied PMID: 19815525 MUTATION: espD deletion mutant of the enterohemorrhagic E. coli (EHEC) strain EDL933 had impaired attachment to HeLa cells [PMID:10456938]. 3748 translocator EspD espD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8480971 ECO26_5285 20140217 573235 protein-coding NCBI-supplied PMID: 19815525 MUTATION: deletion mutant attenuated in humans compared to wild-type EPEC [PMID:10816529]. 3749 translocator EspB espB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8480973 ECO26_5251 20140222 573235 protein-coding NCBI-supplied PMID: 19815525 MUTATION: ler mutants had less adhesion to HeLa cells, ler is a regulator of many virulence genes in the LEE PAI which are needed for adherence [PMID:18794291]. 3750 transcriptional regulator Ler ler Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8481056 ECO26_5517 20140315 573235 protein-coding NCBI-supplied PMID: 19815525 MUTATION: attenuated in mice and humans [PMID:18482721]. 3751 minor component FimH of type 1 fimbriae fimH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8481090 ECO26_2815 20140322 573235 protein-coding NCBI-supplied PMID: 19815525 MUTATION: fliC deletion mutants had reduced adherence in bovine tissue compared to the wild type EHEC and EPEC strains [PMID:17693516]. 3752 flagellin fliC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8481558 ECO26_1346 20140329 573235 protein-coding NCBI-supplied PMID: 19815525 MUTATION: attenuated in mice [PMID:2973985]. 3753 siderophore biosynthesis protein iucB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8481559 ECO26_1347 20140406 573235 protein-coding NCBI-supplied PMID: 19815525 MUTATION: attenuated in mice [PMID:2973985]. 3754 siderophore biosynthesis protein iucC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8481560 ECO26_1348 20140405 573235 protein-coding NCBI-supplied PMID: 19815525 MUTATION: attenuated in mice [PMID:2973985]. 3755 siderophore biosynthesis protein iucD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8481561 ECO26_1349 20140222 573235 protein-coding NCBI-supplied PMID: 19815525 MUTATION: attenuated in mice [PMID:11553558]. 3756 ferric siderophore receptor iutA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8481750 ECO26_5278 20140222 573235 protein-coding NCBI-supplied PMID: 19815525; 20921984 MUTATION: tir deletion strains are unable to adhere to tissue in an in vitro organ culture [PMID:17474908]. 3757 translocated intimin receptor Tir tir Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8482581 ECO26_5283 20140215 573235 protein-coding NCBI-supplied PMID: 19815525; 20921984 MUTATION: deletion of espA in STEC abolished ability to attach to HeLa cells and induce actin rearrangements [PMID:9786192]. 3758 translocator EspA espA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8482582 ECO26_5275 20121017 573235 protein-coding NCBI-supplied PMID: 19815525 MUTATION: deletion mutant is attenuated in infant rabbits [PMID:15731044]. 3759 T3SS effector EspH espH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8482829 ECO26_4745 20140215 573235 protein-coding NCBI-supplied PMID: 19815525 MUTATION: attenuated in mice [PMID:12117951]. 3760 transcriptional activator RfaH rfaH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8483180 ECO26_1084 20140406 573235 protein-coding NCBI-supplied PMID: 19815525 MUTATION: OmpA− strains are unable to cause actin condensation needed for invasion of brain epithelial cells [PMID:10531228]. 3761 outer membrane protein A ompA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8483275 ECO26_1764 20140329 573235 protein-coding NCBI-supplied PMID: 19815525 MUTATION: attenuated in mice [PMID:11553558]. 3762 transporter tonB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8483965 ECO26_4732 20140406 573235 protein-coding NCBI-supplied PMID: 19815525 MUTATION: mutation of dsbA led to degradation of bundilin and an absence of localized adherence to host cells in EPEC [PMID:9224871]. 3763 protein disulfide isomerase I dsbA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8484733 ECO111_1293 20140308 585396 protein-coding NCBI-supplied PMID: 19815525 MUTATION: attenuated in mice [PMID:2973985]. 3715 siderophore biosynthesis protein iucA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8485562 ECO111_3731 20140215 585396 protein-coding NCBI-supplied PMID: 19815525 T3SS secreted effector EspG espG Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8485564 ECO111_3734 20121017 585396 protein-coding NCBI-supplied PMID: 19815525; 20808845 MUTATION: espF mutant of EPEC is deficient in its ability to disrupt electrical resistance across a polarized monolayer of intestinal epithelial cells, suggesting that EspF is an effector molecule required for disrupting intestinal epithelial barrier function [PMID:11238563]. 3717 T3SS secreted effector EspF espF Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8485567 ECO111_3752 20140215 585396 protein-coding NCBI-supplied PMID: 19815525 MUTATION: deletion of escN abolished pathogenicity in infant rabbits compared to wild-type EHEC [PMID:15731044]. 3718 translocator EscN escN Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8485572 ECO111_3772 20130508 585396 protein-coding NCBI-supplied PMID: 19815525 MUTATION: ler mutants had less adhesion to HeLa cells, ler is a regulator of many virulence genes in the LEE PAI which are needed for adherence [PMID:18794291]. 3719 transcriptional regulator Ler ler Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8485768 ECO111_5002 20140222 585396 protein-coding NCBI-supplied PMID: 19815525 MUTATION: deletion mutant lacks the ability to inhibit lymphokine production and lymphocyte proliferation compared to wild type EPEC [PMID:10722613]. 3720 Efa1/LifA-like protein efa1/lifA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8486116 ECO111_3738 20140215 585396 protein-coding NCBI-supplied PMID: 19815525 MUTATION: deletion mutant attenuated in humans compared to wild-type EPEC [PMID:10816529]. 3721 translocon EspB espB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8486117 ECO111_3748 20121017 585396 protein-coding NCBI-supplied PMID: 19815525 MUTATION: deletion mutant is attenuated in infant rabbits [PMID:15731044]. 3722 T3SS secreted effector EspH espH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8486118 ECO111_3745 20130706 585396 protein-coding NCBI-supplied PMID: 19815525 MUTATION: tir deletion strains are unable to adhere to tissue in an in vitro organ culture [PMID:17474908]. 3723 putative translocated intimin receptor Tir tir Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8486355 ECO111_4360 20140405 585396 protein-coding NCBI-supplied PMID: 19815525 MUTATION: dppA mutant was attenuated 10- to 50-fold compared to the wild type for colonization of the bladders and kidneys of mice [PMID:17074858]. 3724 dipeptide transport protein dppA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8486421 ECO111_3743 20140406 585396 protein-coding NCBI-supplied PMID: 19815525 MUTATION: attenuated in humans [PMID:8376594]. 3725 theta intimin eae Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8486431 ECO111_3739 20140217 585396 protein-coding NCBI-supplied PMID: 19815525 MUTATION: espD deletion mutant of the enterohemorrhagic E. coli (EHEC) strain EDL933 had impaired attachment to HeLa cells [PMID:10456938]. 3726 translocon EspD espD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8486432 ECO111_3740 20140217 585396 protein-coding NCBI-supplied PMID: 19815525 MUTATION: deletion of espA in STEC abolished ability to attach to HeLa cells and induce actin rearrangements [PMID:9786192]. 3727 translocon EspA espA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8486516 ECO111_5176 20140222 585396 protein-coding NCBI-supplied PMID: 19815525 MUTATION: attenuated in mice and humans [PMID:18482721]. 3728 minor component FimH of type 1 fimbriae fimH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8486550 ECO111_2503 20140322 585396 protein-coding NCBI-supplied PMID: 19815525 MUTATION: fliC deletion mutants had reduced adherence in bovine tissue compared to the wild type EHEC and EPEC strains [PMID:17693516]. 3729 flagellin fliC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8487016 ECO111_1294 20140405 585396 protein-coding NCBI-supplied PMID: 19815525 MUTATION: attenuated in mice [PMID:2973985]. 3730 siderophore biosynthesis protein iucB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8487017 ECO111_1295 20140406 585396 protein-coding NCBI-supplied PMID: 19815525 MUTATION: attenuated in mice [PMID:2973985]. 3731 siderophore biosynthesis protein iucC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8487018 ECO111_1296 20140405 585396 protein-coding NCBI-supplied PMID: 19815525 MUTATION: attenuated in mice [PMID:2973985]. 3732 siderophore biosynthesis protein iucD Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8487019 ECO111_1297 20140222 585396 protein-coding NCBI-supplied PMID: 19815525 MUTATION: attenuated in mice [PMID:11553558]. 3733 putative ferric siderophore receptor iutA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8488159 ECO111_4668 20140215 585396 protein-coding NCBI-supplied PMID: 19815525 MUTATION: attenuated in mice [PMID:12117951]. 3734 DNA-binding transcriptional antiterminator RfaH rfaH Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8488207 ECO111_3746 20140215 585396 protein-coding NCBI-supplied PMID: 19815525 MUTATION: map EPEC mutants have significantly reduced levels of invasion of HeLa cells [PMID:14531893]. 3735 T3SS secreted effector Map map Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8488643 ECO111_1025 20140406 585396 protein-coding NCBI-supplied PMID: 19815525 MUTATION: OmpA− strains are unable to cause actin condensation needed for invasion of brain epithelial cells [PMID:10531228]. 3736 outer membrane protein A ompA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8488732 ECO111_1986 20140329 585396 protein-coding NCBI-supplied PMID: 19815525 MUTATION: attenuated in mice [PMID:11553558]. 3737 membrane spanning protein TonB tonB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8489430 ECO111_4681 20140406 585396 protein-coding NCBI-supplied PMID: 19815525 MUTATION: mutation of dsbA led to degradation of bundilin and an absence of localized adherence to host cells in EPEC [PMID:9224871]. 3738 protein disulfide isomerase I dsbA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8515760 GYMC10_1581 20140215 481743 protein-coding NCBI-supplied PMID: 23408395 MUTATION: A trpE mutant, in combination with an aroA mutation, is attenuated in mice [PMID:12694904]. 4949 UBA/THIF-type NAD/FAD-binding protein GYMC10_1581 MUTATION: pefC mutants are attenuated in mice [PMID:8557375]. 3835 MUTATION: spvB mutants are attenuated in mice [PMID:11260464]. TOXIN: spvB encodes an ADP-ribosylating enzyme that uses actin as a substrate and depolymerizes actin filaments when expressed in CHO cells [PMID:11260464]. 3836 MUTATION: The spvBC-bearing plasmid was capable of replacing all of the spv genes, as well as the entire virulence plasmid, of serovar Typhimurium for causing systemic infection in BALB/c mice after subcutaneous, but not oral, inoculation. A point mutation in the spvBC plasmid preventing translation but not transcription of spvC eliminated the ability of the plasmid to confer virulence [PMID:11443102]. 3837 MUTATION: rck mutants reduces serum resistance and eukaryotic cell invasion [PMID:8675302]. 3838 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8571459 pEntH10407_p39 20140222 316401 protein-coding NCBI-supplied PMID: 19767599 MUTATION: Deletion mutants of eltA and eltB had decreased levels of inducing cAMP secretion in an in vitro culture system, and had less adherence to IPEC-J2 and Caco-2 cells than the wild-type ETEC [PMID:18978047]. 3690 heat-labile enterotoxin A subunit eltA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8571464 pEntH10407_p38 20140222 316401 protein-coding NCBI-supplied PMID: 19767599 MUTATION: Deletion mutants of eltA and eltB had decreased levels of inducing cAMP secretion in an in vitro culture system, and had less adherence to IPEC-J2 and Caco-2 cells than the wild-type ETEC [PMID:18978047]. 3691 heat-labile enterotoxin B subunit eltB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8607237 ETAE_0886 20130330 498217 protein-coding NCBI-supplied PMID: 19865481; 22227416 MUTATION: An esrB mutant is highly attenuated in fish [PMID:17478097]. 4961 two-component response regulator EsrB, LuxR family esrB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8614197 SAAV_1451 20140405 681288 protein-coding NCBI-supplied PMID: 19884497 MUTATION: An aroA mutant is attenuated in mice [PMID:16714581]. 4934 3-phosphoshikimate 1-carboxyvinyltransferase aroA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8658565 FeHV-1_gp39 20121122 10334 protein-coding NCBI-supplied MUTATION: A thymidine kinase-deficient mutant (C7301dlTK) is attenuated in cats [PMID:8645090]. 4963 thymidine kinase UL23 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8715786 pO26CRL_0032 20140222 376724 protein-coding NCBI-supplied PMID: 19917674 MUTATION: toxB mutants had attenuated adherence to Caco-2 cells [PMID:11598035]. 3678 toxin B toxB Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8715862 pO26CRL_0108 20140217 376724 protein-coding NCBI-supplied PMID: 19917674 MUTATION: hlyC is required for the acylation and therefore activation of the toxin hemolysin which has the ability to lyse several different types of cells [PMID:8793877]. 3679 hemolysin C hlyC Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8715863 pO26CRL_0109 20140329 376724 protein-coding NCBI-supplied PMID: 19917674 MUTATION: attenuated in zebra fish [PMID:20019794]. 3680 hemolysin A hlyA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8748143 LM5578_1155 20140405 653938 protein-coding NCBI-supplied PMID: 20167121 MUTATION: pycA mutant unable to replicate in mammalian cells, attenuated in mice [PMID:20097852]. 4186 pyruvate carboxylase pycA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 8757905 LM5923_1109 20140405 637381 protein-coding NCBI-supplied PMID: 20167121 MUTATION: pycA mutant unable to replicate in mammalian cells, attenuated in mice [PMID:20097852]. 4187 pyruvate carboxylase pycA Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 9130593 lpa_03874 20140329 423212 protein-coding NCBI-supplied PMID: 20236513 MUTATION: letA mutant is non-motile and is attenuated for infecting murine macrophages [PMID:11967072]. 4188 transmission activator LetA lpa_03874 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 9350422 pLM33_p09 20131125 1639 protein-coding NCBI-supplied PMID: 20511420 MUTATION: pLM33_p09 (ctpA) mutant is attenuated in in vivo persistence in mice [PMID:9049996]. 4189 pLM33 0009 Other designations: hypothetical protein pLM33_p09 Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 10040181 FIPV_gp03 20131213 11135 protein-coding NCBI-supplied PMID: 9654687 MUTATION: A 3abc deletion mutant in Feline infectious peritonitis virus (FIPV) was attenuated in kittens [PMID:15047802] 4965 putative 3a protein nsp 3a Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 10040182 FIPV_gp04 20131213 11135 protein-coding NCBI-supplied PMID: 9654687 MUTATION: A 3abc deletion mutant in Feline infectious peritonitis virus (FIPV) was attenuated in kittens [PMID:15047802]. 4966 putative 3b protein nsp 3b Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 10040183 FIPV_gp05 20121122 11135 pseudo NCBI-supplied MUTATION: A 3abc deletion mutant in Feline infectious peritonitis virus (FIPV) was attenuated in kittens [PMID:15047802]. 4967 pseudo nsp 3c Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 10040187 FIPV_gp09 20140322 11135 protein-coding NCBI-supplied PMID: 22438554; 24189622 MUTATION: A 7ab deletion mutant in Feline infectious peritonitis virus is attenuated in kittens [PMID:15047802]. 4968 non-structural protein 7a nsp 7a Bin Zhao, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene 10040188 FIPV_gp10 20140215 11135 protein-coding NCBI-supplied PMID: 3201747 MUTATION: A 7ab deletion mutant in Feline infectious peritonitis virus is attenuated in kittens [PMID:15047802]. 4969 non-structural protein 7b nsp 7b MUTATION: The Ras1 signal transduction pathway controls the ability of the pathogenic fungus Cryptococcus neoformans to grow at high temperatures and to mate [PMID:12455960]. 5354 MUTATION: Phosphatase Ppg1 is crucial for cell integrity [PMID:16194228]. 5350 MUTATION: The regulator of G protein signaling homolog Crg1 is a key regulator of pheromone-responsive mating in Cryptococcus neoformans. A mutation in the CRG1 gene has greatly increased virulence [PMID:15503029]. 5296 MUTATION: The cpa1 mutant is inviable at 39℃ and attenuated for virulence [PMID:11415984]. 5294 MUTATION: The gta1 mutant exhibited impaired growth on all amino acids tested as sole nitrogen sources, with the exception of arginine and proline. Gat1 is not required for C. neoformans survival during macrophage infection or for virulence in a mouse model of cryptococcosis [PMID:20673806][PMID:20673806]. 5307 MUTATION: The avc1? had reduced growth on a selection of carbon sources, capsule inhibition, and poor melanization at 37 degree celsius [PMID:23550133]. 5270 MUTATION: Mpr1 (mpr1Δ) failed to breach the endothelium in an in vitro model of the human blood-brain barrier (BBB) [PMID:24895304]. 5335 MUTATION: This gene participates in mitochondrial protein synthesis [PMID:15765146]. 5377 MUTATION: The Cryptococcus neoformans ILV2 gene, encoding acetolactate synthase. The ilv2 mutants were auxotrophic for isoleucine and valine and the auxotrophy was satisfied by these amino acids only when proline, and not ammonium, was the nitrogen source, indicating nitrogen regulation of amino acid transport [PMID:15133116]. MUTATION: The MET6 gene showed a substantial induction in response to methionine and a dramatic transcriptional induction in response to homocysteine [PMID:15347759]. 5321 5331 MUTATION: Ssn8 functions as a global regulator which negatively regulates diverse physiological and developmental processes and is required for virulence in C. neoformans [PMID:21559476]. 5370 MUTATION: Mutant strains lacking CMTs or expressing Cmt variants defective in Cu-coordination exhibit severely attenuated virulence and reduced pulmonary colonization [PMID:23498952]. 5291 MUTATION: Loss of the C. neoformans Ura4 protein, resulted in an expected uracil/uridine auxotrophy and an unexpected high temperature growth defect [PMID:25011011]. 5382 MUTATION: The cig1Δ mutant was less susceptible than the wild-type strain to noniron metalloporphyrins [PMID:23322859]. 5288 MUTATION: Crz1 is a calcineurin-dependent transcription factor. Δcna1, and a CRZ1/SP1 mutant (Δcrz1) had attenuated cell wall integrity [PMID:23251520]. 5297 MUTATION: The ste6 mutants in either mating-type background showed partially impaired mating functions, and mating was completely abolished in a bilateral mutant cross [PMID:15643070]. 5372 MUTATION: SKN1 are involved in beta-1,6-glucan synthesis, maintenance of cell wall integrity and retention of mannoproteins and known cryptococcal virulence factors in the cell wall of C. neoformans [PMID:20384682]. 5365 MUTATION: Disruption of the C. neoformans PMT4 gene resulted in abnormal growth morphology and defective cell separation and attenuated virulence [PMID:17142566]. 5349 MUTATION: Had no effect on virulence in an animal model of cryptococcosis [PMID:14504286]. 5292 MUTATION: met mutants showed attenuated virulence in a mouse model [PMID:17353245]. 5330 MUTATION: Ccp1 is a mitochondrial antioxidant that catalyzes the degradation of hydrogen peroxide. The mutant showed attenuated resistance to exogenous oxidative stress in vitro but does not diminish the virulence of C.neofromans in a murine model [PMID:15588993]. 5281 MUTATION: The gene encoding a heterotrimeric G-protein beta subunit. This gene is required for mating and haploid fruiting in Cryptococcus neoformans [PMID:10594037]. 5311 MUTATION: Deletion of the VTC4 gene encoding a polyphosphate polymerase blocked the ability of C. neoformans to produce polyphosphate. The vtc4 mutant behaved like the wild-type strain in interactions with macrophages and in the mouse infection model [PMID:24711572]. 5388 MUTATION: Deletion of Rpb4, growth at host temperature was impaired and virulence was attenuated [PMID:23659661]. 5358 MUTATION: Gat201 is a regulator of multiple virulence pathways.GAT201 participates directly or indirectly in the regulation of both capsule induction and melanization [PMID:18854164]. 5308 MUTATION: Orthologs of mammalian SREBP and Scap,, monitor oxygen-dependent sterol synthesis as a measure of cellular oxygen supply. Yeast Scp1 responds to 4-methyl sterols and thus shares properties with mammalian HMG-CoA reductase, a sterol-sensing domain protein whose degradation is regulated by the 4-methyl sterol lanosterol [PMID:17595166]. 5360 MUTATION: This factor is a homolog of the yeast protein Ada2, a member of the Spt-Ada-Gcn5 Acetyltransferase (SAGA) complex that regulates transcription of stress response genes via histone acetylation. The mutant exhibits significant defects in in response to a variety of stress conditions, sexual development and virulence [PMID:22174677]. 5259 MUTATION: Ste7 and Cpk1 kinases were found to act as a co-ordinate signalling module, whereas the Ste12alpha transcription factor functions with a redundant partner or in a branched or parallel signalling pathway [PMID:14614821]. 5373 MUTATION: Deletion of PYK1 blocked for entry of 2- and 3-carbon substrates into gluconeogenesis and attenuated for virulence in a murine inhalation model [PMID:21652778]. 5352 MUTATION: The mutant displayed sensitivity to copper starvation and defects in polysaccharide capsule production and melanization, leading to increased phagocytosis by murine RAW264.7 macrophages [PMID:20824073]. 5299 MUTATION: The deletion of CLP1 leads to a block in sexual development after cell fusion but before filament formation, and cells without CLP1 are unable to grow vegetatively after cell fusion [PMID:17993575]. 5290 MUTATION: The glr1Delta mutant is sensitive to nitrosative stress and macrophage killing in addition to being avirulent in mice [PMID:16524907]. 5309 MUTATION: Needed for Cryptococcus neoformans melanin biosynthesis [PMID:16102007]. 5268 MUTATION: This gene encoding the C. neoformans FKBP12 homolog, Disruption this gene conferred the fungi Rapamycin resistance [PMID:10330150]. 5305 MUTATION: Cryptococcus neoformans CDC43 is important for thermotolerance, morphogenesis, and virulence [PMID:24014765]. 5284 MUTATION: Δsmt1 mutant loses more than 80% of its virulence compared with the wild type and the reconstituted strain [PMID:22151739]. 5366 MUTATION: Pkh2-02-mediated signaling in C. neoformans is crucial for stress tolerance, host-pathogen interactions, and both temperature-dependent and -independent virulence [PMID:23087368]. 5347 MUTATION: The loss of VCX1 does not influence cell wall integrity or capsule size but decreases secretion of the major capsular polysaccharide glucuronoxylomannan (GXM) in culture supernatants.Vcx1 also influences C. neoformans phagocytosis by murine macrophages and is required for full virulence in mice [PMID:20889719]. 5386 MUTATION: The Δaph1 mutant had reduced virulece in both Galleria mellonella and mice model [PMID:25227465]. 5265 MUTATION: CFT2 played no apparent role in iron acquisition;cft2 mutant was attenuated for virulence [PMID:18282105]. 5285 MUTATION: ERG11 is the target of FLC and AFR1, the major transporter of azoles in C. neoformans [PMID:20368972][PMID:20368972]. 5302 MUTATION: RNA interference of ADA1 expression in Cryptococcus neoformans var. grubii serotype A lead to slow-growing and acapsular [PMID:14622425]. 5261 MUTATION: CnΔsec14-1 was hypovirulent in mice and did not disseminate to the CNS by day 14 post infection. Furthermore, macrophage expulsion of live CnΔsec14-1was reduced [PMID:21453402]. 5362 MUTATION: The mutantation of UVE1 leads to a UV hypersensitive phenotype [PMID:24039606]. 5385 MUTATION: RDI1-overexpressing strains exhibited altered morphology compared to that of the wild type, with apparent defects in maintaining proper cell polarity and cytokinesis. RDI1 deletion resulted in increased vacuole size in tissue culture medium and aberrant cell morphology at neutral pH [PMID:18779335]. 5355 MUTATION: The cts1 mutant exhibited defects in cell separation, growth, mating, and haploid fruiting however these were inviable when calcineurin was mutated or inhibited [PMID:14555485]. 5300 MUTATION: Eca1 is involved in maintaining ER function, thus contributing to stress tolerance and virulence acting in parallel with Ca2+-calcineurin signaling [PMID:17502401]. 5301 MUTATION: This gene encodes one of endochitinases of Cryptococcus neoformans and involved in sexual reproduction [PMID:19734369]. 5286 MUTATION: hxt1 mutant strain showed virulence similar to that of the wild-type strain in experiments with Caenorhabditis elegans [PMID:15907385]. 5319 MUTATION: AFR1 affects the resistance of Cryptococcus neoformans to microglia-mediated antifungal activity by delaying phagosomal maturation [PMID:19220870].AFR1 deletion lead to the hypersusceptibility to fluconazole of Cryptococcus neoformans in vitro [PMID:19220870]. 5260 MUTATION: SPE3-lys9 mutants grew slowly at 30 degrees C, were temperature sensitive in rich medium, and died upon lysine starvation [PMID:15189996]. 5367 MUTATION: One of the five components of the homologous RAM-signaling pathway in C. neoformans, deletion of CBK1 gene leading to morphological change of this fungi [PMID:16775005]. 5279 MUTATION: KREgenes are required for b-1,6-glucan synthesis,maintenance of capsule architecture and cell wall proteinanchoring in Cryptococcus neoformans [PMID:20384682]. 5327 MUTATION: The CPL1 gene is required for capsular formation and virulence [PMID:25261494]. 5295 MUTATION: Hxs1 is required for glucose uptake. hxs1Δ mutant exhibited a significant reduction in glucose uptake activity [PMID:23691177]. 5318 MUTATION: Mid1, a binding partner of Cch1,function as a store-operated Ca(2+)-selective channel gated by depletion of endoplasmic reticulum (ER) Ca(2+) stores [PMID:23175710]. 5333 MUTATION: THR1 were essential for the growth of C. neoformans in rich media, when ammonium was the nitrogen source, or when threonine was supplied as an amino acid instead of a dipeptide [PMID:18757810]. 5375 MUTATION: The pex1 and pex6 deletion mutants were unable to localize the fluorescent DsRED-SKL protein to peroxisomal punctate structures, in contrast to wild-type cells. pex1 and pex6 single mutants and a pex1 pex6 double mutant exhibit identical phenotypes, including abolished growth on fatty acids but no growth difference on acetate [PMID:17041184]. 5343 MUTATION: Deletion of PCK1 results in defective growth on lactic acid, normal growth on glucose, and attenuated virulence [PMID:15765146]. 5338 MUTATION: Cdc24 is a Ras1 effector in C. neoformans to mediate the ability of this fungus to grow at high temperature. Ras1-Cdc24 signalling cascade functions specifically through one of the three Cdc42/Rac1 homologues in C. neoformans [PMID:17233829]. 5283 MUTATION: VPS41 plays a key role in regulating starvation response in this pathogenic organism and that defects in cell cycle arrest are associated with attenuated pathogenic fitness in mammalian hosts [PMID:16879414]. 5387 MUTATION: Deletion of each PIK1, RUB1, and ENA1 differentially reduced pulmonary growth and dissemination rates of C. neoformans and extended mice survival [PMID:22846723]. 5344 MUTATION: itr1a itr3c double mutants showed significant virulence attenuation in murine infection models [PMID:21398509]. 5324 MUTATION: ACL1 Gene is responsible for ATP-citrate lyase synthesis and acl1 mutants were unable to cause disease in a murine inhalation model [PMID:23078142]. 5257 MUTATION: Deletion of PDK1, SIN1 or YPK1 but not MPK1 affected cell viability in the presence of sphingolipid biosynthesis inhibitors [PMID:22339665]. 5393 MUTATION: Deletion of SIN1 affected cell viability in the presence of sphingolipid biosynthesis inhibitors [PMID:22339665]. 5363 MUTATION: Endocytic processes were hampered in the sac6Δ mutant, but cell polarity and cytokinesis were not visibly disturbed however had no effect on virulence in mice [PMID:22562467]. 5359 MUTATION: BLP1 gene knock promoted the phagocytosis of Cryptococcus by macrophages in vitro [PMID:21402362]. MUTATION: bck1 mutant had defects in cell wall integrity and high temperature endurance [PMID:16194228]. 5271 5272 MUTATION: Orthologs of mammalian SREBP and Scap.fission yeast Scp1 responds to 4-methyl sterols and thus shares properties with mammalian HMG-CoA reductase, a sterol-sensing domain protein whose degradation is regulated by the 4-methyl sterol lanosterol [PMID:17595166]. 5361 MUTATION: Deletion of UGD1 blocked not only the synthesis of UDP-glucuronic acid but also that of UDP-xylose and modifications in the cell wall [PMID:15590833]. 5380 MUTATION: CAT1 encode putative spore-specific catalases, however cat1 mutant is absent of phenotype of virulence changes in mouse infection models [PMID:16963629]. 5278 MUTATION: The resulting mutants exhibited moderately elevated levels of melanin and capsule production relative to the wild type [PMID:16339715]. 5339 MUTATION: Can2 is the main carbonic anhydrase and suggest a physiological role for bicarbonate during C. neoformans growth [PMID:16400172]. 5277 MUTATION: Xylbeta1,2-transferase (Cxt1p) that participates in capsular polysaccharide biosynthesis is also the sole transferase responsible for adding xylose to C. neoformans glycosphingolipids [PMID:17430900][PMID:17430900]. 5390 MUTATION: PTP1 and PTP2 were found to be stress-inducible genes, which were controlled by the MAPK Hog1 and the transcription factor Atf1. Ptp2 suppressed the hyperphosphorylation of Hog1 and was involved in mediating vegetative growth, sexual differentiation, stress responses, antifungal drug resistance, and virulence factor regulation through the negative-feedback loop of the HOG pathway. In contrast, Ptp1 was not essential for Hog1 regulation, despite its Hog1-dependent induction [PMID:24728196]. 5351 MUTATION: Targeted deletion of ICL1 resulted in a dramatic decline in viability of C. neoformans cells under nitrogen deprivation [PMID:27350614]. 5320 MUTATION: itr1a itr3c double mutants showed significant virulence attenuation in murine infection models [PMID:21398509]. 5323 MUTATION: Downstream regulation of the Rim101 transcription factor and determined potential cell wall processes involved in the capsule attachment defects and altered mechanisms of virulence in the rim101? mutant [PMID:23550133]. 5357 MUTATION: The CnMT1 was identified as one of the metallothioneins (MTs) and played an essential role in C. neoformans copper resistance [PMID:24317230]. 5293 MUTATION: Spo11 and Ubc5 promote sporulation during both bisexual and unisexual reproduction [PMID:23966871]. 5368 MUTATION: URE2 gene product is involved in the utilization of urea by the organism. The mutant had reduced virulence in mouse infection models [PMID:17159224]. 5269 MUTATION: ubp5Δ mutant exhibited severely attenuated virulence and many distinct phenotypes, including decreased capsule formation, hypomelanization, defective sporulation, and elevated sensitivity to several external stressors [PMID:22719877]. 5378 MUTATION: Plc1 is a central regulator of cryptococcal virulence, acting through the protein kinase C/MAPK pathway, that it regulates release of Plb1 from the plasma membrane and is a candidate antifungal drug target [PMID:18532984]. 5348 MUTATION: Cda1 is one of the four putative chitin/polysaccharide deacetylases in C. neoformans. The chitosan production was abolished only in the cda1Δcda2Δcda3Δ triple-deletion strain however CDA1 single deletion was not sufficient to affect the chiitosan levels [PMID:17400891]. 5282 MUTATION: GMT1 is one of the genes encoding GDP-mannose transporters in C. neoformans. Deletion of the GMT1 gene yields cells with small capsules and a defect in capsule induction [PMID:17351078]. 5310 MUTATION: Deletion of each PIK1, RUB1, and ENA1 differentially reduced pulmonary growth and dissemination rates of C. neoformans and extended mice survival [PMID:22846723]. 5345 MUTATION: The Rac paralogs play a primary role in polarized growth via the organization of reactive oxygen species and play only a minor role in the organization of actin [PMID:23748012]. 5353 MUTATION: UGE2 is necessary for C. neoformans cells to utilize galactose as a carbon source at 30 degrees C but is not required for virulence. In contrast, deletion of UGE1 does not affect cell growth on galactose at this temperature [PMID:18820075]. 5381 MUTATION: Ypd1 is required for the viability of C. neoformans via the Hog1 mitogen-activated protein kinase (MAPK) pathway but plays multiple cellular roles in both a Hog1-dependent and -independent manner [PMID:21642509]. 5392 MUTATION: This gene belongs to the polycomb system that assembles repressive subtelomeric domains of H3K27 methylation (H3K27me) in the yeast Cryptococcus neoformans[PMID:25533783]. 5280 MUTATION: The mutant is sensitive to various peroxide stresses while showing wild-type resistance to other oxidant stresses and exhibit wild-type virulence in a mouse model of cryptococcosis [PMID:16079336]. 5314 MUTATION: Znf3 participates in transposon silencing during unisexual reproduction and may serve as a link between RNAi silencing and sexual [PMID:23966871]. 5369 MUTATION: Kic1 in one of the components of RAM signaling pathway.Disruption of this pathway leads to hyperpolarization and attenuated virulence of Cryptococcus neoformans [PMID:16775005]. 5326 MUTATION: One of the genes involved in melanization of Cryptococcus neoformans [PMID:16102007]. 5287 MUTATION: Δarg1 mutants had impaired thermotolerance, compromised cell walls, reduced capsule production and melanization, defective cell separation, and the inability to form mating filaments and attenuated homeostasis and virulence in the Galleria mellonella infection model [PMID:23381992]. 5267 MUTATION: FRE3 was shown to express an iron reductase activity and to play a role in iron-dependent growth of C. neoformans. Overexpression of FRE3 in the two original environmental strains increased growth in the macrophage cell line J774.16 and increased virulence [PMID:24692633]. 5304 MUTATION: The Δapp1 mutant strain showed a decreased virulence in mice deficient for complement C5 (A/Jcr), but it was hypervirulent in mice deficient for T and NK cells (Tgε26) [PMID:14523045]. 5266 MUTATION: The Δall1 mutants produced a shorter exo-PS with less branching and structural complexity [PMID:23565821]. 5263 MUTATION: Antifungal activity of rapamycin and rapamycin analogs is mediated via conserved complexes with FKBP12 and Tor kinase homologs in divergent yeasts [PMID:11600372]. 5376 MUTATION: SXI1alpha establishes alpha cell identity and controls progression through the sexual cycle. Ectopic expression of SXI1alpha in a cells is sufficient to drive a/alpha sexual development [PMID:12464634]. 5374 MUTATION: OVA1 encodes a putative phosphatidylethanolamine-binding protein that appears to negatively influence capsule production and melanin accumulation [PMID:17367210]. 5336 MUTATION: The pex1 and pex6 deletion mutants were unable to localize the fluorescent DsRED-SKL protein to peroxisomal punctate structures, in contrast to wild-type cells. The pex1 mutant exhibits wild-type virulence in a murine inhalation model and in an insect host, demonstrating that peroxisomes are not required for virulence under these conditions [PMID:17041184]. 5341 MUTATION: C. neoformans STE50 gene has both conserved and novel functions during sexual reproduction and monokaryotic fruiting, and these functions are domain-dependent [PMID:21299652]. 5371 MUTATION: Ctr1 is a Cu transporter and this gene was significantly induced under Cu limited conditions [PMID:21819456]. 5298 MUTATION: Disruption of the CIN1 gene had a pleiotropic effect on growth, normal cytokinesis, intracellular transports and the production of several virulence factors. Additionally, Cin1 interacts with cryptococcal Cdc42 and Wsp1 (a WASP homologue) proteins in vitro, suggesting a conserved role in the regulation of the actin cytoskeleton [PMID:20345666]. 5289 MUTATION: Fbp1 mutants showed normal growth and produced normal major virulence factors. Fbp1 is important for fungal sexual reproduction and the mutant showed attenuated virulence in mouse models [PMID:21478432]. 5303 disease A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:21:20Z disease A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:39:44Z disorder disease course The totality of all processes through which a given disease instance is realized. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:55:44Z replace 'OBI:occurrence of disease', need to add logical definition The axioms of OBI occurence of disease: Equivalent classes: realizes some disease Superclasses: 'has part' some 'pathologic process' 'has participant' some (organism and ('has role' some 'host of immune response role')) biological_process realizes some 'host of immune response role' disease course An object aggregate consisting of an organism and all material entities located within the organism, overlapping the organism, or occupying sites formed in part by the organism. Albert Goldfain http://code.google.com/p/ogms/issues/detail?id=3 creation date: 2010-01-25T04:51:11Z extended organism A process that involves an interaction between a host and a pathogen which can be a virus, bacterium, parasite, fungus, etc. Edison Ong, Yongqun He, Yu Lin https://en.wikipedia.org/wiki/Host%E2%80%93pathogen_interaction Potentially we can list 'host-pathogen interaction' as a subclass of GO:interaction with host (http://purl.obolibrary.org/obo/GO_0051701). However, the GO term is a subclass of "interspecies interaction between organisms". Literally, a virus is not considered as an organism, but a virus is a pathogen. Therefore, this GO term (GO_0051701) may not be appropriate as the parent term of 'host-pathogen interaction'. -- Edison and Oliver host pathogen interaction host bacterial pathogen interaction host viral pathogen interaction host parasitic pathogen interaction host fungal pathogen interaction host B. anthracis pathogen interaction host Brucella spp. pathogen interaction host Y. pestis pathogen interaction host F. tularensis pathogen interaction host C. botulinum pathogen interaction host C. jejuni pathogen interaction host E. coli pathogen interaction host M. tuberculosis pathogen interaction host H. influenzae pathogen interaction host C. burnetii pathogen interaction host C. tetani pathogen interaction host Salmonella spp. pathogen interaction host Shigella pathogen interaction host N. meningitidis pathogen interaction host S. pneumoniae pathogen interaction host C. diphtheriae pathogen interaction host A. salmonicida pathogen interaction host S. equi pathogen interaction host M. gallisepticum pathogen interaction host B. avium pathogen interaction host A. pleuropneumoniae pathogen interaction host V. cholerae pathogen interaction host Rickettsia spp. pathogen interaction host B. pertussis pathogen interaction host Y. pseudotuberculosis pathogen interaction host C. pneumoniae pathogen interaction host M. avium pathogen interaction host B. pseudomallei pathogen interaction host Y. enterocolitica pathogen interaction host H. pylori pathogen interaction host B. burgdorferi pathogen interaction host L. monocytogenes pathogen interaction host P. aeruginosa pathogen interaction host S. aureus pathogen interaction host S. agalactiae pathogen interaction host S. pyogenes pathogen interaction host P. multocida pathogen interaction host B. bronchiseptica pathogen interaction host Leptospira spp. pathogen interaction host C. perfringens pathogen interaction host B. mallei pathogen interaction host C. trachomatis pathogen interaction host L. pneumophila pathogen interaction host Bartonella spp. pathogen interaction host Enterococcus spp. pathogen interaction host A. hydrophila pathogen interaction host E. tarda pathogen interaction host Ebola virus pathogen interaction host Human immunodeficiency virus pathogen interaction host Hantavirus pathogen interaction host Influenza virus pathogen interaction host Measles virus pathogen interaction host Rabies virus pathogen interaction host Rotavirus pathogen interaction host Pseudorabies virus pathogen interaction host Classical swine fever virus pathogen interaction host Bovine herpesvirus 1 pathogen interaction host Infectious hematopoietic necrosis virus pathogen interaction host Herpes simplex virus type 1 pathogen interaction host Rift valley fever virus pathogen interaction host SARS-related coronavirus pathogen interaction host Bovine respiratory syncytial virus pathogen interaction host Feline immunodeficiency virus pathogen interaction host Feline herpesvirus 1 pathogen interaction host Gallid herpesvirus 1 pathogen interaction host Feline infectious peritonitis virus pathogen interaction host Vaccinia virus pathogen interaction host Simian immunodeficiency virus pathogen interaction host Myxoma virus pathogen interaction host Ectromelia virus pathogen interaction A virulence factor role that is inherited in a gene that can encode for a protein, and either the gene or the protein will play the role of a virulence factor. Edison Ong, Oliver He virulence factor gene role A role that is inherited in a pathogen molecule that makes the pathogen virulence in terms of colonization, immunoevasion, immunosuppression, entry into or exit out of host cell, and obtaining nutrient from the host. https://en.wikipedia.org/wiki/Virulence_factor Oliver He, Edison Ong virulence factor role A virulence factor role that is inherited in a protein Oliver He, Edison Ong virulence factor protein role human host pathogen interaction human cell host pathogen interaction human cell line cell host pathogen interaction mouse host pathogen interaction mouse cell host pathogen interaction mouse cell line cell host pathogen interaction rabbit host pathogen interaction rabbit cell host pathogen interaction rabbit cell line cell host pathogen interaction hamster host pathogen interaction hamster cell host pathogen interaction hamster cell line cell host pathogen interaction chicken host pathogen interaction chicken cell host pathogen interaction chicken cell line cell host pathogen interaction monkey host pathogen interaction monkey cell host pathogen interaction monkey cell line cell host pathogen interaction cattle host pathogen interaction cattle cell host pathogen interaction cattle cell line cell host pathogen interaction goat host pathogen interaction goat cell host pathogen interaction goat cell line cell host pathogen interaction C. elegans host pathogen interaction C. elegans cell host pathogen interaction C. elegans cell line cell host pathogen interaction E. coli eatA mutant interaction with rabbit E. coli iroB mutant interaction with chicken E. coli iroC mutant interaction with chicken E. coli iroD mutant interaction with chicken E. coli iroN mutant interaction with mouse E. coli iucA mutant interaction with mouse E. coli iucB mutant interaction with mouse E. coli iucC mutant interaction with mouse E. coli iucD mutant interaction with mouse E. coli iutA mutant interaction with mouse E. coli bfpA mutant interaction with human E. coli bfpF mutant interaction with human E. coli perA mutant interaction with human Shigella ipgA mutant interaction with mouse Shigella ipgA mutant interaction with mouse epithelial cell Shigella virG mutant interaction with monkey Shigella virG mutant interaction with monkey epithelial cell Shigella ipgB mutant interaction with mouse Shigella ipgB mutant interaction with mouse epithelial cell Shigella ipaH9.8 mutant interaction with mouse Shigella sepA mutant interaction with rabbit Shigella IpaH7.8 mutant interaction with mouse Shigella IpaH7.8 mutant interaction with mouse macrophage cell M. tuberculosis sigF mutant interaction with mouse M. tuberculosis fbpA mutant interaction with mouse M. tuberculosis panD mutant interaction with mouse M. tuberculosis sigH mutant interaction with mouse M. tuberculosis MT3523 mutant interaction with human M. tuberculosis MT3523 mutant interaction with human macrophage cell M. tuberculosis MT3523 mutant interaction with mouse M. tuberculosis MT3523 mutant interaction with mouse macrophage cell M. tuberculosis hspR mutant interaction with mouse M. tuberculosis katG mutant interaction with mouse M. tuberculosis sodC mutant interaction with mouse M. tuberculosis sodC mutant interaction with mouse macrophage cell M. tuberculosis mgtC mutant interaction with human M. tuberculosis mgtC mutant interaction with human macrophage cell M. tuberculosis mgtC mutant interaction with mouse M. tuberculosis mgtC mutant interaction with mouse macrophage cell M. tuberculosis senX3 mutant interaction with mouse M. tuberculosis regX3 mutant interaction with mouse M. tuberculosis proC mutant interaction with mouse M. tuberculosis trpD mutant interaction with mouse M. tuberculosis lspA mutant interaction with mouse M. tuberculosis sigC mutant interaction with mouse M. tuberculosis sigE mutant interaction with human M. tuberculosis sigE mutant interaction with human macrophage cell M. tuberculosis sigE mutant interaction with mouse M. tuberculosis sigE mutant interaction with mouse macrophage cell M. tuberculosis leuD mutant interaction with mouse M. tuberculosis cysH mutant interaction with mouse M. tuberculosis mma4 mutant interaction with mouse M. tuberculosis sigL mutant interaction with mouse M. tuberculosis erp mutant interaction with mouse M. tuberculosis panC mutant interaction with mouse M. tuberculosis mprA mutant interaction with mouse M. tuberculosis dppD mutant interaction with mouse M. tuberculosis PPE31 mutant interaction with mouse M. tuberculosis pks7 mutant interaction with mouse M. tuberculosis pks10 mutant interaction with mouse M. tuberculosis Rv1710 mutant interaction with mouse M. tuberculosis coaA mutant interaction with mouse M. tuberculosis argJ mutant interaction with mouse M. tuberculosis prrA mutant interaction with mouse M. tuberculosis prrA mutant interaction with mouse macrophage cell M. tuberculosis ompA mutant interaction with mouse M. tuberculosis ompA mutant interaction with mouse macrophage cell M. tuberculosis Rv3651 mutant interaction with mouse M. tuberculosis hemN mutant interaction with mouse M. tuberculosis Rv2387 mutant interaction with mouse M. tuberculosis Rv1747 mutant interaction with mouse M. tuberculosis Rv3631 mutant interaction with mouse M. tuberculosis Rv1930c mutant interaction with mouse M. tuberculosis Rv3616c mutant interaction with mouse M. tuberculosis pepD mutant interaction with mouse M. tuberculosis lysS mutant interaction with mouse M. tuberculosis Rv1931c mutant interaction with mouse M. tuberculosis Rv0950c mutant interaction with mouse M. tuberculosis Rv1111c mutant interaction with mouse M. tuberculosis nirA mutant interaction with mouse M. tuberculosis Rv1939 mutant interaction with mouse M. tuberculosis Rv3676 mutant interaction with human M. tuberculosis Rv3676 mutant interaction with human macrophage cell M. tuberculosis Rv3676 mutant interaction with mouse M. tuberculosis Rv3676 mutant interaction with mouse macrophage cell M. tuberculosis Rv3701c mutant interaction with mouse M. tuberculosis secA2 mutant interaction with mouse M. tuberculosis Rv3717 mutant interaction with mouse M. tuberculosis Rv3615c mutant interaction with mouse M. tuberculosis Rv3615c mutant interaction with mouse macrophage cell M. tuberculosis Rv3614c mutant interaction with mouse M. tuberculosis Rv3614c mutant interaction with mouse macrophage cell M. tuberculosis Rv3683 mutant interaction with mouse M. tuberculosis Rv3723 mutant interaction with mouse M. tuberculosis recN mutant interaction with mouse M. tuberculosis Rv1524 mutant interaction with mouse M. tuberculosis Rv1109c mutant interaction with mouse M. tuberculosis Rv3649 mutant interaction with mouse M. tuberculosis Rv1128c mutant interaction with mouse M. tuberculosis glpX mutant interaction with mouse M. tuberculosis Rv2437 mutant interaction with mouse M. tuberculosis hrcA mutant interaction with mouse M. tuberculosis Rv1144 mutant interaction with mouse M. tuberculosis Rv1974 mutant interaction with mouse M. tuberculosis mce3A mutant interaction with mouse M. tuberculosis plcA mutant interaction with mouse M. tuberculosis plcB mutant interaction with mouse M. tuberculosis plcC mutant interaction with mouse M. tuberculosis Rv1192 mutant interaction with mouse M. tuberculosis furB mutant interaction with mouse M. tuberculosis cysE mutant interaction with mouse M. tuberculosis Rv0386 mutant interaction with mouse M. tuberculosis pks16 mutant interaction with mouse M. tuberculosis Rv1021 mutant interaction with mouse M. tuberculosis Rv1184c mutant interaction with mouse M. tuberculosis fadD21 mutant interaction with mouse M. tuberculosis lpqT mutant interaction with mouse M. tuberculosis mmpL10 mutant interaction with mouse M. tuberculosis kdpD mutant interaction with mouse M. tuberculosis rfbE mutant interaction with mouse M. tuberculosis embA mutant interaction with mouse M. tuberculosis Rv3805c mutant interaction with mouse M. tuberculosis pirG mutant interaction with mouse M. tuberculosis mmpL8 mutant interaction with mouse M. tuberculosis Rv3869 mutant interaction with mouse M. tuberculosis Rv3865 mutant interaction with mouse M. tuberculosis sodA mutant interaction with mouse M. tuberculosis Rv3864 mutant interaction with mouse M. tuberculosis ethR mutant interaction with mouse M. tuberculosis PE35 mutant interaction with mouse M. tuberculosis esxB mutant interaction with mouse M. tuberculosis Rv3868 mutant interaction with mouse M. tuberculosis Rv3866 mutant interaction with mouse M. tuberculosis PPE68 mutant interaction with mouse M. tuberculosis Rv3871 mutant interaction with mouse M. tuberculosis Rv3870 mutant interaction with mouse M. tuberculosis Rv3876 mutant interaction with mouse M. tuberculosis Rv3877 mutant interaction with mouse M. tuberculosis Rv3882c mutant interaction with mouse M. tuberculosis esxA mutant interaction with mouse M. tuberculosis Rv3887c mutant interaction with mouse M. tuberculosis mycP1 mutant interaction with mouse M. tuberculosis Rv3910 mutant interaction with mouse M. tuberculosis pcaA mutant interaction with mouse M. tuberculosis Rv1590 mutant interaction with mouse M. tuberculosis proV mutant interaction with mouse M. tuberculosis bioB mutant interaction with mouse M. tuberculosis bioA mutant interaction with mouse M. tuberculosis bioF1 mutant interaction with mouse M. tuberculosis Rv1560 mutant interaction with mouse M. tuberculosis xthA mutant interaction with mouse M. tuberculosis thiE mutant interaction with mouse M. tuberculosis pknG mutant interaction with mouse M. tuberculosis pks5 mutant interaction with mouse M. tuberculosis Rv1514c mutant interaction with mouse M. tuberculosis Rv0326 mutant interaction with mouse M. tuberculosis Rv1465 mutant interaction with mouse M. tuberculosis Rv1460 mutant interaction with mouse M. tuberculosis ctpD mutant interaction with mouse M. tuberculosis Rv1422 mutant interaction with mouse M. tuberculosis Rv0249c mutant interaction with mouse M. tuberculosis lprG mutant interaction with mouse M. tuberculosis Rv1410c mutant interaction with mouse M. tuberculosis Rv1405c mutant interaction with mouse M. tuberculosis Rv0218 mutant interaction with mouse M. tuberculosis Rv0216 mutant interaction with mouse M. tuberculosis Rv0204c mutant interaction with mouse M. tuberculosis mmpL11 mutant interaction with mouse M. tuberculosis Rv0199 mutant interaction with mouse M. tuberculosis Rv0176 mutant interaction with mouse M. tuberculosis Rv1371 mutant interaction with mouse M. tuberculosis Rv0175 mutant interaction with mouse M. tuberculosis lprK mutant interaction with mouse M. tuberculosis mce1C mutant interaction with mouse M. tuberculosis mce1B mutant interaction with mouse M. tuberculosis yrbE1B mutant interaction with mouse M. tuberculosis fadD5 mutant interaction with mouse M. tuberculosis mce1A mutant interaction with mouse M. tuberculosis fadD33 mutant interaction with mouse M. tuberculosis murI mutant interaction with mouse M. tuberculosis Rv1333 mutant interaction with mouse M. tuberculosis Rv1332 mutant interaction with mouse M. tuberculosis fadA4 mutant interaction with mouse M. tuberculosis Rv0100 mutant interaction with mouse M. tuberculosis fadD10 mutant interaction with mouse M. tuberculosis Rv0098 mutant interaction with mouse M. tuberculosis atpB mutant interaction with mouse M. tuberculosis nrp mutant interaction with mouse M. tuberculosis Rv1284 mutant interaction with mouse M. tuberculosis Rv1272c mutant interaction with mouse M. tuberculosis lpqZ mutant interaction with mouse M. tuberculosis sugC mutant interaction with mouse M. tuberculosis sugB mutant interaction with mouse M. tuberculosis sugA mutant interaction with mouse M. tuberculosis tatB mutant interaction with mouse M. tuberculosis lpqY mutant interaction with mouse M. tuberculosis accD1 mutant interaction with mouse M. tuberculosis Rv0485 mutant interaction with mouse M. tuberculosis Rv2885c mutant interaction with mouse M. tuberculosis Rv3574 mutant interaction with mouse M. tuberculosis ftsY mutant interaction with mouse M. tuberculosis gcvT mutant interaction with mouse M. tuberculosis Rv3551 mutant interaction with mouse M. tuberculosis aceE mutant interaction with mouse M. tuberculosis Rv3519 mutant interaction with mouse M. tuberculosis Rv2472 mutant interaction with mouse M. tuberculosis fadA6 mutant interaction with mouse M. tuberculosis ilvB1 mutant interaction with mouse M. tuberculosis pks15 mutant interaction with mouse M. tuberculosis ppgK mutant interaction with mouse M. tuberculosis ung mutant interaction with mouse M. tuberculosis fadD28 mutant interaction with mouse M. tuberculosis ceoC mutant interaction with mouse M. tuberculosis mmpL7 mutant interaction with mouse M. tuberculosis Rv1204c mutant interaction with mouse M. tuberculosis hspX mutant interaction with mouse M. tuberculosis hspX mutant interaction with mouse macrophage cell M. tuberculosis sigD mutant interaction with human M. tuberculosis sigD mutant interaction with human macrophage cell M. tuberculosis sigD mutant interaction with mouse M. tuberculosis sigD mutant interaction with mouse macrophage cell M. tuberculosis gcp mutant interaction with mouse M. tuberculosis whiB3 mutant interaction with mouse M. tuberculosis fadD26 mutant interaction with mouse M. tuberculosis fadE22 mutant interaction with mouse M. tuberculosis Rv0566c mutant interaction with mouse M. tuberculosis fabG mutant interaction with mouse M. tuberculosis plsC mutant interaction with mouse M. tuberculosis mce2A mutant interaction with mouse M. tuberculosis Rv2707 mutant interaction with mouse M. tuberculosis cyp125 mutant interaction with mouse M. tuberculosis serB2 mutant interaction with mouse M. tuberculosis fadE32 mutant interaction with mouse M. tuberculosis Rv3588c mutant interaction with mouse M. tuberculosis fadE30 mutant interaction with mouse M. tuberculosis Rv2224c mutant interaction with mouse M. tuberculosis Rv2040c mutant interaction with mouse M. tuberculosis Rv2693c mutant interaction with mouse M. tuberculosis Rv3400 mutant interaction with mouse M. tuberculosis lppX mutant interaction with mouse M. tuberculosis drrB mutant interaction with mouse M. tuberculosis Rv1211 mutant interaction with mouse M. tuberculosis Rv2038c mutant interaction with mouse M. tuberculosis Rv3472 mutant interaction with mouse M. tuberculosis Rv2912c mutant interaction with mouse M. tuberculosis Rv3335c mutant interaction with mouse M. tuberculosis Rv0636 mutant interaction with mouse M. tuberculosis Rv3371 mutant interaction with mouse M. tuberculosis mmaA3 mutant interaction with mouse M. tuberculosis amiD mutant interaction with mouse M. tuberculosis mkl mutant interaction with mouse M. tuberculosis fadE28 mutant interaction with mouse M. tuberculosis Rv2206 mutant interaction with mouse M. tuberculosis pks1 mutant interaction with mouse M. tuberculosis drrA mutant interaction with mouse M. tuberculosis end mutant interaction with mouse M. tuberculosis Rv2553c mutant interaction with mouse M. tuberculosis ltp3 mutant interaction with mouse M. tuberculosis Rv2734 mutant interaction with mouse M. tuberculosis yrbE4A mutant interaction with mouse M. tuberculosis cobL mutant interaction with mouse M. tuberculosis cobC mutant interaction with mouse M. tuberculosis mce4A mutant interaction with mouse M. tuberculosis pks12 mutant interaction with mouse M. tuberculosis mce4C mutant interaction with mouse M. tuberculosis Rv2275 mutant interaction with mouse M. tuberculosis lprN mutant interaction with mouse M. tuberculosis Rv3534c mutant interaction with mouse M. tuberculosis Rv3489 mutant interaction with mouse M. tuberculosis ddl mutant interaction with mouse M. tuberculosis lipF mutant interaction with mouse M. tuberculosis cpsA mutant interaction with mouse M. tuberculosis ltp2 mutant interaction with mouse M. tuberculosis Rv3541c mutant interaction with mouse M. tuberculosis Rv2696c mutant interaction with mouse M. tuberculosis Rv3542c mutant interaction with mouse M. tuberculosis drrC mutant interaction with mouse M. tuberculosis Rv2277c mutant interaction with mouse M. tuberculosis proS mutant interaction with mouse M. tuberculosis Rv2857c mutant interaction with mouse M. tuberculosis Rv2813 mutant interaction with mouse M. tuberculosis Rv2998 mutant interaction with mouse M. tuberculosis Rv3087 mutant interaction with mouse M. tuberculosis Rv3258c mutant interaction with mouse M. tuberculosis ctpC mutant interaction with mouse M. tuberculosis Rv3277 mutant interaction with mouse M. tuberculosis mtrA mutant interaction with mouse M. tuberculosis phoP mutant interaction with mouse M. tuberculosis Rv3168 mutant interaction with mouse M. tuberculosis Rv3114 mutant interaction with mouse M. tuberculosis Rv3178 mutant interaction with mouse M. tuberculosis Rv3103c mutant interaction with mouse M. tuberculosis Rv2004c mutant interaction with mouse M. tuberculosis Rv3229c mutant interaction with mouse M. tuberculosis Rv3236c mutant interaction with mouse M. tuberculosis Rv3050c mutant interaction with mouse M. tuberculosis moeB1 mutant interaction with mouse M. tuberculosis Rv3210c mutant interaction with mouse M. tuberculosis Rv2808 mutant interaction with mouse H. pylori cagA mutant interaction with monkey H. pylori vacA mutant interaction with mouse F. tularensis FTL_0837 mutant interaction with mouse F. tularensis FTL_0846 mutant interaction with mouse F. tularensis FTL_1528 mutant interaction with mouse F. tularensis FTL_1096 mutant interaction with mouse F. tularensis FTL_1097 mutant interaction with mouse F. tularensis FTL_1867 mutant interaction with mouse F. tularensis FTL_1672 mutant interaction with mouse F. tularensis FTL_1678 mutant interaction with mouse F. tularensis tig mutant interaction with mouse F. tularensis FTL_0892 mutant interaction with mouse F. tularensis clpX mutant interaction with mouse F. tularensis FTL_0894 mutant interaction with mouse F. tularensis FTL_0899 mutant interaction with mouse F. tularensis FTL_0903 mutant interaction with mouse F. tularensis FTL_0483 mutant interaction with mouse F. tularensis FTL_0485 mutant interaction with mouse F. tularensis FTL_1134 mutant interaction with mouse F. tularensis FTL_1030 mutant interaction with mouse F. tularensis FTL_0768 mutant interaction with mouse F. tularensis FTL_0584 mutant interaction with mouse F. tularensis FTL_0421 mutant interaction with mouse F. tularensis FTL_0428 mutant interaction with mouse F. tularensis FTL_0430 mutant interaction with mouse F. tularensis FTL_0439 mutant interaction with mouse F. tularensis FTL_0950 mutant interaction with mouse F. tularensis FTL_0960 mutant interaction with mouse F. tularensis rpmJ mutant interaction with mouse F. tularensis FTL_0616 mutant interaction with mouse F. tularensis FTL_0617 mutant interaction with mouse F. tularensis FTL_0009 mutant interaction with mouse F. tularensis FTL_0010 mutant interaction with mouse F. tularensis FTL_0012 mutant interaction with mouse F. tularensis secE mutant interaction with mouse F. tularensis FTL_0663 mutant interaction with mouse F. tularensis FTL_1233 mutant interaction with mouse F. tularensis FTL_1240 mutant interaction with mouse F. tularensis FTL_1225 mutant interaction with mouse F. tularensis FTL_0645 mutant interaction with mouse F. tularensis FTL_0723 mutant interaction with mouse F. tularensis FTL_1419 mutant interaction with mouse F. tularensis FTL_0803 mutant interaction with mouse F. tularensis FTL_1075 mutant interaction with mouse F. tularensis FTL_0111 mutant interaction with mouse F. tularensis FTL_0112 mutant interaction with mouse F. tularensis FTL_0113 mutant interaction with mouse F. tularensis FTL_0133 mutant interaction with mouse F. tularensis FTL_1354 mutant interaction with mouse F. tularensis sucC mutant interaction with mouse F. tularensis FTL_1554 mutant interaction with mouse F. tularensis FTL_1601 mutant interaction with mouse F. tularensis FTL_1273 mutant interaction with mouse F. tularensis FTL_1274 mutant interaction with mouse F. tularensis FTL_1275 mutant interaction with mouse F. tularensis FTL_1936 mutant interaction with mouse F. tularensis FTL_1622 mutant interaction with mouse F. tularensis FTL_1623 mutant interaction with mouse F. tularensis rpmA mutant interaction with mouse F. tularensis FTL_1458 mutant interaction with mouse F. tularensis FTL_R0003 mutant interaction with mouse F. tularensis FTL_1504 mutant interaction with mouse F. tularensis FTL_1266 mutant interaction with mouse F. tularensis FTL_0928 mutant interaction with mouse F. tularensis rpsA mutant interaction with mouse F. tularensis glpX mutant interaction with mouse F. tularensis FTL_0514 mutant interaction with mouse F. tularensis FTL_0519 mutant interaction with mouse F. tularensis FTL_0520 mutant interaction with mouse F. tularensis FTL_0094 mutant interaction with mouse F. tularensis rpsU mutant interaction with mouse F. tularensis rplT mutant interaction with mouse F. tularensis FTL_1414 mutant interaction with mouse F. tularensis FTL_1415 mutant interaction with mouse F. tularensis FTL_1416 mutant interaction with mouse F. tularensis FTL_1832 mutant interaction with mouse F. tularensis isftu1 mutant interaction with mouse F. tularensis FTL_1461 mutant interaction with mouse F. tularensis FTL_1473 mutant interaction with mouse F. tularensis FTL_1474 mutant interaction with mouse F. tularensis FTL_1475 mutant interaction with mouse F. tularensis tRNA-Ile1 mutant interaction with mouse F. tularensis FTL_0382 mutant interaction with mouse F. tularensis FTL_0387 mutant interaction with mouse F. tularensis FTL_1947 mutant interaction with mouse F. tularensis FTL_1328 mutant interaction with mouse F. tularensis FTL_0073 mutant interaction with mouse F. tularensis FTL_0525 mutant interaction with mouse F. tularensis FTL_0540 mutant interaction with mouse F. tularensis FTL_0337 mutant interaction with mouse F. tularensis FTL_1392 mutant interaction with mouse F. tularensis FTL_1393 mutant interaction with mouse F. tularensis FTL_0589 mutant interaction with mouse F. tularensis FTL_0592 mutant interaction with mouse F. tularensis FTL_0597 mutant interaction with mouse F. tularensis FTL_0789 mutant interaction with mouse L. monocytogenes lmo2821 mutant interaction with mouse L. monocytogenes lmo2067 mutant interaction with mouse L. monocytogenes gtcA mutant interaction with mouse L. monocytogenes rnhB mutant interaction with mouse L. monocytogenes lmo1269 mutant interaction with mouse L. monocytogenes lmo1271 mutant interaction with mouse L. monocytogenes tig mutant interaction with mouse L. monocytogenes iap mutant interaction with mouse L. monocytogenes inlA mutant interaction with mouse L. monocytogenes aroA mutant interaction with mouse L. monocytogenes clpB mutant interaction with mouse L. monocytogenes lmo1745 mutant interaction with mouse L. monocytogenes lmo1695 mutant interaction with mouse L. monocytogenes aroB mutant interaction with mouse L. monocytogenes lmo1829 mutant interaction with mouse L. monocytogenes lmo1821 mutant interaction with mouse L. monocytogenes inlC mutant interaction with mouse L. monocytogenes lmo1076 mutant interaction with mouse L. monocytogenes pycA mutant interaction with mouse L. monocytogenes dltA mutant interaction with mouse L. monocytogenes lmo0135 mutant interaction with mouse L. monocytogenes clpE mutant interaction with mouse L. monocytogenes sod mutant interaction with mouse L. monocytogenes fri mutant interaction with mouse L. monocytogenes fri mutant interaction with mouse macrophage cell L. monocytogenes inlB mutant interaction with mouse L. monocytogenes prfA mutant interaction with mouse L. monocytogenes plcA mutant interaction with mouse L. monocytogenes hly mutant interaction with mouse L. monocytogenes mpl mutant interaction with mouse L. monocytogenes plcB mutant interaction with mouse L. monocytogenes clpC mutant interaction with mouse L. monocytogenes clpC mutant interaction with mouse macrophage cell L. monocytogenes ami mutant interaction with mouse L. monocytogenes inlG mutant interaction with mouse L. monocytogenes inlH mutant interaction with mouse L. monocytogenes inlE mutant interaction with mouse L. monocytogenes clpP mutant interaction with mouse L. monocytogenes clpP mutant interaction with mouse macrophage cell L. monocytogenes lmo0292 mutant interaction with mouse L. monocytogenes lmo2537 mutant interaction with mouse L. monocytogenes relA mutant interaction with mouse L. monocytogenes lmo0415 mutant interaction with mouse F. tularensis FTT0054 mutant interaction with mouse F. tularensis sodB mutant interaction with mouse F. tularensis sthA mutant interaction with mouse F. tularensis sucB mutant interaction with mouse F. tularensis sucD mutant interaction with mouse F. tularensis ksgA mutant interaction with mouse F. tularensis surA mutant interaction with mouse F. tularensis FTT0105c mutant interaction with mouse F. tularensis tet mutant interaction with mouse F. tularensis glgB mutant interaction with mouse F. tularensis FTT0134 mutant interaction with mouse F. tularensis FTT1441 mutant interaction with mouse F. tularensis lon mutant interaction with mouse F. tularensis lpnB mutant interaction with mouse F. tularensis FTT1489 mutant interaction with mouse F. tularensis FTT1400c mutant interaction with mouse F. tularensis FTT0975 mutant interaction with mouse F. tularensis metIQ mutant interaction with mouse F. tularensis glpe mutant interaction with mouse F. tularensis aroG mutant interaction with mouse F. tularensis aspC1 mutant interaction with mouse F. tularensis cdd mutant interaction with mouse F. tularensis bioD mutant interaction with mouse F. tularensis bioC mutant interaction with mouse F. tularensis bipA mutant interaction with mouse F. tularensis glgC mutant interaction with mouse F. tularensis bioB mutant interaction with mouse F. tularensis capB mutant interaction with mouse F. tularensis bioF mutant interaction with mouse F. tularensis trpG mutant interaction with mouse F. tularensis FTT0708 mutant interaction with mouse F. tularensis FTT0685c mutant interaction with mouse F. tularensis FTT0667 mutant interaction with mouse F. tularensis FTT0645c mutant interaction with mouse F. tularensis carA mutant interaction with mouse F. tularensis FTT1633c mutant interaction with mouse F. tularensis FTT1640c mutant interaction with mouse F. tularensis FTT1314c mutant interaction with mouse F. tularensis FTT1611 mutant interaction with mouse F. tularensis FTT1334c mutant interaction with mouse F. tularensis FTT0615c mutant interaction with mouse F. tularensis FTT0589 mutant interaction with mouse F. tularensis FTT0584 mutant interaction with mouse F. tularensis iglA mutant interaction with mouse F. tularensis prfC mutant interaction with mouse F. tularensis FTT1117c mutant interaction with mouse F. tularensis mtn mutant interaction with mouse F. tularensis FTT1103 mutant interaction with mouse F. tularensis FTT1102 mutant interaction with mouse F. tularensis cadA mutant interaction with mouse F. tularensis yibK mutant interaction with mouse F. tularensis pcs mutant interaction with mouse F. tularensis ruvB mutant interaction with mouse F. tularensis FTT0295 mutant interaction with mouse F. tularensis pdpA mutant interaction with mouse F. tularensis pdpB mutant interaction with mouse F. tularensis pdxY mutant interaction with mouse F. tularensis FTT0256c mutant interaction with mouse F. tularensis FTT0209c mutant interaction with mouse F. tularensis pgm mutant interaction with mouse F. tularensis FTT0509c mutant interaction with mouse F. tularensis sdhC mutant interaction with mouse F. tularensis FTT0455c mutant interaction with mouse F. tularensis parB mutant interaction with mouse F. tularensis FTT0453c mutant interaction with mouse F. tularensis FTT0443 mutant interaction with mouse F. tularensis FTT0398c mutant interaction with mouse F. tularensis FTT0399c mutant interaction with mouse F. tularensis pcp mutant interaction with mouse F. tularensis FTT1258 mutant interaction with mouse F. tularensis htpG mutant interaction with mouse F. tularensis dedA1 mutant interaction with mouse F. tularensis deoB mutant interaction with mouse F. tularensis deoD mutant interaction with mouse F. tularensis fumA mutant interaction with mouse F. tularensis cca mutant interaction with mouse F. tularensis dsbB mutant interaction with mouse F. tularensis gcvH mutant interaction with mouse F. tularensis elbB mutant interaction with mouse F. tularensis iglB mutant interaction with mouse F. tularensis xerC mutant interaction with mouse F. tularensis galE mutant interaction with mouse F. tularensis iglC mutant interaction with mouse F. tularensis rluC mutant interaction with mouse F. tularensis rluB mutant interaction with mouse F. tularensis ribB mutant interaction with mouse F. tularensis ribA mutant interaction with mouse F. tularensis relA mutant interaction with mouse F. tularensis recB mutant interaction with mouse F. tularensis recA mutant interaction with mouse F. tularensis rbfA mutant interaction with mouse F. tularensis qseC mutant interaction with mouse F. tularensis pyrH mutant interaction with mouse F. tularensis pyrF mutant interaction with mouse F. tularensis pyrD mutant interaction with mouse F. tularensis pyrB mutant interaction with mouse F. tularensis putA mutant interaction with mouse F. tularensis purN mutant interaction with mouse F. tularensis purM mutant interaction with mouse F. tularensis purL mutant interaction with mouse F. tularensis purH mutant interaction with mouse F. tularensis purF mutant interaction with mouse F. tularensis purE mutant interaction with mouse F. tularensis FTT1151c mutant interaction with mouse F. tularensis FTT0918 mutant interaction with mouse F. tularensis FTT0910 mutant interaction with mouse F. tularensis FTT0905 mutant interaction with mouse F. tularensis FTT0903 mutant interaction with mouse F. tularensis FTT0891 mutant interaction with mouse F. tularensis FTT0881c mutant interaction with mouse F. tularensis FTT1129c mutant interaction with mouse F. tularensis FTT0843 mutant interaction with mouse F. tularensis FTT1747 mutant interaction with mouse F. tularensis apt mutant interaction with mouse F. tularensis phoH mutant interaction with mouse F. tularensis lpnA mutant interaction with mouse F. tularensis lpxB mutant interaction with mouse F. tularensis FTT0800 mutant interaction with mouse F. tularensis FTT0799 mutant interaction with mouse F. tularensis FTT0798 mutant interaction with mouse F. tularensis FTT0793 mutant interaction with mouse F. tularensis FTT0790 mutant interaction with mouse F. tularensis FTT0797 mutant interaction with mouse F. tularensis FTT0807 mutant interaction with mouse F. tularensis FTT0759 mutant interaction with mouse F. tularensis FTT0792 mutant interaction with mouse F. tularensis FTT0748 mutant interaction with mouse F. tularensis fadD1 mutant interaction with mouse F. tularensis fadB/acbP mutant interaction with mouse F. tularensis feoB mutant interaction with mouse F. tularensis cphB mutant interaction with mouse F. tularensis cphA mutant interaction with mouse F. tularensis uvrA mutant interaction with mouse F. tularensis cyoB mutant interaction with mouse F. tularensis cyoC mutant interaction with mouse F. tularensis cyoD mutant interaction with mouse F. tularensis folD mutant interaction with mouse F. tularensis wbtA mutant interaction with mouse F. tularensis FTT1416c mutant interaction with mouse F. tularensis rpoA2 mutant interaction with mouse F. tularensis rplY mutant interaction with mouse F. tularensis rplW mutant interaction with mouse F. tularensis fopA mutant interaction with mouse F. tularensis rplQ mutant interaction with mouse F. tularensis rplD mutant interaction with mouse F. tularensis FTT1048c mutant interaction with mouse F. tularensis FTT1047c mutant interaction with mouse F. tularensis FTT1015 mutant interaction with mouse F. tularensis secA mutant interaction with mouse F. tularensis wbtD mutant interaction with mouse F. tularensis wbtF mutant interaction with mouse F. tularensis wbtG mutant interaction with mouse F. tularensis wbtH mutant interaction with mouse F. tularensis katG mutant interaction with mouse F. tularensis xasA mutant interaction with mouse F. tularensis xerD mutant interaction with mouse F. tularensis FTT0028c mutant interaction with mouse F. tularensis FTT0029c mutant interaction with mouse F. tularensis FTT0057 mutant interaction with mouse F. tularensis FTT0053 mutant interaction with mouse F. tularensis FTT0056c mutant interaction with mouse F. tularensis yegQ mutant interaction with mouse F. tularensis FTT0101 mutant interaction with mouse F. tularensis yfdH mutant interaction with mouse F. tularensis FTT1152 mutant interaction with mouse F. tularensis ppiC mutant interaction with mouse F. tularensis lolD mutant interaction with mouse F. tularensis FTT1238c mutant interaction with mouse F. tularensis FTT1239 mutant interaction with mouse F. tularensis FTT1236 mutant interaction with mouse F. tularensis FTT1237 mutant interaction with mouse F. tularensis FTT1221 mutant interaction with mouse F. tularensis FTTt19 mutant interaction with mouse F. tularensis manB mutant interaction with mouse F. tularensis FTTr07 mutant interaction with mouse F. tularensis lysA mutant interaction with mouse F. tularensis ispA mutant interaction with mouse F. tularensis bioA mutant interaction with mouse F. tularensis emrA1 mutant interaction with mouse F. tularensis clpP mutant interaction with mouse F. tularensis capC mutant interaction with mouse F. tularensis FTT1676 mutant interaction with mouse F. tularensis sdaC1 mutant interaction with mouse F. tularensis yjjK mutant interaction with mouse F. tularensis hflK mutant interaction with mouse F. tularensis hflX mutant interaction with mouse F. tularensis hisS mutant interaction with mouse F. tularensis FTT0968c mutant interaction with mouse F. tularensis minD mutant interaction with mouse F. tularensis FTT0945 mutant interaction with mouse F. tularensis FTT0944 mutant interaction with mouse F. tularensis FTT0941c mutant interaction with mouse F. tularensis FTT0940c mutant interaction with mouse F. tularensis FTT0928c mutant interaction with mouse F. tularensis minC mutant interaction with mouse F. tularensis ampD mutant interaction with mouse F. tularensis FTT1490 mutant interaction with mouse F. tularensis gcvP1 mutant interaction with mouse F. tularensis clpB mutant interaction with mouse F. tularensis gcvT mutant interaction with mouse F. tularensis FTT0165c mutant interaction with mouse F. tularensis aspC2 mutant interaction with mouse Y. pestis spoT mutant interaction with mouse Y. pestis purH mutant interaction with mouse Y. pestis hfq mutant interaction with mouse Y. pestis hfq mutant interaction with mouse macrophage cell Y. pestis greA mutant interaction with mouse Y. pestis relA mutant interaction with mouse Y. pestis pcm mutant interaction with mouse Y. pestis nlpD mutant interaction with mouse Y. pestis purK mutant interaction with mouse Y. pestis y1136 mutant interaction with mouse Y. pestis pgm mutant interaction with mouse Y. pestis y1436 mutant interaction with mouse Y. pestis y1537 mutant interaction with mouse Y. pestis y1718 mutant interaction with mouse Y. pestis phoP mutant interaction with mouse Y. pestis phoP mutant interaction with mouse macrophage cell Y. pestis yfeB mutant interaction with mouse Y. pestis yfeA mutant interaction with mouse Y. pestis msbB mutant interaction with mouse Y. pestis y2285 mutant interaction with mouse Y. pestis y2316 mutant interaction with mouse Y. pestis ybtP mutant interaction with mouse Y. pestis y2785 mutant interaction with mouse Y. pestis y2786 mutant interaction with mouse Y. pestis psaA mutant interaction with mouse Y. pestis psaE mutant interaction with mouse Y. pestis y3010 mutant interaction with mouse Y. pestis smpB mutant interaction with mouse Y. pestis dnaE mutant interaction with mouse Y. pestis y3395 mutant interaction with mouse Y. pestis thrL mutant interaction with mouse Y. pestis yapE mutant interaction with mouse Y. pestis y3857 mutant interaction with mouse Y. pestis dam mutant interaction with mouse Y. pestis crp mutant interaction with mouse Y. pestis caf1M mutant interaction with mouse B. anthracis atxA mutant interaction with mouse B. anthracis pagA mutant interaction with mouse B. anthracis lef mutant interaction with mouse C. jejuni Cj0019c mutant interaction with chicken C. jejuni Cj0020c mutant interaction with chicken C. jejuni fliA mutant interaction with chicken C. jejuni Cj0248 mutant interaction with chicken C. jejuni motB mutant interaction with chicken C. jejuni motA mutant interaction with chicken C. jejuni Cj0415 mutant interaction with chicken C. jejuni Cj0454c mutant interaction with chicken C. jejuni Cj0456c mutant interaction with chicken C. jejuni Cj0618 mutant interaction with chicken C. jejuni Cj0629 mutant interaction with chicken C. jejuni rpoN mutant interaction with chicken C. jejuni pta mutant interaction with chicken C. jejuni Cj0903c mutant interaction with chicken C. jejuni aas mutant interaction with chicken C. jejuni livJ mutant interaction with chicken C. jejuni cheY mutant interaction with chicken C. jejuni pglF mutant interaction with chicken C. jejuni pglH mutant interaction with chicken C. jejuni fliR mutant interaction with chicken C. jejuni dccR mutant interaction with mouse C. jejuni dnaJ mutant interaction with chicken C. jejuni Cj1279c mutant interaction with chicken C. jejuni Cj1279c mutant interaction with chicken epithelial cell C. jejuni Cj1321 mutant interaction with chicken C. jejuni Cj1324 mutant interaction with chicken C. jejuni Cj1349c mutant interaction with chicken C. jejuni Cj1349c mutant interaction with chicken epithelial cell C. jejuni Cj1461 mutant interaction with human C. jejuni Cj1461 mutant interaction with human epithelial cell C. jejuni flgK mutant interaction with chicken C. jejuni sdaA mutant interaction with chicken C. jejuni peb1A mutant interaction with mouse C. jejuni peb1A mutant interaction with mouse epithelial cell C. jejuni CJE0997 mutant interaction with chicken C. jejuni CJE0998 mutant interaction with chicken C. jejuni pebC mutant interaction with chicken C. jejuni pglH mutant interaction with human C. perfringens plc mutant interaction with mouse C. perfringens virS mutant interaction with mouse B. anthracis clpX mutant interaction with mouse B. anthracis sodC mutant interaction with mouse B. anthracis codY mutant interaction with mouse B. anthracis sigB mutant interaction with mouse Shigella sodB mutant interaction with rabbit Shigella sitA mutant interaction with mouse Shigella aroD mutant interaction with monkey Shigella sigA mutant interaction with rabbit Shigella iucD mutant interaction with rabbit Shigella iucD mutant interaction with chicken Shigella iucC mutant interaction with rabbit Shigella iucC mutant interaction with chicken Shigella iucA mutant interaction with rabbit Shigella iucA mutant interaction with chicken Shigella iutA mutant interaction with chicken Shigella iucB mutant interaction with rabbit Shigella iucB mutant interaction with chicken Shigella ospG mutant interaction with rabbit Shigella ipaH7.8 mutant interaction with mouse Shigella ipaH7.8 mutant interaction with mouse macrophage cell Brucella spp. virB10 mutant interaction with mouse Brucella spp. virB10 mutant interaction with mouse macrophage cell Brucella spp. virB9 mutant interaction with human Brucella spp. virB9 mutant interaction with human macrophage cell Brucella spp. virB9 mutant interaction with human HeLa cell Brucella spp. virB5 mutant interaction with human Brucella spp. virB5 mutant interaction with human macrophage cell Brucella spp. virB4 mutant interaction with mouse Brucella spp. virB4 mutant interaction with mouse macrophage cell Brucella spp. virB2 mutant interaction with mouse Brucella spp. virB2 mutant interaction with mouse macrophage cell Brucella spp. virB1 mutant interaction with mouse Brucella spp. virB1 mutant interaction with mouse macrophage cell Brucella spp. gnd mutant interaction with mouse Brucella spp. narG mutant interaction with human Brucella spp. narG mutant interaction with human macrophage cell Brucella spp. cydB mutant interaction with mouse Brucella spp. pcs mutant interaction with mouse Brucella spp. pcs mutant interaction with mouse macrophage cell Brucella spp. ugpB mutant interaction with human Brucella spp. ugpB mutant interaction with human epithelial cell Brucella spp. ugpB mutant interaction with human HeLa cell Brucella spp. ugpA mutant interaction with mouse Brucella spp. gcvT mutant interaction with human Brucella spp. gcvT mutant interaction with human macrophage cell Brucella spp. eryB mutant interaction with human Brucella spp. eryB mutant interaction with human macrophage cell Brucella spp. eryC mutant interaction with mouse Brucella spp. eryC mutant interaction with mouse macrophage cell Brucella spp. cobW mutant interaction with human Brucella spp. cobW mutant interaction with human macrophage cell Brucella spp. znuA mutant interaction with mouse Brucella spp. znuA mutant interaction with mouse macrophage cell Brucella spp. pheA mutant interaction with mouse Brucella spp. pheA mutant interaction with mouse macrophage cell Brucella spp. bacA mutant interaction with mouse Brucella spp. bacA mutant interaction with mouse macrophage cell Brucella spp. glnA mutant interaction with human Brucella spp. glnA mutant interaction with human macrophage cell Brucella spp. ntrC mutant interaction with mouse Brucella spp. ntrC mutant interaction with mouse macrophage cell Brucella spp. serB mutant interaction with human Brucella spp. serB mutant interaction with human macrophage cell Brucella spp. pncA mutant interaction with mouse Brucella spp. pncA mutant interaction with mouse macrophage cell Brucella spp. lysA mutant interaction with human Brucella spp. lysA mutant interaction with human macrophage cell Brucella spp. bvrR mutant interaction with mouse Brucella spp. bvrR mutant interaction with mouse epithelial cell Brucella spp. bvrR mutant interaction with mouse macrophage cell Brucella spp. bvrS mutant interaction with mouse Brucella spp. bvrS mutant interaction with mouse epithelial cell Brucella spp. bvrS mutant interaction with mouse macrophage cell Brucella spp. pmtA mutant interaction with mouse Brucella spp. pmtA mutant interaction with mouse macrophage cell Y. pestis pla mutant interaction with mouse Y. pestis yopE mutant interaction with mouse Y. pestis yopQ mutant interaction with mouse Y. pestis yopM mutant interaction with mouse Y. pestis yopB mutant interaction with mouse Y. pestis yopB mutant interaction with mouse macrophage cell Y. pestis sycD mutant interaction with mouse Y. pestis lcrV mutant interaction with mouse Y. pestis virF mutant interaction with mouse Y. pestis ypkA mutant interaction with mouse Y. pestis caf1A mutant interaction with mouse Y. pestis arcA mutant interaction with mouse Y. pestis YPO1003 mutant interaction with mouse Y. pestis ssrA mutant interaction with mouse Y. pestis YPO1179 mutant interaction with mouse Y. pestis YPO1387 mutant interaction with mouse Y. pestis YPO1388 mutant interaction with mouse Y. pestis ail mutant interaction with mouse Y. pestis YPO1994 mutant interaction with mouse Y. pestis YPO2027 mutant interaction with mouse Y. pestis slyA mutant interaction with mouse Y. pestis lpp mutant interaction with mouse Y. pestis YPO2471 mutant interaction with mouse Y. pestis YPO2793 mutant interaction with mouse Y. pestis guaA mutant interaction with mouse Y. pestis guaB mutant interaction with mouse Y. pestis YPO2947 mutant interaction with mouse Y. pestis YPO3045 mutant interaction with mouse Y. pestis YPO3398 mutant interaction with mouse Y. pestis YPO3973 mutant interaction with mouse Salmonella spp. ssaV mutant interaction with human Salmonella spp. ssaM mutant interaction with mouse Salmonella spp. sseD mutant interaction with mouse Salmonella spp. sseC mutant interaction with mouse Salmonella spp. spiC mutant interaction with mouse Salmonella spp. spiC mutant interaction with mouse macrophage cell Salmonella spp. fliC mutant interaction with chicken Salmonella spp. aroC mutant interaction with human Salmonella spp. invH mutant interaction with cattle Brucella spp. virb1 mutant interaction with mouse Brucella spp. virb1 mutant interaction with mouse macrophage cell Brucella spp. virb4 mutant interaction with mouse Brucella spp. virb4 mutant interaction with mouse macrophage cell Brucella spp. virb9 mutant interaction with human Brucella spp. virb9 mutant interaction with human macrophage cell Brucella spp. virb9 mutant interaction with human HeLa cell Brucella spp. virb10 mutant interaction with mouse Brucella spp. virb10 mutant interaction with mouse macrophage cell Brucella spp. ftcR mutant interaction with cattle Brucella spp. ftcR mutant interaction with cattle macrophage cell Brucella spp. ftcR mutant interaction with mouse Brucella spp. ftcR mutant interaction with mouse macrophage cell B. anthracis BAS4929 mutant interaction with mouse B. anthracis GBAA4766 mutant interaction with mouse B. anthracis GBAA0552 mutant interaction with mouse B. anthracis phnX mutant interaction with mouse L. monocytogenes degU mutant interaction with mouse L. monocytogenes inlF mutant interaction with mouse L. monocytogenes recQ mutant interaction with mouse L. monocytogenes LMOf2365_0094 mutant interaction with mouse L. monocytogenes LMOf2365_1971 mutant interaction with mouse L. monocytogenes gtcA mutant interaction with mouse epithelial cell L. monocytogenes agrA mutant interaction with mouse L. monocytogenes ctsR mutant interaction with mouse L. monocytogenes prsA-2 mutant interaction with mouse L. pneumophila lpg0742 mutant interaction with mouse L. pneumophila lpg0742 mutant interaction with mouse macrophage cell L. pneumophila cpxR mutant interaction with mouse L. pneumophila cpxR mutant interaction with mouse macrophage cell L. pneumophila mip mutant interaction with human L. pneumophila lpg1905 mutant interaction with human L. pneumophila lpg1905 mutant interaction with human macrophage cell L. pneumophila enhC mutant interaction with mouse L. pneumophila enhC mutant interaction with mouse macrophage cell L. pneumophila dotA mutant interaction with mouse L. pneumophila dotA mutant interaction with mouse macrophage cell L. pneumophila feoB mutant interaction with human L. pneumophila feoB mutant interaction with human macrophage cell L. pneumophila djlA mutant interaction with mouse L. pneumophila djlA mutant interaction with mouse macrophage cell L. pneumophila lpg2515 mutant interaction with mouse L. pneumophila rtxA-2 mutant interaction with mouse L. pneumophila sdhA mutant interaction with mouse L. pneumophila sdhA mutant interaction with mouse macrophage cell L. pneumophila rtxA-1 mutant interaction with mouse Shigella icsA mutant interaction with monkey Shigella icsA mutant interaction with monkey epithelial cell Shigella ipaH mutant interaction with mouse Salmonella spp. sptP mutant interaction with mouse Salmonella spp. sptP mutant interaction with mouse epithelial cell Salmonella spp. tdcA mutant interaction with mouse Salmonella spp. tdcA mutant interaction with mouse epithelial cell C. jejuni motB mutant interaction with mouse C. jejuni cheA mutant interaction with mouse C. jejuni pglB mutant interaction with mouse C. jejuni CJJ81176_0927 mutant interaction with chicken C. jejuni fliI mutant interaction with mouse C. jejuni CJJ81176_0926 mutant interaction with chicken C. jejuni JJD26997_0895 mutant interaction with chicken C. jejuni pebA mutant interaction with chicken C. jejuni JJD26997_0894 mutant interaction with chicken L. pneumophila icmG mutant interaction with mouse C. jejuni racR mutant interaction with chicken C. perfringens pCPF5603_44 mutant interaction with rabbit Vaccinia virus C12L mutant interaction with mouse Vaccinia virus E3L mutant interaction with mouse Vaccinia virus N1L mutant interaction with mouse Vaccinia virus A46R mutant interaction with mouse Measles virus P mutant interaction with monkey Rift valley fever virus RVFVsSgp1 mutant interaction with mouse Human immunodeficiency virus nef mutant interaction with mouse C. perfringens cpe mutant interaction with rabbit Y. pestis yscH mutant interaction with mouse Y. pestis yopK mutant interaction with mouse Y. pestis lcrH mutant interaction with mouse Y. pestis lcrF mutant interaction with mouse B. pseudomallei aroC mutant interaction with mouse B. pseudomallei pabB mutant interaction with mouse B. mallei virG mutant interaction with hamster B. pseudomallei BURPS668_A2153 mutant interaction with mouse B. pseudomallei purM mutant interaction with mouse B. pseudomallei sctU mutant interaction with mouse B. pseudomallei bopA mutant interaction with mouse B. pseudomallei leuB mutant interaction with mouse B. pseudomallei BPSS1509 mutant interaction with mouse B. pseudomallei sctU mutant interaction with hamster B. pseudomallei BPSS2074 mutant interaction with hamster B. pseudomallei bipD mutant interaction with mouse B. pseudomallei BPSS1539 mutant interaction with mouse B. pseudomallei bopE mutant interaction with mouse B. pseudomallei bsaZ mutant interaction with mouse B. pseudomallei bsaZ mutant interaction with mouse macrophage cell B. pseudomallei BPSS0067 mutant interaction with mouse B. pseudomallei BPSS2053 mutant interaction with human B. pseudomallei BPSS2053 mutant interaction with human epithelial cell B. pseudomallei pmlI mutant interaction with mouse B. pseudomallei BPSL1039 mutant interaction with mouse B. pseudomallei BPSL1263 mutant interaction with human B. pseudomallei BPSL1263 mutant interaction with human epithelial cell B. pseudomallei BPSL1263 mutant interaction with human macrophage cell B. pseudomallei lipB mutant interaction with mouse B. pseudomallei hisF mutant interaction with mouse B. pseudomallei wcbN mutant interaction with mouse B. pseudomallei BPSL2825 mutant interaction with mouse B. pseudomallei BPSL0634 mutant interaction with mouse B. pseudomallei BPSL1528 mutant interaction with mouse B. pseudomallei aroB mutant interaction with mouse B. pseudomallei trpG mutant interaction with mouse B. pseudomallei purN mutant interaction with mouse B. pseudomallei wcbB mutant interaction with mouse B. pseudomallei wcbC mutant interaction with mouse B. pseudomallei nth mutant interaction with mouse B. pseudomallei BPSL0872 mutant interaction with human B. pseudomallei BPSL0872 mutant interaction with human epithelial cell B. pseudomallei BPSL0872 mutant interaction with hamster B. pseudomallei BPSL0872 mutant interaction with hamster epithelial cell B. pseudomallei BPSL0395 mutant interaction with mouse B. pseudomallei wzm mutant interaction with mouse B. pseudomallei ilvI mutant interaction with mouse B. pseudomallei fliC mutant interaction with mouse B. pseudomallei wcbD mutant interaction with mouse B. pseudomallei BPSL3147 mutant interaction with mouse B. pseudomallei serC mutant interaction with mouse B. pseudomallei recA mutant interaction with mouse B. pseudomallei BPSL1876 mutant interaction with mouse B. pseudomallei BPSL1705 mutant interaction with mouse B. pseudomallei BPSL1705 mutant interaction with mouse macrophage cell B. mallei BMAA0739 mutant interaction with hamster B. mallei BMAA0743 mutant interaction with hamster B. mallei BMAA0742 mutant interaction with hamster B. mallei BMAA0649 mutant interaction with human B. mallei BMAA0649 mutant interaction with human epithelial cell B. mallei BMAA0740 mutant interaction with hamster E. coli bfpT mutant interaction with human E. coli rfaH mutant interaction with mouse E. coli dppA mutant interaction with mouse E. coli fliC mutant interaction with cattle E. coli fimH mutant interaction with human E. coli fimH mutant interaction with mouse E. coli tonB mutant interaction with mouse E. coli mppA mutant interaction with chicken E. coli sbmA mutant interaction with chicken E. coli ychF mutant interaction with chicken E. coli waaL mutant interaction with chicken E. coli ibeA mutant interaction with human E. coli sitB mutant interaction with chicken E. coli malX mutant interaction with chicken E. coli tia mutant interaction with human E. coli papG mutant interaction with human E. coli kpsS mutant interaction with chicken E. coli wcaE mutant interaction with chicken E. coli APECO1_3367 mutant interaction with chicken E. coli yjjQ mutant interaction with chicken E. coli tktA mutant interaction with chicken E. coli ECP_4655 mutant interaction with human E. coli ECP_4655 mutant interaction with mouse E. coli cnf1 mutant interaction with mouse E. coli ycjM mutant interaction with chicken E. coli wecE mutant interaction with mouse E. coli fimF mutant interaction with mouse E. coli fimD mutant interaction with mouse E. coli fimC mutant interaction with mouse E. coli fimI mutant interaction with mouse E. coli fimB mutant interaction with mouse E. coli manB mutant interaction with mouse E. coli waaW mutant interaction with chicken E. coli kpsC mutant interaction with mouse E. coli pyrD mutant interaction with mouse E. coli phoU mutant interaction with mouse E. coli map mutant interaction with cattle E. coli Z3341 mutant interaction with cattle E. coli Z0275 mutant interaction with cattle E. coli sanA mutant interaction with cattle E. coli mglA mutant interaction with cattle E. coli Z0390 mutant interaction with cattle E. coli Z3496 mutant interaction with cattle E. coli Z0469 mutant interaction with cattle E. coli rdgC mutant interaction with cattle E. coli Z0609 mutant interaction with cattle E. coli evgS mutant interaction with cattle E. coli yfhH mutant interaction with cattle E. coli trxC mutant interaction with cattle E. coli Z0990 mutant interaction with cattle E. coli Z3950 mutant interaction with cattle E. coli recD mutant interaction with cattle E. coli kduI mutant interaction with cattle E. coli Z4200 mutant interaction with cattle E. coli Z3635 mutant interaction with cattle E. coli Z4282 mutant interaction with cattle E. coli speA mutant interaction with cattle E. coli Z4318 mutant interaction with cattle E. coli pitB mutant interaction with cattle E. coli Z1126 mutant interaction with cattle E. coli Z1129 mutant interaction with cattle E. coli tdcE mutant interaction with cattle E. coli Z1182 mutant interaction with cattle E. coli Z1202 mutant interaction with cattle E. coli trxB mutant interaction with cattle E. coli Z1328 mutant interaction with cattle E. coli yqeJ mutant interaction with cattle E. coli ymcC mutant interaction with cattle E. coli pgaA mutant interaction with cattle E. coli agaB mutant interaction with cattle E. coli mdoC mutant interaction with cattle E. coli ypjA mutant interaction with cattle E. coli serA mutant interaction with cattle E. coli Z1829 mutant interaction with cattle E. coli Z5946 mutant interaction with cattle E. coli fimE mutant interaction with cattle E. coli yjhS mutant interaction with cattle E. coli Z5886 mutant interaction with cattle E. coli nrdD mutant interaction with cattle E. coli Z1930 mutant interaction with cattle E. coli yjeJ mutant interaction with cattle E. coli yjcF mutant interaction with cattle E. coli arp mutant interaction with cattle E. coli Z5444 mutant interaction with cattle E. coli ilvG mutant interaction with cattle E. coli narG mutant interaction with cattle E. coli Z2056 mutant interaction with cattle E. coli Z2142 mutant interaction with cattle E. coli Z2144 mutant interaction with cattle E. coli Z2149 mutant interaction with cattle E. coli Z2176 mutant interaction with cattle E. coli ydeK mutant interaction with cattle E. coli Z2203 mutant interaction with cattle E. coli Z2205 mutant interaction with cattle E. coli Z2207 mutant interaction with cattle E. coli yddA mutant interaction with cattle E. coli Z5214 mutant interaction with cattle E. coli Z5212 mutant interaction with cattle E. coli Z5131 mutant interaction with cattle E. coli escC mutant interaction with cattle E. coli Z5121 mutant interaction with cattle E. coli escV mutant interaction with cattle E. coli escN mutant interaction with rabbit E. coli sepQ mutant interaction with cattle E. coli Z5114 mutant interaction with cattle E. coli eae mutant interaction with human E. coli espB mutant interaction with human E. coli yibD mutant interaction with cattle E. coli rhsA mutant interaction with cattle E. coli hrpA mutant interaction with cattle E. coli Z2318 mutant interaction with cattle E. coli dctA mutant interaction with cattle E. coli Z2368 mutant interaction with cattle E. coli yhiJ mutant interaction with cattle E. coli Z3620 mutant interaction with cattle E. coli ycjV mutant interaction with cattle E. coli acnA mutant interaction with cattle E. coli trpB mutant interaction with cattle E. coli Z6010 mutant interaction with cattle E. coli trkA mutant interaction with cattle E. coli Z2702 mutant interaction with cattle E. coli Z2749 mutant interaction with cattle E. coli Z2751 mutant interaction with cattle E. coli celF mutant interaction with cattle E. coli cspC mutant interaction with cattle E. coli Z2984 mutant interaction with cattle E. coli sdiA mutant interaction with cattle E. coli Z3023 mutant interaction with cattle E. coli Z3026 mutant interaction with cattle E. coli Z3062 mutant interaction with cattle E. coli manB mutant interaction with cattle E. coli manC mutant interaction with cattle E. coli fcI mutant interaction with cattle E. coli wbdP mutant interaction with cattle E. coli per mutant interaction with cattle E. coli espP mutant interaction with cattle E. coli tsh mutant interaction with chicken E. coli EHEC-hlyA mutant interaction with cattle Salmonella spp. invE mutant interaction with human Salmonella spp. waaP mutant interaction with mouse V. cholerae pykF mutant interaction with mouse V. cholerae fbp mutant interaction with mouse V. cholerae cyaA mutant interaction with mouse V. cholerae fur mutant interaction with mouse V. cholerae mukB mutant interaction with mouse V. cholerae frdC mutant interaction with mouse V. cholerae rfbB mutant interaction with mouse V. cholerae ubiC mutant interaction with mouse V. cholerae tolB mutant interaction with mouse V. cholerae acpS mutant interaction with mouse V. cholerae tcpT mutant interaction with mouse V. cholerae toxR mutant interaction with mouse V. cholerae carB mutant interaction with mouse V. cholerae gshB mutant interaction with mouse V. cholerae nqrE mutant interaction with mouse V. cholerae fabG mutant interaction with mouse V. cholerae tcpN/toxT mutant interaction with mouse V. cholerae purD mutant interaction with mouse V. cholerae rpoS mutant interaction with mouse V. cholerae trpG mutant interaction with mouse V. cholerae purF mutant interaction with mouse V. cholerae purL mutant interaction with mouse V. cholerae rpoE mutant interaction with mouse V. cholerae relA mutant interaction with mouse V. cholerae lysA mutant interaction with mouse V. cholerae aceF mutant interaction with mouse V. cholerae tcpA mutant interaction with mouse V. cholerae acfC mutant interaction with mouse V. cholerae rfbL mutant interaction with mouse V. cholerae nqrF mutant interaction with mouse V. cholerae galM mutant interaction with mouse V. cholerae recO mutant interaction with mouse V. cholerae ilvD mutant interaction with mouse V. cholerae deoC mutant interaction with mouse V. cholerae acfB mutant interaction with mouse V. cholerae purK mutant interaction with mouse V. cholerae pta mutant interaction with mouse V. cholerae acfA mutant interaction with mouse V. cholerae galK mutant interaction with mouse V. cholerae carA mutant interaction with mouse V. cholerae sspA mutant interaction with mouse V. cholerae bioB mutant interaction with mouse V. cholerae irgA mutant interaction with mouse V. cholerae tcpE mutant interaction with mouse V. cholerae zwf mutant interaction with mouse V. cholerae ydbK mutant interaction with mouse V. cholerae phaC mutant interaction with mouse V. cholerae VCA0688 mutant interaction with mouse V. cholerae VCA0910 mutant interaction with mouse V. cholerae VCA0006 mutant interaction with mouse V. cholerae VCA0903 mutant interaction with mouse V. cholerae VCA0896 mutant interaction with mouse V. cholerae VCA0600 mutant interaction with mouse V. cholerae VCA0578 mutant interaction with mouse V. cholerae VCA0530 mutant interaction with mouse V. cholerae VCA0583 mutant interaction with mouse V. cholerae VCA0930 mutant interaction with mouse V. cholerae VC0028 mutant interaction with mouse V. cholerae VC2426 mutant interaction with mouse V. cholerae VC2433 mutant interaction with mouse V. cholerae tolC mutant interaction with mouse V. cholerae VC2437 mutant interaction with mouse V. cholerae VC2453 mutant interaction with mouse V. cholerae VC2455 mutant interaction with mouse V. cholerae VC2390 mutant interaction with mouse V. cholerae VC2295 mutant interaction with mouse V. cholerae VC2320 mutant interaction with mouse V. cholerae VC2290 mutant interaction with mouse V. cholerae VC2291 mutant interaction with mouse V. cholerae VC2206 mutant interaction with mouse V. cholerae VC2030 mutant interaction with mouse V. cholerae VC2042 mutant interaction with mouse V. cholerae VC2052 mutant interaction with mouse V. cholerae VC2067 mutant interaction with mouse V. cholerae VC1887 mutant interaction with mouse V. cholerae VC1771 mutant interaction with mouse V. cholerae VC1715 mutant interaction with mouse V. cholerae VC1716 mutant interaction with mouse V. cholerae VC1639 mutant interaction with mouse V. cholerae VC1675 mutant interaction with mouse V. cholerae VC1595 mutant interaction with mouse V. cholerae VC0257 mutant interaction with mouse V. cholerae VC0965 mutant interaction with mouse V. cholerae VC1004 mutant interaction with mouse V. cholerae VC1012 mutant interaction with mouse V. cholerae VC0251 mutant interaction with mouse V. cholerae VC0249 mutant interaction with mouse V. cholerae VC0250 mutant interaction with mouse V. cholerae VC1021 mutant interaction with mouse V. cholerae VC1075 mutant interaction with mouse V. cholerae VC1098 mutant interaction with mouse V. cholerae VC0051 mutant interaction with mouse V. cholerae VC0032 mutant interaction with mouse V. cholerae VC0036 mutant interaction with mouse V. cholerae VC0826 mutant interaction with mouse V. cholerae VC0828 mutant interaction with mouse V. cholerae VC0831 mutant interaction with mouse V. cholerae VC0835 mutant interaction with mouse V. cholerae VC0836 mutant interaction with mouse V. cholerae VC0837 mutant interaction with mouse V. cholerae VC0869 mutant interaction with mouse V. cholerae VC0247 mutant interaction with mouse V. cholerae VC0244 mutant interaction with mouse V. cholerae VC1162 mutant interaction with mouse V. cholerae VC1173 mutant interaction with mouse V. cholerae VC0192 mutant interaction with mouse V. cholerae VC0212 mutant interaction with mouse V. cholerae VC0242 mutant interaction with mouse V. cholerae VC0243 mutant interaction with mouse V. cholerae VC0239 mutant interaction with mouse V. cholerae VC1380 mutant interaction with mouse V. cholerae VC0238 mutant interaction with mouse V. cholerae VC0260 mutant interaction with mouse V. cholerae hfq mutant interaction with mouse V. cholerae VC0459 mutant interaction with mouse V. cholerae VC0468 mutant interaction with mouse V. cholerae VC2506 mutant interaction with mouse V. cholerae VC0259 mutant interaction with mouse V. cholerae VC0485 mutant interaction with mouse V. cholerae VC0125 mutant interaction with mouse V. cholerae VC0596 mutant interaction with mouse V. cholerae glmM mutant interaction with mouse V. cholerae VC0647 mutant interaction with mouse V. cholerae VC2544 mutant interaction with mouse V. cholerae VC2647 mutant interaction with mouse V. cholerae VC2660 mutant interaction with mouse V. cholerae VC0724 mutant interaction with mouse V. cholerae VC0727 mutant interaction with mouse V. cholerae VC0523 mutant interaction with mouse V. cholerae VC0095 mutant interaction with mouse V. cholerae VC0132 mutant interaction with mouse Salmonella spp. slyA mutant interaction with mouse Salmonella spp. sodC mutant interaction with mouse Salmonella spp. sopE mutant interaction with mouse Salmonella spp. sopA mutant interaction with cattle Salmonella spp. sopB mutant interaction with cattle Salmonella spp. PSLT072 mutant interaction with mouse Salmonella spp. spvR mutant interaction with mouse Salmonella spp. spvB mutant interaction with mouse Salmonella spp. spvA mutant interaction with mouse Salmonella spp. spvC mutant interaction with mouse Salmonella spp. spvD mutant interaction with mouse Salmonella spp. pefC mutant interaction with mouse Salmonella spp. STM0016 mutant interaction with mouse Salmonella spp. STM0030 mutant interaction with mouse Salmonella spp. dgt mutant interaction with mouse Salmonella spp. yafS mutant interaction with mouse Salmonella spp. STM0298 mutant interaction with mouse Salmonella spp. dinP mutant interaction with mouse Salmonella spp. cyoB mutant interaction with mouse Salmonella spp. clpP mutant interaction with mouse Salmonella spp. gip mutant interaction with mouse Salmonella spp. STM0520 mutant interaction with mouse Salmonella spp. allD mutant interaction with mouse Salmonella spp. fimA mutant interaction with mouse Salmonella spp. fimW mutant interaction with mouse Salmonella spp. nfnB mutant interaction with mouse Salmonella spp. cspE mutant interaction with mouse Salmonella spp. STM0723 mutant interaction with mouse Salmonella spp. slrP mutant interaction with mouse Salmonella spp. STM0972 mutant interaction with mouse Salmonella spp. focA mutant interaction with mouse Salmonella spp. STM1002 mutant interaction with mouse Salmonella spp. sseI mutant interaction with mouse Salmonella spp. ycbG mutant interaction with mouse Salmonella spp. pipD mutant interaction with mouse Salmonella spp. copS mutant interaction with mouse Salmonella spp. csgF mutant interaction with mouse Salmonella spp. csgD mutant interaction with mouse Salmonella spp. csgC mutant interaction with mouse Salmonella spp. solA mutant interaction with mouse Salmonella spp. sifA mutant interaction with mouse Salmonella spp. sifA mutant interaction with mouse epithelial cell Salmonella spp. pagC mutant interaction with mouse Salmonella spp. yeaJ mutant interaction with mouse Salmonella spp. nlpC mutant interaction with mouse Salmonella spp. ydiK mutant interaction with mouse Salmonella spp. ssaC mutant interaction with mouse Salmonella spp. ssaC mutant interaction with mouse macrophage cell Salmonella spp. ssaE mutant interaction with mouse Salmonella spp. sseB mutant interaction with mouse Salmonella spp. sseE mutant interaction with mouse Salmonella spp. sseE mutant interaction with mouse macrophage cell Salmonella spp. sseF mutant interaction with mouse Salmonella spp. sseF mutant interaction with mouse macrophage cell Salmonella spp. sseG mutant interaction with mouse Salmonella spp. sseG mutant interaction with mouse macrophage cell Salmonella spp. ssaN mutant interaction with mouse Salmonella spp. ssaU mutant interaction with mouse Salmonella spp. ydgF mutant interaction with mouse Salmonella spp. STM1549 mutant interaction with mouse Salmonella spp. yddX mutant interaction with mouse Salmonella spp. STM1583 mutant interaction with mouse Salmonella spp. sseJ mutant interaction with mouse Salmonella spp. sseJ mutant interaction with mouse epithelial cell Salmonella spp. STM1669 mutant interaction with mouse Salmonella spp. yciH mutant interaction with mouse Salmonella spp. fadD mutant interaction with mouse Salmonella spp. cspC mutant interaction with mouse Salmonella spp. znuA mutant interaction with mouse Salmonella spp. znuC mutant interaction with mouse Salmonella spp. znuB mutant interaction with mouse Salmonella spp. STM1934 mutant interaction with mouse Salmonella spp. uvrY mutant interaction with mouse Salmonella spp. uvrY mutant interaction with mouse epithelial cell Salmonella spp. uvrY mutant interaction with mouse macrophage cell Salmonella spp. fliQ mutant interaction with mouse Salmonella spp. udg mutant interaction with mouse Salmonella spp. rfbP mutant interaction with mouse Salmonella spp. rfbM mutant interaction with mouse Salmonella spp. rfbC mutant interaction with mouse Salmonella spp. rfbA mutant interaction with mouse Salmonella spp. rfbD mutant interaction with mouse Salmonella spp. rfbB mutant interaction with mouse Salmonella spp. galF mutant interaction with mouse Salmonella spp. wcaM mutant interaction with mouse Salmonella spp. yegQ mutant interaction with mouse Salmonella spp. STM2137 mutant interaction with mouse Salmonella spp. stcD mutant interaction with mouse Salmonella spp. stcC mutant interaction with mouse Salmonella spp. bglX mutant interaction with mouse Salmonella spp. yeiA mutant interaction with mouse Salmonella spp. STM2197 mutant interaction with mouse Salmonella spp. STM2373 mutant interaction with mouse Salmonella spp. shdA mutant interaction with mouse Salmonella spp. ratB mutant interaction with mouse Salmonella spp. yfhL mutant interaction with mouse Salmonella spp. STM2585 mutant interaction with mouse Salmonella spp. STM2680 mutant interaction with mouse Salmonella spp. STM2689 mutant interaction with mouse Salmonella spp. mig-14 mutant interaction with mouse Salmonella spp. yqaE mutant interaction with mouse Salmonella spp. hilA mutant interaction with mouse Salmonella spp. invC mutant interaction with chicken Salmonella spp. invA mutant interaction with chicken Salmonella spp. sopD mutant interaction with cattle Salmonella spp. STM3036 mutant interaction with mouse Salmonella spp. STM3128 mutant interaction with mouse Salmonella spp. STM3192 mutant interaction with mouse Salmonella spp. sspA mutant interaction with cattle Salmonella spp. crp mutant interaction with mouse Salmonella spp. envZ mutant interaction with mouse Salmonella spp. yiaO mutant interaction with mouse Salmonella spp. STM3690 mutant interaction with mouse Salmonella spp. yibD mutant interaction with mouse Salmonella spp. rfaZ mutant interaction with mouse Salmonella spp. misL mutant interaction with mouse Salmonella spp. marT mutant interaction with mouse Salmonella spp. ibpA mutant interaction with mouse Salmonella spp. torD mutant interaction with mouse Salmonella spp. STM3907 mutant interaction with mouse Salmonella spp. ppiC mutant interaction with mouse Salmonella spp. trxA mutant interaction with mouse Salmonella spp. yigG mutant interaction with mouse Salmonella spp. STM3980 mutant interaction with mouse Salmonella spp. yneB mutant interaction with mouse Salmonella spp. yneC mutant interaction with mouse Salmonella spp. STM4155 mutant interaction with mouse Salmonella spp. STM4158 mutant interaction with mouse Salmonella spp. yjaG mutant interaction with mouse Salmonella spp. purD mutant interaction with mouse Salmonella spp. metA mutant interaction with mouse Salmonella spp. STM4206 mutant interaction with mouse Salmonella spp. STM4260 mutant interaction with mouse Salmonella spp. STM4261 mutant interaction with mouse Salmonella spp. yjdB mutant interaction with mouse Salmonella spp. phoN mutant interaction with mouse Salmonella spp. yjeJ mutant interaction with mouse Salmonella spp. idnK mutant interaction with mouse Salmonella spp. sthA mutant interaction with mouse H. influenzae dam mutant interaction with human H. influenzae dam mutant interaction with human epithelial cell H. influenzae pgmB mutant interaction with human H. influenzae pgmB mutant interaction with human epithelial cell H. influenzae dsbA mutant interaction with mouse H. influenzae hbpA mutant interaction with mouse H. influenzae licD mutant interaction with mouse H. influenzae ptsI mutant interaction with mouse H. influenzae arcA mutant interaction with mouse H. influenzae ompA mutant interaction with human Hantavirus HTNVsMgp1 mutant interaction with mouse N. meningitidis pilX mutant interaction with human N. meningitidis pilX mutant interaction with human epithelial cell N. meningitidis pilQ mutant interaction with human N. meningitidis tonB mutant interaction with human N. meningitidis tonB mutant interaction with human epithelial cell N. meningitidis pilF mutant interaction with human N. meningitidis NMA0798 mutant interaction with mouse N. meningitidis NMB0103 mutant interaction with human N. meningitidis lpxA mutant interaction with mouse N. meningitidis NMB0313 mutant interaction with human N. meningitidis NMB0541 mutant interaction with human N. meningitidis pgm mutant interaction with mouse N. meningitidis rfaD mutant interaction with mouse N. meningitidis NMB1012 mutant interaction with human N. meningitidis NMB1829 mutant interaction with human N. meningitidis NMB1726 mutant interaction with human N. meningitidis NMB1638 mutant interaction with human N. meningitidis NMB1638 mutant interaction with human epithelial cell N. meningitidis NMB1966 mutant interaction with human N. meningitidis NMB1966 mutant interaction with human epithelial cell N. meningitidis NMB1966 mutant interaction with mouse N. meningitidis NMB1966 mutant interaction with mouse epithelial cell Rabies virus RABVgp1 mutant interaction with mouse Rabies virus RABVgp2 mutant interaction with mouse Rabies virus RABVgp3 mutant interaction with mouse Rabies virus RABVgp4 mutant interaction with mouse Rotavirus VP4 mutant interaction with mouse S. pneumoniae iga mutant interaction with mouse S. pneumoniae regR mutant interaction with mouse S. pneumoniae spxB mutant interaction with rabbit S. pneumoniae nox mutant interaction with mouse S. pneumoniae ccpA mutant interaction with mouse S. pneumoniae luxS mutant interaction with mouse S. pneumoniae ply mutant interaction with mouse S. pneumoniae zmpB mutant interaction with mouse S. pneumoniae pspC mutant interaction with mouse S. pneumoniae cbpG mutant interaction with human S. pneumoniae cbpG mutant interaction with human epithelial cell S. pneumoniae nanA mutant interaction with mouse S. pneumoniae sodA mutant interaction with mouse S. pneumoniae pspA mutant interaction with mouse S. pneumoniae pgdA mutant interaction with mouse S. pneumoniae lytA mutant interaction with mouse S. pneumoniae ciaR mutant interaction with mouse S. pneumoniae glnA mutant interaction with human S. pneumoniae glnA mutant interaction with human epithelial cell S. pneumoniae codY mutant interaction with mouse S. pneumoniae mutX mutant interaction with mouse S. pneumoniae clpP mutant interaction with mouse S. pneumoniae bacA mutant interaction with mouse S. pneumoniae cbpE mutant interaction with human S. pneumoniae cbpE mutant interaction with human epithelial cell S. pneumoniae purN mutant interaction with mouse S. pneumoniae pepC mutant interaction with mouse S. pneumoniae psaC mutant interaction with mouse S. pneumoniae purB mutant interaction with mouse S. pneumoniae aga mutant interaction with mouse S. pneumoniae potD mutant interaction with mouse S. pneumoniae pavA mutant interaction with mouse S. pneumoniae psaB mutant interaction with mouse S. pneumoniae pbp1A mutant interaction with mouse S. pneumoniae glnP mutant interaction with mouse S. pneumoniae psaA mutant interaction with mouse S. pneumoniae radA mutant interaction with mouse S. pneumoniae SP_1976 mutant interaction with mouse S. pneumoniae SP_2239 mutant interaction with mouse S. pneumoniae SP_0049 mutant interaction with mouse S. pneumoniae purH mutant interaction with mouse S. pneumoniae SP_0057 mutant interaction with mouse S. pneumoniae SP_0063 mutant interaction with mouse S. pneumoniae SP_2231 mutant interaction with mouse S. pneumoniae SP_0071 mutant interaction with mouse S. pneumoniae SP_0078 mutant interaction with mouse S. pneumoniae SP_2210 mutant interaction with mouse S. pneumoniae SP_0092 mutant interaction with mouse S. pneumoniae SP_0095 mutant interaction with mouse S. pneumoniae SP_0100 mutant interaction with mouse S. pneumoniae SP_0102 mutant interaction with mouse S. pneumoniae SP_0110 mutant interaction with mouse S. pneumoniae SP_0117 mutant interaction with mouse S. pneumoniae SP_0121 mutant interaction with mouse S. pneumoniae SP_0128 mutant interaction with mouse S. pneumoniae SP_0136 mutant interaction with mouse S. pneumoniae SP_0141 mutant interaction with mouse S. pneumoniae SP_0145 mutant interaction with mouse S. pneumoniae SP_0146 mutant interaction with mouse S. pneumoniae SP_0150 mutant interaction with mouse S. pneumoniae SP_0156 mutant interaction with mouse S. pneumoniae SP_0157 mutant interaction with mouse S. pneumoniae SP_0160 mutant interaction with mouse S. pneumoniae SP_1964 mutant interaction with mouse S. pneumoniae SP_0177 mutant interaction with mouse S. pneumoniae SP_0198 mutant interaction with mouse S. pneumoniae SP_0199 mutant interaction with mouse S. pneumoniae SP_0240 mutant interaction with mouse S. pneumoniae SP_0242 mutant interaction with mouse S. pneumoniae SP_0246 mutant interaction with mouse S. pneumoniae SP_0247 mutant interaction with mouse S. pneumoniae SP_0251 mutant interaction with mouse S. pneumoniae gldA mutant interaction with mouse S. pneumoniae leuS mutant interaction with mouse S. pneumoniae SP_0265 mutant interaction with mouse S. pneumoniae SP_0267 mutant interaction with mouse S. pneumoniae SP_0268 mutant interaction with mouse S. pneumoniae polC mutant interaction with mouse S. pneumoniae SP_0298 mutant interaction with mouse S. pneumoniae SP_0306 mutant interaction with mouse S. pneumoniae SP_0312 mutant interaction with mouse S. pneumoniae SP_0314 mutant interaction with mouse S. pneumoniae SP_0320 mutant interaction with mouse S. pneumoniae SP_0332 mutant interaction with mouse S. pneumoniae SP_0338 mutant interaction with mouse S. pneumoniae SP_2175 mutant interaction with mouse S. pneumoniae SP_2164 mutant interaction with mouse S. pneumoniae SP_2162 mutant interaction with mouse S. pneumoniae SP_2145 mutant interaction with mouse S. pneumoniae SP_2143 mutant interaction with mouse S. pneumoniae SP_2128 mutant interaction with mouse S. pneumoniae SP_2108 mutant interaction with mouse S. pneumoniae SP_2101 mutant interaction with mouse S. pneumoniae SP_2098 mutant interaction with mouse S. pneumoniae SP_2095 mutant interaction with mouse S. pneumoniae SP_2076 mutant interaction with mouse S. pneumoniae SP_1952 mutant interaction with mouse S. pneumoniae SP_0377 mutant interaction with mouse S. pneumoniae SP_0385 mutant interaction with mouse S. pneumoniae SP_0396 mutant interaction with mouse S. pneumoniae SP_0445 mutant interaction with mouse S. pneumoniae SP_0454 mutant interaction with mouse S. pneumoniae SP_0461 mutant interaction with mouse S. pneumoniae SP_0468 mutant interaction with mouse S. pneumoniae SP_0474 mutant interaction with mouse S. pneumoniae SP_0478 mutant interaction with mouse S. pneumoniae SP_0479 mutant interaction with mouse S. pneumoniae SP_0492 mutant interaction with mouse S. pneumoniae SP_0494 mutant interaction with mouse S. pneumoniae SP_0498 mutant interaction with mouse S. pneumoniae SP_0510 mutant interaction with mouse S. pneumoniae blpA mutant interaction with mouse S. pneumoniae SP_0571 mutant interaction with mouse S. pneumoniae SP_0586 mutant interaction with mouse S. pneumoniae SP_0595 mutant interaction with mouse S. pneumoniae SP_0600 mutant interaction with mouse S. pneumoniae SP_0614 mutant interaction with mouse S. pneumoniae SP_0622 mutant interaction with mouse S. pneumoniae SP_0633 mutant interaction with mouse S. pneumoniae SP_0641 mutant interaction with mouse S. pneumoniae SP_0645 mutant interaction with mouse S. pneumoniae SP_0648 mutant interaction with mouse S. pneumoniae SP_0655 mutant interaction with mouse S. pneumoniae SP_0661 mutant interaction with mouse S. pneumoniae SP_0663 mutant interaction with mouse S. pneumoniae SP_0664 mutant interaction with mouse S. pneumoniae SP_0665 mutant interaction with mouse S. pneumoniae SP_0686 mutant interaction with mouse S. pneumoniae SP_0690 mutant interaction with mouse S. pneumoniae SP_0719 mutant interaction with mouse S. pneumoniae SP_0720 mutant interaction with mouse S. pneumoniae SP_0726 mutant interaction with mouse S. pneumoniae SP_0728 mutant interaction with mouse S. pneumoniae SP_0729 mutant interaction with mouse S. pneumoniae SP_0766 mutant interaction with mouse S. pneumoniae SP_0767 mutant interaction with mouse S. pneumoniae SP_0774 mutant interaction with mouse S. pneumoniae SP_0785 mutant interaction with mouse S. pneumoniae SP_0789 mutant interaction with mouse S. pneumoniae SP_0797 mutant interaction with mouse S. pneumoniae SP_0807 mutant interaction with mouse S. pneumoniae SP_0829 mutant interaction with mouse S. pneumoniae SP_0842 mutant interaction with mouse S. pneumoniae SP_0856 mutant interaction with mouse S. pneumoniae SP_0886 mutant interaction with mouse S. pneumoniae SP_0887 mutant interaction with mouse S. pneumoniae SP_0892 mutant interaction with mouse S. pneumoniae SP_0916 mutant interaction with mouse S. pneumoniae SP_0927 mutant interaction with mouse S. pneumoniae SP_0939 mutant interaction with mouse S. pneumoniae SP_0943 mutant interaction with mouse S. pneumoniae SP_1889 mutant interaction with mouse S. pneumoniae SP_1898 mutant interaction with mouse S. pneumoniae SP_1896 mutant interaction with mouse S. pneumoniae SP_1890 mutant interaction with mouse S. pneumoniae SP_1891 mutant interaction with mouse S. pneumoniae SP_1879 mutant interaction with mouse S. pneumoniae SP_1869 mutant interaction with mouse S. pneumoniae SP_1861 mutant interaction with mouse S. pneumoniae SP_1859 mutant interaction with mouse S. pneumoniae SP_1856 mutant interaction with mouse S. pneumoniae SP_1855 mutant interaction with mouse S. pneumoniae SP_1854 mutant interaction with mouse S. pneumoniae SP_1847 mutant interaction with mouse S. pneumoniae SP_1830 mutant interaction with mouse S. pneumoniae SP_1817 mutant interaction with mouse S. pneumoniae SP_1800 mutant interaction with mouse S. pneumoniae SP_1816 mutant interaction with mouse S. pneumoniae trpD mutant interaction with mouse S. pneumoniae SP_1793 mutant interaction with mouse S. pneumoniae SP_1770 mutant interaction with mouse S. pneumoniae SP_1780 mutant interaction with mouse S. pneumoniae SP_1771 mutant interaction with mouse S. pneumoniae SP_1779 mutant interaction with mouse S. pneumoniae SP_1772 mutant interaction with mouse S. pneumoniae SP_1760 mutant interaction with mouse S. pneumoniae SP_1717 mutant interaction with mouse S. pneumoniae SP_1715 mutant interaction with mouse S. pneumoniae SP_1706 mutant interaction with mouse S. pneumoniae SP_1652 mutant interaction with mouse S. pneumoniae SP_1654 mutant interaction with mouse S. pneumoniae SP_1646 mutant interaction with mouse S. pneumoniae SP_1645 mutant interaction with mouse S. pneumoniae SP_1636 mutant interaction with mouse S. pneumoniae SP_1633 mutant interaction with mouse S. pneumoniae SP_1591 mutant interaction with mouse S. pneumoniae SP_1580 mutant interaction with mouse S. pneumoniae SP_1544 mutant interaction with mouse S. pneumoniae SP_1538 mutant interaction with mouse S. pneumoniae SP_1529 mutant interaction with mouse S. pneumoniae SP_1518 mutant interaction with mouse S. pneumoniae SP_1483 mutant interaction with mouse S. pneumoniae SP_1433 mutant interaction with mouse S. pneumoniae SP_1434 mutant interaction with mouse S. pneumoniae SP_1431 mutant interaction with mouse S. pneumoniae SP_1400 mutant interaction with mouse S. pneumoniae SP_1399 mutant interaction with mouse S. pneumoniae SP_1398 mutant interaction with mouse S. pneumoniae SP_1396 mutant interaction with mouse S. pneumoniae SP_1378 mutant interaction with mouse S. pneumoniae SP_1382 mutant interaction with mouse S. pneumoniae aroD mutant interaction with mouse S. pneumoniae SP_0978 mutant interaction with mouse S. pneumoniae SP_0979 mutant interaction with mouse S. pneumoniae SP_1001 mutant interaction with mouse S. pneumoniae SP_1003 mutant interaction with mouse S. pneumoniae SP_1018 mutant interaction with mouse S. pneumoniae SP_1023 mutant interaction with mouse S. pneumoniae SP_1029 mutant interaction with mouse S. pneumoniae SP_1032 mutant interaction with mouse S. pneumoniae SP_1040 mutant interaction with mouse S. pneumoniae SP_1043 mutant interaction with mouse S. pneumoniae SP_1045 mutant interaction with mouse S. pneumoniae SP_1089 mutant interaction with mouse S. pneumoniae SP_1111 mutant interaction with mouse S. pneumoniae SP_1112 mutant interaction with mouse S. pneumoniae SP_1115 mutant interaction with mouse S. pneumoniae SP_1118 mutant interaction with mouse S. pneumoniae SP_1121 mutant interaction with mouse S. pneumoniae SP_1127 mutant interaction with mouse S. pneumoniae SP_1143 mutant interaction with mouse S. pneumoniae SP_1153 mutant interaction with mouse S. pneumoniae SP_1154 mutant interaction with mouse S. pneumoniae rnhB mutant interaction with mouse S. pneumoniae SP_1174 mutant interaction with mouse S. pneumoniae SP_1175 mutant interaction with mouse S. pneumoniae SP_1193 mutant interaction with mouse S. pneumoniae SP_1202 mutant interaction with mouse S. pneumoniae SP_1278 mutant interaction with mouse S. pneumoniae SP_1281 mutant interaction with mouse S. pneumoniae gidB mutant interaction with mouse S. pneumoniae SP_1286 mutant interaction with mouse S. pneumoniae SP_1292 mutant interaction with mouse S. pneumoniae SP_1321 mutant interaction with mouse S. pneumoniae SP_1328 mutant interaction with mouse S. pneumoniae SP_1343 mutant interaction with mouse S. pneumoniae SP_1344 mutant interaction with mouse S. pneumoniae SP_1941 mutant interaction with mouse S. pneumoniae SP_1970 mutant interaction with mouse S. pneumoniae SP_1998 mutant interaction with mouse S. pneumoniae SP_2201 mutant interaction with mouse S. pneumoniae SP_2236 mutant interaction with mouse S. pneumoniae SP_1923 mutant interaction with mouse S. pneumoniae SP_1956 mutant interaction with mouse S. pneumoniae SP_2190 mutant interaction with mouse S. pneumoniae SP_2176 mutant interaction with mouse S. pneumoniae SP_2182 mutant interaction with mouse S. pneumoniae SP_2167 mutant interaction with mouse S. pneumoniae SP_2159 mutant interaction with mouse S. pneumoniae SP_2146 mutant interaction with mouse S. pneumoniae SP_2142 mutant interaction with mouse S. pneumoniae SP_2136 mutant interaction with mouse S. pneumoniae SP_2131 mutant interaction with mouse S. pneumoniae SP_2105 mutant interaction with mouse S. pneumoniae SP_2086 mutant interaction with mouse S. pneumoniae SP_2060 mutant interaction with mouse S. pneumoniae SP_2052 mutant interaction with mouse S. pneumoniae SP_1939 mutant interaction with mouse S. pneumoniae SP_2002 mutant interaction with mouse S. pneumoniae SP_2017 mutant interaction with mouse S. pneumoniae SP_2022 mutant interaction with mouse S. pneumoniae SP_2039 mutant interaction with mouse C. diphtheriae DIP2010 mutant interaction with human C. diphtheriae DIP2010 mutant interaction with human epithelial cell C. diphtheriae DIP2011 mutant interaction with human C. diphtheriae DIP2011 mutant interaction with human epithelial cell H. pylori homB mutant interaction with human H. pylori homB mutant interaction with human epithelial cell H. pylori hopZ mutant interaction with human H. pylori hopZ mutant interaction with human epithelial cell H. pylori horB mutant interaction with mouse Salmonella spp. fur mutant interaction with mouse Salmonella spp. rpoS mutant interaction with mouse Salmonella spp. relA mutant interaction with mouse Salmonella spp. htrA mutant interaction with mouse Salmonella spp. ompR mutant interaction with mouse Salmonella spp. galE mutant interaction with mouse Salmonella spp. hfq mutant interaction with mouse Salmonella spp. phoP mutant interaction with mouse Salmonella spp. rfaL mutant interaction with mouse Salmonella spp. rfaG mutant interaction with mouse Salmonella spp. spoT mutant interaction with mouse Salmonella spp. aroA mutant interaction with mouse Salmonella spp. iacP mutant interaction with chicken Salmonella spp. sipD mutant interaction with chicken Salmonella spp. sipB mutant interaction with chicken Salmonella spp. ssrA mutant interaction with mouse Salmonella spp. sseA mutant interaction with mouse Salmonella spp. aroD mutant interaction with mouse Rotavirus RVA_s10gp1 mutant interaction with mouse S. pneumoniae piaA mutant interaction with mouse S. pneumoniae igA mutant interaction with mouse S. pneumoniae cpsC mutant interaction with mouse S. pneumoniae purL mutant interaction with mouse S. pneumoniae cpsB mutant interaction with mouse S. pneumoniae zmpC mutant interaction with mouse S. pneumoniae ritR mutant interaction with mouse E. coli eaeA mutant interaction with human E. coli espH mutant interaction with rabbit E. coli FliC mutant interaction with cattle L. monocytogenes LMHCC_0048 mutant interaction with mouse L. monocytogenes LMHCC_0614 mutant interaction with mouse L. monocytogenes srtB mutant interaction with mouse L. monocytogenes LMHCC_2768 mutant interaction with mouse L. monocytogenes LMHCC_2601 mutant interaction with mouse S. pneumoniae htrA mutant interaction with mouse S. pneumoniae psrP mutant interaction with human S. pneumoniae psrP mutant interaction with human epithelial cell S. pneumoniae psrP mutant interaction with mouse S. pneumoniae psrP mutant interaction with mouse epithelial cell B. anthracis nos mutant interaction with mouse B. anthracis asbA mutant interaction with mouse B. anthracis asbA mutant interaction with mouse macrophage cell B. anthracis sodA2 mutant interaction with mouse B. anthracis sodA1 mutant interaction with mouse B. anthracis acpB mutant interaction with mouse B. anthracis capD mutant interaction with mouse B. anthracis capE mutant interaction with mouse B. pseudomallei GBP346_A0742 mutant interaction with mouse B. pseudomallei mviN mutant interaction with human B. pseudomallei mviN mutant interaction with human epithelial cell B. pseudomallei mviN mutant interaction with hamster B. pseudomallei mviN mutant interaction with hamster epithelial cell B. pseudomallei ppsA mutant interaction with mouse B. pseudomallei rpoE mutant interaction with mouse E. coli espK mutant interaction with cattle E. coli nleA mutant interaction with mouse L. monocytogenes Lm4b_01887 mutant interaction with mouse L. monocytogenes Lm4b_00320 mutant interaction with mouse L. monocytogenes srtA mutant interaction with mouse V. cholerae glyA-1 mutant interaction with mouse V. cholerae ccmF mutant interaction with mouse V. cholerae sucA mutant interaction with mouse C. pneumoniae groEL_3 mutant interaction with mouse Y. enterocolitica yopP mutant interaction with mouse Y. enterocolitica lcrV mutant interaction with mouse Y. enterocolitica yscR mutant interaction with mouse Y. enterocolitica yscU mutant interaction with mouse Y. enterocolitica virG mutant interaction with mouse Y. enterocolitica virF mutant interaction with mouse Y. enterocolitica yscC mutant interaction with mouse Y. enterocolitica yscL mutant interaction with mouse Y. enterocolitica sycH mutant interaction with mouse Y. enterocolitica yadA mutant interaction with mouse B. pertussis bhuR mutant interaction with mouse B. pertussis prn mutant interaction with human B. pertussis prn mutant interaction with human HeLa cell B. pertussis cyaA mutant interaction with mouse B. pertussis brkB mutant interaction with mouse B. pertussis brkA mutant interaction with mouse B. pertussis tonB mutant interaction with mouse B. pertussis exbB mutant interaction with mouse B. pertussis ptxA mutant interaction with mouse B. pertussis ptxB mutant interaction with mouse B. pertussis BP0123 mutant interaction with mouse B. pertussis fim3 mutant interaction with mouse B. pertussis BP3072 mutant interaction with human B. pertussis BP3072 mutant interaction with human macrophage cell B. pertussis dnt mutant interaction with mouse B. pertussis bvgR mutant interaction with mouse B. pertussis fhaB mutant interaction with hamster B. pertussis fimD mutant interaction with mouse B. pertussis fauA mutant interaction with mouse M. gallisepticum MGA_0674 mutant interaction with chicken M. gallisepticum MGA_1107 mutant interaction with chicken Y. pseudotuberculosis pYV0047 mutant interaction with mouse Y. pseudotuberculosis pYV0074 mutant interaction with mouse Y. pseudotuberculosis pYV0084 mutant interaction with mouse Y. pseudotuberculosis pYV0094 mutant interaction with mouse Y. pseudotuberculosis cls mutant interaction with mouse Y. pseudotuberculosis ddhC mutant interaction with mouse Y. pseudotuberculosis gmd mutant interaction with mouse Y. pseudotuberculosis ksgA mutant interaction with mouse Y. pseudotuberculosis wzx mutant interaction with mouse Y. pseudotuberculosis wzxE mutant interaction with mouse Y. pseudotuberculosis hfq mutant interaction with mouse Y. enterocolitica pstC mutant interaction with mouse Y. enterocolitica dnaJ mutant interaction with mouse Y. enterocolitica pspC mutant interaction with mouse Y. enterocolitica horYe mutant interaction with mouse Y. enterocolitica irp1 mutant interaction with mouse Y. enterocolitica galE mutant interaction with mouse Y. enterocolitica manB mutant interaction with mouse Y. enterocolitica manC mutant interaction with mouse Y. enterocolitica rfpB mutant interaction with mouse Y. enterocolitica wbcH mutant interaction with mouse Y. enterocolitica wbcF mutant interaction with mouse Y. enterocolitica wbcC mutant interaction with mouse Y. enterocolitica ddhB mutant interaction with mouse Y. enterocolitica ddhA mutant interaction with mouse Y. enterocolitica supX mutant interaction with mouse Y. enterocolitica degP mutant interaction with mouse Y. enterocolitica nlpD mutant interaction with mouse A. pleuropneumoniae apxIC mutant interaction with mouse A. pleuropneumoniae apxIA mutant interaction with mouse A. pleuropneumoniae luxS mutant interaction with mouse Y. pseudotuberculosis YpsIP31758_3820 mutant interaction with mouse Y. pseudotuberculosis YpsIP31758_3046 mutant interaction with mouse Y. pseudotuberculosis yopM mutant interaction with mouse Y. pseudotuberculosis YPK_3908 mutant interaction with mouse Y. pseudotuberculosis YPTS_0345 mutant interaction with mouse Y. pseudotuberculosis YPTS_4218 mutant interaction with mouse Y. pseudotuberculosis YPTS_4278 mutant interaction with mouse Y. pseudotuberculosis YPTS_4292 mutant interaction with mouse Y. pseudotuberculosis YPTS_4207 mutant interaction with mouse Y. pseudotuberculosis YPTS_4221 mutant interaction with mouse S. equi vicK mutant interaction with mouse S. equi szp mutant interaction with mouse S. equi lgt mutant interaction with mouse L. pneumophila lpa_03874 mutant interaction with mouse L. pneumophila lpa_03874 mutant interaction with mouse macrophage cell L. monocytogenes pLM33_p09 mutant interaction with mouse B. burgdorferi ruvB mutant interaction with mouse B. burgdorferi ruvA mutant interaction with mouse B. burgdorferi BB0098 mutant interaction with mouse B. burgdorferi BB0153 mutant interaction with mouse B. burgdorferi BB0198 mutant interaction with mouse B. burgdorferi BB0210 mutant interaction with mouse B. burgdorferi BB0219 mutant interaction with mouse B. burgdorferi BB0268 mutant interaction with mouse B. burgdorferi BB0323 mutant interaction with mouse B. burgdorferi BB0363 mutant interaction with mouse B. burgdorferi BB0797 mutant interaction with mouse P. aeruginosa algR mutant interaction with mouse P. aeruginosa hfq mutant interaction with mouse P. aeruginosa algC mutant interaction with mouse P. aeruginosa wzz mutant interaction with mouse P. aeruginosa galU mutant interaction with mouse P. aeruginosa phzM mutant interaction with mouse P. aeruginosa fur mutant interaction with mouse P. aeruginosa lasR mutant interaction with mouse P. aeruginosa phzS mutant interaction with mouse P. aeruginosa fliC mutant interaction with mouse P. aeruginosa pvdS mutant interaction with rabbit S. pyogenes SPy_0019 mutant interaction with mouse S. pyogenes nga mutant interaction with mouse S. pyogenes sagA mutant interaction with mouse S. pyogenes lsp mutant interaction with mouse S. pyogenes dltA mutant interaction with human S. pyogenes dltA mutant interaction with human epithelial cell S. pyogenes scpA mutant interaction with mouse S. pyogenes sic mutant interaction with human S. pyogenes mga mutant interaction with human S. pyogenes mga mutant interaction with mouse S. pyogenes speB mutant interaction with mouse S. pyogenes gidA mutant interaction with mouse S. pyogenes SPy_1633 mutant interaction with mouse S. pyogenes SPy_1718 mutant interaction with mouse S. pyogenes fba mutant interaction with mouse S. aureus oppF mutant interaction with mouse S. aureus oppD mutant interaction with mouse S. aureus purL mutant interaction with mouse S. aureus SA1062 mutant interaction with mouse S. aureus SA1063 mutant interaction with mouse S. aureus recA mutant interaction with mouse S. aureus thrB mutant interaction with mouse S. aureus citB mutant interaction with mouse S. aureus msrA mutant interaction with mouse S. aureus trpD mutant interaction with mouse S. aureus trpB mutant interaction with mouse S. aureus trpA mutant interaction with mouse S. aureus femA mutant interaction with mouse S. aureus femB mutant interaction with mouse S. aureus opp-2C mutant interaction with mouse S. aureus asd mutant interaction with mouse S. aureus lysA mutant interaction with mouse S. aureus braB mutant interaction with mouse S. aureus odhB mutant interaction with mouse S. aureus dinG mutant interaction with mouse S. aureus SA1453 mutant interaction with mouse S. aureus clpX mutant interaction with mouse S. aureus fbp mutant interaction with mouse S. aureus mprF mutant interaction with mouse S. pyogenes slo mutant interaction with mouse S. agalactiae ciaR mutant interaction with human S. agalactiae ciaR mutant interaction with human macrophage cell S. agalactiae ciaR mutant interaction with mouse S. agalactiae ciaR mutant interaction with mouse macrophage cell S. agalactiae lmb mutant interaction with human S. agalactiae csrS mutant interaction with mouse S. agalactiae csrR mutant interaction with mouse S. agalactiae gbs1020 mutant interaction with human S. agalactiae gbs1020 mutant interaction with human macrophage cell S. agalactiae gbs1020 mutant interaction with mouse S. agalactiae gbs1020 mutant interaction with mouse macrophage cell S. agalactiae cpsD mutant interaction with human S. agalactiae scpB mutant interaction with human S. agalactiae gbs1402 mutant interaction with mouse S. pyogenes M5005_Spy_1305 mutant interaction with mouse S. pyogenes grab mutant interaction with mouse S. pyogenes ccpA mutant interaction with mouse S. pyogenes oppA mutant interaction with mouse S. pyogenes perR mutant interaction with mouse S. agalactiae SAK_0517 mutant interaction with mouse S. agalactiae cpsY mutant interaction with human S. agalactiae lgt mutant interaction with human S. aureus SAOUHSC_01373 mutant interaction with mouse P. aeruginosa mvfR mutant interaction with mouse P. aeruginosa flhB mutant interaction with mouse P. aeruginosa PA14_38610 mutant interaction with mouse P. aeruginosa PA14_37650 mutant interaction with mouse P. aeruginosa PA14_33610 mutant interaction with mouse P. aeruginosa gacA mutant interaction with mouse P. aeruginosa PA14_41070 mutant interaction with mouse P. aeruginosa prpR mutant interaction with mouse P. aeruginosa toxA mutant interaction with mouse P. aeruginosa pilF mutant interaction with mouse P. aeruginosa PA14_35740 mutant interaction with mouse P. aeruginosa katA mutant interaction with mouse P. aeruginosa PA14_03120 mutant interaction with mouse P. aeruginosa PA14_03530 mutant interaction with mouse P. aeruginosa PA14_04850 mutant interaction with mouse P. aeruginosa fabF1 mutant interaction with mouse P. aeruginosa dsbA mutant interaction with mouse P. aeruginosa plcH mutant interaction with mouse P. aeruginosa PA14_37260 mutant interaction with mouse S. aureus tilS mutant interaction with C. elegans S. aureus fbp mutant interaction with C. elegans S. aureus ccpA mutant interaction with mouse S. aureus pyrAA mutant interaction with C. elegans S. aureus SAHV_0924 mutant interaction with C. elegans S. aureus mgrA mutant interaction with mouse S. pyogenes ska mutant interaction with mouse B. burgdorferi bosR mutant interaction with mouse B. burgdorferi cspA mutant interaction with human B. burgdorferi dbpA mutant interaction with mouse B. burgdorferi bbk32 mutant interaction with mouse C. trachomatis CT135 mutant interaction with mouse C. trachomatis incA mutant interaction with mouse P. multocida dcaA mutant interaction with mouse P. multocida dcaA mutant interaction with chicken P. multocida PM0855 mutant interaction with mouse P. multocida PM0855 mutant interaction with chicken P. multocida PM1294 mutant interaction with mouse P. multocida PM1294 mutant interaction with chicken P. multocida purN mutant interaction with mouse P. multocida purN mutant interaction with chicken P. multocida PM1069 mutant interaction with chicken P. multocida deoC mutant interaction with chicken P. multocida pyrF mutant interaction with chicken P. multocida ponC mutant interaction with chicken P. multocida PM0081 mutant interaction with chicken P. multocida dam mutant interaction with mouse P. multocida purF mutant interaction with mouse P. multocida guaA mutant interaction with mouse P. multocida atpG mutant interaction with mouse P. multocida PM1466 mutant interaction with mouse P. multocida dsbB mutant interaction with mouse Pseudorabies virus UL41 mutant interaction with mouse Herpes simplex virus type 1 ICP0 mutant interaction with mouse Herpes simplex virus type 1 gD mutant interaction with mouse Herpes simplex virus type 1 ICP34.5 mutant interaction with mouse Herpes simplex virus type 1 UL41 mutant interaction with mouse Bartonella spp. ialB mutant interaction with human Enterococcus spp. EF3314 mutant interaction with C. elegans Enterococcus spp. EF3314 mutant interaction with C. elegans macrophage cell Enterococcus spp. srtC mutant interaction with mouse Enterococcus spp. scrB-1 mutant interaction with C. elegans Enterococcus spp. scrB-1 mutant interaction with mouse Enterococcus spp. purL mutant interaction with mouse Enterococcus spp. glf mutant interaction with mouse Enterococcus spp. bopD mutant interaction with mouse Enterococcus spp. srtA mutant interaction with mouse Enterococcus spp. prgB mutant interaction with rabbit Enterococcus spp. EF0382 mutant interaction with C. elegans Enterococcus spp. EF1302 mutant interaction with C. elegans Enterococcus spp. psr mutant interaction with C. elegans Enterococcus spp. scrR-1 mutant interaction with C. elegans Enterococcus spp. agrBfs mutant interaction with C. elegans Enterococcus spp. agrBfs mutant interaction with mouse Enterococcus spp. brnQ mutant interaction with C. elegans Enterococcus spp. EF1513 mutant interaction with C. elegans Enterococcus spp. EF2598 mutant interaction with C. elegans Enterococcus spp. recQ-1 mutant interaction with C. elegans Enterococcus spp. recQ-1 mutant interaction with mouse Enterococcus spp. phrB mutant interaction with C. elegans Enterococcus spp. phrB mutant interaction with mouse Enterococcus spp. EF2591 mutant interaction with C. elegans Enterococcus spp. EF0737 mutant interaction with C. elegans Enterococcus spp. EF1623 mutant interaction with C. elegans Enterococcus spp. thyA mutant interaction with C. elegans Enterococcus spp. map mutant interaction with C. elegans Enterococcus spp. EF0376 mutant interaction with C. elegans Enterococcus spp. EF0861 mutant interaction with C. elegans Enterococcus spp. EF1542 mutant interaction with C. elegans Enterococcus spp. EF1590 mutant interaction with C. elegans Enterococcus spp. EF1590 mutant interaction with mouse Enterococcus spp. EF1792 mutant interaction with C. elegans Enterococcus spp. EF2675 mutant interaction with C. elegans Enterococcus spp. EF2957 mutant interaction with C. elegans Leptospira spp. hemO mutant interaction with hamster Influenza virus NS1 mutant interaction with mouse L. monocytogenes Dfp mutant interaction with mouse L. monocytogenes Ptb mutant interaction with mouse Brucella spp. BMEI0066 mutant interaction with mouse Brucella spp. BMEI0066 mutant interaction with mouse macrophage cell B. bronchiseptica aroA mutant interaction with mouse Bovine herpesvirus 1 US8 mutant interaction with cattle M. gallisepticum lpd mutant interaction with chicken L. monocytogenes mogR mutant interaction with mouse F. tularensis guaA mutant interaction with mouse F. tularensis guaB mutant interaction with mouse F. tularensis wbtI mutant interaction with mouse M. tuberculosis lysA mutant interaction with mouse M. tuberculosis mce-2 mutant interaction with mouse M. tuberculosis mce-3 mutant interaction with mouse Salmonella spp. cbiA mutant interaction with chicken Salmonella spp. cobS mutant interaction with chicken Salmonella spp. guaB mutant interaction with mouse Salmonella spp. lon mutant interaction with mouse Salmonella spp. cpxR mutant interaction with mouse Salmonella spp. nuoG mutant interaction with chicken Salmonella spp. ruvB mutant interaction with mouse Salmonella spp. tolA mutant interaction with mouse S. aureus aroA mutant interaction with mouse Y. enterocolitica aroA mutant interaction with mouse B. bronchiseptica bscN mutant interaction with mouse B. bronchiseptica cyaA mutant interaction with mouse B. bronchiseptica trpE mutant interaction with mouse Bovine herpesvirus 1 UL23 mutant interaction with cattle Bovine respiratory syncytial virus glycoprotein G mutant interaction with cattle Brucella spp. manA mutant interaction with mouse Brucella spp. pgk mutant interaction with mouse F. tularensis sodC mutant interaction with mouse F. tularensis purC/purD mutant interaction with mouse F. tularensis FTL0552 mutant interaction with mouse Gallid herpesvirus 1 UL0 mutant interaction with chicken Gallid herpesvirus 1 UL23 mutant interaction with chicken Gallid herpesvirus 1 sORF1 mutant interaction with chicken Herpes simplex virus type 1 US8 mutant interaction with mouse Herpes simplex virus type 1 UL29 mutant interaction with mouse Herpes simplex virus type 1 UL23 mutant interaction with mouse Influenza virus M2 mutant interaction with mouse M. avium relA mutant interaction with goat M. avium relA mutant interaction with cattle Salmonella spp. atpA mutant interaction with mouse Salmonella spp. cpxA mutant interaction with mouse Salmonella spp. lon mutant interaction with chicken Salmonella spp. yjeA mutant interaction with mouse Salmonella spp. surA mutant interaction with mouse SARS-related coronavirus E mutant interaction with hamster Simian immunodeficiency virus nef mutant interaction with monkey Y. enterocolitica sodA mutant interaction with mouse Y. pseudotuberculosis phoP mutant interaction with mouse Myxoma virus MYXV_gp168 mutant interaction with rabbit Vaccinia virus VGF mutant interaction with rabbit Vaccinia virus VGF mutant interaction with mouse Ectromelia virus C13R mutant interaction with mouse quality (PATO) quality morphology A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. morphology shape structure A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form. structure behavioral quality An organismal quality inhering in a bearer by virtue of the bearer's behavior aggregate of the responses or reactions or movements in a given situation. behavioral quality branched physical object quality A quality which inheres in a continuant. physical object quality organismal quality A quality that inheres in an entire organism or part of an organism. organismal quality branchiness laminar handedness A behavioral quality inhering ina bearer by virtue of the bearer's unequal distribution of fine motor skill between its left and right hands or feet. handedness left handedness Handedness where the organism preferentially uses the left hand or foot for tasks requiring the use of a single hand or foot or a dominant hand or foot. left handedness right handedness Handedness where the organism preferentially uses the right hand or foot for tasks requiring the use of a single hand or foot or a dominant hand or foot. right handedness ambidextrous handedness Handedness where the organism exhibits no overall dominance in the use of right or left hand or foot in the performance of tasks that require one hand or foot or a dominant hand or foot. ambidextrous handedness protein A biological macromolecule that is composed of amino acids linked in a linear sequence (a polypeptide chain) and is genetically encoded. Proteins descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic. protein A material entity consisting of multiple components that are causally integrated. May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43 Chris Mungall http://www.jbiomedsem.com/content/4/1/43 system A process that is the means during which the pathogen is transmitted directly or indirectly from its natural reservoir, a susceptible host or source to a new host. transmission_process TRANS:0000000 transmission process A process that is the means during which the pathogen is transmitted directly or indirectly from its natural reservoir, a susceptible host or source to a new host. URL:http://www2a.cdc.gov/phtn/catalog/pdf-file/Epi_Course.pdf An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity. uberon UBERON:0000000 processual entity An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity. span:ProcessualEntity Lower, narrow portion of the uterus where it joins with the top end of the vagina. The narrow caudal end of the uterus that opens into the vagina. [TFD][VHOG] The evolution of mammals is associated with radical changes in their reproductive biology, particularly the structure and function of the female reproductive organs. These changes include the evolution of the uterus, cervix, vagina, placenta and specialized cell types associated with each of those structures.[well established][VHOG] cervical cervix BTO:0001421 BTO:0002249 CALOHA:TS-0134 EFO:0000979 EMAPA:29927 EV:0100114 FMA:17740 GAID:376 MA:0000392 MAT:0000292 MESH:D002584 NCIT:C12311 OpenCyc:Mx4rvVipEJwpEbGdrcN5Y29ycA UMLS:C0007874 VHOG:0001359 galen:CervixUteri canalis cervicis uteri caudal segment of uterus cervical canal of uterus cervix uteri neck of uterus uterine cervix uberon cervical canal cervix of uterus UBERON:0000002 cervix cervix uterine cervix uterine cervix 子宫颈(cervix) 子宫颈(uterine cervix) Lower, narrow portion of the uterus where it joins with the top end of the vagina. The narrow caudal end of the uterus that opens into the vagina. [TFD][VHOG] 2012-09-17 VHOG:0001359 VHOG The evolution of mammals is associated with radical changes in their reproductive biology, particularly the structure and function of the female reproductive organs. These changes include the evolution of the uterus, cervix, vagina, placenta and specialized cell types associated with each of those structures.[well established][VHOG] 2012-09-17 VHOG:0001359 VHOG DOI:10.1098/rspb.2004.2848 Lynch VJ, Roth JJ, Takahashi K, Dunn CW, Nonaka DF, Stopper GF, Wagner GP, Adaptive evolution of HoxA-11 and HoxA-13 at the origin of the uterus in mammals. Proceedings of the Royal Society of London, Series B (2004) cervix EFO:0000979 UMLS:C0007874 ncithesaurus:Cervix canalis cervicis uteri FMA:17740 FMA:TA cervical canal of uterus FMA:17740 cervix uteri EMAPA:29927 neck of uterus FMA:17740 uterine cervix FMA:17740 cervical canal FMA:17740 cervix of uterus BTO:0001421 The olfactory organ of vertebrates, consisting of nares, olfactory epithelia and the structures and skeletal framework of the nasal cavity. Organ that is the specialized structure of the face that contains olfactory neurons. The peripheral olfactory organ is paired[ZFA:0000047]. a protuberance in vertebrates that houses the nostrils, or nares, which admit and expel air for respiration in conjunction with the mouth. Behind the nose are the olfactory mucosa and the sinuses. Behind the nasal cavity, air next passes through the pharynx, shared with the digestive system, and then into the rest of the respiratory system. In humans, the nose is located centrally on the face; on most other mammals, it is on the upper tip of the snout[WP]. GO: The nose is the specialized structure of the face that serves as the organ of the sense of smell and as part of the respiratory system. Includes the nasi externus (external nose) and cavitas nasi (nasal cavity)[Wikipedia:Nose]. the organ that is specialized for smell and is part of the respiratory system the structure of the nose varies across vertebrates. In tetrapods the nose is part of the respiratory system.[PMID:25312359] BTO:0000840 CALOHA:TS-2037 EHDAA2:0001274 EHDAA:1502 EMAPA:16542 EV:0100037 EV:0100370 FMA:46472 GAID:77 MA:0000281 MAT:0000139 MESH:D009666 MIAA:0000139 NCIT:C12756 OpenCyc:Mx4rvViCbJwpEbGdrcN5Y29ycA TAO:0000047 UMLS:C0028429 ZFA:0000047 galen:Nose nasal sac nose peripheral olfactory organ uberon nasus olfactory apparatus proboscis UBERON:0000004 nose FMA ZFA-def ZFA The olfactory organ of vertebrates, consisting of nares, olfactory epithelia and the structures and skeletal framework of the nasal cavity. UBERON:cjm Organ that is the specialized structure of the face that contains olfactory neurons. The peripheral olfactory organ is paired[ZFA:0000047]. ZFA:0000047 a protuberance in vertebrates that houses the nostrils, or nares, which admit and expel air for respiration in conjunction with the mouth. Behind the nose are the olfactory mucosa and the sinuses. Behind the nasal cavity, air next passes through the pharynx, shared with the digestive system, and then into the rest of the respiratory system. In humans, the nose is located centrally on the face; on most other mammals, it is on the upper tip of the snout[WP]. GO: The nose is the specialized structure of the face that serves as the organ of the sense of smell and as part of the respiratory system. Includes the nasi externus (external nose) and cavitas nasi (nasal cavity)[Wikipedia:Nose]. the organ that is specialized for smell and is part of the respiratory system MP:0002233 UMLS:C0028429 ncithesaurus:Nose nasal sac ZFA:0000047 nose MA:0000281 peripheral olfactory organ ZFA:0000047 nasus olfactory apparatus UBERON:cjm FBbt:00005157 chemosensory sensory organ uberon UBERON:0000005 chemosensory organ chemosensory sensory organ FBbt:00005157 A layer of dense irregular connective tissue that lines organs and supports the mucosa, as well as joins the mucosa to the bulk of underlying smooth muscle. [WP,unvetted]. submucosal BTO:0002107 FMA:85391 FMA:85392 NCIT:C13167 UMLS:C0225344 organ submucosa region of submucosa submucosa of organ submucosa of region of organ uberon submucous layer tela submucosa tunica submucosa UBERON:0000009 submucosa A layer of dense irregular connective tissue that lines organs and supports the mucosa, as well as joins the mucosa to the bulk of underlying smooth muscle. [WP,unvetted]. UMLS:C0225344 ncithesaurus:Submucosa organ submucosa FMA:85391 region of submucosa FMA:85392 submucosa of organ FMA:85391 submucosa of region of organ FMA:85392 submucous layer BTO:0002107 tela submucosa BTO:0002107 A major division of the nervous system that contains nerves which connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands. Nervous structures including ganglia outside of the central nervous system. Kimmel et al, 1995.[TAO] Part of nervous system in which nerves extend throughout the body outside of the brain and spinal cord.[AAO] The peripheral nervous system (PNS) is the part of the nervous system connected to the CNS which contains cranial nerves III - XII, spinal, peripheral and autonomic nerves. (CUMBO) (...) specific vertebrate traits within the chordate phylum such as skeletal tissues, PNS, and spectacular head and brain development, are linked to the NC (neural crest) and its derivatives.[well established][VHOG] PNS AAO:0000429 BAMS:PNS BILA:0000081 BTO:0001028 CALOHA:TS-0808 EFO:0000891 EHDAA2:0001445 EHDAA:2893 EMAPA:16665 EV:0100335 FBbt:00005098 FMA:9903 GAID:715 MA:0000218 MAT:0000338 MESH:D017933 MIAA:0000338 NCIT:C12465 TAO:0000142 UMLS:C0206417 UMLS:C1305921 VHOG:0000399 XAO:0000178 ZFA:0000142 pars peripherica systema nervosum periphericum uberon UBERON:0000010 peripheral nervous system cjm A major division of the nervous system that contains nerves which connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands. GO:0007422 Nervous structures including ganglia outside of the central nervous system. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000142 TAO ZFIN:curator Part of nervous system in which nerves extend throughout the body outside of the brain and spinal cord.[AAO] 2012-06-20 AAO:0000429 AAO AAO:BJB The peripheral nervous system (PNS) is the part of the nervous system connected to the CNS which contains cranial nerves III - XII, spinal, peripheral and autonomic nerves. (CUMBO) (...) specific vertebrate traits within the chordate phylum such as skeletal tissues, PNS, and spectacular head and brain development, are linked to the NC (neural crest) and its derivatives.[well established][VHOG] 2012-09-17 VHOG:0000399 VHOG DOI:10.1007/978-0-387-46954-6_6 Dupin E, Creuzet S, Le Douarin NM, The contribution of the neural crest to the vertebrate body. Advances in experimental medicine and biology (2006) PNS UMLS:C0206417 NIFSTD:birnlex_1111 UMLS:C0206417 ncithesaurus:Peripheral_Nervous_System UMLS:C1305921 NIFSTD:birnlex_1111 pars peripherica FMA:9903 FMA:TA systema nervosum periphericum FMA:9903 FMA:TA Part of peripheral nervous system that includes the somatic parts of the cranial and spinal nerves and their ganglia and the peripheral sensory receptors. EFO:0000892 FMA:9904 MA:0002850 MAT:0000099 MIAA:0000099 PNS - somatic somatic nervous system, somatic division somatic part of peripheral nervous system somatic peripheral nervous system uberon UBERON:0000012 somatic nervous system cjm Part of peripheral nervous system that includes the somatic parts of the cranial and spinal nerves and their ganglia and the peripheral sensory receptors. NIFSTD:nlx_anat_100301 somatic nervous system, somatic division NIFSTD:nlx_anat_100301 somatic part of peripheral nervous system UBERON:cjm somatic peripheral nervous system NIFSTD:nlx_anat_100301 The sympathetic nervous system is one of the two divisions of the vertebrate autonomic nervous system (the other being the parasympathetic nervous system). The sympathetic preganglionic neurons have their cell bodies in the thoracic and lumbar regions of the spinal cord and connect to the paravertebral chain of sympathetic ganglia. Innervate heart and blood vessels, sweat glands, viscera and the adrenal medulla. Most sympathetic neurons, but not all, use noradrenaline as a post-ganglionic neurotransmitter [GO]. Part of the autonomic nervous system which has opposing physiological effects of the parasympathetic nervous system. Examples include increasing the heart rate or constricting the blood vessels.[AAO] The part of the autonomic nervous system which chiefly contains adrenergic fibres and tends to control and reduce secretions, decrease the contractility and hence the tone of smooth muscles and provoke the contraction of blood vessels. Essentially, it consists of preganglionic fibres from the thoracic and upper lumbar parts of the spinal cord. These fibres, by means of delicate rami communicantes, cross over to ganglia sited in a pair of ganglionated cords on each side of the vertebral column or to more peripheral ganglia. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] The autonomic nervous system is composed of three divisions: the sympathetic division, the parasympathetic division, and the enteric division. (...) In ray-finned teleost fishes, a sympathetic chain is present, and dual innervation of additional organs can be observed. A similar pattern can be found in amphibians (...). The evolution of the autonomic nervous system has been quite conservative, especially in the tetrapod lineage.[well established][VHOG] has developmental contribution from NC in verteberates (https://github.com/obophenotype/uberon/wiki/The-neural-crest) AAO:0010487 BTO:0001832 CALOHA:TS-2050 EFO:0000893 EHDAA2:0001971 EHDAA:3769 EMAPA:16985 FMA:9906 GAID:710 MA:0000225 MESH:D013564 MIAA:0000100 NCIT:C12795 TAO:0001576 UMLS:C0039044 UMLS:C1269646 VHOG:0000384 ZFA:0001576 pars sympathica divisionis autonomici systematis nervosi sympathetic nervous system sympathetic part of autonomic division of nervous system uberon pars sympathica divisionis autonomici systematis nervosi UBERON:0000013 sympathetic nervous system cjm FMA MA ZFA-modified-from-isa The sympathetic nervous system is one of the two divisions of the vertebrate autonomic nervous system (the other being the parasympathetic nervous system). The sympathetic preganglionic neurons have their cell bodies in the thoracic and lumbar regions of the spinal cord and connect to the paravertebral chain of sympathetic ganglia. Innervate heart and blood vessels, sweat glands, viscera and the adrenal medulla. Most sympathetic neurons, but not all, use noradrenaline as a post-ganglionic neurotransmitter [GO]. GO:0048485 Part of the autonomic nervous system which has opposing physiological effects of the parasympathetic nervous system. Examples include increasing the heart rate or constricting the blood vessels.[AAO] 2012-06-20 AAO:0010487 AAO AAO:BJB The part of the autonomic nervous system which chiefly contains adrenergic fibres and tends to control and reduce secretions, decrease the contractility and hence the tone of smooth muscles and provoke the contraction of blood vessels. Essentially, it consists of preganglionic fibres from the thoracic and upper lumbar parts of the spinal cord. These fibres, by means of delicate rami communicantes, cross over to ganglia sited in a pair of ganglionated cords on each side of the vertebral column or to more peripheral ganglia. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000384 VHOG The autonomic nervous system is composed of three divisions: the sympathetic division, the parasympathetic division, and the enteric division. (...) In ray-finned teleost fishes, a sympathetic chain is present, and dual innervation of additional organs can be observed. A similar pattern can be found in amphibians (...). The evolution of the autonomic nervous system has been quite conservative, especially in the tetrapod lineage.[well established][VHOG] 2012-09-17 VHOG:0000384 VHOG ISBN:978-0471210054 Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.461-463 UMLS:C0039044 NIFSTD:birnlex_2516 UMLS:C0039044 ncithesaurus:Sympathetic_Nervous_System UMLS:C1269646 NIFSTD:birnlex_2516 pars sympathica divisionis autonomici systematis nervosi FMA:9906 FMA:TA pars sympathica divisionis autonomici systematis nervosi Any portion of the organ that covers that body and consists of a layer of epidermis and a layer of dermis. Note the distinction between the entire skin of the body, of which there is only 1 in an organism, and zones of skin, of which there can be many. Examples: skin of knee (...) it is well-established that neural crest cells contribute to both the dermal skeleton (craniofacial bone, teeth, and the caudal fin rays of teleosts) and the integument, including craniofacial dermis and all pigment cells outside the retina (...).[well established][VHOG] we assume that mouse, HOG and GAID all mean zone of skin when they say skin. We also choose skin as an exact synonym, as it is more intuitive EHDAA2:0001844 EHDAA:6530 EMAPA:17525 EV:0100152 FMA:86166 GAID:933 MA:0000151 MAT:0000284 MESH:D012867 MIAA:0000284 OpenCyc:Mx4rvVjX3ZwpEbGdrcN5Y29ycA VHOG:0000860 portion of skin region of skin skin skin region skin zone uberon UBERON:0000014 zone of skin FMA Any portion of the organ that covers that body and consists of a layer of epidermis and a layer of dermis. (...) it is well-established that neural crest cells contribute to both the dermal skeleton (craniofacial bone, teeth, and the caudal fin rays of teleosts) and the integument, including craniofacial dermis and all pigment cells outside the retina (...).[well established][VHOG] 2012-09-17 VHOG:0000860 VHOG DOI:10.1111/j.1469-7580.2008.01043.x Vickaryous MK, Sire JY, The integumentary skeleton of tetrapods: origin, evolution, and development. J Anat (2009) skin MA:0000151 A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures. AEO:0000192 CARO:0000010 FMA:50705 anatomical boundary uberon UBERON:0000015 Except in the case of abstracted fiat boundaries such as the midline plane of an organism, all 2D anatomical entities have a 3 dimensional projection. For example, the surface of the shell of a muscle has a distinct shape that projects into the third dimension. Note that boundaries are 2D structures. They have no thickness - and so can not be sites of gene expression or gene product localisation. For this, use boundary region terms. non-material anatomical boundary CARO A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures. CARO:0000010 anatomical boundary CARO:0000010 An organ of sight that includes the camera-type eyeball and supporting structures such as the lacrimal apparatus, the conjunctiva, the eyelid. A cavitated compound organ that transduces light waves into neural signals.[TAO] The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] FMA distinguishes Eye (subdivision of face) which has its parts an Eyeball (organ), as well as other structures, and the orbit of skull. MA includes eyelid, conjunctiva and lacrimal apparatus as part of MA:eye - consistent with FMA - so we can infer that MA:eye is more like FMA:eye than FMA:eyeball. For other AOs this distinction is less meaningful - e.g. ZFA has no eyelid; XAO has no eyelid, but it has conjuctiva, which is considered part of the xao:eye. GO considers eyelid development part of eye development. See also notes on optic nerve - XAO, AAO and BTO consider this part of the eye. MA considers the eye muscles part of the eye, whereas FMA has a class 'orbital content' for this eye AAO:0010340 BTO:0004688 EHDAA2:0000484 EHDAA:936 EMAPA:16198 FMA:54448 MA:0000261 NCIT:C12401 OpenCyc:Mx8Ngx4rwKSh9pwpEbGdrcN5Y29ycB4rvVil5pwpEbGdrcN5Y29ycB4rvViTvpwpEbGdrcN5Y29ycA TAO:0000107 UMLS:C0015392 UMLS:C1280202 VHOG:0000275 XAO:0000179 ZFA:0000107 regio orbitalis vertebrate eye uberon camera-type eye plus associated structures eyes orbital part of face orbital region UBERON:0000019 camera-type eye definitional An organ of sight that includes the camera-type eyeball and supporting structures such as the lacrimal apparatus, the conjunctiva, the eyelid. GO:0043010 A cavitated compound organ that transduces light waves into neural signals.[TAO] 2012-08-14 TAO:0000107 TAO TAO:wd The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] 2012-09-17 VHOG:0000275 VHOG DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007) FMA distinguishes Eye (subdivision of face) which has its parts an Eyeball (organ), as well as other structures, and the orbit of skull. MA includes eyelid, conjunctiva and lacrimal apparatus as part of MA:eye - consistent with FMA - so we can infer that MA:eye is more like FMA:eye than FMA:eyeball. For other AOs this distinction is less meaningful - e.g. ZFA has no eyelid; XAO has no eyelid, but it has conjuctiva, which is considered part of the xao:eye. GO considers eyelid development part of eye development. See also notes on optic nerve - XAO, AAO and BTO consider this part of the eye. MA considers the eye muscles part of the eye, whereas FMA has a class 'orbital content' for this FMA eye FMA:54448 UMLS:C0015392 NIFSTD:birnlex_1169 UMLS:C0015392 ncithesaurus:Eye UMLS:C1280202 NIFSTD:birnlex_1169 regio orbitalis FMA:54448 FMA:TA eyes TAO:0000107 orbital part of face FMA:54448 orbital region FMA:54448 An organ that is capable of transducing sensory stimulus to the nervous system. AEO:0000094 BSA:0000121 BTO:0000202 CALOHA:TS-2043 EHDAA2:0001824 EHDAA:500 EMAPA:35955 FBbt:00005155 GAID:63 HAO:0000930 MA:0000017 MESH:D012679 NCIT:C33224 UMLS:C0935626 VHOG:0001407 WBbt:0006929 organ of sense organ system organ of sensory organ system organ of sensory system sense organ system organ sensory organ sensory organ system organ sensory system organ sensillum uberon Sinnesorgan sensor UBERON:0000020 sense organ An organ that is capable of transducing sensory stimulus to the nervous system. UMLS:C0935626 ncithesaurus:Organ_of_the_Special_Sense organ of sense organ system OBOL:accepted organ of sensory organ system OBOL:accepted organ of sensory system OBOL:accepted sense organ system organ OBOL:automatic sensory organ system organ OBOL:automatic sensory system organ OBOL:accepted sensillum WBbt:0006929 Sinnesorgan BTO:0000202 Any hollow cylindrical anatomical structure containing a lumen through which substances are transported. not every anatomical conduit is a tube - for example, a bone foramen is an opening in the bone, and there is no distinct separate tube structure. Tubes may transport large mixed objects (for example, a bolus of food in the digestive tube) or they may transport the secretions of a single gland (for example, gland ducts) tubular galen:Tube anatomical tube duct uberon UBERON:0000025 tube Any hollow cylindrical anatomical structure containing a lumen through which substances are transported. Major subdivision of an organism that protrudes from the body[DOS, CARO]. An appendage is an external body part, or natural prolongation, that protrudes from an organism's body, such as a vertebrate's limbs[BILA][BILA:0000018]. Organ or organ part that is attached to the body of an organism. For example a limb[GO, modified][GO:0048736]. appendicular this is currently a subtype of organism subdivision - which would exclude feathers AEO:0000193 BILA:0000018 BTO:0001492 CARO:0010003 EFO:0000799 EHDAA2:0003193 EMAPA:37283 EV:0100155 FBbt:00007000 HAO:0000144 MAT:0000023 MESH:D005121 MIAA:0000023 NCIT:C61460 OpenCyc:Mx4rvViC-JwpEbGdrcN5Y29ycA UMLS:C0598782 VSAO:0000075 XAO:0000218 uberon appendages extremitaet extremity limbs/digits/tail UBERON:0000026 appendage Major subdivision of an organism that protrudes from the body[DOS, CARO]. CARO:DOS An appendage is an external body part, or natural prolongation, that protrudes from an organism's body, such as a vertebrate's limbs[BILA][BILA:0000018]. BILA:0000018 Organ or organ part that is attached to the body of an organism. For example a limb[GO, modified][GO:0048736]. GO:0048736 EMAPA:37283 MA:th UMLS:C0598782 ncithesaurus:Appendage appendages XAO:0000218 extremitaet BTO:0001492 limbs/digits/tail MP:0000001 The head is the anterior-most division of the body [GO]. Organism subdivision that is the part of the body consisting of the cranial and pharyngeal regions.[AAO] Organism subdivision which is the part of the body which consists of the cranial and pharygeal regions.[TAO] Vertebrate evolution has been characterized by a fresh and vast array of cranial structures that collectively form the head.[well established][VHOG] AAO:0010335 AEO:0000106 BILA:0000115 BTO:0000282 CALOHA:TS-0436 EFO:0000964 EHDAA2:0003106 EMAPA:31858 FBbt:00000004 FMA:7154 GAID:61 HAO:0000397 MA:0000023 MAT:0000294 MESH:D006257 MIAA:0000294 NCIT:C12419 OpenCyc:Mx4rEOLm4rgPEdmAAAACs6hRjg OpenCyc:Mx4rvVi6YJwpEbGdrcN5Y29ycA SPD:0000016 TAO:0001114 TGMA:0000002 UMLS:C0018670 VHOG:0001644 WBbt:0005739 XAO:0003024 ZFA:0001114 galen:Head head (volume) adult head uberon cephalic area UBERON:0000033 head The head is the anterior-most division of the body [GO]. GO:0060322 Organism subdivision that is the part of the body consisting of the cranial and pharyngeal regions.[AAO] 2012-06-20 AAO:0010335 AAO AAO:BJB Organism subdivision which is the part of the body which consists of the cranial and pharygeal regions.[TAO] 2012-08-14 TAO:0001114 TAO ZFIN:curator Vertebrate evolution has been characterized by a fresh and vast array of cranial structures that collectively form the head.[well established][VHOG] 2012-09-17 VHOG:0001644 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.82 UMLS:C0018670 NIFSTD:birnlex_1230 UMLS:C0018670 ncithesaurus:Head head (volume) FMA:7154 cephalic area SPD:0000016 multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer. A multi-tissue structure that is comprised of a secretory epithelial layer and a connective tissue layer.[TAO] a smooth membrane consisting of a thin layer of cells which excrete serous fluid. Serous membranes line and enclose several body cavities, known as serous cavities, where they secrete a lubricating fluid which reduces friction from muscle movement. Serosa is not to be confused with adventitia, a connective tissue layer which binds together structures rather than reducing friction between them. Each serous membrane is composed of a secretory epithelial layer and a connective tissue layer underneath. The epithelial layer, known as mesothelium, consists of a single layer of avascular flat nucleated cells (cuboidal epithelium) which produce the lubricating serous fluid. This fluid has a consistency similar to thin mucus. These cells are bound tightly to the underlying connective tissue. The connective tissue layer provides the blood vessels and nerves for the overlying secretory cells, and also serves as the binding layer which allows the whole serous membrane to adhere to organs and other structures.[WP] in FMA, SM = mesothelium + connective tissue. It excludes the cavity. Serous sac = SM + cavity. Note that the SM is a subtype of wall in FMA. FMA:9581 GAID:19 MESH:D012704 NCIT:C13169 TAO:0005425 UMLS:C0036760 ZFA:0005425 tunica serosa wall of serous sac uberon serosa UBERON:0000042 serous membrane multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer. A multi-tissue structure that is comprised of a secretory epithelial layer and a connective tissue layer.[TAO] 2012-08-14 TAO:0005425 TAO a smooth membrane consisting of a thin layer of cells which excrete serous fluid. Serous membranes line and enclose several body cavities, known as serous cavities, where they secrete a lubricating fluid which reduces friction from muscle movement. Serosa is not to be confused with adventitia, a connective tissue layer which binds together structures rather than reducing friction between them. Each serous membrane is composed of a secretory epithelial layer and a connective tissue layer underneath. The epithelial layer, known as mesothelium, consists of a single layer of avascular flat nucleated cells (cuboidal epithelium) which produce the lubricating serous fluid. This fluid has a consistency similar to thin mucus. These cells are bound tightly to the underlying connective tissue. The connective tissue layer provides the blood vessels and nerves for the overlying secretory cells, and also serves as the binding layer which allows the whole serous membrane to adhere to organs and other structures.[WP] in FMA, SM = mesothelium + connective tissue. It excludes the cavity. Serous sac = SM + cavity. Note that the SM is a subtype of wall in FMA. FMA UMLS:C0036760 ncithesaurus:Serosa tunica serosa FMA:9581 wall of serous sac FMA:9581 serosa Dense regular connective tissue that connects muscle to bone[VSAO]. Dense regular connective tissue that connects muscle to bone.[VSAO] Phylogenetically, tendinous tissue first appears in the invertebrate chordate Branchiostoma as myosepta. This two-dimensional array of collagen fibers is highly organized, with fibers running along two primary axes. In hagfish the first linear tendons appear and the myosepta have developed specialized regions with unidirectional fiber orientation - a linear tendon within the flat sheet of myoseptum.[well established][VHOG] in FMA, tendon is an organ component that with parts dense-irregular-connective-tissue of tendon and dense-irregular-connective-tissue of tendon sheath; we follow VSAO in making it a subtype of the former. In VSAO tendons connect muscle to bone; in WP the def states integument (e.g. auricular muscles) - but JB confirms this is not actually tendon but aponeurosis AEO:0000091 BTO:0001356 CALOHA:TS-1021 EHDAA2:0003091 EMAPA:35854 EV:0100149 FMA:9721 GAID:276 MA:0000115 MESH:D013710 NCIT:C13045 OpenCyc:Mx4rvVjefJwpEbGdrcN5Y29ycA UMLS:C0039508 VHOG:0001286 VSAO:0000073 XAO:0000173 ZFA:0005647 galen:Tendon uberon sinew tendo UBERON:0000043 tendon VSAO OG Dense regular connective tissue that connects muscle to bone[VSAO]. GO_REF:0000034 VSAO:0000073 Dense regular connective tissue that connects muscle to bone.[VSAO] 2012-08-14 VSAO:0000073 VSAO PSPUB:0000170 Phylogenetically, tendinous tissue first appears in the invertebrate chordate Branchiostoma as myosepta. This two-dimensional array of collagen fibers is highly organized, with fibers running along two primary axes. In hagfish the first linear tendons appear and the myosepta have developed specialized regions with unidirectional fiber orientation - a linear tendon within the flat sheet of myoseptum.[well established][VHOG] 2012-09-17 VHOG:0001286 VHOG DOI:10.1016/S1095-6433(02)00241-6 Summers AP, Koob TJ, The evolution of tendon - morphology and material properties. Comparative Biochemistry and Physiology-Part A: Molecular and Integrative Physiology (2002) in FMA, tendon is an organ component that with parts dense-irregular-connective-tissue of tendon and dense-irregular-connective-tissue of tendon sheath; we follow VSAO in making it a subtype of the former. In VSAO tendons connect muscle to bone; in WP the def states integument (e.g. auricular muscles) - but JB confirms this is not actually tendon but aponeurosis FMA UMLS:C0039508 ncithesaurus:Tendon sinew tendo A biological tissue mass, most commonly a mass of nerve cell bodies. TODO - check vert vs invert. Other species: Any of a number of aggregations of neurons, glial cells and their processes, surrounded by a glial cell and connective tissue sheath (plural: ganglia). // Subdivision of neural tree (organ) which primarily consists of cell bodies of neurons located outside the neuraxis (brain and spinal cord); together with a nucleus and its associated nerve, it constitutes a neural tree (organ). Examples: spinal ganglion, trigeminal ganglion, superior cervical ganglion, celiac ganglion, inferior hypogastric (pelvic) ganglion. // a cluster of nerve cells and associated glial cells (nuclear location) // Portion of tissue that contains cell bodies of neurons and is located outside the central nervous system. A ganglion is a cluster of neurons. It is part of a nervous system. It may include glial cells. The neurons are arranged in a specific constellation: neuronal somata are concentrated at the surface, thus forming a cell cortex, and neurites are concentrated in the centre of the ganglion to form the neuropil. A ganglion is a distinct unit but several ganglia may be anterio-posteriorly joined by connectives or transversally by commissures Portion of tissue that contains cell bodies of neurons and is located outside the central nervous system.[AAO] Structures containing a collection of nerve cell bodies. (Source: BioGlossary, www.Biology-Text.com)[TAO] Subdivision of nervous system which primarily consists of cell bodies of neurons located outside the neuraxis (brain and spinal cord. Examples: spinal ganglion, trigeminal ganglion, superior cervical ganglion, celiac ganglion, inferior hypogastric (pelvic) ganglion (adapted from Foundational Model of Anatomy)[NIFSTD:nlx_anat_100302]. Cranial sensory placodes are focused areas of the head ectoderm of vertebrates that contribute to the development of the cranial sense organs and their associated ganglia. Placodes have long been considered a key character of vertebrates, and their evolution is proposed to have been essential for the evolution of an active predatory lifestyle by early vertebrates.[well established][VHOG] ganglionic AAO:0010426 AEO:0000135 BAMS:G BTO:0000497 CALOHA:TS-0397 EFO:0000899 EHDAA2:0003135 EHDAA:2897 EHDAA:4662 EHDAA:5621 EHDAA:918 EMAPA:32846 EV:0100372 FBbt:00005137 FMA:5884 MA:0002406 MAT:0000207 MAT:0000343 MESH:D005724 MIAA:0000207 MIAA:0000343 NCIT:C12719 TAO:0000190 TGMA:0001016 UMLS:C0017067 VHOG:0000156 WBbt:0005189 XAO:0000209 ZFA:0000190 uberon ganglia neural ganglion UBERON:0000045 ganglion EHDAA2 Bgee:AN A biological tissue mass, most commonly a mass of nerve cell bodies. A ganglion is a cluster of neurons. It is part of a nervous system. It may include glial cells. The neurons are arranged in a specific constellation: neuronal somata are concentrated at the surface, thus forming a cell cortex, and neurites are concentrated in the centre of the ganglion to form the neuropil. A ganglion is a distinct unit but several ganglia may be anterio-posteriorly joined by connectives or transversally by commissures Portion of tissue that contains cell bodies of neurons and is located outside the central nervous system.[AAO] 2012-06-20 AAO:0010426 AAO AAO:EJS Structures containing a collection of nerve cell bodies. (Source: BioGlossary, www.Biology-Text.com)[TAO] 2012-08-14 TAO:0000190 TAO ZFIN:curator Subdivision of nervous system which primarily consists of cell bodies of neurons located outside the neuraxis (brain and spinal cord. Examples: spinal ganglion, trigeminal ganglion, superior cervical ganglion, celiac ganglion, inferior hypogastric (pelvic) ganglion (adapted from Foundational Model of Anatomy)[NIFSTD:nlx_anat_100302]. NIFSTD:nlx_anat_100302 Cranial sensory placodes are focused areas of the head ectoderm of vertebrates that contribute to the development of the cranial sense organs and their associated ganglia. Placodes have long been considered a key character of vertebrates, and their evolution is proposed to have been essential for the evolution of an active predatory lifestyle by early vertebrates.[well established][VHOG] 2012-09-17 VHOG:0000156 VHOG DOI:10.1016/j.ydbio.2005.02.021 Mazet F, Hutt JA, Milloz J, Millard J, Graham A, Shimeld SM, Molecular evidence from Ciona intestinalis for the evolutionary origin of vertebrate sensory placodes. Developmental Biology (2005) UMLS:C0017067 ncithesaurus:Ganglion neural ganglion BTO:0000497 An eye with one concave chamber. Note that 'simple' does not imply a reduced level of complexity or acuity. TGMA:0000729 uberon UBERON:0000047 simple eye An eye with one concave chamber. Note that 'simple' does not imply a reduced level of complexity or acuity. A tubular structure that contains, conveys body fluid, such as blood or lymph. uberon UBERON:0000055 vessel A tubular structure that contains, conveys body fluid, such as blood or lymph. Muscular duct that propels urine from the kidneys to the urinary bladder, or related organs. Anatomical structure consisting of long narrow duct which carries urine from the kidney to the urinary bladder.[AAO] The duct of amniotes that carries urine from a metanephric kidney to the urinary bladder. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter.[well established][VHOG] ureteral ureteric in humans, consists of adventitial, muscular and mucoa layers AAO:0010254 BTO:0001409 CALOHA:TS-1084 EFO:0000930 EHDAA2:0002139 EHDAA:9341 EMAPA:17950 EV:0100097 FMA:9704 GAID:438 MA:0000378 MAT:0000120 MESH:D014513 MIAA:0000120 NCIT:C12416 OpenCyc:Mx4rvhmm6JwpEbGdrcN5Y29ycA UMLS:C0041951 VHOG:0000605 XAO:0000144 galen:Ureter uberon metanephric duct UBERON:0000056 ureter GO Muscular duct that propels urine from the kidneys to the urinary bladder, or related organs. GO:0090189 Anatomical structure consisting of long narrow duct which carries urine from the kidney to the urinary bladder.[AAO] 2012-06-20 AAO:0010254 AAO AAO:BJB The duct of amniotes that carries urine from a metanephric kidney to the urinary bladder. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] 2012-09-17 VHOG:0000605 VHOG The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter.[well established][VHOG] 2012-09-17 VHOG:0000605 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.543 UMLS:C0041951 ncithesaurus:Ureter metanephric duct ISBN10:0073040584 VHOG:0000605 the fibromuscular tubular canal through which urine is discharged from the bladder to the exterior via the external urinary meatus; in males, the urethra is joined by the ejaculatory ducts and serves as a passageway for semen during ejaculation, as well as a canal for urine during voiding; in females, the urethra is shorter and emerges above the vaginal opening urethral In human males, the urethra travels through the penis, and carries semen as well as urine. In females, the urethra is shorter and emerges above the vaginal opening. BTO:0001426 CALOHA:TS-1132 EFO:0000931 EMAPA:30901 EV:0100099 FMA:19667 GAID:390 MA:0000379 MAT:0000121 MESH:D014521 MIAA:0000121 NCIT:C12417 OpenCyc:Mx4rvVjkypwpEbGdrcN5Y29ycA UMLS:C0041967 VHOG:0001264 XAO:0000153 galen:Urethra uberon UBERON:0000057 urethra pelvic part of UG sinus gives rise to prostatic and membranous parts of urethra Wikipedia Wikipedia the fibromuscular tubular canal through which urine is discharged from the bladder to the exterior via the external urinary meatus; in males, the urethra is joined by the ejaculatory ducts and serves as a passageway for semen during ejaculation, as well as a canal for urine during voiding; in females, the urethra is shorter and emerges above the vaginal opening MGI:anna MP:0000537 UMLS:C0041967 ncithesaurus:Urethra A tubular structure that transports secreted or excreted substances. A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA:0005171]. Most ducts, but not all, are exocrine gland ducts. Some ontologies classify structures such as the oviduct here. AAO:0011123 FBbt:00100314 FMA:30320 NCIT:C12948 TAO:0005171 UMLS:C0687028 XAO:0004000 ZFA:0005171 galen:Duct anatomical duct exocrine duct exocrine gland duct uberon ducts UBERON:0000058 duct A tubular structure that transports secreted or excreted substances. A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA:0005171]. ZFA:0005171 UMLS:C0687028 ncithesaurus:Duct ducts XAO:0004000 A subdivision of the digestive tract that connects the small intestine to the cloaca or anus. Lacks or has few villi[Kardong]. Intestinal surface area also is increased in amphibians and reptiles by internal folds and occasionally by a few villi. The intestine can be divided into a small intestine and a slightly wider large intestine.[well established][VHOG] AAO:0010396 BTO:0000706 CALOHA:TS-1306 EFO:0000840 EMAPA:19252 EV:0100077 FMA:7201 GAID:306 MA:0000333 MESH:A03.492.411.495 MIAA:0000046 NCIT:C12379 OpenCyc:Mx4rvVkF5pwpEbGdrcN5Y29ycA UMLS:C0021851 VHOG:0000054 XAO:0000131 galen:LargeIntestine uberon intestinum crassum UBERON:0000059 large intestine cjm A subdivision of the digestive tract that connects the small intestine to the cloaca or anus. Lacks or has few villi[Kardong]. ISBN10:0073040584 Intestinal surface area also is increased in amphibians and reptiles by internal folds and occasionally by a few villi. The intestine can be divided into a small intestine and a slightly wider large intestine.[well established][VHOG] 2012-09-17 VHOG:0000054 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.566 UMLS:C0021851 ncithesaurus:Large_Intestine intestinum crassum BTO:0000706 Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers. in FMA, serosa is a wall UBERON:0009915 wall EMAPA:25036 FMA:82482 galen:Wall wall of organ uberon organ wall UBERON:0000060 anatomical wall Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers. FMA:82482 in FMA, serosa is a wall FMA wall of organ FMA:82482 organ wall FMA:82482 Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. AAO:0010825 AEO:0000003 BILA:0000003 CARO:0000003 EHDAA2:0003003 EMAPA:0 FBbt:00007001 FMA:305751 FMA:67135 GAID:781 HAO:0000003 MA:0003000 MESH:D000825 TAO:0000037 TGMA:0001823 VHOG:0001759 XAO:0003000 ZFA:0000037 biological structure connected biological structure uberon UBERON:0000061 anatomical structure Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. CARO:0000003 connected biological structure CARO:0000003 Anatomical structure that performs a specific function or group of functions [WP]. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4 CARO:0020004 EFO:0000634 EMAPA:35949 ENVO:01000162 FMA:67498 MA:0003001 NCIT:C13018 OpenCyc:Mx4rv5XMb5wpEbGdrcN5Y29ycA OpenCyc:Mx4rwP3iWpwpEbGdrcN5Y29ycA UMLS:C0178784 WBbt:0003760 uberon anatomical unit body organ element UBERON:0000062 organ Anatomical structure that performs a specific function or group of functions [WP]. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. GO:0048513 UMLS:C0178784 ncithesaurus:Organ element A part of an organ that constitutes a distinct modular sub-unit. In some cases, the organ may also contain other sub-units of identical or similar types, in other cases this may be a distinct entity. FMA distinguishes segment from zone by whether the fiat boundaries are fixed/anchored (segments) or floating (zone). It's not completely clear how to apply this distinction Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball. Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal. FMA:86140 uberon organ region with fixed fiat boundary organ segment segment of organ UBERON:0000063 organ subunit A part of an organ that constitutes a distinct modular sub-unit. In some cases, the organ may also contain other sub-units of identical or similar types, in other cases this may be a distinct entity. Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball. FMA:86140 3 Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal. FMA:86140 1 organ region with fixed fiat boundary FMA:86140 organ segment FMA:86140 segment of organ FMA:86140 A multicellular structure that is a part of an organ. currently defined in a very broad sense, may be replaced by more specific classes in the future AAO:0011124 EFO:0000635 FMA:82472 cardinal organ part uberon regional part of organ UBERON:0000064 organ part A multicellular structure that is a part of an organ. cardinal organ part FMA:82472 regional part of organ NIFSTD:birnlex_16 Anatomical structure that is part of the respiratory system. In mammals consists of upper and lower tracts EHDAA2:0001606 EHDAA:1568 EHDAA:2219 EMAPA:16737 FMA:265130 OpenCyc:Mx4rvvM--pwpEbGdrcN5Y29ycA VHOG:0000393 uberon UBERON:0000065 respiratory tract NCBIBook:NBK10107 Anatomical structure that is part of the respiratory system. In mammals consists of upper and lower tracts The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage. adult stage BTO:0001043 BilaDO:0000004 EFO:0001272 FBdv:00005369 WBls:0000041 XtroDO:0000084 fully formed animal stage juvenile-adult stage uberon UBERON:0000066 fully formed stage The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage. A life cycle stage that starts with fertilization and ends with the fully formed embryo. BilaDO:0000002 EV:0300001 FBdv:00005289 FMA:72652 HsapDv:0000002 MmusDv:0000002 OGES:000000 OGES:000022 WBls:0000003 WBls:0000092 WBls:0000102 XAO:1000012 embryonic stage uberon embryogenesis UBERON:0000068 embryo stage embryo stage 胚胎期 A life cycle stage that starts with fertilization and ends with the fully formed embryo. End of the life of an organism. ncit:Death is an outcome XAO:0000437 XtroDO:0000085 uberon death UBERON:0000071 death stage End of the life of an organism. XAO:0000437 ncit:Death is an outcome ncit An section of a respiratory tract. MA:0000434 has subclasses upper and lower, so it corresponds to a segment of the tract, rather than the tract as a whole EMAPA:16737 FMA:45660 MA:0000434 uberon respiratory tract subdivision of respiratory tract UBERON:0000072 proximo-distal subdivision of respiratory tract An section of a respiratory tract. MA:0000434 has subclasses upper and lower, so it corresponds to a segment of the tract, rather than the tract as a whole MA respiratory tract MA:0000434 Any part or collection of parts of the central or peripheral nervous system. Parts may span both CNS and PNS. Melissa Haendel 2009-06-18T09:00:04Z NCIT:C13040 UMLS:C1518256 part of nervous system uberon UBERON:0000073 regional part of nervous system Any part or collection of parts of the central or peripheral nervous system. Parts may span both CNS and PNS. NIFSTD:birnlex_1157 UMLS:C1518256 ncithesaurus:Nervous_System_Part part of nervous system NIFSTD:birnlex_1157 Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism. UBERON:0010322 FMA:85544 NCIT:C34076 UMLS:C1519343 galen:ComplexSkeletalStructure skeletal system subdivision uberon skeletal system part UBERON:0000075 subdivision of skeletal system cjm Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism. UBERONREF:0000003 UMLS:C1519343 ncithesaurus:Skeletal_System_Part skeletal system subdivision FMA:85544 The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm. merge with non-neural. In vertebrates, the ectoderm has three parts: external ectoderm (also known as surface ectoderm), the neurectoderm (neural crest, and neural tube) (or external ectoderm) forms the following structures: Skin Epithelium of the mouth and nasal cavity saliavary glands, and glands of mouth and nasal cavity Enamel - as a side note dentin and dental pulp are formed from ectomesenchyme which is derived from ectoderm Epithelium of pineal and pituitary glands Lens and cornea of the eye Apical ectodermal ridge inducing development of the limb buds of the embryo. Sensory receptors in epidermis EHDAA2:0001968 EHDAA:1494 EHDAA:350 EHDAA:4784 EHDAA:4790 EHDAA:4796 EHDAA:7860 EMAPA:16096 FMA:87656 NCIT:C34309 UMLS:C1515087 surface (external) ectoderm surface ectoderm uberon UBERON:0000076 external ectoderm EHDAA2 EHDAA2 The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm. MGI:anna MP:0012532 UMLS:C1515087 ncithesaurus:Surface_Ectoderm surface ectoderm MP:0012532 An anatomical structure that develops from the endoderm and the mesoderm. Grouping term for query purposes. Notes that the developmental relationships are being refined such that most structures should develop in whole from at most one layer, but may have contributions from multiple uberon UBERON:0000077 mixed endoderm/mesoderm-derived structure An anatomical structure that develops from the endoderm and the mesoderm. An anatomical structure that develops from the ectoderm, mesoderm and endoderm. Grouping term for query purposes. Notes that the developmental relationships are being refined such that most structures should develop in whole from at most one layer, but may have contributions from multiple uberon UBERON:0000078 mixed ectoderm/mesoderm/endoderm-derived structure An anatomical structure that develops from the ectoderm, mesoderm and endoderm. The second stage of the kidney. It serves as the main excretory organ of aquatic vertebrates and as a temporary embryonic kidney in higher vertebrates. It is composed of the mesonephric duct (also called the Wolffian duct), mesonephric tubules, and associated capillary tufts. A single tubule and its associated capillary tuft is called a mesonephric excretory unit; these units are similar in structure and function to nephrons of the adult kidney. The mesonephros is derived from intermediate mesoderm in the vertebrate embryo. A kidney formed of nephric tubules arising in the middle region of the nephric ridge; a transient embryonic stage that replaces the pronephros, but is itself replaced by the adult metanephros [in mammals; in fishes and amphibians it is the adult kidney]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG] Organ that is the definitive adult kidney. It replaces the earlier pronephros, which degenerates as the mesonephros becomes functional in feeding stage tadpoles.[AAO] As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates. (...) In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros.[well established][VHOG] mesonephric In mammals, the mesonephros is the second of the three embryonic kidneys to be established and exists only transiently. In fish and amphibians, the mesonephros will form the mature kidney By contrast to the pronephros, the histological features of the mammalian mesonephros, with its primitive glomeruli, suggest that it probably functions as a primitive kidney, and is involved in the production of much of the amniotic fluid. Within the two mesonephroi, one located on either side of the dorsal mesentery of the hindgut, a substantial number (in the region of about 40 or more) of cranio-caudally segmented mesonephric tubules are formed. It has, however, been suggested that only the most rostrally located 4-6 pairs of mesonephric tubules drain into the mesonephric portion of the nephric duct. This is now seen to extend along the length of the mesonephroi, being located towards their lateral sides. The mesonephros is also retained over a considerably longer period than the pronephros, but gradually undergoes regression in a cranio-caudal direction. While the rostral part displays clear evidence of regression its more caudal part appears to display evidence of functional activity. Within the medial part of the mesonephros, vesicles are formed, although no glomeruli are formed there in this species. It is, however, difficult to believe that the relatively enormous mesonephroi do not have an excretory role in the mouse, only serving as a base for gonadal differentiation. In the human embryo, the medial part of the mesonephric tubules enlarges, become invaginated by capillaries, and form glomeruli. These then take on an excretory role. In the mouse, the mesonephric ducts appear to be patent throughout their length[GUDMAP, modified] AAO:0010384 BTO:0001542 CALOHA:TS-0624 EFO:0000928 EHDAA2:0001130 EHDAA:1581 EHDAA:5903 EMAPA:16744 FMA:72171 GAID:1308 MESH:D001755 NCIT:C26467 TAO:0000529 UMLS:C0025492 VHOG:0000038 XAO:0000141 ZFA:0000529 Wolffian body mesonephric kidney mesonephroi uberon amphibian adult kidney corpus Wolffi middle kidney opisthonephros opisto nephros opistonephros UBERON:0000080 mesonephros The second stage of the kidney. It serves as the main excretory organ of aquatic vertebrates and as a temporary embryonic kidney in higher vertebrates. It is composed of the mesonephric duct (also called the Wolffian duct), mesonephric tubules, and associated capillary tufts. A single tubule and its associated capillary tuft is called a mesonephric excretory unit; these units are similar in structure and function to nephrons of the adult kidney. The mesonephros is derived from intermediate mesoderm in the vertebrate embryo. GO:0001823 A kidney formed of nephric tubules arising in the middle region of the nephric ridge; a transient embryonic stage that replaces the pronephros, but is itself replaced by the adult metanephros [in mammals; in fishes and amphibians it is the adult kidney]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG] 2012-09-17 VHOG:0000038 VHOG Organ that is the definitive adult kidney. It replaces the earlier pronephros, which degenerates as the mesonephros becomes functional in feeding stage tadpoles.[AAO] 2012-06-20 AAO:0010384 AAO AAO:BJB As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates. (...) In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros.[well established][VHOG] 2012-09-17 VHOG:0000038 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.639 UMLS:C0025492 ncithesaurus:Mesonephros Wolffian body BTO:0001542 GOC:yaf MESH:A16.254.500 mesonephric kidney XAO:0000141 mesonephroi amphibian adult kidney XAO:0000141 corpus Wolffi BTO:0001542 middle kidney BTO:0001542 opisthonephros VHOG:0000038 XAO:0000141 opistonephros In mammals, the metanephros is the excretory organ of the fetus, which develops into the mature kidney and is formed from the rear portion of the nephrogenic cord. The metanephros is an endocrine and metabolic organ that filters the blood and excretes the end products of body metabolism in the form of urine[GO] TODO check developmental relationships A kidney formed of nephric tubules arising in the posterior region of the nephric ridge and drained by a ureter; replaces the embryonic pronephros and mesonephros [in mammals]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG] The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes.[well established][VHOG] metanephric During the fifth week of gestation, the mesonephric duct develops an outpouching, the ureteric bud, near its attachment to the cloaca. This bud, also called the metanephrogenic diverticulum, grows posteriorly and towards the head of the embryo. The elongated stalk of the ureteric bud, the metanephric duct, later forms the ureter. As the cranial end of the bud extends into the intermediate mesoderm, it undergoes a series of branchings to form the collecting duct system of the kidney. It also forms the major and minor calyces and the renal pelvis BTO:0001543 EHDAA2:0001137 EHDAA:3089 EHDAA:5911 EMAPA:17373 EMAPA_RETIRED:17207 FMA:72172 NCIT:C34209 UMLS:C0231049 VHOG:0000039 metanephron uberon definite kidney definitive kidney hind kidney metanephric kidney UBERON:0000081 metanephros definitional GO ISBN:9780878932504 In mammals, the metanephros is the excretory organ of the fetus, which develops into the mature kidney and is formed from the rear portion of the nephrogenic cord. The metanephros is an endocrine and metabolic organ that filters the blood and excretes the end products of body metabolism in the form of urine[GO] GO:0001656 A kidney formed of nephric tubules arising in the posterior region of the nephric ridge and drained by a ureter; replaces the embryonic pronephros and mesonephros [in mammals]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG] 2012-09-17 VHOG:0000039 VHOG The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes.[well established][VHOG] 2012-09-17 VHOG:0000039 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.543 UMLS:C0231049 ncithesaurus:Metanephros metanephron BTO:0001543 definite kidney BTO:0001543 definitive kidney BTO:0001543 hind kidney BTO:0001543 metanephric kidney VHOG:0000039 A mesonephric tubule is an epithelial tube that is part of the mesonephros[GO]. Genital ridge that is next to the mesonephros[WP]. TODO check Any of the renal tubules composing the mesonephros. In mammals they function as excretory structures during the early embryonic development but are later incorporated into the reproductive system. [TFD][VHOG] As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates.[well established][VHOG] AAO:0010389 EHDAA2:0001134 EMAPA:16747 VHOG:0000500 XAO:0000148 uberon renal tubules tubuli mesonephrici UBERON:0000083 mesonephric tubule A mesonephric tubule is an epithelial tube that is part of the mesonephros[GO]. Genital ridge that is next to the mesonephros[WP]. Any of the renal tubules composing the mesonephros. In mammals they function as excretory structures during the early embryonic development but are later incorporated into the reproductive system. [TFD][VHOG] 2012-09-17 VHOG:0000500 VHOG As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates.[well established][VHOG] 2012-09-17 VHOG:0000500 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.639 renal tubules VHOG:0000500 tubuli mesonephrici An epithelial swelling on the Wolffian duct that elongates to invade the adjacent metanephric mesenchyme[MP] Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts. [Embryology, See_Dudek_RW_and_Fix_JD, Third_Edition_(2004)_Philadelphia:_Lippincott_William_and_Wilkins, p.137][VHOG] Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts[VHOG:0000541]. The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter.[well established][VHOG] BTO:0001646 EHDAA2:0002140 EHDAA:3091 EHDAA:5917 EMAPA:17209 NCIT:C34207 UMLS:C1284058 VHOG:0000541 uberon diverticulum diverticulum metanephricum gemma ureterica metanephric bud metanephric diverticulum ureteric ampulla ureteric diverticulum UBERON:0000084 ureteric bud EHDAA2 EHDAA2 ISBN:9780878932504 An epithelial swelling on the Wolffian duct that elongates to invade the adjacent metanephric mesenchyme[MP] MP:0010979 Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts. [Embryology, See_Dudek_RW_and_Fix_JD, Third_Edition_(2004)_Philadelphia:_Lippincott_William_and_Wilkins, p.137][VHOG] 2012-09-17 VHOG:0000541 VHOG Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts[VHOG:0000541]. VHOG:0000541 The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter.[well established][VHOG] 2012-09-17 VHOG:0000541 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.543 UMLS:C1284058 ncithesaurus:Metanephric_Diverticulum diverticulum BTO:0001646 diverticulum metanephricum gemma ureterica metanephric bud BTO:0001646 metanephric diverticulum ureteric diverticulum VHOG:0000541 stage succeeding embryo, including mature structure In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997) BilaDO:0000003 OGES:000010 OGES:000014 OGES:000024 WBls:0000022 WBls:0000093 WBls:0000103 postembryonic stage post-hatching stage uberon postembryonic UBERON:0000092 post-embryonic stage stage succeeding embryo, including mature structure Nonparenchymatous organ that primarily consists of dense connective tissue organized into a sheet which interconnects two or more organs, separates two or more body spaces from one another, or surrounds an organ or body part. Examples: interosseous membrane of forearm, obturator membrane, tympanic membrane, fibrous pericardium, fascia lata, dura mater. [FMA] cjm 2009-07-30T05:19:13Z membrane FMA:7145 membrane of organ uberon UBERON:0000094 membrane organ FMA-def Nonparenchymatous organ that primarily consists of dense connective tissue organized into a sheet which interconnects two or more organs, separates two or more body spaces from one another, or surrounds an organ or body part. Examples: interosseous membrane of forearm, obturator membrane, tympanic membrane, fibrous pericardium, fascia lata, dura mater. [FMA] FMA:7145 portion of neural crest that develops from the dorsal neural tube. It overlaps the vagal neural crest and migrates to populate the pharyngeal arches 3, 4 and 6 (producing structures in the head) and to the heart, forming connective tissue that separates the great vessels of the heart. [Wikipedia] A subpopulation of the cephalic neural crest that emerges from the otic level to the anterior limit of somite 4. It migrates to the heart and is essential for the septation of the outflow track[doi:10.1242/dev.091751]. ZFA treats this as a subtype of NC. cjm 2009-07-30T07:57:38Z TAO:0002173 XAO:0004190 ZFA:0001648 uberon cardiac neural crest complex complexus cristae neuralis cardiacus UBERON:0000095 cardiac neural crest Wikipedia portion of neural crest that develops from the dorsal neural tube. It overlaps the vagal neural crest and migrates to populate the pharyngeal arches 3, 4 and 6 (producing structures in the head) and to the heart, forming connective tissue that separates the great vessels of the heart. [Wikipedia] A subpopulation of the cephalic neural crest that emerges from the otic level to the anterior limit of somite 4. It migrates to the heart and is essential for the septation of the outflow track[doi:10.1242/dev.091751]. ZFA treats this as a subtype of NC. ZFA cardiac neural crest complex complexus cristae neuralis cardiacus The lung vasculature is composed of the tubule structures that carry blood or lymph in the lungs[GO]. FMA:73750 lung vascular network pulmonary vasculature vascular network of lung vasculature of lung uberon UBERON:0000102 lung vasculature The lung vasculature is composed of the tubule structures that carry blood or lymph in the lungs[GO]. GOC:GO lung vascular network OBOL:automatic pulmonary vasculature FMA:73750 vascular network of lung OBOL:automatic vasculature of lung OBOL:automatic An entire span of an organism's life, commencing with the zygote stage and ending in the death of the organism. FBdv:00000000 HsapDv:0000001 MmusDv:0000001 OGES:000011 ncithesaurus:Life entire life cycle entire lifespan life lifespan uberon UBERON:0000104 life cycle An entire span of an organism's life, commencing with the zygote stage and ending in the death of the organism. life cycle stage A spatiotemporal region encompassing some part of the life cycle of an organism. this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here the WBls class 'all stages' belongs here as it is the superclass of other WBls stages we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage BILS:0000105 EFO:0000399 FBdv:00007012 FMA:24120 HsapDv:0000000 MmusDv:0000000 OlatDv:0000010 PdumDv:0000090 WBls:0000002 XAO:1000000 ZFS:0000000 ZFS:0100000 ncithesaurus:Developmental_Stage developmental stage stage uberon UBERON:0000105 life cycle stage A spatiotemporal region encompassing some part of the life cycle of an organism. A stage at which the organism is a single cell produced by means of sexual reproduction. As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG] BILS:0000106 BilaDO:0000005 EFO:0001322 EHDAA:27 FBdv:00005288 NCIT:C12601 PdumDv:0000100 VHOG:0000745 XAO:1000001 ZFS:0000001 1-cell stage fertilized egg stage one cell stage uberon fertilized egg stage one-cell stage zygote zygotum UBERON:0000106 zygote stage A stage at which the organism is a single cell produced by means of sexual reproduction. As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG] 2012-09-17 VHOG:0000745 VHOG ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.107 fertilized egg stage BTO:0000854 one-cell stage VHOG:0000745 zygote VHOG:0000745 zygotum The first few specialized divisions of an activated animal egg; Stage consisting of division of cells in the early embryo. The zygotes of many species undergo rapid cell cycles with no significant growth, producing a cluster of cells the same size as the original zygote. The different cells derived from cleavage are called blastomeres and form a compact mass called the morula. Cleavage ends with the formation of the blastula. BILS:0000107 BilaDO:0000006 EFO:0001290 FBdv:00000054 MESH:A16.254.270 MmusDv:0000004 OGES:000015 OGES:000020 PdumDv:0000200 XAO:1000004 ZFS:0000046 uberon UBERON:0000107 cleavage stage The first few specialized divisions of an activated animal egg; Stage consisting of division of cells in the early embryo. The zygotes of many species undergo rapid cell cycles with no significant growth, producing a cluster of cells the same size as the original zygote. The different cells derived from cleavage are called blastomeres and form a compact mass called the morula. Cleavage ends with the formation of the blastula. GO:0040016 An early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence. consider adding a preceding stage 'morula stage' as part of cleavage BILS:0000108 BilaDO:0000007 EFO:0001282 HsapDv:0000006 MmusDv:0000007 OGES:000003 OGES:000016 OGES:000021 OpenCyc:Mx4rEetFnKP2EdqAAAACs4vPlg WBls:0000005 XAO:1000003 ZFS:0000045 uberon UBERON:0000108 blastula stage An early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence. A stage defined by complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm. BILS:0000109 BilaDO:0000008 EFO:0001296 FBdv:00005317 HsapDv:0000010 MmusDv:0000013 OGES:000004 OGES:000019 WBls:0000010 XAO:1000005 ZFS:0000047 uberon blastocystis trilaminaris stage trilaminar blastocyst stage trilaminar blastoderm stage trilaminar disk stage trilaminar germ stage trilaminar stage UBERON:0000109 gastrula stage BILS A stage defined by complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm. GO:0007369 blastocystis trilaminaris stage trilaminar blastocyst stage trilaminar blastoderm stage trilaminar disk stage trilaminar germ stage trilaminar stage Staged defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system. BILS:0000110 BilaDO:0000009 HsapDv:0000012 MmusDv:0000017 XAO:1000006 uberon UBERON:0000110 neurula stage Staged defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system. GO:0001841 A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism. BILS:0000111 BilaDO:0000010 HsapDv:0000015 MmusDv:0000018 OGES:000005 OGES:000032 uberon segmentation stage UBERON:0000111 organogenesis stage A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism. The stage of being a sexually immature adult animal[XAO:1000010]. In mammals this would include infant (nourishment from lactation) and juvenile (prepubertal no longer dependent on mother) BILS:0000112 BTO:0002168 EFO:0001300 EV:0300051 MmusDv:0000043 OGES:000009 XAO:1000010 XtroDO:0000083 ZFS:0000051 immature stage juvenile stage uberon subadult stage UBERON:0000112 sexually immature stage The stage of being a sexually immature adult animal[XAO:1000010]. XAO:1000010 immature stage VHOG:FB juvenile stage XAO:1000010 subadult stage The stage of being a sexually mature adult animal. adult stage BILS:0000113 EV:0300064 EV:0300070 MIAA:0000403 MmusDv:0000110 OGES:000026 OGES:000027 XAO:1000093 ZFS:0000044 uberon UBERON:0000113 post-juvenile adult stage The stage of being a sexually mature adult animal. the connective tissue located between the respiratory (airway and alveolar) epithelium, the capillary endothelium and pleural mesothelium; it contains basement membrane composed of collagen, elastin, proteoglycans, and fibronectin it functions in the mechanical behavior of the lung, and forms a barrier to regulate the flow of plasma constituents from the capillaries to the airway and alveolar spaces EMAPA:35521 FMA:27533 MA:0001782 connective tissue of lung pulmonary interstitium uberon lung interstitial tissue lung interstitium pulmonary connective tissue pulmonary interstitial tissue UBERON:0000114 lung connective tissue the connective tissue located between the respiratory (airway and alveolar) epithelium, the capillary endothelium and pleural mesothelium; it contains basement membrane composed of collagen, elastin, proteoglycans, and fibronectin ISBN:0-683-40008-8 MGI:anna MP:0002276 connective tissue of lung OBOL:automatic pulmonary interstitium FMA:27533 lung interstitial tissue MA:0001782 pulmonary connective tissue EMAPA:35521 The epithelial layer of the lung. A pseudostratified epithelium, containing basal cells, stem cells of the airway, submucosal glands and cartilage rings, is limited to the trachea and large lobar airways in the mouse (Morrisey and Hogan, 2010). This more complex epithelium extends to terminal bronchioles in the human[doi:10.1242/dev.115469] BTO:0001653 EMAPA:32860 MA:0001783 epithelial tissue of lung epithelium of lung lung epithelial tissue uberon pulmonary epithelium UBERON:0000115 lung epithelium The epithelial layer of the lung. MP:0006382 epithelial tissue of lung OBOL:automatic epithelium of lung OBOL:automatic lung epithelial tissue OBOL:automatic pulmonary epithelium BTO:0001653 A tube in the respiratory system. Examples: bronchus, bronchiole, trachea. in GO lung development is part of respiratory tube development. This can lead to inconsistencies with other ontologies, e.g. VT. The GO structure may be better represented by a tree of tubes (see the FMA class) EMAPA:37946 FMA:12224 segment of tracheobronchial tree respiratory conducting tube segment of tracheobronchial tree tracheobronchial tree segment uberon airway UBERON:0000117 respiratory tube A tube in the respiratory system. Examples: bronchus, bronchiole, trachea. GO:0030323 in GO lung development is part of respiratory tube development. This can lead to inconsistencies with other ontologies, e.g. VT. The GO structure may be better represented by a tree of tubes (see the FMA class) GO EMAPA:37946 MA:th segment of tracheobronchial tree FMA:12224 respiratory conducting tube MP:0004391 segment of tracheobronchial tree FMA:12224 tracheobronchial tree segment FMA:12224 Structure derived from foregut that becomes a lung[GO]. clarify successors - include bronchi? BTO:0001643 EHDAA2:0004089 NCIT:C34260 NCIT:C34282 UMLS:C1514420 UMLS:C1514897 uberon gemma pulmonalis gemma respiratoria lung bud primary lung bud respiratory diverticulum UBERON:0000118 lung bud GO:0060441 EHDAA2 Structure derived from foregut that becomes a lung[GO]. GO:0060431 UMLS:C1514420 ncithesaurus:Primary_Bronchial_Bud UMLS:C1514897 ncithesaurus:Respiratory_Diverticulum gemma pulmonalis gemma respiratoria lung bud primary lung bud GO:0060572 respiratory diverticulum A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses. UBERON:0005163 CARO:0001001 FBbt:00005099 funiculus nerve fiber bundle neural fiber bundle uberon UBERON:0000122 neuron projection bundle A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses. CARO:0001001 FBC:DOS FBbt:00005099 nerve fiber bundle FBbt:00005099 A spatially aggregated collection of nerve cell bodies in the CNS, consisting of one or more subpopulations that share cell type, chemical phenotype, and connections, and including nearby cells that share the same cell type, chemical phenotype, and connections. (CUMBO) Anatomical structure consisting of a discrete aggregate of neuronal soma[GO][GO_REF:0000021]. Proposed CUMBO def from MM: A subcortical part of the nervous system consisting of a relatively compact group of cells that is distinguishable histologically that share a commonality of cytoarchitecture, chemoarchitecturel and connectivity. (comments: I put in 'subcortical' because I don't think we consider either the cerebellar cortex or cerebral cortex to be nuclei. Some people distinguish between a nucleus and a laminar structure (see Wikipedia definition). However, there are structures identified as nuclei that are laminar, e.g., lateral geniculate nucleus, although they are not laminated in all species. Also, I put in 'relatively compact' and 'distiguishable by histology' because we have groups of cells, e.g., cholinergic cell groups, doparminergic cell groups that are related on the 3 criteria but which we don't tend to consider nuclei because they don't occupy an easily defined territory. But all is open to debate. nucleus AEO:0000136 FMA:83686 NCIT:C13197 nervous system nucleus neuraxis nucleus neuronal nucleus nucleus of CNS uberon nucleus of neuraxis UBERON:0000125 neural nucleus A spatially aggregated collection of nerve cell bodies in the CNS, consisting of one or more subpopulations that share cell type, chemical phenotype, and connections, and including nearby cells that share the same cell type, chemical phenotype, and connections. (CUMBO) NIFSTD:nlx_28443 Anatomical structure consisting of a discrete aggregate of neuronal soma[GO][GO_REF:0000021]. GO_REF:0000021 neuraxis nucleus FMA:83686 neuronal nucleus AEO:0000136 nucleus of CNS NIFSTD:nlx_28443 Nucleus that receives projections from or contains neurons that send projections through one of the cranial nerves EMAPA:37066 FMA:54501 cranial neural nucleus nucleus of cranial nerve uberon nucleus nervi cranialis UBERON:0000126 cranial nerve nucleus Nucleus that receives projections from or contains neurons that send projections through one of the cranial nerves NIFSTD:nlx_28532 EMAPA:37066 MA:th cranial neural nucleus FMA:54501 nucleus nervi cranialis the group of motor neurons residing in the pons that innervate the muscles of facial expression FMA has 3 subclasses - left, right and motor nucleus of facial nerve, but no defs. It's not clear how facial nucleus is distinct from facial motor nucleus. BAMS:7 BAMS:7N BAMS:VII BM:Pons-VII DHBA:12420 EHDAA2:0004638 EMAPA:35338 EV:0100267 FMA:54572 MA:0001014 NCIT:C12898 UMLS:C0228740 VHOG:0001412 facial VII nucleus facial nerve nucleus nucleus of facial nerve uberon facial VII motor nucleus UBERON:0000127 facial nucleus definitional the group of motor neurons residing in the pons that innervate the muscles of facial expression ISBN:0838580343 MP:0000909 FMA has 3 subclasses - left, right and motor nucleus of facial nerve, but no defs. It's not clear how facial nucleus is distinct from facial motor nucleus. FMA UMLS:C0228740 ncithesaurus:Facial_Nerve_Nucleus facial VII nucleus MA:0001014 nucleus of facial nerve FMA:54572 facial VII motor nucleus MA:0001014 uberon UBERON:0000153 anterior region of body lexical uberon UBERON:0000154 posterior region of body lexical A thin sheet or layer of pliable tissue, serving as a covering or envelope of a part, as the lining of a cavity, as a partition or septum, or to connect two structures. membrane FMA:30322 FMA:82500 MESH:D008566 NCIT:C12749 membranous organ component uberon UBERON:0000158 membranous layer A thin sheet or layer of pliable tissue, serving as a covering or envelope of a part, as the lining of a cavity, as a partition or septum, or to connect two structures. ncithesaurus:Membrane membranous organ component FMA:82500 The terminal part of the large intestine, continuous proximally with the rectum and distally terminates with the anus. requires alignment with EHDAA2 and complete developmental relationships BTO:0001978 CALOHA:TS-2160 EMAPA:18256 FMA:15703 MA:0000330 NCIT:C12375 UMLS:C0227411 galen:AnalCanal anal canal anal canal viewed anatomically anatomical anal canal uberon anal pad anus canalis analis cloaca cloacal chamber mesenteron pars analis recti UBERON:0000159 anal canal Wikipathways:WP2062 The terminal part of the large intestine, continuous proximally with the rectum and distally terminates with the anus. UMLS:C0227411 ncithesaurus:Anal_Canal canalis analis canalis analis BTO:0001978 pars analis recti BTO:0001978 Segment of the alimentary canal extending from the stomach to the anus and, in humans and other mammals, consists of two segments, the small intestine and the large intestine. This class is probably too inclusive Portion of the alimentary canal bounded anteriorly by the pyloric sphincter and posteriorly by the cloacal sphincter.[AAO] The tract of the alimentary canal. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] intestinal In zebrafish, No stomach, small intestine, or large intestine can be distinguished. However, differences can be found in the morphology of the mucosa columnar epithelial cells and the number of goblet cells, suggesting functional differentiation. The intestine has numerous folds that become progressively shorter in a rostral-to-caudal direction. Proportionally, these folds are significantly larger than the finger-like intestinal villi of mammals and other amniotes (Wallace et al. 2005). Columnar-shaped absorptive enterocytes are the most numerous in the zebrafish intestinal epithelium. Goblet cells are the second most populous epithelial cell type. AAO:0000246 ANISEED:1235303 BSA:0000093 BTO:0000648 CALOHA:TS-0490 EFO:0000834 EMAPA:32874 EV:0100071 FMA:7199 GAID:295 MA:0000328 MA:0001524 MESH:A03.492.411 MIAA:0000043 NCIT:C12736 TAO:0001338 UMLS:C0021853 VHOG:0000056 WBbt:0005772 XAO:0000129 ZFA:0001338 galen:Intestine bowel uberon intestinal tract UBERON:0000160 intestine cjm Segment of the alimentary canal extending from the stomach to the anus and, in humans and other mammals, consists of two segments, the small intestine and the large intestine. GOC:GO Portion of the alimentary canal bounded anteriorly by the pyloric sphincter and posteriorly by the cloacal sphincter.[AAO] 2012-06-20 AAO:0000246 AAO AAO:EJS The tract of the alimentary canal. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000056 VHOG UMLS:C0021853 ncithesaurus:Intestine Anatomical conduit that connects two adjacent body spaces (or a body space with the space surrounding the organism)[FMA,modified]. in FMA, this is an anatomical conduit *space*, rather than anatomical conduit anatomical ostium ostium FMA:3724 anatomical orifice hilum uberon UBERON:0000161 orifice Anatomical conduit that connects two adjacent body spaces (or a body space with the space surrounding the organism)[FMA,modified]. FMA:3724 in FMA, this is an anatomical conduit *space*, rather than anatomical conduit FMA anatomical ostium FMA:3724 anatomical orifice FMA:3724 Common chamber into which the intestines and excretory system opens. Arises during development in all vertebrates, but in many it becomes subdivided, lost or incorporated into other structures adding df link to embryonic cloaca leads to a cycle in uberon-simple, as cloaca is a suberclass of embryonic cloaca A common passage for fecal, urinary, and reproductive discharge in most lower vertebrates as well as the terminal end of the hindgut before division into rectum, bladder, and genital primordia in mammalian embryos. [TFD][VHOG] Anatomical structure which is the common receptacle for the alimentary canal, Wolffian ducts, oviducts, and the bladder.[AAO] A cloaca is apparently a primitive vertebrate feature because it occurs in most primitive gnathostomes and persists in the embryos of almost all vertebrates.[well established][VHOG] cloacal Human beings only have an embryonic cloaca, which is split up into separate tracts during the development of the urinary and reproductive organs hindgut endoderm and proctodeal ectoderm. AAO:0000095 GAID:1206 MESH:D002988 NCIT:C34127 UMLS:C0008987 VHOG:0001186 XAO:0000244 ZFA:0005781 uberon cloacal chamber vent UBERON:0000162 cloaca ZFA AAO Common chamber into which the intestines and excretory system opens. Arises during development in all vertebrates, but in many it becomes subdivided, lost or incorporated into other structures ISBN10:0073040584 most adult placentals have no trace of a cloaca. However, the tenrecs and golden moles, small placental mammals native to Africa, retain a cloaca as adults. A common passage for fecal, urinary, and reproductive discharge in most lower vertebrates as well as the terminal end of the hindgut before division into rectum, bladder, and genital primordia in mammalian embryos. [TFD][VHOG] 2012-09-17 VHOG:0001186 VHOG Anatomical structure which is the common receptacle for the alimentary canal, Wolffian ducts, oviducts, and the bladder.[AAO] 2012-06-20 AAO:0000095 AAO AAO:BJB A cloaca is apparently a primitive vertebrate feature because it occurs in most primitive gnathostomes and persists in the embryos of almost all vertebrates.[well established][VHOG] 2012-09-17 VHOG:0001186 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.572 hindgut endoderm and proctodeal ectoderm. WP UMLS:C0008987 ncithesaurus:Cloaca cloacal chamber AAO:0000095 vent XAO:0000244 endoderm-lined chamber that develops as pouch-like dilation of the caudal end of the hindgut and receives the allantois ventrally and two mesonephric ducts laterally; caudally it ends blindly at the cloacal membrane formed by the union of proctodeal (anal pit) ectoderm and cloacal endoderm, with no intervening mesoderm[MP]. this class represents the embryonic form of the cloaca, as found in both mammals and non-mammals. EHDAA2:0000256 EHDAA:4895 EMAPA:27573 uberon cloaca UBERON:0000163 embryonic cloaca EHDAA2 EHDAA2 endoderm-lined chamber that develops as pouch-like dilation of the caudal end of the hindgut and receives the allantois ventrally and two mesonephric ducts laterally; caudally it ends blindly at the cloacal membrane formed by the union of proctodeal (anal pit) ectoderm and cloacal endoderm, with no intervening mesoderm[MP]. MP:0010115 cloaca the ventral part of the cloaca remaining after septation of the rectum, which further develops into part of the bladder, part of the prostatic part of the male urethra and the urethra and vestibule in females The ventral part of the cloaca after its separation from the rectum, giving rise to the lower part of the bladder in both sexes, to the prostatic portion of the male urethra, and to the urethra and vestibule in the female. [TFD][VHOG] In mammals the lowly monotremes still have a cloaca. Higher types have done away with this structure and have a separate anal outlet for the rectum. The monotreme cloaca shows the initiation of this subdivision. The cloaca has such includes only the distal part, roughly comparable to the proctodeum. The more proximal part is divided into (1) a large dorsal passage into which the intestine opens, the coprodeum, and (2) a ventral portion, the urodeum with which the bladder connects. (...) the development of the placental mammals recapitulates in many respects the phylogenetic story. In the sexually indifferent stage of placental mammal there is a cloaca. While the indifferent stage still persists, a septum develops, and extends out to the closing membrane. This divides the cloaca into two chambers: a coprodeum continuous with the gut above, and a urodeum or urogenital sinus below.[well established][VHOG] the term 'urogenital sinus' may refer to the primitive urogenital sinus present as a transient developmental structure in most mammals or it may refer to a condition in which an unseptated cloaca persists in animals longer than normal urogenital sinus EHDAA2:0004060 EHDAA:5029 EHDAA:5919 EMAPA:17379 NCIT:C34322 UMLS:C0231057 VHOG:0000414 UGS fetal UGS sinus urogenitalis uberon UBERON:0000164 primitive urogenital sinus MP-def the ventral part of the cloaca remaining after septation of the rectum, which further develops into part of the bladder, part of the prostatic part of the male urethra and the urethra and vestibule in females ISBN:0-683-40008-8 MP:0010116 The ventral part of the cloaca after its separation from the rectum, giving rise to the lower part of the bladder in both sexes, to the prostatic portion of the male urethra, and to the urethra and vestibule in the female. [TFD][VHOG] 2012-09-17 VHOG:0000414 VHOG In mammals the lowly monotremes still have a cloaca. Higher types have done away with this structure and have a separate anal outlet for the rectum. The monotreme cloaca shows the initiation of this subdivision. The cloaca has such includes only the distal part, roughly comparable to the proctodeum. The more proximal part is divided into (1) a large dorsal passage into which the intestine opens, the coprodeum, and (2) a ventral portion, the urodeum with which the bladder connects. (...) the development of the placental mammals recapitulates in many respects the phylogenetic story. In the sexually indifferent stage of placental mammal there is a cloaca. While the indifferent stage still persists, a septum develops, and extends out to the closing membrane. This divides the cloaca into two chambers: a coprodeum continuous with the gut above, and a urodeum or urogenital sinus below.[well established][VHOG] 2012-09-17 VHOG:0000414 VHOG ISBN:978-0721676678 Romer AS, Vertebrate body (1970)p.388-89 and Figure 300 the term 'urogenital sinus' may refer to the primitive urogenital sinus present as a transient developmental structure in most mammals or it may refer to a condition in which an unseptated cloaca persists in animals longer than normal MP urogenital sinus MP:0010116 UMLS:C0231057 ncithesaurus:Urogenital_Sinus UGS MP:0010116 fetal UGS sinus urogenitalis mouth The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks). Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO] Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG] oral some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips AAO:0010355 BTO:0001090 BTO:0004698 CALOHA:TS-1315 EFO:0000825 EHDAA2:0001326 EHDAA:542 EMAPA:16262 FBbt:00003126 FMA:49184 GAID:75 MA:0000341 MA:0002474 MAT:0000038 MESH:D009055 MIAA:0000038 OpenCyc:Mx4rvVidh5wpEbGdrcN5Y29ycA TADS:0000040 TAO:0000547 TAO:0000590 TGMA:0000131 VHOG:0000280 VHOG:0000812 XAO:0003029 ZFA:0000547 ZFA:0000590 galen:Mouth regio oralis adult mouth uberon cavital oralis cavitas oris cavum oris mouth cavity oral region oral vestibule rima oris stoma stomatodaeum trophic apparatus vestibule of mouth vestibulum oris UBERON:0000165 mouth the mouth contains structures such as jaw skeleton that may not strictly be considered tract parts exceptions in some taxa The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks). Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO] 2012-06-20 AAO:0010355 AAO AAO:BJB Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG] 2012-09-17 VHOG:0000812 VHOG DOI:10.1038/nature07309 Hejnol A, Martindale MQ, Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature (2008) in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips FMA regio oralis BTO:0004698 regio oralis FMA:49184 FMA:TA cavital oralis cavitas oris BTO:0001090 cavum oris BTO:0001090 mouth cavity BTO:0001090 oral region EHDAA2:0001326 oral vestibule BTO:0001090 rima oris BTO:0001090 stomatodaeum VHOG:0000812 trophic apparatus vestibule of mouth BTO:0001090 vestibulum oris BTO:0001090 The orifice that connects the mouth to the exterior of the body. (...) mouth development is very similar in protostomes and 'basal' deuterostomes, whereas the chordate mouth seems to develop at a new position. Recent data for echinoderms and hemichordates further suggest that this change in mouth position may result from change in the influence of a conserved ectodermal patterning system on mouth development. It has been suggested that the mouths of vertebrates and urochordates may constitute a 'new' mouth.[well established][VHOG] FMA:59806 oral fissure oral orifice uberon mouth oral part of face UBERON:0000166 oral opening FMA The orifice that connects the mouth to the exterior of the body. (...) mouth development is very similar in protostomes and 'basal' deuterostomes, whereas the chordate mouth seems to develop at a new position. Recent data for echinoderms and hemichordates further suggest that this change in mouth position may result from change in the influence of a conserved ectodermal patterning system on mouth development. It has been suggested that the mouths of vertebrates and urochordates may constitute a 'new' mouth.[well established][VHOG] 2012-09-17 VHOG:0000280 VHOG DOI:10.1016/j.semcdb.2007.06.002 Christiaen L, Jaszczyszyn Y, Kerfant M, Kanob S, Thermes V, Joly JS, Evolutionary modification of mouth position in deuterostomes. Seminars in Cell and Developmental Biology (2007) oral fissure FMA:59806 oral orifice FMA:59806 mouth Anatomical cavity at the start of the digestive tract that that is enclosed by the mouth. The boundaries and contents vary depending on the species. In vertebrates, the boundaries are the oral opening, the cheeks, the palate and (if present) the palatoglossal arch - if this is not present then the mouth and pharynx form the oropharyngeal cavity. The buccal cavity contains the teeth, tongue and palate (when present) Anatomical cavity bounded anteriorly by the mouth and posteriorly by the derivatives of the branchial arches.[AAO] The cavity of the mouth, bounded by the jaw bones and associated structures (muscles and mucosa). [TFD][VHOG] Echinoderms, hemichordates, and chordates are called deuterostomes because the mouth arises not from the blastopore but from a second invagination at the anterior end of the larva that pushes in to connect with the archenteron.[well established][VHOG] AAO:0000053 AAO:0000960 BSA:0000107 CALOHA:TS-1315 EFO:0001975 EHDAA2:0001324 EHDAA:6970 EMAPA:17411 EMAPA:18399 EV:0100057 FMA:20292 HAO:0000669 NCIT:C12421 TAO:0001027 TGMA:0000102 UMLS:C0226896 VHOG:0000188 WBbt:0005255 XAO:0000126 ZFA:0001027 buccal cavity cavity of mouth uberon bucca UBERON:0000167 oral cavity Anatomical cavity at the start of the digestive tract that that is enclosed by the mouth. The boundaries and contents vary depending on the species. In vertebrates, the boundaries are the oral opening, the cheeks, the palate and (if present) the palatoglossal arch - if this is not present then the mouth and pharynx form the oropharyngeal cavity. The buccal cavity contains the teeth, tongue and palate (when present) ISBN10:0073040584 Anatomical cavity bounded anteriorly by the mouth and posteriorly by the derivatives of the branchial arches.[AAO] 2012-06-20 AAO:0000960 AAO AAO:EJS The cavity of the mouth, bounded by the jaw bones and associated structures (muscles and mucosa). [TFD][VHOG] 2012-09-17 VHOG:0000188 VHOG Echinoderms, hemichordates, and chordates are called deuterostomes because the mouth arises not from the blastopore but from a second invagination at the anterior end of the larva that pushes in to connect with the archenteron.[well established][VHOG] 2012-09-17 VHOG:0000188 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.32 UMLS:C0226896 ncithesaurus:Oral_Cavity buccal cavity FMA:20292 ISBN10:0073040584 A section dividing a colon along a proximal-distal axis. FMA:222905 uberon segment of colon UBERON:0000168 proximal-distal subdivision of colon 4 cjm A section dividing a colon along a proximal-distal axis. segment of colon FMA:222905 1 1 1 1 The pair of anatomical structures comprised of a left lung and right lung. FMA:68877 OpenCyc:Mx4rvVjKy5wpEbGdrcN5Y29ycA lungs lungs pair pulmones set of lungs uberon UBERON:0000170 pair of lungs pair of lungs 肺对 FMA-abduced The pair of anatomical structures comprised of a left lung and right lung. pulmones FMA:68877 FMA:TA Organ that functions in gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms. EMAPA:17607 SPD:0000428 TGMA:0001247 apparatus respiratorius organ breathing organ organ of apparatus respiratorius organ of respiratory system respiratory organ respiratory system organ uberon gas exchange organ UBERON:0000171 respiration organ Organ that functions in gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms. GO:0007585 apparatus respiratorius organ OBOL:automatic organ of apparatus respiratorius OBOL:automatic organ of respiratory system OBOL:automatic respiratory system organ OBOL:automatic A portion of organism substance that is the product of an excretion process that will be eliminated from the body. An excretion process is elimination by an organism of the waste products that arise as a result of metabolic activity UBERON:0000324 UBERON:0007550 AEO:0000184 BTO:0000491 EHDAA2_RETIRED:0003184 ENVO:02000022 FMA:9674 galen:Excretion excreted substance portion of excreted substance waste substance uberon excretion UBERON:0000174 excreta A portion of organism substance that is the product of an excretion process that will be eliminated from the body. An excretion process is elimination by an organism of the waste products that arise as a result of metabolic activity GO:0007588 portion of excreted substance FMA:9674 waste substance AEO:0000184 excretion BTO:0000491 blood A fluid that is composed of blood plasma and erythrocytes. This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid. A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO] Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO] relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG] AAO:0000046 BTO:0000089 CALOHA:TS-0079 EFO:0000296 EHDAA2:0000176 EHDAA:418 EMAPA:16332 ENVO:02000027 EV:0100047 FMA:9670 GAID:965 MA:0000059 MESH:D001769 MIAA:0000315 NCIT:C12434 OpenCyc:Mx4rvVjI8JwpEbGdrcN5Y29ycA TAO:0000007 UMLS:C0005767 VHOG:0000224 XAO:0000124 ZFA:0000007 galen:Blood portion of blood vertebrate blood uberon whole blood UBERON:0000178 blood Bgee:AN A fluid that is composed of blood plasma and erythrocytes. FMA:9670 A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO] 2012-08-14 TAO:0000007 TAO ZFIN:curator Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO] 2012-06-20 AAO:0000046 AAO AAO:LAP relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] 2012-06-20 AAO:0000046 AAO Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG] 2012-09-17 VHOG:0000224 VHOG DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual review of cell and developmental biology (2006) UMLS:C0005767 ncithesaurus:Blood whole blood BTO:0000089 Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs. cjm 2009-04-08T04:38:19Z CARO:0000081 uberon blood or blood analog circulating fluid UBERON:0000179 haemolymphatic fluid Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs. A layer of membrane around a tendon. It has 2 layers: synovial sheath + fibrous tendon sheath TODO - add layer relations. 'tendon sheath' GAT in FMA. BTO:0000051 FMA:45087 FMA:76715 NCIT:C96299 UMLS:C0224856 synovial tendon sheath uberon vagina tendinis UBERON:0000304 tendon sheath A layer of membrane around a tendon. It has 2 layers: synovial sheath + fibrous tendon sheath UMLS:C0224856 ncithesaurus:Tendon_Sheath synovial tendon sheath FMA:45087 vagina tendinis Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence. TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula UBERON:0007011 BILA:0000059 BTO:0000128 GAID:1294 MESH:A16.254.270.274 OGEM:000006 OpenCyc:Mx4rEetFnKP2EdqAAAACs4vPlg blastula embryo uberon blastosphere UBERON:0000307 blastula Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence. blastula embryo BILA:0000059 blastosphere A substance produced by the cervix and endocervical glands[BTO]. Thick acidic mucus that blocks the cervical os after mestruation[WP]. This 'infertile' mucus blocks spermatozoa from entering the uterus. BTO:0000242 FMA:83689 MESH:D002582 cervix mucus uberon UBERON:0000316 cervical mucus A substance produced by the cervix and endocervical glands[BTO]. Thick acidic mucus that blocks the cervical os after mestruation[WP]. This 'infertile' mucus blocks spermatozoa from entering the uterus. BTO:0000242 cervix mucus OBOL:automatic Mucosa that is part of a colon. The mucosa of the colon is lined by a simple columnar epithelium with a thin brush border and numerous goblet cells. UBERON:0003347 UBERON:0004981 BTO:0000271 CALOHA:TS-0164 EFO:0003038 EMAPA:27375 FMA:14984 FMA:85388 MA:0003194 colon mucosa colon mucous membrane colonic mucosa colonic mucous membrane large bowel mucosa mucosa of colon mucosa of large bowel uberon UBERON:0000317 colonic mucosa Mucosa that is part of a colon. The mucosa of the colon is lined by a simple columnar epithelium with a thin brush border and numerous goblet cells. colon mucosa FMA:14984 colon mucous membrane OBOL:automatic colonic mucous membrane FMA:14984 large bowel mucosa OBOL:automatic mucosa of colon FMA:14984 mucosa of large bowel OBOL:automatic The branched tubular glands found in the mucosa of the fundus and body of the stomach which contain parietal cells that secrete hydrochloric acid and zymogenic cells that produce pepsin. BTO:0000503 EMAPA:27181 FMA:14919 uberon UBERON:0000325 gastric gland cjm ISBN10:0073040584 The branched tubular glands found in the mucosa of the fundus and body of the stomach which contain parietal cells that secrete hydrochloric acid and zymogenic cells that produce pepsin. MGI:anna The wall of the digestive tract. This encompasses all parts of the digestive tract with the exception of the lumen (cavity). We model the digestive tract as consisting of two parts: the wall and the lumen. BTO:0000547 FMA:45653 digestive tract wall wall of digestive tract wall of gut uberon wall of alimentary tract UBERON:0000328 gut wall The wall of the digestive tract. This encompasses all parts of the digestive tract with the exception of the lumen (cavity). wall of gut FMA:45653 A gland that is part of the intestinal mucosa. Examples include the intestinal crypts, duodenal gland[cjm]. Note that some sources treat 'intestinal gland' as synonymous with crypts BTO:0000640 FMA:15052 bowel mucosa gland bowel mucosa of organ gland bowel mucous membrane gland bowel organ mucosa gland gland of bowel mucosa gland of bowel mucosa of organ gland of bowel mucous membrane gland of bowel organ mucosa gland of intestinal mucosa gland of intestine mucosa gland of intestine mucosa of organ gland of intestine mucous membrane gland of intestine organ mucosa gland of mucosa of bowel gland of mucosa of intestine gland of mucosa of organ of bowel gland of mucosa of organ of intestine gland of mucous membrane of bowel gland of mucous membrane of intestine gland of organ mucosa of bowel gland of organ mucosa of intestine glandula intestinalis intestinal mucosa gland intestine mucosa gland intestine mucosa of organ gland intestine mucous membrane gland intestine organ mucosa gland mucosa of bowel gland mucosa of intestine gland mucosa of organ of bowel gland mucosa of organ of intestine gland mucous membrane of bowel gland mucous membrane of intestine gland organ mucosa of bowel gland organ mucosa of intestine gland uberon glandulae intestinales UBERON:0000333 intestinal gland A gland that is part of the intestinal mucosa. Examples include the intestinal crypts, duodenal gland[cjm]. bowel mucosa gland OBOL:automatic bowel mucosa of organ gland OBOL:automatic bowel mucous membrane gland OBOL:automatic bowel organ mucosa gland OBOL:automatic gland of bowel mucosa OBOL:automatic gland of bowel mucosa of organ OBOL:automatic gland of bowel mucous membrane OBOL:automatic gland of bowel organ mucosa OBOL:automatic gland of intestinal mucosa OBOL:automatic gland of intestine mucosa OBOL:automatic gland of intestine mucosa of organ OBOL:automatic gland of intestine mucous membrane OBOL:automatic gland of intestine organ mucosa OBOL:automatic gland of mucosa of bowel OBOL:automatic gland of mucosa of intestine OBOL:automatic gland of mucosa of organ of bowel OBOL:automatic gland of mucosa of organ of intestine OBOL:automatic gland of mucous membrane of bowel OBOL:automatic gland of mucous membrane of intestine OBOL:automatic gland of organ mucosa of bowel OBOL:automatic gland of organ mucosa of intestine OBOL:automatic glandula intestinalis FMA:15052 intestinal mucosa gland OBOL:automatic intestine mucosa gland OBOL:automatic intestine mucosa of organ gland OBOL:automatic intestine mucous membrane gland OBOL:automatic intestine organ mucosa gland OBOL:automatic mucosa of bowel gland OBOL:automatic mucosa of intestine gland OBOL:automatic mucosa of organ of bowel gland OBOL:automatic mucosa of organ of intestine gland OBOL:automatic mucous membrane of bowel gland OBOL:automatic mucous membrane of intestine gland OBOL:automatic organ mucosa of bowel gland OBOL:automatic organ mucosa of intestine gland OBOL:automatic A lining of mostly endodermal origin, covered in epithelium, which is involved in absorption and secretion. They line various body cavities that are exposed to the external environment and internal organs. It is at several places continuous with skin: at the nostrils, the lips, the ears, the genital area, and the anus. The sticky, thick fluid secreted by the mucous membranes and gland is termed mucus. The term mucous membrane refers to where they are found in the body and not every mucous membrane secretes mucus[WP] mucosal FMA has mucosa vs region of mucosa; these are subtypes of Mucosa: Mucosa of gallbladder, tongue, .... The following are subtypes of Region of mucosa: Mucosa of zone of stomach, trachea, bronchus, dorsum of tongue.... Depends on whether the covered area is an organ or organ component. Uberon does not regard organ vs organ component as crucial distinction and thus collapses these into a single class deliberately AEO:0000199 BTO:0000886 CALOHA:TS-2031 EHDAA2_RETIRED:0003234 EV:0100382 FMA:85355 FMA:85358 GAID:297 MESH:D009092 NCIT:C13166 OpenCyc:Mx4rvmKNOpwpEbGdrcN5Y29ycA UMLS:C0026724 galen:Mucosa mucosa of organ mucosa of organ part mucosal region mucous membrane organ mucosa uberon region of mucosa tunica mucosa UBERON:0000344 mucosa A lining of mostly endodermal origin, covered in epithelium, which is involved in absorption and secretion. They line various body cavities that are exposed to the external environment and internal organs. It is at several places continuous with skin: at the nostrils, the lips, the ears, the genital area, and the anus. The sticky, thick fluid secreted by the mucous membranes and gland is termed mucus. The term mucous membrane refers to where they are found in the body and not every mucous membrane secretes mucus[WP] FMA has mucosa vs region of mucosa; these are subtypes of Mucosa: Mucosa of gallbladder, tongue, .... The following are subtypes of Region of mucosa: Mucosa of zone of stomach, trachea, bronchus, dorsum of tongue.... Depends on whether the covered area is an organ or organ component. Uberon does not regard organ vs organ component as crucial distinction and thus collapses these into a single class deliberately FMA UMLS:C0026724 ncithesaurus:Mucosa mucosa of organ FMA:85355 mucosa of organ part FMA:85358 mucosal region FMA:85358 mucous membrane FMA:85355 organ mucosa FMA:85355 region of mucosa FMA:85358 tunica mucosa tunica mucosa BTO:0000886 A mucosa that is part of a pharynx [Automatically generated definition]. UBERON:0003344 BTO:0001047 EMAPA:26957 FMA:55031 MA:0003143 mucosa of organ of pharynx mucosa of pharynx mucous membrane of pharynx organ mucosa of pharynx pharynx mucosa pharynx mucosa of organ pharynx mucous membrane pharynx organ mucosa tunica mucosa pharyngea tunica mucosa pharyngis uberon mucous membrane of the pharynx UBERON:0000355 pharyngeal mucosa A mucosa that is part of a pharynx [Automatically generated definition]. OBOL:automatic mucosa of organ of pharynx OBOL:automatic mucosa of pharynx OBOL:automatic mucous membrane of pharynx FMA:55031 mucous membrane of pharynx OBOL:automatic organ mucosa of pharynx OBOL:automatic pharynx mucosa OBOL:automatic pharynx mucosa of organ OBOL:automatic pharynx mucous membrane OBOL:automatic pharynx organ mucosa OBOL:automatic tunica mucosa pharyngea FMA:55031 FMA:TA mucous membrane of the pharynx BTO:0001047 The sensory nerve subdivision of the trigeminal nerve that transmits sensory information from the palate, upper teeth and gingiva, the skin between the palpebral fissure and the mouth, and from the nasal cavity and maxillary sinuses. Medial ramus (sensory) of the trigeminal nerve.[AAO] relationship loss: part_of trunk maxillary-mandibularis (AAO:0010669)[AAO] AAO:0010670 BTO:0001378 EHDAA2:0002087 EMAPA:17799 FMA:52724 GAID:836 MA:0001103 MESH:D008442 OpenCyc:Mx4rvWNU9JwpEbGdrcN5Y29ycA VHOG:0001346 maxillary division [V2] maxillary division [Vb] maxillary division of fifth cranial nerve maxillary division of trigeminal nerve (Vb; V2) maxillary nerve [V2] maxillary nerve [Vb] nervus maxillaris (Vb; V2) nervus maxillaris [v2] nervus maxillaris [vb] ramus maxillaris (ramus V2) second division of fifth cranial nerve second division of trigeminal nerve trigeminal V nerve maxillary division uberon n. maxillaris nervus maxillaris trigeminal nerve maxillary division UBERON:0000377 maxillary nerve The sensory nerve subdivision of the trigeminal nerve that transmits sensory information from the palate, upper teeth and gingiva, the skin between the palpebral fissure and the mouth, and from the nasal cavity and maxillary sinuses. MP:0009799 Medial ramus (sensory) of the trigeminal nerve.[AAO] 2012-06-20 AAO:0010670 AAO AAO:EJS relationship loss: part_of trunk maxillary-mandibularis (AAO:0010669)[AAO] 2012-06-20 AAO:0010670 AAO maxillary division [V2] FMA:52724 maxillary division [Vb] FMA:52724 maxillary division of fifth cranial nerve FMA:52724 maxillary division of trigeminal nerve (Vb; V2) FMA:52724 maxillary nerve [V2] FMA:52724 maxillary nerve [Vb] FMA:52724 nervus maxillaris (Vb; V2) FMA:52724 nervus maxillaris [v2] FMA:52724 FMA:TA nervus maxillaris [vb] FMA:52724 FMA:TA ramus maxillaris (ramus V2) AAO:0010670 second division of fifth cranial nerve FMA:52724 second division of trigeminal nerve FMA:52724 trigeminal V nerve maxillary division MA:0001103 n. maxillaris nervus maxillaris BTO:0001378 trigeminal nerve maxillary division EMAPA:17799 A mucosa that is part of a respiratory airway. BTO:0001390 FMA:7471 mucosa of organ of trachea mucosa of organ of windpipe mucosa of trachea mucosa of windpipe mucous membrane of trachea mucous membrane of windpipe organ mucosa of trachea organ mucosa of windpipe trachea mucosa trachea mucosa of organ trachea mucous membrane trachea organ mucosa tracheal mucous membrane tunica mucosa (tracheae) tunica mucosa tracheae windpipe mucosa windpipe mucosa of organ windpipe mucous membrane windpipe organ mucosa uberon UBERON:0000379 tracheal mucosa A mucosa that is part of a respiratory airway. OBOL:automatic mucosa of organ of trachea OBOL:automatic mucosa of organ of windpipe OBOL:automatic mucosa of trachea OBOL:automatic mucosa of windpipe OBOL:automatic mucous membrane of trachea FMA:7471 mucous membrane of trachea OBOL:automatic mucous membrane of windpipe OBOL:automatic organ mucosa of trachea OBOL:automatic organ mucosa of windpipe OBOL:automatic trachea mucosa OBOL:automatic trachea mucosa of organ OBOL:automatic trachea mucous membrane OBOL:automatic trachea organ mucosa OBOL:automatic tracheal mucous membrane FMA:7471 tunica mucosa (tracheae) FMA:7471 tunica mucosa tracheae FMA:7471 FMA:TA windpipe mucosa OBOL:automatic windpipe mucosa of organ OBOL:automatic windpipe mucous membrane OBOL:automatic windpipe organ mucosa OBOL:automatic The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified]. consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77 Anatomical system that consists of the muscles of the body.[VSAO] we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA AAO:0000307 BILA:0000088 BTO:0001369 BTO:0001485 EFO:0000801 EMAPA:35578 FBbt:00005069 FMA:72954 MA:0002888 MAT:0000025 MIAA:0000025 VSAO:0000033 XAO:0004042 muscle system muscle system of body muscular system musculature system set of all muscles set of muscles of body vertebrate muscular system uberon muskelsystem UBERON:0000383 musculature of body The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified]. VSAO:0000033 Anatomical system that consists of the muscles of the body.[VSAO] 2012-08-14 VSAO:0000033 VSAO VSAO:curator we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA MA muscular system FMA:72954 musculature system BILA:0000088 set of all muscles FMA:72954 set of muscles of body FMA:72954 vertebrate muscular system BTO:0001369 muskelsystem BTO:0001485 Tissue that surrounds the lens nucleus BTO:0001632 CALOHA:TS-0542 FMA:58970 MESH:A09.371.509.225 cortex of lens uberon UBERON:0000389 lens cortex Tissue that surrounds the lens nucleus cortex of lens FMA:58970 The core of the crystalline lens, surrounded by the cortex. BTO:0001633 FMA:58971 MESH:A09.371.509.670 nucleus of lens uberon UBERON:0000390 lens nucleus The core of the crystalline lens, surrounded by the cortex. BTO:0001633 nucleus of lens FMA:58971 An epithelium that is part of a colon [Automatically generated definition]. Intestinal epithelium which lines the lumen of the posterior intestine.[TAO] BTO:0001709 CALOHA:TS-0163 EMAPA:18941 FMA:17302 MA:0003195 TAO:0005128 ZFA:0005128 colon epithelial tissue colon epithelium epithelial tissue of colon epithelial tissue of large bowel epithelium of colon epithelium of large bowel large bowel epithelial tissue large bowel epithelium posterior intestine epithelium uberon UBERON:0000397 colonic epithelium An epithelium that is part of a colon [Automatically generated definition]. OBOL:automatic Intestinal epithelium which lines the lumen of the posterior intestine.[TAO] 2012-08-14 TAO:0005128 TAO ZFIN:curator colon epithelial tissue OBOL:automatic colon epithelium FMA:17302 colon epithelium OBOL:automatic epithelial tissue of colon OBOL:automatic epithelial tissue of large bowel OBOL:automatic epithelium of colon OBOL:automatic epithelium of large bowel OBOL:automatic large bowel epithelial tissue OBOL:automatic large bowel epithelium OBOL:automatic posterior intestine epithelium ZFA:0005128 The nasal vestibule is the most anterior part of the nasal cavity. It's enclosed by the cartilages of nose and lined by the same epithelium of the skin. The other part of the nasal cavity, which is lined by the respiratory epithelium, is called nasal cavity proper. [WP,unvetted]. BTO:0001761 CALOHA:TS-0660 FMA:59644 vestibular part of nasal cavity uberon vestibulum nasale vestibulum nasi UBERON:0000402 nasal vestibule The nasal vestibule is the most anterior part of the nasal cavity. It's enclosed by the cartilages of nose and lined by the same epithelium of the skin. The other part of the nasal cavity, which is lined by the respiratory epithelium, is called nasal cavity proper. [WP,unvetted]. vestibular part of nasal cavity FMA:59644 vestibulum nasale BTO:0001761 vestibulum nasi vestibulum nasi BTO:0001761 A gland in which the principal secretory cells are serous secreting cells. glands that secrete watery albuminous material that often contains enzymes[MP:0008052]. BTO:0001837 EMAPA:37950 FMA:62889 uberon UBERON:0000409 serous gland A gland in which the principal secretory cells are serous secreting cells. glands that secrete watery albuminous material that often contains enzymes[MP:0008052]. MP:0008052 EMAPA:37950 MA:th A mucosa that is part of a bronchus [Automatically generated definition]. BTO:0001846 FMA:62652 bronchi mucosa bronchi mucosa of organ bronchi mucous membrane bronchi organ mucosa bronchial trunk mucosa bronchial trunk mucosa of organ bronchial trunk mucous membrane bronchial trunk organ mucosa bronchus mucosa bronchus mucosa of organ bronchus mucous membrane bronchus organ mucosa mucosa of bronchi mucosa of bronchial trunk mucosa of bronchus mucosa of organ of bronchi mucosa of organ of bronchial trunk mucosa of organ of bronchus mucous membrane of bronchi mucous membrane of bronchial trunk mucous membrane of bronchus organ mucosa of bronchi organ mucosa of bronchial trunk organ mucosa of bronchus tunica mucosa bronchi uberon UBERON:0000410 bronchial mucosa A mucosa that is part of a bronchus [Automatically generated definition]. OBOL:automatic bronchi mucosa OBOL:automatic bronchi mucosa of organ OBOL:automatic bronchi mucous membrane OBOL:automatic bronchi organ mucosa OBOL:automatic bronchial trunk mucosa OBOL:automatic bronchial trunk mucosa of organ OBOL:automatic bronchial trunk mucous membrane OBOL:automatic bronchial trunk organ mucosa OBOL:automatic bronchus mucosa OBOL:automatic bronchus mucosa of organ OBOL:automatic bronchus mucous membrane OBOL:automatic bronchus organ mucosa OBOL:automatic mucosa of bronchi OBOL:automatic mucosa of bronchial trunk OBOL:automatic mucosa of bronchus OBOL:automatic mucosa of organ of bronchi OBOL:automatic mucosa of organ of bronchial trunk OBOL:automatic mucosa of organ of bronchus OBOL:automatic mucous membrane of bronchi OBOL:automatic mucous membrane of bronchial trunk OBOL:automatic mucous membrane of bronchus FMA:62652 mucous membrane of bronchus OBOL:automatic organ mucosa of bronchi OBOL:automatic organ mucosa of bronchial trunk OBOL:automatic organ mucosa of bronchus OBOL:automatic tunica mucosa bronchi FMA:62652 FMA:TA A gland in which the principal secretory cells are mucus secreting cells. In frogs and salamanders, this is the smaller of the two types of gland, the other being the granular (poison) gland. In these species the mucous gland is a cluster of cells that release secretion into a common duct[Kardong] AAO:0010601 BTO:0001979 EMAPA:37913 FMA:62888 glandula mucosa uberon muciparous gland mucous secreting gland mucus gland mucus-secreting gland UBERON:0000414 mucous gland A gland in which the principal secretory cells are mucus secreting cells. In frogs and salamanders, this is the smaller of the two types of gland, the other being the granular (poison) gland. In these species the mucous gland is a cluster of cells that release secretion into a common duct[Kardong] NCBITaxon:8292 ISBN10:0073040584 EMAPA:37913 MA:th glandula mucosa muciparous gland BTO:0001979 An anatomical wall that is part of an artery [Automatically generated definition]. BTO:0002009 FMA:14155 galen:ArterialWall arterial wall wall of artery uberon UBERON:0000415 artery wall An anatomical wall that is part of an artery [Automatically generated definition]. OBOL:automatic arterial wall FMA:14155 wall of artery FMA:14155 A portion of organism substance that is produced by exocrine glands. BTO has two distunct classes, with exocrine glandular secretion a subtype of secretion - however, all examples in BTO directly under secretion appear to be exocrine gland secretions UBERON:0006540 secretion AEO:0001005 BTO:0002977 BTO:0002979 EMAPA:36535 FMA:9675 MA:0002504 MESH:D012634 NCIT:C34062 UMLS:C1516992 galen:Secretion bodily secretion exocrine gland fluid/secretion secreted substance uberon exocrine gland fluid exocrine gland fluid or secretion exocrine gland secretion external secretion UBERON:0000456 secretion of exocrine gland A portion of organism substance that is produced by exocrine glands. BTO has two distunct classes, with exocrine glandular secretion a subtype of secretion - however, all examples in BTO directly under secretion appear to be exocrine gland secretions BTO secretion FMA:9675 UMLS:C1516992 ncithesaurus:Exocrine_Gland_Fluid_or_Secretion bodily secretion MESH:D012634 exocrine gland fluid/secretion MA:0002504 external secretion BTO:0002977 The region of the opening of the uterine cervix into the uterine cavity. BTO:0003002 FMA:86485 NCIT:C12309 UMLS:C0227837 uberon UBERON:0000458 endocervix The region of the opening of the uterine cervix into the uterine cavity. BTO:0003002 UMLS:C0227837 ncithesaurus:Endocervix An anatomical wall that is part of a uterus [Automatically generated definition]. BTO:0003083 FMA:17560 anatomical wall of uterus uterus anatomical wall uterus wall wall of uterus uberon UBERON:0000459 uterine wall An anatomical wall that is part of a uterus [Automatically generated definition]. OBOL:automatic anatomical wall of uterus OBOL:automatic uterus anatomical wall OBOL:automatic uterus wall OBOL:automatic wall of uterus OBOL:automatic organism substance Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body. AAO:0010839 AEO:0000004 BILA:0000004 CALOHA:TS-2101 CARO:0000004 EHDAA2:0003004 EMAPA:35178 FBbt:00007019 FMA:9669 HAO:0000004 MA:0002450 NCIT:C13236 SPD:0000008 TAO:0001487 TGMA:0001824 VHOG:0001726 XAO:0004001 ZFA:0001487 galen:BodySubstance body fluid or substance body substance organism substance portion of body substance portion of organism substance uberon UBERON:0000463 organism substance this relationship may be too strong and may be weakened in future Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body. body fluid or substance MA:0002450 body substance FMA:9669 organism substance CARO:0000004 portion of body substance FMA:9669 portion of organism substance ZFA:0001487 Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures. lumen space AAO:0010110 AEO:0000005 BILA:0000005 CARO:0000005 EHDAA2:0003005 FBbt:00007017 FMA:5897 HAO:0000005 NCIT:C94478 TAO:0001668 TGMA:0001825 UMLS:C0524461 VHOG:0001728 XAO:0003190 ZFA:0001643 lumen space uberon anatomical spaces UBERON:0000464 anatomical space Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures. UMLS:C0524461 ncithesaurus:Lumen_Space anatomical spaces ZFA:0001643 material anatomical entity Anatomical entity that has mass. AAO:0010264 AEO:0000006 BILA:0000006 CARO:0000006 EHDAA2:0003006 FBbt:00007016 FMA:67165 HAO:0000006 TAO:0001836 TGMA:0001826 VHOG:0001721 uberon UBERON:0000465 material anatomical entity Anatomical entity that has mass. Anatomical entity that has no mass. AAO:0010265 AEO:0000007 BILA:0000007 CARO:0000007 EHDAA2:0003007 FBbt:00007015 FMA:67112 HAO:0000007 TAO:0001835 TGMA:0001827 VHOG:0001727 immaterial physical anatomical entity uberon UBERON:0000466 immaterial anatomical entity Anatomical entity that has no mass. immaterial physical anatomical entity FMA:67112 Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function. system AAO:0000007 AEO:0000011 BILA:0000011 BSA:0000049 CALOHA:TS-2088 CARO:0000011 EHDAA2:0003011 EHDAA:392 EMAPA:16103 EV:0100000 FBbt:00004856 FMA:7149 HAO:0000011 MA:0000003 NCIT:C12919 OpenCyc:Mx4rCWM0QCtDEdyAAADggVbxzQ TAO:0001439 TGMA:0001831 UMLS:C0460002 VHOG:0001725 WBbt:0005746 WBbt:0005763 XAO:0003002 ZFA:0001439 galen:AnatomicalSystem body system connected anatomical system organ system uberon anatomical systems UBERON:0000467 anatomical system Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function. CARO:0000011 system GO:0048731 UMLS:C0460002 ncithesaurus:Organ_System body system NIFSTD:birnlex_14 connected anatomical system CARO:0000011 anatomical systems ZFA:0001439 Anatomical structure that is an individual member of a species and consists of more than one cell. TODO - split body and mc organism? body continues after death stage organismal organism AAO:0010026 AEO:0000191 BILA:0000012 BSA:0000038 BTO:0000042 CARO:0000012 EFO:0002906 EHDAA2:0003103 EHDAA2:0003191 EHDAA:1 EMAPA:25765 EV:0100016 FBbt:00000001 FMA:256135 HAO:0000012 NCIT:C13041 TADS:0000001 TAO:0001094 TGMA:0001832 VHOG:0000671 WBbt:0007833 XAO:0003004 ZFA:0001094 galen:Organism ncithesaurus:Whole_Organism multi-cellular organism animal uberon Koerper body whole body whole organism UBERON:0000468 multicellular organism Anatomical structure that is an individual member of a species and consists of more than one cell. CARO:0000012 organism FBbt:00000001 VHOG:0000671 WBbt:0007833 multi-cellular organism CARO:0000012 animal BTO:0000042 Koerper BTO:0001489 body AEO:0000103 FMA:256135 NCIT:C13041 whole body BTO:0001489 whole organism FBbt:00000001 The organs and associated structures associated with bearing offspring in a female animal. By far, sexual reproduction is the more common pattern among living vertebrate forms and its widespread occurrence suggests that it is the plesiomorphic, or primitive, reproductive mode among the vertebrates.[well established][VHOG] BTO:0000083 CALOHA:TS-1303 EFO:0000969 EHDAA2:0000506 EHDAA:8116 EMAPA:17959 EV:0100110 FBbt:00004864 FMA:45663 GAID:364 HAO:0000324 MA:0000381 MESH:D005836 MIAA:0000028 NCIT:C12402 OpenCyc:Mx4rvVipTZwpEbGdrcN5Y29ycA TGMA:0000635 UMLS:C0700038 VHOG:0000726 WBbt:0006748 WikipediaCategory:Female_reproductive_system XAO:0000156 female organism genitalia female organism reproductive system genitalia of female organism reproductive system of female organism uberon female genital system female genital tract female genitalia female genitals female reproductive tract gynaecological tissue systema genitale femininum UBERON:0000474 female reproductive system The organs and associated structures associated with bearing offspring in a female animal. MP:0001119 By far, sexual reproduction is the more common pattern among living vertebrate forms and its widespread occurrence suggests that it is the plesiomorphic, or primitive, reproductive mode among the vertebrates.[well established][VHOG] 2012-09-17 VHOG:0000726 VHOG ISBN:978-0792383369 Lombardi J, Comparative vertebrate reproduction (1998) p.43 UMLS:C0700038 ncithesaurus:Female_Reproductive_System female organism genitalia OBOL:automatic female organism reproductive system OBOL:automatic genitalia of female organism OBOL:automatic reproductive system of female organism OBOL:automatic female genitals XAO:0000156 female reproductive tract MA:0000381 gynaecological tissue BTO:0000083 systema genitale femininum BTO:0000083 Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument. Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency AAO:0010053 AEO:0000032 BILA:0000032 CALOHA:TS-2084 CARO:0000032 EFO:0000808 EHDAA2:0003032 EMAPA:36031 FBbt:00007009 FMA:7153 HAO:0000032 MA:0002433 MAT:0000293 MESH:D001829 MIAA:0000293 NCIT:C32221 OpenCyc:Mx4rvViAHJwpEbGdrcN5Y29ycA TAO:0001308 TGMA:0001840 UMLS:C0229962 VHOG:0001758 XAO:0003013 ZFA:0001308 galen:BodyPart anatomic region uberon body part body region cardinal body part UBERON:0000475 organism subdivision CARO Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument. CARO:0000032 CARO:DOS UMLS:C0229962 ncithesaurus:Body_Part anatomic region MA:0002433 body region FMA:7153 cardinal body part FMA:7153 Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue. AAO:0010268 AEO:0000040 BILA:0000040 CARO:0000040 EHDAA2:0003040 FBbt:00007013 FMA:63863 HAO:0000040 TAO:0000382 TGMA:0001841 XAO:0003162 ZFA:0000382 uberon acellular anatomical structures UBERON:0000476 acellular anatomical structure CARO Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue. acellular anatomical structures ZFA:0000382 anatomical cluster Anatomical group that has its parts adjacent to one another. Will be obsoleted in CARO v2 [https://github.com/obophenotype/caro/issues/3] AAO:0010009 AEO:0000041 BILA:0000041 CARO:0000041 EHDAA2:0003041 FBbt:00007277 FMA:49443 HAO:0000041 TADS:0000605 TAO:0001478 TGMA:0001842 VHOG:0001737 XAO:0003160 ZFA:0001478 uberon UBERON:0000477 anatomical cluster Anatomical group that has its parts adjacent to one another. A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis. AAO:0010020 AEO:0000042 BILA:0000042 CALOHA:TS-2119 CARO:0000042 EHDAA2:0003042 EHDAA:46 FBbt:00005835 FMA:85537 HAO:0000042 NCIT:C34055 TAO:0000020 TGMA:0001843 UMLS:C1282438 VHOG:0000292 XAO:0004005 ZFA:0000020 extra-embryonic structure uberon extraembryonic structures extraembryonic tissue UBERON:0000478 see also conceptus extraembryonic component in EHDAA2. extraembryonic structure A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis. CARO:DOS UMLS:C1282438 ncithesaurus:Extraembryonic_Structure extraembryonic structures ZFA:0000020 tissue Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. changed label and definition to reflect CARO2 AAO:0000607 AAO:0010054 AEO:0000043 BILA:0000043 CALOHA:TS-2090 CARO:0000043 EHDAA2:0003043 EMAPA:35868 FBbt:00007003 FMA:9637 HAO:0000043 MA:0003002 MESH:D014024 NCIT:C12801 TAO:0001477 TGMA:0001844 UMLS:C0040300 VHOG:0001757 WBbt:0005729 XAO:0003040 ZFA:0001477 galen:Tissue portion of tissue tissue portion simple tissue uberon UBERON:0000479 tissue CARO Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. CARO:0000043 UMLS:C0040300 ncithesaurus:Tissue portion of tissue CARO:0000043 simple tissue AEO:0000043 multi-tissue structure Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types. AAO:0010048 AEO:0000055 BILA:0000055 CARO:0000055 EHDAA2:0003055 FBbt:00007010 HAO:0000055 TAO:0001488 TGMA:0001847 VHOG:0001762 XAO:0003037 ZFA:0001488 uberon multi-tissue structures UBERON:0000481 multi-tissue structure CARO Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types. CARO:0000055 multi-tissue structures ZFA:0001488 epithelium Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO]. The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG] epithelial AAO:0000144 AAO:0010055 AEO:0000066 BILA:0000066 BTO:0000416 CALOHA:TS-0288 CARO:0000066 EHDAA2:0003066 EMAPA:32738 FBbt:00007005 FMA:9639 GAID:402 HAO:0000066 MA:0003060 MESH:D004848 NCIT:C12710 TAO:0001486 UMLS:C0014609 VHOG:0000387 XAO:0003045 ZFA:0001486 epithelial tissue portion of epithelium uberon UBERON:0000483 epithelium Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO]. The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG] 2012-09-17 VHOG:0000387 VHOG ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.59 UMLS:C0014609 ncithesaurus:Epithelium portion of epithelium FMA:9639 Unilaminar epithelium that consists of a single layer of cuboidal cells. needs to be synchronized with CL - there is no distinct cuboidal cell in CL AAO:0010064 AEO:0000067 BILA:0000067 CARO:0000067 EHDAA2:0003067 FMA:45566 HAO:0000067 NCIT:C33553 TAO:0001497 UMLS:C0836134 XAO:0004009 ZFA:0001497 epithelium simplex cuboideum uberon simple cuboidal epithelia UBERON:0000484 simple cuboidal epithelium Unilaminar epithelium that consists of a single layer of cuboidal cells. UMLS:C0836134 ncithesaurus:Simple_Cuboidal_Epithelium simple cuboidal epithelia ZFA:0001497 Unilaminar epithelium, which consists of a single layer of columnar cells. Examples: ciliated columnar epithelium, gastric epithelium, microvillus columnar epithelium.[FMA] columnar epithelium columnar epithlium AAO:0010063 AEO:0000068 BILA:0000068 CARO:0000068 EHDAA2_RETIRED:0003068 FBbt:00007027 FMA:45567 HAO:0000068 NCIT:C33552 TAO:0001496 UMLS:C0836135 XAO:0004008 ZFA:0001496 epithelium simplex columnare simple columnar epithelium uberon simple columnar epithelia UBERON:0000485 simple columnar epithelium Unilaminar epithelium, which consists of a single layer of columnar cells. Examples: ciliated columnar epithelium, gastric epithelium, microvillus columnar epithelium.[FMA] FMA:FMA columnar epithelium EHDAA2:0003068 columnar epithlium AEO:0000068 UMLS:C0836135 ncithesaurus:Simple_Columnar_Epithelium simple columnar epithelia ZFA:0001496 Epithelium which consists of more than one layer of epithelial cells that may or may not be in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, ciliated stratified columnar epithelium.[FMA] Epithelium that consists of more than one layer of epithelial cells.[CARO] AAO:0010059 AEO:0000069 BILA:0000069 BTO:0002074 CARO:0000069 EHDAA2:0003069 FMA:45562 HAO:0000069 NCIT:C33622 TAO:0001494 UMLS:C0682575 XAO:0004006 ZFA:0001494 stratified epithelium uberon laminated epithelium UBERON:0000486 multilaminar epithelium Epithelium which consists of more than one layer of epithelial cells that may or may not be in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, ciliated stratified columnar epithelium.[FMA] FMA:FMA Epithelium that consists of more than one layer of epithelial cells.[CARO] 2012-06-20 CARO:0000069 CARO FMA:45562 UMLS:C0682575 ncithesaurus:Stratified_Epithelium laminated epithelium BTO:0002074 Unilaminar epithelium which consists of a single layer of squamous cells. Examples: pulmonary alveolar epithelium, endothelium.[FMA] Unilaminar epithelium that consists of a single layer of squamous cells.[CARO] AAO:0010066 AEO:0000070 BILA:0000070 BTO:0002073 CARO:0000070 EHDAA2:0003070 FMA:45565 HAO:0000070 NCIT:C13178 TAO:0001498 UMLS:C0836133 XAO:0004010 ZFA:0001498 epithelium simplex squamosum uberon simple squamous epithelia UBERON:0000487 simple squamous epithelium Unilaminar epithelium which consists of a single layer of squamous cells. Examples: pulmonary alveolar epithelium, endothelium.[FMA] FMA:45565 Unilaminar epithelium that consists of a single layer of squamous cells.[CARO] 2012-06-20 CARO:0000070 CARO FMA:45565 UMLS:C0836133 ncithesaurus:Simple_Squamous_Epithelium simple squamous epithelia ZFA:0001498 Epithelium that consists of epithelial cells not arranged in one ore more layers. AAO:0010057 AEO:0000071 BILA:0000071 CARO:0000071 EHDAA2:0003071 FMA:61741 HAO:0000071 TAO:0001493 XAO:0004004 ZFA:0001493 heterogenous epithelium uberon atypical epithelia UBERON:0000488 atypical epithelium Epithelium that consists of epithelial cells not arranged in one ore more layers. atypical epithelia ZFA:0001493 Compound organ that contains one or more macroscopic anatomical spaces. this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future AAO:0010016 AEO:0000072 BILA:0000072 CARO:0000072 EHDAA2:0003072 FMA:55671 HAO:0000072 TAO:0001490 TGMA:0001857 VHOG:0001730 XAO:0003165 ZFA:0001490 cavitated organ uberon cavitated compound organs UBERON:0000489 cavitated compound organ Compound organ that contains one or more macroscopic anatomical spaces. cavitated organ FMA:55671 cavitated compound organs ZFA:0001490 Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA] consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable Epithelium that consists of a single layer of epithelial cells.[CARO] AAO:0010062 AEO:0000073 BILA:0000073 BTO:0002073 CARO:0000073 EHDAA2:0003073 FMA:45561 HAO:0000073 NCIT:C33554 TAO:0001495 UMLS:C0682574 XAO:0004007 ZFA:0001495 simple epithelium uberon unilaminar epithelia UBERON:0000490 unilaminar epithelium Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA] FMA:45561 Epithelium that consists of a single layer of epithelial cells.[CARO] 2012-06-20 CARO:0000073 CARO FMA:45561 UMLS:C0682574 ncithesaurus:Simple_Epithelium simple epithelium FMA:45561 unilaminar epithelia ZFA:0001495 Mucus is a bodily fluid consisting of a slippery secretion of the lining of the mucous membranes in the body. It is a viscous colloid containing antiseptic enzymes (such as lysozyme) and immunoglobulins. Mucus is produced by goblet cells in the mucous membranes that cover the surfaces of the membranes. It is made up of mucins and inorganic salts suspended in water. mucoid mucous CALOHA:TS-2144 ENVO:02000040 FMA:66938 GAID:1164 MESH:D009093 NCIT:C13259 OpenCyc:Mx4rvVjHq5wpEbGdrcN5Y29ycA UMLS:C0026727 galen:Mucus uberon UBERON:0000912 mucus Mucus is a bodily fluid consisting of a slippery secretion of the lining of the mucous membranes in the body. It is a viscous colloid containing antiseptic enzymes (such as lysozyme) and immunoglobulins. Mucus is produced by goblet cells in the mucous membranes that cover the surfaces of the membranes. It is made up of mucins and inorganic salts suspended in water. UMLS:C0026727 ncithesaurus:Mucus Subdivision of trunk that lies between the head and the abdomen. note that we use the slightly verbose term 'thoracic segment of trunk' to avoid confusuon with insect thorax. todo - taxonomic constraints. Also, in FMA 'thorax' is a synonym for chest EMAPA:35862 FMA:259209 MA:0000022 thorax uberon anterior subdivision of trunk upper body upper trunk UBERON:0000915 thoracic segment of trunk FMA Subdivision of trunk that lies between the head and the abdomen. thorax MA:0000022 upper trunk FMA:259209 The subdivision of the vertebrate body between the thorax and pelvis. The ventral part of the abdomen contains the abdominal cavity and visceral organs. The dorsal part includes the abdominal section of the vertebral column. Vertebrate specific. In arthropods 'abdomen' is the most distal section of the body which lies behind the thorax or cephalothorax. If need be we can introduce some grouping class abdominal celiac BTO:0000020 CALOHA:TS-0001 EFO:0000968 EMAPA:35102 EV:0100011 FMA:9577 GAID:16 MA:0000029 MAT:0000298 MESH:A01.047 MIAA:0000298 OpenCyc:Mx4rvVjgyZwpEbGdrcN5Y29ycA galen:Abdomen abdominopelvic region abdominopelvis uberon adult abdomen belly celiac region UBERON:0000916 abdomen MA The subdivision of the vertebrate body between the thorax and pelvis. The ventral part of the abdomen contains the abdominal cavity and visceral organs. The dorsal part includes the abdominal section of the vertebral column. abdominopelvic region FMA:9577 abdominopelvis FMA:9577 Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. embryonic Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo AAO:0011035 AEO:0000169 BILA:0000056 BSA:0000039 BTO:0000379 CALOHA:TS-0229 EFO:0001367 EHDAA2:0000002 EHDAA2_RETIRED:0003236 EHDAA:38 EMAPA:16039 FBbt:00000052 FMA:69068 GAID:963 MAT:0000226 MESH:D004622 MIAA:0000019 NCIT:C28147 OGEM:000001 OpenCyc:Mx4rwP1ceZwpEbGdrcN5Y29ycA UMLS:C0013935 VHOG:0001766 XAO:0000113 ZFA:0000103 embryonic organism uberon developing organism developmental tissue UBERON:0000922 embryo Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. BTO:0000379 FB:FBrf0039741 FB:FBrf0041814 GO:0009790 Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo ZFA UMLS:C0013935 ncithesaurus:Embryo embryonic organism BILA:0000056 developing organism BILA:0000056 A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm. The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] embryonic tissue AAO:0000480 BILA:0000035 BTO:0000556 EMAPA:36033 FBbt:00000110 FMA:69069 GAID:1303 MESH:A16.254.425 NCIT:C12950 NCIT:C54105 TAO:0001122 UMLS:C0920502 UMLS:C1708239 VHOG:0001223 XAO:0003011 ZFA:0001122 germinal layer primary germ layer uberon embryonic germ layer embryonic germ layers UBERON:0000923 Classically the germ layers are ectoderm, mesoderm and endoderm. Alternatively: primary = ectoderm, endoderm; secondary=mesoderm; tertiary=dorsal mesoderm, NC[https://github.com/obophenotype/uberon/wiki/The-neural-crest] germ layer A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm. The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] 2012-09-17 VHOG:0001223 VHOG ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 embryonic tissue FMA:69069 UMLS:C0920502 ncithesaurus:Embryonic_Tissue UMLS:C1708239 ncithesaurus:Germinal_Layer germinal layer ncithesaurus:Germinal_Layer primary germ layer GO:0001704 ZFA:0001122 Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO] The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] ectodermal AAO:0000137 BILA:0000036 BTO:0000315 CALOHA:TS-0216 EFO:0000414 EHDAA2:0000428 EMAPA:16069 EV:0100003 FBbt:00000111 FMA:69070 GAID:1304 MAT:0000155 MAT:0000173 MESH:A16.254.425.273 MIAA:0000173 NCIT:C12703 TAO:0000016 UMLS:C0013574 VHOG:0000153 XAO:0000001 ZFA:0000016 embryonic ectoderm uberon UBERON:0000924 ectoderm Bgee:AN Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO] 2012-06-20 AAO:0000137 AAO AAO:EJS The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] 2012-09-17 VHOG:0000153 VHOG ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 UMLS:C0013574 ncithesaurus:Ectoderm embryonic ectoderm VHOG:0000153 Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] endodermal AAO:0000139 BILA:0000038 BTO:0000800 CALOHA:TS-0273 EFO:0002545 EHDAA2:0000436 EMAPA:16062 EV:0100005 FBbt:00000125 FMA:69071 GAID:1305 MAT:0000175 MESH:A16.254.425.407 MIAA:0000175 NCIT:C12706 TAO:0000017 UMLS:C0014144 VHOG:0000154 XAO:0000090 ZFA:0000017 uberon entoderm UBERON:0000925 endoderm Bgee:AN Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] 2012-09-17 VHOG:0000154 VHOG ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 UMLS:C0014144 ncithesaurus:Endoderm entoderm The middle germ layer of the embryo, between the endoderm and ectoderm. Primary germ layer that is the middle of the embryonic germ layers.[AAO] The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] mesodermal sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates UBERON:0003263 AAO:0000304 BILA:0000037 BTO:0000839 CALOHA:TS-0623 EFO:0001981 EHDAA2:0001128 EHDAA:124 EHDAA:160 EHDAA:183 EMAPA:16083 EV:0100006 FBbt:00000126 FMA:69072 GAID:522 MAT:0000174 MESH:A16.254.425.660 MIAA:0000174 NCIT:C12750 TAO:0000041 UMLS:C0025485 VHOG:0000152 XAO:0000050 ZFA:0000041 uberon embryonic mesoderm entire mesoderm mesodermal mantle UBERON:0000926 mesoderm sometimes not considered primary Bgee:AN The middle germ layer of the embryo, between the endoderm and ectoderm. Primary germ layer that is the middle of the embryonic germ layers.[AAO] 2012-06-20 AAO:0000304 AAO AAO:EJS The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] 2012-09-17 VHOG:0000152 VHOG ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates UMLS:C0025485 ncithesaurus:Mesoderm embryonic mesoderm VHOG:0000152 entire mesoderm Anterior part of the embryonic digestive tract that develops into a mouth. The stomodeum includes as parts an invagination of the ectoderm and the stomodeal cavity. consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO] the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx stomodeal This class groups together disparate structures as all being the anterior part of the early metazoan digestive tract and precursor of the mouth. However, the developmental processes vary, so this class may be split in future. E.g. in mammals it is a rostral depression surrounded by prominences. Outgrowth of the prominences produces a stomodeal cavity. stomodeal-hypophyseal primordium BTO:0004224 EHDAA2:0001929 EMAPA:16263 FBbt:00000439 FMA:295846 NCIT:C34306 TAO:0001290 TGMA:0000135 UMLS:C1514977 XAO:0000269 ZFA:0001290 mouth primordium primitive oral cavity stomatodeum stomodaeum uberon mouth pit oral ectoderm oral pit UBERON:0000930 stomodeum Anterior part of the embryonic digestive tract that develops into a mouth. The stomodeum includes as parts an invagination of the ectoderm and the stomodeal cavity. Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO] 2012-08-14 TAO:0001290 TAO ZFIN:curator the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx MP:0012522 NCBITaxon:40674 stomodeal-hypophyseal primordium XAO:0000269 UMLS:C1514977 ncithesaurus:Stomodeum mouth primordium XAO:0000269 primitive oral cavity stomatodeum mouth pit EMAPA:16263 oral ectoderm ZFA:0001290,ZFIN:ZDB-PUB-100726-23 oral pit EMAPA:16263 Inward fold on the surface of the embryonic ectoderm that develops into an ectodermal terminal part of the digestive tract. removed WBbt:0006795 'proctodeum' - junction between the alimentary and genital tracts in the male. An inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[TAO] Inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[AAO] proctodeal AAO:0011087 EHDAA2:0000121 EMAPA:25038 FBbt:00000123 NCIT:C34278 TAO:0000066 UMLS:C0231054 VHOG:0000139 XAO:0001019 ZFA:0000066 embryonic proctodaeum proctodaeum amnioproctodeal invagination uberon anal pit anus porus UBERON:0000931 proctodeum EHDAA2 EHDAA2 Inward fold on the surface of the embryonic ectoderm that develops into an ectodermal terminal part of the digestive tract. ZFA:0000066 An inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[TAO] 2012-08-14 TAO:0000066 TAO ZFIN:curator Inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[AAO] 2012-06-20 AAO:0011087 AAO ZFA:0000066 UMLS:C0231054 ncithesaurus:Proctodeum amnioproctodeal invagination FBbt:00000123 anal pit VHOG:0000139 anus porus XAO:0001019 stomach An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium. Portion of alimentary canal with increased circular and longitudinal smooth muscle. Bounded posteriorly by the pyloric sphincter. Mucosal lining has increased folding.[AAO] It appears that the stomach has an ancient origin. The stomach first appears in the fish lineage. The prevertebrate chordates do not have a true stomach, whereas the cartilaginous and bony fish do. Although most fish do have a true stomach, some fish species appear to have lost the stomach secondarily. The remaining vertebrate lineages do have a true stomach (at least in the adult animal), although there is great variation in the size and shape of the stomach.[well established][VHOG] We restrict this to the vertebrate specific structure - see the grouping class 'food storage organ' for analogous structures in other species. Teleosts: Zebrafish is functionally stomach-less, but may retain ontogenic footprint. Although the precise shape and size of the stomach varies widely among different vertebrates, the relative positions of the oesophageal and duodenal openings remain relatively constant. As a result, the organ always curves somewhat to the left before curving back to meet the pyloric sphincter. However, lampreys, hagfishes, chimaeras, lungfishes, and some teleost fish have no stomach at all, with the oesophagus opening directly into the intestine. The gastric lining is usually divided into two regions, an anterior portion lined by fundic glands, and a posterior with pyloric glands. Cardiac glands are unique to mammals, and even then are absent in a number of species. The distributions of these glands vary between species, and do not always correspond with the same regions as in man. Furthermore, in many non-human mammals, a portion of the stomach anterior to the cardiac glands is lined with epithelium essentially identical to that of the oesophagus. Ruminants, in particular, have a complex stomach, the first three chambers of which are all lined with oesophageal mucosa AAO:0000579 ANISEED:1235297 BTO:0001307 CALOHA:TS-0980 EFO:0000837 EHDAA2:0001915 EHDAA:2993 EMAPA:17021 EV:0100070 FMA:7148 GAID:293 MA:0000353 MAT:0000051 MESH:A03.492.766 MIAA:0000051 NCIT:C12391 OpenCyc:Mx4rvVjlqpwpEbGdrcN5Y29ycA TAO:0002121 UMLS:C0038351 VHOG:0000408 XAO:0000128 galen:Stomach stomach chamber uberon anterior intestine gaster mesenteron ventriculus UBERON:0000945 stomach stomach 胃 cjm cjm An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium. ISBN10:0073040584 Portion of alimentary canal with increased circular and longitudinal smooth muscle. Bounded posteriorly by the pyloric sphincter. Mucosal lining has increased folding.[AAO] 2012-06-20 AAO:0000579 AAO AAO:EJS It appears that the stomach has an ancient origin. The stomach first appears in the fish lineage. The prevertebrate chordates do not have a true stomach, whereas the cartilaginous and bony fish do. Although most fish do have a true stomach, some fish species appear to have lost the stomach secondarily. The remaining vertebrate lineages do have a true stomach (at least in the adult animal), although there is great variation in the size and shape of the stomach.[well established][VHOG] 2012-09-17 VHOG:0000408 VHOG DOI:10.1046/j.1525-142x.2000.00076.x Smith DM, Grasty RC, Theodosiou NA, Tabin CJ, Nascone-Yoder NM, Evolutionary relationships between the amphibian, avian, and mammalian stomachs. Evolution and development (2000) We restrict this to the vertebrate specific structure - see the grouping class 'food storage organ' for analogous structures in other species. Teleosts: Zebrafish is functionally stomach-less, but may retain ontogenic footprint. Although the precise shape and size of the stomach varies widely among different vertebrates, the relative positions of the oesophageal and duodenal openings remain relatively constant. As a result, the organ always curves somewhat to the left before curving back to meet the pyloric sphincter. However, lampreys, hagfishes, chimaeras, lungfishes, and some teleost fish have no stomach at all, with the oesophagus opening directly into the intestine. The gastric lining is usually divided into two regions, an anterior portion lined by fundic glands, and a posterior with pyloric glands. Cardiac glands are unique to mammals, and even then are absent in a number of species. The distributions of these glands vary between species, and do not always correspond with the same regions as in man. Furthermore, in many non-human mammals, a portion of the stomach anterior to the cardiac glands is lined with epithelium essentially identical to that of the oesophagus. Ruminants, in particular, have a complex stomach, the first three chambers of which are all lined with oesophageal mucosa WP:Stomach#In_other_animals UMLS:C0038351 ncithesaurus:Stomach gaster BTO:0001307 ventriculus aorta The main trunk of the systemic arterial system that carries blood from the heart to all the organs and other structures of the body, bringing oxygenated blood to all parts of the body in the systemic circulation This class is currently a mixed bag, encompassing (1) the entirety of the mammalian aorta together with (2) the developmental and phylogenetic homologs of its segments: the ventral aorta and dorsal aortae. The main artery of the circulatory system which carries oxygenated blood from the heart to all the arteries of the body except those of the lungs.[AAO] When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG] aortic All amniotes have a broadly similar arrangement to that of humans, albeit with a number of individual variations. In fish, however, there are two separate vessels referred to as aortas. The ventral aorta carries de-oxygenated blood from the heart to the gills; part of this vessel forms the ascending aorta in tetrapods (the remainder forms the pulmonary artery). A second, dorsal aorta carries oxygenated blood from the gills to the rest of the body, and is homologous with the descending aorta of tetrapods. The two aortas are connected by a number of vessels, one passing through each of the gills. Amphibians also retain the fifth connecting vessel, so that the aorta has two parallel arches AAO:0010213 BTO:0000135 CALOHA:TS-0046 EFO:0000265 EMAPA:18601 EV:0100027 FMA:3734 GAID:469 MA:0000062 MAT:0000035 MESH:D001011 MIAA:0000035 NCIT:C12669 OpenCyc:Mx4rvVjvTpwpEbGdrcN5Y29ycA UMLS:C0003483 VHOG:0001523 XAO:0003010 galen:Aorta trunk of aortic tree trunk of systemic arterial tree dorsal aorta uberon arteria maxima UBERON:0000947 aorta MA EHDAA2 The main trunk of the systemic arterial system that carries blood from the heart to all the organs and other structures of the body, bringing oxygenated blood to all parts of the body in the systemic circulation ISBN:0-683-40008-8 MESH:A07.231.114.056 MP:0000272 This class is currently a mixed bag, encompassing (1) the entirety of the mammalian aorta together with (2) the developmental and phylogenetic homologs of its segments: the ventral aorta and dorsal aortae. WP The main artery of the circulatory system which carries oxygenated blood from the heart to all the arteries of the body except those of the lungs.[AAO] 2012-06-20 AAO:0010213 AAO AAO:BJB When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG] 2012-09-17 VHOG:0001523 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620 UMLS:C0003483 ncithesaurus:Aorta dorsal aorta ZFA:0000014 arteria maxima heart A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ. Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO] Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO] relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO] As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG] cardiac AAO:0010210 BILA:0000020 BTO:0000562 CALOHA:TS-0445 EFO:0000815 EHDAA2:0000738 EHDAA:420 EMAPA:16105 EV:0100018 FMA:7088 GAID:174 MA:0000072 MAT:0000036 MESH:D006321 MIAA:0000036 NCIT:C12727 OpenCyc:Mx4rvVjvDpwpEbGdrcN5Y29ycA TAO:0000114 UMLS:C0018787 VHOG:0000276 XAO:0000064 ZFA:0000114 galen:Heart chambered heart vertebrate heart branchial heart uberon Herz@de cardium UBERON:0000948 Taxon notes:" the ascidian tube-like heart lacks chambers....The ascidian heart is formed after metamorphosis as a simple tube-like structure with a single-layered myoepithelium that is continuous with a single-layered pericar- dial wall. It lacks chambers and endocardium.... The innovation of the chambered heart was a key event in vertebrate evolution, because the chambered heart generates one-way blood flow with high pressure, a critical requirement for the efficient blood supply of large-body vertebrates... all extant vertebrates have hearts with two or more chambers (Moorman and Christoffels 2003)" https://doi.org/10.1101/gad.1485706 heart MA A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ. Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO] 2012-08-14 TAO:0000114 TAO ZFIN:curator Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO] 2012-06-20 AAO:0010210 AAO AAO:BJB relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO] 2012-06-20 AAO:0010210 AAO As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG] 2012-09-17 VHOG:0000276 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481 UMLS:C0018787 ncithesaurus:Heart chambered heart branchial heart Herz@de BTO:0000562 cardium EMAPA:16105 Anatomical system that consists of the glands and parts of glands that produce endocrine secretions and help to integrate and control bodily metabolic activity. Anatomical system containing glands which regulates bodily functions though the secretion of hormones.[AAO] Multicellular organisms have complex endocrine systems, allowing responses to environmental stimuli, regulation of development, reproduction, and homeostasis. Nuclear receptors (NRs), a metazoan-specific family of ligand-activated transcription factors, play central roles in endocrine responses, as intermediates between signaling molecules and target genes. The NR family includes ligand-bound and orphan receptors, that is, receptors with no known ligand or for which there is no ligand Pocket. Understanding NR evolution has been further improved by comparison of several completed genomes, particularly those of deuterostomes and ecdysozoans. In contrast, evolution of NR ligands is still much debated. One hypothesis proposes that several independent gains and losses of ligand-binding ability in NRs occurred in protostomes and deuterostomes. A second hypothesis, pertaining to the NR3 subfamily (vertebrate steroid hormone receptors and estrogen related receptor), proposes that before the divergence of protostomes and deuterostomes, there was an ancestral steroid receptor (AncSR) that was ligand-activated and that orphan receptors secondarily lost the ability to bind a ligand. (...) Our analysis reveals that steroidogenesis has been independently elaborated in the 3 main bilaterian lineages (...).[well established][VHOG] endocrine AAO:0010279 CALOHA:TS-1301 EFO:0002969 EHDAA2:0002224 EMAPA:35306 EV:0100128 FBbt:00005068 FMA:9668 GAID:439 MA:0000012 MESH:D004703 NCIT:C12705 TAO:0001158 UMLS:C0014136 VHOG:0000098 XAO:0000158 ZFA:0001158 endocrine glandular system endocrine system systema endocrinum uberon UBERON:0000949 endocrine system Anatomical system that consists of the glands and parts of glands that produce endocrine secretions and help to integrate and control bodily metabolic activity. NLM:endocrine+system Anatomical system containing glands which regulates bodily functions though the secretion of hormones.[AAO] 2012-06-20 AAO:0010279 AAO AAO:BJB Multicellular organisms have complex endocrine systems, allowing responses to environmental stimuli, regulation of development, reproduction, and homeostasis. Nuclear receptors (NRs), a metazoan-specific family of ligand-activated transcription factors, play central roles in endocrine responses, as intermediates between signaling molecules and target genes. The NR family includes ligand-bound and orphan receptors, that is, receptors with no known ligand or for which there is no ligand Pocket. Understanding NR evolution has been further improved by comparison of several completed genomes, particularly those of deuterostomes and ecdysozoans. In contrast, evolution of NR ligands is still much debated. One hypothesis proposes that several independent gains and losses of ligand-binding ability in NRs occurred in protostomes and deuterostomes. A second hypothesis, pertaining to the NR3 subfamily (vertebrate steroid hormone receptors and estrogen related receptor), proposes that before the divergence of protostomes and deuterostomes, there was an ancestral steroid receptor (AncSR) that was ligand-activated and that orphan receptors secondarily lost the ability to bind a ligand. (...) Our analysis reveals that steroidogenesis has been independently elaborated in the 3 main bilaterian lineages (...).[well established][VHOG] 2012-09-17 VHOG:0000098 VHOG DOI:10.1073/pnas.0812138106 Markov GV, Tavares R, Dauphin-Villemant C, Demeneix BA, Baker ME, Laudet V, Independent elaboration of steroid hormone signaling pathways in metazoans. PNAS (2009) UMLS:C0014136 ncithesaurus:Endocrine_System endocrine glandular system EHDAA2:0002224 brain The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP]. requires review for applicability to invertebrate structures, e.g. synganglion Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO] Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO] The part of the central nervous system contained within the cranium, comprising the forebrain, midbrain, hindbrain, and metencephalon. It is derived from the anterior part of the embryonic neural tube (or the encephalon). Does not include retina. (CUMBO) (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG] AAO:0010478 ABA:Brain BAMS:Br BAMS:Brain BILA:0000135 BTO:0000142 CALOHA:TS-0095 DHBA:10155 EFO:0000302 EHDAA2:0000183 EHDAA:2641 EHDAA:6485 EMAPA:16894 EV:0100164 FBbt:00005095 FMA:50801 GAID:571 HBA:4005 MA:0000168 MAT:0000098 MBA:8 MBA:997 MESH:D001921 MIAA:0000098 NCIT:C12439 OpenCyc:Mx4rvVjT65wpEbGdrcN5Y29ycA PBA:3999 TAO:0000008 UMLS:C0006104 UMLS:C1269537 VHOG:0000157 XAO:0000010 ZFA:0000008 galen:Brain http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=21 uberon encephalon suprasegmental levels of nervous system suprasegmental structures synganglion the brain UBERON:0000955 brain GO FMA Bgee:AN The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP]. Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO] 2012-08-14 TAO:0000008 TAO ZFIN:curator Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO] 2012-06-20 AAO:0010478 AAO AAO:BJB The part of the central nervous system contained within the cranium, comprising the forebrain, midbrain, hindbrain, and metencephalon. It is derived from the anterior part of the embryonic neural tube (or the encephalon). Does not include retina. (CUMBO) (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000157 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 UMLS:C0006104 NIFSTD:birnlex_796 UMLS:C0006104 ncithesaurus:Brain UMLS:C1269537 NIFSTD:birnlex_796 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=21 NIFSTD:birnlex_796 encephalon BTO:0000142 suprasegmental levels of nervous system NeuroNames:21 suprasegmental structures NeuroNames:21 the brain NeuroNames:21 the transparent anterior portion of the fibrous coat of the eye that serves as the chief refractory structure corneal Compared to terrestial animals, the cornea of zebrafish is relatively flat. It consists of nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals. In fish, and aquatic vertebrates in general, the cornea plays no role in focusing light, since it has virtually the same refractive index as water AAO:0010344 BTO:0000286 CALOHA:TS-0171 EFO:0000377 EHDAA2:0000316 EHDAA:10199 EMAPA:17161 EV:0100341 FMA:58238 GAID:892 MA:0000266 MESH:D003315 NCIT:C12342 OpenCyc:Mx4rvViBa5wpEbGdrcN5Y29ycA TAO:0000640 UMLS:C0010031 VHOG:0000164 XAO:0000180 ZFA:0000640 cornea of camera-type eye uberon corneas tunica cornea UBERON:0000964 cornea XAO MA MA FMA-isa definitional the transparent anterior portion of the fibrous coat of the eye that serves as the chief refractory structure ISBN:0-683-40008-8 MESH:A09.371.060.217 MP:0001312 UMLS:C0010031 ncithesaurus:Cornea cornea of camera-type eye GO:0061303 corneas ZFA:0000640 Transparent part of camera-type eye that helps to refract light to be focused on the retina. The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] This class excludes compound eye corneal lenses. AAO:0010348 BTO:0000723 CALOHA:TS-0545 EHDAA:9057 EMAPA:17838 EV:0100343 FMA:58241 MA:0000275 MAT:0000141 MESH:A09.371.509 MIAA:0000141 NCIT:C12743 OpenCyc:Mx4rvVj0fZwpEbGdrcN5Y29ycA RETIRED_EHDAA2:0000975 TAO:0000035 UMLS:C0023317 VHOG:0000169 XAO:0000008 ZFA:0000035 camera-type eye lens eye lens lens lens crystallina uberon crystalline lens lenses ocular lens UBERON:0000965 The lens is avascular and nourished by diffusion from the aqueous and vitreous lens of camera-type eye Transparent part of camera-type eye that helps to refract light to be focused on the retina. The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] 2012-09-17 VHOG:0000169 VHOG DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007) UMLS:C0023317 ncithesaurus:Crystalline_Lens camera-type eye lens GO:0002088 eye lens lens lens crystallina crystalline lens BTO:0000723 lenses ZFA:0000035 ocular lens BTO:0000723 The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates. The portion of the eye developing from the optic primordium and including the neural retina and the retinal pigment layer. Kimmel et al, 1995.[TAO] The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] retinal AAO:0010352 BAMS:R BTO:0001175 CALOHA:TS-0865 EFO:0000832 EHDAA2:0001627 EHDAA:4757 EMAPA:17168 EV:0100348 FMA:58301 GAID:755 MA:0000276 MAT:0000142 MBA:304325711 MESH:D012160 MIAA:0000142 NCIT:C12343 NIFSTD_RETIRED:birnlex_1156 OpenCyc:Mx4rvViTfpwpEbGdrcN5Y29ycA TAO:0000152 UMLS:C0035298 UMLS:C1278894 VHOG:0000229 XAO:0000009 ZFA:0000152 inner layer of eyeball retina of camera-type eye tunica interna of eyeball uberon Netzhaut retinas UBERON:0000966 Currently this class encompasses only verteberate AOs but could in theory also include cephalopod - we may want to make a more specific class for vertebrate retina. note that this class excludes ommatidial retinas, as the retina must be part of an eyeball. Use the parent class photoreceptor array / light-sensitive tissue for arthropods retina EHDAA2 The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates. ZFIN:curator The portion of the eye developing from the optic primordium and including the neural retina and the retinal pigment layer. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000152 TAO ZFIN:curator The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] 2012-09-17 VHOG:0000229 VHOG DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007) UMLS:C0035298 NIFSTD:birnlex_1153 UMLS:C0035298 ncithesaurus:Retina UMLS:C1278894 NIFSTD:birnlex_1153 retina of camera-type eye GO:0060041 Netzhaut BTO:0001175 retinas ZFA:0000152 An organ that detects light. This class encompasses a variety of light-detecting structures from different phyla with no implication of homology, from the compound insect eye to the vertebrate camera-type eye (distinct classes are provided for each) ocular optic Note that whilst this is classified as an organ, it is in fact more of a unit composed of different structures: in Drosophila, it includes the interommatidial bristle as a part; we consider here the vertebrate eye to include the eyeball/eye proper as a part, with the eye having as parts (when present): eyelids, conjuctiva, BILA:0000017 BTO:0000439 CALOHA:TS-0309 EFO:0000827 EV:0100336 FBbt:00005162 GAID:69 MAT:0000140 MESH:D005123 MIAA:0000140 OpenCyc:Mx4rvViTvpwpEbGdrcN5Y29ycA uberon light-detecting organ visual apparatus UBERON:0000970 eye An organ that detects light. visual apparatus EV:0100336 An organism subdivision that extends from the head to the pectoral girdle, encompassing the cervical vertebral column. true necks are considered to be present when the pectoral girdle is separate from the skull - Tiktaalik is the earliest known fish to have a true neck. cervical AEO:0000108 BTO:0000420 CALOHA:TS-2045 EFO:0000967 EHDAA2:0003108 EMAPA:35587 FMA:7155 GAID:86 MA:0000024 MAT:0000297 MESH:D009333 MIAA:0000297 NCIT:C13063 OpenCyc:Mx4rvVjLF5wpEbGdrcN5Y29ycA UMLS:C0027530 galen:Neck uberon collum neck (volume) UBERON:0000974 neck An organism subdivision that extends from the head to the pectoral girdle, encompassing the cervical vertebral column. ISBN:9780674021839 UMLS:C0027530 ncithesaurus:Neck collum neck (volume) FMA:7155 Anatomical cluster that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO]. Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO] Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO] articulation joint AEO:0000182 BTO:0001686 CALOHA:TS-2023 EFO:0000948 EMAPA:35456 FMA:7490 GAID:102 MA:0000319 MAT:0000188 MESH:D007596 MIAA:0000188 NCIT:C13044 OpenCyc:Mx4rvVjjdpwpEbGdrcN5Y29ycA RETIRED_EHDAA2:0003182 TAO:0000367 UMLS:C0022417 VHOG:0001276 VSAO:0000101 XAO:0000171 ZFA:0001596 galen:Joint uberon articular joint joints UBERON:0000982 skeletal joint Anatomical cluster that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO]. GO_REF:0000034 VSAO:0000101 Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO] 2012-08-14 VSAO:0000101 VSAO PSPUB:0000170 Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO] 2012-08-14 TAO:0000367 TAO TAO:pem articulation VSAO:0000101 joint FMA:7490 VSAO:0000101 UMLS:C0022417 ncithesaurus:Joint articular joint BTO:0001686 joints ZFA:0001596 The part of the central nervous system lying between the medulla oblongata and the midbrain, ventral to the cerebellum. The pons is not present in zebrafish. In this ontology we currently have some structures which are applicable to zebrafish appearing as parts of the pons. Currently we only include the weaker dubious_for_taxon relationship ubtil this is resolved The part of the central nervous system lying between the medulla oblongata and the midbrain, ventral to the cerebellum. [TFD][VHOG] During the embryonic development of birds and mammals, neuroblasts migrate from the cerebellum into the ventral part of the rhombencephalon and differentiate into pontine and other nuclei, which relay information from between the cerebrum and cerebellum, and a conspicuous band of transverse fibers. This region is known as the pons. A pons does not differentiate in reptiles and anamniotes (...).[well established][VHOG] BAMS:PONS BAMS:Pons BM:Pons BTO:0001101 CALOHA:TS-0813 DHBA:10661 EFO:0001394 EHDAA2:0004394 EMAPA:17563 EV:0100253 FMA:67943 GAID:578 HBA:9131 MA:0000204 MAT:0000115 MBA:771 MESH:D011149 MIAA:0000115 NCIT:C12511 UMLS:C0032639 UMLS:C1280999 VHOG:0001176 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=547 pons Varolii pons of Varolius uberon pons cerebri UBERON:0000988 pons neuronames The part of the central nervous system lying between the medulla oblongata and the midbrain, ventral to the cerebellum. VHOG:0001176 The part of the central nervous system lying between the medulla oblongata and the midbrain, ventral to the cerebellum. [TFD][VHOG] 2012-09-17 VHOG:0001176 VHOG During the embryonic development of birds and mammals, neuroblasts migrate from the cerebellum into the ventral part of the rhombencephalon and differentiate into pontine and other nuclei, which relay information from between the cerebrum and cerebellum, and a conspicuous band of transverse fibers. This region is known as the pons. A pons does not differentiate in reptiles and anamniotes (...).[well established][VHOG] 2012-09-17 VHOG:0001176 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.474 UMLS:C0032639 NIFSTD:birnlex_733 UMLS:C0032639 ncithesaurus:Pons_Varolii UMLS:C1280999 NIFSTD:birnlex_733 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=547 NIFSTD:birnlex_733 pons Varolii ncithesaurus:Pons_Varolii pons cerebri NeuroNames:547 Anatomical system that has as its parts the organs concerned with reproduction. consider splitting genitalia from reproductive system Anatomical system which consists of organs and tissues associated with sexual reproduction of the organism.[AAO] Arguably, one of the most important aspects of urbilaterian organogenesis would have been gonadogenesis, since Urbilateria must have successfully generated gametes and developed a strategy for extrusion and fertilization, in order to be the ancestor of all living Bilateria.[well established][VHOG] AAO:0010258 BILA:0000103 BTO:0000081 CALOHA:TS-1318 EFO:0000809 EHDAA2:0001603 EHDAA:5923 EMAPA:17381 EV:0100100 FBbt:00004857 FMA:7160 GAID:363 HAO:0000374 HAO:0000895 MA:0000326 MIAA:0000305 NCIT:C12841 OpenCyc:Mx4rvVja4ZwpEbGdrcN5Y29ycA TAO:0000632 UMLS:C1261210 VHOG:0000182 WBbt:0005747 XAO:0000142 ZFA:0000632 uberon Geschlechtsorgan animal reproductive system genital system genital tract genitalia organa genitalia reproductive tissue reproductive tract systemata genitalia UBERON:0000990 reproductive system Anatomical system that has as its parts the organs concerned with reproduction. Anatomical system which consists of organs and tissues associated with sexual reproduction of the organism.[AAO] 2012-06-20 AAO:0010258 AAO AAO:BJB Arguably, one of the most important aspects of urbilaterian organogenesis would have been gonadogenesis, since Urbilateria must have successfully generated gametes and developed a strategy for extrusion and fertilization, in order to be the ancestor of all living Bilateria.[well established][VHOG] 2012-09-17 VHOG:0000182 VHOG PMID:21672850 Extavour CGM, Gray anatomy: phylogenetic patterns of somatic gonad structures and reproductive strategies across Bilateria. Integrative and Comparative Biology (2007) UMLS:C1261210 ncithesaurus:Reproductive_System Geschlechtsorgan BTO:0000081 animal reproductive system BTO:0000081 genitalia organa genitalia BTO:0000081 reproductive tissue BTO:0000081 systemata genitalia Reproductive organ that produces and releases eggs (ovary) or sperm (testis). Anatomical structure which produces gametes as well as certain sex hormones controlled by the pituitary gonadotropins.[AAO] The part of the reproductive system that produces and releases eggs (ovary) or sperm (testis).[TAO] Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved.[uncertain][VHOG] gonadal FMA xref is a 'general anatomical term' AAO:0000213 BILA:0000123 BSA:0000079 BTO:0000534 EMAPA:17383 FBbt:00004858 FMA:18250 GAID:368 HAO:0000379 MA:0002420 MESH:D006066 NCIT:C12725 OpenCyc:Mx4rwQvdiZwpEbGdrcN5Y29ycA TAO:0000413 UMLS:C0018067 VHOG:0000397 WBbt:0005175 XAO:0003146 ZFA:0000413 gonada uberon gonads UBERON:0000991 gonad Reproductive organ that produces and releases eggs (ovary) or sperm (testis). ISBN:0140512888 ZFA:0000413 ZFIN:curator Anatomical structure which produces gametes as well as certain sex hormones controlled by the pituitary gonadotropins.[AAO] 2012-06-20 AAO:0000213 AAO AAO:BJB The part of the reproductive system that produces and releases eggs (ovary) or sperm (testis).[TAO] 2012-08-14 TAO:0000413 TAO ZFIN:curator Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved.[uncertain][VHOG] 2012-09-17 VHOG:0000397 VHOG DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T, Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009) FMA xref is a 'general anatomical term' FMA UMLS:C0018067 ncithesaurus:Gonad gonads ZFA:0000413 ovary the gonad of a female organism which contains germ cells Either of paired female reproductive organs involved in production of ova and female sex hormones.[AAO] Female reproductive organ.[TAO] (...) while it is likely that Urbilateria lacked a complex somatic reproductive system, it is at present impossible to speculate on whether or not it possessed a true gonad, let alone any other somatic adaptations for reproduction (reference 1); Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved (reference 2).[uncertain][VHOG] ovarian Ovaries of some kind are found in the female reproductive system of many animals that employ sexual reproduction, including invertebrates. However, they develop in a very different way in most invertebrates than they do in vertebrates, and are not truly homologous. Many of the features found in human ovaries are common to all vertebrates, including the presence of follicular cells, tunica albuginea, and so on. However, many species produce a far greater number of eggs during their lifetime than do humans, so that, in fish and amphibians, there may be hundreds, or even millions of fertile eggs present in the ovary at any given time. In these species, fresh eggs may be developing from the germinal epithelium throughout life. Corpora lutea are found only in mammals, and in some elasmobranch fish; in other species, the remnants of the follicle are quickly resorbed by the ovary. In birds, reptiles, and monotremes, the egg is relatively large, filling the follicle, and distorting the shape of the ovary at maturity. Amphibians and reptiles have no ovarian medulla; the central part of the ovary is a hollow, lymph-filled space. The ovary of teleosts is also often hollow, but in this case, the eggs are shed into the cavity, which opens into the oviduct. Although most normal female vertebrates have two ovaries, this is not the case in all species. In birds and platypuses, the right ovary never matures, so that only the left is functional. In some elasmobranchs, the reverse is true, with only the right ovary fully developing. In the primitive jawless fish, and some teleosts, there is only one ovary, formed by the fusion of the paired organs in the embryo AAO:0000371 BILA:0000125 BSA:0000080 BTO:0000975 CALOHA:TS-0730 EFO:0000973 EHDAA2:0001360 EHDAA:8124 EMAPA:17962 EV:0100111 FBbt:00004865 FMA:7209 GAID:367 MA:0000384 MESH:D010053 MIAA:0000125 NCIT:C12404 OpenCyc:Mx4rvVi9QJwpEbGdrcN5Y29ycA TAO:0000403 UMLS:C0029939 VHOG:0000251 XAO:0000258 ZFA:0000403 animal ovary female gonad female organism genitalia gonad female organism genitalia gonada female organism reproductive system gonad female organism reproductive system gonada female reproductive system gonad female reproductive system gonada genitalia of female organism gonad genitalia of female organism gonada gonad of female organism genitalia gonad of female organism reproductive system gonad of female reproductive system gonad of genitalia of female organism gonad of reproductive system of female organism gonada of female organism genitalia gonada of female organism reproductive system gonada of female reproductive system gonada of genitalia of female organism gonada of reproductive system of female organism ovum-producing ovary reproductive system of female organism gonad reproductive system of female organism gonada uberon ovaries ovarium UBERON:0000992 female gonad female gonad ovary 雌性生殖腺 the gonad of a female organism which contains germ cells ISBN:0-683-40008-8 MP:0001126 Either of paired female reproductive organs involved in production of ova and female sex hormones.[AAO] 2012-06-20 AAO:0000371 AAO AAO:BJB Female reproductive organ.[TAO] 2012-08-14 TAO:0000403 TAO ZFIN:curator (...) while it is likely that Urbilateria lacked a complex somatic reproductive system, it is at present impossible to speculate on whether or not it possessed a true gonad, let alone any other somatic adaptations for reproduction (reference 1); Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved (reference 2).[uncertain][VHOG] 2012-09-17 VHOG:0000251 VHOG DOI:10.1093/icb/icm052 Extavour CGM, Gray anatomy: phylogenetic patterns of somatic gonad structures and reproductive strategies across the Bilateria. Integrative and Comparative Biology (2007), DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T and Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009) Ovaries of some kind are found in the female reproductive system of many animals that employ sexual reproduction, including invertebrates. However, they develop in a very different way in most invertebrates than they do in vertebrates, and are not truly homologous. Many of the features found in human ovaries are common to all vertebrates, including the presence of follicular cells, tunica albuginea, and so on. However, many species produce a far greater number of eggs during their lifetime than do humans, so that, in fish and amphibians, there may be hundreds, or even millions of fertile eggs present in the ovary at any given time. In these species, fresh eggs may be developing from the germinal epithelium throughout life. Corpora lutea are found only in mammals, and in some elasmobranch fish; in other species, the remnants of the follicle are quickly resorbed by the ovary. In birds, reptiles, and monotremes, the egg is relatively large, filling the follicle, and distorting the shape of the ovary at maturity. Amphibians and reptiles have no ovarian medulla; the central part of the ovary is a hollow, lymph-filled space. The ovary of teleosts is also often hollow, but in this case, the eggs are shed into the cavity, which opens into the oviduct. Although most normal female vertebrates have two ovaries, this is not the case in all species. In birds and platypuses, the right ovary never matures, so that only the left is functional. In some elasmobranchs, the reverse is true, with only the right ovary fully developing. In the primitive jawless fish, and some teleosts, there is only one ovary, formed by the fusion of the paired organs in the embryo WP UMLS:C0029939 ncithesaurus:Ovary animal ovary EFO:0000973 female organism genitalia gonad OBOL:automatic female organism genitalia gonada OBOL:automatic female organism reproductive system gonad OBOL:automatic female organism reproductive system gonada OBOL:automatic female reproductive system gonad OBOL:automatic female reproductive system gonada OBOL:automatic genitalia of female organism gonad OBOL:automatic genitalia of female organism gonada OBOL:automatic gonad of female organism genitalia OBOL:automatic gonad of female organism reproductive system OBOL:automatic gonad of female reproductive system OBOL:automatic gonad of genitalia of female organism OBOL:automatic gonad of reproductive system of female organism OBOL:automatic gonada of female organism genitalia OBOL:automatic gonada of female organism reproductive system OBOL:automatic gonada of female reproductive system OBOL:automatic gonada of genitalia of female organism OBOL:automatic gonada of reproductive system of female organism OBOL:automatic ovum-producing ovary GO:0061039 reproductive system of female organism gonad OBOL:automatic reproductive system of female organism gonada OBOL:automatic ovaries ovarium A tube or collection of tubes in an animal from the ovaries to the outside of the body. sometimes oviduct is used interchangeably with follaopian tube. Here they are different - the oviduct connects the gonad to the outside in a variety of animals. The mammal-class fallopian tube is derived from the mullerian duct and connects the gonads/infubdibulum to the uterus A passage through which ova leave the maternal body or pass to an organ communicating with the exterior of the body. [TFD][VHOG] In all remaining vertebrates (i.e., coelacanths, lungfishes, amphibians, reptiles, birds, and mammals), the oviduct arises in ontogeny as a longitudinal, groovelike invagination of the coelomic epithelium on the lateral surface of the mesonephros.[well established][VHOG] The only female vertebrates to lack oviducts are the jawless fishes. In these species, the single fused ovary releases eggs directly into the body cavity. The fish eventually extrudes the eggs through small genital pores towards the rear of the body[WP] in birds divided into infundibulum, magnum, isthmus, uterus, and vagina AAO:0010533 BSA:0000083 BTO:0000980 EFO:0000974 EMAPA:18984 GAID:366 MAT:0000126 MESH:D010057 MIAA:0000126 NCIT:C77957 TAO:0000560 UMLS:C0029954 VHOG:0001136 XAO:0003052 ZFA:0000560 ovarian duct ovarian tube uterine tube uberon female reproductive tracts oviducts tuba uterina tuba uterinae tubular parts of female reproductive system UBERON:0000993 oviduct A tube or collection of tubes in an animal from the ovaries to the outside of the body. A passage through which ova leave the maternal body or pass to an organ communicating with the exterior of the body. [TFD][VHOG] 2012-09-17 VHOG:0001136 VHOG In all remaining vertebrates (i.e., coelacanths, lungfishes, amphibians, reptiles, birds, and mammals), the oviduct arises in ontogeny as a longitudinal, groovelike invagination of the coelomic epithelium on the lateral surface of the mesonephros.[well established][VHOG] 2012-09-17 VHOG:0001136 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.687-688 UMLS:C0029954 ncithesaurus:Oviduct ovarian duct ovarian tube female reproductive tracts oviducts ZFA:0000560 tuba uterina BTO:0000980 tuba uterinae BTO:0000980 tubular parts of female reproductive system uterus the female muscular organ of gestation in which the developing embryo or fetus is nourished until birth The hollow muscular organ in female mammals in which the blastocyst normally becomes embedded and in which the developing embryo and fetus is nourished. Its cavity opens into the vagina below and into a uterine tube on either side. [TFD][VHOG] An infundibulum, uterine tube, uterus, and vagina also differentiate along the oviducts of eutherian mammals.[well established][VHOG] uterine Most animals that lay eggs, such as birds and reptiles, have an oviduct instead of a uterus. In monotremes, mammals which lay eggs and include the platypus, either the term uterus or oviduct is used to describe the same organ, but the egg does not develop a placenta within the mother and thus does not receive further nourishment after formation and fertilization. Marsupials have two uteruses, each of which connect to a lateral vagina and which both use a third, middle 'vagina' which functions as the birth canal. Marsupial embryos form a choriovitelline 'placenta' (which can be thought of as something between a monotreme egg and a 'true' placenta), in which the egg's yolk sac supplies a large part of the embryo's nutrition but also attaches to the uterine wall and takes nutrients from the mother's bloodstream. Two uteruses usually form initially in a female fetus, and in placental mammals they may partially or completely fuse into a single uterus depending on the species. In many species with two uteruses, only one is functional. Humans and other higher primates such as chimpanzees, along with horses, usually have a single completely fused uterus, although in some individuals the uteruses may not have completely fused [Wikipedia:Uterus] BTO:0001424 CALOHA:TS-1102 EFO:0000975 EMAPA:29915 EV:0100113 FMA:17558 GAID:172 MA:0000389 MAT:0000127 MESH:D014599 MIAA:0000127 NCIT:C12405 OpenCyc:Mx4rvViojJwpEbGdrcN5Y29ycA UMLS:C0042149 VHOG:0001137 galen:Uterus uberon UBERON:0000995 uterus cjm the female muscular organ of gestation in which the developing embryo or fetus is nourished until birth MGI:csmith MP:0001120 The hollow muscular organ in female mammals in which the blastocyst normally becomes embedded and in which the developing embryo and fetus is nourished. Its cavity opens into the vagina below and into a uterine tube on either side. [TFD][VHOG] 2012-09-17 VHOG:0001137 VHOG An infundibulum, uterine tube, uterus, and vagina also differentiate along the oviducts of eutherian mammals.[well established][VHOG] 2012-09-17 VHOG:0001137 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.678 UMLS:C0042149 ncithesaurus:Uterus vagina A fibromuscular tubular tract leading from the uterus to the exterior of the body in female placental mammals and marsupials, or to the cloaca in female birds, monotremes, and some reptiles[WP]. Organ with organ cavity which connects the cervical canal of uterus to the vestibule of vagina.[FMA] The genital canal in the female, leading from the opening of the vulva to the cervix of the uterus. [TFD][VHOG] The distal end of the oviducts differentiates as a vagina in Metatheria and Eutheria.[well established][VHOG] vaginal 'The distal end of the oviducts differentiates as a vagina in Metatheria and Eutheria.' Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective, Third Edition (2001) Orlando Fla.: Harcourt College Publishers, p.688 BTO:0000243 CALOHA:TS-1103 EFO:0000976 EMAPA:18986 EV:0100117 FMA:19949 GAID:381 MA:0000394 MAT:0000128 MESH:D014621 MIAA:0000128 NCIT:C12407 OpenCyc:Mx4rvVj1B5wpEbGdrcN5Y29ycA UMLS:C0042232 VHOG:0001138 galen:Vagina uberon distal oviductal region distal portion of oviduct vaginae UBERON:0000996 vagina cjm FMA Wikipedia A fibromuscular tubular tract leading from the uterus to the exterior of the body in female placental mammals and marsupials, or to the cloaca in female birds, monotremes, and some reptiles[WP]. Organ with organ cavity which connects the cervical canal of uterus to the vestibule of vagina.[FMA] 2012-11-29 FMA:19949 FMA The genital canal in the female, leading from the opening of the vulva to the cervix of the uterus. [TFD][VHOG] 2012-09-17 VHOG:0001138 VHOG The distal end of the oviducts differentiates as a vagina in Metatheria and Eutheria.[well established][VHOG] 2012-09-17 VHOG:0001138 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.688 UMLS:C0042232 ncithesaurus:Vagina vaginae The outer epithelial layer of the skin that is superficial to the dermis. A cellular, multilayered epithelium derived from the ectoderm. Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. Le Guellec et al, 2004.[TAO] The outer epithelial layer of the external integument of the body that is derived from the embryonic epiblast.[AAO] relationship loss: subclass external integument structures (AAO:0000961)[AAO] (...) outer epithelia in all metazoan animals are homologous. (...) The ancestor of all metazoans likely had an epidermis with a basal extracellular matrix (ECM), an apical extracellular glycocalyx, and one cilium with a striated rootlet per cell.[well established][VHOG] epidermal Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. In terrestrial vertebrates the epidermis often forms an outer keratinized or cornified layer, the stratum corneum. Interaction between the epideris and dermis gives rise to feathers (birds), hair and mammary glands (mammals), teeth and scales (placoid: chondrichthyans; cosmoids, ganoid, cycloid in bony fishes). epidermis skin AAO:0000143 BTO:0000404 CALOHA:TS-0283 EFO:0000954 EMAPA:17528 EV:0100153 FMA:70596 GAID:932 MA:0000153 MAT:0000154 MESH:D004817 MIAA:0000154 NCIT:C12708 TAO:0000105 UMLS:C0014520 VHOG:0000077 XAO:0000028 ZFA:0000105 vertebrate epidermis uberon UBERON:0001003 skin epidermis The outer epithelial layer of the skin that is superficial to the dermis. ISBN10:0073040584 A cellular, multilayered epithelium derived from the ectoderm. Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. Le Guellec et al, 2004.[TAO] 2012-08-14 TAO:0000105 TAO ZFIN:curator The outer epithelial layer of the external integument of the body that is derived from the embryonic epiblast.[AAO] 2012-06-20 AAO:0000143 AAO AAO:BJB relationship loss: subclass external integument structures (AAO:0000961)[AAO] 2012-06-20 AAO:0000143 AAO (...) outer epithelia in all metazoan animals are homologous. (...) The ancestor of all metazoans likely had an epidermis with a basal extracellular matrix (ECM), an apical extracellular glycocalyx, and one cilium with a striated rootlet per cell.[well established][VHOG] 2012-09-17 VHOG:0000077 VHOG ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.71-72 UMLS:C0014520 ncithesaurus:Epidermis Functional system which consists of structures involved in respiration. The anatomical system in which the exchange of oxygen and carbon dioxide between the organism and its environment.[AAO] There is no doubt that the primitive pattern of vertebrate air-breathing is the buccal pulse pump found in actinopterygian fishes.[well established][VHOG] AAO:0000541 BTO:0000203 CALOHA:TS-1319 EFO:0000804 EHDAA2:0001604 EHDAA:2203 EMAPA:16727 EV:0100036 FMA:7158 GAID:78 MA:0000327 MAT:0000030 MESH:D012137 MIAA:0000030 NCIT:C12779 OpenCyc:Mx4rvVjzFJwpEbGdrcN5Y29ycA TAO:0000272 UMLS:C0035237 VHOG:0000202 XAO:0000117 ZFA:0000272 apparatus respiratorius respiratory system uberon Atmungssystem apparatus respiratorius systema respiratorium UBERON:0001004 respiratory system Functional system which consists of structures involved in respiration. The anatomical system in which the exchange of oxygen and carbon dioxide between the organism and its environment.[AAO] 2012-06-20 AAO:0000541 AAO AAO:BJB There is no doubt that the primitive pattern of vertebrate air-breathing is the buccal pulse pump found in actinopterygian fishes.[well established][VHOG] 2012-09-17 VHOG:0000202 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.599 and Figure 18-23 UMLS:C0035237 ncithesaurus:Respiratory_System Atmungssystem BTO:0000203 apparatus respiratorius BTO:0000203 systema respiratorium An airway through which respiratory air passes in organisms. This class generically groups trachea and analagous structures throughout metazoa. Consider renaming, as the term could be taken to mean lumen of tracheal system (e.g. in SNOMED). As a grouping class this is quite vague, as it is not clear where the airway begins and ends airway airways FMA:265130 uberon UBERON:0001005 respiratory airway An airway through which respiratory air passes in organisms. airway airways Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes. An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO] digestive many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class AAO:0000129 BILA:0000082 BTO:0000058 CALOHA:TS-1293 EFO:0000793 EV:0100056 FBbt:00005055 FMA:7152 GAID:278 MA:0002431 MAT:0000018 MESH:D004064 MIAA:0000018 TADS:0000170 TAO:0000339 WBbt:0005748 XAO:0000125 ZFA:0000339 galen:DigestiveSystem ncithesaurus:Digestive_System uberon alimentary system alimentary tract gastrointestinal system gut UBERON:0001007 digestive system Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes. FB:gg NLM:alimentary+system An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO] 2012-06-20 AAO:0000129 AAO AAO:BJB many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class MA The renal system in an anatomical system that maintains fluid balance and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products.. In various sources such as Encyclopedia Britannica, the excretory and urinary systems are indeed the same system (see wikipedia talk page); we merge two BTO classes here An anatomical system which consists of organs and tissues which produce, store, and excrete urine.[AAO] Evolution of vertebrate renal anatomy appears quite conservative when compared, for example, to evolution of respiratory and cardiovascular systems in vertebrates. Major anatomical changes in vertebrates kidneys separate those of birds and mammals from kidneys of lower vertebrates. General increase in animal size from fish to mammals is reflected by an increase in total number of nephrons per kidney, rather than by constant change in tubular dimensions.[well established][VHOG] In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels This definition is inclusive of the organs of the vertebrate renal system, as well as the Malpighian tubules of insects, and allows for future incorporation of structures such as the antennal glands of crustaceans AAO:0010257 BILA:0000015 BTO:0001244 BTO:0003092 CALOHA:TS-1323 EFO:0000803 EHDAA2:0001601 EHDAA:5901 EMAPA:17366 EV:0100095 FBbt:00005056 FMA:7159 GAID:391 MA:0000325 MAT:0000027 MESH:D014551 MIAA:0000027 NCIT:C12413 TADS:0000162 TAO:0000163 UMLS:C1508753 VHOG:0000723 WBbt:0005736 XAO:0000143 ZFA:0000163 galen:UrinaryTract excretory system renal system systema urinaria systema urinarium urinary system urinary tract uberon renal or urinary system renal/urinary system UBERON:0001008 renal system The renal system in an anatomical system that maintains fluid balance and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products.. GO:0072001 An anatomical system which consists of organs and tissues which produce, store, and excrete urine.[AAO] 2012-06-20 AAO:0010257 AAO AAO:BJB Evolution of vertebrate renal anatomy appears quite conservative when compared, for example, to evolution of respiratory and cardiovascular systems in vertebrates. Major anatomical changes in vertebrates kidneys separate those of birds and mammals from kidneys of lower vertebrates. General increase in animal size from fish to mammals is reflected by an increase in total number of nephrons per kidney, rather than by constant change in tubular dimensions.[well established][VHOG] 2012-09-17 VHOG:0000723 VHOG ISBN:978-3540428541 Kapoor BG, Bhavna Khanna, Ichthyology Handbook (2004) p.406 In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels GO This definition is inclusive of the organs of the vertebrate renal system, as well as the Malpighian tubules of insects, and allows for future incorporation of structures such as the antennal glands of crustaceans UMLS:C1508753 ncithesaurus:Urinary_System renal system GO:0001977 systema urinaria FMA:7159 systema urinarium BTO:0003092 renal or urinary system EHDAA:5901 organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP]. the cardiovascular system and the lymphatic system are parts of the circulatory system Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO] We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG] AAO:0000959 CALOHA:TS-2103 FBbt:00005057 OpenCyc:Mx4rvVjzG5wpEbGdrcN5Y29ycA VHOG:0001248 uberon systema cardiovasculare UBERON:0001009 circulatory system organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP]. WBbt coelomocyte currently classified as circulating cell Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO] 2012-06-20 AAO:0000959 AAO AAO:BJB We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG] 2012-09-17 VHOG:0001248 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.493 systema cardiovasculare adipose tissue Portion of connective tissue composed of adipocytes enmeshed in areolar tissue Connective tissue in which fat is stored.[TAO] Tissue that contains adipocytes, used for cushioning, thermal insulation, lubrication (primarily in the pericardium) and energy storage.[AAO] relationship loss: subclass connective tissue proper (AAO:0000099)[AAO] Adipose tissue is unique to vertebrates. It is found in mostmammals, birds, reptiles and amphibians, and a variety is found in some species of fish. Furthermore, in insects the fat body found in larvae as well as in adults shares some homology with adipose tissue.[well established][VHOG] adipose In humans, adipose tissue is located beneath the skin (subcutaneous fat), around internal organs (visceral fat), in bone marrow (yellow bone marrow) and in breast tissue. Adipose tissue is found in specific locations, which are referred to as adipose depots. Adipose tissue contains several cell types, with the highest percentage of cells being adipocytes, which contain fat droplets. Other cell types include fibroblasts, macrophages, and endothelial cells. Adipose tissue contains many small blood vessels.; Mice have eight major adipose depots, four of which are within the abdominal cavity. The paired gonadal depots are attached to the uterus and ovaries in females and the epididymis and testes in males; the paired retroperitoneal depots are found along the dorsal wall of the abdomen, surrounding the kidney, and, when massive, extend into the pelvis. The mesenteric depot forms a glue-like web that supports the intestines, and the omental depot, which originates near the stomach and spleen, and, when massive, extends into the ventral abdomen. in FMA this is dense irregular connective tissue AAO:0000001 AEO:000020 BTO:0001487 CALOHA:TS-0013 EFO:0000790 EHDAA2:0003120 EMAPA:35112 EV:0100381 FMA:20110 GAID:920 MA:0000009 MAT:0000015 MESH:D000273 MIAA:0000015 NCIT:C12472 OpenCyc:Mx4rvVjc_ZwpEbGdrcN5Y29ycA TAO:0002134 UMLS:C0001527 VHOG:0001284 XAO:0003049 ZFA:0005345 galen:FattyTissue fat fat tissue fatty tissue uberon adipose bodyfat fatty depot UBERON:0001013 adipose tissue FMA Portion of connective tissue composed of adipocytes enmeshed in areolar tissue MESH:A10.165.114 MGI:cwg MP:0000003 Connective tissue in which fat is stored.[TAO] 2012-08-14 TAO:0002134 TAO ZFIN:curator Tissue that contains adipocytes, used for cushioning, thermal insulation, lubrication (primarily in the pericardium) and energy storage.[AAO] 2012-06-20 AAO:0000001 AAO AAO:LAP relationship loss: subclass connective tissue proper (AAO:0000099)[AAO] 2012-06-20 AAO:0000001 AAO Adipose tissue is unique to vertebrates. It is found in mostmammals, birds, reptiles and amphibians, and a variety is found in some species of fish. Furthermore, in insects the fat body found in larvae as well as in adults shares some homology with adipose tissue.[well established][VHOG] 2012-09-17 VHOG:0001284 VHOG DOI:10.1017/S0029665107005423 Haugen F, Drevon CA, The interplay between nutrients and the adipose tissue. The Proceedings of the Nutrition Society (2007) in FMA this is dense irregular connective tissue FMA UMLS:C0001527 ncithesaurus:Adipose_Tissue fat MA:0000009 adipose BTO:0001487 bodyfat BTO:0001487 A subdivision of the muscular system corresponding to a subdisivision of an organism. In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here. AAO:0011066 BTO:0000887 EFO:0001949 EMAPA:32715 EMAPA:35577 FMA:32558 MA:0000165 NCIT:C13056 OpenCyc:Mx4rvVjmr5wpEbGdrcN5Y29ycA TAO:0000548 UMLS:C0026845 VSAO:0005038 WBbt:0005737 ZFA:0000548 muscle group muscles set musculature musculi set of muscles set of skeletal muscles uberon muscle system muscles musculature system UBERON:0001015 musculature A subdivision of the muscular system corresponding to a subdisivision of an organism. In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here. FMA UMLS:C0026845 ncithesaurus:Muscle musculi FMA:32558 FMA:TA set of muscles FMA:32558 set of skeletal muscles MA:0000165 The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO]. A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO] Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO] Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG] nervous neural AAO:0000324 BILA:0000079 BTO:0001484 CALOHA:TS-1313 EFO:0000802 EHDAA2:0001246 EHDAA:826 EMAPA:16469 EV:0100162 FBbt:00005093 FMA:7157 GAID:466 MA:0000016 MAT:0000026 MESH:D009420 MIAA:0000026 NCIT:C12755 OpenCyc:Mx4rvViT_pwpEbGdrcN5Y29ycA TAO:0000396 UMLS:C0027763 VHOG:0000402 WBbt:0005735 XAO:0000177 ZFA:0000396 neurological system nerve net uberon systema nervosum UBERON:0001016 nervous system Bgee:AN The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO]. ISBN:0-14-051288-8 ISBN:3110148986 NLM:nervous+system WB:rynl ZFIN:curator A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO] 2012-08-14 TAO:0000396 TAO ZFIN:curator Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO] 2012-06-20 AAO:0000324 AAO AAO:BJB Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG] 2012-09-17 VHOG:0000402 VHOG ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.117 UMLS:C0027763 ncithesaurus:Nervous_System neurological system GO:0050877 nerve net systema nervosum The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. Part of the nervous system which includes the brain and spinal cord.[AAO] The brain and spinal cord. Kimmel et al, 1995.[TAO] The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO). (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG] AAO:0000090 BAMS:CNS BILA:0000080 BTO:0000227 CALOHA:TS-0150 EFO:0000908 EHDAA2:0000225 EHDAA:828 EMAPA:16470 EMAPA:16754 EV:0100163 FBbt:00005094 FMA:55675 GAID:570 MA:0000167 MAT:0000457 MESH:D002490 NCIT:C12438 OpenCyc:Mx4rvzYt3pwpEbGdrcN5Y29ycA TAO:0000012 UMLS:C0927232 VHOG:0000293 XAO:0000215 ZFA:0000012 CNS systema nervosum centrale cerebrospinal axis uberon neuraxis UBERON:0001017 central nervous system FBbt cjm Bgee:AN The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. GO:0021551 Part of the nervous system which includes the brain and spinal cord.[AAO] 2012-06-20 AAO:0000090 AAO AAO:BJB The brain and spinal cord. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000012 TAO ZFIN:curator The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO). NIFSTD:birnlex_1099 (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG] 2012-09-17 VHOG:0000293 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 (reference 1), ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 (reference 2), DOI:10.1016/j.cell.2007.02.040 Denes AS, Jekely G, Steinmetz PRH, Raible F, Snyman H, Prud'homme B, Ferrier DEK, Balavoine G and Arendt D, Molecular architecture of annelid nerve cord supports common origin of nervous system centralization in Bilateria. Cell (2007) (reference 3) UMLS:C0927232 NIFSTD:birnlex_1099 UMLS:C0927232 ncithesaurus:Central_Nervous_System CNS systema nervosum centrale FMA:55675 FMA:TA cerebrospinal axis FMA:55675 neuraxis FMA:55675 An enclosed, cable-like bundle of axons in the peripheral nervous system originating in a nerve root in the central nervous system (or a condensed nervous structure) connecting with peripheral structures. A portion of tissue which is a fasiculated group of axons.[TAO] nervous AAO:0011070 AEO:0000137 BAMS:n BSA:0000098 BTO:0000925 BTO:0001027 CALOHA:TS-0772 EHDAA2:0003137 EHDAA:2851 EHDAA:3776 EHDAA:4657 EMAPA:32808 EMAPA:32815 EV:0100371 FBbt:00005105 FMA:65132 FMA:65239 GAID:747 GAID:758 MA:0000217 MA:0000228 MESH:D010525 NCIT:C12466 NCIT:C12768 OpenCyc:Mx4rwP3lkpwpEbGdrcN5Y29ycA TAO:0007009 UMLS:C0027740 UMLS:C0031119 VHOG:0000901 XAO:0000204 XAO:0003047 ZFA:0007009 galen:Nerve nerves peripheral nerve uberon neural subtree UBERON:0001021 nerve FBbt An enclosed, cable-like bundle of axons in the peripheral nervous system originating in a nerve root in the central nervous system (or a condensed nervous structure) connecting with peripheral structures. FBbt:00005105 A portion of tissue which is a fasiculated group of axons.[TAO] 2012-08-14 TAO:0007009 TAO ZFIN:curator UMLS:C0027740 ncithesaurus:Nerve UMLS:C0031119 ncithesaurus:Peripheral_Nerve nerves TAO:0007009 peripheral nerve neural subtree FMA:65132 A nerve that transmits from sensory receptors on the surface of the body to the central nervous system. AEO:0000201 EHDAA2:0003200 FBbt:00005136 FMA:5868 OpenCyc:Mx4rv0GdXpwpEbGdrcN5Y29ycA nervus sensorius uberon afferent nerve UBERON:0001027 sensory nerve A nerve that transmits from sensory receptors on the surface of the body to the central nervous system. UBERON:cjm nervus sensorius Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information. An early step in the evolution of neural crest, therefore, may have been the origin of a specific dorsal neural cell population contributing to sensory processing; this would predate the divergence of the amphioxus and vertebrate lineages.[well established][VHOG] note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs AAO:0000555 BAMS:SEN BILA:0000099 EFO:0000805 EHDAA2:0003094 EMAPA:16192 FBbt:00007692 FMA:75259 MA:0002442 MAT:0000031 MIAA:0000031 TAO:0000282 VHOG:0001674 XAO:0003194 ZFA:0000282 organa sensuum sense organ subsystem sense organs sense organs set sensory subsystem sensory systems uberon organa sensuum sensory organ system set of sense organs UBERON:0001032 sensory system Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information. An early step in the evolution of neural crest, therefore, may have been the origin of a specific dorsal neural cell population contributing to sensory processing; this would predate the divergence of the amphioxus and vertebrate lineages.[well established][VHOG] 2012-09-17 VHOG:0001674 VHOG DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000) organa sensuum FMA:75259 FMA:TA sense organs FMA:75259 sense organs set FMA:75259 sensory systems TAO:0000282 organa sensuum set of sense organs FMA:75259 The sensory system for the sense of taste. The sensory system for the sense of taste[NIFSTD:nlx_anat_090803]. The sensory system used for the sense of taste.[AAO] gustatory in ZFA and MA this is a subtype of sensory system. we should change sensory system to disambiguate parts and wholes AAO:0010577 BILA:0000143 EFO:0000830 FMA:7194 MA:0002446 MAT:0000275 MIAA:0000275 TAO:0001101 XAO:0003197 ZFA:0001101 gustatory organ system taste system uberon UBERON:0001033 gustatory system The sensory system for the sense of taste. NIFSTD:nlx_anat_090803 The sensory system for the sense of taste[NIFSTD:nlx_anat_090803]. NIFSTD:nlx_anat_090803 The sensory system used for the sense of taste.[AAO] 2012-06-20 AAO:0010577 AAO AAO:EJS in ZFA and MA this is a subtype of sensory system. we should change sensory system to disambiguate parts and wholes ZFA Anterior subdivision of a digestive tract. Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. In vertebrates the term may refer to a developmental structure The anterior portion of the primitive digestive tube of the embryo that lies cephalic to the junction of the yolk stalk, consists of endodermal tissue, and gives rise to the the pharynx, lower respiratory system, esophagus, stomach, duodenum proximal to the biliary tract, liver, pancreas, biliary tract, and gall bladder. The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] AAO:0011042 BILA:0000085 BTO:0000507 EHDAA2:0000557 EHDAA:520 EMAPA:16548 FBbt:00005379 FMA:45616 MA:0001526 NCIT:C34180 TGMA:0001014 UMLS:C0231051 VHOG:0000285 XAO:0000232 uberon praeenteron proenteron UBERON:0001041 foregut Anterior subdivision of a digestive tract. The anterior portion of the primitive digestive tube of the embryo that lies cephalic to the junction of the yolk stalk, consists of endodermal tissue, and gives rise to the the pharynx, lower respiratory system, esophagus, stomach, duodenum proximal to the biliary tract, liver, pancreas, biliary tract, and gall bladder. MP:0000474 The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000285 VHOG ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 UMLS:C0231051 ncithesaurus:Foregut praeenteron proenteron A portion of the respiratory and digestive tracts; its distal limit is the superior part of the esophagus and it connects the nasal and oral cavities with the esophagus and larynx; it contains the valleculae and the pyriform recesses; its upper limits are the nasal cavity and cranial base.[FEED]. A funnel-shaped fibromuscular tube that conducts food to the ESOPHAGUS, and air to the LARYNYX and LUNGS. It is located posterior to the NASAL CAVITY; ORAL CAVITY; and LARYNX, and extends from the SKULL BASE to the inferior border of the CRICOID CARTILAGE anteriorly and to the inferior border of the C6 vertebra posteriorly. It is divided into the NASOPHARYNX; OROPHARYNX; and HYPOPHARYNX (laryngopharynx)[MESH:A03.867]. Anatomical cavity bounded by the derivatives of the branchial arches.[AAO] Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills. Kimmel et al, 1995.[TAO] Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills[ZFA:0000056, ZFIN:ZDB-PUB-961014-576]. The portion of the alimentary canal between the mouth and the oesophagus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: develops_from respiratory system (UBERON:0001004)[AAO] relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: part_of respiratory system (UBERON:0001004)[AAO] (...) the earliest vertebrates possessed unjointed internal and external branchial arches, and musculature encircling the pharynx.[well established][VHOG] MA/FMA pharynx not part of digestive/alimentary system, we are consistent with this scheme pharynx AAO:0000967 BTO:0001049 CALOHA:TS-0785 EFO:0000836 EHDAA2:0001458 EHDAA:2947 EMAPA:16706 EV:0100065 FMA:46688 GAID:155 MA:0000432 MESH:A03.867 NCIT:C12425 OpenCyc:Mx4rvViv7ZwpEbGdrcN5Y29ycA TAO:0000056 UMLS:C0031354 VHOG:0000462 XAO:0003227 ZFA:0000056 galen:Pharynx uberon UBERON:0001042 Consider generalizing to deuterostome pharynx chordate pharynx EHDAA2 A portion of the respiratory and digestive tracts; its distal limit is the superior part of the esophagus and it connects the nasal and oral cavities with the esophagus and larynx; it contains the valleculae and the pyriform recesses; its upper limits are the nasal cavity and cranial base.[FEED]. A funnel-shaped fibromuscular tube that conducts food to the ESOPHAGUS, and air to the LARYNYX and LUNGS. It is located posterior to the NASAL CAVITY; ORAL CAVITY; and LARYNX, and extends from the SKULL BASE to the inferior border of the CRICOID CARTILAGE anteriorly and to the inferior border of the C6 vertebra posteriorly. It is divided into the NASOPHARYNX; OROPHARYNX; and HYPOPHARYNX (laryngopharynx)[MESH:A03.867]. MESH:A03.867 Anatomical cavity bounded by the derivatives of the branchial arches.[AAO] 2012-06-20 AAO:0000967 AAO AAO:EJS Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000056 TAO ZFIN:curator Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills[ZFA:0000056, ZFIN:ZDB-PUB-961014-576]. ZFIN:ZDB-PUB-961014-576 The portion of the alimentary canal between the mouth and the oesophagus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000462 VHOG relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: develops_from respiratory system (UBERON:0001004)[AAO] 2012-06-20 AAO:0000967 AAO relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: part_of respiratory system (UBERON:0001004)[AAO] 2012-06-20 AAO:0000967 AAO (...) the earliest vertebrates possessed unjointed internal and external branchial arches, and musculature encircling the pharynx.[well established][VHOG] 2012-09-17 VHOG:0000462 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) Box essay 13.1 and Box figure I, p.502-503 MA/FMA pharynx not part of digestive/alimentary system, we are consistent with this scheme MA pharynx FMA:46688 UMLS:C0031354 ncithesaurus:Pharynx Middle subdivision of a digestive tract[CJM]. In vertebrates: The middle part of the alimentary canal from the stomach, or entrance of the bile duct, to, or including, the large intestine[GO]. Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. We may explicitly make this a developmental class The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] In humans: originates from the foregut at the opening of the bile duct into the duodenum and continues through the small intestine and much of the large intestine until the transition to the hindgut about two-thirds of the way through the transverse colon in FMA this represents an embryonic region. BILA:0000086 BTO:0000863 EFO:0001950 EHDAA2:0001185 EHDAA:983 EMAPA:16255 FBbt:00005383 FMA:45617 MA:0001564 NCIT:C34210 TGMA:0001036 UMLS:C0231052 VHOG:0000290 XAO:0000103 uberon mesenteron UBERON:0001045 midgut Middle subdivision of a digestive tract[CJM]. In vertebrates: The middle part of the alimentary canal from the stomach, or entrance of the bile duct, to, or including, the large intestine[GO]. GO:0007494 The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000290 VHOG ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 In humans: originates from the foregut at the opening of the bile duct into the duodenum and continues through the small intestine and much of the large intestine until the transition to the hindgut about two-thirds of the way through the transverse colon WP in FMA this represents an embryonic region. FMA UMLS:C0231052 ncithesaurus:Midgut mesenteron The caudalmost subdivision of a digestive tract. Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future (vertebrates have some contribution from NC - https://github.com/obophenotype/uberon/wiki/The-neural-crest). We may explicitly make this a developmental class the caudal portion of the primitive digestive tube of the embryo The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] in FMA this class has no children. In MA it has a single child hindgut epithelium AAO:0011052 BILA:0000087 BTO:0000510 EHDAA2:0000779 EHDAA:975 EMAPA:16715 FBbt:00005384 FMA:45618 MA:0001527 NCIT:C34188 TGMA:0001020 UMLS:C0231053 VHOG:0000459 XAO:0000104 uberon metenteron UBERON:0001046 hindgut Wikipedia The caudalmost subdivision of a digestive tract. the caudal portion of the primitive digestive tube of the embryo MP:0008786 The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000459 VHOG ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 in FMA this class has no children. In MA it has a single child hindgut epithelium FMA UMLS:C0231053 ncithesaurus:Hindgut metenteron Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue[FBbt, Hartenstein, V. (2004)]. AEO:0000171 BTO:0001886 EFO:0001652 EHDAA2:0003171 FBbt:00005495 FMA:86589 MAT:0000482 NCIT:C34275 UMLS:C0678727 XAO:0003043 uberon bud future organ placode primordia rudiment UBERON:0001048 primordium EHDAA2 Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue[FBbt, Hartenstein, V. (2004)]. BTO:0001886 FB:DJS FB:FBrf0089570 UMLS:C0678727 ncithesaurus:Primordium placode FBbt:00005495 primordia XAO:0003043 In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted]. Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO] The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG] (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium AAO:0010617 BTO:0001057 CALOHA:TS-2371 DHBA:10154 EHDAA2:0001254 EHDAA:2869 EHDAA:908 EMAPA:16164 EMAPA:16757 FMA:293882 MAT:0000069 MIAA:0000069 NCIT:C34226 TAO:0001135 UMLS:C0231024 VHOG:0000307 XAO:0003204 ZFA:0001135 uberon neural primordium presumptive central nervous system tubus neuralis UBERON:0001049 neural tube EHDAA2 In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted]. Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO] 2012-06-20 AAO:0010617 AAO AAO:JOR The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG] 2012-09-17 VHOG:0000307 VHOG (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] 2012-09-17 VHOG:0000307 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium GO:0021915 UMLS:C0231024 ncithesaurus:Neural_Tube tubus neuralis rectum the terminal portion of the intestinal tube, terminating with the anus The terminal portion of the large intestine between the ileo-pelvic colon and the anus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] rectal In the lungfish, sharks and rays the rectum opens into the cloaca which also receives wastes (urine) from the kidneys and material from the reproductive organs. In bony fish the rectum reaches the outside environment through the anus, which is normally situated just in front the urinary and reproductive openings. However in some fish the digestive tract may be curled back on itself, and in the Electric Eel (Electrophorus electricus) the anus is situated in the fish's throat. -- http://www.earthlife.net/fish/digestion.html AAO:0010401 BTO:0001158 CALOHA:TS-1180 EFO:0000848 EHDAA2:0001592 EHDAA:5836 EMAPA:17896 EV:0100081 FMA:14544 GAID:311 MA:0000336 MAT:0000050 MESH:A03.492.411.495.767 MIAA:0000050 NCIT:C12390 OpenCyc:Mx4rvVjaU5wpEbGdrcN5Y29ycA UMLS:C0034896 VHOG:0001751 XAO:0000238 galen:Rectum terminal portion of intestine uberon intestinum rectum rectal sac terminal portion of large intestine UBERON:0001052 rectum 4 cjm MA EHDAA2 ISBN10:0073040584 the terminal portion of the intestinal tube, terminating with the anus ISBN:0-683-40008-8 MP:0000492 The terminal portion of the large intestine between the ileo-pelvic colon and the anus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0001751 VHOG UMLS:C0034896 ncithesaurus:Rectum intestinum rectum BTO:0001158 Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. AAO:0010841 AEO:0000000 BILA:0000000 CARO:0000000 EHDAA2:0002229 FBbt:10000000 FBbt_root:00000000 FMA:62955 HAO:0000000 MA:0000001 NCIT:C12219 TAO:0100000 TGMA:0001822 UMLS:C1515976 WBbt:0000100 XAO:0000000 ZFA:0100000 uberon UBERON:0001062 anatomical entity Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. FMA:62955 UMLS:C1515976 ncithesaurus:Anatomic_Structure_System_or_Substance A zone of skin that is part of a back [Automatically generated definition]. TODO - distinguish between entire skin of region and arbitrary zone of skin on region EMAPA:36392 FMA:10462 FMA:22985 MA:0000498 back skin back zone of skin skin, dorsal region zone of skin of back uberon UBERON:0001068 skin of back MA MA A zone of skin that is part of a back [Automatically generated definition]. OBOL:automatic back zone of skin OBOL:automatic skin, dorsal region zone of skin of back OBOL:automatic A terminal branch of the left or right common carotid artery which supplies oxygenated blood to to the throat, neck glands, tongue, face, mouth, ear, scalp and dura mater of the meninges[MP] not homologous to the external carotid of zebrafish (Goodrich, 1958) - http://zfish.nichd.nih.gov/zfatlas/Intro%20Page/comparative.html; check XAO AAO:0010218 AAO:0010416 BTO:0004696 EFO:0001953 EHDAA2:0000461 EMAPA:18611 FMA:10635 GAID:480 MA:0001929 MESH:D002342 NCIT:C32551 OpenCyc:Mx4rwVJkPZwpEbGdrcN5Y29ycA UMLS:C0007275 VHOG:0000265 XAO:0000345 external carotid uberon arteria carotis externa UBERON:0001070 external carotid artery https://sourceforge.net/tracker/?func=detail&aid=3486863&group_id=76834&atid=1127722 MA FMA EHDAA2 FMA A terminal branch of the left or right common carotid artery which supplies oxygenated blood to to the throat, neck glands, tongue, face, mouth, ear, scalp and dura mater of the meninges[MP] MGI:anna UMLS:C0007275 ncithesaurus:External_Carotid_Artery external carotid AAO:0010218 arteria carotis externa It ascends beneath the anterior margin of the trapezius, distributing branches to it, and to the neighboring muscles and lymph glands in the neck, and anastomosing with the superficial branch of the descending branch of the occipital artery. EMAPA:37117 FMA:10665 MA:0002052 NCIT:C53005 UMLS:C0226271 superficial branch of transverse cervical artery uberon UBERON:0001071 The transverse cervical artery splits into two branches, a superficial one and a deep one[WP] superficial cervical artery It ascends beneath the anterior margin of the trapezius, distributing branches to it, and to the neighboring muscles and lymph glands in the neck, and anastomosing with the superficial branch of the descending branch of the occipital artery. EMAPA:37117 MA:th UMLS:C0226271 ncithesaurus:Superficial_Cervical_Artery superficial branch of transverse cervical artery A vein that carries deoxygenated blood from the lower half of the body into the right atrium of the heart. Trunk of systemic vein which is formed by the union of the right common iliac vein and the left common iliac vein and terminates in the right atrium[FMA]. Phylogenetic modifications within this basic pattern of arteries and veins are largely correlated with functional changes. In the transition from water to land, gills gave way to lungs, accompanied by the establishment of a pulmonary circulation. In some fishes and certainly in tetrapods, the cardinal veins become less involved in blood return. Instead, the composite, prominent postcava (posterior vena cava) arose to drain the posterior part of the body and the precava (anterior vena cava) developed to drain the anterior part of the body.[well established][VHOG] AAO:0011083 BTO:0002682 EHDAA2:0000611 EMAPA:18416 FMA:10951 GAID:548 MA:0000480 MESH:D014682 NCIT:C12815 UMLS:C0042458 VHOG:0001194 XAO:0000388 galen:InferiorVenaCava inferior caval vein inferior vena cava posterior vena cava uberon caudal vena cava postcava vena cava inferior UBERON:0001072 posterior vena cava lexical A vein that carries deoxygenated blood from the lower half of the body into the right atrium of the heart. Trunk of systemic vein which is formed by the union of the right common iliac vein and the left common iliac vein and terminates in the right atrium[FMA]. FMA:10951 Phylogenetic modifications within this basic pattern of arteries and veins are largely correlated with functional changes. In the transition from water to land, gills gave way to lungs, accompanied by the establishment of a pulmonary circulation. In some fishes and certainly in tetrapods, the cardinal veins become less involved in blood return. Instead, the composite, prominent postcava (posterior vena cava) arose to drain the posterior part of the body and the precava (anterior vena cava) developed to drain the anterior part of the body.[well established][VHOG] 2012-09-17 VHOG:0001194 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.454-455 UMLS:C0042458 ncithesaurus:Inferior_Vena_Cava inferior caval vein inferior vena cava posterior vena cava caudal vena cava VHOG:0001194 vena cava inferior vena cava inferior BTO:0002682 Endocardium that is part of the cardiac ventricle. EMAPA:32747 FMA:12148 MA:0000079 TAO:0002247 VHOG:0000607 ZFA:0001615 cardiac ventricle endocardium endocardium of cardiac ventricle endocardium of heart ventricle endocardium of lower chamber of heart endocardium of ventricle of heart heart ventricle endocardium lower chamber of heart endocardium ventricle endocardium ventricle of heart endocardium ventricular endocardium uberon ventricle endocardial tissue UBERON:0001081 endocardium of ventricle Endocardium that is part of the cardiac ventricle. ZFIN:curator cardiac ventricle endocardium OBOL:automatic endocardium of cardiac ventricle OBOL:automatic endocardium of heart ventricle OBOL:automatic endocardium of lower chamber of heart OBOL:automatic endocardium of ventricle of heart OBOL:automatic heart ventricle endocardium OBOL:automatic lower chamber of heart endocardium OBOL:automatic ventricle of heart endocardium OBOL:automatic ventricle endocardial tissue VHOG:0000607 Muscular layer of the cardiac ventricle composed of a compact myocardial layer surrounding the trabecular layer. Muscular layer of the cardiac ventricle composed of a compact myocardial layer surrounding the trabecular layer Hu et al. 2001.[TAO] As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[uncertain][VHOG] EFO:0003088 EMAPA:32748 FMA:12151 MA:0000082 TAO:0005061 VHOG:0000604 ZFA:0005061 ventricle myocardium ventricular myocardium uberon ventricle cardiac muscle UBERON:0001083 myocardium of ventricle Muscular layer of the cardiac ventricle composed of a compact myocardial layer surrounding the trabecular layer. ZFIN:curator Muscular layer of the cardiac ventricle composed of a compact myocardial layer surrounding the trabecular layer Hu et al. 2001.[TAO] 2012-08-14 TAO:0005061 TAO ZFIN:curator As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[uncertain][VHOG] 2012-09-17 VHOG:0000604 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481 ventricle cardiac muscle VHOG:0000604 A zone of skin that is part of a head [Automatically generated definition]. TODO - distinguish between entire skin of region and arbitrary zone of skin on region FMA:12166 FMA:24756 MA:0000582 NCIT:C52757 UMLS:C0205029 adult head zone of skin head skin head zone of skin zone of skin of adult head zone of skin of head uberon UBERON:0001084 skin of head A zone of skin that is part of a head [Automatically generated definition]. OBOL:automatic UMLS:C0205029 ncithesaurus:Head_Skin adult head zone of skin OBOL:automatic head zone of skin OBOL:automatic zone of skin of adult head OBOL:automatic zone of skin of head OBOL:automatic A zone of skin that is part of a trunk [Automatically generated definition]. TODO - distinguish between entire skin of region and arbitrary zone of skin on region EMAPA:37278 FMA:12167 FMA:23093 MA:0000517 NCIT:C12295 UMLS:C0205031 torso zone of skin trunk skin trunk zone of skin zone of skin of torso zone of skin of trunk uberon UBERON:0001085 skin of trunk A zone of skin that is part of a trunk [Automatically generated definition]. OBOL:automatic EMAPA:37278 MA:th UMLS:C0205031 ncithesaurus:Skin_of_the_Trunk torso zone of skin OBOL:automatic trunk zone of skin OBOL:automatic zone of skin of torso OBOL:automatic zone of skin of trunk OBOL:automatic urine Excretion that is the output of a kidney kidney excreta from some taxa (e.g. in aves) may not be liquid BTO:0001419 CALOHA:TS-1092 EFO:0001939 EMAPA:36554 ENVO:00002047 FMA:12274 GAID:1189 MA:0002545 MAT:0000058 MESH:D014556 MIAA:0000058 NCIT:C13283 OpenCyc:Mx4rvVjGppwpEbGdrcN5Y29ycA UMLS:C0042036 galen:Urine uberon UBERON:0001088 urine Excretion that is the output of a kidney UMLS:C0042036 ncithesaurus:Urine synovial fluid Joint fluid is a transudate of plasma that is actively secreted by synovial cells. Portion of organism substance that is a clear fluid that occupies the space in synovial joints.[TAO] It provides nutrients and lubrication for articular cartilage The fluid contains hyaluronan secreted by fibroblast-like cells in the synovial membrane, lubricin (proteoglycan 4; PRG4) secreted by the surface chondrocytes of the articular cartilage and interstitial fluid filtered from the blood plasma BTO:0001339 CALOHA:TS-0996 ENVO:02000039 FMA:12277 GAID:265 MA:0002544 MESH:D013582 NCIT:C33718 TAO:0005154 UMLS:C0039097 ZFA:0005154 galen:SynovialFluid joint fluid uberon UBERON:0001090 synovial fluid FMA Joint fluid is a transudate of plasma that is actively secreted by synovial cells. Portion of organism substance that is a clear fluid that occupies the space in synovial joints.[TAO] 2012-08-14 TAO:0005154 TAO ZFIN:curator UMLS:C0039097 ncithesaurus:Synovial_Fluid joint fluid Muscle tissue composed of cardiac muscle cells, forming the muscles of the heart[ZFA,modified]. check relationship with myocardium. part_of in MA - but we also have a more specific class 'cardiac muscle tissue of myocardium'. Check ncit UBERON:0007096 AAO:0010245 AEO:0000142 BILA:0000134 BTO:0000199 CALOHA:TS-0440 EHDAA2:0003142 EMAPA:32688 FMA:14068 TAO:0005280 ZFA:0005280 galen:CardiacMuscle galen:CardiacMuscleTissue ncithesaurus:Heart_Muscle cardiac muscle cardiac muscle muscle tissue cardiac muscle textus muscularis heart muscle muscle tissue heart muscle textus muscularis heart myocardium muscle tissue heart myocardium textus muscularis muscle of heart muscle tissue muscle of heart textus muscularis muscle tissue of cardiac muscle muscle tissue of heart muscle muscle tissue of heart myocardium muscle tissue of muscle of heart muscle tissue of myocardium myocardium muscle tissue myocardium textus muscularis textus muscularis of cardiac muscle textus muscularis of heart muscle textus muscularis of heart myocardium textus muscularis of muscle of heart textus muscularis of myocardium uberon cardiac musculature UBERON:0001133 cardiac muscle tissue ZFA Muscle tissue composed of cardiac muscle cells, forming the muscles of the heart[ZFA,modified]. ZFA:0005280 cardiac muscle muscle tissue OBOL:automatic cardiac muscle textus muscularis OBOL:automatic heart muscle muscle tissue OBOL:automatic heart muscle textus muscularis OBOL:automatic heart myocardium muscle tissue OBOL:automatic heart myocardium textus muscularis OBOL:automatic muscle of heart muscle tissue OBOL:automatic muscle of heart textus muscularis OBOL:automatic muscle tissue of cardiac muscle OBOL:automatic muscle tissue of heart muscle OBOL:automatic muscle tissue of heart myocardium OBOL:automatic muscle tissue of muscle of heart OBOL:automatic muscle tissue of myocardium OBOL:automatic myocardium muscle tissue OBOL:automatic myocardium textus muscularis OBOL:automatic textus muscularis of cardiac muscle OBOL:automatic textus muscularis of heart muscle OBOL:automatic textus muscularis of heart myocardium OBOL:automatic textus muscularis of muscle of heart OBOL:automatic textus muscularis of myocardium OBOL:automatic cardiac musculature BILA:0000134 skeletal muscle tissue Muscle tissue that consists primarily of skeletal muscle fibers. TODO - add skeletal muscle organ? See GO:0060538 skeletal muscle organ development. Todo - group FBbt:00005073 - somatic muscle. Muscle, composed of long cylindrical, multinucleated cells that attaches to the skeleton via tendons.[TAO] Tissue which consists of skeletal muscle fibers surrounded by endomysium. Examples: Skeletal muscle tissue of biceps, Skeletal muscle tissue of diaphragm[FMA] This result implies the following views in terms of evolutionary differentiation: (1) Arthropod striated muscle and vertebrate skeletal and cardiac muscles share a common ancestor. In other words, they did not evolve independently (...) (5) The divergence of vertebrate skeletal and cardiac muscles/vertebrate smooth muscle and nonmuscle is at least before that of vertebrates/arthropods. In other words, emergence of skeletal and cardiac musle type tissues preceded the vertebrate/arthropod divergence (ca. 700 MYA).[well established][VHOG] skeletal muscle EMAPA:32716 FMA:14069 MA:0002439 NCIT:C13050 UMLS:C0242692 uberon skeletal muscle system somatic muscle UBERON:0001134 skeletal muscle tissue Muscle tissue that consists primarily of skeletal muscle fibers. Muscle, composed of long cylindrical, multinucleated cells that attaches to the skeleton via tendons.[TAO] 2012-08-14 TAO:0005277 TAO ZFIN:curator Tissue which consists of skeletal muscle fibers surrounded by endomysium. Examples: Skeletal muscle tissue of biceps, Skeletal muscle tissue of diaphragm[FMA] FMA:14069 FMA This result implies the following views in terms of evolutionary differentiation: (1) Arthropod striated muscle and vertebrate skeletal and cardiac muscles share a common ancestor. In other words, they did not evolve independently (...) (5) The divergence of vertebrate skeletal and cardiac muscles/vertebrate smooth muscle and nonmuscle is at least before that of vertebrates/arthropods. In other words, emergence of skeletal and cardiac musle type tissues preceded the vertebrate/arthropod divergence (ca. 700 MYA).[well established][VHOG] 2012-09-17 VHOG:0000319 VHOG PMID:10368962 Oota S, Saitou N, Phylogenetic relationship of muscle tissues deduced from superimposition of gene trees. Mol Biol Evol (1999) UMLS:C0242692 ncithesaurus:Skeletal_Muscle_Tissue skeletal muscle system BTO:0001103 somatic muscle BTO:0001103 Muscle tissue which is unstriated, composed primarily of smooth muscle fibers surrounded by a reticulum of collagen and elastic fibers. Smooth muscle differs from striated muscle in the much higher actin/myosin ratio, the absence of conspicuous sarcomeres and the ability to contract to a much smaller fraction of its resting length[GO]. A non-striated muscle that is composed of spindle-shaped cells. Smooth muscle usually is organized into sheets that line cavitated organs.[TAO] Involuntary muscle tissue consisting of uninucleate spindle-shaped fibers.[AAO] (...) the first bilateral animals possessed only smooth muscles with the molecular repertoire necessary to build a striated muscle. (...) it is more parsimonious to regard striated muscle cells as a sister cell type to the smooth muscle cells. In this scenario, striated and smooth muscles would have arisen in the stem lineage that led to the Nephrozoa (i.e. all Bilateria exclusive the acoelomorphs) (Hejnol et al., 2009), from an 'acoel-like' smooth muscle, by segregation and divergence of functions and through differential recruitment of additional genes[well established][VHOG] GO uses visceral and smooth interchangeably. However visceral can also be used in the sense of the viscera. Many fly annotations to smooth muscle terms. If we want to be inclusive of insects have to have a general definition of tissue that includes cells. AAO:0010244 AEO:0000141 BTO:0001260 CALOHA:TS-0943 EFO:0000889 EHDAA2:0003141 EMAPA:32717 EV:0100378 FBbt:00003525 FMA:14070 GAID:167 MA:0000166 MAT:0000303 MESH:D009130 MIAA:0000303 NCIT:C12437 OpenCyc:Mx4rvvSS3pwpEbGdrcN5Y29ycA TAO:0005274 UMLS:C1267092 VHOG:0001246 WBbt:0005781 XAO:0000175 ZFA:0005274 galen:SmoothMuscle galen:SmoothMuscleTissue involuntary muscle non-striated muscle smooth muscle textus muscularis nonstriatus visceral muscle visceral muscle tissue uberon textus muscularis levis; textus muscularis nonstriatus UBERON:0001135 smooth muscle tissue Muscle tissue which is unstriated, composed primarily of smooth muscle fibers surrounded by a reticulum of collagen and elastic fibers. Smooth muscle differs from striated muscle in the much higher actin/myosin ratio, the absence of conspicuous sarcomeres and the ability to contract to a much smaller fraction of its resting length[GO]. GO:0006939 A non-striated muscle that is composed of spindle-shaped cells. Smooth muscle usually is organized into sheets that line cavitated organs.[TAO] 2012-08-14 TAO:0005274 TAO ZFIN:curator Involuntary muscle tissue consisting of uninucleate spindle-shaped fibers.[AAO] 2012-06-20 AAO:0010244 AAO AAO:CAM (...) the first bilateral animals possessed only smooth muscles with the molecular repertoire necessary to build a striated muscle. (...) it is more parsimonious to regard striated muscle cells as a sister cell type to the smooth muscle cells. In this scenario, striated and smooth muscles would have arisen in the stem lineage that led to the Nephrozoa (i.e. all Bilateria exclusive the acoelomorphs) (Hejnol et al., 2009), from an 'acoel-like' smooth muscle, by segregation and divergence of functions and through differential recruitment of additional genes[well established][VHOG] 2012-09-17 VHOG:0001246 VHOG DOI:10.1002/jez.b.21416 Chiodin M, Achatz JG, Wanninger A, Martinez P, Molecular architecture of muscles in an acoel and its evolutionary implications. Journal of Experimental Zoology (2011) UMLS:C1267092 ncithesaurus:Smooth_Muscle_Tissue textus muscularis nonstriatus FMA:14070 FMA:TA visceral muscle visceral muscle tissue textus muscularis levis; textus muscularis nonstriatus Simple squamous epithelium of mesodermal origin which lines serous membranes. Examples: mesothelium of pleura, mesothelium of peritoneum[FMA]. http://en.wikipedia.org/wiki/ The mesothelium is a membrane that forms the lining of several body cavities: the pleura (thoracal cavity), peritoneum (abdominal cavity including the mesentery) and pericardium (heart sac). Mesothelial tissue also surrounds the male internal reproductive organs (the tunica vaginalis testis) and covers the internal reproductive organs of women (the tunica serosa uteri). AEO:0000111 BTO:0002422 CALOHA:TS-1183 EHDAA2_RETIRED:0003111 EHDAA:2331 EHDAA:2349 EHDAA:295 EHDAA:6073 EHDAA:640 EHDAA:646 EMAPA:32856 FMA:14074 MA:0000565 NCIT:C33105 UMLS:C0086610 uberon UBERON:0001136 mesothelium Simple squamous epithelium of mesodermal origin which lines serous membranes. Examples: mesothelium of pleura, mesothelium of peritoneum[FMA]. http://en.wikipedia.org/wiki/ The mesothelium is a membrane that forms the lining of several body cavities: the pleura (thoracal cavity), peritoneum (abdominal cavity including the mesentery) and pericardium (heart sac). Mesothelial tissue also surrounds the male internal reproductive organs (the tunica vaginalis testis) and covers the internal reproductive organs of women (the tunica serosa uteri). FMA:14074 UMLS:C0086610 ncithesaurus:Mesothelium A major subdivision of an organism that is the entire part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. In vertebrares this includes the vertebral column.. dorsal In humans, called the back, a large posterior area of the human body, rising from the top of the buttocks to the back of the neck and the shoulders. It is the surface opposite to the chest, its height being defined by the vertebral column (commonly referred to as the spine or backbone) and its breadth being supported by the ribcage and shoulders. The spinal canal runs through the spine and provides nerves to the rest of the body BTO:0001713 CALOHA:TS-2223 EFO:0001405 FMA:14181 GAID:30 MESH:A01.176 NCIT:C13062 OpenCyc:Mx4rvVkEU5wpEbGdrcN5Y29ycA UMLS:C0004600 galen:Back back back of body proper dorsal part of organism uberon UBERON:0001137 dorsum A major subdivision of an organism that is the entire part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. In vertebrares this includes the vertebral column.. BSPO:0000063 UBERONREF:0000006 UMLS:C0004600 ncithesaurus:Back back FMA:14181 back of body proper FMA:14181 Either of the pair of major vessels which arise from the renal hilus and return blood from the kidneys, suprarenal gland and the ureter to the inferior vena cava. The renal veins are veins that drain the kidney. They connect the kidney to the inferior vena cava. It is usually singular to each kidney, except in the condition 'multiple renal veins'. It also divides into 2 divisions upon entering the kidney: the anterior branch which receives blood from the anterior portion of the kidney and, the posterior branch which receives blood from the posterior portion. Often, each renal vein will have a branch that receives blood from the ureter. [WP,unvetted][Wikipedia:Renal_vein]. in EHDAA2, the renal vein is part of the kidney BTO:0002681 EHDAA2:0001602 EHDAA:8722 EMAPA:28376 FMA:14334 GAID:544 MA:0002210 MESH:D012082 NCIT:C33462 OpenCyc:Mx4rvdUXKJwpEbGdrcN5Y29ycA UMLS:C0035092 galen:RenalVein kidney vein renal venous tree vein of kidney uberon venae renales UBERON:0001140 renal vein Either of the pair of major vessels which arise from the renal hilus and return blood from the kidneys, suprarenal gland and the ureter to the inferior vena cava. ISBN:0-683-40008-8 MGI:csmith MP:0011323 The renal veins are veins that drain the kidney. They connect the kidney to the inferior vena cava. It is usually singular to each kidney, except in the condition 'multiple renal veins'. It also divides into 2 divisions upon entering the kidney: the anterior branch which receives blood from the anterior portion of the kidney and, the posterior branch which receives blood from the posterior portion. Often, each renal vein will have a branch that receives blood from the ureter. [WP,unvetted][Wikipedia:Renal_vein]. in EHDAA2, the renal vein is part of the kidney EHDAA2 UMLS:C0035092 ncithesaurus:Renal_Vein kidney vein OBOL:automatic vein of kidney OBOL:automatic venae renales A renal vein that drains the right kidney A vein that drains blood from the right kidney into the inferior vena cava[ncithesaurus]. EMAPA:37381 FMA:14335 MA:0002212 NCIT:C52695 OpenCyc:Mx8Ngh4rvgHsHZwpEbGdrcN5Y29ycB4rvdUXKJwpEbGdrcN5Y29ycA UMLS:C0508000 uberon UBERON:0001141 right renal vein A renal vein that drains the right kidney A vein that drains blood from the right kidney into the inferior vena cava[ncithesaurus]. ncithesaurus:Right_Renal_Vein EMAPA:37381 MA:th UMLS:C0508000 ncithesaurus:Right_Renal_Vein A renal vein that drains the left kidney A vein that drains blood from the left kidney into the inferior vena cava[ncithesaurus]. EMAPA:37166 FMA:14336 MA:0002211 NCIT:C52693 OpenCyc:Mx8Ngh4rvgIFoJwpEbGdrcN5Y29ycB4rvdUXKJwpEbGdrcN5Y29ycA UMLS:C0508001 uberon UBERON:0001142 left renal vein A renal vein that drains the left kidney A vein that drains blood from the left kidney into the inferior vena cava[ncithesaurus]. ncithesaurus:Left_Renal_Vein EMAPA:37166 MA:th UMLS:C0508001 ncithesaurus:Left_Renal_Vein A vein that carries deoxygenated blood from its corresponding ovary to inferior vena cava or one of its tributaries. EMAPA:18644 FMA:14346 MA:0002186 NCIT:C53058 OpenCyc:Mx4rvrST5ZwpEbGdrcN5Y29ycA UMLS:C0226720 female reproductive system gonad vein female reproductive system gonada vein gonad of female reproductive system vein gonada of female reproductive system vein ovary vein vein of female reproductive system gonad vein of female reproductive system gonada vein of gonad of female reproductive system vein of gonada of female reproductive system vein of ovary uberon vena ovarica dextra vena ovarica sinistra UBERON:0001145 ovarian vein A vein that carries deoxygenated blood from its corresponding ovary to inferior vena cava or one of its tributaries. UMLS:C0226720 ncithesaurus:Ovarian_Vein female reproductive system gonad vein OBOL:automatic female reproductive system gonada vein OBOL:automatic gonad of female reproductive system vein OBOL:automatic gonada of female reproductive system vein OBOL:automatic ovary vein OBOL:automatic vein of female reproductive system gonad OBOL:automatic vein of female reproductive system gonada OBOL:automatic vein of gonad of female reproductive system OBOL:automatic vein of gonada of female reproductive system OBOL:automatic vein of ovary OBOL:automatic vena ovarica dextra vena ovarica sinistra colon Last portion of the large intestine before it becomes the rectum. TODO - abstract this such that it legitimately covers all vertebrates The last portion of the digestive system, it extracts water and salt from solid wastes before they are eliminated from the body.[AAO] The posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates. Wallace et al, 2005.[TAO] Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] colonic In mammals, the colon consists of four sections: the ascending colon, the transverse colon, the descending colon, and the sigmoid colon[WP] In zebrafish, the posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates[ZFIN] it extracts water and salt from solid wastes before they are eliminated from the body[WP] AAO:0010400 BTO:0000269 CALOHA:TS-0158 EFO:0000361 EMAPA:18939 EV:0100079 FMA:14543 GAID:309 MA:0000335 MAP:0000001 MAT:0000526 MESH:A03.492.411.495.356 NCIT:C12382 OpenCyc:Mx4rvgLEM5wpEbGdrcN5Y29ycA TAO:0000706 UMLS:C0009368 VHOG:0000648 XAO:0000243 ZFA:0000706 galen:Colon large bowel posterior intestine uberon hindgut UBERON:0001155 colon colon 结肠 3 cjm FMA Last portion of the large intestine before it becomes the rectum. ZFIN:curator The last portion of the digestive system, it extracts water and salt from solid wastes before they are eliminated from the body.[AAO] 2012-06-20 AAO:0010400 AAO UBERON:0001155 The posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates. Wallace et al, 2005.[TAO] 2012-08-14 TAO:0000706 TAO ZFIN:curator Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] 2012-09-17 VHOG:0000648 VHOG ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 UMLS:C0009368 ncithesaurus:Colon sigmoid colon The part of the large intestine that is closest to the rectum and anus. It forms a loop that averages about 40 cm. in length, and normally lies within the pelvis, but on account of its freedom of movement it is liable to be displaced into the abdominal cavity. BTO:0000645 CALOHA:TS-2044 EFO:0000846 EMAPA:36391 FMA:14548 MAT:0000314 MESH:A03.492.411.495.356.668 MIAA:0000314 NCIT:C12384 NCIT:C33550 OpenCyc:Mx4rwHX_-5wpEbGdrcN5Y29ycA UMLS:C0227391 UMLS:C0682612 galen:SigmoidColon uberon colon sigmoideum pelvic colon sigmoid colon sigmoid flexure UBERON:0001159 sigmoid colon FMA Wikipedia The part of the large intestine that is closest to the rectum and anus. It forms a loop that averages about 40 cm. in length, and normally lies within the pelvis, but on account of its freedom of movement it is liable to be displaced into the abdominal cavity. UMLS:C0227391 ncithesaurus:Sigmoid_Colon UMLS:C0682612 ncithesaurus:Sigmoid_Flexure colon sigmoideum the layered structure that makes up the stomach, typiclly consists of a serous coat, a muscular coat, a mucous membrane, and other tissue layers in between EMAPA:35826 FMA:14582 MA:0002692 galen:WallOfStomach anatomical wall of stomach anatomical wall of ventriculus gastric wall stomach anatomical wall stomach wall ventriculus anatomical wall ventriculus wall wall of ventriculus uberon UBERON:0001167 wall of stomach the layered structure that makes up the stomach, typiclly consists of a serous coat, a muscular coat, a mucous membrane, and other tissue layers in between MGI:csmith MP:0010783 anatomical wall of stomach OBOL:automatic anatomical wall of ventriculus OBOL:automatic stomach anatomical wall OBOL:automatic ventriculus anatomical wall OBOL:automatic ventriculus wall OBOL:automatic wall of ventriculus OBOL:automatic An anatomical wall that is part of a large intestine [Automatically generated definition]. EMAPA:35470 FMA:14619 MA:0002695 anatomical wall of large intestine large intestinal wall large intestine anatomical wall large intestine wall uberon UBERON:0001169 wall of large intestine An anatomical wall that is part of a large intestine [Automatically generated definition]. OBOL:automatic anatomical wall of large intestine OBOL:automatic large intestine anatomical wall OBOL:automatic One of two laterally paired arteries that supplies the kidneys. These are large arteries that branch from the dorsal aorta in primitive vertebrates. renal arteries vary widely even in humans. Sub-structures should be checked for taxon variability. Artery which supplies blood via branches to the gonads, oviducts, and kidneys.[AAO] The renal arteries normally arise off the side of the abdominal aorta, immediately below the superior mesenteric artery, and supply the kidneys with blood. Each is directed across the crus of the diaphragm, so as to form nearly a right angle with the aorta. The renal arteries carry a large portion of total blood flow to the kidneys. Up to a third of total cardiac output can pass through the renal arteries to be filtered by the kidneys. The arterial supply of the kidneys is variable and there may be one or more renal arteries supplying each kidney. It is located above the renal vein. It has a radius of approximately 0.25cm, 0.26 cm at the root. The measured mean diameter can differ depending on the imaging method used. For example, the diameter was found to be 5.04 ± 0.74 mm using ultrasound, but 5.68 ± 1.19 mm using angiography. [WP,unvetted].[Wikipedia] AAO:0010223 BTO:0001165 EFO:0002552 EHDAA2:0004100 EHDAA:5321 EHDAA:8594 EMAPA:28373 FMA:14751 GAID:507 MA:0002035 MESH:D012077 NCIT:C12778 OpenCyc:Mx4rveOFHpwpEbGdrcN5Y29ycA RETIRED_EHDAA2:0001600 TAO:0000420 UMLS:C0035065 ZFA:0000420 galen:RenalArtery renal arterial tree uberon arteria renalis renal arteries UBERON:0001184 renal artery One of two laterally paired arteries that supplies the kidneys. These are large arteries that branch from the dorsal aorta in primitive vertebrates. ISBN10:0073040584 Artery which supplies blood via branches to the gonads, oviducts, and kidneys.[AAO] 2012-06-20 AAO:0010223 AAO AAO:BJB The renal arteries normally arise off the side of the abdominal aorta, immediately below the superior mesenteric artery, and supply the kidneys with blood. Each is directed across the crus of the diaphragm, so as to form nearly a right angle with the aorta. The renal arteries carry a large portion of total blood flow to the kidneys. Up to a third of total cardiac output can pass through the renal arteries to be filtered by the kidneys. The arterial supply of the kidneys is variable and there may be one or more renal arteries supplying each kidney. It is located above the renal vein. It has a radius of approximately 0.25cm, 0.26 cm at the root. The measured mean diameter can differ depending on the imaging method used. For example, the diameter was found to be 5.04 ± 0.74 mm using ultrasound, but 5.68 ± 1.19 mm using angiography. [WP,unvetted].[Wikipedia] Wikipedia UMLS:C0035065 ncithesaurus:Renal_Artery arteria renalis renal arteries Renal artery that supplies the right kidney EMAPA:37380 FMA:14752 MA:0002037 NCIT:C52740 OpenCyc:Mx4rtW8I0KgEEdudWQACs5b6Bw OpenCyc:Mx8Ngh4rvgHsHZwpEbGdrcN5Y29ycB4rveOFHpwpEbGdrcN5Y29ycA UMLS:C0226332 right renal arterial tree uberon UBERON:0001185 The right [renal artery] passes behind the inferior vena cava, the right renal vein, the head of the pancreas, and the descending part of the duodenum[WP] right renal artery Renal artery that supplies the right kidney EMAPA:37380 MA:th UMLS:C0226332 ncithesaurus:Right_Renal_Artery Renal artery that supplies the left kidney EMAPA:37098 FMA:14753 MA:0002036 NCIT:C52741 OpenCyc:Mx4rtW8I0agEEdudWQACs5b6Bw OpenCyc:Mx8Ngh4rvgIFoJwpEbGdrcN5Y29ycB4rveOFHpwpEbGdrcN5Y29ycA UMLS:C0226333 left renal arterial tree uberon UBERON:0001186 The left [renal artery] is somewhat higher than the right; it lies behind the left renal vein, the body of the pancreas and the splenic vein, and is crossed by the inferior mesenteric vein[WP] left renal artery Renal artery that supplies the left kidney EMAPA:37098 MA:th UMLS:C0226333 ncithesaurus:Left_Renal_Artery An artery that supplies an ovary. In human anatomy, the ovarian artery is a blood vessel that supplies oxygenated blood to the ovary. It arises from the abdominal aorta below the renal artery, and does not pass out of the abdomiproperty_value external_definitioncavity. It can be found in the suspensory ligament of the ovary. [WP]. EMAPA:18620 FMA:14761 MA:0002012 NCIT:C33242 OpenCyc:Mx4rwOa9PZwpEbGdrcN5Y29ycA UMLS:C0226411 ovarian arterial tree uberon arteria ovarica UBERON:0001190 ovarian artery An artery that supplies an ovary. OBOL:automatic In human anatomy, the ovarian artery is a blood vessel that supplies oxygenated blood to the ovary. It arises from the abdominal aorta below the renal artery, and does not pass out of the abdomiproperty_value external_definitioncavity. It can be found in the suspensory ligament of the ovary. [WP]. UMLS:C0226411 ncithesaurus:Ovarian_Artery arteria ovarica The mucosal layer that lines the stomach. The gastric mucosa is the mucous membrane layer of the stomach which contains the glands and the gastric pits. In men it is about 1 mm thick and its surface is smooth, soft, and velvety. It consists of epithelium, lamina propria, and the muscularis mucosae. In its fresh state, it is of a pinkish tinge at the pyloric end and of a red or reddish-brown color over the rest of its surface. In infancy it is of a brighter hue, the vascular redness being more marked. It is thin at the cardiac extremity, but thicker toward the pylorus. During the contracted state of the organ it is thrown into numerous plaits or rugae, which, for the most part, have a longitudinal direction, and are most marked toward the pyloric end of the stomach, and along the greater curvature. These folds are entirely obliterated when the organ becomes distended. When examined with a lens, the inner surface of the mucous membrane presents a peculiar honeycomb appearance from being covered with funnel-like depressions or foveolae of a polygonal or hexagonal form, which vary from 0.12 to 0.25 mm. in diameter. These are the ducts of the gastric glands, and at the bottom of each may be seen one or more minute orifices, the openings of the gland tubes. Gastric glands are simple or branched tubular glands that emerge on the deeper part of the gastric foveola, inside the gastric areas and outlined by the folds of the mucosa. There are three types of glands: cardiac glands (in the proximal part of the stomach), oxyntic glands (the dominating type of gland), and pyloric glands. The cardiac glands mainly contain mucus producing cells. The bottom part of the oxyntic glands is dominated by zymogen (chief) cells that produce pepsinogen (an inactive precursor of the pepsin enzyme). Parietal cells, which secrete hydrochloric acid are scattered in the glands, with most of them in the middle part. The upper part of the glands consist of mucous neck cells; in this part the dividing cells are seen. The pyloric glands contain mucus-secreting cells. Several types of endocrine cells are found in all regions of the gastric mucosa. In the pyloric glands contain gastrin producing cells (G cells); this hormone stimulates acid production from the parietal cells. ECL (enterochromaffine-like) cells, found in the oxyntic glands release histamine, which also is a powerful stimulant of the acid secretion. The A cells produce glucagon, which mobilizes the hepatic glycogen, and the enterochromaffin cells that produce serotonin, which stimulates the contraction of the smooth muscles. The surface of the mucous membrane is covered by a single layer of columnar epithelium . This epithelium commences very abruptly at the cardiac orifice, where there is a sudden transition from the stratified epithelium of the esophagus. The epithelial lining of the gland ducts is of the same character and is continuous with the general lining of the stomach. [WP,unvetted][Wikipedia:Gastric_mucosa]. BTO:0001308 CALOHA:TS-0404 EMAPA:35817 FMA:14907 GAID:321 MA:0002683 MESH:A03.492.766.440 NCIT:C32656 OpenCyc:Mx8NhB4rvcD6KJwpEbGdrcN5Y29ycB4rvmKNOpwpEbGdrcN5Y29ycB4rvVj5FpwpEbGdrcN5Y29ycB4rvVjlqpwpEbGdrcN5Y29ycA UMLS:C0017136 galen:GastricMucosa gastric mucosa gastric mucous membrane mucosa of organ of stomach mucosa of organ of ventriculus mucosa of ventriculus mucous membrane of stomach mucous membrane of ventriculus organ mucosa of stomach organ mucosa of ventriculus stomach mucosa stomach mucosa of organ stomach mucous membrane stomach organ mucosa tunica mucosa (gaster) tunica mucosa gastricae ventriculus mucosa ventriculus mucosa of organ ventriculus mucous membrane ventriculus organ mucosa uberon Magenschleimhaut tunica mucosa gastris UBERON:0001199 mucosa of stomach The mucosal layer that lines the stomach. The gastric mucosa is the mucous membrane layer of the stomach which contains the glands and the gastric pits. In men it is about 1 mm thick and its surface is smooth, soft, and velvety. It consists of epithelium, lamina propria, and the muscularis mucosae. In its fresh state, it is of a pinkish tinge at the pyloric end and of a red or reddish-brown color over the rest of its surface. In infancy it is of a brighter hue, the vascular redness being more marked. It is thin at the cardiac extremity, but thicker toward the pylorus. During the contracted state of the organ it is thrown into numerous plaits or rugae, which, for the most part, have a longitudinal direction, and are most marked toward the pyloric end of the stomach, and along the greater curvature. These folds are entirely obliterated when the organ becomes distended. When examined with a lens, the inner surface of the mucous membrane presents a peculiar honeycomb appearance from being covered with funnel-like depressions or foveolae of a polygonal or hexagonal form, which vary from 0.12 to 0.25 mm. in diameter. These are the ducts of the gastric glands, and at the bottom of each may be seen one or more minute orifices, the openings of the gland tubes. Gastric glands are simple or branched tubular glands that emerge on the deeper part of the gastric foveola, inside the gastric areas and outlined by the folds of the mucosa. There are three types of glands: cardiac glands (in the proximal part of the stomach), oxyntic glands (the dominating type of gland), and pyloric glands. The cardiac glands mainly contain mucus producing cells. The bottom part of the oxyntic glands is dominated by zymogen (chief) cells that produce pepsinogen (an inactive precursor of the pepsin enzyme). Parietal cells, which secrete hydrochloric acid are scattered in the glands, with most of them in the middle part. The upper part of the glands consist of mucous neck cells; in this part the dividing cells are seen. The pyloric glands contain mucus-secreting cells. Several types of endocrine cells are found in all regions of the gastric mucosa. In the pyloric glands contain gastrin producing cells (G cells); this hormone stimulates acid production from the parietal cells. ECL (enterochromaffine-like) cells, found in the oxyntic glands release histamine, which also is a powerful stimulant of the acid secretion. The A cells produce glucagon, which mobilizes the hepatic glycogen, and the enterochromaffin cells that produce serotonin, which stimulates the contraction of the smooth muscles. The surface of the mucous membrane is covered by a single layer of columnar epithelium . This epithelium commences very abruptly at the cardiac orifice, where there is a sudden transition from the stratified epithelium of the esophagus. The epithelial lining of the gland ducts is of the same character and is continuous with the general lining of the stomach. [WP,unvetted][Wikipedia:Gastric_mucosa]. UMLS:C0017136 ncithesaurus:Gastric_Mucosa mucosa of organ of stomach OBOL:automatic mucosa of organ of ventriculus OBOL:automatic mucosa of ventriculus OBOL:automatic mucous membrane of ventriculus OBOL:automatic organ mucosa of stomach OBOL:automatic organ mucosa of ventriculus OBOL:automatic stomach mucosa of organ OBOL:automatic stomach mucous membrane OBOL:automatic stomach organ mucosa OBOL:automatic tunica mucosa gastricae FMA:14907 FMA:TA ventriculus mucosa OBOL:automatic ventriculus mucosa of organ OBOL:automatic ventriculus mucous membrane OBOL:automatic ventriculus organ mucosa OBOL:automatic Magenschleimhaut BTO:0001308 tunica mucosa gastris tunica mucosa gastris BTO:0001308 the fibrous connective tissue layer beneath the stomach mucosa BTO:0002110 EMAPA:35825 FMA:14908 MA:0002685 NCIT:C32663 UMLS:C0227211 gastric submucosa stomach submucosa submucosa of ventriculus tela submucosa (gaster) tela submucosa gastricae ventriculus submucosa uberon submucous layer of stomach tela submucosa ventriculi UBERON:0001200 submucosa of stomach the fibrous connective tissue layer beneath the stomach mucosa MGI:csmith MP:0010794 UMLS:C0227211 ncithesaurus:Gastric_Submucosa submucosa of ventriculus OBOL:automatic tela submucosa gastricae FMA:14908 FMA:TA ventriculus submucosa OBOL:automatic submucous layer of stomach BTO:0002110 tela submucosa ventriculi BTO:0002110 the outermost layer of the stomach wall, consisting of layers of connective tissue continuous with the peritoneum TODO - check serosa/peritoneum EMAPA:35822 FMA:14914 MA:0001626 NCIT:C32662 UMLS:C1517453 anatomical wall of stomach serosa anatomical wall of stomach serous membrane anatomical wall of ventriculus serosa anatomical wall of ventriculus serous membrane gastric wall serosa gastric wall serous membrane serosa of anatomical wall of stomach serosa of anatomical wall of ventriculus serosa of gastric wall serosa of stomach anatomical wall serosa of stomach wall serosa of ventriculus anatomical wall serosa of ventriculus wall serosa of wall of stomach serosa of wall of ventriculus serous coat of stomach serous membrane of anatomical wall of stomach serous membrane of anatomical wall of ventriculus serous membrane of gastric wall serous membrane of stomach anatomical wall serous membrane of stomach wall serous membrane of ventriculus anatomical wall serous membrane of ventriculus wall serous membrane of wall of stomach serous membrane of wall of ventriculus stomach anatomical wall serosa stomach anatomical wall serous membrane stomach serosa stomach wall serosa stomach wall serous membrane tunica serosa (gaster) tunica serosa gastricae ventriculus anatomical wall serosa ventriculus anatomical wall serous membrane ventriculus wall serosa ventriculus wall serous membrane visceral peritoneum of stomach wall of stomach serosa wall of stomach serous membrane wall of ventriculus serosa wall of ventriculus serous membrane uberon gastric serosa UBERON:0001201 serosa of stomach the outermost layer of the stomach wall, consisting of layers of connective tissue continuous with the peritoneum MGI:csmith MP:0010793 UMLS:C1517453 ncithesaurus:Gastric_Serosal_Surface anatomical wall of stomach serosa OBOL:automatic anatomical wall of stomach serous membrane OBOL:automatic anatomical wall of ventriculus serosa OBOL:automatic anatomical wall of ventriculus serous membrane OBOL:automatic gastric wall serosa OBOL:automatic gastric wall serous membrane OBOL:automatic serosa of anatomical wall of stomach OBOL:automatic serosa of anatomical wall of ventriculus OBOL:automatic serosa of gastric wall OBOL:automatic serosa of stomach anatomical wall OBOL:automatic serosa of stomach wall OBOL:automatic serosa of ventriculus anatomical wall OBOL:automatic serosa of ventriculus wall OBOL:automatic serosa of wall of stomach OBOL:automatic serosa of wall of ventriculus OBOL:automatic serous membrane of anatomical wall of stomach OBOL:automatic serous membrane of anatomical wall of ventriculus OBOL:automatic serous membrane of gastric wall OBOL:automatic serous membrane of stomach anatomical wall OBOL:automatic serous membrane of stomach wall OBOL:automatic serous membrane of ventriculus anatomical wall OBOL:automatic serous membrane of ventriculus wall OBOL:automatic serous membrane of wall of stomach OBOL:automatic serous membrane of wall of ventriculus OBOL:automatic stomach anatomical wall serosa OBOL:automatic stomach anatomical wall serous membrane OBOL:automatic stomach wall serosa OBOL:automatic stomach wall serous membrane OBOL:automatic tunica serosa gastricae FMA:14914 FMA:TA ventriculus anatomical wall serosa OBOL:automatic ventriculus anatomical wall serous membrane OBOL:automatic ventriculus wall serosa OBOL:automatic ventriculus wall serous membrane OBOL:automatic wall of stomach serosa OBOL:automatic wall of stomach serous membrane OBOL:automatic wall of ventriculus serosa OBOL:automatic wall of ventriculus serous membrane OBOL:automatic A mucosa that is part of a large intestine [Automatically generated definition]. CALOHA:TS-2106 EMAPA:35467 FMA:14969 MA:0002688 NCIT:C32926 UMLS:C0734203 large intestinal mucosa large intestine mucosa large intestine mucosa of organ large intestine mucous membrane large intestine organ mucosa mucosa of organ of large intestine mucous membrane of large intestine organ mucosa of large intestine tunica mucosa intestini crassi uberon UBERON:0001207 mucosa of large intestine A mucosa that is part of a large intestine [Automatically generated definition]. OBOL:automatic UMLS:C0734203 ncithesaurus:Large_Intestinal_Mucosa large intestine mucosa of organ OBOL:automatic large intestine mucous membrane OBOL:automatic large intestine organ mucosa OBOL:automatic mucosa of organ of large intestine OBOL:automatic organ mucosa of large intestine OBOL:automatic tunica mucosa intestini crassi FMA:14969 FMA:TA A submucosa that is part of a large intestine [Automatically generated definition]. BTO:0002111 EMAPA:37560 FMA:14970 MA:0002690 NCIT:C32930 UMLS:C0734204 large intestinal submucosa large intestine submucosa tela submucosa intestini crassi uberon submucous layer of large intestine UBERON:0001208 submucosa of large intestine A submucosa that is part of a large intestine [Automatically generated definition]. OBOL:automatic EMAPA:37560 MA:th UMLS:C0734204 ncithesaurus:Large_Intestinal_Submucosa tela submucosa intestini crassi FMA:14970 FMA:TA submucous layer of large intestine BTO:0002111 A serous membrane that is part of a large intestine [Automatically generated definition]. TODO - check serosa/peritoneum EMAPA:37557 FMA:14975 MA:0001546 NCIT:C32929 UMLS:C1517727 large intestinal serosa large intestine serosa large intestine serous membrane serous coat of large intestine serous membrane of large intestine tunica serosa intestini crassi visceral peritoneum of large intestine uberon UBERON:0001209 serosa of large intestine A serous membrane that is part of a large intestine [Automatically generated definition]. OBOL:automatic EMAPA:37557 MA:th UMLS:C1517727 ncithesaurus:Large_Intestinal_Serosal_Surface large intestine serous membrane OBOL:automatic serous membrane of large intestine OBOL:automatic tunica serosa intestini crassi FMA:14975 FMA:TA A blood vessel that drains blood from the large intestine that usually terminates when reaching the splenic vein, which goes on to form the portal vein with the superior mesenteric vein (SMV). Anatomical variations include the IMV draining into the confluence of the SMV and splenic vein and the IMV draining in the SMV. The IMV lies to the right of the similarly name artery, the inferior mesenteric artery, which originates from the abdominal aorta. [WP,unvetted]. BTO:0002782 EHDAA2:0000819 EHDAA:8712 EMAPA:18642 FMA:15391 MA:0002178 NCIT:C32782 OpenCyc:Mx4rvcV53ZwpEbGdrcN5Y29ycA UMLS:C0226754 VHOG:0001118 uberon lower mesenteric vein vena mesenterica inferior UBERON:0001215 inferior mesenteric vein FMA/obol A blood vessel that drains blood from the large intestine that usually terminates when reaching the splenic vein, which goes on to form the portal vein with the superior mesenteric vein (SMV). Anatomical variations include the IMV draining into the confluence of the SMV and splenic vein and the IMV draining in the SMV. The IMV lies to the right of the similarly name artery, the inferior mesenteric artery, which originates from the abdominal aorta. [WP,unvetted]. UMLS:C0226754 ncithesaurus:Inferior_Mesenteric_Vein lower mesenteric vein BTO:0002782 vena mesenterica inferior An ureter that is part of a right side of organism [Automatically generated definition]. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EMAPA:37373 FMA:15571 MA:0001685 NCIT:C49327 UMLS:C0227682 uberon UBERON:0001222 right ureter An ureter that is part of a right side of organism [Automatically generated definition]. OBOL:automatic EMAPA:37373 MA:th UMLS:C0227682 ncithesaurus:Right_Ureter An ureter that is part of a left side of organism [Automatically generated definition]. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EMAPA:37372 FMA:15572 MA:0001684 NCIT:C49324 UMLS:C0227683 uberon UBERON:0001223 left ureter An ureter that is part of a left side of organism [Automatically generated definition]. OBOL:automatic EMAPA:37372 MA:th UMLS:C0227683 ncithesaurus:Left_Ureter A funnel shaped proximal portion of the ureter that is formed by convergence of the major calices [MP]. CALOHA:TS-2230 EMAPA:17948 FMA:15575 GAID:426 MA:0000374 MESH:D007682 NCIT:C12887 UMLS:C0227666 galen:RenalPelvis kidney pelvis pelvis of ureter uberon p. renallis pyelum UBERON:0001224 In this ontology, the renal pelvis is represented as the area of part-overlap between the kidney and the ureter renal pelvis MA FMA A funnel shaped proximal portion of the ureter that is formed by convergence of the major calices [MP]. MP:0004194 UMLS:C0227666 ncithesaurus:Renal_Pelvis p. renallis pyelum MP:0004194 Mucosal layer that lines the intestine. BTO:0000642 EMAPA:35440 FMA:15695 GAID:296 MA:0001537 MESH:A03.492.411.369 NCIT:C49241 UMLS:C0021839 bowel mucosa bowel mucosa of organ bowel mucous membrane bowel organ mucosa intestine mucosa intestine mucosa of organ intestine mucous membrane intestine organ mucosa mucosa of bowel mucosa of intestine mucosa of organ of bowel mucosa of organ of intestine mucous membrane of bowel mucous membrane of intestine organ mucosa of bowel organ mucosa of intestine tunica mucosa intestini uberon UBERON:0001242 intestinal mucosa Mucosal layer that lines the intestine. UBERON:cjm UMLS:C0021839 ncithesaurus:Intestinal_Mucosa bowel mucosa OBOL:automatic bowel mucosa of organ OBOL:automatic bowel mucous membrane OBOL:automatic bowel organ mucosa OBOL:automatic intestine mucosa of organ OBOL:automatic intestine mucous membrane OBOL:automatic intestine organ mucosa OBOL:automatic mucosa of bowel OBOL:automatic mucosa of organ of bowel OBOL:automatic mucosa of organ of intestine OBOL:automatic mucous membrane of bowel OBOL:automatic mucous membrane of intestine OBOL:automatic organ mucosa of bowel OBOL:automatic organ mucosa of intestine OBOL:automatic A serous membrane that is part of a wall of intestine [Automatically generated definition]. TODO - check serosa/peritoneum EMAPA:37619 FMA:15701 MA:0001538 anatomical wall of bowel serosa anatomical wall of bowel serous membrane anatomical wall of intestine serosa anatomical wall of intestine serous membrane bowel anatomical wall serosa bowel anatomical wall serous membrane bowel wall serosa bowel wall serous membrane intestinal serosa intestinal wall serosa intestinal wall serous membrane intestine anatomical wall serosa intestine anatomical wall serous membrane intestine serosa intestine wall serosa intestine wall serous membrane serosa of anatomical wall of bowel serosa of anatomical wall of intestine serosa of bowel anatomical wall serosa of bowel wall serosa of intestinal wall serosa of intestine anatomical wall serosa of intestine wall serosa of wall of bowel serosa of wall of intestine serous membrane of anatomical wall of bowel serous membrane of anatomical wall of intestine serous membrane of bowel anatomical wall serous membrane of bowel wall serous membrane of intestinal wall serous membrane of intestine anatomical wall serous membrane of intestine wall serous membrane of wall of bowel serous membrane of wall of intestine visceral peritoneum of intestine wall of bowel serosa wall of bowel serous membrane wall of intestine serosa wall of intestine serous membrane uberon UBERON:0001243 serosa of intestine A serous membrane that is part of a wall of intestine [Automatically generated definition]. OBOL:automatic EMAPA:37619 MA:th anatomical wall of bowel serosa OBOL:automatic anatomical wall of bowel serous membrane OBOL:automatic anatomical wall of intestine serosa OBOL:automatic anatomical wall of intestine serous membrane OBOL:automatic bowel anatomical wall serosa OBOL:automatic bowel anatomical wall serous membrane OBOL:automatic bowel wall serosa OBOL:automatic bowel wall serous membrane OBOL:automatic intestinal wall serosa OBOL:automatic intestinal wall serous membrane OBOL:automatic intestine anatomical wall serosa OBOL:automatic intestine anatomical wall serous membrane OBOL:automatic intestine wall serosa OBOL:automatic intestine wall serous membrane OBOL:automatic serosa of anatomical wall of bowel OBOL:automatic serosa of anatomical wall of intestine OBOL:automatic serosa of bowel anatomical wall OBOL:automatic serosa of bowel wall OBOL:automatic serosa of intestinal wall OBOL:automatic serosa of intestine anatomical wall OBOL:automatic serosa of intestine wall OBOL:automatic serosa of wall of bowel OBOL:automatic serosa of wall of intestine OBOL:automatic serous membrane of anatomical wall of bowel OBOL:automatic serous membrane of anatomical wall of intestine OBOL:automatic serous membrane of bowel anatomical wall OBOL:automatic serous membrane of bowel wall OBOL:automatic serous membrane of intestinal wall OBOL:automatic serous membrane of intestine anatomical wall OBOL:automatic serous membrane of intestine wall OBOL:automatic serous membrane of wall of bowel OBOL:automatic serous membrane of wall of intestine OBOL:automatic wall of bowel serosa OBOL:automatic wall of bowel serous membrane OBOL:automatic wall of intestine serosa OBOL:automatic wall of intestine serous membrane OBOL:automatic Orifice at the opposite end of an animal's digestive tract from the mouth. Its function is to expel feces, unwanted semi-solid matter produced during digestion, which, depending on the type of animal, may be one or more of: matter which the animal cannot digest, such as bones; food material after all the nutrients have been extracted, for example cellulose or lignin; ingested matter which would be toxic if it remained in the digestive tract; and dead or excess gut bacteria and other endosymbionts. anal In the lungfish, sharks and rays the rectum opens into the cloaca which also receives wastes (urine) from the kidneys and material from the reproductive organs. In bony fish the rectum reaches the outside environment through the anus, which is normally situated just in front the urinary and reproductive openings. However in some fish the digestive tract may be curled back on itself, and in the Electric Eel (Electrophorus electricus) the anus is situated in the fish's throat. -- http://www.earthlife.net/fish/digestion.html BTO:0001680 CALOHA:TS-2005 EV:0100082 FBbt:00003148 FMA:15711 GAID:312 MA:0000331 MESH:A03.492.411.495.767.288 NCIT:C43362 OpenCyc:Mx4rvVjaEZwpEbGdrcN5Y29ycA TADS:0000066 TGMA:0001279 UMLS:C0003461 WBbt:0005364 galen:Anus anal opening anal orifice opening of terminal part of digestive tract uberon proctodeum UBERON:0001245 anus Orifice at the opposite end of an animal's digestive tract from the mouth. Its function is to expel feces, unwanted semi-solid matter produced during digestion, which, depending on the type of animal, may be one or more of: matter which the animal cannot digest, such as bones; food material after all the nutrients have been extracted, for example cellulose or lignin; ingested matter which would be toxic if it remained in the digestive tract; and dead or excess gut bacteria and other endosymbionts. ZFIN:curator UMLS:C0003461 ncithesaurus:Anus An adventitia that is part of a ureter. EMAPA:28114 FMA:15892 MA:0002652 external adventitia of ureter tunica adventitia (ureter) tunica adventitia ureteris ureter adventitia ureteral adventitia uberon UBERON:0001252 adventitia of ureter An adventitia that is part of a ureter. OBOL:automatic tunica adventitia (ureter) FMA:15892 FMA:TA tunica adventitia ureteris FMA:15892 FMA:TA urinary bladder distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion[MP]. A saccular organ in which urine accumulates before discharge from the body. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] Anatomical structure which consists of a membranous sac used to temporarily store urine until it is excreted from the body.[AAO] In tetrapods, the urinary bladder arises as an outpocketing of the cloaca. (...) The tetrapod urinary bladder appears first among amphibians and is present in Sphenodon, turtles, most lizards, ostriches among birds, and all mammals.[well established][VHOG] vesical The urinary bladder evolved in tetrapods. Birds to not possess a true urinary bladder, although Palaeognathae have an undifferentiated cloacal outpocketing that serves a similar function[https://github.com/obophenotype/uberon/issues/454] bladder AAO:0000623 BTO:0001418 CALOHA:TS-1090 EFO:0000290 EHDAA2:0000174 EHDAA:9328 EMAPA:18321 EV:0100098 FMA:15900 GAID:0000004 MA:0000380 MAT:0000122 MESH:A05.810.161 MIAA:0000122 NCIT:C12414 OpenCyc:Mx4rvVjMmZwpEbGdrcN5Y29ycA UMLS:C0005682 VHOG:0000740 XAO:0000154 galen:UrinaryBladder vesica urinaria uberon urocyst vesica UBERON:0001255 urinary bladder BTO FMA upper part of UG sinus distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion[MP]. MGI:anna A saccular organ in which urine accumulates before discharge from the body. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] 2012-09-17 VHOG:0000740 VHOG Anatomical structure which consists of a membranous sac used to temporarily store urine until it is excreted from the body.[AAO] 2012-06-20 AAO:0000623 AAO AAO:BJB In tetrapods, the urinary bladder arises as an outpocketing of the cloaca. (...) The tetrapod urinary bladder appears first among amphibians and is present in Sphenodon, turtles, most lizards, ostriches among birds, and all mammals.[well established][VHOG] 2012-09-17 VHOG:0000740 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.577-78 bladder EHDAA2:0000174 UMLS:C0005682 ncithesaurus:Bladder vesica urinaria urocyst vesica BTO:0001418 An anatomical wall that lines the insider of a urinary bladder. BTO:0001462 EMAPA:35175 FMA:15902 MA:0002493 NCIT:C48941 UMLS:C0458421 anatomical wall of bladder anatomical wall of urinary bladder bladder anatomical wall bladder wall urinary bladder anatomical wall urinary bladder wall wall of bladder uberon UBERON:0001256 wall of urinary bladder An anatomical wall that lines the insider of a urinary bladder. UMLS:C0458421 ncithesaurus:Bladder_Wall anatomical wall of bladder OBOL:automatic anatomical wall of urinary bladder OBOL:automatic bladder anatomical wall OBOL:automatic bladder wall OBOL:automatic urinary bladder anatomical wall OBOL:automatic wall of bladder OBOL:automatic The constricted portion of the urinary bladder, formed by the meeting of its inferolateral surfaces proximal to the opening of the urethra[MP]. EMAPA:36078 FMA:15912 MA:0002491 NCIT:C12336 UMLS:C0227716 galen:UrinaryBladderNeck bladder neck cervix vesicae collum vesicae neck of bladder urinary bladder neck vesical neck uberon cervix vesicae urinariae UBERON:0001258 neck of urinary bladder The constricted portion of the urinary bladder, formed by the meeting of its inferolateral surfaces proximal to the opening of the urethra[MP]. MP:anna UMLS:C0227716 ncithesaurus:Bladder_Neck cervix vesicae FMA:15912 FMA:TA collum vesicae FMA:15912 FMA:TA cervix vesicae urinariae the mucous membrane lining the urinary bladder EFO:0000293 EMAPA:35897 FMA:15928 MA:0001692 NCIT:C32205 UMLS:C0227691 galen:MucousMembraneOfUrinaryBladder bladder mucosa bladder mucous membrane bladder organ mucosa mucosa of bladder mucous membrane of bladder mucous membrane of urinary bladder tunica mucosa (vesica urinaria) tunica mucosa vesicae tunica mucosa vesicae urinariae urinary bladder mucosa urinary bladder mucous membrane uberon UBERON:0001259 mucosa of urinary bladder the mucous membrane lining the urinary bladder MGI:anna MP:0011766 UMLS:C0227691 ncithesaurus:Bladder_Mucosa bladder mucous membrane OBOL:automatic bladder organ mucosa OBOL:automatic mucosa of bladder OBOL:automatic tunica mucosa (vesica urinaria) FMA:15928 FMA:TA tunica mucosa vesicae FMA:15928 FMA:TA tunica mucosa vesicae urinariae MP:MP urinary bladder mucous membrane OBOL:automatic A serous membrane that is part of a urinary bladder [Automatically generated definition]. TODO - check serosa/peritoneum EMAPA:28661 FMA:15932 MA:0001696 bladder serosa bladder serous membrane serosa of bladder serous coat of bladder serous coat of urinary bladder serous membrane of bladder serous membrane of urinary bladder tunica serosa (vesica urinaria) tunica serosa vesicae urinary bladder serosa urinary bladder serous membrane visceral peritoneum of urinary bladder uberon UBERON:0001260 serosa of urinary bladder A serous membrane that is part of a urinary bladder [Automatically generated definition]. OBOL:automatic bladder serous membrane OBOL:automatic serous membrane of bladder OBOL:automatic serous membrane of urinary bladder OBOL:automatic tunica serosa (vesica urinaria) FMA:15932 FMA:TA tunica serosa vesicae FMA:15932 FMA:TA urinary bladder serous membrane OBOL:automatic An anatomical wall that is part of a intestine [Automatically generated definition]. we place two MA classes here due to the official ncit2ma mapping to intestinal wall tissue; not clear how bowel and intestine are different BTO:0000647 EMAPA:35444 FMA:15949 MA:0001525 MA:0002693 NCIT:C49478 UMLS:C1708548 anatomical wall of bowel anatomical wall of intestine bowel anatomical wall bowel wall intestinal wall intestine anatomical wall intestine wall wall of bowel uberon bowel wall UBERON:0001262 wall of intestine An anatomical wall that is part of a intestine [Automatically generated definition]. OBOL:automatic UMLS:C1708548 ncithesaurus:Intestinal_Wall_Tissue anatomical wall of bowel OBOL:automatic anatomical wall of intestine OBOL:automatic bowel anatomical wall OBOL:automatic bowel wall OBOL:automatic intestine anatomical wall OBOL:automatic wall of bowel OBOL:automatic bowel wall MA:0001525 The organism subdivision that includes the pelvic girdle skeleton and associated soft tissue. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). Examples: There are only two instances in an organism, right and left pectoral girdle regions. this class describes the subdivision of the limb/fin, NOT the skeleton within. See also: skeleton of pectoral girdle (UBERON:0007831). See also comments on obo-anatomy mail list. Note that even though the class includes soft tissue it is more restrictive than 'pelvis' which also includes structures in cavities etc. TODO this needs to be better documented Subdivision of lower limb or fin which links the limb/fin to the body[FMA,modified]. There is only one instance of the pelvic girdle region per organism.[VSAO] EMAPA:37862 FMA:16581 NCIT:C33291 UMLS:C0684083 VSAO:0000304 uberon girdle - pelvic pelvic girdle UBERON:0001271 pelvic girdle region The organism subdivision that includes the pelvic girdle skeleton and associated soft tissue. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). Examples: There are only two instances in an organism, right and left pectoral girdle regions. FMA:16581 FMA:23217 UBERONREF:0000003 Subdivision of lower limb or fin which links the limb/fin to the body[FMA,modified]. There is only one instance of the pelvic girdle region per organism.[VSAO] 2012-08-14 VSAO:0000304 VSAO EMAPA:37862 MA:th UMLS:C0684083 ncithesaurus:Pelvic_Girdle pelvic girdle The epithelial layer of the stomach . in FMA this is classified as simple columnar, MA divides this into squamous and glandular BTO:0000500 CALOHA:TS-2068 EHDAA2:0001918 EMAPA:17023 FMA:17091 MA:0001610 VHOG:0001433 epithelial tissue of stomach epithelial tissue of ventriculus epithelium of ventriculus stomach epithelial tissue stomach epithelium ventriculus epithelial tissue ventriculus epithelium uberon gastric epithelium UBERON:0001276 epithelium of stomach The epithelial layer of the stomach . MP:0000471 in FMA this is classified as simple columnar, MA divides this into squamous and glandular FMA epithelial tissue of stomach OBOL:automatic epithelial tissue of ventriculus OBOL:automatic epithelium of ventriculus OBOL:automatic stomach epithelial tissue OBOL:automatic stomach epithelium OBOL:automatic ventriculus epithelial tissue OBOL:automatic ventriculus epithelium OBOL:automatic gastric epithelium BTO:0000500 Epithelial layer that lines the intestine. Simple columnar epithelium that lines the intestine, sometimes pseudostratified, with absorptive brush-border cells and mucous goblet cells clearly visible. Crosnier et al. 2005[TAO] BTO:0000781 EMAPA:32873 FMA:17229 MA:0001536 NCIT:C49240 TAO:0005124 UMLS:C0226890 ZFA:0005124 bowel epithelial tissue bowel epithelium epithelial tissue of bowel epithelial tissue of intestine epithelium of bowel epithelium of intestine intestine epithelial tissue villous epithelium uberon intestine epithelium UBERON:0001277 intestinal epithelium Epithelial layer that lines the intestine. UBERON:cjm Simple columnar epithelium that lines the intestine, sometimes pseudostratified, with absorptive brush-border cells and mucous goblet cells clearly visible. Crosnier et al. 2005[TAO] 2012-08-14 TAO:0005124 TAO ZFIN:curator UMLS:C0226890 ncithesaurus:Intestinal_Epithelium bowel epithelial tissue OBOL:automatic bowel epithelium OBOL:automatic epithelial tissue of bowel OBOL:automatic epithelial tissue of intestine OBOL:automatic epithelium of bowel OBOL:automatic epithelium of intestine OBOL:automatic intestine epithelial tissue OBOL:automatic villous epithelium ZFA:0005124 An epithelium that is part of a large intestine [Automatically generated definition]. CALOHA:TS-2105 EMAPA:35466 FMA:17301 MA:0001545 epithelial tissue of large intestine large intestinal epithelium large intestine epithelial tissue large intestine epithelium uberon UBERON:0001278 epithelium of large intestine An epithelium that is part of a large intestine [Automatically generated definition]. OBOL:automatic epithelial tissue of large intestine OBOL:automatic large intestine epithelial tissue OBOL:automatic the glandular mucous membrane lining of the uterine cavity that is hormonally responsive during the estrous/menstrual cycle and during pregnancy The mucous membrane lining the uterus. [TFD][VHOG] The maternal part of the placenta (of eutherian mammals) is the vascularized and glandular uterine lining, or endometrium.[well established][VHOG] endometrial Animals that have estrous cycles reabsorb the endometrium if conception does not occur during that cycle. Animals that have menstrual cycles shed the endometrium through menstruation instead in FMA this is subdivided into basal and outer BTO:0001422 CALOHA:TS-0276 EFO:0000980 EMAPA:29917 EV:0100115 FMA:17742 GAID:377 MA:0000390 MAT:0000319 MESH:D004717 MIAA:0000319 NCIT:C12313 UMLS:C0014180 VHOG:0001285 tunica mucosa (endometrium) tunica mucosa uteri uterine endometrium uberon uterine mucosa uterine mucous membrane UBERON:0001295 endometrium FMA the glandular mucous membrane lining of the uterine cavity that is hormonally responsive during the estrous/menstrual cycle and during pregnancy MESH:A05.360.319.679.490 MGI:smb MP:0004896 The mucous membrane lining the uterus. [TFD][VHOG] 2012-09-17 VHOG:0001285 VHOG The maternal part of the placenta (of eutherian mammals) is the vascularized and glandular uterine lining, or endometrium.[well established][VHOG] 2012-09-17 VHOG:0001285 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.144 in FMA this is subdivided into basal and outer FMA UMLS:C0014180 ncithesaurus:Endometrium tunica mucosa (endometrium) FMA:17742 tunica mucosa uteri uterine endometrium BTO:0001422 uterine mucous membrane BTO:0001422 Outer serosa layer of the uterus. TODO - check for parallel structure with peritoneum EMAPA:37792 FMA:17744 MA:0001729 NCIT:C33298 UMLS:C0227824 perimetrium serous coat of uterus serous membrane of uterus tunica serosa (perimetrium) tunica serosa uteri uterine serosa uterus serosa uterus serous membrane visceral peritoneum of uterus uberon UBERON:0001297 serosa of uterus Outer serosa layer of the uterus. EMAPA:37792 MA:th UMLS:C0227824 ncithesaurus:Perimetrium perimetrium serous coat of uterus serous membrane of uterus OBOL:automatic tunica serosa uteri FMA:17744 FMA:TA uterus serous membrane OBOL:automatic A fallopian tube that is part of a right side of organism [Automatically generated definition]. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern non-functional in monotremes[ISBN-13:978-0226870137] EMAPA:37369 FMA:18483 MA:0001717 NCIT:C33475 UMLS:C0227900 right fallopian tube right oviduct uberon UBERON:0001302 right uterine tube A fallopian tube that is part of a right side of organism [Automatically generated definition]. OBOL:automatic EMAPA:37369 MA:th UMLS:C0227900 ncithesaurus:Right_Fallopian_Tube A fallopian tube that is part of a left side of organism [Automatically generated definition]. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EMAPA:37368 FMA:18484 MA:0001716 NCIT:C32959 UMLS:C0227902 left fallopian tube left oviduct uberon UBERON:0001303 left uterine tube A fallopian tube that is part of a left side of organism [Automatically generated definition]. OBOL:automatic EMAPA:37368 MA:th UMLS:C0227902 ncithesaurus:Left_Fallopian_Tube An artery that supplies blood to the upper urinary bladder. The first part of the superior vesical artery represents the terminal section of the previous portion of the umbilical artery (fetal hypogastric artery)[WP] EMAPA:37123 FMA:18839 MA:0002080 NCIT:C52686 UMLS:C0226376 arteria vesicali superior arteria vesicalis superior uberon arteriae vesicales superiores UBERON:0001312 superior vesical artery An artery that supplies blood to the upper urinary bladder. EMAPA:37123 MA:th UMLS:C0226376 ncithesaurus:Superior_Vesical_Artery arteria vesicali superior arteria vesicalis superior arteriae vesicales superiores A vein that begins near the upper part of the greater sciatic foramen, passes upward behind and slightly medial to the hypogastric artery and, at the brim of the pelvis, joins with the external iliac to form the common iliac vein. [WP,unvetted]. EHDAA2:0000874 EMAPA:37148 FMA:18884 MA:0002139 MA:0002145 NCIT:C32847 UMLS:C0226764 VHOG:0000749 galen:InternalIliacVein uberon hypogastric vein v. hypogastrica v. iliaca interna UBERON:0001317 internal iliac vein MA A vein that begins near the upper part of the greater sciatic foramen, passes upward behind and slightly medial to the hypogastric artery and, at the brim of the pelvis, joins with the external iliac to form the common iliac vein. [WP,unvetted]. EMAPA:37148 MA:th UMLS:C0226764 ncithesaurus:Internal_Iliac_Vein hypogastric vein MA:0002139 v. hypogastrica v. iliaca interna One the veins that drains the vaginal venous plexus, into the hypogastric veins. [WP,modified]. EMAPA:37796 FMA:18899 MA:0002251 vagina vein vein of vagina uberon UBERON:0001319 vaginal vein FMA/obol One the veins that drains the vaginal venous plexus, into the hypogastric veins. [WP,modified]. EMAPA:37796 MA:th vagina vein OBOL:automatic vein of vagina OBOL:automatic Muscle (organ) which is a part of the pelvis. Examples: levator ani, EMAPA:18184 EMAPA:37481 FMA:19086 MA:0000534 muscle organ of pelvis pelvic muscle pelvis muscle pelvis muscle organ uberon UBERON:0001325 muscle of pelvis FMAdef MA Muscle (organ) which is a part of the pelvis. Examples: levator ani, FMA:19086 EMAPA:37481 MA:th muscle organ of pelvis OBOL:automatic pelvic muscle FMA:19086 pelvis muscle organ OBOL:automatic A urethra that is part of a female reproductive system. BTO:0004088 EMAPA:28747 FMA:19669 MA:0002637 NCIT:C32591 UMLS:C0458485 uberon urethra feminina urethra muliebris UBERON:0001334 female urethra A urethra that is part of a female reproductive system. UMLS:C0458485 ncithesaurus:Female_Urethra urethra feminina BTO:0004088 urethra muliebris BTO:0004088 Any of the numerous small mucous-secreting glands located in the wall of the male or female urethra that help protect the epithelium from the corrosive urine NCIT:C12339 paraurethral gland belongs here EMAPA:37784 FMA:19683 MA:0001688 gland of urethra urethra gland urethra gland (male or female) urethral mucuous gland uberon UBERON:0001338 urethral gland MP Any of the numerous small mucous-secreting glands located in the wall of the male or female urethra that help protect the epithelium from the corrosive urine MP:anna NCIT:C12339 paraurethral gland belongs here NCIT EMAPA:37784 MA:th gland of urethra OBOL:automatic The epithelial layer of the vagina. FMA: nonkeratinizing stratified squamous epithelium; BTO: Vaginal epithelium is stratified squamous epithelium having a thickness of 15-200 microns; MA has single subclass (squamous) BTO:0000422 CALOHA:TS-1325 EMAPA:30991 FMA:19978 MA:0001730 NCIT:C49313 UMLS:C0920840 epithelial tissue of vagina vagina epithelial tissue vagina epithelium vaginal epithelium uberon epithelium, vaginal UBERON:0001344 epithelium of vagina The epithelial layer of the vagina. MP:0001140 FMA: nonkeratinizing stratified squamous epithelium; BTO: Vaginal epithelium is stratified squamous epithelium having a thickness of 15-200 microns; MA has single subclass (squamous) FMA UMLS:C0920840 ncithesaurus:Vaginal_Epithelium epithelial tissue of vagina OBOL:automatic vagina epithelial tissue OBOL:automatic epithelium, vaginal BTO:0000422 The anus and surrounding regions. Encompasses both internal and external regions, where present Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] EFO:0000847 EHDAA2:0000122 EHDAA:2931 EMAPA:16831 MA:0000329 MAT:0000042 MIAA:0000042 NCIT:C32069 UMLS:C0230120 VHOG:0000395 WBbt:0006919 uberon posterior posterior end of organism UBERON:0001353 anal region cjm The anus and surrounding regions. Encompasses both internal and external regions, where present Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] 2012-09-17 VHOG:0000395 VHOG ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 UMLS:C0230120 ncithesaurus:Anal_Region A zone of skin that is part of a pelvis [Automatically generated definition]. EMAPA:37282 FMA:22984 MA:0000546 pelvic skin pelvis skin pelvis zone of skin zone of skin of pelvis uberon UBERON:0001415 skin of pelvis A zone of skin that is part of a pelvis [Automatically generated definition]. OBOL:automatic EMAPA:37282 MA:th pelvis zone of skin OBOL:automatic zone of skin of pelvis OBOL:automatic A zone of skin that is part of an abdomen [Automatically generated definition]. EFO:0000214 FMA:22988 FMA:23000 MA:0000523 NCIT:C52758 UMLS:C0222166 abdomen skin abdomen zone of skin abdominal skin skin of abdomen proper zone of skin of abdomen uberon UBERON:0001416 skin of abdomen A zone of skin that is part of an abdomen [Automatically generated definition]. OBOL:automatic UMLS:C0222166 ncithesaurus:Abdominal_Skin abdomen zone of skin OBOL:automatic skin of abdomen proper FMA:22988 zone of skin of abdomen OBOL:automatic A zone of skin that is part of a neck [Automatically generated definition]. EMAPA:37277 FMA:23021 FMA:23022 MA:0000590 NCIT:C52756 UMLS:C0205030 neck (volume) zone of skin neck skin neck zone of skin zone of skin of neck zone of skin of neck (volume) uberon UBERON:0001417 skin of neck A zone of skin that is part of a neck [Automatically generated definition]. OBOL:automatic EMAPA:37277 MA:th UMLS:C0205030 ncithesaurus:Neck_Skin neck (volume) zone of skin OBOL:automatic neck zone of skin OBOL:automatic zone of skin of neck OBOL:automatic zone of skin of neck (volume) OBOL:automatic A zone of skin that is part of a thorax [Automatically generated definition]. EMAPA:37765 FMA:23028 FMA:23029 MA:0000564 thoracic skin thorax skin thorax zone of skin zone of skin of thorax uberon upper body skin UBERON:0001418 skin of thorax A zone of skin that is part of a thorax [Automatically generated definition]. OBOL:automatic EMAPA:37765 MA:th thorax zone of skin OBOL:automatic zone of skin of thorax OBOL:automatic An organism subdivision that includes the pectoral girdle skeleton and associated soft tissue. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). Examples: There are only two instances in an organism, right and left pectoral girdle regions. this class describes the organism subdivision, NOT the skeleton within. See also: skeleton of pectoral girdle (UBERON:0007831). An organism subdivision that includes the pectoral girdle skeleton. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). There is only one instance of the pectoral girdle region per organism.[VSAO] Note that this class describes the central subdivision of the pectoral girdle complex, NOT the skeleton within.[VSAO] EMAPA:37856 FMA:23217 VSAO:0000305 galen:ShoulderGirdle cingulum membri superioris girdle - pectoral cingulum membri superioris shoulder girdle upper limb girdle uberon pectoral girdle pectoral region UBERON:0001421 pectoral girdle region An organism subdivision that includes the pectoral girdle skeleton and associated soft tissue. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). Examples: There are only two instances in an organism, right and left pectoral girdle regions. FMA:23217 UBERONREF:0000003 An organism subdivision that includes the pectoral girdle skeleton. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). There is only one instance of the pectoral girdle region per organism.[VSAO] 2012-08-14 VSAO:0000305 VSAO Note that this class describes the central subdivision of the pectoral girdle complex, NOT the skeleton within.[VSAO] 2012-09-06 VSAO:0000305 VSAO Curator EMAPA:37856 MA:th cingulum membri superioris FMA:23217 FMA:TA cingulum membri superioris FMA:TA shoulder girdle FMA:23217 upper limb girdle FMA:23217 Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system. Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO] Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO] System that provides physical support to the organism.[AAO] By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG] skeletal GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates AAO:0000566 BTO:0001486 CALOHA:TS-1320 EFO:0000806 EHDAA2:0003168 EMAPA:35773 FMA:23881 MA:0000018 NCIT:C12788 OpenCyc:Mx4rvVi1rpwpEbGdrcN5Y29ycA TAO:0000434 UMLS:C0037253 VHOG:0001254 VSAO:0000027 XAO:0003060 ZFA:0000434 skeleton system set of all bones and joints uberon Skelettsystem UBERON:0001434 skeletal system https://github.com/obophenotype/uberon/wiki/The-skeletal-system Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system. GO_REF:0000034 VSAO:0000027 Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO] 2012-08-14 TAO:0000434 TAO TAO:wd Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO] 2012-08-14 VSAO:0000027 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 PSPUB:0000170 System that provides physical support to the organism.[AAO] 2012-06-20 AAO:0000566 AAO AAO:LAP By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG] 2012-09-17 VHOG:0001254 VHOG DOI:10.1159/000324245 Donoghue PCJ, Sansom IJ, Origin and early evolution of vertebrate skeletonization. Microscopy research and technique (2002) GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates GO UMLS:C0037253 ncithesaurus:Skeletal_System set of all bones and joints Skelettsystem BTO:0001486 FMA:24218 XAO:0000040 head subdivision uberon head region region of head UBERON:0001444 subdivision of head A subdivision of the head that has as parts the layers deep to the surface of the anterior surface, including the mouth, eyes, and nose (when present). In vertebrates, this includes the facial skeleton and structures superficial to the facial skeleton (cheeks, mouth, eyeballs, skin of face, etc). Subdivision of head which consists of the viscerocranium and all layers superficial to it. Examples: There is only one face. The area that extends from the median ocellus to the oral foramen[HAO]. facial The face develops from outward growth of tissue located rostral to the cranium & pharynx. The lower jaw and most of the upper jaw are formed by growth of the first pharyngeal (branchial) arch. The upper incisor region and the nose and forehead (frontal region) are formed from tissue located rostral to the neural tube (frontonasal prominence) BTO:0003369 CALOHA:TS-2216 EMAPA:32763 FMA:24728 GAID:64 HAO:0000316 MA:0002473 MESH:D005145 NCIT:C13071 OpenCyc:Mx4rvVi5GZwpEbGdrcN5Y29ycA UMLS:C0015450 galen:Face uberon facia/facies visage UBERON:0001456 face A subdivision of the head that has as parts the layers deep to the surface of the anterior surface, including the mouth, eyes, and nose (when present). In vertebrates, this includes the facial skeleton and structures superficial to the facial skeleton (cheeks, mouth, eyeballs, skin of face, etc). Subdivision of head which consists of the viscerocranium and all layers superficial to it. Examples: There is only one face. FMA:24728 The area that extends from the median ocellus to the oral foramen[HAO]. HAO:0000316 NCBITaxon:7399 The face develops from outward growth of tissue located rostral to the cranium & pharynx. The lower jaw and most of the upper jaw are formed by growth of the first pharyngeal (branchial) arch. The upper incisor region and the nose and forehead (frontal region) are formed from tissue located rostral to the neural tube (frontonasal prominence) vanat.cvm.umn.edu/TFFlectPDFs/LectFaceDevelop.pdf UMLS:C0015450 ncithesaurus:Face facia/facies visage BTO:0003369 A zone of skin that is part of a lip [Automatically generated definition]. EMAPA:37643 FMA:24764 MA:0001579 NCIT:C12291 UMLS:C0222101 lip skin lip zone of skin zone of skin of lip uberon skin of lips UBERON:0001458 skin of lip A zone of skin that is part of a lip [Automatically generated definition]. OBOL:automatic EMAPA:37643 MA:th UMLS:C0222101 ncithesaurus:Skin_of_the_Lip lip zone of skin OBOL:automatic zone of skin of lip OBOL:automatic skin of lips Skeletal element that is composed of bone tissue. Also called osseous tissue, (Latin: os). Is a type of hard endoskeletal connective tissue found in many vertebrate animals. Bone is the main tissue of body organs that support body structures, protect internal organs, (in conjunction with muscles) facilitate movement; and are involved with cell formation, calcium metabolism, and mineral storage.[AAO] Portion of tissue which is calcified connective tissue making up the structural elements of the skeletal system.[TAO] Skeletal element that is composed of bone tissue.[VSAO] relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] The 'new animal phylogeny' reveals that many of the groups known to biomineralize sit among close relatives that do not, and it favours an interpretation of convergent or parallel evolution for biomineralization in animals. (...) Whether this 'biomineralization toolkit'of genes reflects a parallel co-option of a common suite of genes or the inheritance of a skeletogenic gene regulatory network from a biomineralizing common ancestor remains an open debate.[debated][VHOG] AAO:0000047 AEO:0000082 BTO:0000140 CALOHA:TS-0088 EFO:0000298 EHDAA2:0003082 EMAPA:32782 ENVO:00002039 EV:0100140 FMA:30317 FMA:5018 GAID:92 MA:0001459 MAT:0000299 MIAA:0000299 NCIT:C12366 OpenCyc:Mx4rvViDlpwpEbGdrcN5Y29ycA OpenCyc:Mx4rvVkCG5wpEbGdrcN5Y29ycA TAO:0001514 UMLS:C0262950 VHOG:0001190 VSAO:0000057 XAO:0000169 ZFA:0001514 galen:Bone bone organ uberon bone bones UBERON:0001474 bone element VSAO-modified Skeletal element that is composed of bone tissue. GO_REF:0000034 PSPUB:0000170 VSAO:0000057 Also called osseous tissue, (Latin: os). Is a type of hard endoskeletal connective tissue found in many vertebrate animals. Bone is the main tissue of body organs that support body structures, protect internal organs, (in conjunction with muscles) facilitate movement; and are involved with cell formation, calcium metabolism, and mineral storage.[AAO] 2012-06-20 AAO:0000047 AAO AAO:LAP Portion of tissue which is calcified connective tissue making up the structural elements of the skeletal system.[TAO] 2012-08-14 TAO:0001514 TAO ZFIN:curator Skeletal element that is composed of bone tissue.[VSAO] 2012-08-14 VSAO:0000057 VSAO PSPUB:0000170 relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] 2012-06-20 AAO:0000047 AAO The 'new animal phylogeny' reveals that many of the groups known to biomineralize sit among close relatives that do not, and it favours an interpretation of convergent or parallel evolution for biomineralization in animals. (...) Whether this 'biomineralization toolkit'of genes reflects a parallel co-option of a common suite of genes or the inheritance of a skeletogenic gene regulatory network from a biomineralizing common ancestor remains an open debate.[debated][VHOG] 2012-09-17 VHOG:0001190 VHOG DOI:10.1159/000324245 Murdock DJ, Donoghue PC, Evolutionary Origins of Animal Skeletal Biomineralization. Cells Tissues Organs (2011) UMLS:C0262950 ncithesaurus:Bone bone organ FMA:5018 bone AEO:0000082 BTO:0000140 MA:0001459 VHOG:0001190 bones ZFA:0001514 An articular capsule (or joint capsule) is an envelope surrounding a synovial joint. [WP,unvetted]. check ncita EMAPA:37621 FMA:34836 GAID:263 MA:0001519 MESH:D017746 NCIT:C32259 NCIT:C84388 UMLS:C0206207 galen:JointCapsule capsula articularis fibrous capsule of joint joint capsule joint fibrous capsule uberon capsulae articulares UBERON:0001484 articular capsule An articular capsule (or joint capsule) is an envelope surrounding a synovial joint. [WP,unvetted]. check ncita ncit EMAPA:37621 MA:th UMLS:C0206207 ncithesaurus:Joint_Capsule capsula articularis FMA:34836 FMA:TA capsulae articulares Any muscle organ that is part of a pelvic girdle [Automatically generated definition]. Note that in MA, this is a subclass of pelvis muscle; in FMA this is a hindlimb muscle, but recall in FMA hindlimb includes the girdle. UBERON:0003271 EHDAA:8326 EMAPA:18184 EMAPA:18185 FMA:37367 MA:0000537 RETIRED_EHDAA2:0001430 girdle-pelvic muscle organ muscle organ of girdle-pelvic muscle organ of pelvic girdle muscle organ of pelvic girdle bone pelvic girdle muscle pelvic girdle muscle organ pelvic girdle skeletal muscle uberon UBERON:0001497 muscle of pelvic girdle Any muscle organ that is part of a pelvic girdle [Automatically generated definition]. OBOL:automatic Note that in MA, this is a subclass of pelvis muscle; in FMA this is a hindlimb muscle, but recall in FMA hindlimb includes the girdle. MA girdle-pelvic muscle organ OBOL:automatic muscle organ of girdle-pelvic OBOL:automatic muscle organ of pelvic girdle OBOL:automatic muscle organ of pelvic girdle bone OBOL:automatic pelvic girdle muscle organ OBOL:automatic pelvic girdle skeletal muscle EMAPA:18185 The descending aorta is the portion of the aorta in a two-pass circulatory system from the arch of aorta to the point where it divides into the common iliac arteries[GO]. The descending aorta is part of the aorta, the largest artery in the body. The descending aorta is the part of the aorta beginning at the aortic arch that runs down through the chest and abdomen. The descending aorta is divided into two portions, the thoracic and abdominal, in correspondence with the two great cavities of the trunk in which it is situated. Within the abdomen, the descending aorta branches into the two common iliac arteries which serve the legs. [WP,unvetted]. results from fusion of left and right dorsal aortae EMAPA:18606 FMA:3784 MA:0002571 NCIT:C32455 OpenCyc:Mx4rv4EE35wpEbGdrcN5Y29ycA UMLS:C0011666 pars descendens aortae uberon aorta descendens pars descendens aortae UBERON:0001514 descending aorta FMA Wikipedia The descending aorta is the portion of the aorta in a two-pass circulatory system from the arch of aorta to the point where it divides into the common iliac arteries[GO]. The descending aorta is part of the aorta, the largest artery in the body. The descending aorta is the part of the aorta beginning at the aortic arch that runs down through the chest and abdomen. The descending aorta is divided into two portions, the thoracic and abdominal, in correspondence with the two great cavities of the trunk in which it is situated. Within the abdomen, the descending aorta branches into the two common iliac arteries which serve the legs. [WP,unvetted]. GO:0035906 UMLS:C0011666 ncithesaurus:Descending_Aorta pars descendens aortae FMA:3784 aorta descendens aorta descendens pars descendens aortae the part of the aorta that extends from the origin at the heart to the diaphragm, and from which arises numerous branches that supply oxygenated blood to the chest cage and the organs within the chest BTO:0000157 EFO:0002525 EMAPA:18603 FMA:3786 GAID:471 MA:0002569 MESH:D001013 NCIT:C33766 OpenCyc:Mx4rveb9TpwpEbGdrcN5Y29ycA UMLS:C1522460 galen:ThoracicAorta aorta thoracica thoracic part of aorta uberon aorta thoracalis pars thoracica aortae UBERON:0001515 thoracic aorta FMA the part of the aorta that extends from the origin at the heart to the diaphragm, and from which arises numerous branches that supply oxygenated blood to the chest cage and the organs within the chest MP:0010468 UMLS:C1522460 ncithesaurus:Thoracic_Aorta aorta thoracica FMA:3786 FMA:TA aorta thoracalis pars thoracica aortae Abdominal part of aorta: the distal part of the descending aorta, which is the continuation of the thoracic part and gives rise to the inferior phrenic, lumbar, median sacral, superior and inferior mesenteric, middle suprarenal, renal, and testicular or ovarian arteries, and celiac trunk[BTO]. The abdominal aorta is the largest artery in the abdominal cavity. As part of the aorta, it is a direct continuation of descending aorta(of the thorax). [WP,unvetted]. Many of the branches of the abdominal aorta in mammals may be branches of the dorsal aorta in other vertebrates BTO:0002976 EFO:0002524 EMAPA:17856 FMA:3789 GAID:470 MA:0000474 MESH:D001012 NCIT:C32038 OpenCyc:Mx4rvYhWCZwpEbGdrcN5Y29ycA UMLS:C0003484 galen:AbdominalAorta abdominal part of aorta descending abdominal aorta pars abdominalis aortae uberon abdominal part of aorta aorta abdominalis pars abdominalis aortae UBERON:0001516 abdominal aorta FMA Abdominal part of aorta: the distal part of the descending aorta, which is the continuation of the thoracic part and gives rise to the inferior phrenic, lumbar, median sacral, superior and inferior mesenteric, middle suprarenal, renal, and testicular or ovarian arteries, and celiac trunk[BTO]. The abdominal aorta is the largest artery in the abdominal cavity. As part of the aorta, it is a direct continuation of descending aorta(of the thorax). [WP,unvetted]. BTO:0002976 UMLS:C0003484 ncithesaurus:Abdominal_Aorta abdominal part of aorta FMA:3789 descending abdominal aorta FMA:3789 pars abdominalis aortae FMA:3789 abdominal part of aorta BTO:0002976 aorta abdominalis aorta abdominalis BTO:0002976 pars abdominalis aortae pars abdominalis aortae BTO:0002976 A bilaterally paired branched artery that originates from the aortic arches and divides into and includes as parts the internal and external carotid arteries[cjm]. we follow the FMA and treat the artery as a tree-structure - here we include the internal and external as parts. For the part that excludes the branches, see 'trunk of common carotid artery' This class represents the adult and developing structures' in birds and reptiles, develops from arch III and parts of ventral and dorsal aortae carotid artery CALOHA:TS-0116 EHDAA2:0000217 EHDAA:7331 EMAPA:17855 FMA:3939 GAID:479 MA:0001926 MESH:D017536 NCIT:C32352 UMLS:C0162859 VHOG:0000272 carotid artery system common carotid artery trunk of common carotid tree uberon a. carotis communis UBERON:0001530 common carotid artery plus branches FMA Wikipedia A bilaterally paired branched artery that originates from the aortic arches and divides into and includes as parts the internal and external carotid arteries[cjm]. carotid artery FMA:3939 UMLS:C0162859 ncithesaurus:Common_Carotid_Artery carotid artery system EHDAA2:0000217 common carotid artery FMA:3939 trunk of common carotid tree FMA:3939 a. carotis communis A tube extending from the mouth to the anus. The alimentary or digestive tract, and associated organs.[TAO] The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] FMA also has a term 'gastrointestinal tract', but this includes the liver. we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509 we following Kardong in naming the entire tube from mouth to anus the alimentary canal. Kardong calls the portion of this tract that excludes buccal cavity and pharynx the 'alimentary canal', consider adding an extra class for this gut AAO:0010023 BILA:0000083 BTO:0000511 BTO:0000545 EHDAA2:0000726 EHDAA:518 EMAPA:16247 FBbt:00003125 FMA:45615 MA:0000917 NCIT:C34082 OpenCyc:Mx4rvVi0GpwpEbGdrcN5Y29ycA TAO:0000112 TGMA:0001819 UMLS:C0017189 VHOG:0000309 WBbt:0005743 ZFA:0000112 galen:AlimentaryTract digestive tube enteric tract alimentary canal alimentary tract uberon digestive canal gut tube UBERON:0001555 digestive tract NCBIBook:NBK10107 A tube extending from the mouth to the anus. The alimentary or digestive tract, and associated organs.[TAO] 2012-08-14 TAO:0000112 TAO ZFIN:curator The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000309 VHOG ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 FMA also has a term 'gastrointestinal tract', but this includes the liver. FMA we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509 MA UMLS:C0017189 ncithesaurus:Gastrointestinal_Tract enteric tract ZFA:0000112 digestive canal BTO:0000058 Subdivision of urinary system which consists of the urinary bladder and the urethra. FMA:45659 MA:0002636 galen:LowerUrinaryTract uberon UBERON:0001556 lower urinary tract Subdivision of urinary system which consists of the urinary bladder and the urethra. FMA:45659 The segment of the respiratory tract that starts proximally with the nose and ends distally with the cricoid cartilage, before continuing to the trachea. Some specify that the glottis (vocal cords) is the defining line between the upper and lower respiratory tracts;[2] yet even others make the line at the cricoid cartilage. The FMA includes nose, nasopharynx, oropharynx and larynx[WP] EHDAA2:0002136 EMAPA:17669 FMA:45661 MA:0000442 OpenCyc:Mx4rtT2HwgJMEdyAAADggVbxzQ VHOG:0000406 uberon UBERON:0001557 upper respiratory tract The segment of the respiratory tract that starts proximally with the nose and ends distally with the cricoid cartilage, before continuing to the trachea. Some specify that the glottis (vocal cords) is the defining line between the upper and lower respiratory tracts;[2] yet even others make the line at the cricoid cartilage. The FMA includes nose, nasopharynx, oropharynx and larynx[WP] FMA The segment of the respiratory tract that starts proximally with the trachea and includes all distal structures including the lungs[WP,modified] EHDAA2:0001036 EMAPA:16738 FMA:45662 MA:0000435 OpenCyc:Mx4rQRqjUgAKEdyHxgDggVfs8g VHOG:0000382 lower respiratory system uberon UBERON:0001558 lower respiratory tract The segment of the respiratory tract that starts proximally with the trachea and includes all distal structures including the lungs[WP,modified] FMA:45733 organ neck uberon UBERON:0001560 neck of organ FMA The muscles associated with the larynx. BTO:0001626 EMAPA:35473 FMA:46562 GAID:144 MA:0001768 MESH:D007821 NCIT:C32934 UMLS:C0023054 laryngeal muscle larynx muscle larynx muscle organ muscle organ of larynx musculi laryngeales uberon UBERON:0001568 muscle of larynx prolog The muscles associated with the larynx. MP:0002263 UMLS:C0023054 ncithesaurus:Laryngeal_Muscle larynx muscle organ OBOL:automatic muscle organ of larynx OBOL:automatic A muscle innervated by a facial nerve. FMA:46751 GAID:143 MA:0003160 MESH:D005152 MFMO:0000005 NCIT:C13073 UMLS:C0015460 XAO:0001013 face muscle face muscle organ facial muscle facial muscle proper facial nerve innervated muscle facial nerve muscle muscle of face muscle organ of face uberon cranial-facial muscle cranio-facial muscle craniofacial muscle mimetic muscles muscle of facil expression muscles of facial expression musculi faciei UBERON:0001577 facial muscle FEED Wikipedia A muscle innervated by a facial nerve. FEED:rd UMLS:C0015460 ncithesaurus:Facial_Muscle face muscle FMA:46751 face muscle organ OBOL:automatic facial muscle FMA:46751 facial muscle XAO:0001013 facial nerve innervated muscle muscle of face FMA:46751 muscle organ of face OBOL:automatic cranial-facial muscle EMAPA:25133 cranio-facial muscle EMAPA:25133 craniofacial muscle EMAPA:25133 mimetic muscles muscle of facil expression muscles of facial expression musculi faciei A vein that carries deoxygenated blood from the upper half of the body into the right atrium of the heart. Phylogenetic modifications within this basic pattern of arteries and veins are largely correlated with functional changes. In the transition from water to land, gills gave way to lungs, accompanied by the establishment of a pulmonary circulation. In some fishes and certainly in tetrapods, the cardinal veins become less involved in blood return. Instead, the composite, prominent postcava (posterior vena cava) arose to drain the posterior part of the body and the precava (anterior vena cava) developed to drain the anterior part of the body.[well established][VHOG] The mouse has both left and right anterior vena cava. adult humans only have a right. Postnatally the left regresses and becomes non-functional (Wessels and Sedmera 2003). In the mouse, The right pulmonary vein passes dorsal to the right superior vena cava, the left pulmonary dorsal to the left superior vena cava (Biology of the Laboratory Mouse, Green). BTO:0002683 EHDAA2:0001962 EHDAA:8726 EMAPA:18417 FMA:4720 GAID:549 MA:0000481 MESH:D014683 NCIT:C12816 UMLS:C0042459 VHOG:0001195 galen:SuperiorVenaCava superior caval vein superior vena cava uberon cranial vena cava precava vena cava superior vena maxima UBERON:0001585 anterior vena cava lexical A vein that carries deoxygenated blood from the upper half of the body into the right atrium of the heart. Phylogenetic modifications within this basic pattern of arteries and veins are largely correlated with functional changes. In the transition from water to land, gills gave way to lungs, accompanied by the establishment of a pulmonary circulation. In some fishes and certainly in tetrapods, the cardinal veins become less involved in blood return. Instead, the composite, prominent postcava (posterior vena cava) arose to drain the posterior part of the body and the precava (anterior vena cava) developed to drain the anterior part of the body.[well established][VHOG] 2012-09-17 VHOG:0001195 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.454-455 UMLS:C0042459 ncithesaurus:Superior_Vena_Cava superior caval vein superior vena cava FMA:4720 cranial vena cava VHOG:0001195 vena cava superior vena cava superior BTO:0002683 vena maxima One of two jugular veins that collect the blood from the brain, the superficial parts of the face, and the neck. [WP,unvetted]. Vein which receives many veins draining the palate, brain, and the orbital, nasal, and auditory regions.[AAO] AAO:0010236 EHDAA2:0000877 EHDAA:5407 EMAPA:17620 FMA:4724 MA:0002157 NCIT:C32849 OpenCyc:Mx4rvqdb95wpEbGdrcN5Y29ycA RETIRED_EHDAA2:0000878 UMLS:C0226550 XAO:0000382 galen:InternalJugularVein internal jugular internal jugular venous tree uberon vena jugularis interna UBERON:0001586 internal jugular vein One of two jugular veins that collect the blood from the brain, the superficial parts of the face, and the neck. [WP,unvetted]. Vein which receives many veins draining the palate, brain, and the orbital, nasal, and auditory regions.[AAO] 2012-06-20 AAO:0010236 AAO AAO:BJB UMLS:C0226550 ncithesaurus:Internal_Jugular_Vein internal jugular EHDAA2:0000877 vena jugularis interna The bronchial veins are small vessels that return blood from the larger bronchi and structures at the roots of the lungs. The right side drains into the azygos vein, while the left side drains into the left superior intercostal vein or the accessory hemiazygos vein. The bronchial veins are counterparts to the bronchial arteries. The veins, however, do not return all of the blood supplied by the arteries; much of the blood that is carried in the bronchial arteries is returned to the heart via the pulmonary veins. [WP,unvetted]. EMAPA:36284 FMA:4749 MA:0002088 NCIT:C53031 UMLS:C0226650 bronchial venous tree uberon UBERON:0001592 bronchial vein The bronchial veins are small vessels that return blood from the larger bronchi and structures at the roots of the lungs. The right side drains into the azygos vein, while the left side drains into the left superior intercostal vein or the accessory hemiazygos vein. The bronchial veins are counterparts to the bronchial arteries. The veins, however, do not return all of the blood supplied by the arteries; much of the blood that is carried in the bronchial arteries is returned to the heart via the pulmonary veins. [WP,unvetted]. UMLS:C0226650 ncithesaurus:Bronchial_Vein The ciliary muscle is a ring of smooth muscle in the middle layer of the eye that controls the eye's accommodation for viewing objects at varying distances and regulates the flow of aqueous humour through Schlemm's canal. [WP,unvetted]. BTO:0000654 EMAPA:35240 FMA:49151 MA:0001269 NCIT:C32315 UMLS:C0559230 musculus ciliarus uberon Bowman`s muscles ciliaris musculus ciliaris UBERON:0001605 ciliary muscle MA FMA FMA The ciliary muscle is a ring of smooth muscle in the middle layer of the eye that controls the eye's accommodation for viewing objects at varying distances and regulates the flow of aqueous humour through Schlemm's canal. [WP,unvetted]. UMLS:C0559230 ncithesaurus:Ciliary_Muscle musculus ciliarus BTO:0000654 Bowman`s muscles BTO:0000654 ciliaris musculus ciliaris . revisit this, see issue #331 The muscle cells of the iris are smooth muscle in mammals and amphibians, but are striated muscle in birds and reptiles. Many fish have neither, and, as a result, their irides are unable to dilate and contract, so that the pupil always remains of a fixed size[Romer, via WP] in aves, stromal mesenchymal cells may migrate to the iris and become skeletal EMAPA:35448 FMA:49154 MA:0001287 iris muscle iris muscle organ muscle organ of iris uberon UBERON:0001606 muscle of iris FMA . iris muscle organ OBOL:automatic muscle organ of iris OBOL:automatic A branch of the external carotid artery that supplies structures of the face. [WP,unvetted]. EMAPA:19213 FMA:49549 MA:0001950 NCIT:C32578 OpenCyc:Mx4rwCt95ZwpEbGdrcN5Y29ycA UMLS:C0226109 uberon arteria maxillaris externa external maxillary artery UBERON:0001612 facial artery A branch of the external carotid artery that supplies structures of the face. [WP,unvetted]. UMLS:C0226109 ncithesaurus:Facial_Artery arteria maxillaris externa An artery that supplies deep structures of the face. It comes just out behind the neck of the mandible. [WP,unvetted]. ...1st pair undergoes partial regression, the remnants of which becomes part of the maxillary arteries EHDAA2:0001069 EHDAA:7357 EMAPA:17311 FMA:49675 GAID:498 MA:0001919 MESH:D008438 NCIT:C34205 OpenCyc:Mx4rwDDJ45wpEbGdrcN5Y29ycA UMLS:C0024949 uberon arteria maxillaris internal maxillary artery UBERON:0001616 maxillary artery An artery that supplies deep structures of the face. It comes just out behind the neck of the mandible. [WP,unvetted]. ...1st pair undergoes partial regression, the remnants of which becomes part of the maxillary arteries UMLS:C0024949 ncithesaurus:Maxillary_Artery arteria maxillaris Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO]. Portion of tissue composed of contractile fibers.[TAO] It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG] muscular muscle AAO:0011066 EMAPA:32715 EMAPA:37474 EV:0100146 FMA:5022 GAID:131 MA:0000015 OpenCyc:Mx4rv2kf-5wpEbGdrcN5Y29ycA TAO:0005145 VHOG:0001245 XAO:0000172 ZFA:0005145 galen:Muscle uberon UBERON:0001630 muscle organ Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO]. GO:0007517 Portion of tissue composed of contractile fibers.[TAO] 2012-08-14 TAO:0005145 TAO ZFIN:curator It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG] 2012-09-17 VHOG:0001245 VHOG ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.75 muscle ZFA:0005145 EMAPA:37474 MA:th An epithelial tube or tree of tibes that transports blood away from the heart[modified from AEO definition]. Note that in FMA an artery is a tree, whereas AEO/JB defines it as a tube; FMA includes a separate class for what it calls the trunk. Classification in this ontology may currently (Jan 2012) represent a mix of both schemes, although we are gradually revising in the direction of the AEO scheme. Part of the circulatory system composed of blood vessels which carry oxygenated blood away from the heart to the rest of the body.[AAO] The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] arterial AAO:0010211 AEO:0000208 BTO:0000573 CALOHA:TS-0054 EFO:0000814 EHDAA2:0000143 EHDAA2:0003253 EMAPA:35147 EV:0100026 FMA:50720 GAID:468 MA:0000064 MAT:0000034 MESH:D001158 MIAA:0000034 NCIT:C12372 OpenCyc:Mx4rvVjknZwpEbGdrcN5Y29ycA TAO:0000005 UMLS:C0003842 VHOG:0001251 XAO:0000114 ZFA:0000005 galen:Artery arterial subtree arterial tree organ part arteries uberon arterial system arterial vessel UBERON:0001637 artery An epithelial tube or tree of tibes that transports blood away from the heart[modified from AEO definition]. AEO:JB Part of the circulatory system composed of blood vessels which carry oxygenated blood away from the heart to the rest of the body.[AAO] 2012-06-20 AAO:0010211 AAO AAO:BJB The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] 2012-09-17 VHOG:0001251 VHOG DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006) UMLS:C0003842 ncithesaurus:Artery arteries TAO:0000005 vein Any of the tubular branching vessels that carry blood from the capillaries toward the heart. TODO - check with MA - vein vs venous blood vessel Part of the circulatory system composed of blood vessels which carry blood from other organs, tissues, and cells to the heart.[AAO] The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] venous venous subtree venous vessel AAO:0010212 AEO:0000209 BTO:0000234 CALOHA:TS-1108 EFO:0000816 EHDAA2:0003254 EMAPA:35906 EV:0100031 FMA:50723 GAID:492 MA:0000067 MAT:0000037 MESH:D014680 MIAA:0000037 NCIT:C12814 OpenCyc:Mx4rvVjkWpwpEbGdrcN5Y29ycA TAO:0000082 UMLS:C0042449 VHOG:0001743 XAO:0000115 ZFA:0000082 galen:Vein venous tree organ part uberon vascular element vena venae UBERON:0001638 vein Any of the tubular branching vessels that carry blood from the capillaries toward the heart. Part of the circulatory system composed of blood vessels which carry blood from other organs, tissues, and cells to the heart.[AAO] 2012-06-20 AAO:0010212 AAO AAO:BJB The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] 2012-09-17 VHOG:0001743 VHOG DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006) UMLS:C0042449 ncithesaurus:Vein vascular element EMAPA:th vena venae VHOG:0001743 Cranial nerve that has three branches - the ophthalmic (supplying the skin of the nose and upper jaw), the maxillary and the mandibular (supplying the lower jaw). Nerve consists of motor and sensory components. Ganglion cells of the sensory component form the proximal part of the trigeminal (Gasserian) ganglion. From the ganglion 3 major rami innervate jaws, snout, and buccal roof.[AAO] We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG] the ophthalmic usually usually merges with the other two. In some vertebrates, the ophthalmic emerges from the brain separately[Kardong] The trigeminal nerve has 3 branches in mammals - similar branches are present in nonmammalian vertebrates, but in some a separate profundus nerve that corresponds to opthalmic branch in mammls 5n AAO:0010470 BAMS:5n BAMS:Vn BAMS:nV BM:VN BTO:0001072 EFO:0001402 EHDAA2:0002084 EHDAA:3738 EMAPA:17576 FMA:50866 GAID:726 HBA:9322 MA:0001100 MBA:901 MESH:D014276 MFMO:0000093 NCIT:C12806 OpenCyc:Mx4rwMF8CJwpEbGdrcN5Y29ycA TAO:0000697 UMLS:C0040996 VHOG:0000704 XAO:0003092 ZFA:0000697 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=549 fifth cranial nerve nervus trigeminus nervus trigeminus [v] trigeminal V trigeminal nerve [V] trigeminal nerve tree trigeminal v nerve uberon CN-V cranial nerve V nerve V nervus trigeminus trigeminus UBERON:0001645 trigeminal nerve Wikipedia Cranial nerve that has three branches - the ophthalmic (supplying the skin of the nose and upper jaw), the maxillary and the mandibular (supplying the lower jaw). ISBN:0471209627 Nerve consists of motor and sensory components. Ganglion cells of the sensory component form the proximal part of the trigeminal (Gasserian) ganglion. From the ganglion 3 major rami innervate jaws, snout, and buccal roof.[AAO] 2012-06-20 AAO:0010470 AAO AAO:EJS We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000704 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.625 the ophthalmic usually usually merges with the other two. In some vertebrates, the ophthalmic emerges from the brain separately[Kardong] The trigeminal nerve has 3 branches in mammals - similar branches are present in nonmammalian vertebrates, but in some a separate profundus nerve that corresponds to opthalmic branch in mammls ISBN10:0471888893 5n NIFSTD:NeuroNames_abbrevSource UMLS:C0040996 NIFSTD:birnlex_869 UMLS:C0040996 ncithesaurus:Trigeminal_Nerve http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=549 NIFSTD:birnlex_869 nervus trigeminus nervus trigeminus [v] FMA:50866 FMA:TA trigeminal V EHDAA2:0002084 nerve V NeuroNames:549 nervus trigeminus BTO:0001072 trigeminus BTO:0001072 Cranial nerve that branches into the supraorbital (supplying the skin of the eye region and the lateral line organs here), the palatine (to the roof of the buccal cavity), and the hyomandibular (dividing into the jugular and mental branches). Slender nerve composed of branchiomotor and visceral efferent fibers innervating the mouth and various muscles within the jaw. Sensory components innervate the bucccal roof and somatomotor components innervate the depressor musculature and muscle interhyoideus.[AAO] We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG] 7n AAO:0010472 BAMS:7n BAMS:VIIn BAMS:Viin BAMS:nVII BM:Pons-VIIN EHDAA2:0000489 EHDAA:3729 EMAPA:17796 FMA:50868 GAID:719 HBA:9328 MA:0001091 MBA:798 MESH:D005154 NCIT:C12714 OpenCyc:Mx4rvthgEpwpEbGdrcN5Y29ycA TAO:0000664 UMLS:C0015462 VHOG:0000706 XAO:0003094 ZFA:0000664 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=551 branchiomeric cranial nerve face nerve facial VII facial VII nerve facial nerve [VII] facial nerve tree nerve of face nervus facialis nervus facialis [vii] seventh cranial nerve uberon CN-VII cranial nerve VII facial nerve or its root facial nerve/root nerve VII nervus facialis UBERON:0001647 facial nerve ZFA Wikipedia Wikipedia Cranial nerve that branches into the supraorbital (supplying the skin of the eye region and the lateral line organs here), the palatine (to the roof of the buccal cavity), and the hyomandibular (dividing into the jugular and mental branches). ISBN:0471209627 Slender nerve composed of branchiomotor and visceral efferent fibers innervating the mouth and various muscles within the jaw. Sensory components innervate the bucccal roof and somatomotor components innervate the depressor musculature and muscle interhyoideus.[AAO] 2012-06-20 AAO:0010472 AAO AAO:DSM We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000706 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.625 7n NIFSTD:NeuroNames_abbrevSource UMLS:C0015462 NIFSTD:birnlex_827 UMLS:C0015462 ncithesaurus:Facial_Nerve http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=551 NIFSTD:birnlex_827 face nerve OBOL:automatic facial VII EHDAA2:0000489 nerve of face OBOL:automatic nervus facialis ZFA:0000664 nervus facialis [vii] FMA:50868 FMA:TA facial nerve or its root BAMS:7n facial nerve/root BAMS:7n nerve VII NeuroNames:551 nervus facialis Cranial nerve that branches into the ramus communicans (to the skin), the pretrematic (to the walls of the pharynx and mouth, viscero-sensory fibers), and the larval post-trematic branch (lost in the adult). Small nerve consisting of branchiomotor and visceral efferent and afferent fibers which innervate the m. subarculais rectus I, dorsal buccal mucosa, and the tongue.[AAO] We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG] 9n AAO:0010474 BAMS:9n BAMS:IXn BTO:0004979 EHDAA2:0000709 EHDAA:3733 EMAPA:17268 FMA:50870 GAID:827 HBA:9334 MA:0001093 MBA:808 MESH:D005930 NCIT:C12723 OpenCyc:Mx4rwIr5X5wpEbGdrcN5Y29ycA TAO:0000668 UMLS:C0017679 UMLS:C1305752 VHOG:0000701 XAO:0003096 ZFA:0000668 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=701 glossopharyngeal IX glossopharyngeal IX nerve glossopharyngeal nerve [IX] glossopharyngeal nerve tree nervus glossopharyngeus nervus glossopharyngeus [ix] ninth cranial nerve uberon CN-IX cranial nerve IX nerve IX nervus glossopharyngeus UBERON:0001649 glossopharyngeal nerve motor Wikipedia Cranial nerve that branches into the ramus communicans (to the skin), the pretrematic (to the walls of the pharynx and mouth, viscero-sensory fibers), and the larval post-trematic branch (lost in the adult). ISBN:0471209627 Small nerve consisting of branchiomotor and visceral efferent and afferent fibers which innervate the m. subarculais rectus I, dorsal buccal mucosa, and the tongue.[AAO] 2012-06-20 AAO:0010474 AAO AAO:EJS We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000701 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.625 9n NIFSTD:NeuroNames_abbrevSource UMLS:C0017679 NIFSTD:birnlex_899 UMLS:C0017679 ncithesaurus:Glossopharyngeal_Nerve UMLS:C1305752 NIFSTD:birnlex_899 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=701 NIFSTD:birnlex_899 glossopharyngeal IX EHDAA2:0000709 nervus glossopharyngeus ZFA:0000668 nervus glossopharyngeus [ix] FMA:50870 FMA:TA CN-IX nerve IX NeuroNames:701 nervus glossopharyngeus The pulmonary artery that supplies the right lung. TODO - add class 'pulmonary artery tree organ' EMAPA:37378 FMA:50872 MA:0002500 NCIT:C33489 UMLS:C0923924 galen:RightPulmonaryArtery right main pulmonary artery right pulmonary arterial tree uberon arteria pulmonalis dextra UBERON:0001651 right pulmonary artery The pulmonary artery that supplies the right lung. UBERON:cjm EMAPA:37378 MA:th UMLS:C0923924 ncithesaurus:Right_Pulmonary_Artery arteria pulmonalis dextra The pulmonary artery that supplies the left lung. TODO - add class 'pulmonary artery tree organ' EMAPA:37097 FMA:50873 MA:0002032 NCIT:C32971 UMLS:C0923925 galen:LeftPulmonaryArtery left main pulmonary artery left pulmonary arterial tree uberon arteria pulmonalis sinistra UBERON:0001652 left pulmonary artery The pulmonary artery that supplies the left lung. UBERON:cjm EMAPA:37097 MA:th UMLS:C0923925 ncithesaurus:Left_Pulmonary_Artery arteria pulmonalis sinistra The anterior facial vein (facial vein) commences at the side of the root of the nose, and is a direct continuation of the angular vein where it also receives a small nasal branch. It lies behind the facial artery and follows a less tortuous course. It receives blood from the external palatine vein before it either joins the anterior branch of the retromandibular vein to form the common facial vein, or drains directly into the internal jugular vein. [WP,unvetted]. Vein which collects blood from muscles of the head and drains into the external jugular vein.[AAO] MA and NCITA also has 'anterior facial vein' AAO:0010513 EMAPA:19220 FMA:50874 MA:0002115 NCIT:C32579 OpenCyc:Mx4rvziz3JwpEbGdrcN5Y29ycA UMLS:C0226532 face vein vein of face uberon anterior facial vein vena facialis anterior UBERON:0001653 facial vein FMA The anterior facial vein (facial vein) commences at the side of the root of the nose, and is a direct continuation of the angular vein where it also receives a small nasal branch. It lies behind the facial artery and follows a less tortuous course. It receives blood from the external palatine vein before it either joins the anterior branch of the retromandibular vein to form the common facial vein, or drains directly into the internal jugular vein. [WP,unvetted]. Vein which collects blood from muscles of the head and drains into the external jugular vein.[AAO] 2012-06-20 AAO:0010513 AAO AAO:BJB MA and NCITA also has 'anterior facial vein' MA UMLS:C0226532 ncithesaurus:Facial_Vein face vein OBOL:automatic vein of face OBOL:automatic anterior facial vein vena facialis anterior The cranial ganglion that is associated with and extends fibers into the trigeminal nerve. consider renaming this 'trigeminal ganglion complex'. The complex may be fused (amniotes) partially fused (xenopus) or separate (sharks) A prominent collection of touch-sensory neurons of the trigeminal or fifth cranial nerve, positioned beside the brain between the eye and the ear. Kimmel et al, 1995.[TAO] In Xenopus, the profundal and the trigeminal ganglia are separate distally but fused at their proximal end as they condense around NF stage 24. AAO:0011107 BAMS:5Gn BAMS:GV BTO:0001231 EFO:0000903 EHDAA2:0002085 EHDAA:2113 EMAPA:16797 FMA:52618 GAID:725 MA:0001080 MAT:0000511 MESH:D012668 NCIT:C62642 TAO:0000295 UMLS:C0040995 VHOG:0000694 XAO:0000427 XAO:0000428 ZFA:0000295 5th ganglion Gasserian ganglion fifth ganglion ganglion of trigeminal complex semilunar ganglion trigeminal V ganglion fused trigeminal ganglion uberon Gasser's ganglion Gasserian ganglia gV ganglion of trigeminal nerve ganglion semilunare ganglion trigeminale trigeminal ganglia trigeminus ganglion UBERON:0001675 trigeminal ganglion ncithesaurus Bgee:AN The cranial ganglion that is associated with and extends fibers into the trigeminal nerve. A prominent collection of touch-sensory neurons of the trigeminal or fifth cranial nerve, positioned beside the brain between the eye and the ear. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000295 TAO ZFIN:curator In Xenopus, the profundal and the trigeminal ganglia are separate distally but fused at their proximal end as they condense around NF stage 24. XAO:0004093 UMLS:C0040995 ncithesaurus:Trigeminal_Ganglion 5th ganglion ZFA:0000295 Gasserian ganglion fifth ganglion ZFA:0000295 ganglion of trigeminal complex semilunar ganglion ISBN10:0471888893 trigeminal V ganglion MA:0001080 fused trigeminal ganglion NCBITaxon:32524 Gasser's ganglion BTO:0001231 Gasserian ganglia ganglion of trigeminal nerve BTO:0001231 ganglion semilunare ganglion trigeminale ganglion trigeminale BTO:0001231 trigeminal ganglia the bone at the lower, posterior part of the skull formed from the sclerotome of the occipital somites. It is not present in living or fossil agnathans or cartilaginous fishes, but appears to have arisen in parallel in many bony fishes. Incorporation of the occipital ver- tebrae into the skull was associated with the annexation of the upper part of the spinal cord into the brain, together with the first 2 spinal nerves as cranial nerves XI and XII fusion of basi-, exo- and supra-occipitals (and maybe tabular) EMAPA:25112 FMA:52735 GAID:227 MA:0001468 MESH:D009777 NCIT:C12757 OpenCyc:Mx4rwQtsiZwpEbGdrcN5Y29ycA UMLS:C0028784 uberon occipital complex occipital squama os occipitale UBERON:0001676 occipital bone FMA FMA basi paired exo and supra occipital bones MA-modified interparietal (postparietal) the bone at the lower, posterior part of the skull ISBN:0-683-40008-8 MP:0005269 formed from the sclerotome of the occipital somites. It is not present in living or fossil agnathans or cartilaginous fishes, but appears to have arisen in parallel in many bony fishes. Incorporation of the occipital ver- tebrae into the skull was associated with the annexation of the upper part of the spinal cord into the brain, together with the first 2 spinal nerves as cranial nerves XI and XII fusion of basi-, exo- and supra-occipitals (and maybe tabular) Kardong UMLS:C0028784 ncithesaurus:Occipital_Bone occipital complex os occipitale the large, irregular bone located at the base and side of the skull; consists of three parts at birth: squamous, tympanic, and petrous In many mammals, as in humans, the petrosal, ectotympanic and squamosal bones synostose to form the temporal bone + styloid process fusion of squamosal + angular (tympanic annulus) [derm.] + petrosal (prootic + opisthotic) The temporal bone consists of four parts: * Squama temporalis * Mastoid portion * Petrous portion (Petrosal ridge) * Tympanic part[WP]. Note the Temporal bone is not explicitly categorized to a part of the cranium in FMA EHDAA:6035 EMAPA:17682 FMA:52737 GAID:232 MA:0001476 MESH:D013701 NCIT:C12797 OpenCyc:Mx4rvbkAk5wpEbGdrcN5Y29ycA UMLS:C0039484 VHOG:0000800 uberon os temporale UBERON:0001678 temporal bone FMA petrosal squamosal plus angular temporal series styloid process FMA-abduced-lr the large, irregular bone located at the base and side of the skull; consists of three parts at birth: squamous, tympanic, and petrous ISBN:0-683-40008-8 MP:0005272 fusion of squamosal + angular (tympanic annulus) [derm.] + petrosal (prootic + opisthotic) chond. The temporal bone consists of four parts: * Squama temporalis * Mastoid portion * Petrous portion (Petrosal ridge) * Tympanic part[WP]. [WP] Note the Temporal bone is not explicitly categorized to a part of the cranium in FMA FMA UMLS:C0039484 ncithesaurus:Temporal_Bone os temporale Sense organ in vertebrates that is specialized for the detection of sound, and the maintenance of balance. Includes the outer ear and middle ear, which collect and transmit sound waves; and the inner ear, which contains the organs of balance and (except in fish) hearing. Also includes the pinna, the visible part of the outer ear, present in some mammals. The organ of hearing and of equilibrium. [TFD][VHOG] Both vertebrate and invertebrate auditory organs are thought to have evolved from primitive mechanosensors, but the nature of the ancestral structure and the evolutionary trajectories followed in distinct animal lineages remain unknown. In particular, we do not know how many types of mechanosensor existed in the protostome-deuterostome ancestor from which insects and vertebrates evolved or whether the PDA had an auditory organ.[well established][VHOG] auricular AAO:0011014 BTO:0000368 CALOHA:TS-1165 EFO:0000826 EHDAA2:0000423 EHDAA:502 EMAPA:16193 EV:0100353 FMA:52780 GAID:62 MA:0000236 MAT:0000138 MESH:D004423 MIAA:0000138 NCIT:C12394 OpenCyc:Mx4rvViXS5wpEbGdrcN5Y29ycA OpenCyc:Mx4rvVjL05wpEbGdrcN5Y29ycA UMLS:C0013443 UMLS:C0521421 VHOG:0000330 XAO:0000189 galen:Ear uberon auditory apparatus auris UBERON:0001690 ear Sense organ in vertebrates that is specialized for the detection of sound, and the maintenance of balance. Includes the outer ear and middle ear, which collect and transmit sound waves; and the inner ear, which contains the organs of balance and (except in fish) hearing. Also includes the pinna, the visible part of the outer ear, present in some mammals. GO:0042471 The organ of hearing and of equilibrium. [TFD][VHOG] 2012-09-17 VHOG:0000330 VHOG Both vertebrate and invertebrate auditory organs are thought to have evolved from primitive mechanosensors, but the nature of the ancestral structure and the evolutionary trajectories followed in distinct animal lineages remain unknown. In particular, we do not know how many types of mechanosensor existed in the protostome-deuterostome ancestor from which insects and vertebrates evolved or whether the PDA had an auditory organ.[well established][VHOG] 2012-09-17 VHOG:0000330 VHOG DOI:10.1002/dvdy.20207 Boekhoff-Falk G, Hearing in Drosophila: Development of Johnston's organ and emerging parallels to vertebrate ear development. Developmental Dynamics (2005) UMLS:C0013443 NIFSTD:birnlex_1062 UMLS:C0013443 ncithesaurus:Ear UMLS:C0521421 NIFSTD:birnlex_1062 auris BTO:0000368 the group of sensory neuron cell bodies associated with the facial nerve (seventh cranial nerve) resolve facial VII vs geniculate (see EHDAA2) These (the epibranchial placodes) are focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches in all vertebrates, and they produce the neuroblasts which migrate and condense to form the distal cranial ganglia: the geniculate, petrosal and nodose ganglia. (...) The one substantial difference between the vertebrate pharyngeal arches and those of the protochordates is the presence of the epibranchial placodes but the evolution of these structures was undoubtedly driven by the endoderm.[well established][VHOG] geniculate BAMS:GgVII EFO:0003669 EHDAA2:0000491 EHDAA2:0004623 EHDAA:5567 EHDAA:6644 EMAPA:17569 FMA:53414 GAID:718 MA:0001076 MESH:D005830 NCIT:C12721 TAO:0001291 UMLS:C0017406 VHOG:0000707 ZFA:0001291 facial VII ganglion gVII ganglion genicularum genicular ganglion uberon facial ganglion ganglion geniculi ganglion geniculi nervi facialis geniculate ganglion internal genu UBERON:0001700 geniculate ganglion ncithesaurus EHDAA2:0004623 ZFA EHDAA2:0004623 EHDAA2:0000491 the group of sensory neuron cell bodies associated with the facial nerve (seventh cranial nerve) ISBN:0-683-40008-8 MP:0001082 These (the epibranchial placodes) are focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches in all vertebrates, and they produce the neuroblasts which migrate and condense to form the distal cranial ganglia: the geniculate, petrosal and nodose ganglia. (...) The one substantial difference between the vertebrate pharyngeal arches and those of the protochordates is the presence of the epibranchial placodes but the evolution of these structures was undoubtedly driven by the endoderm.[well established][VHOG] 2012-09-17 VHOG:0000707 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) geniculate UMLS:C0017406 ncithesaurus:Geniculate_Ganglion facial VII ganglion MA:0001076 gVII ZFA:0001291 ganglion genicularum FMA:53414 genicular ganglion genicular ganglion FMA:53414 facial ganglion ZFA:0001291 ganglion geniculi ganglion geniculi nervi facialis geniculate ganglion MA:0001076 internal genu The group of neuron cell bodies associated with the ninth cranial nerve. These (the epibranchial placodes) are focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches in all vertebrates, and they produce the neuroblasts which migrate and condense to form the distal cranial ganglia: the geniculate, petrosal and nodose ganglia. (...) The one substantial difference between the vertebrate pharyngeal arches and those of the protochordates is the presence of the epibranchial placodes but the evolution of these structures was undoubtedly driven by the endoderm.[well established][VHOG] EHDAA2:0000710 EHDAA:2838 EMAPA:16795 FMA:53471 MA:0001077 TAO:0001301 VHOG:0000702 ZFA:0001301 ganglion of glossopharyngeal nerve ganglion of glosspharyngeal nerve glossopharyngeal IX ganglion petrosal ganglion uberon gIX UBERON:0001701 glossopharyngeal ganglion ZFA dorsal EHDAA2 ISBN10:0471888893 ZFA ventrolateral EHDAA2 ISBN10:0471888893 ZFA The group of neuron cell bodies associated with the ninth cranial nerve. MP:0001096 These (the epibranchial placodes) are focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches in all vertebrates, and they produce the neuroblasts which migrate and condense to form the distal cranial ganglia: the geniculate, petrosal and nodose ganglia. (...) The one substantial difference between the vertebrate pharyngeal arches and those of the protochordates is the presence of the epibranchial placodes but the evolution of these structures was undoubtedly driven by the endoderm.[well established][VHOG] 2012-09-17 VHOG:0000702 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) ganglion of glosspharyngeal nerve FMA:53471 glossopharyngeal IX ganglion MA:0001077 petrosal ganglion ZFA:0001301 Subdivision of skeletal system that surrounds and protects the brain. Includes the skull base, sensory capsules and the central part of the skull roof. Anatomical cluster that consists of the cartilages and bones that surround the brain.[TAO] neurocranial It includes the following bones: Ethmoid bone, Frontal bone, Occipital bone, Parietal bone, Sphenoid bone, Temporal bone. The term cranium can be ambiguous, in that it can refer to the neurocranium, or the neurocranium and the Facial skeleton The cartilaginous parts of the neurocranium undergo endochondral ossification in most species; ossification has been lost in cartilaginous fishes, but the cartilaginous condition of the skull of lampreys is considered to be primitive (Kardong, 1995)[PMID:11523816]. The neurocranium arises from paraxial mesoderm in the head (first five somites and the unsegmented somitomeres rostral to the first somite) and from ectoderm via the neural crest. In Chondrichthyes and other cartilaginous vertebrates this portion of the cranium does not ossify; it is not replaced via endochondral ossification[WP]. It seems MA uses 'neurocranium' as a synonym for chondrocranium. Note there are currently some structures part of both viscero and neurocranium - ethmoid, zyogomatic, ... AAO:0010153 EHDAA2:0000243 EMAPA:17681 FMA:53672 MA:0000317 TAO:0001580 XAO:0003170 ZFA:0001580 brain box uberon brain case brain pan braincase UBERON:0001703 neurocranium FMA Subdivision of skeletal system that surrounds and protects the brain. Includes the skull base, sensory capsules and the central part of the skull roof. TAO:MAH ZFA:0001580 Anatomical cluster that consists of the cartilages and bones that surround the brain.[TAO] 2012-08-14 TAO:0001580 TAO TAO:MAH The cartilaginous parts of the neurocranium undergo endochondral ossification in most species; ossification has been lost in cartilaginous fishes, but the cartilaginous condition of the skull of lampreys is considered to be primitive (Kardong, 1995)[PMID:11523816]. The neurocranium arises from paraxial mesoderm in the head (first five somites and the unsegmented somitomeres rostral to the first somite) and from ectoderm via the neural crest. In Chondrichthyes and other cartilaginous vertebrates this portion of the cranium does not ossify; it is not replaced via endochondral ossification[WP]. WP It seems MA uses 'neurocranium' as a synonym for chondrocranium. Note there are currently some structures part of both viscero and neurocranium - ethmoid, zyogomatic, ... MA brain case ZFA:0001580 brain pan braincase ZFA:0001580 An anatomical cavity that is part of the olfactory apparatus. This includes the space bounded anteriorly by the nares and posteriorly by the choanae, when these structures are present. define the boundaries of this cavity for a variety of species and check that parthood relations are not too strong. Saclike space internal to the nasal capsule lined by respiratory and sensory epithelium and glandular tissue.[AAO] a large air filled space above and behind the nose in the middle of the face[WP][Wikipedia:Nasal_cavity]. Despite significant modification to the nasal cavity within Archosauria and its extreme hypertrophy and supraorbital development in Lambeosaurinae, the neural olfactory system and the olfactory region of the nasal cavity proper retain their plesiomorphic positions and associations, suggesting that this system is highly conserved in vertebrate evolution.[well established][VHOG] in humans, the cavity includes and starts at the nares and reaches all the way through to the and includes the choanae, the posterior nasal apertures AAO:0000314 BTO:0002096 EHDAA2:0001226 EHDAA:6801 EMAPA:17604 FMA:54378 GAID:350 MA:0000284 MESH:D009296 NCIT:C12424 TAO:0000130 UMLS:C0027423 VHOG:0000271 ZFA:0000130 cavity of nose cavity of olfactory apparatus nasal canal nasal conduit space nasal fossa olfactory chamber cavity uberon cavitas nasalis cavitas nasi cavum nasi nasal pit olfactory cavity olfactory chamber olfactory pit UBERON:0001707 nasal cavity cjm An anatomical cavity that is part of the olfactory apparatus. This includes the space bounded anteriorly by the nares and posteriorly by the choanae, when these structures are present. Saclike space internal to the nasal capsule lined by respiratory and sensory epithelium and glandular tissue.[AAO] 2012-06-20 AAO:0000314 AAO AAO:LAP a large air filled space above and behind the nose in the middle of the face[WP][Wikipedia:Nasal_cavity]. Despite significant modification to the nasal cavity within Archosauria and its extreme hypertrophy and supraorbital development in Lambeosaurinae, the neural olfactory system and the olfactory region of the nasal cavity proper retain their plesiomorphic positions and associations, suggesting that this system is highly conserved in vertebrate evolution.[well established][VHOG] 2012-09-17 VHOG:0000271 VHOG DOI:10.1666/0094-8373(2006)032[0109:NCHACC]2.0.CO;2 Evans DC, Nasal cavity homologies and cranial crest function in lambeosaurine dinosaurs. Paleobiology (2006) in humans, the cavity includes and starts at the nares and reaches all the way through to the and includes the choanae, the posterior nasal apertures HP UMLS:C0027423 ncithesaurus:Nasal_Cavity cavity of olfactory apparatus nasal canal ZFA:0000130 nasal conduit space nasal fossa olfactory chamber cavity cavitas nasalis BTO:0002096 cavitas nasi cavitas nasi BTO:0002096 cavum nasi olfactory chamber olfactory pit ZFA:0000130 Subdivision of skeleton which includes upper and lower jaw skeletons. TODO - move ZFA:0001227 (it is the entire jaw skeleton). Skeletal and cartilage elements of the first pharyngeal arch.[TAO] There are cellular contributions from all three embryonic germ layers: pharyngeal mesoderm, endoderm and neural crest that migrates out of the ectoderm (Noden, 1983). in FMA, the jaw is an organism subdivision cluster, and includes mucosal tissue such as the gingiva as parts. It appears to be skeletal in MA (and has teeth as parts). It is reasonable to assume that ZFA and XAO consider the upper and lower jaws to be skeletal elements or clusters. EHDAA2 also considers these clusters. TODO - follow EHDAA2 model. These arbitrary differences in terminology and classification have to be reconciled with the genuine well-known biological differences in the skeletal elements across vertebrates AAO:0000988 BTO:0001749 EMAPA:35455 FMA:54396 GAID:214 MA:0001905 MESH:D007568 NCIT:C48821 OpenCyc:Mx4rvVjjEZwpEbGdrcN5Y29ycA TAO:0001227 UMLS:C0022359 ZFA:0001227 galen:Jaw jaw jaw cartilage mandibular arch skeleton uberon anterior splanchnocranium jaws mandibular arch oral jaw skeleton pharyngeal arch 1 skeleton visceral arch 1 UBERON:0001708 jaw skeleton cjm Subdivision of skeleton which includes upper and lower jaw skeletons. Skeletal and cartilage elements of the first pharyngeal arch.[TAO] 2012-08-14 TAO:0001227 TAO ZFIN:curator in FMA, the jaw is an organism subdivision cluster, and includes mucosal tissue such as the gingiva as parts. It appears to be skeletal in MA (and has teeth as parts). It is reasonable to assume that ZFA and XAO consider the upper and lower jaws to be skeletal elements or clusters. EHDAA2 also considers these clusters. TODO - follow EHDAA2 model. These arbitrary differences in terminology and classification have to be reconciled with the genuine well-known biological differences in the skeletal elements across vertebrates FMA UMLS:C0022359 ncithesaurus:Jaw jaw MA:0001905 jaw cartilage ZFA:0001227 mandibular arch skeleton ZFA:0001227 mandibular arch TAO:0001227 Subdivision of head that consists of the lower jaw skeletal elements plus associated soft tissue (skin, lips, muscle)[cjm]. Inferior mandibular arch located on the anterior and lateral sides of the skull.[AAO] Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG] Note isa/partof difference MA/FMA AAO:0000272 EFO:0003660 EHDAA2:0001018 EHDAA:7995 EMAPA:17906 FMA:59398 MESH:D008334 VHOG:0000453 ncithesaurus:Lower_Jaw mandibular part of mouth uberon lower part of mouth mandibular series UBERON:0001710 See notes for jaw w.r.t skeletal element vs subdivision of head lower jaw region Subdivision of head that consists of the lower jaw skeletal elements plus associated soft tissue (skin, lips, muscle)[cjm]. Inferior mandibular arch located on the anterior and lateral sides of the skull.[AAO] 2012-06-20 AAO:0000272 AAO AAO:LAP Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG] 2012-09-17 VHOG:0000453 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) Note isa/partof difference MA/FMA MA mandibular part of mouth FMA:59398 the groups of nerve cell bodies associated with the twelve cranial nerves Ganglion which is located in the head.[TAO] UBERON:0003213 UBERON:0026601 BTO:0000106 EFO:0000902 EMAPA:16659 FMA:54502 MA:0000213 MA:0000214 MAT:0000200 MIAA:0000200 TAO:0000013 VHOG:0000076 XAO:0000027 ZFA:0000013 cranial ganglion cranial ganglion part of peripheral nervous system cranial ganglion/nerve cranial nerve ganglion cranial neural ganglion cranial neural tree organ ganglion ganglion of cranial nerve ganglion of cranial neural tree organ uberon cranial ganglia head ganglion presumptive cranial ganglia UBERON:0001714 cranial ganglion the groups of nerve cell bodies associated with the twelve cranial nerves ISBN:0-683-40008-8 MGI:csmith MP:0001081 Ganglion which is located in the head.[TAO] 2012-08-14 TAO:0000013 TAO ZFIN:curator cranial ganglion part of peripheral nervous system NIFSTD:birnlex_2597 cranial neural tree organ ganglion OBOL:automatic ganglion of cranial nerve FMA:54502 ganglion of cranial neural tree organ OBOL:automatic presumptive cranial ganglia ZFA:0000013 A specialized receptor organ that is a collection of cells spanning the gustatory epithelium. A chemoreceptive organ.[AAO] One of a number of receptor cell nests located in the epithelium of the papillae of the tongue and in the soft palate, epiglottis, and pharynx that mediate the sense of taste. [TFD][VHOG] Experients in amphibia have shown that an intrinsic feature of the pharyngeal endoderm is its ability to generate taste buds and this capacity must have been acquired by the endoderm at the origin of the vertebrates.[well established][VHOG] In humans, saste buds may be found on the tongue, soft palatte, epiglottis and upper pharynx. In other species they may be found in more unusual places, such as the trunk, or on the barbels or fins of fish. arise by inductive interactions between epithelial cells and invading gustatory cells from chorda tympani (facial), glossophrayngeal and vagues nerves ISBN10:1607950324 (todo - request cell terms from CL) AAO:0010573 BTO:0000989 CALOHA:TS-1015 EMAPA:35850 FMA:54825 GAID:815 MA:0001591 MESH:A08.800.550.700.120.800 NCIT:C96518 OpenCyc:Mx4rvVjan5wpEbGdrcN5Y29ycA TAO:0001074 UMLS:C0039337 VHOG:0000130 XAO:0000445 ZFA:0001074 tastebud uberon caliculus gustatorius taste buds taste-bud tastebuds UBERON:0001727 taste bud NIF A specialized receptor organ that is a collection of cells spanning the gustatory epithelium. A chemoreceptive organ.[AAO] 2012-06-20 AAO:0010573 AAO AAO:EJS One of a number of receptor cell nests located in the epithelium of the papillae of the tongue and in the soft palate, epiglottis, and pharynx that mediate the sense of taste. [TFD][VHOG] 2012-09-17 VHOG:0000130 VHOG Experients in amphibia have shown that an intrinsic feature of the pharyngeal endoderm is its ability to generate taste buds and this capacity must have been acquired by the endoderm at the origin of the vertebrates.[well established][VHOG] 2012-09-17 VHOG:0000130 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) UMLS:C0039337 NIFSTD:birnlex_4101 UMLS:C0039337 ncithesaurus:Taste_Bud tastebud caliculus gustatorius caliculus gustatorius taste buds taste-bud tastebuds A anatomical space that is enclosed by a pharynx. See notes for pharynx - as a grouping class this is probably too bad. We exclude WBbt:0005790 (pharyngeal lumen) because of the developmental relationship TOODO check AAO:0010435 BSA:0000113 BTO:0002097 EMAPA:18381 FMA:54935 XAO:0000105 lumen of pharynx pharyngeal cavity uberon cavitas pharyngealis cavitas pharyngis UBERON:0001731 cavity of pharynx XAO A anatomical space that is enclosed by a pharynx. OBOL:automatic cavitas pharyngealis cavitas pharyngis BTO:0002097 A continuation of the pharynx that is involved in breathing, sound production, and protecting the trachea against food aspiration. An anatomical cluster consisting of the epiglottus, the arytenoid cartilages, the thyroid cartilage, the cricoid cartilage and the muscles, membranes, and ligaments connecting them, and also of the mucosal covering these structures.[FEED] Anatomical structure consisting of a narrowly triangular chamber supported by a series of semicircular cartilages in which part of the sound-production system is located.[AAO] (In anura) a dorsal pair of arytenoid cartilages (...), which support vocal cords, and a ventral pair (often fused) of cricoid cartilage (...). These cartilages are regarded as derivatives of posterior visceral arches of ancestors. Together they constitute the larynx, a structure characteristic of tetrapods. (...) (In mammals) Paired arytenoid cartilages help support and control the vocal cords. The cricoid cartilage is single. Two additional cartilages are present that are lacking in other vertebrates: a large ventral thyroid cartilage (...) and a cartilage in the epiglottis.[well established][VHOG] laryngeal AAO:0000268 BTO:0001208 CALOHA:TS-0532 EFO:0000838 EHDAA2:0004063 EMAPA:18333 EV:0100039 FMA:55097 GAID:108 MA:0000414 MAT:0000187 MESH:D007830 MIAA:0000187 NCIT:C12420 OpenCyc:Mx4rvViOnZwpEbGdrcN5Y29ycA UMLS:C0023078 VHOG:0001279 XAO:0003081 galen:Larynx uberon Kehlkopf@de UBERON:0001737 larynx EHDAA2 A continuation of the pharynx that is involved in breathing, sound production, and protecting the trachea against food aspiration. An anatomical cluster consisting of the epiglottus, the arytenoid cartilages, the thyroid cartilage, the cricoid cartilage and the muscles, membranes, and ligaments connecting them, and also of the mucosal covering these structures.[FEED] 2012-07-02 FEED http://www.feedexp.org Anatomical structure consisting of a narrowly triangular chamber supported by a series of semicircular cartilages in which part of the sound-production system is located.[AAO] 2012-06-20 AAO:0000268 AAO AAO:BJB (In anura) a dorsal pair of arytenoid cartilages (...), which support vocal cords, and a ventral pair (often fused) of cricoid cartilage (...). These cartilages are regarded as derivatives of posterior visceral arches of ancestors. Together they constitute the larynx, a structure characteristic of tetrapods. (...) (In mammals) Paired arytenoid cartilages help support and control the vocal cords. The cricoid cartilage is single. Two additional cartilages are present that are lacking in other vertebrates: a large ventral thyroid cartilage (...) and a cartilage in the epiglottis.[well established][VHOG] 2012-09-17 VHOG:0001279 VHOG ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.239-241 UMLS:C0023078 ncithesaurus:Larynx Kehlkopf@de BTO:0001208 The cartilaginous structures that support the larynx. (In anura) a dorsal pair of arytenoid cartilages (...), which support vocal cords, and a ventral pair (often fused) of cricoid cartilage (...). These cartilages are regarded as derivatives of posterior visceral arches of ancestors. Together they constitute the larynx, a structure characteristic of tetrapods. (...) (In mammals) Paired arytenoid cartilages help support and control the vocal cords. The cricoid cartilage is single. Two additional cartilages are present that are lacking in other vertebrates: a large ventral thyroid cartilage (...) and a cartilage in the epiglottis.[well established][VHOG] BTO:0003660 EHDAA:8157 EMAPA:18697 FMA:55108 GAID:107 MA:0001758 MESH:A02.165.507 NCIT:C12281 UMLS:C0023050 VHOG:0001550 cartilage of larynx cartilagines laryngeales larynx cartilage uberon UBERON:0001739 laryngeal cartilage The cartilaginous structures that support the larynx. MP:0002256 (In anura) a dorsal pair of arytenoid cartilages (...), which support vocal cords, and a ventral pair (often fused) of cricoid cartilage (...). These cartilages are regarded as derivatives of posterior visceral arches of ancestors. Together they constitute the larynx, a structure characteristic of tetrapods. (...) (In mammals) Paired arytenoid cartilages help support and control the vocal cords. The cricoid cartilage is single. Two additional cartilages are present that are lacking in other vertebrates: a large ventral thyroid cartilage (...) and a cartilage in the epiglottis.[well established][VHOG] 2012-09-17 VHOG:0001550 VHOG ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.239-241 UMLS:C0023050 ncithesaurus:Laryngeal_Cartilage cartilage of larynx FMA:55108 cartilagines laryngeales larynx cartilage VHOG:0001550 Cranial nerve that branches into the lateral (to body sense organs) and the intestino-accessorial (to the skin, muscles of shoulder, hyoid, larynx, gut, lungs, and heart). Nerve consisting of branchiomotor and visceral efferent fibers which branch and innervate the smooth muscles and glands of the heart, lungs, esophagus, and stomach as well as some throat muscles. Sensory fibers supply mucosa of the mouth and pharynx.[AAO] We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG] 10n AAO:0010475 BAMS:10n BAMS:Xn BTO:0003472 EFO:0002549 EMAPA:37797 FMA:5731 GAID:721 HBA:9337 MA:0001106 MBA:917 MESH:D014630 NCIT:C12812 OpenCyc:Mx4rviHk2ZwpEbGdrcN5Y29ycA TAO:0000453 UMLS:C0042276 UMLS:C1305910 VHOG:0000737 XAO:0003097 ZFA:0000453 galen:VagusNerve http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=702 nervus vagus [x] tenth cranial nerve vagus vagus X nerve vagus nerve [X] vagus nerve tree uberon CN-X cranial nerve X nerve X nervus vagus pneuomgastric nerve vagal nerve vagus nerve or its root UBERON:0001759 vagus nerve motor Wikipedia Cranial nerve that branches into the lateral (to body sense organs) and the intestino-accessorial (to the skin, muscles of shoulder, hyoid, larynx, gut, lungs, and heart). ISBN:0471209627 Nerve consisting of branchiomotor and visceral efferent fibers which branch and innervate the smooth muscles and glands of the heart, lungs, esophagus, and stomach as well as some throat muscles. Sensory fibers supply mucosa of the mouth and pharynx.[AAO] 2012-06-20 AAO:0010475 AAO AAO:EJS We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000737 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.625 10n NIFSTD:NeuroNames_abbrevSource EMAPA:37797 MA:th UMLS:C0042276 NIFSTD:birnlex_801 UMLS:C0042276 ncithesaurus:Vagus_Nerve UMLS:C1305910 NIFSTD:birnlex_801 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=702 NIFSTD:birnlex_801 nervus vagus [x] FMA:5731 FMA:TA vagus X nerve MA:0001106 nerve X NeuroNames:702 nervus vagus nervus vagus BTO:0003472 pneuomgastric nerve BTO:0003472 vagus nerve or its root BAMS:10n the space in the eye, filled with aqueous humor, and bounded anteriorly by the cornea and a small portion of the sclera and posteriorly by a small portion of the ciliary body, the iris, and part of the crystalline lens The part of the eyeball between the cornea and the iris, filled with aqueous humor. [TFD][VHOG] space in EHDAA2 - consider adding Cavity of anterior chamber of eyeball BTO:0002084 EHDAA2:0000129 EHDAA:9033 EMAPA:18231 FMA:58078 GAID:889 MA:0000262 MESH:D000867 NCIT:C12667 UMLS:C0003151 VHOG:0001431 anterior chamber anterior chamber of eye camera anterior eye anterior chamber uberon camera anterior bulbi camera anterior bulbi oculi camera oculi anterior UBERON:0001766 anterior chamber of eyeball FMA the space in the eye, filled with aqueous humor, and bounded anteriorly by the cornea and a small portion of the sclera and posteriorly by a small portion of the ciliary body, the iris, and part of the crystalline lens MESH:A09.371.060.067 MP:0005205 The part of the eyeball between the cornea and the iris, filled with aqueous humor. [TFD][VHOG] 2012-09-17 VHOG:0001431 VHOG space in EHDAA2 - consider adding Cavity of anterior chamber of eyeball EHDAA2 UMLS:C0003151 ncithesaurus:Anterior_Chamber_of_the_Eye anterior chamber HP:0000593 MP:0010709 camera anterior bulbi BTO:0002084 camera anterior bulbi oculi camera oculi anterior BTO:0002084 the pigmented middle of the three concentric layers that make up an eye, consisting of the iris, ciliary body and choroid[WP,edited]. TODO - check child terms, isa vs partof. See also MA:0001284 ! tunica vasculosa plexus uveal CALOHA:TS-2228 EMAPA:35901 FMA:58103 GAID:912 MA:0002480 MESH:D014602 NCIT:C12811 UMLS:C0042160 tunica vasculosa of eyeball uvea uveal tract uberon pars iridica retinae tunica vasculatis oculi tunica vasculosa bulbi vascular layer of eyeball UBERON:0001768 uvea FMA the pigmented middle of the three concentric layers that make up an eye, consisting of the iris, ciliary body and choroid[WP,edited]. MP:0005197 UMLS:C0042160 ncithesaurus:Uvea tunica vasculosa of eyeball FMA:58103 uvea FMA:58103 uveal tract FMA:58103 pars iridica retinae tunica vasculatis oculi tunica vasculosa bulbi vascular layer of eyeball FMA:58103 the adjustable membrane, composed of the stroma and pigmented epithelium, located just in front of the crystalline lens within the eye The opaque muscular contractile diaphragm suspended in the aqueous humour in front of the lens of the eye. The organ is perforated by the pupil and continues peripherally with the ciliary body. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] iridial The avian iris and ciliary body undergoes a transition from smooth-to-striated muscle during embryonic development [doi:dx.doi.org/10.1006/dbio.1998.9019] AAO:0010347 BTO:0000653 CALOHA:TS-0491 EFO:0004245 EMAPA:19154 EV:0100345 FMA:58235 GAID:917 MA:0000273 MESH:D007498 NCIT:C12737 OpenCyc:Mx4rvVjbppwpEbGdrcN5Y29ycA TAO:0001238 UMLS:C0022077 VHOG:0000101 XAO:0000185 ZFA:0001238 uberon anterior uvea irides irises UBERON:0001769 iris XAO the adjustable membrane, composed of the stroma and pigmented epithelium, located just in front of the crystalline lens within the eye ISBN:0-683-40008-8 MP:0001322 The opaque muscular contractile diaphragm suspended in the aqueous humour in front of the lens of the eye. The organ is perforated by the pupil and continues peripherally with the ciliary body. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000101 VHOG The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] 2012-09-17 VHOG:0000101 VHOG DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007) UMLS:C0022077 ncithesaurus:Iris irides irises VHOG:0000101 the smooth stratified squamous epithelium that covers the outer surface of the cornea Portion of tissue comprised of four to six layers of nonkeratinized, stratified squamous cells and represents approximately 60% of the thickness of the cornea.[TAO] In Humans: It consists of several layers of cells. The cells of the deepest layer are columnar; then follow two or three layers of polyhedral cells, the majority of which are prickle cells similar to those found in the stratum mucosum of the cuticle. Lastly, there are three or four layers of squamous cells, with flattened nuclei In zebrafish: nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals BTO:0000287 CALOHA:TS-0173 EFO:0001917 EHDAA2:0000319 EMAPA:17162 FMA:58263 GAID:895 MA:0001243 MESH:D019573 NCIT:C12928 TAO:0002187 UMLS:C0459875 ZFA:0001683 anterior corneal epithelium cornea epithelial tissue cornea epithelium epithelial tissue of cornea epithelium anterius (cornea) epithelium anterius corneae epithelium corneæ anterior layer epithelium of cornea external epithelium of cornea uberon anterior endothelium of cornea e. anterius corneae endothelium anterius corneae endothelium camerae anterioris bulbi endothelium corneale epithelium posterius corneae UBERON:0001772 corneal epithelium ISBN:0781772214 the smooth stratified squamous epithelium that covers the outer surface of the cornea MESH:A09.371.060.217.325 MGI:smb MP:0006000 Portion of tissue comprised of four to six layers of nonkeratinized, stratified squamous cells and represents approximately 60% of the thickness of the cornea.[TAO] 2012-08-14 TAO:0002187 TAO ZFIN:ZDB-PUB-061010-3 UMLS:C0459875 ncithesaurus:Corneal_Epithelium cornea epithelial tissue OBOL:automatic cornea epithelium OBOL:automatic epithelial tissue of cornea OBOL:automatic epithelium anterius corneae FMA:58263 FMA:TA anterior endothelium of cornea BTO:0000287 e. anterius corneae endothelium anterius corneae BTO:0000287 endothelium camerae anterioris bulbi BTO:0000287 endothelium corneale BTO:0000287 epithelium posterius corneae BTO:0000287 Opaque fibrous outer layer of the eyeball[ZFA,Kardong,WP]. The sclera, also known as the white part of the eye, is the opaque (usually white, though certain animals, such as horses and lizards, can have black sclera), fibrous, protective, outer layer of the eye containing collagen and elastic fiber. It is derived from the neural crest. In children, it is thinner and shows some of the underlying pigment, appearing slightly blue. In the elderly, however, fatty deposits on the sclera can make it appear slightly yellow. The sclera forms the posterior five sixths of the connective tissue coat of the globe. It is continuous with the dura mater and the cornea, and maintains the shape of the globe, offering resistance to internal and external forces, and provides an attachment for the extraocular muscle insertions. The sclera is perforated by plenty of nerves and vessels passing through the posterior scleral foramen, the hole that is formed by the optic nerve. At the optic disk the outer two-thirds of the sclera continues with the dura mater (outer coat of the brain) via the dural sheath of the optic nerve. The inner third joins with some choroidal tissue to form a plate (lamina cribrosa) across the optic nerve with perforations through which the optic fibers (fasciculi). The thickness of the sclera varies from 1mm at the posterior pole to 0.3 mm just behind the rectus muscle insertions. The sclera's blood vessels are mainly on the surface, and together with the conjunctiva (which lies on top) This is a thin layer covering the sclera. Along with the vessels of the conjunctiva, those of the sclera renders the inflamed eye bright red. [WP,unvetted][Wikipedia:Sclera]. The tough, usually white, outer coat of the eyeball, covering all the posterior surface and continuous anteriorly with the cornea. [TFD][VHOG] scleral in fish, reptiles and monotremes the connective tissue of the sclera is skeletal continuous with the dura mater and the cornea; The sclera forms the posterior five-sixths of the connective tissue coat of the globe. Majority derives from NC that surrounds optic cup of neurectoderm; a small temporal portion develops from the mesoderm that contributes to striated extra-ocular muscles and vascular endothelia[Rada&Johnson]. Seko et al demonstrate chondrogenic potential and identify this as connective tissue[doi:10.1371/journal.pone.0003709]. AAO:0010354 BTO:0001606 EMAPA:19027 EV:0100342 FMA:58269 GAID:911 MA:0000280 MESH:D012590 NCIT:C12784 OpenCyc:Mx4rv7yR55wpEbGdrcN5Y29ycA UMLS:C0036410 VHOG:0001274 XAO:0000183 ZFA:0005563 uberon scleral capsule UBERON:0001773 Disease notes: implicated in rheumatoid arthritis. sclera FMA ISBN:0781772214 Opaque fibrous outer layer of the eyeball[ZFA,Kardong,WP]. ZFIN:ZDB-PUB-050701-15 The sclera, also known as the white part of the eye, is the opaque (usually white, though certain animals, such as horses and lizards, can have black sclera), fibrous, protective, outer layer of the eye containing collagen and elastic fiber. It is derived from the neural crest. In children, it is thinner and shows some of the underlying pigment, appearing slightly blue. In the elderly, however, fatty deposits on the sclera can make it appear slightly yellow. The sclera forms the posterior five sixths of the connective tissue coat of the globe. It is continuous with the dura mater and the cornea, and maintains the shape of the globe, offering resistance to internal and external forces, and provides an attachment for the extraocular muscle insertions. The sclera is perforated by plenty of nerves and vessels passing through the posterior scleral foramen, the hole that is formed by the optic nerve. At the optic disk the outer two-thirds of the sclera continues with the dura mater (outer coat of the brain) via the dural sheath of the optic nerve. The inner third joins with some choroidal tissue to form a plate (lamina cribrosa) across the optic nerve with perforations through which the optic fibers (fasciculi). The thickness of the sclera varies from 1mm at the posterior pole to 0.3 mm just behind the rectus muscle insertions. The sclera's blood vessels are mainly on the surface, and together with the conjunctiva (which lies on top) This is a thin layer covering the sclera. Along with the vessels of the conjunctiva, those of the sclera renders the inflamed eye bright red. [WP,unvetted][Wikipedia:Sclera]. The tough, usually white, outer coat of the eyeball, covering all the posterior surface and continuous anteriorly with the cornea. [TFD][VHOG] 2012-09-17 VHOG:0001274 VHOG UMLS:C0036410 ncithesaurus:Sclera A skeletal muscle organ that is part of the trunk region. Note that this class excludes smooth muscle elements in the trunk region, such as the internal anal sphincter. This appears to be consistent with other ontologies such as FMA and ZFA which appear to only include skeletal muscles here. In fact the MA class 'trunk muscle' is classified as a 'set of skeletal muscles'. Many ontologies do not appear to have a coherent distinction between an individual muscle and the musculature (i.e. the set of muscles in a region), so we group all together here. AAO:0000611 EMAPA:35888 FMA:58274 MA:0000514 TAO:0000473 XAO:0003230 ZFA:0000473 body musculature muscle of trunk muscle organ of torso muscle organ of trunk torso muscle organ trunk muscle trunk muscle organ trunk musculature uberon UBERON:0001774 skeletal muscle of trunk prolog A skeletal muscle organ that is part of the trunk region. body musculature ZFA:0000473 muscle of trunk FMA:58274 muscle organ of torso OBOL:automatic muscle organ of trunk OBOL:automatic torso muscle organ OBOL:automatic trunk muscle organ OBOL:automatic the thickened portion of the vascular tunic, which lies between the choroid and the iris, composed of ciliary muscle and ciliary processes The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] AAO:0010341 BTO:0000260 CALOHA:TS-0694 EMAPA:19065 EV:0100346 FMA:58295 GAID:916 MA:0000264 MESH:D002924 NCIT:C12345 UMLS:C0008779 VHOG:0000102 XAO:0000186 ocular ciliary body uberon anterior uvea ciliary bodies corpus ciliare UBERON:0001775 ciliary body ISBN:0781772214 the thickened portion of the vascular tunic, which lies between the choroid and the iris, composed of ciliary muscle and ciliary processes ISBN:0-683-40008-8 MP:0005099 The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] 2012-09-17 VHOG:0000102 VHOG DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007) UMLS:C0008779 ncithesaurus:Ciliary_Body ciliary bodies VHOG:0000102 corpus ciliare corpus ciliare vascular layer containing connective tissue, of the eye lying between the retina and the sclera. The choroid provides oxygen and nourishment to the outer layers of the retina. Along with the ciliary body and iris, the choroid forms the uveal tract[WP]. check choroid vs choroid layer; check ZFA/TAO placement - no homology assertion in VHOG. Note this is entirely in the posterior region of eyeball in ZFA choroidal MP treats posterior uvea and optic choroid as distinct BTO:0001829 CALOHA:TS-2054 EMAPA:19077 EV:0100347 FMA:58298 GAID:913 MA:0000263 MESH:D002829 NCIT:C12344 TAO:0005229 UMLS:C0008520 VHOG:0001568 ZFA:0005229 choroid choroid coat choroidea eye choroid posterior uvea uberon chorioid choroidea optic choroid UBERON:0001776 optic choroid MA Wikipedia lexical vascular layer containing connective tissue, of the eye lying between the retina and the sclera. The choroid provides oxygen and nourishment to the outer layers of the retina. Along with the ciliary body and iris, the choroid forms the uveal tract[WP]. MP treats posterior uvea and optic choroid as distinct MP UMLS:C0008520 ncithesaurus:Choroid choroid MA:0000263 choroid coat choroidea eye choroid VHOG:0001568 posterior uvea chorioid BTO:0001829 choroidea optic choroid ZFA:0005229 A double layer covering the ciliary body that produces aqueous humor. BTO:0001770 CALOHA:TS-0695 EMAPA:35239 FMA:58464 MA:0001238 NCIT:C32314 UMLS:C0459736 ciliary body epithelium epithelium of ciliary body ocular ciliary epithelium uberon UBERON:0001778 ciliary epithelium FMA MA Wikipedia A double layer covering the ciliary body that produces aqueous humor. UMLS:C0459736 ncithesaurus:Ciliary_Epithelium ciliary body epithelium FMA:58464 epithelium of ciliary body FMA:58464 the any of the paired peripheral nerves formed by the union of the dorsal and ventral spinal roots from each spinal cord segment[MP,modified] Any of the paired nerves emerging from the spinal cord, each attached to the cord by two roots: ventral and dorsal, and passing out between the vertebrae. [TFD][VHOG] AAO:0011101 BAMS:spin BTO:0000870 EHDAA2:0001898 EMAPA:16989 FMA:5858 GAID:841 MA:0000233 MESH:D013127 NCIT:C12792 OpenCyc:Mx4rwK_iFJwpEbGdrcN5Y29ycA UMLS:C0037941 VHOG:0000824 XAO:0003101 backbone nerve nerve of backbone nerve of spinal column nerve of spine nerve of vertebral column spinal column nerve spinal nerve tree spine nerve vertebral column nerve uberon nervi spinales spinal nerves UBERON:0001780 spinal nerve the any of the paired peripheral nerves formed by the union of the dorsal and ventral spinal roots from each spinal cord segment[MP,modified] MESH:A08.800.800.720 MP:0001077 Any of the paired nerves emerging from the spinal cord, each attached to the cord by two roots: ventral and dorsal, and passing out between the vertebrae. [TFD][VHOG] 2012-09-17 VHOG:0000824 VHOG UMLS:C0037941 ncithesaurus:Spinal_Nerve backbone nerve OBOL:automatic nerve of backbone OBOL:automatic nerve of spinal column OBOL:automatic nerve of spine OBOL:automatic nerve of vertebral column OBOL:automatic spinal column nerve OBOL:automatic spine nerve OBOL:automatic vertebral column nerve OBOL:automatic nervi spinales spinal nerves BAMS:spin Any of the layers that make up the retina[MP]. MA does not treat internal/external limiting memranes as layers - these are classified as laminae. Here we follow other ontologies in grouping with other layers. MA also treats retinal pigment epithelium and neural retina epithelium as distinct from the layers. We follow ontologies such as FMA and ZFA in first dividing into pigmented and neural layers - these are also classified as layers, giving us over the usual 10 layers AAO:0010353 EMAPA:35742 FMA:58617 MA:0001319 NCIT:C49328 UMLS:C0459649 XAO:0000266 retina layer retina neuronal layer retinal layer retinal neuronal layer uberon UBERON:0001781 layer of retina Any of the layers that make up the retina[MP]. MP:0003727 MA does not treat internal/external limiting memranes as layers - these are classified as laminae. Here we follow other ontologies in grouping with other layers. MA also treats retinal pigment epithelium and neural retina epithelium as distinct from the layers. We follow ontologies such as FMA and ZFA in first dividing into pigmented and neural layers - these are also classified as layers, giving us over the usual 10 layers MA UMLS:C0459649 ncithesaurus:Retina_Layer retina neuronal layer MP:0006069 retinal neuronal layer MP:0006069 Cranial nerves are nerves that emerge directly from the brain, in contrast to spinal nerves, which emerge from segments of the spinal cord. classified as neural tree organ, not nerve in FMA. CN II poses a challenge here as it is not strictly a nerve, yet is expected to be classified under CN. Twelve pairs of cranial nerves exit/enter the cranium through openings in the skull. The nerves contain efferent axons with motor and glandular functions, as well as afferent axons from cranial ganglia with sensory functions. The nerves are numbered in a rostral to caudal sequence, with the exception of the lateral line nerves.[TAO] We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...).[well established][VHOG] See https://github.com/obophenotype/mouse-anatomy-ontology/issues/6 AAO:0000108 BAMS:cran BTO:0001104 EHDAA2:0000323 EMAPA:17264 FMA:5865 GAID:802 HBA:9299 MA:0000215 MBA:967 MESH:D003391 NCIT:C12700 OpenCyc:Mx4rvWvJVpwpEbGdrcN5Y29ycA TAO:0000641 UMLS:C0010268 UMLS:C1269897 VHOG:0000279 XAO:0000429 XAO:0003089 ZFA:0000641 cranial neural tree organ uberon cranial nerves nervus cranialis UBERON:0001785 cranial nerve Cranial nerves are nerves that emerge directly from the brain, in contrast to spinal nerves, which emerge from segments of the spinal cord. Twelve pairs of cranial nerves exit/enter the cranium through openings in the skull. The nerves contain efferent axons with motor and glandular functions, as well as afferent axons from cranial ganglia with sensory functions. The nerves are numbered in a rostral to caudal sequence, with the exception of the lateral line nerves.[TAO] 2012-08-14 TAO:0000641 TAO ZFIN:curator We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...).[well established][VHOG] 2012-09-17 VHOG:0000279 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 UMLS:C0010268 NIFSTD:birnlex_1623 UMLS:C0010268 ncithesaurus:Cranial_Nerve UMLS:C1269897 NIFSTD:birnlex_1623 nervus cranialis A thick watery refractive medium that fills the space between the lens and the cornea[WP]. The fluid produced by the ciliary process in the eye and occupying the anterior and posterior chambers. It provides nourishment for the lens and cornea and maintains the ocular pressure, and hence the optical integrity of the eyeball. [TFD][VHOG] (...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (...) A watery aqueous humor fills the spaces in the eye in front of the lens (...) (reference 2).[well established][VHOG] FMA says A+P chambers, and MA states A chamber. ZFA states A chamber and tha it is produced primarily by dorsal ciliary epithelial cells.To be investigated across taxa. EHDAA2:0000139 EHDAA:10196 EMAPA:18232 ENVO:02000024 FMA:58819 GAID:890 MA:0001236 MESH:D001082 NCIT:C13190 OpenCyc:Mx4rvdGd-5wpEbGdrcN5Y29ycA UMLS:C0003662 VHOG:0000548 ZFA:0005564 aqueous humor aqueous humour humor aquosus uberon UBERON:0001796 aqueous humor of eyeball FMA def states A and P located_in in EHDAA2 VHOG A thick watery refractive medium that fills the space between the lens and the cornea[WP]. The fluid produced by the ciliary process in the eye and occupying the anterior and posterior chambers. It provides nourishment for the lens and cornea and maintains the ocular pressure, and hence the optical integrity of the eyeball. [TFD][VHOG] 2012-09-17 VHOG:0000548 VHOG (...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (...) A watery aqueous humor fills the spaces in the eye in front of the lens (...) (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000548 VHOG DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.424 and p.426 and p.429 and Figure 12-24 FMA says A+P chambers, and MA states A chamber. ZFA states A chamber and tha it is produced primarily by dorsal ciliary epithelial cells.To be investigated across taxa. FMA UMLS:C0003662 ncithesaurus:Aqueous_Humor aqueous humour EHDAA2:0000139 humor aquosus FMA:58819 FMA:TA The clusters of neurons in the somatic peripheral nervous system which contain the cell bodies of sensory nerve axons, interneurons and non-neuronal supporting cells. AEO:0001000 BTO:0005630 EMAPA:36596 FMA:5885 MA:0002566 MESH:D017950 NCIT:C13060 UMLS:C0206429 ganglion sensorium uberon UBERON:0001800 sensory ganglion The clusters of neurons in the somatic peripheral nervous system which contain the cell bodies of sensory nerve axons, interneurons and non-neuronal supporting cells. MP:0000960 UMLS:C0206429 ncithesaurus:Sensory_Ganglion ganglion sensorium any of the parts of the eye that lie in front of, or ventral to, the lens (inclusive) EMAPA:36594 FMA:58865 MA:0002484 MESH:D000869 NCIT:C12668 UMLS:C0003153 ZFA:0005566 anterior eye segment anterior segment eye anterior segment of eye anterior segment of the eye eye anterior segment segmentum anterius (bulbus oculi) uberon segmentum anterius bulbi oculi UBERON:0001801 anterior segment of eyeball FMA cjm lexical any of the parts of the eye that lie in front of, or ventral to, the lens (inclusive) ISBN:0-683-40008-8 MESH:A09.371.060 MP:0005193 UMLS:C0003153 ncithesaurus:Anterior_Eye_Segment anterior segment eye ZFA:0005566 segmentum anterius bulbi oculi any of the parts of the eye that lie in back of, or dorsal to, the lens (but not inclusive) EMAPA:36595 FMA:58868 MA:0002485 NCIT:C12906 UMLS:C0278450 ZFA:0005567 eye posterior segment posterior eye segment posterior segment eye posterior segment of eye posterior segment of the eye segmentum posterius (bulbus oculi) uberon segmentum posterius bulbi oculi UBERON:0001802 posterior segment of eyeball FMA cjm lexical any of the parts of the eye that lie in back of, or dorsal to, the lens (but not inclusive) ISBN:0-683-40008-8 MP:0005195 UMLS:C0278450 ncithesaurus:Posterior_Eye_Segment posterior segment eye ZFA:0005567 segmentum posterius bulbi oculi A layer of epithelial cells that is part of the eye. this class is the superclass of the anterior epithelium and equatorial epithlium, although the term 'lens epithelium' may refer specifically to the former BTO:0001873 CALOHA:TS-0543 EMAPA:32871 FMA:58871 MA:0001301 TAO:0001326 XAO:0004094 ZFA:0001326 epithelial tissue of eye lens epithelial tissue of lens epithelium lentis epithelium of eye lens eye lens epithelial tissue eye lens epithelium lens epithelial tissue lens epithelium uberon UBERON:0001803 epithelium of lens A layer of epithelial cells that is part of the eye. epithelial tissue of eye lens OBOL:automatic epithelial tissue of lens OBOL:automatic epithelium lentis FMA:58871 FMA:TA epithelium of eye lens OBOL:automatic eye lens epithelial tissue OBOL:automatic eye lens epithelium OBOL:automatic lens epithelial tissue OBOL:automatic the elastic, clear, membrane-like structure, that is outer most layer of the lens The transparent membrane which surrounds the lens of the eye. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] (...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (...) A watery aqueous humor fills the spaces in the eye in front of the lens (...) (reference 2).[well established][VHOG] synthesized by the lens epithelium and its main components are Type IV collagen and sulfated glycosaminoglycans (GAGs). [Wikipedia:Capsule_of_lens FMA classifies this is a capsule and hence an organ part. In contrast we classify this as acellular EHDAA2:0000977 EMAPA:18237 FMA:58881 MA:0001300 NCIT:C32975 UMLS:C0229232 VHOG:0000550 ZFA:0005574 capsula lentis lens capsule uberon UBERON:0001804 capsule of lens EHDAA2 the elastic, clear, membrane-like structure, that is outer most layer of the lens MGI:smb MP:0003236 The transparent membrane which surrounds the lens of the eye. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000550 VHOG (...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (...) A watery aqueous humor fills the spaces in the eye in front of the lens (...) (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000550 VHOG DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.424 and p.426 and p.429 and Figure 12-24 FMA classifies this is a capsule and hence an organ part. In contrast we classify this as acellular FMA UMLS:C0229232 ncithesaurus:Lens_Capsule capsula lentis ganglion that has dendrites that form a junction between autonomic nerves originating from the central nervous system and autonomic nerves innervating their target organs in the periphery. There are two subtypes, sympathetic ganglion and parasympathetic ganglion. AEO:0001001 CALOHA:TS-2340 EMAPA:17157 EMAPA:18221 FMA:5889 MA:0000220 MESH:D005725 NCIT:C12720 UMLS:C0017068 autonomic nervous system ganglion ganglion of autonomic nervous system ganglion of visceral nervous system visceral nervous system ganglion uberon ganglion autonomicum UBERON:0001805 autonomic ganglion ganglion that has dendrites that form a junction between autonomic nerves originating from the central nervous system and autonomic nerves innervating their target organs in the periphery. There are two subtypes, sympathetic ganglion and parasympathetic ganglion. UMLS:C0017068 ncithesaurus:Autonomic_Ganglion autonomic nervous system ganglion OBOL:automatic ganglion of autonomic nervous system OBOL:automatic ganglion of visceral nervous system OBOL:automatic visceral nervous system ganglion OBOL:automatic ganglion autonomicum A ganglion of the sympathetic nervous system. Examples: paravertebral and the prevertebral ganglia, which include the sympathetic chain ganglia, the superior, middle, and inferior cervical ganglia, and the aorticorenal, celiac, and stellate ganglia AAO:0010773 BTO:0001333 CALOHA:TS-0994 EHDAA2:0001969 EMAPA:17157 FMA:5890 MA:0000226 NCIT:C12467 UMLS:C0017071 ganglion of sympathetic nervous system ganglion of sympathetic part of autonomic division of nervous system ganglion sympatheticum sympathetic nervous system ganglion sympathetic part of autonomic division of nervous system ganglion uberon ganglion sympathicum UBERON:0001806 sympathetic ganglion ISBN10:0073040584 A ganglion of the sympathetic nervous system. Examples: paravertebral and the prevertebral ganglia, which include the sympathetic chain ganglia, the superior, middle, and inferior cervical ganglia, and the aorticorenal, celiac, and stellate ganglia MP:0001008 UMLS:C0017071 ncithesaurus:Sympathetic_Ganglion ganglion of sympathetic nervous system OBOL:automatic ganglion of sympathetic part of autonomic division of nervous system OBOL:automatic sympathetic nervous system ganglion OBOL:automatic sympathetic part of autonomic division of nervous system ganglion OBOL:automatic ganglion sympathicum ganglion sympathicum BTO:0001333 One of the cartilage structures in the nose that provide form and support[WP]. CALOHA:TS-0655 EMAPA:37681 FMA:59502 MA:0001883 NCIT:C49593 UMLS:C0225415 cartilage of nose uberon UBERON:0001823 nasal cartilage MA One of the cartilage structures in the nose that provide form and support[WP]. EMAPA:37681 MA:th UMLS:C0225415 ncithesaurus:Nasal_Cartilage The mucous lining of the larynx, which is composed of squamous epithelium in the upper larynx and ciliated columnar epithelium in the lower larynx. EMAPA:18334 FMA:59662 GAID:301 MA:0001766 MESH:D007820 NCIT:C49246 UMLS:C0023053 laryngeal mucosa larynx mucosa larynx mucosa of organ larynx mucous membrane larynx organ mucosa mucosa of organ of larynx mucous membrane of larynx organ mucosa of larynx tunica mucosa laryngis uberon laryngeal mucous membrane UBERON:0001824 mucosa of larynx The mucous lining of the larynx, which is composed of squamous epithelium in the upper larynx and ciliated columnar epithelium in the lower larynx. MP:0002261 UMLS:C0023053 ncithesaurus:Laryngeal_Mucosa larynx mucosa of organ OBOL:automatic larynx mucous membrane OBOL:automatic larynx organ mucosa OBOL:automatic mucosa of organ of larynx OBOL:automatic organ mucosa of larynx OBOL:automatic tunica mucosa laryngis FMA:59662 FMA:TA laryngeal mucous membrane EMAPA:18334 The mucous membrane that lines the nasal cavity[MP]. TODO - check lining vs part of. split olfactory and nasal mucosa? BTO:0000912 CALOHA:TS-0657 EMAPA:36026 FMA:59684 GAID:302 mucosa of nose mucous membrane of nose tunica mucosa nasalis tunica mucosa nasi uberon nasal mucosa UBERON:0001826 nasal cavity mucosa The mucous membrane that lines the nasal cavity[MP]. MP:0002238 mucosa of nose FMA:59684 mucous membrane of nose FMA:59684 tunica mucosa nasi FMA:59684 FMA:TA One of the two fleshy folds which surround the opening of the mouth. Surface structure that is one of the two fleshy folds surrounding the opening of the mouth.[TAO] labial BTO:0001647 CALOHA:TS-0558 EMAPA:32839 FMA:59816 GAID:76 MA:0000343 MESH:D008046 NCIT:C12220 OpenCyc:Mx4rvVi4U5wpEbGdrcN5Y29ycA TAO:0007006 UMLS:C0023759 VHOG:0000677 ZFA:0007006 galen:Lip uberon labia oris lips UBERON:0001833 lip ZFA BTO FMA-implicit VHOG ZFA cjm One of the two fleshy folds which surround the opening of the mouth. Surface structure that is one of the two fleshy folds surrounding the opening of the mouth.[TAO] 2012-08-14 TAO:0007006 TAO ZFIN:curator UMLS:C0023759 ncithesaurus:Lip labia oris Lip that covers the lower portion of the mouth.[TAO]. Lip that covers the lower portion of the mouth.[TAO] UBERON:0003392 EHDAA2:0001020 EMAPA:17909 FMA:59818 MA:0000921 NCIT:C94572 OpenCyc:Mx4rv842UpwpEbGdrcN5Y29ycA TAO:0002060 UMLS:C0458583 ZFA:0005225 lower jaw lip uberon labium inferius oris UBERON:0001835 lower lip Lip that covers the lower portion of the mouth.[TAO]. TAO:0002060 Lip that covers the lower portion of the mouth.[TAO] 2012-08-14 TAO:0002060 TAO TAO:wd UMLS:C0458583 ncithesaurus:Lower_Lip lower jaw lip labium inferius oris Complex labyrinthine structure that comprises sensory endorgans specialized for vestibular, auditory, and acoustico-vestibular sensation. The auditory (hearing) and vestibular (balance) organ of the fish, equivalent to the inner ear of amniotes. (See Anatomical Atlas entry for ear by T. Whitfield.)[TAO] The labyrinth, or inner ear, evolved very early in vertebrate history and, with many variations in configuration but none of basic design and function, has been retained by all vertebrates.[well established][VHOG] AAO:0000238 BTO:0000630 CALOHA:TS-0478 EFO:0001363 EHDAA2:0000831 EHDAA:504 EMAPA:16194 EV:0100361 FMA:60909 GAID:871 MA:0000237 MAT:0000145 MESH:D007758 MIAA:0000145 NCIT:C12499 OpenCyc:Mx4rwJ8SsJwpEbGdrcN5Y29ycA TAO:0000217 UMLS:C0022889 UMLS:C1268973 VHOG:0000284 XAO:0000192 ZFA:0000217 galen:InnerEar inner ear uberon auris interna labyrinth otocyst UBERON:0001846 internal ear definitional Complex labyrinthine structure that comprises sensory endorgans specialized for vestibular, auditory, and acoustico-vestibular sensation. ZFIN:curator The auditory (hearing) and vestibular (balance) organ of the fish, equivalent to the inner ear of amniotes. (See Anatomical Atlas entry for ear by T. Whitfield.)[TAO] 2012-08-14 TAO:0000217 TAO ZFIN:curator The labyrinth, or inner ear, evolved very early in vertebrate history and, with many variations in configuration but none of basic design and function, has been retained by all vertebrates.[well established][VHOG] 2012-09-17 VHOG:0000284 VHOG ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.366 UMLS:C0022889 NIFSTD:birnlex_1196 UMLS:C0022889 ncithesaurus:Internal_Ear UMLS:C1268973 NIFSTD:birnlex_1196 auris interna BTO:0000630 The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)[GO]. developmental relationships need revised Middle part of the brain composed of the optic tectum and penducular region.[AAO] The brain region between the forebrain anteriorly and the hindbrain posteriorly, including the tectum dorsally and the midbrain tegmentum ventrally. Kimmel et al, 1995.[TAO] Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG] mesencephalic part of brainstem in ABA - we reject this in favor of ISBN10:0471888893 which has an implicit overlaps relationships MB AAO:0010149 BAMS:MES BM:MB BTO:0000138 CALOHA:TS-0630 DHBA:10648 DMBA:16649 EFO:0000919 EHDAA2:0001162 EHDAA:3694 EMAPA:16974 EV:0100242 FMA:61993 HBA:9001 MA:0000207 MAT:0000106 MBA:313 MESH:D008636 MIAA:0000106 NCIT:C12510 OpenCyc:Mx4rvsBUqpwpEbGdrcN5Y29ycA RETIRED_EHDAA2:0001104 TAO:0000128 UMLS:C0025462 VHOG:0000069 XAO:0000014 ZFA:0000128 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=462 uberon mesencephalon UBERON:0001891 midbrain definitional Bgee:AN The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)[GO]. GO:0030901 Middle part of the brain composed of the optic tectum and penducular region.[AAO] 2012-06-20 AAO:0010149 AAO AAO:BJB The brain region between the forebrain anteriorly and the hindbrain posteriorly, including the tectum dorsally and the midbrain tegmentum ventrally. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000128 TAO ZFIN:curator Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG] 2012-09-17 VHOG:0000069 VHOG DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999) part of brainstem in ABA - we reject this in favor of ISBN10:0471888893 which has an implicit overlaps relationships ABA MB NIFSTD:NeuroNames_abbrevSource UMLS:C0025462 NIFSTD:birnlex_1667 UMLS:C0025462 ncithesaurus:Mesencephalon http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=462 NIFSTD:birnlex_1667 mesencephalon A segment of the developing hindbrain[ZFA]. In the vertebrate embryo, a rhombomere is a transiently divided segment of the developing neural tube, within the hindbrain region (a neuromere) in the area that will eventually become the rhombencephalon. The rhombomeres appear as a series of slightly constricted swellings in the neural tube, caudal to the cephalic flexure.[WP]. A segment of the developing hindbrain. Kimmel et al, 1995.[TAO] Rhombomeric segmentation is found in all living vertebrates and is of fundamental importance to the development of the vertebrate head.[well established][VHOG] In human embryonic development, the rhombomeres are present by day 29 DHBA divides this into A(1-3),B(4),C(5-7) and D(8) hindbrain segment segment of hindbrain DHBA:12664 EFO:0003617 EMAPA:16148 FMA:295666 MAT:0000272 MIAA:0000272 RETIRED_EHDAA2:0000669 TAO:0001064 VHOG:0000672 XAO:0004079 ZFA:0001064 hindbrain neuromere hindbrain neuromeres rhombomere uberon future rhombencephalon rhombomeres UBERON:0001892 rhombomere A segment of the developing hindbrain[ZFA]. In the vertebrate embryo, a rhombomere is a transiently divided segment of the developing neural tube, within the hindbrain region (a neuromere) in the area that will eventually become the rhombencephalon. The rhombomeres appear as a series of slightly constricted swellings in the neural tube, caudal to the cephalic flexure.[WP]. ZFIN:curator A segment of the developing hindbrain. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0001064 TAO ZFIN:curator Rhombomeric segmentation is found in all living vertebrates and is of fundamental importance to the development of the vertebrate head.[well established][VHOG] 2012-09-17 VHOG:0000672 VHOG DOI:10.1006/dbio.2002.0831 Mazet F, Shimeld SM, The Evolution of Chordate Neural Segmentation. Developmental Biology (2002) hindbrain segment ZFA:0001064 segment of hindbrain ZFA:0001064 hindbrain neuromeres DHBA:HNM future rhombencephalon MIAA:0000272 rhombomeres VHOG:0000672 Rostral segment of the hindbrain that has as its parts the pons (where present) and the cerebellum[WP,modified]. Anterior part of the hindbrain ventral to the cerebellum[NIFSTD:birnlex_965]. The anterior of two brain vesicles formed by specialization of the rhombencephalon in the developing embryo. It gives rise to cerebellum and pons. [TFD][VHOG] The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG] epencephalon BAMS:Met BTO:0000673 CALOHA:TS-2029 DHBA:10655 EHDAA2:0001149 EHDAA:5498 EMAPA:17071 FMA:62003 GAID:594 HBA:4833 MA:0000197 MESH:D020540 NCIT:C32741 UMLS:C0376353 UMLS:C1516904 VHOG:0000741 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=543 epencephalon-2 uberon UBERON:0001895 the terms metencephalon and myelencephalon are only meaningful in mammals and birds[Neuroanatomy of the Zebrafish Brain]. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata and thus these are not distinguished in ZFA[ZFA]. metencephalon definitional Rostral segment of the hindbrain that has as its parts the pons (where present) and the cerebellum[WP,modified]. Anterior part of the hindbrain ventral to the cerebellum[NIFSTD:birnlex_965]. NIFSTD:birnlex_965 The anterior of two brain vesicles formed by specialization of the rhombencephalon in the developing embryo. It gives rise to cerebellum and pons. [TFD][VHOG] 2012-09-17 VHOG:0000741 VHOG The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000741 VHOG ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.381-382, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500 epencephalon ncithesaurus:Epencephalon UMLS:C0376353 NIFSTD:birnlex_965 UMLS:C1516904 ncithesaurus:Epencephalon http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=543 NIFSTD:birnlex_965 epencephalon-2 FMA:62003 Organ component of neuraxis that has as its parts the medullary reticular formation, inferior olivary complex and cochlear nuclear complex, among other structures[FMA]. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate[GO]. Posterior portion of the hindbrain which controls respiration, heartbeat, digestion, and swallowing as well as some locomotor responses.[AAO] The posterior region of the brain that is continuous with the spinal cord. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-17, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] Classical anatomical studies subdivided the vertebrate rhombencephalon into pons and medulla oblongata. (...) The medulla oblongata appears therefore as a tagma, that is, a group of segmental units (pseudorhombomeres, in this case) sharing some morphological and molecular characteristics, and in some aspects different from the segmental units present in adjoining brain regions, pons and spinal cord.[well established][VHOG] bulb medulla AAO:0010486 BAMS:MY BAMS:Md BM:Me BTO:0000041 CALOHA:TS-0607 DMBA:17352 EFO:0000924 EHDAA2:0001088 EHDAA:7588 EMAPA:17550 EV:0100275 FMA:62004 GAID:590 MA:0000206 MAT:0000111 MAT:0000367 MBA:354 MESH:D008526 MIAA:0000111 NCIT:C12442 OpenCyc:Mx4rvVjxSJwpEbGdrcN5Y29ycA OpenCyc:Mx4rwCqnXJwpEbGdrcN5Y29ycA TAO:0000545 UMLS:C0025148 UMLS:C1269575 VHOG:0000181 XAO:0003100 ZFA:0000545 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=698 bulbus uberon medulla oblonzata metepencephalon UBERON:0001896 medulla oblongata Organ component of neuraxis that has as its parts the medullary reticular formation, inferior olivary complex and cochlear nuclear complex, among other structures[FMA]. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate[GO]. FMA:62004 GO:0021550 Posterior portion of the hindbrain which controls respiration, heartbeat, digestion, and swallowing as well as some locomotor responses.[AAO] 2012-06-20 AAO:0010486 AAO AAO:BJB The posterior region of the brain that is continuous with the spinal cord. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-17, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] 2012-09-17 VHOG:0000181 VHOG Classical anatomical studies subdivided the vertebrate rhombencephalon into pons and medulla oblongata. (...) The medulla oblongata appears therefore as a tagma, that is, a group of segmental units (pseudorhombomeres, in this case) sharing some morphological and molecular characteristics, and in some aspects different from the segmental units present in adjoining brain regions, pons and spinal cord.[well established][VHOG] 2012-09-17 VHOG:0000181 VHOG DOI:10.1016/j.ydbio.2008.08.017 Marin F, Aroca P, Puelles L, Hox gene colinear expression in the avian medulla oblongata is correlated with pseudorhombomeric domains. Developmental Biology (2008) medulla ABA:MY UMLS:C0025148 NIFSTD:birnlex_957 UMLS:C0025148 ncithesaurus:Medulla_Oblongata UMLS:C1269575 NIFSTD:birnlex_957 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=698 NIFSTD:birnlex_957 bulbus FMA:62004 FMA:TA medulla oblonzata metepencephalon FMA:62004 the epithelial lining of the trachea which contains numerous ciliated cells UBERON:0003227 BTO:0001389 CALOHA:TS-1061 EHDAA2:0002069 EHDAA:5007 EMAPA:16855 EMAPA:18409 FMA:62015 MA:0001862 NCIT:C33797 UMLS:C1179002 VHOG:0001045 epithelial tissue of trachea epithelial tissue of windpipe epithelium of windpipe trachea epithelial tissue trachea epithelium tracheal epithelium windpipe epithelial tissue windpipe epithelium uberon UBERON:0001901 epithelium of trachea the epithelial lining of the trachea which contains numerous ciliated cells ISBN:0-397-51047-0 MGI:cwg MP:0002285 UMLS:C1179002 ncithesaurus:Tracheal_Epithelium epithelial tissue of trachea OBOL:automatic epithelial tissue of windpipe OBOL:automatic epithelium of windpipe OBOL:automatic trachea epithelial tissue OBOL:automatic windpipe epithelial tissue OBOL:automatic windpipe epithelium OBOL:automatic An endothelium that is part of a capillary [Automatically generated definition]. BTO:0004954 CALOHA:TS-0112 EMAPA:36292 FMA:62114 MA:0000711 NCIT:C49215 UMLS:C0006904 blood capillary endothelium capillary endothelium capillary vessel endothelium endothelium of blood capillary endothelium of capillary vessel uberon UBERON:0001915 endothelium of capillary An endothelium that is part of a capillary [Automatically generated definition]. OBOL:automatic UMLS:C0006904 ncithesaurus:Capillary_Endothelium blood capillary endothelium OBOL:automatic capillary vessel endothelium OBOL:automatic endothelium of blood capillary OBOL:automatic endothelium of capillary vessel OBOL:automatic An endothelium that is part of an arteriole [Automatically generated definition]. EMAPA:36286 FMA:62115 MA:0000705 NCIT:C49192 UMLS:C1179024 arteriole endothelium uberon UBERON:0001916 endothelium of arteriole An endothelium that is part of an arteriole [Automatically generated definition]. OBOL:automatic UMLS:C1179024 ncithesaurus:Arteriole_Endothelium An endothelium that is part of an artery [Automatically generated definition]. The endothelium is the thin layer of cells that lines the interior surface of blood vessels, forming an interface between circulating blood in the lumen and the rest of the vessel wall.[AAO] Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG] AAO:0011013 BTO:0004757 EMAPA:35148 FMA:62116 MA:0000707 NCIT:C49194 UMLS:C1179025 VHOG:0001215 XAO:0000357 arterial endothelium artery endothelium uberon UBERON:0001917 endothelium of artery An endothelium that is part of an artery [Automatically generated definition]. OBOL:automatic The endothelium is the thin layer of cells that lines the interior surface of blood vessels, forming an interface between circulating blood in the lumen and the rest of the vessel wall.[AAO] 2012-06-20 AAO:0011013 AAO XAO:curator Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG] 2012-09-17 VHOG:0001215 VHOG ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207 UMLS:C1179025 ncithesaurus:Artery_Endothelium An endothelium that is part of a venule [Automatically generated definition]. EMAPA:36290 FMA:62117 MA:0000716 NCIT:C49319 UMLS:C1179026 venule endothelium uberon UBERON:0001918 endothelium of venule An endothelium that is part of a venule [Automatically generated definition]. OBOL:automatic UMLS:C1179026 ncithesaurus:Venule_Endothelium An endothelium that is part of a vein [Automatically generated definition]. Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG] AAO:0011110 BTO:0004756 EMAPA:36288 FMA:62118 MA:0000712 NCIT:C49317 UMLS:C1179027 VHOG:0001216 XAO:0000358 vein endothelium venous endothelium uberon veinous endothelium UBERON:0001919 endothelium of vein An endothelium that is part of a vein [Automatically generated definition]. OBOL:automatic Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG] 2012-09-17 VHOG:0001216 VHOG ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207 UMLS:C1179027 ncithesaurus:Vein_Endothelium veinous endothelium VHOG:0001216 Ventral part of the midbrain, separated from the hindbrain by the isthmus[ISBN10:0471888893]. Subdivision of the midbrain lying anterior to the tectum and posterior to the substantia nigra and cerebral peduncle[FMA] The part of the midbrain extending from the substantia nigra to the cerebral aqueduct in a horizontal section of the midbrain. It forms the floor of the midbrain that surrounds the cerebral aqueduct[WP]. Together, our results reveal a shared basic organization in the tegmental domains of the diencephalon and midbrain of developing lamprey, indicating early appearance of the domain in vertebrate phylogeny.[well established][VHOG] MTg tegmentum BAMS:MTg BTO:0003388 DHBA:12195 EFO:0000921 EHDAA2:0004475 EMAPA:18215 FMA:62393 HBA:9002 MA:0000212 MAT:0000452 TAO:0000160 UMLS:C0039441 VHOG:0001367 XAO:0004271 ZFA:0000160 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=491 tegmentum mesencephali tegmentum of midbrain uberon mesencephalic tegmentum tegmentum mesencephalicum UBERON:0001943 'tegmentum' is used generically for the ventral part of the brainstem (ISBN10:0471888893). We use the label 'midbrain tegmentum' to denote the midbrain structure. In NIFSTD tegmentum is a composite structure and there is a separate class for midbrain tegmentum and pontine tegmentum midbrain tegmentum ZFA Ventral part of the midbrain, separated from the hindbrain by the isthmus[ISBN10:0471888893]. Subdivision of the midbrain lying anterior to the tectum and posterior to the substantia nigra and cerebral peduncle[FMA] The part of the midbrain extending from the substantia nigra to the cerebral aqueduct in a horizontal section of the midbrain. It forms the floor of the midbrain that surrounds the cerebral aqueduct[WP]. FMA:FMA ISBN10:0471888893 Together, our results reveal a shared basic organization in the tegmental domains of the diencephalon and midbrain of developing lamprey, indicating early appearance of the domain in vertebrate phylogeny.[well established][VHOG] 2012-09-17 VHOG:0001367 VHOG DOI:10.1016/j.brainresbull.2005.05.001 Villar-Cheda B, Abalo XM, Anadon R, Rodicio MC, The tegmental proliferation region in the sea lamprey. Brain Research Bulletin (2005) MTg NIFSTD:NeuroNames_abbrevSource tegmentum ISBN10:0471888893 UMLS:C0039441 NIFSTD:birnlex_1200 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=491 NIFSTD:birnlex_1200 tegmentum mesencephali mesencephalic tegmentum VHOG:0001367 tegmentum mesencephalicum NeuroNames:491 A multi-tissue structure that is part of a spinal cord. NCIT:C33969 UMLS:C1268166 uberon spinal cord part UBERON:0001948 regional part of spinal cord A multi-tissue structure that is part of a spinal cord. OBOL:automatic UMLS:C1268166 ncithesaurus:Spinal_Cord_Part The hyaline cartilaginous structures that support the bronchi, present as irregular rings in the larger bronchi (and not as regular as in the trachea), and as small plates and islands in the smaller bronchi; as the branching continues through the bronchial tree, the amount of hyaline cartilage in the walls decreases until it is absent in the smallest bronchioles[MP]. EMAPA:35192 FMA:62649 MA:0001835 NCIT:C49209 UMLS:C0225604 bronchi cartilage bronchial cartilage bronchial cartilage ring bronchial trunk cartilage bronchus cartilage cartilage of bronchi cartilage of bronchial trunk cartilagines bronchiales uberon UBERON:0001956 cartilage of bronchus MP The hyaline cartilaginous structures that support the bronchi, present as irregular rings in the larger bronchi (and not as regular as in the trachea), and as small plates and islands in the smaller bronchi; as the branching continues through the bronchial tree, the amount of hyaline cartilage in the walls decreases until it is absent in the smallest bronchioles[MP]. MP:0010988 UMLS:C0225604 ncithesaurus:Bronchus_Cartilage bronchi cartilage OBOL:automatic bronchial cartilage ring MP:0010988 bronchial trunk cartilage OBOL:automatic cartilage of bronchi OBOL:automatic cartilage of bronchial trunk OBOL:automatic cartilagines bronchiales A submucosa that is part of a bronchus [Automatically generated definition]. BTO:0002108 EMAPA:37449 FMA:62653 MA:0001837 NCIT:C49214 UMLS:C0225601 bronchi submucosa bronchial submucosa bronchial trunk submucosa bronchus submucosa submucosa of bronchi submucosa of bronchial trunk tela submucosa bronchi uberon submucous layer of bronchi UBERON:0001957 submucosa of bronchus A submucosa that is part of a bronchus [Automatically generated definition]. OBOL:automatic EMAPA:37449 MA:th UMLS:C0225601 ncithesaurus:Bronchus_Submucosa bronchi submucosa OBOL:automatic bronchial trunk submucosa OBOL:automatic submucosa of bronchi OBOL:automatic submucosa of bronchial trunk OBOL:automatic tela submucosa bronchi FMA:62653 FMA:TA submucous layer of bronchi BTO:0002108 The liquid component of blood, in which erythrocytes are suspended. plasma portion of plasma BTO:0000131 CALOHA:TS-0800 EFO:0001905 EMAPA:35690 FMA:62970 GAID:1178 MA:0002501 MAT:0000052 MESH:D010949 MIAA:0000052 NCIT:C13356 OpenCyc:Mx4rEg4ZYrIbEduAAAAOpmP6tw UMLS:C0032105 blood plasm portion of blood plasma uberon UBERON:0001969 blood plasma The liquid component of blood, in which erythrocytes are suspended. plasma MA:0002501 portion of plasma FMA:62970 UMLS:C0032105 ncithesaurus:Plasma . BTO:0000501 FMA:62972 GAID:1160 MA:0002519 MESH:D005750 NCIT:C32661 UMLS:C0017133 galen:GastricJuice stomach secretion uberon succus gastricus UBERON:0001971 gastric juice . UMLS:C0017133 ncithesaurus:Gastric_Secretion succus gastricus BTO:0000501 One of the minute vessels that collect deoxygenated blood from the capillary plexuses returns it to the veins Multi-tissue structure part of the blood vasculature formed by the anastomosis of capillaries. Venules carry blood toward the heart.[TAO] BTO:0002626 EMAPA:35917 FMA:63130 MA:0000071 MESH:A07.231.432.952 NCIT:C12818 TAO:0005315 UMLS:C0042520 VHOG:0001765 ZFA:0005315 uberon venula UBERON:0001979 venule One of the minute vessels that collect deoxygenated blood from the capillary plexuses returns it to the veins MESH:A07.231.432.952 MP:0004125 Multi-tissue structure part of the blood vasculature formed by the anastomosis of capillaries. Venules carry blood toward the heart.[TAO] 2012-08-14 TAO:0005315 TAO ZFIN:curator UMLS:C0042520 ncithesaurus:Venule venula The smallest division of the artery located between the muscular arteries and the capillaries[GO]. Multi-tissue structure part of the blood vasculature, feeds into capillaries. Arterioles carry blood away from the heart.[TAO] Small, terminal branch of an artery which generally connects to capillaries.[AAO] AAO:0010253 BTO:0001997 EMAPA:35146 FMA:63182 MA:0000063 MESH:D001160 NCIT:C12672 TAO:0002138 UMLS:C0003847 VHOG:0001763 ZFA:0005255 uberon arteriola UBERON:0001980 arteriole MA The smallest division of the artery located between the muscular arteries and the capillaries[GO]. GO:0014830 Multi-tissue structure part of the blood vasculature, feeds into capillaries. Arterioles carry blood away from the heart.[TAO] 2012-08-14 TAO:0002138 TAO ZFIN:curator Small, terminal branch of an artery which generally connects to capillaries.[AAO] 2012-06-20 AAO:0010253 AAO AAO:BJB UMLS:C0003847 ncithesaurus:Arteriole arteriola A vessel through which blood circulates in the body. consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG] Any of the vessels through which blood circulates in the body.[AAO] The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] annelids have blood vessels, but this class is not applicable to annelids. FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX vascular element AAO:0011004 AEO:0000207 BTO:0001102 CALOHA:TS-0080 EFO:0000817 EHDAA2:0003252 EHDAA:240 EMAPA:32743 EMAPA:35993 FMA:50722 FMA:63183 GAID:169 MA:0000060 MAT:0000393 MESH:D001808 NCIT:C12679 OpenCyc:Mx4rvVjxlpwpEbGdrcN5Y29ycA TAO:0002137 UMLS:C0005847 VHOG:0001250 XAO:0001011 ZFA:0005314 region of vascular tree organ vascular tree organ region uberon vas sanguineum UBERON:0001981 blood vessel EHDAA2 GO:0072360 A vessel through which blood circulates in the body. BTO:0001102 Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG] 2012-09-17 VHOG:0001250 VHOG Any of the vessels through which blood circulates in the body.[AAO] 2012-06-20 AAO:0011004 AAO AAO:EJS The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] 2012-09-17 VHOG:0001250 VHOG DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006) FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX FMA vascular element EMAPA:35993 UMLS:C0005847 ncithesaurus:Blood_Vessel region of vascular tree organ FMA:50722 vascular tree organ region FMA:50722 vas sanguineum Any of the smallest blood vessels connecting arterioles with venules. not all sources agree capillary is a blood vessel - consider adopting EMAPA superclass of vascular element Any of the tiny blood vessels connecting the arterioles to the venules.[AAO] The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] capillaries lack tunica media and tunica adventitia; only the endothelial wall of the tunica intima belongs AAO:0010252 BTO:0002045 CALOHA:TS-2006 EFO:0001906 EMAPA:35198 EV:0100035 FMA:63194 MA:0000065 MESH:A07.231.432.410 NCIT:C12685 OpenCyc:Mx4rvWEU-5wpEbGdrcN5Y29ycA TAO:0005250 UMLS:C0935624 VHOG:0001253 XAO:0000116 ZFA:0005250 blood capillary capillary vessel uberon UBERON:0001982 capillary FMA MA XAO ZFA Any of the smallest blood vessels connecting arterioles with venules. ISBN10:0073040584 Any of the tiny blood vessels connecting the arterioles to the venules.[AAO] 2012-06-20 AAO:0010252 AAO AAO:BJB The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] 2012-09-17 VHOG:0001253 VHOG DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006) UMLS:C0935624 ncithesaurus:Capillary A monolayer of specialized, flattened, mitochondria-rich cells that lines the posterior surface of the cornea and faces the anterior chamber of the eye[WP]. CALOHA:TS-0172 EMAPA:35935 FMA:63882 GAID:891 MA:0001242 MESH:D004728 NCIT:C12707 TAO:0002186 UMLS:C0014259 ZFA:0001687 cornea endothelium endothelium of cornea uberon epithelium posterius corneae UBERON:0001985 corneal endothelium A monolayer of specialized, flattened, mitochondria-rich cells that lines the posterior surface of the cornea and faces the anterior chamber of the eye[WP]. UMLS:C0014259 ncithesaurus:Corneal_Endothelium cornea endothelium OBOL:automatic endothelium of cornea OBOL:automatic epithelium posterius corneae A layer of epithelium that lines the heart, blood vessels (endothelium, vascular), lymph vessels (endothelium, lymphatic), and the serous cavities of the body[MESH]. Simple squamous epithelium which lines blood and lymphatic vessels and the heart[FMA] endothelial BTO:0000393 CALOHA:TS-0278 EFO:0002548 FMA:63916 GAID:520 MESH:D004727 NCIT:C12481 UMLS:C0014257 galen:Endothelium uberon UBERON:0001986 The term 'endothelium' has been either restricted to the continuous cell layer of the vertebrates, as we are assuming here, or applied to all the cells able to adhere to the luminal surface of the vascular basement membrane (Casley-Smith 1980) endothelium FMA-text-def A layer of epithelium that lines the heart, blood vessels (endothelium, vascular), lymph vessels (endothelium, lymphatic), and the serous cavities of the body[MESH]. Simple squamous epithelium which lines blood and lymphatic vessels and the heart[FMA] FMA:63916 MESH:A10.272.491 UMLS:C0014257 ncithesaurus:Endothelium feces Portion of semisolid bodily waste discharged through the anus[MW,modified] Excretion in semisolid state processed by the intestine.[FMA] fecal excreta BTO:0000440 CALOHA:TS-2345 ENVO:00002003 FMA:64183 GAID:1199 MA:0002509 MAT:0000053 MESH:D005243 MIAA:0000053 NCIT:C13234 OpenCyc:Mx4rvVjJMZwpEbGdrcN5Y29ycA UMLS:C0015733 galen:Feces faeces fecal material fecal matter matières fécales@fr merde@fr partie de la merde@fr piece of shit porción de mierda@es portion of excrement portion of faeces portion of fecal material portion of fecal matter portion of feces portionem cacas stool teil der fäkalien@de cow dung cow pat dung fewmet frass guano portion of dung portion of guano portion of scat scat spraint uberon droppings excrement ordure spoor UBERON:0001988 feces Portion of semisolid bodily waste discharged through the anus[MW,modified] Excretion in semisolid state processed by the intestine.[FMA] FMA:64183 UMLS:C0015733 ncithesaurus:Feces piece of shit portionem cacas cow dung cow pat fewmet frass guano spraint excrement BTO:0000440 Cartilage tissue primarily composed of type II collagen (thin fibrils) and a glassy appearance. Cartilage (tissue) which consists of chondrocytes and collagen, the intercellular matrix of which is an amorphous gel with a perichondrium[FMA:64783]. Cartilage tissue primarily composed of type II collagen (thin fibrils) and a glassy appearance.[VSAO] EMAPA:35414 FMA:64783 MA:0000109 NCIT:C32746 UMLS:C0225362 VSAO:0000094 XAO:0004029 hyaline cartilage uberon chondroid cartilage UBERON:0001994 hyaline cartilage tissue FMA Cartilage tissue primarily composed of type II collagen (thin fibrils) and a glassy appearance. GO_REF:0000034 PSPUB:0000170 VSAO:0000094 Cartilage (tissue) which consists of chondrocytes and collagen, the intercellular matrix of which is an amorphous gel with a perichondrium[FMA:64783]. FMA:64783 Cartilage tissue primarily composed of type II collagen (thin fibrils) and a glassy appearance.[VSAO] 2012-08-14 VSAO:0000094 VSAO PSPUB:0000170 UMLS:C0225362 ncithesaurus:Hyaline_Cartilage hyaline cartilage MA:0000109 chondroid cartilage An artery that carries deoxygenated blood from heart to the lungs. They are the only arteries (other than umbilical arteries in the fetus) that carry deoxygenated blood.. Major artery which supplies blood to the lungs.[AAO] One of two arteries, leaving from the heart, the left one supplying the left lung and the right one supplying the right lung. [TFD][VHOG] On the other hand, in the sister clade of the actinopterygians, the sarcopterygians, the gill circulation is supplemented with lung ventilation. As a result, the pulmonary artery and vein and a functional ductus arteriosus arose as a major evolutionary innovation from the sixth arch, giving the organism a flexible shunt to balance blood supply to and from gills and lungs according to environmental conditions.[well established][VHOG] In the human heart, the pulmonary trunk (pulmonary artery or main pulmonary artery) begins at the base of the right ventricle. It is short and wide - approximately 5 cm (2 inches) in length and 3 cm (1.2 inches) in diameter. It then branches into two pulmonary arteries (left and right), which deliver deoxygenated blood to the corresponding lung[WP] AAO:0010221 BTO:0000778 CALOHA:TS-0839 EFO:0001399 EHDAA2:0001575 EHDAA:4351 EMAPA:17008 FMA:66326 GAID:505 MA:0002031 MESH:D011651 NCIT:C12774 OpenCyc:Mx4rvVjbIpwpEbGdrcN5Y29ycA UMLS:C0034052 VHOG:0000982 XAO:0004162 galen:PulmonaryArtery pulmonary arterial tree pulmonary arterial tree organ part uberon arteria pulmonalis pulmonary arterial subtree truncus pulmonalis UBERON:0002012 pulmonary artery Wikipedia EHDAA2 XAO EHDAA2 An artery that carries deoxygenated blood from heart to the lungs. They are the only arteries (other than umbilical arteries in the fetus) that carry deoxygenated blood.. Major artery which supplies blood to the lungs.[AAO] 2012-06-20 AAO:0010221 AAO AAO:BJB One of two arteries, leaving from the heart, the left one supplying the left lung and the right one supplying the right lung. [TFD][VHOG] 2012-09-17 VHOG:0000982 VHOG On the other hand, in the sister clade of the actinopterygians, the sarcopterygians, the gill circulation is supplemented with lung ventilation. As a result, the pulmonary artery and vein and a functional ductus arteriosus arose as a major evolutionary innovation from the sixth arch, giving the organism a flexible shunt to balance blood supply to and from gills and lungs according to environmental conditions.[well established][VHOG] 2012-09-17 VHOG:0000982 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620 UMLS:C0034052 ncithesaurus:Pulmonary_Artery pulmonary arterial tree FMA:66326 pulmonary arterial tree organ part FMA:66326 arteria pulmonalis pulmonary arterial subtree FMA:66326 truncus pulmonalis the tough fibrous layer surrounding the kidney which is covered in a thick layer of perirenal adipose tissue that functions to provide some protection from trauma and damage provides some protection from trauma and damage. The renal capsule relates to the other layers in the following order (moving from innermost to outermost): renal medulla renal cortex renal capsule perinephric fat (or 'perirenal fat') renal fascia paranephric fat (or 'pararenal fat') peritoneum (anteriorly), and transversalis fascia (posteriorly).[Wikipedia:Kidney_capsule] EMAPA:18679 FMA:66610 MA:0000370 NCIT:C12885 UMLS:C0227637 galen:CapsuleOfKidney capsula fibrosa renis capsule of kidney fibrous capsule of kidney renal capsule uberon UBERON:0002015 kidney capsule the tough fibrous layer surrounding the kidney which is covered in a thick layer of perirenal adipose tissue that functions to provide some protection from trauma and damage MGI:anna MP:0011383 UMLS:C0227637 ncithesaurus:Renal_Capsule capsula fibrosa renis FMA:66610 FMA:TA fibrous capsule of kidney FMA:66610 renal capsule GO:0072127 Pulmonary veins are blood vessels that transport blood from the lungs to the heart[GO]. Any of the veins which collect blood from the lungs and some small vesicles received from the esophagus.[AAO] One of two pairs of large vessels that return oxygenated blood from each lung to the left atrium of the heart. [TFD][VHOG] the veins that return oxygenated blood from the lungs to the left atrium of the heart On the other hand, in the sister clade of the actinopterygians, the sarcopterygians, the gill circulation is supplemented with lung ventilation. As a result, the pulmonary artery and vein and a functional ductus arteriosus arose as a major evolutionary innovation from the sixth arch, giving the organism a flexible shunt to balance blood supply to and from gills and lungs according to environmental conditions.[well established][VHOG] AAO:0010521 BTO:0001799 CALOHA:TS-0840 EHDAA2:0001579 EHDAA:2629 EMAPA:18645 FMA:66643 GAID:543 MA:0002206 MESH:D011667 NCIT:C12776 UMLS:C0034090 VHOG:0001133 XAO:0000394 galen:PulmonaryVein pulmonary venous tree organ part uberon venae pulmonales UBERON:0002016 pulmonary vein Pulmonary veins are blood vessels that transport blood from the lungs to the heart[GO]. GO:0060577 Any of the veins which collect blood from the lungs and some small vesicles received from the esophagus.[AAO] 2012-06-20 AAO:0010521 AAO AAO:BJB One of two pairs of large vessels that return oxygenated blood from each lung to the left atrium of the heart. [TFD][VHOG] 2012-09-17 VHOG:0001133 VHOG the veins that return oxygenated blood from the lungs to the left atrium of the heart MP:0002726,MGI:cwg On the other hand, in the sister clade of the actinopterygians, the sarcopterygians, the gill circulation is supplemented with lung ventilation. As a result, the pulmonary artery and vein and a functional ductus arteriosus arose as a major evolutionary innovation from the sixth arch, giving the organism a flexible shunt to balance blood supply to and from gills and lungs according to environmental conditions.[well established][VHOG] 2012-09-17 VHOG:0001133 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620 UMLS:C0034090 ncithesaurus:Pulmonary_Vein venae pulmonales A cranial nerve that originates from neurons in the medulla and in the cervical spinal cord. A small motor nerve which emerges from the lateral wall of the medulla with the roots of the vagus nerve, and innervates a single pectoral suspensory muscle, the m.cucullaris. Cranial nerve that innervates the sternocleidomastoid and trapezius complex of muscles. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-1, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] Small motor nerve which innervates a single pectoral suspensory muscle, the m. cucullaris.[AAO] Cranial nerves XI and XII evolved in the common ancestor to amniotes (non-amphibian tetrapods) thus totalling twelve pairs.[well established][VHOG] In mice, the spinal branch of this motor nerve innervates the trapezius and the sternocleidomastoid muscles. The cranial branch joins the vagus nerve and innervates the same targets as the vagus nerve FMA has distinct cranial and spinal parts - WP says 'Traditional descriptions of the accessory nerve divide it into two parts: a spinal part and a cranial part.[1] However, because the cranial component rapidly joins the vagus nerve, becoming an integral part of said nerve, modern descriptions often consider the cranial component to be part of the vagus nerve and not part of the accessory nerve proper.[2] AAO:0010476 BAMS:11n BAMS:XIn EHDAA2:0000106 EHDAA:2855 EMAPA:17265 FMA:6720 FMA:80284 GAID:825 HBA:9340 MA:0001088 MBA:717 MESH:D000055 NCIT:C32041 OpenCyc:Mx4rwTEwI5wpEbGdrcN5Y29ycA UMLS:C0000905 UMLS:C1305777 VHOG:0000699 XAO:0004214 Willis' nerve accessory XI accessory XI nerve accessory nerve accessory nerve [XI] cervical accessory nerve cranial nerve XI eleventh cranial nerve nervus accessorius [XI] pars spinalis nervus accessorius radix spinalis nervus accessorius spinal accessory nerve spinal accessory nerve tree spinal part of accessory nerve uberon CN-XI accessory spinal nerve UBERON:0002019 accessory XI nerve A cranial nerve that originates from neurons in the medulla and in the cervical spinal cord. NIFSTD:birnlex_812 http://code.google.com/p/xenopus-anatomy-ontology/issues/detail?id=7 VHOG Wikipedia A small motor nerve which emerges from the lateral wall of the medulla with the roots of the vagus nerve, and innervates a single pectoral suspensory muscle, the m.cucullaris. ISBN:080184780X XAO:0004214 Cranial nerve that innervates the sternocleidomastoid and trapezius complex of muscles. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-1, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] 2012-09-17 VHOG:0000699 VHOG Small motor nerve which innervates a single pectoral suspensory muscle, the m. cucullaris.[AAO] 2012-06-20 AAO:0010476 AAO AAO:EJS Cranial nerves XI and XII evolved in the common ancestor to amniotes (non-amphibian tetrapods) thus totalling twelve pairs.[well established][VHOG] 2012-09-17 VHOG:0000699 VHOG In mice, the spinal branch of this motor nerve innervates the trapezius and the sternocleidomastoid muscles. The cranial branch joins the vagus nerve and innervates the same targets as the vagus nerve GO FMA has distinct cranial and spinal parts - WP says 'Traditional descriptions of the accessory nerve divide it into two parts: a spinal part and a cranial part.[1] However, because the cranial component rapidly joins the vagus nerve, becoming an integral part of said nerve, modern descriptions often consider the cranial component to be part of the vagus nerve and not part of the accessory nerve proper.[2] FMA UMLS:C0000905 NIFSTD:birnlex_812 UMLS:C0000905 ncithesaurus:Accessory_Nerve UMLS:C1305777 NIFSTD:birnlex_812 accessory XI EHDAA2:0000106 cranial nerve XI NIFSTD:birnlex_812 eleventh cranial nerve NIFSTD:birnlex_812 nervus accessorius [XI] FMA:6720 FMA:TA pars spinalis nervus accessorius FMA:6720 FMA:TA radix spinalis nervus accessorius FMA:6720 FMA:TA spinal accessory nerve FMA:6720 CN-XI VHOG:0000699 accessory spinal nerve BAMS:XIn A nervous system structure composed primarily of nerve cell bodies (somas). May also include dendrites and the initial unmyelinated portion of axons. Multi-tissue comprised of neurons, dendrites, axon terminals, glial cells, and capillaries.[TAO] AEO:0001012 EHDAA2:0003136 EHDAA2_RETIRED:0004658 EMAPA:37596 FMA:67242 HBA:4006 MA:0001112 NCIT:C32695 OpenCyc:Mx4rwDdKMpwpEbGdrcN5Y29ycA TAO:0002197 UMLS:C0018220 VHOG:0001768 ZFA:0001681 gray matter gray matter of neuraxis grey matter grey matter of neuraxis grey substance neuronal grey matter substantia grisea uberon gray mater grisea UBERON:0002020 gray matter A nervous system structure composed primarily of nerve cell bodies (somas). May also include dendrites and the initial unmyelinated portion of axons. Multi-tissue comprised of neurons, dendrites, axon terminals, glial cells, and capillaries.[TAO] 2012-08-14 TAO:0002197 TAO ZFIN:curator EMAPA:37596 MA:th UMLS:C0018220 ncithesaurus:Gray_Matter gray matter of neuraxis FMA:67242 neuronal grey matter AEO:0001012 substantia grisea FMA:67242 FMA:TA gray mater ZFA:0001681 grisea The most posterior of the three principal regions of the brain. In mammals and birds the hindbrain is divided into a rostral metencephalon and a caudal myelencephalon. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata (From: Neuroanatomy of the Zebrafish Brain)[ZFA]. Organ component of neuraxis that has as its parts the pons, cerebellum and medulla oblongata[FMA]. Posterior part of the brain consisting of the cerebellum and medulla oblongata.[AAO] The most posterior of the three principal regions of the brain, forming the rhombencephalon and all or most of the metencephalon. Kimmel et al, 1995.[TAO] relationship loss: develops_from hindbrain neural tube (TAO:0007043)[TAO] Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG] rhombencephalic in MA, brainstem and hindbrain and part-of siblings under brain, consistent with FMA and NIF. See also notes for cerebellum. We weaken the relation in ABA to overlaps AAO:0010150 BAMS:HB BTO:0000672 CALOHA:TS-0457 DHBA:10653 DMBA:16808 EFO:0000923 EHDAA2:0000746 EHDAA:3514 EHDAA:6487 EMAPA:16916 FMA:67687 MA:0000195 MAT:0000107 MBA:1065 MESH:D012249 MIAA:0000107 NCIT:C40336 TAO:0000029 UMLS:C0035507 UMLS:C1522180 VHOG:0000070 XAO:0000015 ZFA:0000029 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=540 uberon rhombencephalon UBERON:0002028 hindbrain modified-source-relation ABA Bgee:AN The most posterior of the three principal regions of the brain. In mammals and birds the hindbrain is divided into a rostral metencephalon and a caudal myelencephalon. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata (From: Neuroanatomy of the Zebrafish Brain)[ZFA]. Organ component of neuraxis that has as its parts the pons, cerebellum and medulla oblongata[FMA]. ZFA:0000029 ZFIN:curator Posterior part of the brain consisting of the cerebellum and medulla oblongata.[AAO] 2012-06-20 AAO:0010150 AAO AAO:BJB The most posterior of the three principal regions of the brain, forming the rhombencephalon and all or most of the metencephalon. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000029 TAO ZFIN:curator relationship loss: develops_from hindbrain neural tube (TAO:0007043)[TAO] 2012-08-14 TAO:0000029 TAO Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG] 2012-09-17 VHOG:0000070 VHOG DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999) in MA, brainstem and hindbrain and part-of siblings under brain, consistent with FMA and NIF. See also notes for cerebellum. We weaken the relation in ABA to overlaps MA UMLS:C0035507 NIFSTD:birnlex_942 UMLS:C0035507 ncithesaurus:Hind-Brain UMLS:C1522180 NIFSTD:birnlex_942 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=540 NIFSTD:birnlex_942 An epithelium that is part of a bronchus [Automatically generated definition]. BTO:0001845 CALOHA:TS-1240 EFO:0000307 EMAPA:32691 FMA:67782 MA:0001839 NCIT:C32231 UMLS:C0599333 bronchi epithelial tissue bronchi epithelium bronchial epithelium bronchial trunk epithelial tissue bronchial trunk epithelium bronchus epithelial tissue bronchus epithelium epithelial tissue of bronchi epithelial tissue of bronchial trunk epithelial tissue of bronchus epithelium of bronchi epithelium of bronchial trunk uberon UBERON:0002031 epithelium of bronchus An epithelium that is part of a bronchus [Automatically generated definition]. OBOL:automatic UMLS:C0599333 ncithesaurus:Bronchial_Epithelium bronchi epithelial tissue OBOL:automatic bronchi epithelium OBOL:automatic bronchial trunk epithelial tissue OBOL:automatic bronchial trunk epithelium OBOL:automatic bronchus epithelial tissue OBOL:automatic epithelial tissue of bronchi OBOL:automatic epithelial tissue of bronchial trunk OBOL:automatic epithelial tissue of bronchus OBOL:automatic epithelium of bronchi OBOL:automatic epithelium of bronchial trunk OBOL:automatic Muscle tissue that contains fibers that are divided by transverse bands into striations. Voluntary muscle tissue arranged in bundles of fibers.[AAO] AAO:0010762 AEO:0000140 CALOHA:TS-2047 EHDAA2:0003140 EMAPA:36390 FMA:67905 MA:0002438 NCIT:C12436 OpenCyc:Mx4rwAoze5wpEbGdrcN5Y29ycA UMLS:C1331262 WBbt:0005779 galen:StriatedMuscle striated muscle uberon UBERON:0002036 striated muscle tissue Muscle tissue that contains fibers that are divided by transverse bands into striations. CL:0000737 GOC:dph GOC:mtg_muscle Voluntary muscle tissue arranged in bundles of fibers.[AAO] 2012-06-20 AAO:0010762 AAO AAO:CAM UMLS:C1331262 ncithesaurus:Striated_Muscle_Tissue A systemic artery that supplies the lung with with oxygenated blood. EMAPA:18608 FMA:68109 GAID:477 MA:0001923 MESH:D001981 NCIT:C32230 OpenCyc:Mx4r4sy0UiNbEd2AAAACs6hRXg UMLS:C0006257 bronchial arterial tree uberon arteriae bronchiales rami bronchiales partis thoracicae aortae UBERON:0002040 Although there is much variation, there are usually two bronchial arteries that run to the left lung, and one to the right lung. bronchial artery A systemic artery that supplies the lung with with oxygenated blood. UBERON:cjm UMLS:C0006257 ncithesaurus:Bronchial_Artery arteriae bronchiales rami bronchiales partis thoracicae aortae The pontine raphe nucleus is one of the raphe nuclei. It is located in the pontine tegmentum. [WP,unvetted]. BAMS:PnR BAMS:RA-PONS BAMS:RPn DHBA:12471 DHBA:12475 FMA:68875 HBA:9159 MA:0001022 MBA:238 UMLS:C0175423 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=589 raphe of pons raphe pontis uberon nucleus raphe pontis nucleus raphes pontis raphe (mediana pontina) raphe pontis nucleus UBERON:0002047 pontine raphe nucleus Wikipedia The pontine raphe nucleus is one of the raphe nuclei. It is located in the pontine tegmentum. [WP,unvetted]. UMLS:C0175423 NIFSTD:birnlex_1110 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=589 NIFSTD:birnlex_1110 raphe pontis FMA:68875 FMA:TA nucleus raphe pontis NeuroNames:589 nucleus raphes pontis raphe (mediana pontina) NeuroNames:589 lung Respiration organ that develops as an oupocketing of the esophagus. Either of two organs which allow gas exchange absorbing oxygen from inhaled air and releasing carbon dioxide with exhaled air.[AAO] Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata. (...) In actinopterygian fishes, apart from Cladistia, the ventral intestinal pocket migrates dorsally and becomes the swim-bladder, a mainly hydrostatical organ (reference 1); Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung (reference 2).[well established][VHOG] pulmonary respiration organ in all air-breathing animals, including most tetrapods, a few fish and a few snails. In mammals and the more complex life forms, the two lungs are located in the chest on either side of the heart. Their principal function is to transport oxygen from the atmosphere into the bloodstream, and to release carbon dioxide from the bloodstream into the atmosphere. This exchange of gases is accomplished in the mosaic of specialized cells that form millions of tiny, exceptionally thin-walled air sacs called alveoli. // Avian lungs do not have alveoli as mammalian lungs do, they have Faveolar lungs. They contain millions of tiny passages known as para-bronchi, connected at both ends by the dorsobronchi AAO:0000275 AAO:0010567 BTO:0000763 CALOHA:TS-0568 EFO:0000934 EHDAA2:0001042 EHDAA:1554 EHDAA:2205 EMAPA:16728 EV:0100042 FMA:7195 GAID:345 MA:0000415 MAT:0000135 MESH:D008168 MIAA:0000135 NCIT:C12468 OpenCyc:Mx4rvVjKy5wpEbGdrcN5Y29ycA UMLS:C0024109 VHOG:0000310 XAO:0000119 galen:Lung pulmo uberon UBERON:0002048 Snakes and limbless lizards typically possess only the right lung as a major respiratory organ; the left lung is greatly reduced, or even absent. Amphisbaenians, however, have the opposite arrangement, with a major left lung, and a reduced or absent right lung [WP] lung some species only have a single lung Respiration organ that develops as an oupocketing of the esophagus. Either of two organs which allow gas exchange absorbing oxygen from inhaled air and releasing carbon dioxide with exhaled air.[AAO] 2012-06-20 AAO:0010567 AAO AAO:SBH Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata. (...) In actinopterygian fishes, apart from Cladistia, the ventral intestinal pocket migrates dorsally and becomes the swim-bladder, a mainly hydrostatical organ (reference 1); Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000310 VHOG ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.210, DOI:10.1371/journal.pone.0024019 Zheng W, Wang Z, Collins JE, Andrews RM, Stemple D, Gong Z, Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung. PLoS One (2011) UMLS:C0024109 ncithesaurus:Lung pulmo An interconnected tubular multi-tissue structure contains fluid that is actively transported around the organism[ZFA]. Examples: vasculature of lung, vasculature of face. see also: vascular system. Consider merging? vascular BTO:0003718 FMA:69050 TAO:0005249 ZFA:0005249 vascular network uberon UBERON:0002049 vasculature FMA An interconnected tubular multi-tissue structure contains fluid that is actively transported around the organism[ZFA]. Examples: vasculature of lung, vasculature of face. ZFA:0005249 vascular network FMA:69050 Anatomical structure that is part of an embryo. Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO] Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO] Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO] in FMA embryo is_a embryonic structure AAO:0000138 BILA:0000034 BTO:0000174 CALOHA:TS-2110 EFO:0000461 FBbt:00004208 FMA:69067 GAID:407 MESH:D004628 NCIT:C13229 RETIRED_EHDAA2:0003169 TAO:0001105 UMLS:C0013948 VSAO:0000178 XAO:0003042 ZFA:0001105 developing embryonic structure embryonic anatomical structure uberon developing structure embryonale Struktur embryonic structures UBERON:0002050 embryonic structure Anatomical structure that is part of an embryo. BTO:0000174 ZFIN:curator Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO] 2012-06-20 AAO:0000138 AAO AAO:BJB Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO] 2012-08-14 TAO:0001105 TAO ZFIN:curator Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO] 2012-08-14 VSAO:0000178 VSAO ZFIN:curator in FMA embryo is_a embryonic structure FMA UMLS:C0013948 ncithesaurus:Embryonic_Structure developing embryonic structure FBbt:00004208 embryonic anatomical structure RETIRED_EHDAA2:0003169 embryonale Struktur BTO:0000174 embryonic structures ZFA:0001105 The truncus arteriosus and bulbus cordis are divided by the aorticopulmonary septum. The truncus arteriosus gives rise to the ascending aorta and the pulmonary trunk. The bulbus cordis gives rise to the smooth parts (outflow tract) of the left and right ventricles. assume spelling error for ncit EHDAA2:0004143 EMAPA:35887 FMA:70301 GAID:554 MA:0000103 MESH:D014338 NCIT:C34317 OpenCyc:Mx4rquH9YKgNEdudWQACs5b6Bw UMLS:C1519589 uberon UBERON:0002061 truncus arteriosus EHDAA2 FMA MA EHDAA2 EHDAA2 The truncus arteriosus and bulbus cordis are divided by the aorticopulmonary septum. The truncus arteriosus gives rise to the ascending aorta and the pulmonary trunk. The bulbus cordis gives rise to the smooth parts (outflow tract) of the left and right ventricles. assume spelling error for ncit ncit UMLS:C1519589 ncithesaurus:Trancus_Arteriosus dermis The dermis is a layer of skin between the epidermis (with which it makes up the skin) and subcutaneous tissues, and is composed of two layers, the papillary and reticular dermis[WP]. Consider adding a layer-of-skin grouping class for all skin layers A collagenous layer of the skin subjacent to the epidermis and covering the hypodermis. It contains various types of cells (e.g. fibroblasts, pigment cells, nerve, blood vessels and scales. Le Guellec et al, 2004.[TAO] When approaching controversies surrounding skin evolution, we need to remember that the skin consists of two layers, an epidermis and a dermis, not a single evolving structure. (...) It is little wonder that controversies about homology exist. If we think of the epidermis, the dermis, and their interactions as an evolving unit, then their specialized products (hair, feathers, and reptilian scales) are broadly homologous.[well established][VHOG] dermal AAO:0000128 BTO:0000294 CALOHA:TS-2076 EFO:0000953 EMAPA:17527 EV:0100154 FMA:70323 GAID:1321 MA:0000152 MAT:0000153 MESH:D020405 MIAA:0000153 NCIT:C12701 TAO:0001119 UMLS:C0011646 VHOG:0000108 XAO:0000217 ZFA:0001119 vertebrate dermis uberon corium cutis UBERON:0002067 dermis FMA definitional The dermis is a layer of skin between the epidermis (with which it makes up the skin) and subcutaneous tissues, and is composed of two layers, the papillary and reticular dermis[WP]. ZFIN:curator A collagenous layer of the skin subjacent to the epidermis and covering the hypodermis. It contains various types of cells (e.g. fibroblasts, pigment cells, nerve, blood vessels and scales. Le Guellec et al, 2004.[TAO] 2012-08-14 TAO:0001119 TAO ZFIN:curator When approaching controversies surrounding skin evolution, we need to remember that the skin consists of two layers, an epidermis and a dermis, not a single evolving structure. (...) It is little wonder that controversies about homology exist. If we think of the epidermis, the dermis, and their interactions as an evolving unit, then their specialized products (hair, feathers, and reptilian scales) are broadly homologous.[well established][VHOG] 2012-09-17 VHOG:0000108 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.231-232 see also p.209 and p.228 and Figure 6-1 UMLS:C0011646 ncithesaurus:Dermis corium corium BTO:0000294 cutis BTO:0000294 hypodermis Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP]. A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells. Le Guellec et al, 2004.[TAO] A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells[FMA:70544]. hypodermal subcutaneous subcutaneus BTO has 'subcutis', as part of dermis. We follow FMA in having distinct classes for hypodermis and superficial fascia, and including these as part of the non-skin intgeument. BTO:0001314 CALOHA:TS-2366 EMAPA:37505 FMA:70544 NCIT:C33645 TAO:0001136 UMLS:C0278403 ZFA:0001136 hypoderm vertebrate hypodermis uberon sub-tegumental tissue subcutaneous tissue subcutis subtegumental tissue superficial fascia tela subcutanea UBERON:0002072 hypodermis ZFA FMA-modified Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP]. A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells. Le Guellec et al, 2004.[TAO] 2012-08-14 TAO:0001136 TAO ZFIN:curator A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells[FMA:70544]. FMA:70544 BTO has 'subcutis', as part of dermis. We follow FMA in having distinct classes for hypodermis and superficial fascia, and including these as part of the non-skin intgeument. BTO EMAPA:37505 MA:th UMLS:C0278403 ncithesaurus:Subcutis sub-tegumental tissue BTO:0004525 subcutaneous tissue subtegumental tissue BTO:0004525 superficial fascia tela subcutanea An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen. An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO] general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs. AAO:0010386 BTO:0001491 EHDAA:512 EMAPA:16245 FMA:7085 MA:0000019 MESH:D014781 NCIT:C28287 RETIRED_EHDAA2:0002201 UMLS:C0042779 XAO:0003034 visceral organ visceral organ system uberon Organsystem@de splanchnic tissue viscera visceral tissue UBERON:0002075 viscus An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen. BTO:0001491 An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO] 2012-06-20 AAO:0010386 AAO BTO:0001491 general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs. FMA UMLS:C0042779 ncithesaurus:Viscera visceral organ RETIRED_EHDAA2:0002201 visceral organ system MA:0000019 Organsystem@de BTO:0001491 splanchnic tissue BTO:0001491 visceral tissue BTO:0001491 A cardiac ventricle that is in the right side of the heart. The muscular chamber on the right and in front of the left ventricle. It generally receives venous blood from the right atrium and conveys it into the pulmonary artery. [(1988)_Dorian_AF, Amsterdam, Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B._Anatomy, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier's_Encyclopaedic_Dictionary_of_Medicine][VHOG] https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern In mammals continuous with the pulmonary arteries BTO:0001630 CALOHA:TS-0443 EHDAA2:0000196 EMAPA:17340 FMA:7098 MA:0000093 NCIT:C12870 OpenCyc:Mx4rRMlc0KgNEdudWQACs5b6Bw OpenCyc:Mx8Ngh4rvgHsHZwpEbGdrcN5Y29ycB4rvVjj1pwpEbGdrcN5Y29ycA UMLS:C0225883 VHOG:0000717 galen:RightVentricle cardiac right ventricle right ventricle right ventricle of heart uberon right cardiac ventricle ventriculus dexter UBERON:0002080 heart right ventricle cjm A cardiac ventricle that is in the right side of the heart. The muscular chamber on the right and in front of the left ventricle. It generally receives venous blood from the right atrium and conveys it into the pulmonary artery. [(1988)_Dorian_AF, Amsterdam, Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B._Anatomy, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier's_Encyclopaedic_Dictionary_of_Medicine][VHOG] 2012-09-17 VHOG:0000717 VHOG UMLS:C0225883 ncithesaurus:Right_Ventricle right ventricle FMA:7098 right cardiac ventricle EMAPA:17340 ventriculus dexter Cardiac chamber through which blood leaves the heart. A chamber of the heart that receives blood from one or more atria and pumps it by muscular contraction into the arteries.[AAO] One of four heart chambers.[TAO] In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...)[well established][VHOG] ventricle AAO:0010249 BTO:0000862 CALOHA:TS-0444 EFO:0000317 EHDAA2:0004164 EHDAA:1912 EMAPA:17331 EV:0100020 FMA:7100 GAID:568 MA:0000091 MAT:0000497 MESH:D006352 NCIT:C12730 OpenCyc:Mx4rvVjj1pwpEbGdrcN5Y29ycA TAO:0000009 UMLS:C0018827 VHOG:0000435 XAO:0003193 ZFA:0000009 galen:Ventricle heart ventricle lower chamber of heart ventricle of heart uberon UBERON:0002082 cardiac ventricle Bgee:AN Cardiac chamber through which blood leaves the heart. A chamber of the heart that receives blood from one or more atria and pumps it by muscular contraction into the arteries.[AAO] 2012-06-20 AAO:0010249 AAO AAO:BJB One of four heart chambers.[TAO] 2012-08-14 TAO:0000009 TAO ZFIN:curator In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...)[well established][VHOG] 2012-09-17 VHOG:0000435 VHOG ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.428 UMLS:C0018827 ncithesaurus:Cardiac_Ventricle A cardiac ventricle that is in the left side of the heart. Thick-walled muscular chamber constituting the left border and apex of the heart. It receives oxygenated blood from the left atrium through the mitral orifice and send it off into the aorta. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] The vertebrate heart initially forms as a tube from a population of precursor cells termed the first heart field (FHF). Cells from the adjacent second heart field (SHF) are then progressively added to the developing heart. In avian and mammalian hearts, the FHF contributes mainly to the left ventricle, whereas the SHF gives rise to the outflow tract and large portions of the right ventricle and atria. Both fields arise from common mesodermal progenitors, although the detailed lineage relationships between FHF and SHF remain uncertain.[well established][VHOG] https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern In mammals continuous with aorta BTO:0001629 CALOHA:TS-0439 EHDAA2:0002178 EMAPA:17337 FMA:7101 MA:0000092 NCIT:C12871 OpenCyc:Mx4rtW8v46gEEdudWQACs5b6Bw OpenCyc:Mx8Ngh4rvgIFoJwpEbGdrcN5Y29ycB4rvVjj1pwpEbGdrcN5Y29ycA UMLS:C0225897 VHOG:0000718 galen:LeftVentricle cardiac left ventricle left cardiac ventricle left ventricle left ventricle of heart uberon ventriculus sinister cordis UBERON:0002084 heart left ventricle GO A cardiac ventricle that is in the left side of the heart. Thick-walled muscular chamber constituting the left border and apex of the heart. It receives oxygenated blood from the left atrium through the mitral orifice and send it off into the aorta. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000718 VHOG The vertebrate heart initially forms as a tube from a population of precursor cells termed the first heart field (FHF). Cells from the adjacent second heart field (SHF) are then progressively added to the developing heart. In avian and mammalian hearts, the FHF contributes mainly to the left ventricle, whereas the SHF gives rise to the outflow tract and large portions of the right ventricle and atria. Both fields arise from common mesodermal progenitors, although the detailed lineage relationships between FHF and SHF remain uncertain.[well established][VHOG] 2012-09-17 VHOG:0000718 VHOG DOI:10.1126/science.1190181 Stolfi A, Gainous TB, Young JJ, Mori A, Levine M, Christiaen L, Early chordate origins of the vertebrate second heart field. Science (2010) UMLS:C0225897 ncithesaurus:Left_Ventricle left ventricle FMA:7101 ventriculus sinister cordis The postcranial subdivision of skeleton structural components forming the long axis of the vertebrate body; in Danio, consisting of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins; in human consists of the bones of the vertebral column, the thoracic cage and the pelvis[ZFA+FMA]. Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO] The axial skeleton is formed by the vertebral column, a metameric, semi-flexible, arched bar located in the dorsal part of the trunk, and is formed by a series of cartilaginous or bony vertebrae. It provides suspension for the appendicular skeleton and protection for the spinal nerve cord.[AAO] The post-cranial structural components forming the long axis of the vertebrate body; usually consists of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins.[TAO] The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods.[well established][VHOG] axial skeleton AAO:0000034 EFO:0000942 EHDAA2:0000161 EHDAA:5049 EMAPA:17214 EMAPA:37721 FMA:71221 MA:0002986 MAT:0000148 MIAA:0000148 TAO:0000317 VHOG:0000317 VSAO:0000093 XAO:0003073 ZFA:0000317 post-cranial axial skeleton uberon UBERON:0002090 previous some AOs had used the term 'axial skeleton' to include the skull. This is being resolved (see tracker items above). Status: MA - fixed. postcranial axial skeleton http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton The postcranial subdivision of skeleton structural components forming the long axis of the vertebrate body; in Danio, consisting of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins; in human consists of the bones of the vertebral column, the thoracic cage and the pelvis[ZFA+FMA]. ZFA:0000317 Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO] 2012-08-14 VSAO:0000093 VSAO PSPUB:0000170 The axial skeleton is formed by the vertebral column, a metameric, semi-flexible, arched bar located in the dorsal part of the trunk, and is formed by a series of cartilaginous or bony vertebrae. It provides suspension for the appendicular skeleton and protection for the spinal nerve cord.[AAO] 2012-06-20 AAO:0000034 AAO AAO:LAP The post-cranial structural components forming the long axis of the vertebrate body; usually consists of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins.[TAO] 2012-08-14 TAO:0000317 TAO ZFIN:curator The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods.[well established][VHOG] 2012-09-17 VHOG:0000317 VHOG DOI:10.1186/1742-9994-8-4 Schilling N, Evolution of the axial system in craniates: morphology and function of the perivertebral musculature. Frontiers in Zoology (2011) axial skeleton FMA:71221 EMAPA:37721 MA:th Subdivision of skeleton which which consists of all the skeletal elements in in the pectoral and pelvic appendage complexes[cjm]. Skeletal subdivision consisting of all the skeletal elements in the pectoral and pelvic appendage complexes.[VSAO] Skeletal system that consists of the paired fins (pectoral or pelvic fins).[TAO] The pectoral and pelvic girdles, which articulate with the axial skeleton, together with their associated limbs, the forelimbs and hind limbs, form the appendicular skeleton.[AAO] ontologies differ in whether they treat the term appendicular skeleton as being the entire set of bones in the limbs, or whether the fore and hind limbs/fins are treated as seperate appendicular skeletons. Here we follow FMA, and treat the appendicular skeleton as the sum total of skeletal elements in the organism (this is evidenced by the fact that in FMA, skeleton of left/right upper/lower limb is part_of a appendicular skeleton, and subtypes of 'subdivision of appendicular skeleton'). We have separate classes such as 'skeleton of limb', and 'skeleton of hindlimb' for the 4 parts of the appendicular skeleton. In future the ZFA/TAO classes may be moved. AAO:0000747 EFO:0000951 EMAPA:32729 FMA:71222 MA:0000290 MAT:0000278 MIAA:0000278 NCIT:C49477 UMLS:C0222646 VHOG:0001666 VSAO:0000076 XAO:0003166 appendicular skeleton entire appendicular skeleton paired fin skeleton uberon skeleton appendiculare UBERON:0002091 appendicular skeleton https://github.com/obophenotype/uberon/wiki/Appendages-and-the-appendicular-skeleton Subdivision of skeleton which which consists of all the skeletal elements in in the pectoral and pelvic appendage complexes[cjm]. UBERONREF:0000003 Skeletal subdivision consisting of all the skeletal elements in the pectoral and pelvic appendage complexes.[VSAO] 2012-08-14 VSAO:0000076 VSAO PSPUB:0000170 Skeletal system that consists of the paired fins (pectoral or pelvic fins).[TAO] 2012-08-14 TAO:0000027 TAO TAO:wd The pectoral and pelvic girdles, which articulate with the axial skeleton, together with their associated limbs, the forelimbs and hind limbs, form the appendicular skeleton.[AAO] 2012-06-20 AAO:0000747 AAO AAO:LAP ontologies differ in whether they treat the term appendicular skeleton as being the entire set of bones in the limbs, or whether the fore and hind limbs/fins are treated as seperate appendicular skeletons. Here we follow FMA, and treat the appendicular skeleton as the sum total of skeletal elements in the organism (this is evidenced by the fact that in FMA, skeleton of left/right upper/lower limb is part_of a appendicular skeleton, and subtypes of 'subdivision of appendicular skeleton'). We have separate classes such as 'skeleton of limb', and 'skeleton of hindlimb' for the 4 parts of the appendicular skeleton. In future the ZFA/TAO classes may be moved. FMA UMLS:C0222646 ncithesaurus:Appendicular_Skeleton entire appendicular skeleton paired fin skeleton skeleton appendiculare Cardiac septum which separates the right ventricle from the left ventricle.[FMA] The partition separating the right and left ventricles of the heart. [TFD][VHOG] The two most progressive vertebrate classes, the birds and mammals, have completed the ventricular septum and at long last have completely separated the two blood streams along the length of the major heart chambers. This development has obviously been brought about independently in the two cases, since mammals and birds have evolved independently from primitive reptiles.[well established][VHOG] involves the recruitment of myocardial cells as well as of non- muscular mesenchymal cells (Kaufman and Bard, 1999) BTO:0002483 EFO:0001956 EHDAA:2603 EMAPA:17333 FMA:7133 MA:0000085 NCIT:C32874 OpenCyc:Mx4rwA7lp5wpEbGdrcN5Y29ycA UMLS:C0225870 VHOG:0000386 galen:InterventricularSeptum heart interventricular septum heart ventricular septum uberon interventricular septum of heart interventriculare cordis intraventricular septum s. interventriculare cordis septum inferius septum membranaceum ventricle septum ventricular septum UBERON:0002094 interventricular septum Cardiac septum which separates the right ventricle from the left ventricle.[FMA] FMA:7133 The partition separating the right and left ventricles of the heart. [TFD][VHOG] 2012-09-17 VHOG:0000386 VHOG The two most progressive vertebrate classes, the birds and mammals, have completed the ventricular septum and at long last have completely separated the two blood streams along the length of the major heart chambers. This development has obviously been brought about independently in the two cases, since mammals and birds have evolved independently from primitive reptiles.[well established][VHOG] 2012-09-17 VHOG:0000386 VHOG ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.430 involves the recruitment of myocardial cells as well as of non- muscular mesenchymal cells (Kaufman and Bard, 1999) ISBN10:0124020607 UMLS:C0225870 ncithesaurus:Interventricular_Septum heart interventricular septum MA:0000085 heart ventricular septum MA:0000085 interventricular septum of heart BTO:0002483 interventriculare cordis BTO:0002483 intraventricular septum s. interventriculare cordis septum inferius septum membranaceum ventricular septum ventricular septum MA:0000085 skin of body The organ covering the body that consists of the dermis and epidermis. consider 'integumentary system' for invertebrates MA uses the term skin to refer to what is called here: zone of skin BTO:0001253 CALOHA:TS-0934 EFO:0000962 EHDAA2:0001844 EMAPA:17525 FMA:7163 MESH:D012867 MFMO:0000099 NCIT:C12470 OpenCyc:Mx4rvVjX3ZwpEbGdrcN5Y29ycA UMLS:C1123023 XAO:0000023 galen:Skin entire skin skin organ uberon entire integument integument integumental organ pelt skin UBERON:0002097 skin of body Wikipathways:WP2062 The organ covering the body that consists of the dermis and epidermis. UBERON:cjm MA uses the term skin to refer to what is called here: zone of skin FMA UMLS:C1123023 ncithesaurus:Skin The thin membranous structure between the two heart atria or the thick muscular structure between the two heart ventricles. 'Terrestrial vertebrates have divided hearts in which septae separate the oxygenated and deoxygenated blood within the pulmonary and systemic circulations' in GO, septum morphogenesis is part of cardiac chamber morphogenesis; need to add axioms to infer this EMAPA:35400 FMA:7180 GAID:562 MA:0000083 MESH:D006346 NCIT:C49485 UMLS:C0018819 XAO:0004141 cardiac septa heart septa heart septum septum of heart uberon spiral septa UBERON:0002099 cardiac septum The thin membranous structure between the two heart atria or the thick muscular structure between the two heart ventricles. MESH:A07.541.459 in GO, septum morphogenesis is part of cardiac chamber morphogenesis; need to add axioms to infer this GO UMLS:C0018819 ncithesaurus:Heart_Septum cardiac septa heart septa spiral septa XAO:0004141 Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present. Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO] Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO] AAO:0010339 BILA:0000116 BTO:0001493 CALOHA:TS-1071 EFO:0000966 EMAPA:31857 FMA:7181 MA:0000004 MAT:0000296 MIAA:0000296 NCIT:C33816 OpenCyc:Mx4rvVkJjpwpEbGdrcN5Y29ycA TAO:0001115 UMLS:C0460005 XAO:0000054 XAO:0003025 ZFA:0001115 galen:Trunk thoracolumbar region torso trunk region uberon Rumpf UBERON:0002100 trunk Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present. TAO:0001115 UBERONREF:0000006 Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO] 2012-06-20 AAO:0010339 AAO AAO:BJB Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO] 2012-08-14 TAO:0001115 TAO ZFIN:curator UMLS:C0460005 ncithesaurus:Trunk trunk region XAO:0000054 Rumpf BTO:0001493 The sensory system subserving the sense of vision. The sensory system used for sight.[AAO] UBERON:0007036 AAO:0000632 BILA:0000140 EMAPA:36003 FMA:7191 MA:0002444 NCIT:C12888 OpenCyc:Mx4rvViCtpwpEbGdrcN5Y29ycA TAO:0001127 UMLS:C0587900 XAO:0003198 ZFA:0001127 photosensory system visual organ system uberon UBERON:0002104 visual system The sensory system subserving the sense of vision. NIFSTD:FMAID_7191 The sensory system used for sight.[AAO] 2012-06-20 AAO:0000632 AAO AAO:EJS UMLS:C0587900 ncithesaurus:Visual_System photosensory system BILA:0000140 Sensory system responsible for the perception of spatial orientation and auditory stimuli. The sensory system used for balance and hearing.[AAO] AAO:0000631 EMAPA:36002 EMAPA:37985 FMA:78500 TAO:0001138 XAO:0003195 ZFA:0001138 auditory organ system vestibuloauditory system uberon auditory system auditory/vestibular system vestibuloauditory system UBERON:0002105 vestibulo-auditory system Sensory system responsible for the perception of spatial orientation and auditory stimuli. ZFA:0001138 The sensory system used for balance and hearing.[AAO] 2012-06-20 AAO:0000631 AAO AAO:EJS EMAPA:37985 MA:th A portion of smooth muscle tissue that is part of an artery [Automatically generated definition]. BTO:0000087 CALOHA:TS-1198 EMAPA:36285 FMA:72024 MA:0000708 NCIT:C49195 UMLS:C1706851 arterial smooth muscle artery smooth muscle artery smooth muscle tissue smooth muscle of artery uberon arterial smooth muscle cell UBERON:0002111 artery smooth muscle tissue A portion of smooth muscle tissue that is part of an artery [Automatically generated definition]. OBOL:automatic UMLS:C1706851 ncithesaurus:Artery_Smooth_Muscle_Tissue arterial smooth muscle BTO:0000087 smooth muscle of artery FMA:72024 arterial smooth muscle cell BTO:0000087 A paired organ of the urinary tract which has the production of urine as its primary function. One of either of a pair of structures lying on either side of the dorsal aorta in which fluid balance is regulated and waste is excreted out in the form of urine.[AAO] renal AAO:0000250 BTO:0000671 CALOHA:TS-0510 EFO:0000929 EMAPA:17373 EV:0100096 FMA:7203 GAID:423 MA:0000368 MAT:0000119 MESH:D007668 MIAA:0000119 NCIT:C12415 OpenCyc:Mx4rvVjlYpwpEbGdrcN5Y29ycA UMLS:C0022646 XAO:0003267 galen:Kidney reniculate kidney uberon UBERON:0002113 kidney kidney 肾 FMA definitional A paired organ of the urinary tract which has the production of urine as its primary function. One of either of a pair of structures lying on either side of the dorsal aorta in which fluid balance is regulated and waste is excreted out in the form of urine.[AAO] 2012-06-20 AAO:0000250 AAO AAO:BJB UMLS:C0022646 ncithesaurus:Kidney reniculate kidney An ovary that is part of a right side of organism [Automatically generated definition]. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EMAPA:37367 FMA:7213 MA:0001705 NCIT:C33487 UMLS:C0227873 uberon UBERON:0002118 right ovary An ovary that is part of a right side of organism [Automatically generated definition]. OBOL:automatic EMAPA:37367 MA:th UMLS:C0227873 ncithesaurus:Right_Ovary An ovary that is part of a left side of organism [Automatically generated definition]. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern In some elasmobranchs, the left ovary does not mature, with only the right ovary fully developing. In the primitive jawless fish, and some teleosts, there is only one ovary, formed by the fusion of the paired organs in the embryo EMAPA:37366 FMA:7214 MA:0001704 NCIT:C32969 UMLS:C0227874 uberon UBERON:0002119 left ovary An ovary that is part of a left side of organism [Automatically generated definition]. OBOL:automatic In some elasmobranchs, the left ovary does not mature, with only the right ovary fully developing. In the primitive jawless fish, and some teleosts, there is only one ovary, formed by the fusion of the paired organs in the embryo EMAPA:37366 MA:th UMLS:C0227874 ncithesaurus:Left_Ovary In mammals, the pronephros is the first of the three embryonic kidneys to be established and exists only transiently. In lower vertebrates such as fish and amphibia, the pronephros is the fully functional embryonic kidney and is indispensible for larval life[GO]. A kidney formed of nephric tubules arising in the anterior region of the nephric ridge; forms only as a transient embryonic structure. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.748][VHOG] Organ that serves as a transient kidney, providing osmoregulation during early developmental stages and then degenerating during metamorphosis.[AAO] The embryonic kidney, present at the level of the third somite, is composed of two glomeruli fused at the midline, two pronephric tubules, and paired bilateral pronephric ducts that modify the composition of the blood filtrate before delivering it to the cloaca for excretion.Kimmel et al, 1995.[TAO] In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros.[well established][VHOG] pronephric UBERON:0005794 AAO:0011089 BTO:0001541 EFO:0000927 EHDAA2:0001570 EHDAA:1017 EMAPA:16579 FMA:72170 MAT:0000117 MIAA:0000117 NCIT:C34280 TAO:0000151 UMLS:C0231048 VHOG:0000037 XAO:0002000 ZFA:0000151 pronephric kidney uberon archinephron embryonic kidney pronephron UBERON:0002120 Once the more complex mesonephros forms the pronephros undergoes apoptosis in amphibians. In fishes the nephron degenerates but the organ remains and becomes a component of the immune system[Wikipedia:Pronephros]. // TODO - check developmental relationships. Note that we previously include the ZFA/XAO terms under the more specific 'pronephric kidney', but these are now merged. TODO GCI: relationship: capable_of GO:0030104 pronephros GO OG ZFA In mammals, the pronephros is the first of the three embryonic kidneys to be established and exists only transiently. In lower vertebrates such as fish and amphibia, the pronephros is the fully functional embryonic kidney and is indispensible for larval life[GO]. GO:0048793 A kidney formed of nephric tubules arising in the anterior region of the nephric ridge; forms only as a transient embryonic structure. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.748][VHOG] 2012-09-17 VHOG:0000037 VHOG Organ that serves as a transient kidney, providing osmoregulation during early developmental stages and then degenerating during metamorphosis.[AAO] 2012-06-20 AAO:0011089 AAO XAO:curator The embryonic kidney, present at the level of the third somite, is composed of two glomeruli fused at the midline, two pronephric tubules, and paired bilateral pronephric ducts that modify the composition of the blood filtrate before delivering it to the cloaca for excretion.Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000151 TAO ZFIN:curator In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros.[well established][VHOG] 2012-09-17 VHOG:0000037 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.637 UMLS:C0231048 ncithesaurus:Pronephros pronephric kidney XAO:0002000 archinephron BTO:0001541 embryonic kidney BTO:0001541 pronephron BTO:0001541 A a collection of brainstem nuclei that functions in multiple aspects of hearing and is an important component of the ascending and descending auditory pathways of the auditory system. In mice, the superior olivary nucleus is a small cylindrical mass on the dorsal surface of the lateral part of the trapezoid body of the pons, and it is situated immediately above the inferior olivary nucleus. It receives projections from the cochlear nucleus and thus is involved in the perception of sound[GO:0021718] The SOC displays a significant interspecies variation, being largest in bats and rodents and smaller in primates. BAMS:SOC DHBA:12462 EMAPA:35840 EV:0100263 FMA:72247 HBA:9177 MA:0001026 MBA:398 UMLS:C0175427 VHOG:0001381 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=569 nucleus olivaris superior superior olivary nuclei uberon regio olivaris superioris superior olivary nucleus superior olivary nucleus (Barr & Kiernan) superior olive UBERON:0002128 superior olivary complex NIFSTD A a collection of brainstem nuclei that functions in multiple aspects of hearing and is an important component of the ascending and descending auditory pathways of the auditory system. ISBN:0-19-502694-2 UMLS:C0175427 NIFSTD:birnlex_1307 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=569 NIFSTD:birnlex_1307 nucleus olivaris superior FMA:72247 FMA:TA superior olivary nuclei FMA:72247 regio olivaris superioris NeuroNames:569 superior olivary nucleus FMA:72247 superior olivary nucleus (Barr & Kiernan) NeuroNames:569 superior olive FMA:72247 ISBN:0-19-502694-2 The locus ceruleus is a dense cluster of neurons within the dorsorostral pons. This nucleus is the major location of neurons that release norepinephrine throughout the brain, and is responsible for physiological responses to stress and panic[GO]. Bluish region in the superior angle of the fourth ventricle floor, corresponding to melanin-like pigmented nerve cells which lie lateral to the ponto-mesencephalic central gray (griseum centrale). It is also known as nucleus pigmentosus pontis[GAID]. TODO - check ZFA/pons. also GO says part of dorsorostral pons BAMS:CAE BAMS:LC BM:Pons-LC BTO:0001408 DHBA:12819 DMBA:16972 EFO:0001963 EMAPA:35502 FMA:72478 GAID:577 HBA:9148 MA:0001017 MBA:147 MESH:D008125 NCIT:C97333 TAO:0000539 UMLS:C0023951 ZFA:0000539 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=583 blue nucleus caerulean nucleus locus caeruleus locus coeruleu locus coeruleus nucleus caeruleus nucleus of locus caeruleus nucleus pigmentosus pontis substantia ferruginea uberon loci coeruleus locus cinereus locus coeruleus (Vicq d'Azyr) nucleus loci caerulei UBERON:0002148 locus ceruleus check ZFA NIFSTD The locus ceruleus is a dense cluster of neurons within the dorsorostral pons. This nucleus is the major location of neurons that release norepinephrine throughout the brain, and is responsible for physiological responses to stress and panic[GO]. Bluish region in the superior angle of the fourth ventricle floor, corresponding to melanin-like pigmented nerve cells which lie lateral to the ponto-mesencephalic central gray (griseum centrale). It is also known as nucleus pigmentosus pontis[GAID]. GAID:577 GO:0021703 UMLS:C0023951 NIFSTD:birnlex_905 UMLS:C0023951 ncithesaurus:Locus_Coeruleus http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=583 NIFSTD:birnlex_905 blue nucleus NIFSTD:birnlex_905 locus caeruleus NIFSTD:birnlex_905 nucleus caeruleus FMA:72478 FMA:TA nucleus pigmentosus pontis NIFSTD:birnlex_905 substantia ferruginea NIFSTD:birnlex_905 loci coeruleus ZFA:0000539 locus cinereus BTO:0001408 locus coeruleus (Vicq d'Azyr) NeuroNames:583 nucleus loci caerulei NeuroNames:583 Nucleus containing parasympathetic neurons giving rise to the parasympathetic division of the facial nerve, innervating the salivary glands (Brodal, Neurological Anatomy, 3rd ed., 1981, pg 703). BAMS:SSN BAMS:SuS DHBA:12435 EHDAA2:0004646 EMAPA:37756 FMA:72482 HBA:9194 MA:0001027 MBA:462 UMLS:C0175447 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=590 superior salivary nucleus uberon nucleus salivarius superior nucleus salivatorius cranialis nucleus salivatorius rostralis nucleus salivatorius superior UBERON:0002149 superior salivatory nucleus definitional Nucleus containing parasympathetic neurons giving rise to the parasympathetic division of the facial nerve, innervating the salivary glands (Brodal, Neurological Anatomy, 3rd ed., 1981, pg 703). NIFSTD:birnlex_1131 EMAPA:37756 MA:th UMLS:C0175447 NIFSTD:birnlex_1131 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=590 NIFSTD:birnlex_1131 superior salivary nucleus GO:0021753 nucleus salivarius superior NeuroNames:590 nucleus salivatorius cranialis NeuroNames:590 nucleus salivatorius rostralis NeuroNames:590 nucleus salivatorius superior NeuroNames:590 The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers[GO]. Layer that lines the lumen of the heart.[TAO] Part of the heart comprised of thin serous membrane, composed of endothelial tissue, that lines the interior of the heart.[AAO] Tunica intima which has as its parts the endothelium of endocardium and the fibroelastic connective tissue that surrounds the cavity of a cardiac chamber. UBERON:0006225 AAO:0010408 BTO:0000387 CALOHA:TS-2075 EFO:0000821 EHDAA2:0004153 EMAPA:17868 EMAPA:32686 EV:0100021 FMA:7280 GAID:550 MA:0000076 MAT:0000455 MESH:D004699 NCIT:C13004 OpenCyc:Mx4rsWA75K1cEduAAADggVaqvw TAO:0001320 UMLS:C0014124 VHOG:0000084 XAO:0000066 ZFA:0001320 galen:Endocardium endocardial lining endocardial tissue heart endocardium uberon heart endocardial tissue UBERON:0002165 fixed in GO to reflect FMA. See email to David/Varsha June 18 2010 endocardium Bgee:AN The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers[GO]. GO:0003157 Layer that lines the lumen of the heart.[TAO] 2012-08-14 TAO:0001320 TAO ZFIN:curator Part of the heart comprised of thin serous membrane, composed of endothelial tissue, that lines the interior of the heart.[AAO] 2012-06-20 AAO:0010408 AAO AAO:BJB Tunica intima which has as its parts the endothelium of endocardium and the fibroelastic connective tissue that surrounds the cavity of a cardiac chamber. FMA:7280 UMLS:C0014124 ncithesaurus:Endocardium endocardial lining EMAPA:32686 endocardial tissue EMAPA:17868 heart endocardial tissue VHOG:0000084 Lung which consists of the right upper lobe, middle lobe and right lower lobe.[FMA] Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG] https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EHDAA2:0001730 EHDAA:4969 EMAPA:17661 FMA:7309 MA:0000426 NCIT:C33483 OpenCyc:Mx8Ngh4rvgHsHZwpEbGdrcN5Y29ycB4rvVjKy5wpEbGdrcN5Y29ycA UMLS:C0225706 VHOG:0000301 uberon UBERON:0002167 right lung Lung which consists of the right upper lobe, middle lobe and right lower lobe.[FMA] FMA:FMA Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG] 2012-09-17 VHOG:0000301 VHOG ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.210 UMLS:C0225706 ncithesaurus:Right_Lung Lung which consists of the left upper lobe and left lower lobe.[FMA] Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG] https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EHDAA2:0000943 EHDAA:4947 EMAPA:17653 FMA:7310 MA:0000425 NCIT:C32967 OpenCyc:Mx8Ngh4rvgIFoJwpEbGdrcN5Y29ycB4rvVjKy5wpEbGdrcN5Y29ycA UMLS:C0225730 VHOG:0000618 uberon UBERON:0002168 left lung Lung which consists of the left upper lobe and left lower lobe.[FMA] FMA:FMA Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG] 2012-09-17 VHOG:0000618 VHOG ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.210 UMLS:C0225730 ncithesaurus:Left_Lung the upper conducting airways of the lung; these airways arise from the terminus of the trachea Each of the two primary divisions of the trachea leading respectively into the right and the left lung. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] bronchial In humans, the main bronchus is histologically identical to trachea; 2ary and 3ary bronchi are not; epithelium becomes simple columnar, goblet cell number decreases, elastic fibers in lamina propria increases, distribution more uniform. Muscular layer between mucosa and submucosa appears. cartilage rings become discontinuous plates connected by fibrous connective tissue BTO:0001340 CALOHA:TS-1229 EFO:0000932 EMAPA:32689 EV:0100041 FMA:7409 GAID:346 MA:0000436 MAT:0000133 MESH:D001980 MIAA:0000133 NCIT:C12683 UMLS:C0006255 VHOG:0000262 XAO:0000121 bronchi bronchial trunk uberon bronchial tissue UBERON:0002185 bronchus the upper conducting airways of the lung; these airways arise from the terminus of the trachea ISBN:0-397-51047-0 MESH:A04.411.125 MGI:cwg MP:0002264 Each of the two primary divisions of the trachea leading respectively into the right and the left lung. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000262 VHOG UMLS:C0006255 ncithesaurus:Bronchus bronchi bronchial trunk FMA:7409 bronchial tissue BTO:0001340 A portion of adipose tissue that is part of the hypodermis, beneath the dermis. the superficial portion of the subcutaneous tissue which is specialized for fat storage[MP:0011156] UBERON:0008875 panniculus adiposus BTO:0004042 EMAPA:35829 FMA:74315 MA:0000473 fatty layer of subcutaneous tissue hypodermis fat layer panniculus adiposus (tela subcutanea) panniculus adiposus telae subcutaneae subcutaneous fat layer uberon fatty layer of superficial fascia subcutaneous fat UBERON:0002190 subcutaneous adipose tissue A portion of adipose tissue that is part of the hypodermis, beneath the dermis. the superficial portion of the subcutaneous tissue which is specialized for fat storage[MP:0011156] MP:0011156 panniculus adiposus MP:0011156 fatty layer of subcutaneous tissue FMA:74315 hypodermis fat layer MP:0011156 panniculus adiposus (tela subcutanea) FMA:74315 FMA:TA panniculus adiposus telae subcutaneae FMA:74315 FMA:TA subcutaneous fat layer MP:0011156 fatty layer of superficial fascia FMA:74315 subcutaneous fat BTO:0004042 Anatomical cluster consisting of the hematopoietic system and the lymphoid system, or its analogs. CALOHA:TS-2018 EHDAA2:0004615 EMAPA:18765 FMA:74562 MA:0000013 hematolymphoid system lymphomyeloid complex uberon haemolymphoid system UBERON:0002193 hemolymphoid system MA Anatomical cluster consisting of the hematopoietic system and the lymphoid system, or its analogs. The dermis, epidermis and hypodermis. in FMA intergument = skin+superficial fascia(hypodermis), skin=dermis+epidermis+hair_nail. Note that the definition provided here excludes the more general sense of the term 'integument' used in invertebrates; consider 'integumental system'. Note that the VSAO class appears to include adnexa by its definition. Anatomical system that protects the body from damage, comprising the skin and its appendages.[AAO] Surface structure that is the outer protective covering of the body.[VSAO] The outer protective barrier that separates the animal from its aquatic environment. Le Guellec et al, 2004.[TAO] integumental integumentary AAO:0000239 BTO:0000634 EMAPA:37504 FMA:74657 TAO:0000368 VSAO:0000029 ZFA:0000368 galen:Integument dermis plus epidermis plus hypodermis integumentum commune skin and subcutaneous tissue skin plus hypodermis the integument uberon Hautsystem@de dermal system dermoid system skin tegument vertebrate integument UBERON:0002199 integument FMA FMA The dermis, epidermis and hypodermis. Anatomical system that protects the body from damage, comprising the skin and its appendages.[AAO] 2012-06-20 AAO:0000239 AAO AAO:EJS Surface structure that is the outer protective covering of the body.[VSAO] 2012-08-14 VSAO:0000029 VSAO PSPUB:0000170 The outer protective barrier that separates the animal from its aquatic environment. Le Guellec et al, 2004.[TAO] 2012-08-14 TAO:0000368 TAO ZFIN:curator EMAPA:37504 MA:th integumentum commune FMA:74657 FMA:TA the integument FMA:74657 Hautsystem@de BTO:0000634 dermal system BTO:0000634 dermoid system BTO:0000634 tegument BTO:0000634 Vasculature that is part of a head [Automatically generated definition]. EFO:0003656 FMA:74710 TAO:0001267 XAO:0004152 ZFA:0001267 adult head vascular network adult head vasculature cranial vasculature head vascular network vascular network of adult head vascular network of head vasculature of adult head uberon head vasculature UBERON:0002200 vasculature of head Vasculature that is part of a head [Automatically generated definition]. OBOL:automatic adult head vascular network OBOL:automatic adult head vasculature OBOL:automatic head vascular network OBOL:automatic vascular network of adult head OBOL:automatic vascular network of head OBOL:automatic vasculature of adult head OBOL:automatic A vasculature that is part of a trunk [Automatically generated definition]. FMA:74712 TAO:0005024 ZFA:0005024 torso vascular network torso vasculature trunk vascular network trunk vasculature vascular network of torso vascular network of trunk vasculature of torso uberon UBERON:0002201 vasculature of trunk A vasculature that is part of a trunk [Automatically generated definition]. OBOL:automatic torso vascular network OBOL:automatic torso vasculature OBOL:automatic trunk vascular network OBOL:automatic vascular network of torso OBOL:automatic vascular network of trunk OBOL:automatic vasculature of torso OBOL:automatic A submucosa that is part of a trachea. BTO:0002115 EMAPA:35879 FMA:7472 MA:0001860 NCIT:C49307 UMLS:C0225586 submucosa of windpipe trachea submucosa tracheal submucosa windpipe submucosa uberon submucous layer of trachea UBERON:0002202 submucosa of trachea A submucosa that is part of a trachea. OBOL:automatic UMLS:C0225586 ncithesaurus:Trachea_Submucosa submucosa of windpipe OBOL:automatic windpipe submucosa OBOL:automatic submucous layer of trachea BTO:0002115 Vasculature that is part of the eye region. not part of the eye in ZFA. Note this changed to a blood vessel in ZFA FMA:74743 TAO:0007057 ZFA:0007057 eye vascular network ocular blood vessel ocular vasculature vascular network of eye uberon eye vasculature optic vasculature UBERON:0002203 vasculature of eye ISBN:0781772214 Vasculature that is part of the eye region. OBOL:automatic not part of the eye in ZFA. Note this changed to a blood vessel in ZFA ZFA eye vascular network OBOL:automatic ocular blood vessel ZFA:0007057 vascular network of eye OBOL:automatic Anatomical system that consists of the muscular and skeletal systems. Anatomical system that provides locomotion and physical support to the organism.[AAO] There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG] musculoskeletal AAO:0010546 CALOHA:TS-1311 EMAPA:32714 EV:0100139 FMA:7482 GAID:98 MA:0002418 MESH:D009141 NCIT:C12754 OpenCyc:Mx4rQRpVNgAKEdyHxgDggVfs8g UMLS:C0026860 VHOG:0001275 VSAO:0000031 XAO:0000168 musculo-skeletal system uberon UBERON:0002204 musculoskeletal system check ctenophore Anatomical system that consists of the muscular and skeletal systems. VSAO:0000031 VSAO:curator Anatomical system that provides locomotion and physical support to the organism.[AAO] 2012-06-20 AAO:0010546 AAO AAO:EJS There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG] 2012-09-17 VHOG:0001275 VHOG DOI:10.1002/jez.b.21246 Shearman RM, Burke AC, The lateral somitic frontier in ontogeny and phylogeny. Journal of Experimental Zoology (2009) UMLS:C0026860 ncithesaurus:Musculoskeletal_System Nonsynovial joint in which the articulating bones or cartilages are connected by cartilage. Examples: Spheno-occipital synchondrosis, first sternocostal joint, pubic symphysis.[FMA] EMAPA:36581 FMA:7496 MA:0000320 TAO:0005155 ZFA:0005155 articulatio cartilaginea uberon junctura cartilaginea UBERON:0002213 cartilaginous joint FMA Nonsynovial joint in which the articulating bones or cartilages are connected by cartilage. Examples: Spheno-occipital synchondrosis, first sternocostal joint, pubic symphysis.[FMA] FMA:FMA junctura cartilaginea Joint in which the articulating bones or cartilages are connected by an articular capsule which encloses a synovial membrane and a synovial cavity. Examples: Temporomandibular joint, knee joint.[FMA] Is a joint that is located at the point of contact of articulating bones allowing movement. The joint has a capsule containing synovial fluid surrounding the articulating bone surfaces.[TAO] AEO:0000183 CALOHA:TS-2138 EHDAA2:0003183 FMA:7501 MA:0000322 NCIT:C32461 OpenCyc:Mx4rv2bBV5wpEbGdrcN5Y29ycA TAO:0005153 ZFA:0005153 galen:SynovialJoint articulatio synoviale diarthroses diarthrosis diarthrosis joint uberon diarthrodial joints UBERON:0002217 synovial joint Joint in which the articulating bones or cartilages are connected by an articular capsule which encloses a synovial membrane and a synovial cavity. Examples: Temporomandibular joint, knee joint.[FMA] FMA:7501 Is a joint that is located at the point of contact of articulating bones allowing movement. The joint has a capsule containing synovial fluid surrounding the articulating bone surfaces.[TAO] 2012-08-14 TAO:0005153 TAO ZFIN:Curator diarthroses ZFA:0005153 diarthrodial joints ZFA:0005153 The part of the coelemic cavity lumen that is enclosed by the walls of the thorax. In many species, the diaphragm separates thoracic and abdominal cavities EMAPA:36497 FMA:7565 GAID:93 MA:0000032 MESH:A01.911.800 NCIT:C12905 OpenCyc:Mx4rmvyleLfEEduAAAACs6hRXg OpenCyc:Mx4rvhU_TpwpEbGdrcN5Y29ycA UMLS:C0230139 cavitas thoracis cavity of chest cavity of thorax chest cavity pectoral cavity space of thoracic compartment thoracic lumen uberon UBERON:0002224 thoracic cavity The part of the coelemic cavity lumen that is enclosed by the walls of the thorax. UBERON:cjm UMLS:C0230139 ncithesaurus:Thoracic_Cavity cavitas thoracis space of thoracic compartment FMA:7565 Part of the central nervous system located in the vertebral canal continuous with and caudal to the brain; demarcated from brain by plane of foramen magnum. It is composed of an inner core of gray matter in which nerve cells predominate, and an outer layer of white matter in which myelinated nerve fibers predominate, and surrounds the central canal. (CUMBO) TODO - add superclass to unify with VNC? Part of the central nervous system which descends from the hindbrain within the vertebral column.[AAO] (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG] AAO:0010151 BAMS:SP BAMS:Spinal BM:SpC BTO:0001279 CALOHA:TS-0953 DHBA:12890 DMBA:17651 EFO:0000110 EHDAA2:0001255 EHDAA:2863 EMAPA:17577 EV:0100316 FMA:7647 GAID:695 MA:0000216 MAT:0000183 MESH:D013116 MIAA:0000183 NCIT:C12464 OpenCyc:Mx4rvVjjk5wpEbGdrcN5Y29ycA TAO:0000075 UMLS:C0037925 VHOG:0000601 XAO:0000020 ZFA:0000075 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=22 uberon SpC cerebro-cerebellar fissure cerebrocerebellar fissure fissura cerebro-cerebellaris fissura cerebrocerebellaris medulla spinalis spinal cord structure spinal medulla UBERON:0002240 spinal cord definitional definitional Part of the central nervous system located in the vertebral canal continuous with and caudal to the brain; demarcated from brain by plane of foramen magnum. It is composed of an inner core of gray matter in which nerve cells predominate, and an outer layer of white matter in which myelinated nerve fibers predominate, and surrounds the central canal. (CUMBO) NIFSTD:birnlex_1709 Part of the central nervous system which descends from the hindbrain within the vertebral column.[AAO] 2012-06-20 AAO:0010151 AAO AAO:BJB (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000601 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 UMLS:C0037925 NIFSTD:birnlex_1709 UMLS:C0037925 ncithesaurus:Spinal_Cord http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=22 NIFSTD:birnlex_1709 SpC cerebro-cerebellar fissure NeuroNames:22 cerebrocerebellar fissure NeuroNames:22 fissura cerebro-cerebellaris NeuroNames:22 fissura cerebrocerebellaris NeuroNames:22 medulla spinalis medulla spinalis BTO:0001279 spinal cord structure ZFA:0000075 spinal medulla BTO:0001279 Endoskeletal elements that encase the brain, nose, inner ear[cjm]. that part of the neurocranium formed by endochondral ossification and comprising the bones of the base of the skull[TFD]. we follow the standard evolutionary classification and treat this as endoskeletal. This means what MA calls 'chondrocranium' must in fact be neurocranium, as it includes parts of the dermatocranium (e.g. frontal, parietal) Anatomical cluster that is part of the cranium and composed of cartilage and cartilage replacement bones.[AAO] Anatomical cluster that is part of the cranium and composed of cartilage and cartilage replacement bones.[TAO] chondrocranial covers the brain dorsally in chondrichthyans AAO:0010169 EHDAA2:0000243 EMAPA:17681 TAO:0001424 VHOG:0000288 ZFA:0001424 uberon calvarium neurocranium UBERON:0002241 chondrocranium Endoskeletal elements that encase the brain, nose, inner ear[cjm]. that part of the neurocranium formed by endochondral ossification and comprising the bones of the base of the skull[TFD]. Anatomical cluster that is part of the cranium and composed of cartilage and cartilage replacement bones.[AAO] 2012-06-20 AAO:0010169 AAO AAO:BJB Anatomical cluster that is part of the cranium and composed of cartilage and cartilage replacement bones.[TAO] 2012-08-14 TAO:0001424 TAO ZFIN:curator calvarium MA:0000317 neurocranium MA:0000317 An organ that houses olfactory neurons and is responsible for the sense of smell. Examples include the vertebrate nose and the Drosophila dorsal organ. An olfactory organ overlaps with the olfactory system, because some parts of the nose (e.g. nasal skeleton) are parts of the skeletal system, which is spatially disjoint fma general anatomical term. xao has no subtypes (but Johnstons organ develops from this). An olfactory organ overlaps with the olfactory system, because some parts of the nose (e.g. nasal skeleton) are parts of the skeletal system, which is spatially disjoint AAO:0010180 BTO:0001772 FBbt:00005158 FMA:77659 VHOG:0000287 XAO:0000273 olfactory organ olfactory sense organ olfactory sensory organ main olfactory organ primary olfactory organ uberon olfactory neuroepithelium organ olfactus organum olfactorium UBERON:0002268 olfactory organ An organ that houses olfactory neurons and is responsible for the sense of smell. Examples include the vertebrate nose and the Drosophila dorsal organ. UBERON:cjm olfactory organ BTO:0001772 olfactory sensory organ FBbt:00005158 olfactory neuroepithelium BTO:0001772 organ olfactus BTO:0001772 organum olfactorium BTO:0001772 A composite substructure of the brainstem that consists of the midbrain reticular formation, the pontine reticular formation and the medullary reticular formation ( Carpenter-1983 ). this class denotes the generic structure, and not a specific one such as medullary or pontine reticular formation. It is essential for governing some of the basic functions of higher organisms, and is one of the phylogenetically oldest portions of the brain. FMA has a spinal cord reticular formation but we follow NNs (classical) to restrict this to brainstem structures. This means we also include the MA class for brainstem reticular formation here. FMA has subtypes of reticular formation but we treat this as a composite structure BAMS:RET EMAPA:35188 FMA:77719 MA:0003185 MESH:D012154 brain stem reticular formation brainstem reticular formation reticular formation (classical) reticular formation of the brainstem uberon UBERON:0002275 reticular formation A composite substructure of the brainstem that consists of the midbrain reticular formation, the pontine reticular formation and the medullary reticular formation ( Carpenter-1983 ). NeuroNames:1223 FMA has a spinal cord reticular formation but we follow NNs (classical) to restrict this to brainstem structures. This means we also include the MA class for brainstem reticular formation here. FMA has subtypes of reticular formation but we treat this as a composite structure FMA brain stem reticular formation NeuroNames:1223 brainstem reticular formation MA:0003185 brainstem reticular formation NeuroNames:1223 reticular formation (classical) NeuroNames:1223 reticular formation of the brainstem NeuroNames:1223 Stalk-like part of the brain that includes amongst its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,MP,generalized]. Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain.[TAO] Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,adopted][ZFA:0001707]. the stalk-like part of the brain that comprises the midbrain (aka mesencephalon), the pons (aka pons Varolii), and the medulla oblongata, and connects the cerebral hemispheres with the cervical spinal cord[MP] BAMS:BS BTO:0000146 CALOHA:TS-0093 EFO:0001962 EMAPA:32678 EV:0100241 FMA:79876 MA:0000169 MBA:343 MESH:D001933 NCIT:C12441 TAO:0002156 UMLS:C0006121 VHOG:0001457 ZFA:0001707 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=236 brain stem truncus encephali uberon accessory medullary lamina of pallidum lamella pallidi incompleta lamina medullaris accessoria lamina medullaris incompleta pallidi lamina pallidi incompleta truncus encephalicus UBERON:0002298 'brainstem' is a loose term that sometimes refers to the ventral parts o the brain except for any part of the telencephalon - sometimes it includes the diencephalon or subpallial telencephalon structures (ISBN10:0471888893). Here we use it in a more restriced sense, to include only the medulla oblongata, pons (when present) and the midbrain tegmentum (following the ZFA definitions). brainstem Stalk-like part of the brain that includes amongst its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,MP,generalized]. ISBN10:0471888893 MP:0005277 ZFA:0001707 Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain.[TAO] 2012-08-14 TAO:0002156 TAO ISBN:3764351209 Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,adopted][ZFA:0001707]. ZFA:0001707 the stalk-like part of the brain that comprises the midbrain (aka mesencephalon), the pons (aka pons Varolii), and the medulla oblongata, and connects the cerebral hemispheres with the cervical spinal cord[MP] MP:0005277 UMLS:C0006121 NIFSTD:birnlex_1565 UMLS:C0006121 ncithesaurus:Brain_Stem http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=236 NIFSTD:birnlex_1565 brain stem ABA:BS truncus encephali accessory medullary lamina of pallidum NeuroNames:236 lamella pallidi incompleta NeuroNames:236 lamina medullaris accessoria NeuroNames:236 lamina medullaris incompleta pallidi NeuroNames:236 lamina pallidi incompleta NeuroNames:236 truncus encephalicus BTO:0000146 A neural nucleus that is part of the brain. EMAPA:35185 FMA:83840 MA:0000811 NCIT:C49346 UMLS:C1706993 ZFA:0005575 brain nucleus uberon brain nuclei UBERON:0002308 nucleus of brain A neural nucleus that is part of the brain. UMLS:C1706993 ncithesaurus:Brain_Nucleus brain nuclei ZFA:0005575 The ridge-shaped grey matter of the spinal cord that extends longitudunally through the center of each half of the spinal cord, and are largely or entirely composed of nerve cell bodies and their dendrites and some supportive tissue. BAMS:Scgrey DHBA:146035048 EMAPA:35792 FMA:256580 MA:0000002 NCIT:C32696 UMLS:C0475853 gray matter of spinal cord gray substance of spinal cord grey matter of spinal cord grey substance of spinal cord spinal cord gray matter spinal cord grey matter spinal cord grey substance substantia grisea medullae spinalis uberon UBERON:0002315 gray matter of spinal cord The ridge-shaped grey matter of the spinal cord that extends longitudunally through the center of each half of the spinal cord, and are largely or entirely composed of nerve cell bodies and their dendrites and some supportive tissue. MP:0008503 UMLS:C0475853 ncithesaurus:Gray_Matter_of_the_Spinal_Cord gray matter of spinal cord OBOL:automatic gray substance of spinal cord FMA:256580 spinal cord gray matter OBOL:automatic spinal cord grey substance OBOL:automatic substantia grisea medullae spinalis FMA:256580 FMA:TA The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities. check the FMA placement here; ncit placement of body cavity here probably not correct Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA]. The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO]. In mammals it forms the peritoneal, pleural, and pericardial cavities UBERON:0000169 body cavity AEO:0000186 BTO:0001707 EHDAA2:0000267 FBbt:00005060 FMA:85006 NCIT:C25444 RETIRED_EHDAA2:0003186 TAO:0001438 UMLS:C0333343 ZFA:0001438 galen:BodyCavity coelomic cavity coelomic cavity lumen main body cavity space of body compartment ventral body cavity uberon celom coelom coelome hemocoel UBERON:0002323 coelemic cavity lumen definitional The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities. BTO:0001707 Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA]. 2012-09-12 ZFA:0001438 ZFA ZFIN:curator The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO]. 2012-09-12 BTO:0001707 BTO BTO body cavity BTO:0001707 UMLS:C0333343 ncithesaurus:Cavity coelomic cavity EHDAA2:0000267 coelomic cavity lumen EHDAA2:0000267 space of body compartment FMA:85006 ventral body cavity NCBITaxon:7742 celom BTO:0001707 coelome BTO:0001707 hemocoel FBbt:00005060 Any muscle organ that is part of a back [Automatically generated definition]. EMAPA:35161 FMA:85216 MA:0000496 back muscle back muscle organ muscle organ of back uberon UBERON:0002324 muscle of back prolog Any muscle organ that is part of a back [Automatically generated definition]. OBOL:automatic back muscle organ OBOL:automatic muscle organ of back OBOL:automatic The urethra is a renal system organ that carries urine from the bladder to outside the body. The epithelium is the tubular, planar layer of cells through which the urine passes.. EMAPA:31518 FMA:85275 MA:0001686 NCIT:C49309 UMLS:C1710584 epithelial tissue of urethra urethra epithelial tissue urethra epithelium uberon urethral epithelium urethral plate urethral seam UBERON:0002325 epithelium of urethra GO The urethra is a renal system organ that carries urine from the bladder to outside the body. The epithelium is the tubular, planar layer of cells through which the urine passes.. GO:0061071 UMLS:C1710584 ncithesaurus:Urethra_Epithelium epithelial tissue of urethra OBOL:automatic urethra epithelial tissue OBOL:automatic urethral plate EMAPA:31518 urethral seam EMAPA:31518 A flexible rod-shaped body found in embryos of all chordates. It is composed of cells derived from the mesoderm and defines the primitive axis of the embryo. In some chordates, it persists throughout life as the main axial support of the body, while in most vertebrates it becomes the nucleus pulposus of the intervertebral disc. The notochord is found ventral to the neural tube. Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO] Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO] Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO] relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO] (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG] notochordal In between vertebra the notochord becomes the nucleus pulposus, under it degenerates, and at anterior end in some species its tissue merges with some of the cranial bones.. Some organisms retain a post-embryonic notochord. AAO:0000327 BTO:0001768 CALOHA:TS-0690 EHDAA2:0001277 EHDAA:1241 EHDAA:6021 EMAPA:16191 EV:0100002 FMA:85521 GAID:1311 MAT:0000281 MESH:A16.254.610 NCIT:C12463 TAO:0000135 UMLS:C0028439 VHOG:0000199 VSAO:0000032 XAO:0000055 ZFA:0000135 embryonic notocord notocord uberon notochorda UBERON:0002328 The notochord appears early in embryogeny and plays an important role in promoting or organizing the embryonic development of nearby structures. In most adult chordates the notochord disappears or becomes highly modified. In some non-vertebrate chordates and fishes the notochord persists as a laterally flexible but incompressible skeletal rod that prevents telescopic collapse of the body during swimming[TOLWEB] notochord VSAO ZFA EHDAA2 A flexible rod-shaped body found in embryos of all chordates. It is composed of cells derived from the mesoderm and defines the primitive axis of the embryo. In some chordates, it persists throughout life as the main axial support of the body, while in most vertebrates it becomes the nucleus pulposus of the intervertebral disc. The notochord is found ventral to the neural tube. ISBN:0815318960 Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO] 2012-08-14 VSAO:0000032 VSAO PSPUB:0000170 Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000135 TAO ZFIN:curator Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO] 2012-06-20 AAO:0000327 AAO AAO:LAP relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO] 2012-06-20 AAO:0000327 AAO (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG] 2012-09-17 VHOG:0000199 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 UMLS:C0028439 ncithesaurus:Notochord notocord ZFA:0000135 notochorda Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm. currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk Post-cranial axial segments which form sclerotome and dermomyotome.[AAO] Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO] relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO] relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO] relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO] (...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG] somitic mesodermal cluster AAO:0010569 AEO:0001015 BTO:0001558 EHDAA2:0003436 EHDAA:366 EHDAA:699 EMAPA:31169 FMA:85522 GAID:1306 MAT:0000068 MESH:A16.254.425.660.750 MIAA:0000068 NCIT:C34302 TAO:0000155 UMLS:C0376449 VHOG:0000191 XAO:0000058 ZFA:0000155 uberon epimere epimere mesoderm epithelial somite somites somitic mesoderm somitus UBERON:0002329 When the somite becomes segmented from the segmental plate, it is composed of an epithelial sac enclosing mesenchymal somitocoel cells. Thereafter the somite differentiates into two parts, the ventro-medial mesenchymal sclerotome and the dorso-lateral epithelial dermomyotome. This change in the epithelial somite depends on surrounding tissue [PMID:15906248] somite EHDAA2 ZFA Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm. Post-cranial axial segments which form sclerotome and dermomyotome.[AAO] 2012-06-20 AAO:0010569 AAO AAO:EJS Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000155 TAO ZFIN:curator relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO] 2012-08-14 TAO:0000155 TAO relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO] 2012-08-14 TAO:0000155 TAO relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO] 2012-06-20 AAO:0010569 AAO (...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000191 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.40, DOI:10.1093/icb/43.1.137 Balavoine G, Adoutte A, The segmented urbilateria: a testable scenario. Integrative and Comparative Biology (2003) mesodermal cluster GO:0001756 UMLS:C0376449 ncithesaurus:Somite epimere ISBN10:0073040584 epithelial somite somites somitus Anatomical system that consists of the glands and parts of glands that produce exocrine secretions and help to integrate and control bodily metabolic activity. Exocrine glands are glands that secrete their products (hormones) into ducts (duct glands). They are the counterparts to endocrine glands, which secrete their products (hormones) directly into the bloodstream (ductless glands) or release hormones (paracrines) that affect only target cells nearby the release site. [Wikipedia]. CALOHA:TS-2057 EHDAA2:0002225 EMAPA:35329 FMA:85539 MA:0002411 NCIT:C12957 UMLS:C1516995 WikipediaCategory:Exocrine_system exocrine glandular system uberon UBERON:0002330 exocrine system Anatomical system that consists of the glands and parts of glands that produce exocrine secretions and help to integrate and control bodily metabolic activity. Exocrine glands are glands that secrete their products (hormones) into ducts (duct glands). They are the counterparts to endocrine glands, which secrete their products (hormones) directly into the bloodstream (ductless glands) or release hormones (paracrines) that affect only target cells nearby the release site. [Wikipedia]. UMLS:C1516995 ncithesaurus:Exocrine_System exocrine glandular system EHDAA2:0002225 An arterial trunk which is continuous with the heart and branches into the pulmonary arteries. An arterial trunk with origin from the right ventricle of the heart, and dividing into the right and left pulmonary arteries, which enter the corresponding lungs and branch with the bronchi. [TFD][VHOG] As in birds, the conus arteriosus split during embryonic development in mammals to produce the pulmonary trunk and single aortic trunk of the adult.[well established][VHOG] EHDAA2:0001576 EHDAA:9831 EMAPA:17015 FMA:8612 MA:0002033 NCIT:C116918 OpenCyc:Mx4rv-6d0ZwpEbGdrcN5Y29ycA VHOG:0001134 galen:PulmonaryTrunk pulmonary artery (trunk) trunk of pulmonary arterial tree uberon main pulmonary artery UBERON:0002333 pulmonary trunk MA An arterial trunk which is continuous with the heart and branches into the pulmonary arteries. An arterial trunk with origin from the right ventricle of the heart, and dividing into the right and left pulmonary arteries, which enter the corresponding lungs and branch with the bronchi. [TFD][VHOG] 2012-09-17 VHOG:0001134 VHOG As in birds, the conus arteriosus split during embryonic development in mammals to produce the pulmonary trunk and single aortic trunk of the adult.[well established][VHOG] 2012-09-17 VHOG:0001134 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481 main pulmonary artery A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams). A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO] Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO] A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831] We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG] AAO:0010578 BTO:0001764 CALOHA:TS-0676 EHDAA2:0004419 EMAPA:32737 FMA:86666 GAID:1310 MAT:0000066 MESH:A16.254.600 MIAA:0000066 NCIT:C34222 TAO:0000045 UMLS:C0027789 VHOG:0000057 XAO:0000048 ZFA:0000045 NC uberon crista neuralis neural crest material UBERON:0002342 Gene notes: Many factors and genes, such as Pax3 (Tremblay et al., 1995), slug (Nieto et al., 1994), AP-2 (Zhang et al., 1996; Schorle et al., 1996), and Wnt-1/3a (Ikeya et al., 1997) are expressed in the dorsal most region of the neural tube, and have been shown to be involved in the generation of neural crest cells. neural crest XAO BTO A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. MP:0009846 ISBN10:0073040584 A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000045 TAO ZFIN:curator Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO] 2012-06-20 AAO:0010578 AAO AAO:EJS A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831] We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG] 2012-09-17 VHOG:0000057 VHOG DOI:10.1111/j.1469-7580.2012.01495.x Hall BK, Gillis JA, Incremental evolution of the neural crest, neural crest cells and neural crest-derived skeletal tissues. J Anat (2012) UMLS:C0027789 ncithesaurus:Neural_Crest NC XAO:0000048 crista neuralis neural crest material VHOG:0000057 Set of all muscles in abdomen. distinction between abdomen muscle and abdomen musculature FMA:71294 FMA:86917 TAO:0001327 ZFA:0001327 abdominal musculature muscle group of abdomen muscles of abdomen musculature of abdomen musculature of abdominal wall set of muscles of abdomen uberon UBERON:0002343 abdomen musculature Set of all muscles in abdomen. OBOL:automatic muscle group of abdomen FMA:71294 muscles of abdomen FMA:71294 musculature of abdominal wall FMA:86917 set of muscles of abdomen FMA:71294 Embryonic ectoderm that gives rise to nervous tissue. (...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG] neurectodermal we prefer neurectoderm to neural ectoderm since placodal ectoderm is not classified here AAO:0011074 BILA:0000039 CALOHA:TS-1212 EHDAA2:0001248 EHDAA:1498 EHDAA:255 EMAPA:16073 EV:0100004 FBbt:00001061 FMA:87657 MAT:0000176 MIAA:0000176 NCIT:C34228 TAO:0001120 UMLS:C1518271 VHOG:0000150 XAO:0000042 ZFA:0001120 neural ectoderm neuroectoderm uberon epithelium tubi neuralis; neuroectoderma neuaral ectoderm presumptive central nervous system ventral neurogenic region UBERON:0002346 neurectoderm Embryonic ectoderm that gives rise to nervous tissue. (...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG] 2012-09-17 VHOG:0000150 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) UMLS:C1518271 ncithesaurus:Neuroectoderm epithelium tubi neuralis; neuroectoderma ventral neurogenic region VHOG:0000150 the middle layer of the heart, comprised mainly of striated cardiac muscle fibers TODO - check 'Myocardum proper' in FMA. We superclass the more generic class for now. FMA has is_a muscle layer - should we add this? ZFA and BTO both have is_a 'cardiac muscle' (tissue?). But in U we also follow FMA and have cardiac muscle tissue of myocardium (there is also Fibrocollagenous connective tissue of myocardium), which would be identical (see issue-10). Note that GO also treats left/right ventricular cardiac muscle tissue synonymous with ventricular myocardium Robust muscular tunic of the heart which forms the basic part of its walls. Its external surface is covered by the pericardium and its internal one by the endocardium. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] The middle layer of the heart, consisting of cardiac muscle.[AAO] myocardial AAO:0010410 BSA:0000089 BTO:0000901 CALOHA:TS-0440 EFO:0000819 EHDAA2:0004150 EMAPA:32688 EV:0100022 FMA:9462 GAID:173 MA:0000164 MAT:0000453 MESH:D009206 NCIT:C12371 OpenCyc:Mx4ro36AFrCvEduAAAAOpmP6tw RETIRED_EHDAA2:0001220 TAO:0001319 UMLS:C0027061 VHOG:0000083 XAO:0000065 ZFA:0001319 galen:Myocardium heart myocardium muscle of heart uberon cardiac muscle heart muscle UBERON:0002349 myocardium the middle layer of the heart, comprised mainly of striated cardiac muscle fibers ISBN:0-683-40008-8 MP:0005329 Robust muscular tunic of the heart which forms the basic part of its walls. Its external surface is covered by the pericardium and its internal one by the endocardium. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000083 VHOG The middle layer of the heart, consisting of cardiac muscle.[AAO] 2012-06-20 AAO:0010410 AAO AAO:BJB UMLS:C0027061 ncithesaurus:Myocardium muscle of heart FMA:9462 cardiac muscle ZFA:0001319 heart muscle FMA:9462 heart muscle ZFA:0001319 The cardiac conduction system consists of specialized cardiomyocytes that regulate the frequency of heart beat[GO] EHDAA2 divides the system from the tissue The fish heart displays clear polarity of contraction in a posterior-to-anterior direction. The contraction waves originate in the sinus venosus and terminate in the conus arteriosus. The nodal phenotype persists in the inflow region of the heart, varying from the venosinus to the sinoatrial junctional areas in different species . Similar to the mammalian situation, pacemaker tissue with a lower intrinsic rhythmicity is also found at the atrioventricular junction.[uncertain][VHOG] EFO:0003909 EHDAA2:0004185 EMAPA:35428 EV:0100025 FMA:9476 MA:0000094 MESH:D006329 TAO:0005063 VHOG:0001271 ZFA:0005063 cardiac conducting system cardiac conduction system cardiac impulse conducting system cardionector complexus stimulans cordis heart conduction system impulse conducting system systema conducente cordis uberon central conduction system UBERON:0002350 conducting system of heart FMA The cardiac conduction system consists of specialized cardiomyocytes that regulate the frequency of heart beat[GO] GO:0003161 The fish heart displays clear polarity of contraction in a posterior-to-anterior direction. The contraction waves originate in the sinus venosus and terminate in the conus arteriosus. The nodal phenotype persists in the inflow region of the heart, varying from the venosinus to the sinoatrial junctional areas in different species . Similar to the mammalian situation, pacemaker tissue with a lower intrinsic rhythmicity is also found at the atrioventricular junction.[uncertain][VHOG] 2012-09-17 VHOG:0001271 VHOG DOI:10.1152/physrev.00006.2003 Moorman AFM, Christoffels VM, Cardiac Chamber Formation: Development, Genes, and Evolution. Physiological Reviews (2003) cardiac conducting system VHOG:0001271 cardiac impulse conducting system GO:0003161 complexus stimulans cordis FMA:9476 FMA:TA heart conduction system GO:0003161 impulse conducting system MA:0000094 systema conducente cordis FMA:9476 FMA:TA The lower segment of the trunk, inferioposterior to the abdomen proper, in the transition area between the trunk and the lower limbs. pelvic MA and FMA differ in what they consider to be parts of the pelvis. MA includes ureter, urethra, urinary bladder, reproductive organs BTO:0001006 CALOHA:TS-2227 EFO:0002805 EMAPA:35931 EV:0100012 FMA:9578 GAID:87 MA:0000030 MESH:A01.673 NCIT:C12767 OpenCyc:Mx4rvVjiTJwpEbGdrcN5Y29ycA UMLS:C0030797 galen:Pelvis lesser pelvis pelvic region pelvis pelvis region true pelvis uberon UBERON:0002355 pelvic region of trunk The lower segment of the trunk, inferioposterior to the abdomen proper, in the transition area between the trunk and the lower limbs. MA and FMA differ in what they consider to be parts of the pelvis. MA includes ureter, urethra, urinary bladder, reproductive organs MA UMLS:C0030797 ncithesaurus:Pelvis lesser pelvis FMA:9578 pelvis FMA:9578 MA:0000030 true pelvis FMA:9578 A gland that secretes products (excluding hormones and other chemical messengers) into ducts (duct glands) which lead directly into the external environment[WP]. Typical exocrine glands include sweat glands, salivary glands, mammary glands, stomach, liver, pancreas Currently this is logically defined by the system it belongs to, but a better system may be base this on presence/absence of ducts. However, the dual nature of the liver should be taken into consideration here. Consider adding subclasses AEO:0000097 BTO:0000765 CALOHA:TS-2012 EHDAA2:0003097 EMAPA:35327 FMA:9596 GAID:34 MA:0002564 MESH:D005088 NCIT:C12712 UMLS:C0015282 ducted gland glandula exocrina uberon UBERON:0002365 exocrine gland A gland that secretes products (excluding hormones and other chemical messengers) into ducts (duct glands) which lead directly into the external environment[WP]. Typical exocrine glands include sweat glands, salivary glands, mammary glands, stomach, liver, pancreas UMLS:C0015282 ncithesaurus:Exocrine_Gland ducted gland AEO:0000097 glandula exocrina Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified]. AEO:0000098 BTO:0001488 CALOHA:TS-1300 EHDAA2:0003098 EMAPA:35999 FMA:9602 GAID:335 MA:0002563 MESH:D004702 NCIT:C12704 OpenCyc:Mx4rvbkiRZwpEbGdrcN5Y29ycA UMLS:C0014133 ductless gland glandula endocrina uberon ductless gland glandulae endocrinae UBERON:0002368 endocrine gland Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified]. UMLS:C0014133 ncithesaurus:Endocrine_Gland ductless gland AEO:0000098 ductless gland glandulae endocrinae Any skeletal muscle that is part of the head region. UBERON:0003899 AAO:0000107 BTO:0000021 EFO:0003524 EHDAA2:0000322 EMAPA:18172 FMA:9616 MA:0000578 ZFA:0001652 cephalic muscle cephalic musculature head muscle head muscle organ muscle of head muscle organ of adult head muscle organ of head musculus caput adult head muscle organ uberon cranial muscle head muscles UBERON:0002376 defined generically so could in theory encompass FBbt:00003260 'skeletal muscle of head', or the muscle of a starfish Aristotle's lantern, but we restrict this to craniates. Skeletal muscles of the head originate from the non-segmented head mesoderm (Noden, 1983; Wachtler et al., 1984) cranial muscle EHDAA2-abduced Any skeletal muscle that is part of the head region. cephalic muscle ZFA:0001652 head muscle MA:0000578 head muscle organ OBOL:automatic muscle of head FMA:9616 muscle organ of adult head OBOL:automatic muscle organ of head OBOL:automatic adult head muscle organ OBOL:automatic cranial muscle ZFA:0001652 Any muscle that is part of the cervical (neck) region. EMAPA:36050 FMA:9617 GAID:149 MA:0000587 MESH:D009334 NCIT:C33163 UMLS:C0027532 muscle organ of neck muscle organ of neck (volume) neck (volume) muscle organ neck muscle neck muscle organ uberon UBERON:0002377 muscle of neck prolog Any muscle that is part of the cervical (neck) region. UMLS:C0027532 ncithesaurus:Neck_Muscle muscle organ of neck OBOL:automatic muscle organ of neck (volume) OBOL:automatic neck (volume) muscle organ OBOL:automatic neck muscle organ OBOL:automatic Muscle (organ) which is a part of the abdomen. Examples: external oblique, rectus abdominis. BTO:0001261 EMAPA:35103 FMA:9620 GAID:89 MA:0000520 MESH:D000009 NCIT:C32040 OpenCyc:Mx4rvlygNJwpEbGdrcN5Y29ycA UMLS:C0000739 abdomen muscle abdomen muscle organ abdominal muscle abdominal wall muscle muscle organ of abdomen uberon abdominal wall musculature UBERON:0002378 muscle of abdomen prolog Muscle (organ) which is a part of the abdomen. Examples: external oblique, rectus abdominis. UMLS:C0000739 ncithesaurus:Abdominal_Muscle abdomen muscle organ OBOL:automatic muscle organ of abdomen OBOL:automatic abdominal wall musculature EMAPA:35103 Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance. One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO] Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO] Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO] MA also has set of connective tissues AAO:0000098 BTO:0000421 CALOHA:TS-2009 EFO:0000952 EMAPA:35251 FMA:9640 GAID:100 MA:0000011 MAT:0000301 MESH:D003238 MIAA:0000301 NCIT:C12374 OpenCyc:Mx4rv-aBgZwpEbGdrcN5Y29ycA TAO:0001641 UMLS:C0009780 VSAO:0000017 XAO:0001017 ZFA:0001632 galen:ConnectiveTissue portion of connective tissue textus connectivus uberon Bindegewebe UBERON:0002384 connective tissue Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance. GO_REF:0000034 PSPUB:0000170 VSAO:0000017 One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO] 2012-06-20 AAO:0000098 AAO AAO:LAP Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO] 2012-08-14 TAO:0001641 TAO TAO:wd Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO] 2012-08-14 VSAO:0000017 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 PSPUB:0000170 MA also has set of connective tissues MA UMLS:C0009780 ncithesaurus:Connective_Tissue portion of connective tissue FMA:9640 Bindegewebe BTO:0000421 Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO]. One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO] AAO:0000306 AEO:0000122 CALOHA:TS-0642 EHDAA2:0003122 EMAPA:32715 FMA:9641 MA:0002437 MESH:D009132 NCIT:C12435 UMLS:C2328219 galen:MuscleTissue muscular tissue portion of muscle tissue textus muscularis uberon UBERON:0002385 Vertebrate muscle is categorized into three major muscle types defined by their structural and functional properties: skeletal, cardiac and smooth. In Dmel the counterparts are somatic, heart/cardiac and visceral. Here we take a cell type based approach. muscle tissue Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO]. GO:0060537 One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO] 2012-06-20 AAO:0000306 AAO AAO:LAP UMLS:C2328219 ncithesaurus:Muscle_Tissue muscular tissue portion of muscle tissue FMA:9641 Anatomical system that is involved in the production of hematopoietic cells. Anatomical system that consists of the blood and blood forming tissues.[AAO] Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG] hematopoietic In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes AAO:0011002 BTO:0000570 CALOHA:TS-0449 EFO:0000798 EMAPA:35402 EV:0100045 FMA:9667 GAID:1008 MA:0002434 MAT:0000022 MESH:D006413 MIAA:0000022 NCIT:C12909 TAO:0005023 UMLS:C0018957 VHOG:0001624 XAO:0000122 ZFA:0005023 haematological system haemopoietic system organa haemopoietica uberon Blutbildungssystem haematopoietic system hematological system hematolymphoid system hemopoietic system UBERON:0002390 hematopoietic system FMA definitional Anatomical system that is involved in the production of hematopoietic cells. Anatomical system that consists of the blood and blood forming tissues.[AAO] 2012-06-20 AAO:0011002 AAO AAO:EJS Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG] 2012-09-17 VHOG:0001624 VHOG DOI:10.1016/j.coph.2010.05.004 Ellett F, Lieschke GJ, Zebrafish as a model for vertebrate hematopoiesis. Current Opinion in Pharmacology (2010) In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes WP UMLS:C0018957 ncithesaurus:Hematopoietic_System Blutbildungssystem BTO:0000570 The autonomic nervous system is composed of neurons that are not under conscious control, and is comprised of two antagonistic components, the sympathetic and parasympathetic nervous systems. The autonomic nervous system regulates key functions including the activity of the cardiac (heart) muscle, smooth muscles (e.g. of the gut), and glands[GO]. Nervous system including a portion of the central and peripheral systems and presiding over the control and coordination of the vegetative functions of the organism. It innervates smooth and cardiac muscles and glandular tissues and is responsible for many actions which are more or less automatic (e.g. secretion, vasoconstriction etc.). It consists of the sympathetic and parasympathetic nervous systems. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] Part of the peripheral nervous system which regulates involuntary functions of the body and consists of the sympathetic and parasympathetic system.[AAO] From comparative analyses of craniate brains, a morphotype of the brain in the earliest craniate stock can be constructed. In marked contrast to cephalochordates, the ancestral craniate morphotype had a plethora of unique features, which included a telencephalon with pallial and subpallial parts, paired olfactory bulbs with substantial projections to most or all of the telencephalic pallium, paired lateral eyes and ears, a lateral line system for both electroreception and mechanoreception, spinal cord dorsal root ganglia, and an autonomic nervous system.[well established][VHOG] FMA splits this into peripheral and nervous parts; GO has ANS directly under NS; PNS is a sib AAO:0000033 BTO:0002507 CALOHA:TS-2001 EHDA:10095 EHDAA2:0000158 EHDAA:3767 EMAPA:16984 FMA:65553 GAID:706 MA:0000219 MESH:D001341 NCIT:C12673 TAO:0001574 UMLS:C0004388 UMLS:C1305381 VHOG:0000396 ZFA:0001574 autonomic division of peripheral nervous system autonomic part of peripheral nervous system divisio autonomica systematis nervosi peripherici pars autonomica systematis nervosi peripherici peripheral autonomic nervous system visceral nervous system uberon ANS divisio autonomica systematis nervosi peripherici UBERON:0002410 autonomic nervous system cjm EMAPA MA NIFSTD ZFA-modified-from-isa The autonomic nervous system is composed of neurons that are not under conscious control, and is comprised of two antagonistic components, the sympathetic and parasympathetic nervous systems. The autonomic nervous system regulates key functions including the activity of the cardiac (heart) muscle, smooth muscles (e.g. of the gut), and glands[GO]. GO:0048483 Nervous system including a portion of the central and peripheral systems and presiding over the control and coordination of the vegetative functions of the organism. It innervates smooth and cardiac muscles and glandular tissues and is responsible for many actions which are more or less automatic (e.g. secretion, vasoconstriction etc.). It consists of the sympathetic and parasympathetic nervous systems. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000396 VHOG Part of the peripheral nervous system which regulates involuntary functions of the body and consists of the sympathetic and parasympathetic system.[AAO] 2012-06-20 AAO:0000033 AAO AAO:BJB From comparative analyses of craniate brains, a morphotype of the brain in the earliest craniate stock can be constructed. In marked contrast to cephalochordates, the ancestral craniate morphotype had a plethora of unique features, which included a telencephalon with pallial and subpallial parts, paired olfactory bulbs with substantial projections to most or all of the telencephalic pallium, paired lateral eyes and ears, a lateral line system for both electroreception and mechanoreception, spinal cord dorsal root ganglia, and an autonomic nervous system.[well established][VHOG] 2012-09-17 VHOG:0000396 VHOG DOI:10.1002/1097-0185(20000615)261:3<111::AID-AR6>3.0.CO;2-F Butler AB, Chordate evolution and the origin of craniates: An old brain in a new head. AnaT Rec (New Anat) (2000) FMA splits this into peripheral and nervous parts; GO has ANS directly under NS; PNS is a sib FMA UMLS:C0004388 NIFSTD:birnlex_1123 UMLS:C0004388 ncithesaurus:Autonomic_Nervous_System UMLS:C1305381 NIFSTD:birnlex_1123 autonomic division of peripheral nervous system FMA:65553 autonomic part of peripheral nervous system FMA:65553 divisio autonomica systematis nervosi peripherici FMA:TA pars autonomica systematis nervosi peripherici FMA:TA peripheral autonomic nervous system FMA:65553 ANS divisio autonomica systematis nervosi peripherici Connected anatomical system that forms a barrier between an animal and its environment. In vertebrates, the integumental system consists of the epidermis, dermis plus associated glands and adnexa such as hair and scales. In invertebrates, the integumental system may include cuticle. (...) the integument of many tetrapods is reinforced by a morphologically and structurally diverse assemblage of skeletal elements. These elements are widely understood to be derivatives of the once all-encompassing dermal skeleton of stem-gnathostomes (...).[well established][VHOG] UBERON:0007029 AEO:0000154 BILA:0000118 CALOHA:TS-1299 CARO:0002001 EFO:0000807 EHDAA2:0000836 EHDAA2_RETIRED:0003154 EHDAA:6520 EMAPA:17524 EV:0100151 FBbt:00004969 FMA:72979 HAO:0000421 MA:0000014 MAT:0000033 MESH:D034582 MIAA:0000033 NCIT:C12907 TADS:0000108 UMLS:C0037267 VHOG:0000403 XAO:0000176 galen:Surface integumentary system uberon body surface dermal system external covering of organism integumentum commune organism surface surface UBERON:0002416 integumental system Connected anatomical system that forms a barrier between an animal and its environment. In vertebrates, the integumental system consists of the epidermis, dermis plus associated glands and adnexa such as hair and scales. In invertebrates, the integumental system may include cuticle. CARO:0002001 (...) the integument of many tetrapods is reinforced by a morphologically and structurally diverse assemblage of skeletal elements. These elements are widely understood to be derivatives of the once all-encompassing dermal skeleton of stem-gnathostomes (...).[well established][VHOG] 2012-09-17 VHOG:0000403 VHOG DOI:10.1111/j.1469-7580.2008.01043.x Vickaryous MK, Sire JY, The integumentary skeleton of tetrapods: origin, evolution, and development. J Anat (2009) UMLS:C0037267 ncithesaurus:Integumentary_System integumentary system FMA:72979 dermal system MIAA:0000033 integumentum commune organism surface EHDAA2:0003154 surface BILA:0000118 The abdominal segment of the torso. EMAPA:35104 FMA:259211 MA:0000021 uberon abdomen/pelvis/perineum lower body lower trunk lumbar region UBERON:0002417 abdominal segment of trunk FMA The abdominal segment of the torso. abdomen/pelvis/perineum MA:0000021 lower body MA:0000021 lower trunk FMA:259211 lumbar region Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts. A type of dense connective tissue. It is composed of cells called chondrocytes which are dispersed in a firm gel-like ground substance, called the matrix. Cartilage is avascular (contains no blood vessels) and nutrients are diffused through the matrix. Cartilage is found in the joints, the rib cage, the ear, the nose, in the throat and between intervertebral disks. It makes up virtually the entire skeleton in chondrichthyes.[AAO] Portion of tissue which is connective tissue composed of collagen and/or elastin fibers and chondrocytes. Cartilage is avascular and provides both skeletal functions and a framework upon which bone is deposited.[TAO] Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts.[VSAO] relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] Phylogenetic analysis suggests that cartilage arose independently in cnidarians, hemichordates, vertebrates, arthropods, annelids, brachiopods, and molluscs - or a common ancestor of brachiopods and molluscs (...). Analyses of cartilage as a tissue and of the development of invertebrate cartilages are consistent with homology between invertebrate and vertebrate cartilage. From the discussion above, it will be clear that understanding genetic changes underlying cartilage evolution is key to determining whether the multiple origins of cartilage represent parallel evolution.[well established][VHOG] AAO:0000060 AEO:0000087 BTO:0000206 EFO:0000949 EHDAA2:0003087 EMAPA:32730 EV:0100141 FMA:37377 GAID:99 MA:0000104 MAT:0000189 MESH:D002356 MIAA:0000189 NCIT:C12373 NCIT:C32268 OpenCyc:Mx4rvVjeOZwpEbGdrcN5Y29ycA TAO:0001501 UMLS:C0007301 VHOG:0001207 VSAO:0000040 XAO:0000170 ZFA:0005622 galen:Cartilage cartilage tissue cartilaginous tissue chondrogenic tissue uberon cartilage cartilages portion of cartilage tissue UBERON:0002418 Previous: "A portion of connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate[GO]. Regular connective tissue, which consists of chondrocytes and related cells, the intercellular matrix of which is chondrified. Examples: hyaline cartilage, fibrocartilage, elastic cartilage[FMA]. an avascular supporting and articular skeletal tissue. It also functions as the primary endoskeletal support in vertebrate embryos. Cartilage is deposited by and is composed of chondroblasts and chondrocytes separated by an extracellular matrix, which may or may not mineralize depending on cartilage type, age, or taxon[Hall and Witten]." See also FMA:71500 Set of cartilages, FMA:55107 Cartilage organ, FMA:12264 Articular cartilage. // elements made from cartilage, cartilage-like, or chondroid tissues evolved in invertebrates[H&W] cartilage tissue Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts. GO_REF:0000034 PSPUB:0000170 VSAO:0000040 A type of dense connective tissue. It is composed of cells called chondrocytes which are dispersed in a firm gel-like ground substance, called the matrix. Cartilage is avascular (contains no blood vessels) and nutrients are diffused through the matrix. Cartilage is found in the joints, the rib cage, the ear, the nose, in the throat and between intervertebral disks. It makes up virtually the entire skeleton in chondrichthyes.[AAO] 2012-06-20 AAO:0000060 AAO AAO:LAP Portion of tissue which is connective tissue composed of collagen and/or elastin fibers and chondrocytes. Cartilage is avascular and provides both skeletal functions and a framework upon which bone is deposited.[TAO] 2012-08-14 TAO:0001501 TAO ZFIN:curator Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts.[VSAO] 2012-08-14 VSAO:0000040 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 PSPUB:0000170 relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] 2012-06-20 AAO:0000060 AAO Phylogenetic analysis suggests that cartilage arose independently in cnidarians, hemichordates, vertebrates, arthropods, annelids, brachiopods, and molluscs - or a common ancestor of brachiopods and molluscs (...). Analyses of cartilage as a tissue and of the development of invertebrate cartilages are consistent with homology between invertebrate and vertebrate cartilage. From the discussion above, it will be clear that understanding genetic changes underlying cartilage evolution is key to determining whether the multiple origins of cartilage represent parallel evolution.[well established][VHOG] 2012-09-17 VHOG:0001207 VHOG DOI:10.1111/j.1525-142X.2011.00520.x Hall BK, Parallelism, deep homology, and evo-devo. Evolution and Development (2012) UMLS:C0007301 ncithesaurus:Cartilage cartilage tissue FMA:37377 chondrogenic tissue VSAO:0000040 cartilages VHOG:0001207 portion of cartilage tissue FMA:37377 A gland that is part of a skin of body [Automatically generated definition]. check FMA, use plural for now as general class not there EMAPA:35774 FMA:71878 MA:0000146 glandulae cutis uberon set of skin glands skin glands skin glands set UBERON:0002419 skin gland A gland that is part of a skin of body [Automatically generated definition]. OBOL:automatic glandulae cutis FMA:71878 FMA:TA set of skin glands FMA:71878 skin glands skin glands set An epithelium that is part of the mouth and lines the oral cavity, typically stratified squamous, and may be para-, ortho- or non- keratinized. Primary barrier between oral environment and deeper tissues consider including separate class for developmental structure (adult human is stratified; in EHDAA2 is unilaminar) The epithelium that lines the oral cavity. The oral epithelium epithelial cells with many short microvilli as well as mucous cells, rodlet cells and taste buds[ZFIN:ZDB-PUB-060921-12, ZFIN:ZDB-PUB-091204-24]. the avian oral epithelium has the developmental capacity to initiate tooth developmental programs with underlying grafts of non-avian oral ectomesenchyme AAO:0010357 BTO:0001775 CALOHA:TS-0715 EHDAA2:0001325 EHDAA:2187 EMAPA:16839 EMAPA:26942 FMA:265152 MA:0000344 NCIT:C49595 TAO:0000816 UMLS:C1709332 VHOG:0000187 XAO:0003201 ZFA:0000816 epithelium of mucosa of mouth epithelium of oral mucosa uberon UBERON:0002424 oral epithelium AAO-modified An epithelium that is part of the mouth and lines the oral cavity, typically stratified squamous, and may be para-, ortho- or non- keratinized. Primary barrier between oral environment and deeper tissues The epithelium that lines the oral cavity. The oral epithelium epithelial cells with many short microvilli as well as mucous cells, rodlet cells and taste buds[ZFIN:ZDB-PUB-060921-12, ZFIN:ZDB-PUB-091204-24]. ZFA:0000816 the avian oral epithelium has the developmental capacity to initiate tooth developmental programs with underlying grafts of non-avian oral ectomesenchyme UMLS:C1709332 ncithesaurus:Oral_Cavity_Epithelium epithelium of mucosa of mouth FMA:265152 epithelium of oral mucosa FMA:265152 A blood vessel that is part of a choroid [Automatically generated definition]. EMAPA:17828 FMA:76550 MA:0001237 blood vessel of choroid blood vessel of choroid coat blood vessel of choroidea blood vessel of posterior uvea choroid blood vessel choroid blood vessels choroid blood vessels set choroid coat blood vessel choroidea blood vessel posterior uvea blood vessel vasa sanguinea choroideae uberon set of choroid blood vessels UBERON:0002443 cannot find singular in FMA, using Set class choroidal blood vessel A blood vessel that is part of a choroid [Automatically generated definition]. OBOL:automatic blood vessel of choroid OBOL:automatic blood vessel of choroid coat OBOL:automatic blood vessel of choroidea OBOL:automatic blood vessel of posterior uvea OBOL:automatic choroid blood vessel OBOL:automatic choroid coat blood vessel OBOL:automatic choroidea blood vessel OBOL:automatic posterior uvea blood vessel OBOL:automatic vasa sanguinea choroideae FMA:76550 FMA:TA set of choroid blood vessels FMA:76550 The mucous secreting gland associated with the mucuous membrane lining the uterus. simple or branched tubular BTO:0003433 BTO:0004518 EMAPA:29919 MA:0001726 NCIT:C33842 UMLS:C1183035 endometrial gland endometrial mucuous gland endometrium gland glandulae uterinae uterine gland uberon glandulae uterinae UBERON:0002451 endometrial gland MP The mucous secreting gland associated with the mucuous membrane lining the uterus. UMLS:C1183035 ncithesaurus:Uterine_Gland endometrial gland BTO:0003433 glandulae uterinae FMA:71647 FMA:TA glandulae uterinae Arteries that supply the spinal cord. EHDAA2:0001890 EHDAA:4355 EMAPA:18241 MA:0002043 NCIT:C33587 TAO:0000682 UMLS:C0447043 ZFA:0000682 spinal arteries uberon UBERON:0002458 spinal artery Arteries that supply the spinal cord. UMLS:C0447043 ncithesaurus:Spinal_Artery spinal arteries ZFA:0000682 A tributary of the iliac vein that drains the urinary bladder. EMAPA:37205 MA:0002263 venae vesicales vesical veins vesical veins set uberon UBERON:0002460 vesical vein A tributary of the iliac vein that drains the urinary bladder. UBERON:cjm EMAPA:37205 MA:th venae vesicales FMA:70911 FMA:TA vesical veins Clear to pale yellow watery secretions from the glands lining the small intestine walls. Secretion is stimulated by the mechanical pressure of partly digested food in the intestine. BTO:0000644 FMA:62974 GAID:1162 MA:0002515 MESH:D007419 NCIT:C32875 UMLS:C0021849 intestinal secretion succus entericus uberon intestinal juice UBERON:0002466 intestine secretion Clear to pale yellow watery secretions from the glands lining the small intestine walls. Secretion is stimulated by the mechanical pressure of partly digested food in the intestine. UMLS:C0021849 ncithesaurus:Intestinal_Secretion intestinal secretion FMA:62974 succus entericus intestinal juice BTO:0000644 Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts. see https://github.com/obophenotype/uberon/issues/27 Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.[VSAO] CALOHA:TS-2011 EMAPA:35179 FMA:224804 MA:0002780 MESH:D001842 NCIT:C13076 UMLS:C0391978 VSAO:0000047 XAO:0004040 ZFA:0005621 galen:BoneTissue calcium tissue osseous tissue osteogenic tissue mineralized bone tissue uberon bone portion of bone tissue UBERON:0002481 bone tissue VSAO Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts. GO_REF:0000034 PSPUB:0000170 VSAO:0000047 Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.[VSAO] 2012-08-14 VSAO:0000047 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 PSPUB:0000170 UMLS:C0391978 ncithesaurus:Bone_Tissue osteogenic tissue VSAO:curator mineralized bone tissue XAO:0004040 bone MESH:A02.835.232 portion of bone tissue FMA:224804 An epithelium that is part of a iris [Automatically generated definition]. EMAPA:35447 FMA:58517 MA:0002826 epithelial tissue of iris epithelium of iris epithelium pigmentosum (iris) epithelium pigmentosum iridis iris epithelial tissue iris epithelium pigmented epithelium of iris uberon iris pigmented epithelium UBERON:0002506 iris epithelium FMA MA An epithelium that is part of a iris [Automatically generated definition]. OBOL:automatic epithelial tissue of iris OBOL:automatic epithelium of iris OBOL:automatic epithelium pigmentosum (iris) FMA:58517 epithelium pigmentosum iridis FMA:58517 FMA:TA iris epithelial tissue OBOL:automatic iris epithelium FMA:58517 pigmented epithelium of iris FMA:58517 iris pigmented epithelium MA:0002826 Replacement bone that forms within cartilage. placement in this class to be inferred Replacement bone that forms within cartilage.[VSAO] some structures, e.g. in ZFA are both intramembrane and endochondral AAO:0010776 AEO:0000083 BTO:0002157 EHDAA2:0003083 FMA:24321 TAO:0001591 VSAO:0000145 XAO:0004018 ZFA:0001591 ossified chondrogenic bone uberon cartilaginous bone endochondral bones UBERON:0002513 endochondral bone https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern VSAO VSAO Replacement bone that forms within cartilage. GO:0001958 GO_REF:0000034 VSAO:0000145 Replacement bone that forms within cartilage.[VSAO] 2012-08-14 VSAO:0000145 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 PSPUB:0000170 some structures, e.g. in ZFA are both intramembrane and endochondral ZFA ossified chondrogenic bone VSAO:0000145 cartilaginous bone BTO:0002157 endochondral bones ZFA:0001591 Connective tissue composed of elastic fibers. FMA:20113 GAID:926 MA:0002853 MESH:D004547 NCIT:C32495 elastic connective tissue textus connectivus elasticus elastic fiber uberon UBERON:0002521 elastic tissue Connective tissue composed of elastic fibers. textus connectivus elasticus The middle layer of an artery or vein. [WP,unvetted]. BTO:0002011 EMAPA:36298 FMA:55590 GAID:170 MA:0002855 MESH:D017540 NCIT:C33821 UMLS:C0162867 uberon tunica media vasorum UBERON:0002522 May be composed of smooth muscle and elastic tissue tunica media MA cjm cjm The middle layer of an artery or vein. [WP,unvetted]. UMLS:C0162867 ncithesaurus:Tunica_Media tunica media vasorum tunica media vasorum BTO:0002011 The innermost layer of a blood vessel which is a lining of endothelial cells facing the lumen[Kardong]. the FMA class represents a more generic layer which is the superclass of the layer found in both blood vessels and lymph vessels (and also endocardium) - we should probably follow this structure the FMA class represents a structure which may have both epithelium and fibroelastic connective tissue as parts The tunica intima (or just intima) is the innermost layer of an artery or vein. It is made up of one layer of endothelial cells and is supported by an internal elastic lamina. The endothelial cells are in direct contact with the blood flow. The inner coat (tunica intima) can be separated from the middle by a little maceration, or it may be stripped off in small pieces; but, on account of its friability, it cannot be separated as a complete membrane. It is a fine, transparent, colorless structure which is highly elastic, and, after death, is commonly corrugated into longitudinal wrinkles. The inner coat consists of: A layer of pavement endothelium, the cells of which are polygonal, oval, or fusiform, and have very distinct round or oval nuclei. This endothelium is brought into view most distinctly by staining with silver nitrate. A subendothelial layer, consisting of delicate connective tissue with branched cells lying in the interspaces of the tissue; in arteries of less than 2 mm. in diameter the subendothelial layer consists of a single stratum of stellate cells, and the connective tissue is only largely developed in vessels of a considerable size. An elastic or fenestrated layer, which consists of a membrane containing a net-work of elastic fibers, having principally a longitudinal direction, and in which, under the microscope, small elongated apertures or perforations may be seen, giving it a fenestrated appearance. It was therefore called by Henle the fenestrated membrane. This membrane forms the chief thickness of the inner coat, and can be separated into several layers, some of which present the appearance of a network of longitudinal elastic fibers, and others a more membranous character, marked by pale lines having a longitudinal direction. In minute arteries the fenestrated membrane is a very thin layer; but in the larger arteries, and especially in the aorta, it has a very considerable thickness. [WP,unvetted].[Wikipedia] BTO:0002012 EMAPA:36297 FMA:55589 GAID:523 MA:0002861 MESH:D017539 NCIT:C33820 UMLS:C0162864 uberon Bichat's tunic intima tunica intima vasorum UBERON:0002523 tunica intima FMA check for exceptions, e.g. capillaries ISBN10:0073040584 The innermost layer of a blood vessel which is a lining of endothelial cells facing the lumen[Kardong]. ISBN10:0073040584 NCIT:C33820 The tunica intima (or just intima) is the innermost layer of an artery or vein. It is made up of one layer of endothelial cells and is supported by an internal elastic lamina. The endothelial cells are in direct contact with the blood flow. The inner coat (tunica intima) can be separated from the middle by a little maceration, or it may be stripped off in small pieces; but, on account of its friability, it cannot be separated as a complete membrane. It is a fine, transparent, colorless structure which is highly elastic, and, after death, is commonly corrugated into longitudinal wrinkles. The inner coat consists of: A layer of pavement endothelium, the cells of which are polygonal, oval, or fusiform, and have very distinct round or oval nuclei. This endothelium is brought into view most distinctly by staining with silver nitrate. A subendothelial layer, consisting of delicate connective tissue with branched cells lying in the interspaces of the tissue; in arteries of less than 2 mm. in diameter the subendothelial layer consists of a single stratum of stellate cells, and the connective tissue is only largely developed in vessels of a considerable size. An elastic or fenestrated layer, which consists of a membrane containing a net-work of elastic fibers, having principally a longitudinal direction, and in which, under the microscope, small elongated apertures or perforations may be seen, giving it a fenestrated appearance. It was therefore called by Henle the fenestrated membrane. This membrane forms the chief thickness of the inner coat, and can be separated into several layers, some of which present the appearance of a network of longitudinal elastic fibers, and others a more membranous character, marked by pale lines having a longitudinal direction. In minute arteries the fenestrated membrane is a very thin layer; but in the larger arteries, and especially in the aorta, it has a very considerable thickness. [WP,unvetted].[Wikipedia] Wikipedia UMLS:C0162864 ncithesaurus:Tunica_Intima Bichat's tunic BTO:0002012 intima BTO:0002012 tunica intima vasorum BTO:0002012 an organ that functions as a secretory or excretory organ glandular UBERON:MIAA_0000021 AAO:0000212 AEO:0000096 BTO:0000522 EFO:0000797 EHDAA2:0003096 EHDAA:2161 EHDAA:4475 EHDAA:6522 EMAPA:18425 FBbt:00100317 FMA:7146 FMA:86294 HAO:0000375 MA:0003038 MAT:0000021 MIAA:0000021 NCIT:C13319 OpenCyc:Mx4rwP3vyJwpEbGdrcN5Y29ycA UMLS:C1285092 WikipediaCategory:Glands galen:Gland glandular organ uberon Druese glandula UBERON:0002530 gland an organ that functions as a secretory or excretory organ MGI:csmith MP:0002163 UMLS:C1285092 ncithesaurus:Gland glandular organ Druese BTO:0000522 glandula glandula BTO:0000522 In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA] MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG] BTO:0004593 FMA:296704 MAT:0000067 MIAA:0000067 VHOG:0000243 epiblast uberon blastocyst ectoblast epiblastus primitive ectoderm UBERON:0002532 epiblast (generic) In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA] ZFIN:curator In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG] 2012-09-17 VHOG:0000243 VHOG DOI:10.1146/annurev.cellbio.042308.113344 Zorn AM, Wells JM, Vertebrate endoderm development and organ formation. Annual Review of Cell Developmental Biology (2009) epiblast VHOG:0000243 ectoblast MP:0003886 epiblastus primitive ectoderm VHOG:0000243 One of a series of paired bulges that develop along the lateral walls of the foregut. The pharyngeal arches have developmental contributions from endoderm, mesoderm, and neural crest cells and are separated by anterior lateral endoderm out-pockets known as pharyngeal pouches. One of a series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO] A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down.[well established][VHOG] Numbered cranial to caudal. different in mammals. branchial arch = ZFA:0001613 pharyngeal arch 3-7. generally gill arch 1 = pharyngeal arch 3. terminology varies as to whether branchial arch follows gill or pharyngeal numbering AAO:0010359 BTO:0001785 EFO:0000959 EHDAA:571 EMAPA:16117 FMA:293015 GAID:1292 MAT:0000242 MESH:A16.254.160 MIAA:0000242 NCIT:C34249 TAO:0001306 UMLS:C0080322 VHOG:0000155 XAO:0000096 ZFA:0001306 pharyngeal arches branchial arch uberon arcus pharyngei visceral arch UBERON:0002539 pharyngeal arch EHDAA2 One of a series of paired bulges that develop along the lateral walls of the foregut. The pharyngeal arches have developmental contributions from endoderm, mesoderm, and neural crest cells and are separated by anterior lateral endoderm out-pockets known as pharyngeal pouches. ZFA:yb One of a series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO] 2012-06-20 AAO:0010359 AAO NLM:branchial+arch A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down.[well established][VHOG] 2012-09-17 VHOG:0000155 VHOG DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005) UMLS:C0080322 ncithesaurus:Pharyngeal_Arch pharyngeal arches branchial arch BTO:0001785 MP:0002884 arcus pharyngei Ectodermal placode that develops in the head into a part of the sensory nervous system. With a few exceptions (lens, adenohypophyseal), cranial placodes are neurogenic. Do not merge with neurogenic placode Comparisons of developmental gene expression suggest that the anterior ectoderm in amphioxus may be homologous to the vertebrate olfactory placode, the only vertebrate placode with primary, not secondary, neurons The term placode or placodes also applies to developing organs such as teeth, mammary glands, hair follicles, feathers and scales. We include a separate parent class for this. to avoid confusion, we include neurogenic placode as a subclass ectodermal placode placode AAO:0010466 EFO:0001650 FMA:293966 MAT:0000369 MIAA:0000369 XAO:0000305 ectodermal cranial placode uberon cranial placodes UBERON:0002546 cranial placode cjm Ectodermal placode that develops in the head into a part of the sensory nervous system. With a few exceptions (lens, adenohypophyseal), cranial placodes are neurogenic. Comparisons of developmental gene expression suggest that the anterior ectoderm in amphioxus may be homologous to the vertebrate olfactory placode, the only vertebrate placode with primary, not secondary, neurons ectodermal placode FMA:293966 placode ectodermal cranial placode UBERON:cjm cranial placodes XAO:0000305 Anatomical space which contains portions of one or more body substances and is bounded by the internal surface of one maximally connected anatomical structure. Examples: cranial cavity, pharyngeal recess space, nasal cavity, tooth socket, cavity of serous sac, lumen of stomach, lumen of artery, fornix of vagina. cavity EMAPA:37442 FMA:67552 MA:0002447 NCIT:C34007 galen:Cavity uberon UBERON:0002553 anatomical cavity Anatomical space which contains portions of one or more body substances and is bounded by the internal surface of one maximally connected anatomical structure. Examples: cranial cavity, pharyngeal recess space, nasal cavity, tooth socket, cavity of serous sac, lumen of stomach, lumen of artery, fornix of vagina. FMA:67552 EMAPA:37442 MA:th FMA:12237 cavity of organ uberon UBERON:0002558 organ cavity cavity of organ FMA:12237 The cavity that is enclosed by the central nervous system. In vertebrates this is the cavity that includes as parts ventricular cavities and the central canal of the spinal cord that develops from the lumen of the neura tube FMA:75007 cavity of neuraxis cavity of ventricular system of neuraxis neuraxis cavity neuraxis lumen uberon UBERON:0002561 lumen of central nervous system The cavity that is enclosed by the central nervous system. In vertebrates this is the cavity that includes as parts ventricular cavities and the central canal of the spinal cord that develops from the lumen of the neura tube cavity of neuraxis FMA:75007 cavity of ventricular system of neuraxis FMA:75007 neuraxis cavity FMA:75007 Anatomical divisons of the brain according to one or more criteria, e.g. cytoarchitectural, gross anatomy. Parts may be contiguous in 3D or not, e.g., basal ganglia. FMA:55676 NCIT:C13031 UMLS:C0445620 anatomical structure of brain biological structure of brain brain anatomical structure brain biological structure brain part neuraxis segment neuroanatomical region segment of brain uberon UBERON:0002616 regional part of brain Anatomical divisons of the brain according to one or more criteria, e.g. cytoarchitectural, gross anatomy. Parts may be contiguous in 3D or not, e.g., basal ganglia. NIFSTD:birnlex_1167 UMLS:C0445620 ncithesaurus:Brain_Part anatomical structure of brain OBOL:automatic biological structure of brain OBOL:automatic brain anatomical structure OBOL:automatic brain biological structure OBOL:automatic neuraxis segment FMA:55676 segment of brain NIFSTD:birnlex_1167 A nucleus of brain that is part of a trigeminal nuclear complex. massive inconsistencies between GO, MA, wikipedia. Part of pons in MA, but this leads to inconsistencies with ABA. BM:V BTO:0001074 CALOHA:TS-2077 EMAPA:35883 EV:0100271 FMA:71247 GAID:604 MA:0001028 MESH:D014278 NCIT:C12807 UMLS:C0040999 VHOG:0001353 nucleus of trigeminal nuclear complex trigeminal V nucleus trigeminal nuclear complex nucleus trigeminal nucleus uberon nucleus mesencephalicus nervi trigemini nucleus mesencephalicus trigeminalis nucleus tractus mesencephali nervi trigeminalis UBERON:0002925 trigeminal nucleus A nucleus of brain that is part of a trigeminal nuclear complex. OBOL:automatic massive inconsistencies between GO, MA, wikipedia. Part of pons in MA, but this leads to inconsistencies with ABA. GO https://github.com/obophenotype/mouse-anatomy-ontology/issues/58 UMLS:C0040999 ncithesaurus:Trigeminal_Nucleus nucleus of trigeminal nuclear complex FMA:71247 trigeminal V nucleus MA:0001028 trigeminal nuclear complex nucleus FMA:71247 trigeminal nucleus FMA:71248 nucleus mesencephalicus nervi trigemini BTO:0001074 nucleus mesencephalicus trigeminalis BTO:0001074 nucleus tractus mesencephali nervi trigeminalis BTO:0001074 A sensory epithelium that is part of a gustatory system. FMA:62412 uberon UBERON:0002926 gustatory epithelium NIFSTD A sensory epithelium that is part of a gustatory system. OBOL:automatic Dorsal portion of the pons, containing cranial nervee nuclei, ascending and descending tracts and reticular nuclei. It is continuous with the reticular formation of the medulla (Carpenter, A Core Text of Neuroanatomy, 3rd ed, 1985, pg 133). involved in the initiation of REM sleep [Wikipedia:Pontine_tegmentum] BAMS:PTg DHBA:12416 FMA:71108 HBA:9135 UMLS:C0228426 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=557 dorsal pons dorsal portion of pons tegmental portion of pons tegmentum of pons tegmentum pontis uberon pars dorsalis pontis pars posterior pontis tegmentum pontis UBERON:0003023 pontine tegmentum Dorsal portion of the pons, containing cranial nervee nuclei, ascending and descending tracts and reticular nuclei. It is continuous with the reticular formation of the medulla (Carpenter, A Core Text of Neuroanatomy, 3rd ed, 1985, pg 133). NIFSTD:birnlex_923 UMLS:C0228426 NIFSTD:birnlex_923 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=557 NIFSTD:birnlex_923 dorsal portion of pons FMA:71108 tegmental portion of pons FMA:71108 tegmentum of pons FMA:71108 tegmentum pontis FMA:71108 FMA:TA pars dorsalis pontis NeuroNames:557 pars posterior pontis NeuroNames:557 tegmentum pontis A wall, dividing a cavity or structure into smaller ones[WP]. septal AAO:0011127 FMA:86461 OpenCyc:Mx4rrqot_on_EdaAAAACs0uFOQ septa uberon UBERON:0003037 general anatomical term in FMA septum A wall, dividing a cavity or structure into smaller ones[WP]. septa A thick plate of cells derived from the neural ectoderm in the head region of the embryo that develops into the olfactory region of the nasal cavity. We conclude this section by listing some of the many synapomorphies of craniates, including (...) (2) neurogenic placodes (...).[well established][VHOG] AAO:0011076 EFO:0003420 EHDAA2:0001232 EHDAA:1504 EMAPA:16543 FMA:293971 TAO:0000048 VHOG:0000186 XAO:0000005 ZFA:0000048 olfactory placodes placoda nasalis placoda olfactoria uberon nasal I placode nasal placode UBERON:0003050 Olfactory placodes are the only ectodermal placodes to produce glia, a cell type typically derived from neural crest // Note that NBK53171 classifies this as non-neurogenic olfactory placode NCBIBook:NBK53171 ZFA EHDAA2 A thick plate of cells derived from the neural ectoderm in the head region of the embryo that develops into the olfactory region of the nasal cavity. XAO:0000005 We conclude this section by listing some of the many synapomorphies of craniates, including (...) (2) neurogenic placodes (...).[well established][VHOG] 2012-09-17 VHOG:0000186 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 olfactory placodes placoda nasalis placoda olfactoria An epithelial sac of invaginated ectoderm formed from the otic placode that gives rise to the structures of the inner ear[MP] Epithelial sac present beside the fifth rhombomere; forms the semicircular canals dorsally and the otolith organs ventrally, and houses the acoustico-vestibular sensory epithelia (maculae) of hair cells. Kimmel et al, 1995. (Also see Anatomical Atlas entry for ear by T. Whitfield.)[TAO] One of the paired sacs of invaginated ectoderm that develop into the membranous labyrinth of the internal ear. [Biology_online][VHOG] The inner ear develops embryonically in all vertebrates as an invagination of the ectodermal otic placode to form an otic vesicle.[well established][VHOG] MP defines as epithelial sac, but EHDAA defines as multi-tissue; See https://github.com/obophenotype/uberon/issues/1305 UBERON:0004373 AAO:0011080 BTO:0002661 EHDAA2:0001342 EMAPA:16669 FMA:302920 NCIT:C34240 TAO:0000051 UMLS:C1518678 VHOG:0001148 XAO:0000006 ZFA:0000051 otic vesicle uberon OV acoustic vesicle auditory vesicle otocyst UBERON:0003051 ear vesicle An epithelial sac of invaginated ectoderm formed from the otic placode that gives rise to the structures of the inner ear[MP] MP:0009806 Epithelial sac present beside the fifth rhombomere; forms the semicircular canals dorsally and the otolith organs ventrally, and houses the acoustico-vestibular sensory epithelia (maculae) of hair cells. Kimmel et al, 1995. (Also see Anatomical Atlas entry for ear by T. Whitfield.)[TAO] 2012-08-14 TAO:0000051 TAO ZFIN:curator One of the paired sacs of invaginated ectoderm that develop into the membranous labyrinth of the internal ear. [Biology_online][VHOG] 2012-09-17 VHOG:0001148 VHOG The inner ear develops embryonically in all vertebrates as an invagination of the ectodermal otic placode to form an otic vesicle.[well established][VHOG] 2012-09-17 VHOG:0001148 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.413 MP defines as epithelial sac, but EHDAA defines as multi-tissue; See https://github.com/obophenotype/uberon/issues/1305 MP UMLS:C1518678 ncithesaurus:Otic_Vesicle otic vesicle MP:0004311 acoustic vesicle VHOG:0001148 auditory vesicle BTO:0002661 otocyst MP:0004311 The part of the brain that is the morphological boundary between the midbrain and hindbrain and that is the location of an organizing center which patterns the midbrain and hindbrain primordia of the neural plate. consider adding class for organizer. Consider adding separate class for isthmus as a structure Lampreys also have an MHB [midbrain hindbrain boundary], expressing a similar repertoire of regulatory gene cognates as in gnathostomes.[well established][VHOG] AAO:0011064 DMBA:16810 EHDAA2:0004395 EHDAA:5789 EMAPA:32857 NCIT:C93172 TAO:0000042 VHOG:0000649 XAO:0000016 ZFA:0000042 MHB mid-hindbrain boundary mid-hindbrain junction midbrain hindbrain boundary uberon isthmic organizer territory isthmo-cerebellar region isthmus isthmus/MHB UBERON:0003052 midbrain-hindbrain boundary ZFA ZFA ZFA The part of the brain that is the morphological boundary between the midbrain and hindbrain and that is the location of an organizing center which patterns the midbrain and hindbrain primordia of the neural plate. GO:0021555 Lampreys also have an MHB [midbrain hindbrain boundary], expressing a similar repertoire of regulatory gene cognates as in gnathostomes.[well established][VHOG] 2012-09-17 VHOG:0000649 VHOG DOI:10.1016/j.ydbio.2005.02.008 Murakami Y, Uchida K, Rijli FM and Kuratani S, Evolution of the brain developmental plan: Insights from agnathans. Developmental Biology (2005) isthmic organizer territory XAO:0000016 isthmo-cerebellar region VHOG:0000649 isthmus/MHB Geisha:syn NCBITaxon:8782 A temporary epithelium that derives from the outer layer of the ectdoerm and is shed once the inner layer differentiates to form a true epidermis. The outermost epidermal layer covering the fish at embryonic stages; derived from the EVL and thought to eventually be replaced by the superficial stratum of the epidermis. Sometimes used synonymously with EVL. Le Guellec et al, 2004.[TAO] relationship type change: OBO_REL:part_of ectoderm (TAO:0000016) CHANGED TO: develops_from ectoderm (UBERON:0000924)[TAO] In mice, the first non-basal layer formed at ~E9.5; it is a temporary structure composed of simple squamous epithelium that serves as the first barrier to the embryo's physical environment, exists throughout the entire keratinocyte stratification process, and sheds off at ~E17, when it is replaced by corneocytes[MP] In some mammals, Eyelid Fusion is thought to be driven by a population of cells which are derived from the periderm, the outermost layer of the developing epidermis Originally the epidermis is one layer thick, in most vertebrates it soon becomes a two-layered structure. The outer layer gives rise to the periderm. The periderm goes through distinct developmental phases and is ultimately sloughed into the amniotic fluid when differentiation of the underlying epidermal layers is complete. The function of the periderm is not known, but is thought to be related to transport/exchange between the fetus and the amniotic fluid (http://courses.washington.edu/hubio567/devbio/periderm.html) EHDAA2:0001846 EHDAA:6538 FMA:295662 NCIT:C34247 TAO:0001185 UMLS:C1518973 VHOG:0001680 XAO:0000029 ZFA:0001185 skin periderm uberon EVL epidermis epithelial layer epidermis outer layer epitrichium periderm UBERON:0003055 periderm EHDAA2 EHDAA2 ZFA A temporary epithelium that derives from the outer layer of the ectdoerm and is shed once the inner layer differentiates to form a true epidermis. ISBN:9780878932504 The outermost epidermal layer covering the fish at embryonic stages; derived from the EVL and thought to eventually be replaced by the superficial stratum of the epidermis. Sometimes used synonymously with EVL. Le Guellec et al, 2004.[TAO] 2012-08-14 TAO:0001185 TAO ZFIN:curator relationship type change: OBO_REL:part_of ectoderm (TAO:0000016) CHANGED TO: develops_from ectoderm (UBERON:0000924)[TAO] 2012-08-14 TAO:0001185 TAO UMLS:C1518973 ncithesaurus:Periderm skin periderm EHDAA2:0001846 EVL ZFA:0001185 epitrichium MP:0013530 The portion of neural plate anterior to the mid-hindbrain junction. (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] AAO:0011084 TAO:0007016 VHOG:0001200 XAO:0000045 ZFA:0007016 uberon anterior neural plate UBERON:0003056 pre-chordal neural plate The portion of neural plate anterior to the mid-hindbrain junction. XB:curator (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] 2012-09-17 VHOG:0001200 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 The portion of neural plate posterior to the mid-hindbrain junction. (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] TAO:0007017 VHOG:0001201 XAO:0000046 ZFA:0007017 uberon posterior neural plate UBERON:0003057 chordal neural plate The portion of neural plate posterior to the mid-hindbrain junction. XB:curator (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] 2012-09-17 VHOG:0001201 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO] It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG] AAO:0011086 EFO:0001982 EMAPA:16189 EMAPA:16752 TAO:0000279 VHOG:0000559 XAO:0000057 ZFA:0000279 segmental plate unsegmented paraxial mesoderm uberon PSM presumptive somite mesoderm somitogenic mesoderm somitomeric mesoderm unsegmented mesenchyme UBERON:0003059 presomitic mesoderm Bgee:AN Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. ZFIN:curator Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000279 TAO ZFIN:curator It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG] 2012-09-17 VHOG:0000559 VHOG DOI:10.1006/dbio.2001.0460 Schubert M, Holland LZ, Dale Stokes M and Holland ND, Three Amphoxius Wnt Genes (AmphiWnt3, AmphiWnt5, and AmphiWnt6) Associated with the Tail Bud: the Evolution of Somitogenesis in Chordates. Developmental Biology (2001) unsegmented paraxial mesoderm somitomeric mesoderm GO:0002075 unsegmented mesenchyme VHOG:0000559 In mammals, the pronephric duct is the predecessor of the Wolffian duct[WP]. Duct of the embryonic kidney, present bilaterally ventral to the somites and leading to the anal region where it empties separately from, and just posterior to the anus. Kimmel et al, 1995.[TAO] The first-formed kidney duct, which drains the kidney of most anamniotes and becomes the ductus deferens of male amniotes. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-3, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] (...) in all craniates, the archinephric duct develops in embryogeny.[well established][VHOG] AAO:0011088 NCIT:C34279 TAO:0000150 UMLS:C1283945 VHOG:0000082 XAO:0000063 ZFA:0000150 uberon archinephric duct ductus pronephricus pronephric ducts UBERON:0003060 The pronephric duct collects the filtrate from the pronephric tubules and opens to the exterior of the pronephric kidney[GOC:mtg_kidney_jan10, http://www.ncbi.nlm.nih.gov/pubmed/15647339, XAO:0000063, ZFA:0000150] pronephric duct GO Wikipedia XAO In mammals, the pronephric duct is the predecessor of the Wolffian duct[WP]. Duct of the embryonic kidney, present bilaterally ventral to the somites and leading to the anal region where it empties separately from, and just posterior to the anus. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000150 TAO ZFIN:curator The first-formed kidney duct, which drains the kidney of most anamniotes and becomes the ductus deferens of male amniotes. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-3, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] 2012-09-17 VHOG:0000082 VHOG (...) in all craniates, the archinephric duct develops in embryogeny.[well established][VHOG] 2012-09-17 VHOG:0000082 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.686 UMLS:C1283945 ncithesaurus:Pronephric_Duct archinephric duct VHOG:0000082 ductus pronephricus pronephric ducts ZFA:0000150 Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted]. Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO] Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO] relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO] Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG] EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac ventral lateral plate mesoderm AAO:0011006 EFO:0003489 EHDAA:207 NCIT:C34113 TAO:0000094 TE:E5.11.2.0.0.0.4 UMLS:C1511224 VHOG:0000085 XAO:0000067 ZFA:0000094 blood islands uberon VBI caudal hematopoietic tissue posterior ICM posterior blood island ventral blood island UBERON:0003061 blood island Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted]. Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000094 TAO ZFIN:curator Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO] 2012-06-20 AAO:0011006 AAO AAO:EJS relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO] 2012-08-14 TAO:0000094 TAO Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000085 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.450, DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual Review of Cell and Developmental Biology (2006) EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac EHDAA2 UMLS:C1511224 ncithesaurus:Blood_Island blood islands A horseshoe-shaped thickening of the endoderm at the cranial (rostral) end of the primitive streak formed by the involution of Spemann's organizer cells which, together with the notochord, induces the formation of the neural plate from the overlying ectodermal cells and contributes mesodermal type cells to the surrounding tissue TODO - check; developmental relationship to anterior hypoblast in ZFA? Axial hypoblast located anterior to the chorda mesoderm; the polster is its most anterior region. Kimmel et al, 1995.[TAO] Axial mesoderm that lies anterior to the notochord and that underlies the forebrain. [Amphioxus_goosecoid_and_the_evolution_of_the_head_organizer_and_prechordal_plate._Evolution_and_Development_(2008)_2(6):303-310, Neidert_AH, Panopoulou_G_and_Langeland_JA][VHOG] There are two opposing models that can potentially explain the differences in gsc (goosecoid) expression between amphioxus and vertebrates. In one model, the vertebrate gsc expression pattern more closely resembles the common ancestral state and the amphioxus gsc expression pattern is a derivation associated with its unique morphology. (...) In an alternate model, the amphioxus gsc expression pattern most closely represents the common ancestral state and the vertebrate pattern is derived. This model suggests that the evolution of vertebrates was accompanied by the segregation of gsc expression, from a more general domain underlying the entire brain anlage to a distinct forebrain organizer domain and subsequent prechordal plate. We feel this second model is more parsimonious than the first model in that what would be novel anterior gsc expression in vertebrates directly correlates with a novel vertebrate anterior structure, the prechordal plate.[well established][VHOG] UBERON:0004881 head mesenchyme head mesoderm AAO:0011085 EHDAA2:0001493 EHDAA:181 FMA:295532 TAO:0000060 VHOG:0000086 XAO:0000079 ZFA:0000060 uberon UBERON:0003063 prechordal plate ZFA PMID:16313393 A horseshoe-shaped thickening of the endoderm at the cranial (rostral) end of the primitive streak formed by the involution of Spemann's organizer cells which, together with the notochord, induces the formation of the neural plate from the overlying ectodermal cells and contributes mesodermal type cells to the surrounding tissue ISBN:0838580343 MP:0004387 Axial hypoblast located anterior to the chorda mesoderm; the polster is its most anterior region. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000060 TAO ZFIN:curator Axial mesoderm that lies anterior to the notochord and that underlies the forebrain. [Amphioxus_goosecoid_and_the_evolution_of_the_head_organizer_and_prechordal_plate._Evolution_and_Development_(2008)_2(6):303-310, Neidert_AH, Panopoulou_G_and_Langeland_JA][VHOG] 2012-09-17 VHOG:0000086 VHOG There are two opposing models that can potentially explain the differences in gsc (goosecoid) expression between amphioxus and vertebrates. In one model, the vertebrate gsc expression pattern more closely resembles the common ancestral state and the amphioxus gsc expression pattern is a derivation associated with its unique morphology. (...) In an alternate model, the amphioxus gsc expression pattern most closely represents the common ancestral state and the vertebrate pattern is derived. This model suggests that the evolution of vertebrates was accompanied by the segregation of gsc expression, from a more general domain underlying the entire brain anlage to a distinct forebrain organizer domain and subsequent prechordal plate. We feel this second model is more parsimonious than the first model in that what would be novel anterior gsc expression in vertebrates directly correlates with a novel vertebrate anterior structure, the prechordal plate.[well established][VHOG] 2012-09-17 VHOG:0000086 VHOG DOI:10.1046/j.1525-142x.2000.00073.x Neidert AH, Panopoulou G and Langeland JA, Amphioxus goosecoid and the evolution of the head organizer and prechordal plate. Evolution and Development (2008) head mesenchyme XAO:0000079 head mesoderm XAO:0000079 The intermediate mesoderm is located between the lateral mesoderm and the paraxial mesoderm. It develops into the kidney and gonads. Mesoderm between somite and lateral plate. Traditionally thought to give rise to the urogenital system.[AAO] (...)the mesoderm of a developing vertebrate transitionally differentiates into the following sub-types: Chordamesoderm (also known as axial mesoderm) which later on gives rise to notochord in all chordates, Paraxial mesoderm, Intermediate mesoderm, Lateral plate mesoderm (reference 1); The mesoderm is present in Bilateria, therefore they are sometimes called triploblasts. Ectoderm and endoderm are usually organized as epithelial layers, while mesoderm can be epithelial or a compact, three-dimensional tissue.[well established][VHOG] all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). AAO:0010575 EMAPA:16056 EMAPA:16178 FMA:293147 NCIT:C34193 TAO:0001206 UMLS:C1284010 VHOG:0000087 XAO:0000085 ZFA:0001206 uberon IM intermediate mesenchyme intermediate plate intermediate plate mesoderm mesenchyma intermedium UBERON:0003064 intermediate mesoderm AAO EMAPA XAO The intermediate mesoderm is located between the lateral mesoderm and the paraxial mesoderm. It develops into the kidney and gonads. GOC:curators Mesoderm between somite and lateral plate. Traditionally thought to give rise to the urogenital system.[AAO] 2012-06-20 AAO:0010575 AAO AAO:EJS (...)the mesoderm of a developing vertebrate transitionally differentiates into the following sub-types: Chordamesoderm (also known as axial mesoderm) which later on gives rise to notochord in all chordates, Paraxial mesoderm, Intermediate mesoderm, Lateral plate mesoderm (reference 1); The mesoderm is present in Bilateria, therefore they are sometimes called triploblasts. Ectoderm and endoderm are usually organized as epithelial layers, while mesoderm can be epithelial or a compact, three-dimensional tissue.[well established][VHOG] 2012-09-17 VHOG:0000087 VHOG http://en.wikipedia.org/wiki/Mesoderm, ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.43 all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). ZFA UMLS:C1284010 ncithesaurus:Intermediate_Mesoderm intermediate mesenchyme intermediate plate EMAPA:16178 intermediate plate mesoderm mesenchyma intermedium The second pharyngeal arch will form the hyoid apparatus. The cranial neural crest cells that populate the second pharyngeal arch emerge primarily from rhombomere 4 and will form skeletal elements. The second of the series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO] A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] in XAO, develops from visceral pouch 2 2 AAO:0010363 EHDAA2:0000050 EHDAA:611 EMAPA:16272 FMA:293017 NCIT:C34288 TAO:0001596 VHOG:0000297 XAO:0000098 ZFA:0001611 2nd pharyngeal arch arcus pharyngeus secundus branchial arch 2 hyoid arch pharyngeal arch 2 second branchial arch second pharyngeal arch second visceral arch visceral arch 2 uberon 2nd arch 2nd visceral arch hyoid bars pharyngeal arches 2 UBERON:0003066 pharyngeal arch 2 The second pharyngeal arch will form the hyoid apparatus. The cranial neural crest cells that populate the second pharyngeal arch emerge primarily from rhombomere 4 and will form skeletal elements. ZFIN:yb The second of the series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO] 2012-06-20 AAO:0010363 AAO XAO:EJS A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] 2012-09-17 VHOG:0000297 VHOG DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005) in XAO, develops from visceral pouch 2 XAO arcus pharyngeus secundus branchial arch 2 hyoid arch XAO:0000098 second branchial arch second visceral arch visceral arch 2 2nd arch EHDAA2:0000050 2nd visceral arch VHOG:0000297 pharyngeal arches 2 VHOG:0000297 Lateral neurogenic placodes positioned dorsal of the epibranchial placodes. In summary, the collective term 'placodes' refers to some rather different structures, probably with different evolutionary origins. Some sensory placodes (at least the otic and olfactory) may have homologues in basal chordates. Even if this is so, it is apparent that they were elaborated considerably during early vertebrate evolution. Epibranchial and dorsolateral placodes appear to be new; we infer that their origin depended on the evolution of specific inductive signals.[well established][VHOG] TAO:0001310 VHOG:0000103 XAO:0000187 ZFA:0001310 dorsolateral placodes uberon UBERON:0003067 The only remaining dorsolateral placode in land vertebrates is the otic/octaval placode dorsolateral placode NCBIBook:NBK53175 Lateral neurogenic placodes positioned dorsal of the epibranchial placodes. ZFIN:curator In summary, the collective term 'placodes' refers to some rather different structures, probably with different evolutionary origins. Some sensory placodes (at least the otic and olfactory) may have homologues in basal chordates. Even if this is so, it is apparent that they were elaborated considerably during early vertebrate evolution. Epibranchial and dorsolateral placodes appear to be new; we infer that their origin depended on the evolution of specific inductive signals.[well established][VHOG] 2012-09-17 VHOG:0000103 VHOG DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000) dorsolateral placodes ZFA:0001310 The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord. The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] AAO:0011017 EFO:0003647 TAO:0001204 VHOG:0000107 XAO:0000205 ZFA:0001204 uberon chordamesoderm UBERON:0003068 axial mesoderm The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord. GO:0048318 The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] 2012-09-17 VHOG:0000107 VHOG chordamesoderm A cranial placode which, once specified, invaginates to form an otic cup, which eventually separates from the surface ectoderm to form the otic vesicle or otocyst, a rounded structure without appar- ent polarity. As the otic placode invaginates into a cup neuroblasts delaminate from the anterior ventral aspect of the otic epithelium to give rise to neurons of the vestibulocochlear (statoacoustic) ganglion of cranial nerve VIII[NBK] Primordium of the ear epithelium before it hollows into the otic vesicle, present beside the hindbrain rudiment in the midsegmentation period. Kimmel et al, 1995. (Also see Anatomical Atlas entry for ear by T. Whitfield.)[TAO] We conclude this section by listing some of the many synapomorphies of craniates, including (...) (2) neurogenic placodes (...).[well established][VHOG] With the exception of the pigment cells of the stria vascularis and the secretory epithelium of the cochlea, which are of neural crest origin, all compo- nents of the inner ear derive from the otic placode. In most species the thickening of the ectoderm into a placode occurs in a region adjacent to rhombomere 5 (reviewed in Ohyama et al., 2007), while in amphibians the otic placode is centered onto rhombomere 4 (Ruiz i Altaba and Jessell, 1991). AAO:0011079 EFO:0003429 EHDAA2:0001339 EHDAA:506 EMAPA:16195 FMA:293973 NCIT:C34239 TAO:0000138 UMLS:C1518677 VHOG:0000235 XAO:0000223 ZFA:0000138 placoda otica uberon auditory placode ear placode ear/otic placode octaval VIII placode octaval placode UBERON:0003069 otic placode invaginates NCBIBook:NBK53175 A cranial placode which, once specified, invaginates to form an otic cup, which eventually separates from the surface ectoderm to form the otic vesicle or otocyst, a rounded structure without appar- ent polarity. As the otic placode invaginates into a cup neuroblasts delaminate from the anterior ventral aspect of the otic epithelium to give rise to neurons of the vestibulocochlear (statoacoustic) ganglion of cranial nerve VIII[NBK] NCBIBook:NBK53175 Primordium of the ear epithelium before it hollows into the otic vesicle, present beside the hindbrain rudiment in the midsegmentation period. Kimmel et al, 1995. (Also see Anatomical Atlas entry for ear by T. Whitfield.)[TAO] 2012-08-14 TAO:0000138 TAO ZFIN:curator We conclude this section by listing some of the many synapomorphies of craniates, including (...) (2) neurogenic placodes (...).[well established][VHOG] 2012-09-17 VHOG:0000235 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 With the exception of the pigment cells of the stria vascularis and the secretory epithelium of the cochlea, which are of neural crest origin, all compo- nents of the inner ear derive from the otic placode. In most species the thickening of the ectoderm into a placode occurs in a region adjacent to rhombomere 5 (reviewed in Ohyama et al., 2007), while in amphibians the otic placode is centered onto rhombomere 4 (Ruiz i Altaba and Jessell, 1991). NCBIBook:NBK53175 UMLS:C1518677 ncithesaurus:Otic_Placodes placoda otica octaval VIII placode ISBN10:0471888893 octaval placode ISBN10:0471888893 A neurogenic placode that arises at the level of the midbrain-hindbrain boundary and develops into a trigeminal ganglion. The ectodermal precursor of the trigeminal ganglion. The profundal and the trigeminal ganglia are separate distally but fused at their proximal end as they condense around NF stage 24.[XAO] The ectodermal rudiment of the trigeminal ganglion, distinguishable during much of the segmentation period. Kimmel et al, 1995.[TAO] The dorsolateral placodes (trigeminal and vestibular) develop from ectoderm lateral to the brain (...). In summary, the collective term 'placodes' refers to some rather different structures, probably with different evolutionary origins. Some sensory placodes (at least the otic and olfactory) may have homologues in basal chordates. Even if this is so, it is apparent that they were elaborated considerably during early vertebrate evolution. Epibranchial and dorsolateral placodes appear to be new; we infer that their origin depended on the evolution of specific inductive signals.[well established][VHOG] Consider naming this 'trigeminal placode complex'. Also, Fig9-5 of ISBN10:0471888893 calls this the profundus placode; XAO says 'profundal and the trigeminal ganglia are separate distally but fused at their proximal end...' EFO:0003433 EHDAA2:0004209 TAO:0000162 VHOG:0000109 XAO:0000225 ZFA:0000162 trigeminal V placode trigeminal placode uberon profundus V placode profundus placode trigeminal placodes UBERON:0003070 trigeminal placode complex ISBN10:0471888893 A neurogenic placode that arises at the level of the midbrain-hindbrain boundary and develops into a trigeminal ganglion. The ectodermal precursor of the trigeminal ganglion. The profundal and the trigeminal ganglia are separate distally but fused at their proximal end as they condense around NF stage 24.[XAO] XAO The ectodermal rudiment of the trigeminal ganglion, distinguishable during much of the segmentation period. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000162 TAO ZFIN:curator The dorsolateral placodes (trigeminal and vestibular) develop from ectoderm lateral to the brain (...). In summary, the collective term 'placodes' refers to some rather different structures, probably with different evolutionary origins. Some sensory placodes (at least the otic and olfactory) may have homologues in basal chordates. Even if this is so, it is apparent that they were elaborated considerably during early vertebrate evolution. Epibranchial and dorsolateral placodes appear to be new; we infer that their origin depended on the evolution of specific inductive signals.[well established][VHOG] 2012-09-17 VHOG:0000109 VHOG DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000) trigeminal placode EHDAA2:0004209 VHOG:0000109 XAO:0000225 ZFA:0000162 profundus V placode ISBN10:0471888893 profundus placode ISBN10:0471888893 trigeminal placodes ZFA:0000162 Portion of tissue that is part of the anterior neural keel and will form the optic vesicle[ZFA]. A paired ectodermal placode that becomes invaginated to form the embryonic lens vesicles. TODO - check that GO's optic placode is the same as ZFA's eye primordium; we may want to have separate term for ocular primordium precursor. XAO has both optic field and eye primordium. UBERON:0005060 AAO:0011038 EFO:0003541 EHDAA2:0004431 TAO:0000570 XAO:0000227 XAO:0004090 ZFA:0000570 eye placode occular primordium ocular primordium optic placode optic placode of camera-type eye optic primordium uberon eye anlage eye field optic field optic placodes UBERON:0003071 eye primordium EHDAA2 XAO Portion of tissue that is part of the anterior neural keel and will form the optic vesicle[ZFA]. A paired ectodermal placode that becomes invaginated to form the embryonic lens vesicles. GO:0046619 ZFA:0000570 TODO - check that GO's optic placode is the same as ZFA's eye primordium; we may want to have separate term for ocular primordium precursor. XAO has both optic field and eye primordium. GO eye placode OBOL:automatic optic placode GO:0046619 optic placode of camera-type eye GO:0046619 eye anlage XAO:0000227 optic placodes Multi-tissue structure that is comprised of neural and non-neural epithelial layers which will form the retina and retinal pigmented epithelium of the mature eye[ZFA]. double walled structured formed by expansion and invagination of the distal end of the optic vesicle that develops into the pigmented and sensory layers of the retina while the mouth of the optic cup eventually forms the pupil of the eye[MP]. (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup.[well established][VHOG] BTO:0005351 EHDAA2:0001303 EHDAA:2912 EMAPA:16674 NCIT:C34233 TAO:0001202 UMLS:C0231109 VHOG:0000167 ZFA:0001202 uberon eye cup eyecup ocular cup ophtalmic cup UBERON:0003072 optic cup ZFA ZFA Multi-tissue structure that is comprised of neural and non-neural epithelial layers which will form the retina and retinal pigmented epithelium of the mature eye[ZFA]. double walled structured formed by expansion and invagination of the distal end of the optic vesicle that develops into the pigmented and sensory layers of the retina while the mouth of the optic cup eventually forms the pupil of the eye[MP]. MP:0004269 Optic_cup_(embryology) ZFA:0001202 (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup.[well established][VHOG] 2012-09-17 VHOG:0000167 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 UMLS:C0231109 ncithesaurus:Optic_Cup eyecup BTO:0005351 ocular cup VHOG:0000167 ophtalmic cup BTO:0005351 A thickened portion of ectoderm which serves as the precursor to the lens. SOX2 and Pou2f1 are involved in its development[WP]. Ectodermal primordium of the lens of the eye. Kimmel et al, 1995.[TAO] (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG] Classical transplantation experiments using amphibian embryos suggested that the optic vesicle is the source of lens-inducing signals sufficient to generate lens tissues in competent ectoderm (reviewed in Grainger et al., 1996). More recent findings suggest a multistep model for lens induction. There is now good evidence that lens specification occurs at the neurula stage, before the optic vesicle contact the surface ectoderm, and that neural crest cell migration in the frontonasal region is required to restrict the position of the lens placode (Bailey et al., 2006) AAO:0011055 EFO:0003494 EHDAA2:0000982 EHDAA:2908 EMAPA:16672 FMA:296767 NCIT:C34202 TAO:0000122 UMLS:C1517770 VHOG:0000166 XAO:0000240 ZFA:0000122 uberon lens placodes placoda lentis UBERON:0003073 lens placode NCBIBook:NBK53175 A thickened portion of ectoderm which serves as the precursor to the lens. SOX2 and Pou2f1 are involved in its development[WP]. ZFIN:curator Ectodermal primordium of the lens of the eye. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000122 TAO ZFIN:curator (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG] 2012-09-17 VHOG:0000166 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 Classical transplantation experiments using amphibian embryos suggested that the optic vesicle is the source of lens-inducing signals sufficient to generate lens tissues in competent ectoderm (reviewed in Grainger et al., 1996). More recent findings suggest a multistep model for lens induction. There is now good evidence that lens specification occurs at the neurula stage, before the optic vesicle contact the surface ectoderm, and that neural crest cell migration in the frontonasal region is required to restrict the position of the lens placode (Bailey et al., 2006) NCBIBook:NBK53175 UMLS:C1517770 ncithesaurus:Lens_Placodes lens placodes ZFA:0000122 placoda lentis Paired organ that connects the primitive kidney Wolffian body (or mesonephros) to the cloaca and serves as the anlage for certain male reproductive organs. the Wolffian duct is what remains of the pronephric duct after the atrophy of the pronephros[WP]. In Zebrafish: Duct of the adult kidney (mesonephros), present bilaterally ventral to the somites and leading to the cloacal chamber[ZFA]. Consider adding subclasses for male and female specific variants TODO - mesonephric portion of the nephric duct Anatomical structure consisting of either of a pair of longitudinal ducts which carry urine and in males, sperm, to the cloaca.[AAO] The first-formed kidney duct, which drains the kidney of most anamniotes and becomes the ductus deferens of male amniotes. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-3, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] (...) in all craniates, the archinephric duct develops in embryogeny.[well established][VHOG] In the male the Wolffian duct persists, and forms for example the epididymis, the ductus deferens, the ejaculatory duct, seminal vesicle and efferent ducts. AAO:0000637 EHDAA2:0001243 EHDAA:1590 EMAPA:16577 GAID:1315 MESH:A16.254.940 NCIT:C26469 TAO:0000546 UMLS:C0043204 VHOG:0000082 XAO:0000242 ZFA:0000546 Wolffian duct uberon Leydig's duct archinephric duct ductus mesonephricus; ductus Wolffi renal duct UBERON:0003074 mesonephric duct GO EHDAA2 Paired organ that connects the primitive kidney Wolffian body (or mesonephros) to the cloaca and serves as the anlage for certain male reproductive organs. the Wolffian duct is what remains of the pronephric duct after the atrophy of the pronephros[WP]. In Zebrafish: Duct of the adult kidney (mesonephros), present bilaterally ventral to the somites and leading to the cloacal chamber[ZFA]. ZFIN:curator Anatomical structure consisting of either of a pair of longitudinal ducts which carry urine and in males, sperm, to the cloaca.[AAO] 2012-06-20 AAO:0000637 AAO AAO:BJB The first-formed kidney duct, which drains the kidney of most anamniotes and becomes the ductus deferens of male amniotes. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-3, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] 2012-09-17 VHOG:0000082 VHOG (...) in all craniates, the archinephric duct develops in embryogeny.[well established][VHOG] 2012-09-17 VHOG:0000082 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.686 UMLS:C0043204 ncithesaurus:Mesonephric_Duct Wolffian duct GOC:yaf ZFA:0000546 Leydig's duct archinephric duct VHOG:0000082 ductus mesonephricus; ductus Wolffi A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA] The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO] (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] AAO:0011072 BTO:0001765 DHBA:10153 DMBA:15565 EHDAA:346 EHDAA:902 EMAPA:35593 FMA:293879 NCIT:C34225 RETIRED_EHDAA2:0001252 TAO:0000132 UMLS:C0920623 VHOG:0000068 XAO:0000249 ZFA:0000132 uberon lamina neuralis presumptive central nervous system UBERON:0003075 neural plate Wikipedia Bgee:AN A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA] ISBN:0815318960 OMD:neural+plate ZFIN:curator The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000132 TAO ZFIN:curator (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] 2012-09-17 VHOG:0000068 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 UMLS:C0920623 ncithesaurus:Neural_Plate lamina neuralis (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] AAO:0011082 TAO:0007037 VHOG:0001383 XAO:0000250 ZFA:0007037 uberon UBERON:0003076 posterior neural tube lexical (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] 2012-09-17 VHOG:0001383 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO] Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO] Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG] note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here) AAO:0010568 EFO:0003515 EMAPA:16183 EMAPA:16751 FMA:293145 NCIT:C34244 TAO:0000255 UMLS:C1284009 VHOG:0000114 XAO:0000259 ZFA:0000255 paraxial mesenchyme somitic mesoderm uberon mesoderma paraxiale UBERON:0003077 paraxial mesoderm EHDAA2 Bgee:AN The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO] GO:0048339 Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO] 2012-06-20 AAO:0010568 AAO AAO:EJS Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG] 2012-09-17 VHOG:0000114 VHOG DOI:10.1002/dvdy.21177 Kusakabe R and Kuratani S. Evolutionary perspectives from development of mesodermal components in the lamprey. Developmental dynamics (2007) note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here) ZFA UMLS:C1284009 ncithesaurus:Paraxial_Mesoderm paraxial mesenchyme ZFA:0000255 somitic mesoderm ISBN:9780878932504 mesoderma paraxiale Focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches and that produce the neuroblasts that migrate and condense to form the distal cranial ganglia. Focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches and that produce the neuroblasts that migrate and condense to form the distal cranial ganglia. [Graham_A, The_development_and_evolution_of_the_pharyngeal_arches._J_Anat_(2001)_199:_133-141][VHOG] These (the epibranchial placodes) are focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches in all vertebrates, and they produce the neuroblasts which migrate and condense to form the distal cranial ganglia: the geniculate, petrosal and nodose ganglia. (...) The one substantial difference between the vertebrate pharyngeal arches and those of the protochordates is the presence of the epibranchial placodes but the evolution of these structures was undoubtedly driven by the endoderm.[well established][VHOG] Epibranchial placodes-derived neurons innervate internal organs to transmit information such as heart rate, blood pressure, and visceral distension from the periphery to the central nervous system (Baker and Bronner-Fraser, 2001). From rostral to caudal the epibranchial placodes comprise the geniculate, petrosal, and nodose placodes, each associated in sequence with the first, second and third branchial clefts. Each placode contributes sensory neurons to cranial nerves VII (facial nerve), IX (glossopharyngeal nerve), and X (vagal nerve), respectively in XAO this develops_from dorsolateral placode, but in NBK53175, this is a separate group AAO:0011036 EFO:0003455 FMA:293968 TAO:0001294 VHOG:0000117 XAO:0000284 ZFA:0001294 epibranchial placodes uberon ventrolateral placode UBERON:0003078 epibranchial placode NCBIBook:NBK53175 ZFA ZFA EHDAA2-abduced Focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches and that produce the neuroblasts that migrate and condense to form the distal cranial ganglia. VHOG:0000117 Focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches and that produce the neuroblasts that migrate and condense to form the distal cranial ganglia. [Graham_A, The_development_and_evolution_of_the_pharyngeal_arches._J_Anat_(2001)_199:_133-141][VHOG] 2012-09-17 VHOG:0000117 VHOG These (the epibranchial placodes) are focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches in all vertebrates, and they produce the neuroblasts which migrate and condense to form the distal cranial ganglia: the geniculate, petrosal and nodose ganglia. (...) The one substantial difference between the vertebrate pharyngeal arches and those of the protochordates is the presence of the epibranchial placodes but the evolution of these structures was undoubtedly driven by the endoderm.[well established][VHOG] 2012-09-17 VHOG:0000117 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A, The development and evolution of the pharyngeal arches. J Anat (2001) Epibranchial placodes-derived neurons innervate internal organs to transmit information such as heart rate, blood pressure, and visceral distension from the periphery to the central nervous system (Baker and Bronner-Fraser, 2001). From rostral to caudal the epibranchial placodes comprise the geniculate, petrosal, and nodose placodes, each associated in sequence with the first, second and third branchial clefts. Each placode contributes sensory neurons to cranial nerves VII (facial nerve), IX (glossopharyngeal nerve), and X (vagal nerve), respectively NCBIBook:NBK53175 in XAO this develops_from dorsolateral placode, but in NBK53175, this is a separate group XAO epibranchial placodes ZFA:0001294 ventrolateral placode ISBN10:0471888893 TODO - add grouping class for the anterior end of the neural tube at all stages (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] AAO:0011012 TAO:0007038 VHOG:0001384 XAO:0000307 ZFA:0007038 uberon UBERON:0003080 anterior neural tube lexical (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] 2012-09-17 VHOG:0001384 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP]. Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO] The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG] subclass of mesoderm in ZFA. UBERON:0006258 AAO:0010574 EHDAA2:0000919 EHDAA:379 EMAPA:16179 FMA:293149 NCIT:C34199 TAO:0000121 UMLS:C1517749 VHOG:0000118 XAO:0000311 ZFA:0000121 LPM lateral mesoderm uberon lateral plate lateral plate mesenchyme mesoderma laminae lateralis UBERON:0003081 lateral plate mesoderm EHDAA2 EHDAA2 VHOG Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP]. MP:0010117 Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO] 2012-06-20 AAO:0010574 AAO AAO:EJS The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] 2012-09-17 VHOG:0000118 VHOG A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG] 2012-09-17 VHOG:0000118 VHOG DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000) subclass of mesoderm in ZFA. ZFA UMLS:C1517749 ncithesaurus:Lateral_Mesoderm LPM ZFA:0000121 lateral mesoderm GO:0048368 lateral plate mesenchyme EHDAA2:0000919 mesoderma laminae lateralis A transitional population of migrating mesenchymal cells that derive from somites and that will become muscle cells. The term 'myotome' is also used to describe the muscles served by a single nerve root / spinal segment - consider adding new class, myomere. Portion of the somites giving rise to body wall muscle masses. Kimmel et al, 1995.[TAO] In all vertebrates, the skeletal muscle of the body axis is chiefly derived from an early embryonic compartment, known as the myotome.[well established][VHOG] AAO:0011067 AEO:0001018 BTO:0000742 EHDAA2_RETIRED:0003431 EHDAA:1721 EHDAA:1727 EHDAA:1733 EHDAA:1739 EMAPA:32841 FMA:295658 NCIT:C34214 TAO:0001056 UMLS:C1513802 VHOG:0001244 XAO:0000315 ZFA:0001056 myomeres uberon muscle plate myomere myotome region myotomes myotomus UBERON:0003082 myotome AEO EHDAA2-abduced A transitional population of migrating mesenchymal cells that derive from somites and that will become muscle cells. AEO:0001018 Portion of the somites giving rise to body wall muscle masses. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0001056 TAO ZFIN:curator In all vertebrates, the skeletal muscle of the body axis is chiefly derived from an early embryonic compartment, known as the myotome.[well established][VHOG] 2012-09-17 VHOG:0001244 VHOG DOI:10.1038/sj.embor.embor920 Hollway GE, Currie PD, Myotome meanderings. Cellular morphogenesis and the making of muscle. EMBO Rep.(2003) UMLS:C1513802 ncithesaurus:Myotome_Region myomeres TAO:0001056 myotomus Trunk portion of the neural crest. The trunk neural crest lies between the vagal and sacral neural crest and gives rise to two groups of cells. One group migrates dorsolateral and populates the skin, forming pigment cells and the other migrates ventrolateral through the anterior sclerotome to become the epinephrine-producing cells of the adrenal gland and the neurons of the sympathetic nervous system. Some cells remain in the sclerotome to form the dorsal root ganglia [Wikipedia]. Post-cranial portion of the neural crest. Exact anatomical derivations not experimentally resolved in amphibians.[AAO] We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] AAO:0010582 EFO:0003605 EHDAA2:0001901 TAO:0001024 VHOG:0000062 XAO:0000319 ZFA:0001024 TNC uberon trunk crest UBERON:0003083 trunk neural crest Trunk portion of the neural crest. The trunk neural crest lies between the vagal and sacral neural crest and gives rise to two groups of cells. One group migrates dorsolateral and populates the skin, forming pigment cells and the other migrates ventrolateral through the anterior sclerotome to become the epinephrine-producing cells of the adrenal gland and the neurons of the sympathetic nervous system. Some cells remain in the sclerotome to form the dorsal root ganglia [Wikipedia]. ISBN:0815318960 Post-cranial portion of the neural crest. Exact anatomical derivations not experimentally resolved in amphibians.[AAO] 2012-06-20 AAO:0010582 AAO AAO:EJS We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] 2012-09-17 VHOG:0000062 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 TNC XAO:0000319 Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone. should probably be merged with heart rudiment. Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO] The fused aspects of ventral mesoderm, which have migrated from either side of the prechordal plate, and fused ventrally, just behind the cement gland. They will give rise to the endocardium at NF stage 27&28.[AAO] relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO] AAO:0011044 BTO:0001887 NCIT:C34276 TAO:0000028 UMLS:C1514450 XAO:0000336 ZFA:0000028 uberon cardiac field fused heart primordium UBERON:0003084 heart primordium Obol ZFA ZFA XAO Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone. ZFIN:curator Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO] 2012-08-14 TAO:0000028 TAO ZFIN:curator The fused aspects of ventral mesoderm, which have migrated from either side of the prechordal plate, and fused ventrally, just behind the cement gland. They will give rise to the endocardium at NF stage 27&28.[AAO] 2012-06-20 AAO:0011044 AAO XAO:curator relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO] 2012-08-14 TAO:0000028 TAO UMLS:C1514450 ncithesaurus:Primordium_of_the_Heart cardiac field ZFA:0000028 Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]. Skeletogenic portion of somites.[AAO] The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG] part_of somite in XAO AAO:0010571 AEO:0000212 EHDAA2:0003439 EMAPA:31159 FMA:295652 NCIT:C34287 TAO:0001080 UMLS:C0183176 VHOG:0000680 XAO:0000397 ZFA:0001080 sclerotomes uberon sclerotomus UBERON:0003089 sclerotome EHDAA2 EHDAA2 ZFA Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]. XB:curator Skeletogenic portion of somites.[AAO] 2012-06-20 AAO:0010571 AAO AAO:EJS The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG] 2012-09-17 VHOG:0000680 VHOG DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000) part_of somite in XAO XAO UMLS:C0183176 ncithesaurus:Sclerotome sclerotomes TAO:0001080 sclerotomus neural crest cells (NCCs) originating in the anterior part of the developing embryo and residing between the mid-diencephalon and the forming hindbrain; cranial NCCs migrate dorsolaterally to form the craniofacial mesenchyme that differentiates into various craniofacial cartilages and bones, cranial neurons, glia, and connective tissues of the face; these cells enter the pharyngeal pouches and arches where they give rise to thymic cells, bones of the middle ear and jaw (mandible), and the odontoblasts of the tooth primordia; like their counterparts in the trunk, cranial NCCs also contribute to the developing peripheral nervous system, along with the pigmented cell (i.e. melanocyte) lineage. Anterior most portion of the neural crest. Migrates in three highly conserved streams: mandibular, hyoid and branchial.[AAO] Neural crest that is part of the head.[TAO] We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] AAO:0010580 EFO:0003645 EHDAA2:0004420 EMAPA:16091 TAO:0001194 VHOG:0000063 XAO:0001001 ZFA:0001194 CNC cephalic neural crest cranial NCC population head NCC population uberon crista neuralis cranialis head crest head neural crest UBERON:0003099 cranial neural crest neural crest cells (NCCs) originating in the anterior part of the developing embryo and residing between the mid-diencephalon and the forming hindbrain; cranial NCCs migrate dorsolaterally to form the craniofacial mesenchyme that differentiates into various craniofacial cartilages and bones, cranial neurons, glia, and connective tissues of the face; these cells enter the pharyngeal pouches and arches where they give rise to thymic cells, bones of the middle ear and jaw (mandible), and the odontoblasts of the tooth primordia; like their counterparts in the trunk, cranial NCCs also contribute to the developing peripheral nervous system, along with the pigmented cell (i.e. melanocyte) lineage. MGI:anna Anterior most portion of the neural crest. Migrates in three highly conserved streams: mandibular, hyoid and branchial.[AAO] 2012-06-20 AAO:0010580 AAO AAO:EJS Neural crest that is part of the head.[TAO] 2012-08-14 TAO:0001194 TAO ZFIN:curator We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] 2012-09-17 VHOG:0000063 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 CNC XAO:0001001 cephalic neural crest EMAPA:16091 crista neuralis cranialis Gonochoristic organism that can produce female gametes. AAO:0010030 BILA:0000028 CARO:0000028 FBbt:00007011 FMA:67812 HAO:0000028 TAO:0000303 TGMA:0001839 XAO:0003005 ZFA:0000303 female human body uberon female UBERON:0003100 female organism Gonochoristic organism that can produce female gametes. CARO:0000028 female human body FMA:67812 female TAO:0000303 Anatomical structure that overlaps the outer epithelial layer and is adjacent to the space surrounding the organism. consider obsoleting. See issue/1305 Organism subdivision which is the collection of anatomical structures on the body surface.[ZFA] AAO:0010337 AEO_RETIRED:0000010 EHDAA2_RETIRED:0003010 TAO:0000292 VSAO:0000001 XAO:0003028 ZFA:0000292 galen:SurfaceRegion anatomical surface feature uberon surface feature surface region surface structures UBERON:0003102 surface structure Anatomical structure that overlaps the outer epithelial layer and is adjacent to the space surrounding the organism. Organism subdivision which is the collection of anatomical structures on the body surface.[ZFA] 2012-08-14 TAO:0000292 TAO ZFIN:curator anatomical surface feature EHDAA2:0003010 surface structures ZFA:0000292 Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types. this class was introduced for consistency with CARO. However, in this ontology we typically classify organs directly under 'organ' rather than subdividing into compound and simple organs AAO:0010015 AEO:0000024 BILA:0000024 CARO:0000024 EHDAA2:0003024 HAO:0000024 TADS:0000598 TAO:0000496 TGMA:0001837 VHOG:0001723 XAO:0003041 ZFA:0000496 uberon organ UBERON:0003103 compound organ Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types. CARO:0000024 Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage[XAO]. A mesh-like cell arrangement, less compact than an epithelium[ZFA]. The part of the embryonic mesoderm, consisting of loosely packed, unspecialized cells set in a gelatinous ground substance, from which connective tissue, bone, cartilage, and the circulatory and lymphatic systems develop[BTO]. the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO] Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO] mesenchymal AAO:0010427 AEO:0000145 BTO:0001393 CALOHA:TS-0620 EHDAA2:0003145 EV:0100007 NCIT:C13301 TAO:0000393 UMLS:C0162415 VHOG:0000170 XAO:0003046 ZFA:0000393 mesenchymal tissue mesenchyme tissue portion of mesenchymal tissue portion of mesenchyme tissue uberon mesenchyma UBERON:0003104 mesenchyme Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage[XAO]. A mesh-like cell arrangement, less compact than an epithelium[ZFA]. The part of the embryonic mesoderm, consisting of loosely packed, unspecialized cells set in a gelatinous ground substance, from which connective tissue, bone, cartilage, and the circulatory and lymphatic systems develop[BTO]. BTO:0001393 ZFIN:curator A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000393 TAO ZFIN:curator Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO] 2012-06-20 AAO:0010427 AAO AAO:EJS UMLS:C0162415 ncithesaurus:Mesenchyme mesenchyma Subdivision of skeleton that includes all dermal bones in the cranial skeleton[ZFA,modified]. wikipedia treats skull roof and dermatocranium as synonymous, but some sources treat the roof as being part of the dermatocranium - see UBERONREF:0000007 Anatomical cluster that is part of the cranium and composed of dermally derived bones.[TAO] Anatomical cluster that is part of the cranium which consists of dermally derived bones.[AAO] AAO:0010154 TAO:0000863 VHOG:0001665 XAO:0003169 ZFA:0000863 dendrocranium exocranium dermal skull roof dermatocranial cover roof of skull skull roof uberon dermal bone cranium dermal part of skull dermal skull bones roofing bones of the skull skull exoskeleton UBERON:0003113 dermatocranium Subdivision of skeleton that includes all dermal bones in the cranial skeleton[ZFA,modified]. ZFA:0000863 Anatomical cluster that is part of the cranium and composed of dermally derived bones.[TAO] 2012-08-14 TAO:0000863 TAO ZFIN:curator Anatomical cluster that is part of the cranium which consists of dermally derived bones.[AAO] 2012-06-20 AAO:0010154 AAO AAO:BJB dendrocranium TAO:0000863 exocranium UBERONREF:0000007 dermal skull roof roof of skull skull roof dermal bone cranium ZFA:0000863 roofing bones of the skull contributes to development of the cartilage of the larynx, laryngeal, pharyngeal, and soft palate muscles, superior parathyroid gland, and C-cells of the thymus The second pharyngeal/branchial arch; arises as a thickening of the pharygeal wall between the first and second branchial clefts; contains the second aortic arch; forms part of the hyoid bone, tongue and facial musculature.[AAO] A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] in XAO, called branchial arch 2 and df VP4 4 AAO:0010366 EHDAA2:0000086 EHDAA:1663 EMAPA:16760 FMA:293035 TAO:0001599 VHOG:0000299 XAO:0000449 ZFA:0001607 4th branchial arch 4th pharyngeal arch 4th visceral arch fourth pharyngeal arch gill arch 2 second gill arch visceral arch 4 uberon 4th arch branchial arch 2 fourth visceral arch second branchial arch UBERON:0003115 pharyngeal arch 4 contributes to development of the cartilage of the larynx, laryngeal, pharyngeal, and soft palate muscles, superior parathyroid gland, and C-cells of the thymus MP:0006340 The second pharyngeal/branchial arch; arises as a thickening of the pharygeal wall between the first and second branchial clefts; contains the second aortic arch; forms part of the hyoid bone, tongue and facial musculature.[AAO] 2012-06-20 AAO:0010366 AAO ISBN:0-02-377110-0 A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] 2012-09-17 VHOG:0000299 VHOG DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005) in XAO, called branchial arch 2 and df VP4 XAO 4th branchial arch gill arch 2 ZFA:0001607 second gill arch ZFA:0001607 4th arch EHDAA2:0000086 branchial arch 2 AAO:0010366 ZFA:0001607 fourth visceral arch VHOG:0000299 second branchial arch ZFA:0001607 The 6th pharyngeal arch. contributes to the development of the sternocleidomastoid and trapezius muscles The forth in a series of paired bars in the wall of the pharynx, within which are formed the forth aortic arch and the cartilage bar of the visceral skeleton, forms and supports the gills.[AAO] A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] 6 UBERON:0004349 AAO:0010368 EHDAA2:0004075 EMAPA:32766 FMA:293047 TAO:0001601 VHOG:0001205 XAO:0000453 ZFA:0001609 6th arch gill arch 4 sixth branchial arch visceral arch 6 uberon 6th pharyngeal arch 6th visceral arch branchial arch 4 fourth branchial arch sixth pharyngeal arch sixth visceral arch UBERON:0003117 pharyngeal arch 6 The 6th pharyngeal arch. contributes to the development of the sternocleidomastoid and trapezius muscles MP:0006347 The forth in a series of paired bars in the wall of the pharynx, within which are formed the forth aortic arch and the cartilage bar of the visceral skeleton, forms and supports the gills.[AAO] 2012-06-20 AAO:0010368 AAO ISBN:0-02-377110-0 A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] 2012-09-17 VHOG:0001205 VHOG DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M, Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005) 6th arch EHDAA2:0004075 gill arch 4 ZFA:0001609 visceral arch 6 ZFA:0001609 6th pharyngeal arch VHOG:0001205 6th visceral arch VHOG:0001205 branchial arch 4 AAO:0010368 ZFA:0001609 fourth branchial arch sixth pharyngeal arch VHOG:0001205 sixth visceral arch XAO:0000453 The vessels formed within the first pair of branchial arches in embryogenesis Disappears early in development in tetrapods ZFA states that The paired aortic arch 1 arteries branch off of the ventral aorta, and empty into the right and left lateral dorsal aortas UBERON:0004371 AAO:0010415 EHDAA2:0000007 EMAPA:16202 EMAPA:16685 TAO:0005005 VHOG:0000149 XAO:0000342 ZFA:0005005 1st arch artery AA1 aortic arch 1 first aortic arch first branchial arch artery mandibular aortic arch uberon 1st aortic arch artery 1st branchial arch artery 1st pharyngeal arch artery first arch artery UBERON:0003118 pharyngeal arch artery 1 The vessels formed within the first pair of branchial arches in embryogenesis MP:0010355 ZFA states that The paired aortic arch 1 arteries branch off of the ventral aorta, and empty into the right and left lateral dorsal aortas ZFA 1st arch artery EMAPA:16685 AA1 ZFA:0005005 aortic arch 1 ZFA:0005005 first aortic arch XAO:0000342 mandibular aortic arch ZFA:0005005 1st aortic arch artery EMAPA:16685 1st branchial arch artery EMAPA:16685 1st pharyngeal arch artery EMAPA:16685 first arch artery EMAPA:16685 The vessels formed within the second pair of branchial arches in embryogenesis The first and second arches disappear early, but the dorsal end of the second gives origin to the stapedial artery, a vessel which atrophies in humans but persists in some mammals. It passes through the ring of the stapes and divides into supraorbital, infraorbital, and mandibular branches which follow the three divisions of the trigeminal nerve. The infraorbital and mandibular arise from a common stem, the terminal part of which anastomoses with the external carotid. On the obliteration of the stapedial artery this anastomosis enlarges and forms the internal maxillary artery, and the branches of the stapedial artery are now branches of this vessel. The common stem of the infraorbital and mandibular branches passes between the two roots of the auriculotemporal nerve and becomes the middle meningeal artery; the original supraorbital branch of the stapedial is represented by the orbital twigs of the middle meningeal[WP][Wikipedia:Aortic_arches#Arches_1_and_2]. The second in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 2 that is part of hyoid arch.[AAO] UBERON:0004372 AAO:0010418 EHDAA2:0000051 EMAPA:16203 EMAPA:16686 TAO:0005006 VHOG:0000148 XAO:0000343 ZFA:0005006 2nd arch artery AA2 aortic arch 2 hyoid aortic arch second aortic arch second branchial arch artery uberon 2nd aortic arch artery 2nd branchial arch artery 2nd pharyngeal arch artery UBERON:0003119 pharyngeal arch artery 2 The vessels formed within the second pair of branchial arches in embryogenesis MP:0010356 The first and second arches disappear early, but the dorsal end of the second gives origin to the stapedial artery, a vessel which atrophies in humans but persists in some mammals. It passes through the ring of the stapes and divides into supraorbital, infraorbital, and mandibular branches which follow the three divisions of the trigeminal nerve. The infraorbital and mandibular arise from a common stem, the terminal part of which anastomoses with the external carotid. On the obliteration of the stapedial artery this anastomosis enlarges and forms the internal maxillary artery, and the branches of the stapedial artery are now branches of this vessel. The common stem of the infraorbital and mandibular branches passes between the two roots of the auriculotemporal nerve and becomes the middle meningeal artery; the original supraorbital branch of the stapedial is represented by the orbital twigs of the middle meningeal[WP][Wikipedia:Aortic_arches#Arches_1_and_2]. The second in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 2 that is part of hyoid arch.[AAO] 2012-06-20 AAO:0010418 AAO ISBN:0-02-377110-0 2nd arch artery EHDAA2:0000051 AA2 ZFA:0005006 aortic arch 2 ZFA:0005006 hyoid aortic arch ZFA:0005006 second aortic arch XAO:0000343 2nd aortic arch artery EMAPA:16686 2nd branchial arch artery EMAPA:16686 2nd pharyngeal arch artery EMAPA:16686 The vessels formed within the fourth pair of branchial arches in embryogenesis Aortic arches 3 and 4 are not remodeled but are retained largely intact as the branchial arteries providing circulation through the gills. These areches are direct branches from the ventral aorta to the lateral dorsal aorta. Isogai et al. 2001.[TAO] The forth in a series paired arterial connections between the dorsal and ventral aortae, lies within the 4th branchial arch. The paired aortic arch 4 arteries branch directly from the ventral aorta to the lateral dorsal aorta, and are retained as the branchial arteries providing circulation through the gills in the adult.[AAO] The fourth right arch forms the right subclavian as far as the origin of its internal mammary branch; while the fourth left arch constitutes the arch of the aorta between the origin of the left carotid artery and the termination of the ductus arteriosus[WP][Wikipedia:Aortic_arches#Arch_4]. Normally, the left fourth arch becomes the aortic arch, the right fourth arch contributes to the innominate artery[http://emedicine.medscape.com/article/899609-overview] in birds it is the right fourth arch which forms the permanent aorta UBERON:0004350 AAO:0010420 EHDAA2:0000087 EMAPA:17004 TAO:0005008 XAO:0000355 ZFA:0005008 4th arch artery AA4 aortic arch 4 fourth aortic arch fourth branchial arch artery uberon 4th aortic arch artery 4th branchial arch artery 4th pharyngeal arch artery systemic arch UBERON:0003121 proximal right subclavian pharyngeal arch artery 4 The vessels formed within the fourth pair of branchial arches in embryogenesis MP:0006354 Aortic arches 3 and 4 are not remodeled but are retained largely intact as the branchial arteries providing circulation through the gills. These areches are direct branches from the ventral aorta to the lateral dorsal aorta. Isogai et al. 2001.[TAO] 2012-08-14 TAO:0005008 TAO ZFIN:curator The forth in a series paired arterial connections between the dorsal and ventral aortae, lies within the 4th branchial arch. The paired aortic arch 4 arteries branch directly from the ventral aorta to the lateral dorsal aorta, and are retained as the branchial arteries providing circulation through the gills in the adult.[AAO] 2012-06-20 AAO:0010420 AAO ISBN:0-02-377110-0 The fourth right arch forms the right subclavian as far as the origin of its internal mammary branch; while the fourth left arch constitutes the arch of the aorta between the origin of the left carotid artery and the termination of the ductus arteriosus[WP][Wikipedia:Aortic_arches#Arch_4]. 4th arch artery EHDAA2:0000087 AA4 ZFA:0005008 aortic arch 4 ZFA:0005008 fourth aortic arch XAO:0000355 4th aortic arch artery EMAPA:17004 4th branchial arch artery EMAPA:17004 4th pharyngeal arch artery EMAPA:17004 systemic arch ISBN10:0073040584 XAO:0000355 The vessels formed within the sixth pair of branchial arches in embryogenesis The fifth and sixth arches, which come on-line at approximately 2.5 dpf, have a common trunk from the ventral aorta and drain to the midline dorsal aorta via an independent route. The fifth and sixth aortic arches supply the trunk and tail with oxigenated blood. Isogai et al. 2001.[TAO] The sixth in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 6 artery is paired and has a common trunk with aortic arch 5 from the ventral aorta, and drains via a separate branch of the lateral dorsal aorta. It forms part of the pulmonary arteries, and in the later embryo, the ductus arteriosis. Aortic arches 5 and 6 together supply the trunk and tail with oxygenated blood.[AAO] The sixth right arch disappears; the sixth left arch gives off the pulmonary arteries and forms the ductus arteriosus; this duct remains pervious during the whole of fetal life, but then closes within the first few days after birth due to increased O2 concentration. Oxygen concentration causes the production of bradykinin which causes the ductus to constrict occluding all flow. Within 1-3 months, the ductus is obliterated and becomes the ligamentum arteriosus. His showed that in the early embryo the right and left arches each gives a branch to the lungs, but that later both pulmonary arteries take origin from the left arch[WP][Wikipedia:Aortic_arches#Arch_6]. the distal left sixth arch becomes the ductus arteriosus, the proximal sixth arches bilaterally contribute to the proximal branch pulmonary arteries UBERON:0004351 AAO:0010422 EHDAA2:0000102 EMAPA:17005 TAO:0005016 VHOG:0000144 XAO:0000353 ZFA:0005016 6th arch artery AA6 aortic arch 6 sixth aortic arch sixth branchial arch artery uberon 6th aortic arch artery 6th branchial arch artery 6th pharyngeal arch artery pulmonary arch UBERON:0003123 pharyngeal arch artery 6 The vessels formed within the sixth pair of branchial arches in embryogenesis MP:0006355 The fifth and sixth arches, which come on-line at approximately 2.5 dpf, have a common trunk from the ventral aorta and drain to the midline dorsal aorta via an independent route. The fifth and sixth aortic arches supply the trunk and tail with oxigenated blood. Isogai et al. 2001.[TAO] 2012-08-14 TAO:0005016 TAO ZFIN:curator The sixth in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 6 artery is paired and has a common trunk with aortic arch 5 from the ventral aorta, and drains via a separate branch of the lateral dorsal aorta. It forms part of the pulmonary arteries, and in the later embryo, the ductus arteriosis. Aortic arches 5 and 6 together supply the trunk and tail with oxygenated blood.[AAO] 2012-06-20 AAO:0010422 AAO ISBN:0-02-377110-0 The sixth right arch disappears; the sixth left arch gives off the pulmonary arteries and forms the ductus arteriosus; this duct remains pervious during the whole of fetal life, but then closes within the first few days after birth due to increased O2 concentration. Oxygen concentration causes the production of bradykinin which causes the ductus to constrict occluding all flow. Within 1-3 months, the ductus is obliterated and becomes the ligamentum arteriosus. His showed that in the early embryo the right and left arches each gives a branch to the lungs, but that later both pulmonary arteries take origin from the left arch[WP][Wikipedia:Aortic_arches#Arch_6]. the distal left sixth arch becomes the ductus arteriosus, the proximal sixth arches bilaterally contribute to the proximal branch pulmonary arteries 6th arch artery EMAPA:17005 AA6 ZFA:0005016 aortic arch 6 ZFA:0005016 sixth aortic arch XAO:0000353 6th aortic arch artery EMAPA:17005 6th branchial arch artery EMAPA:17005 6th pharyngeal arch artery EMAPA:17005 pulmonary arch ISBN10:0073040584 The trachea is the portion of the airway that attaches to the bronchi as it branches [GO:dph]. An elongated tube which carries air to and from the lungs.[AAO] The respiratory tube between the larynx and the bronchi. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] In primitive fishes and most tetrapods, the lungs of adults are usually paired. They lie ventral to the digestive tract and are connected to the outside environment through the trachea.[well established][VHOG] tracheal In birds, the trachea runs from the pharynx to the syrinx, from which the primary bronchi diverge. Swans have an unusually elongated trachea, part of which is coiled beneath the sternum; this may act as a resonator to amplify sound. In some birds, the cartilagenous rings are complete, and may even be ossified. In amphibians, the trachea is normally extremely short, and leads directly into the lungs, without clear primary bronchi. A longer trachea is, however found in some long-necked salamanders, and in caecilians. While there are irregular cartilagenous nodules on the amphibian trachea, these do not form the rings found in amniotes. The only vertebrate to have lungs, but no trachea, is Polypterus, in which the lungs arise directly from the pharynx. in mouse 15-18 C-rings, 15-20 in human. AAO:0010140 BTO:0001388 CALOHA:TS-1060 EFO:0000935 EHDAA2:0002066 EHDAA:3078 EMAPA:16853 EV:0100040 FMA:7394 GAID:361 MA:0000441 MAT:0000137 MESH:D014132 MIAA:0000137 NCIT:C12428 OpenCyc:Mx4rvViOX5wpEbGdrcN5Y29ycA UMLS:C0040578 VHOG:0000371 XAO:0000118 cartilaginous trachea vertebrate trachea windpipe uberon tracheal tubule UBERON:0003126 trachea EHDAA2 The trachea is the portion of the airway that attaches to the bronchi as it branches [GO:dph]. GO:0060438 An elongated tube which carries air to and from the lungs.[AAO] 2012-06-20 AAO:0010140 AAO AAO:BJB The respiratory tube between the larynx and the bronchi. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] 2012-09-17 VHOG:0000371 VHOG In primitive fishes and most tetrapods, the lungs of adults are usually paired. They lie ventral to the digestive tract and are connected to the outside environment through the trachea.[well established][VHOG] 2012-09-17 VHOG:0000371 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.409 in mouse 15-18 C-rings, 15-20 in human. ISBN10:0123813611 UMLS:C0040578 ncithesaurus:Trachea vertebrate trachea tracheal tubule BTO:0001388 Upper portion of the skull that excludes the mandible (when present in the organism). cranial the inclusion of the FMA class here is probably not quite correct, as this class includes as parts sutures, whereas this is not part of the bones of the cranium The term cranium can be ambiguous, in that it can refer to the neurocranium, or the neurocranium and the Facial skeleton BTO:0001328 EFO:0000831 EHDAA:6029 EMAPA:17680 FMA:71325 MA:0000316 MAT:0000340 MIAA:0000340 OpenCyc:Mx4rvVlEyJwpEbGdrcN5Y29ycA VHOG:0000334 bones of cranium ossa cranii set of bones of cranium skull minus mandible upper part of skull uberon calvarium epicranial plate skeletal system of head UBERON:0003128 cranium FMA-inferred Upper portion of the skull that excludes the mandible (when present in the organism). the inclusion of the FMA class here is probably not quite correct, as this class includes as parts sutures, whereas this is not part of the bones of the cranium FMA The term cranium can be ambiguous, in that it can refer to the neurocranium, or the neurocranium and the Facial skeleton WP bones of cranium FMA:71325 ossa cranii FMA:71325 FMA:TA set of bones of cranium FMA:71325 calvarium BTO:0001328 Anatomical structure that is part of the head consisting entirely of cranium and mandible[WP]. in FMA the skull is divided into orbit, neurocranium (8 parts), viscerocranium (26 parts). Here we have a separate overlapping division into cranium and mandible. in many ontologies, the structure called the cranium is inclusive of the mandible/lower jaw skeleton A skull that is missing a mandible is only a cranium; this is the source of a very commonly made error in terminology. Those animals having skulls are called craniates BTO:0001295 CALOHA:TS-2344 EHDAA2:0000325 EMAPA:17680 FMA:46565 GAID:82 MESH:D012886 NCIT:C12789 OpenCyc:Mx4rvVjOsZwpEbGdrcN5Y29ycA UMLS:C0037303 WikipediaCategory:Skull galen:Skull uberon cranial skeleton skeletal system of head UBERON:0003129 skull FMA Anatomical structure that is part of the head consisting entirely of cranium and mandible[WP]. in FMA the skull is divided into orbit, neurocranium (8 parts), viscerocranium (26 parts). Here we have a separate overlapping division into cranium and mandible. FMA A skull that is missing a mandible is only a cranium; this is the source of a very commonly made error in terminology. Those animals having skulls are called craniates WP UMLS:C0037303 ncithesaurus:Skull An organ involved in reproduction GO uses genitalia for the singular organ EMAPA:17381 EMAPA:37731 MA:0001752 MESH:D005835 NCIT:C25177 OpenCyc:Mx4rwO39aJwpEbGdrcN5Y29ycA TGMA:0000591 UMLS:C0017420 WBbt:0008422 genital organ reproductive system organ sex organ uberon genitalia UBERON:0003133 reproductive organ An organ involved in reproduction UBERON:xp GO uses genitalia for the singular organ GO EMAPA:37731 MA:th UMLS:C0017420 ncithesaurus:Genitalia genitalia A female organ involved in reproduction EMAPA:28540 MA:0000544 female organism reproductive organ female organism reproductive structure female organism reproductive system organ female organism sex organ female reproductive gland/organ female reproductive system organ female sex organ reproductive organ of female organism reproductive structure of female organism reproductive system organ of female organism sex organ of female organism uberon UBERON:0003134 female reproductive organ A female organ involved in reproduction UBERON:xp female organism reproductive organ OBOL:automatic female organism reproductive structure OBOL:automatic female organism reproductive system organ OBOL:automatic female organism sex organ OBOL:automatic female reproductive gland/organ MA:0000544 reproductive organ of female organism OBOL:automatic reproductive structure of female organism OBOL:automatic reproductive system organ of female organism OBOL:automatic sex organ of female organism OBOL:automatic Any sense organ that functions in (some) detection of chemical stimulus involved in sensory perception of taste (GO:0050912). FBbt:00005159 FMA:77853 gustatory organ system organ gustatory system organ organ of gustatory organ system organ of gustatory system organ of taste system taste organ taste system organ uberon UBERON:0003212 gustatory organ Any sense organ that functions in (some) detection of chemical stimulus involved in sensory perception of taste (GO:0050912). FBC:auto_generated_definition gustatory organ system organ OBOL:automatic gustatory system organ OBOL:automatic organ of gustatory organ system OBOL:automatic organ of gustatory system OBOL:automatic organ of taste system OBOL:automatic taste system organ OBOL:automatic Septum that divides the ovary, the basal portion of a carpel or group of fused carpels, that encloses the ovule(s)[GO]. uberon UBERON:0003218 ovary septum Septum that divides the ovary, the basal portion of a carpel or group of fused carpels, that encloses the ovule(s)[GO]. GO:0080126 one of the two embryological structures that give rise to the kidney (the other is the ureteric bud). The metanephric blastema mostly develops into nephrons, but can also form parts of the collecting duct system.[WP]. Metanephric mesenchyme is the tissue made up of loosely connected mesenchymal cells in the metanephros[GO] A mass of intermediate mesodermal cells around the distal end of the ureteric bud that gives rise to nephrons in the metanephric kidney. [TFD][VHOG] When the ureteric buds emerge from the nephric duct, they enter the metanephrogenic mesenchyme. The ureteric buds induce this mesenchymal tissue to condense around them and differentiate into the nephrons of the mammalian kidney. As this mesenchyme differentiates, it tells the ureteric bud to branch and grow.[well established][VHOG] EHDAA2:0004062 EHDAA:4041 EHDAA:5021 EHDAA:5915 EMAPA:17375 VHOG:0000540 metanephric blastema metanephric mesoderm metanephrogenic mesenchyme metanephros associated mesenchyme uberon UBERON:0003220 Genes: The positional specification of the metanephrogenic mesenchyme is negatively regulated by Foxc1 and Foxc2. Next the permanent kidney forming metanephrogenic mesenchyme is specified by Hox11 genes. The competence to respond to ureteric bud inducers is regulated by WT1. GDNF secretion restricted to posterior region by Robo2 and Sprouty1. The receptors for GDNF are synthesized in the nephric ducts and later in ureteric buds [ISBN:9780878932504 "Developmental Biology"] metanephric mesenchyme ISBN:9780878932504 one of the two embryological structures that give rise to the kidney (the other is the ureteric bud). The metanephric blastema mostly develops into nephrons, but can also form parts of the collecting duct system.[WP]. Metanephric mesenchyme is the tissue made up of loosely connected mesenchymal cells in the metanephros[GO] GO:0072075 A mass of intermediate mesodermal cells around the distal end of the ureteric bud that gives rise to nephrons in the metanephric kidney. [TFD][VHOG] 2012-09-17 VHOG:0000540 VHOG When the ureteric buds emerge from the nephric duct, they enter the metanephrogenic mesenchyme. The ureteric buds induce this mesenchymal tissue to condense around them and differentiate into the nephrons of the mammalian kidney. As this mesenchyme differentiates, it tells the ureteric bud to branch and grow.[well established][VHOG] 2012-09-17 VHOG:0000540 VHOG ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.462 metanephric blastema metanephric mesoderm metanephrogenic mesenchyme EHDAA:5021 metanephros associated mesenchyme RETIRED_EHDAA2:0001139 An epithelium that is part of a lower jaw [Automatically generated definition]. EHDAA2:0001019 EHDAA:7999 EMAPA:35516 VHOG:0000802 epithelial tissue of lower jaw epithelial tissue of ventral mandibular arch epithelium of ventral mandibular arch lower jaw epithelial tissue lower jaw epithelium ventral mandibular arch epithelial tissue ventral mandibular arch epithelium uberon UBERON:0003236 epithelium of lower jaw An epithelium that is part of a lower jaw [Automatically generated definition]. OBOL:automatic epithelial tissue of lower jaw OBOL:automatic epithelial tissue of ventral mandibular arch OBOL:automatic epithelium of ventral mandibular arch OBOL:automatic lower jaw epithelial tissue OBOL:automatic lower jaw epithelium OBOL:automatic ventral mandibular arch epithelial tissue OBOL:automatic ventral mandibular arch epithelium OBOL:automatic An epithelium that is part of a otic placode [Automatically generated definition]. check ZFA, placemeant, appears to refer to both adult structures and primordium EHDAA2:0001341 EHDAA:510 EMAPA:16197 VHOG:0000636 ZFA:0007068 epithelial tissue of otic placode otic epithelium otic placode epithelial tissue otic placode epithelium uberon UBERON:0003249 epithelium of otic placode An epithelium that is part of a otic placode [Automatically generated definition]. OBOL:automatic epithelial tissue of otic placode OBOL:automatic otic epithelium otic placode epithelial tissue OBOL:automatic otic placode epithelium OBOL:automatic An endoderm that is part of a foregut [Automatically generated definition]. TODO - check EHDAA2:0004568 EHDAA:524 foregut endoderm uberon UBERON:0003258 endoderm of foregut An endoderm that is part of a foregut [Automatically generated definition]. OBOL:automatic foregut endoderm OBOL:automatic An endoderm that is part of a midgut [Automatically generated definition]. TODO - check EHDAA:987 EMAPA:16257 RETIRED_EHDAA2:0001194 VHOG:0001080 midgut endoderm uberon UBERON:0003259 endoderm of midgut An endoderm that is part of a midgut [Automatically generated definition]. OBOL:automatic midgut endoderm OBOL:automatic An endoderm that is part of a hindgut [Automatically generated definition]. TODO - check EHDAA:979 RETIRED_EHDAA2:0000781 hindgut endoderm uberon UBERON:0003260 endoderm of hindgut An endoderm that is part of a hindgut [Automatically generated definition]. OBOL:automatic hindgut endoderm OBOL:automatic A portion of skeletal muscle tissue that is part of a eye [Automatically generated definition]. EHDAA2:0000486 EHDAA:2923 EMAPA:17844 eye skeletal muscle eye skeletal muscle tissue skeletal muscle tissue of eye uberon eye skeletal muscle group UBERON:0003269 skeletal muscle tissue of eye A portion of skeletal muscle tissue that is part of a eye [Automatically generated definition]. OBOL:automatic eye skeletal muscle OBOL:automatic eye skeletal muscle tissue OBOL:automatic skeletal muscle tissue of eye OBOL:automatic eye skeletal muscle group EHDAA2:0000486 A subdivision of the skeleton that corresponds to the lower part of the mouth. The lower jaw skeleton includes the following elements, when present: lower jaw teeth, the mandible and other lower jaw bones, and Meckel's cartilage. The ventral portion of the first pharyngeal arch, comprising the lower jaw.[TAO] The jaw joint of all jawed vertebrates, except for mammals, involves the quadrate and articular bones, or the posterior ends of the palatoquadrate and mandibular cartilages; A correlate of the conversion of the articular and quadrate bones to the malleus and incus is that all adult mammals have a jaw joint that lies between the dentary of the lower jaw and the squamosal bone of the skull roof.[well established][VHOG] Inclusion of the FMA class 'lower jaw' is debatable - this mostly corresponds to the lower jaw skeleton (with 'maxillary part of mouth' corresponding to the upper jaw region); however, the FMA class also includes gingiva. See also: https://github.com/obophenotype/mouse-anatomy-ontology/issues/102 lower jaw mandible AAO:0000274 EHDAA2:0004606 EHDAA:8005 EMAPA:17906 EMAPA:17910 FMA:54398 MA:0001906 TAO:0001273 VHOG:0000428 XAO:0003084 ZFA:0001273 lower jaw skeleton uberon mandibles mandibular series UBERON:0003278 skeleton of lower jaw EHDAA2 VHOG-modified A subdivision of the skeleton that corresponds to the lower part of the mouth. The lower jaw skeleton includes the following elements, when present: lower jaw teeth, the mandible and other lower jaw bones, and Meckel's cartilage. The ventral portion of the first pharyngeal arch, comprising the lower jaw.[TAO] 2012-08-14 TAO:0001273 TAO ZFIN:curator The jaw joint of all jawed vertebrates, except for mammals, involves the quadrate and articular bones, or the posterior ends of the palatoquadrate and mandibular cartilages; A correlate of the conversion of the articular and quadrate bones to the malleus and incus is that all adult mammals have a jaw joint that lies between the dentary of the lower jaw and the squamosal bone of the skull roof.[well established][VHOG] 2012-09-17 VHOG:0000428 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.241 and p.101 Inclusion of the FMA class 'lower jaw' is debatable - this mostly corresponds to the lower jaw skeleton (with 'maxillary part of mouth' corresponding to the upper jaw region); however, the FMA class also includes gingiva. See also: https://github.com/obophenotype/mouse-anatomy-ontology/issues/102 FMA lower jaw MA:0001906 lower jaw ZFA:0001273 mandible ZFA:0001273 lower jaw skeleton AAO:0000274 mandibles TAO:0001273 mandibular series ZFA:0001273 An endothelium that is part of a trachea. EHDAA:3082 RETIRED_EHDAA2:0002068 endothelium of windpipe trachea endothelium windpipe endothelium uberon UBERON:0003279 endothelium of trachea An endothelium that is part of a trachea. OBOL:automatic endothelium of windpipe OBOL:automatic trachea endothelium OBOL:automatic windpipe endothelium OBOL:automatic A gland that is part of a foregut [Automatically generated definition]. EHDAA2:0000567 EHDAA:950 EMAPA:16557 VHOG:0000650 foregut gland uberon UBERON:0003294 gland of foregut A gland that is part of a foregut [Automatically generated definition]. OBOL:automatic foregut gland OBOL:automatic Racemose mucous glands beneath the mucous membrane of the pharynx. BTO:0004849 EHDAA2:0001461 EHDAA:2967 FMA:55075 pharynx gland uberon glandulae pharyngeae UBERON:0003295 pharyngeal gland BTO Racemose mucous glands beneath the mucous membrane of the pharynx. Biology-Online_Dictionary:http://www.biology-online.org/dictionary/ pharynx gland EHDAA2:0001461 glandulae pharyngeae BTO:0004849 A gland that is part of a integumental system [Automatically generated definition]. EHDAA2:0000837 EHDAA:6522 EMAPA:17758 MA:0000144 VHOG:0000654 integumental gland integumental system gland integumentary gland uberon UBERON:0003297 gland of integumental system A gland that is part of a integumental system [Automatically generated definition]. OBOL:automatic integumental gland integumental system gland integumentary gland A blood island that is part of a mesoderm. in EHDAA2, gives rise to blood and dorsal aorta UBERON:0003305 EHDAA2:0003241 EHDAA:170 EMAPA:16115 mesoderm blood islands uberon mesenchyme blood island UBERON:0003304 mesoderm blood island EHDAA2 EHDAA2 A blood island that is part of a mesoderm. OBOL:automatic in EHDAA2, gives rise to blood and dorsal aorta EHDAA2 mesoderm blood islands EHDAA2:0003241 mesenchyme blood island OBOL:automatic Mesenchyme that is part of a developing camera-type eye. TODO - change mesenchyme relationships to precursor_of EHDAA2:0000485 EHDAA:2910 EMAPA:16673 VHOG:0001084 mesenchyme of eye uberon UBERON:0003314 eye mesenchyme EHDAA2 Mesenchyme that is part of a developing camera-type eye. OBOL:automatic mesenchyme of eye OBOL:automatic Mesenchyme that is part of a developing ovary [Automatically generated definition]. EHDAA2:0001362 EHDAA:8128 VHOG:0001441 female reproductive system gonad mesenchyme female reproductive system gonada mesenchyme gonad of female reproductive system mesenchyme gonada of female reproductive system mesenchyme mesenchyme of female reproductive system gonad mesenchyme of female reproductive system gonada mesenchyme of gonad of female reproductive system mesenchyme of gonada of female reproductive system ovary mesenchyme uberon UBERON:0003315 mesenchyme of ovary Mesenchyme that is part of a developing ovary [Automatically generated definition]. OBOL:automatic female reproductive system gonad mesenchyme OBOL:automatic female reproductive system gonada mesenchyme OBOL:automatic gonad of female reproductive system mesenchyme OBOL:automatic gonada of female reproductive system mesenchyme OBOL:automatic mesenchyme of female reproductive system gonad OBOL:automatic mesenchyme of female reproductive system gonada OBOL:automatic mesenchyme of gonad of female reproductive system OBOL:automatic mesenchyme of gonada of female reproductive system OBOL:automatic ovary mesenchyme OBOL:automatic Mesenchyme that is part of a developing lower jaw [Automatically generated definition]. EHDAA2:0001024 EHDAA:8003 EMAPA:17916 VHOG:0001069 lower jaw mesenchyme mesenchyme of ventral mandibular arch ventral mandibular arch mesenchyme uberon UBERON:0003324 mesenchyme of lower jaw EHDAA2 Mesenchyme that is part of a developing lower jaw [Automatically generated definition]. OBOL:automatic lower jaw mesenchyme OBOL:automatic mesenchyme of ventral mandibular arch OBOL:automatic ventral mandibular arch mesenchyme OBOL:automatic A submucosa that is part of an anal canal [Automatically generated definition]. EMAPA:27217 EMAPA:27227 EMAPA:27535 FMA:85399 anal canal submucosa anal canal viewed anatomically submucosa anal region submucosa anatomical anal canal submucosa submucosa of anal canal viewed anatomically submucosa of anal region submucosa of anatomical anal canal uberon UBERON:0003329 submucosa of anal canal A submucosa that is part of an anal canal [Automatically generated definition]. OBOL:automatic anal canal submucosa OBOL:automatic anal canal viewed anatomically submucosa OBOL:automatic anal region submucosa OBOL:automatic anatomical anal canal submucosa OBOL:automatic submucosa of anal canal viewed anatomically OBOL:automatic submucosa of anal region OBOL:automatic submucosa of anatomical anal canal OBOL:automatic The submucous layer of the wall of the rectum. BTO:0002114 EMAPA:27083 FMA:15034 rectal submucosa rectum submucosa tela submucosa recti uberon UBERON:0003330 submucosa of rectum The submucous layer of the wall of the rectum. BTO:0002114 rectal submucosa FMA:15034 rectum submucosa OBOL:automatic tela submucosa recti BTO:0002114 A submucosa that is part of a colon [Automatically generated definition]. EMAPA:27379 FMA:14985 MA:0003200 colon submucosa colonic submucosa large bowel submucosa submucosa of large bowel uberon UBERON:0003331 submucosa of colon A submucosa that is part of a colon [Automatically generated definition]. OBOL:automatic colon submucosa OBOL:automatic colonic submucosa FMA:14985 large bowel submucosa OBOL:automatic submucosa of large bowel OBOL:automatic A serous membrane that is part of a rectum [Automatically generated definition]. EMAPA:27087 FMA:15039 rectal serosa rectum serosa rectum serous membrane serous membrane of rectum visceral peritoneum of rectum uberon UBERON:0003334 serosa of rectum A serous membrane that is part of a rectum [Automatically generated definition]. OBOL:automatic rectal serosa FMA:15039 rectum serosa OBOL:automatic rectum serous membrane OBOL:automatic serous membrane of rectum OBOL:automatic visceral peritoneum of rectum FMA:15039 A serous membrane that is part of a colon [Automatically generated definition]. EMAPA:27387 FMA:14990 MA:0003199 colon serosa colon serous membrane colonic serosa large bowel serosa large bowel serous membrane serosa of large bowel serous membrane of colon serous membrane of large bowel visceral peritoneum of colon uberon UBERON:0003335 serosa of colon A serous membrane that is part of a colon [Automatically generated definition]. OBOL:automatic colon serosa OBOL:automatic colon serous membrane OBOL:automatic colonic serosa FMA:14990 large bowel serosa OBOL:automatic large bowel serous membrane OBOL:automatic serosa of large bowel OBOL:automatic serous membrane of colon OBOL:automatic serous membrane of large bowel OBOL:automatic visceral peritoneum of colon FMA:14990 A spatially aggregated collection of nerve cell bodies in the PNS, consisting of one or more subpopulations that share cell type, chemical phenotype, and connections. (CUMBO). we follow MA in including separate classes for ganglion and peripheral nervous system, even though for vertebrates gangia are always in the PNS BTO:0001123 EMAPA:32814 MA:0001161 peripheral nervous system ganglion uberon UBERON:0003338 ganglion of peripheral nervous system A spatially aggregated collection of nerve cell bodies in the PNS, consisting of one or more subpopulations that share cell type, chemical phenotype, and connections. (CUMBO). NIFSTD:birnlex_2548 we follow MA in including separate classes for ganglion and peripheral nervous system, even though for vertebrates gangia are always in the PNS MA peripheral nervous system ganglion OBOL:automatic A ganglion that is part of a central nervous system [Automatically generated definition]. this has no subclasses in FMA. In EHDAA2 and EMAPA it has only the cranial ganglia EHDAA2:0000227 EMAPA:16658 FMA:83843 central nervous system ganglion ganglion of neuraxis neuraxis ganglion uberon UBERON:0003339 ganglion of central nervous system A ganglion that is part of a central nervous system [Automatically generated definition]. OBOL:automatic this has no subclasses in FMA. In EHDAA2 and EMAPA it has only the cranial ganglia FMA central nervous system ganglion OBOL:automatic ganglion of neuraxis OBOL:automatic neuraxis ganglion OBOL:automatic A mucosa that is part of an anal canal [Automatically generated definition]. EMAPA:27531 FMA:74654 NCIT:C60784 UMLS:C0227414 anal canal mucosa anal canal mucosa of organ anal canal mucous membrane anal canal organ mucosa anal canal viewed anatomically mucosa anal canal viewed anatomically mucosa of organ anal canal viewed anatomically mucous membrane anal canal viewed anatomically organ mucosa anal mucosa anal mucous membrane anal region mucosa anal region mucosa of organ anal region mucous membrane anal region organ mucosa anatomical anal canal mucosa anatomical anal canal mucosa of organ anatomical anal canal mucous membrane anatomical anal canal organ mucosa mucosa of anal canal viewed anatomically mucosa of anal region mucosa of anatomical anal canal mucosa of organ of anal canal mucosa of organ of anal canal viewed anatomically mucosa of organ of anal region mucosa of organ of anatomical anal canal mucous membrane of anal canal mucous membrane of anal canal viewed anatomically mucous membrane of anal region mucous membrane of anatomical anal canal organ mucosa of anal canal organ mucosa of anal canal viewed anatomically organ mucosa of anal region organ mucosa of anatomical anal canal uberon UBERON:0003342 mucosa of anal canal A mucosa that is part of an anal canal [Automatically generated definition]. OBOL:automatic UMLS:C0227414 ncithesaurus:Anal_Mucosa anal canal mucosa OBOL:automatic anal canal mucosa of organ OBOL:automatic anal canal mucous membrane OBOL:automatic anal canal organ mucosa OBOL:automatic anal canal viewed anatomically mucosa OBOL:automatic anal canal viewed anatomically mucosa of organ OBOL:automatic anal canal viewed anatomically mucous membrane OBOL:automatic anal canal viewed anatomically organ mucosa OBOL:automatic anal mucosa FMA:74654 anal mucous membrane FMA:74654 anal region mucosa OBOL:automatic anal region mucosa of organ OBOL:automatic anal region mucous membrane OBOL:automatic anal region organ mucosa OBOL:automatic anatomical anal canal mucosa OBOL:automatic anatomical anal canal mucosa of organ OBOL:automatic anatomical anal canal mucous membrane OBOL:automatic anatomical anal canal organ mucosa OBOL:automatic mucosa of anal canal viewed anatomically OBOL:automatic mucosa of anal region OBOL:automatic mucosa of anatomical anal canal OBOL:automatic mucosa of organ of anal canal OBOL:automatic mucosa of organ of anal canal viewed anatomically OBOL:automatic mucosa of organ of anal region OBOL:automatic mucosa of organ of anatomical anal canal OBOL:automatic mucous membrane of anal canal OBOL:automatic mucous membrane of anal canal viewed anatomically OBOL:automatic mucous membrane of anal region OBOL:automatic mucous membrane of anatomical anal canal OBOL:automatic organ mucosa of anal canal OBOL:automatic organ mucosa of anal canal viewed anatomically OBOL:automatic organ mucosa of anal region OBOL:automatic organ mucosa of anatomical anal canal OBOL:automatic A mucosa that is part of a oral opening [Automatically generated definition]. EMAPA:26937 mucosa of oral opening mucosa of oral part of face mucosa of organ of oral opening mucosa of organ of oral part of face mucosa of organ of oral region mucosa of organ of subdivision of mouth mucosa of subdivision of mouth mucous membrane of oral opening mucous membrane of oral part of face mucous membrane of oral region mucous membrane of subdivision of mouth oral opening mucosa oral opening mucosa of organ oral opening mucous membrane oral opening organ mucosa oral part of face mucosa oral part of face mucosa of organ oral part of face mucous membrane oral part of face organ mucosa oral region mucosa oral region mucosa of organ oral region mucous membrane oral region organ mucosa organ mucosa of oral opening organ mucosa of oral part of face organ mucosa of oral region organ mucosa of subdivision of mouth subdivision of mouth mucosa subdivision of mouth mucosa of organ subdivision of mouth mucous membrane subdivision of mouth organ mucosa uberon UBERON:0003343 mucosa of oral region A mucosa that is part of a oral opening [Automatically generated definition]. OBOL:automatic mucosa of oral opening OBOL:automatic mucosa of oral part of face OBOL:automatic mucosa of organ of oral opening OBOL:automatic mucosa of organ of oral part of face OBOL:automatic mucosa of organ of oral region OBOL:automatic mucosa of organ of subdivision of mouth OBOL:automatic mucosa of subdivision of mouth OBOL:automatic mucous membrane of oral opening OBOL:automatic mucous membrane of oral part of face OBOL:automatic mucous membrane of oral region OBOL:automatic mucous membrane of subdivision of mouth OBOL:automatic oral opening mucosa OBOL:automatic oral opening mucosa of organ OBOL:automatic oral opening mucous membrane OBOL:automatic oral opening organ mucosa OBOL:automatic oral part of face mucosa OBOL:automatic oral part of face mucosa of organ OBOL:automatic oral part of face mucous membrane OBOL:automatic oral part of face organ mucosa OBOL:automatic oral region mucosa OBOL:automatic oral region mucosa of organ OBOL:automatic oral region mucous membrane OBOL:automatic oral region organ mucosa OBOL:automatic organ mucosa of oral opening OBOL:automatic organ mucosa of oral part of face OBOL:automatic organ mucosa of oral region OBOL:automatic organ mucosa of subdivision of mouth OBOL:automatic subdivision of mouth mucosa OBOL:automatic subdivision of mouth mucosa of organ OBOL:automatic subdivision of mouth mucous membrane OBOL:automatic subdivision of mouth organ mucosa OBOL:automatic A mucosa that is part of a rectum [Automatically generated definition]. CALOHA:TS-2107 EMAPA:27081 FMA:15033 MA:0003218 mucosa of organ of rectum mucous membrane of rectum organ mucosa of rectum rectal mucosa rectal mucous membrane rectum mucosa rectum mucosa of organ rectum mucous membrane rectum organ mucosa uberon UBERON:0003346 mucosa of rectum A mucosa that is part of a rectum [Automatically generated definition]. OBOL:automatic mucosa of organ of rectum OBOL:automatic mucous membrane of rectum OBOL:automatic organ mucosa of rectum OBOL:automatic rectal mucosa FMA:15033 rectal mucous membrane FMA:15033 rectum mucosa OBOL:automatic rectum mucosa of organ OBOL:automatic rectum mucous membrane OBOL:automatic rectum organ mucosa OBOL:automatic A layer of epithelial cells on the surface of the mucosa. BTO:0003752 uberon lamina epithelialis mucosa lamina epithelialis mucosae UBERON:0003350 lies on top of lamina propria epithelium of mucosa A layer of epithelial cells on the surface of the mucosa. BTO:0003752 lamina epithelialis mucosa BTO:0003752 lamina epithelialis mucosae BTO:0003752 An epithelium that is part of a pharynx [Automatically generated definition]. Epithelium lining the pharynx consisting largely of simple columnar epithelium with a short segment (1mm) of stratified squamous epithelium on the ventral side. Chen et al, 2007.[TAO] BSA:0000112 BTO:0005240 EMAPA:16708 MA:0002725 RETIRED_EHDAA2:0001460 TAO:0001174 XAO:0003202 ZFA:0001174 epithelial tissue of pharynx epithelium of pharynx pharynx epithelial tissue pharynx epithelium uberon UBERON:0003351 pharyngeal epithelium ZFA ZFA An epithelium that is part of a pharynx [Automatically generated definition]. OBOL:automatic Epithelium lining the pharynx consisting largely of simple columnar epithelium with a short segment (1mm) of stratified squamous epithelium on the ventral side. Chen et al, 2007.[TAO] 2012-08-14 TAO:0001174 TAO ZFIN:curator epithelial tissue of pharynx OBOL:automatic epithelium of pharynx OBOL:automatic pharynx epithelial tissue OBOL:automatic pharynx epithelium OBOL:automatic An epithelium that is part of a midgut. BTO:0005053 EHDAA2:0001195 EMAPA:16569 MA:0003205 epithelial tissue of midgut midgut epithelial tissue midgut epithelium uberon UBERON:0003352 epithelium of midgut BTO An epithelium that is part of a midgut. OBOL:automatic epithelial tissue of midgut OBOL:automatic midgut epithelial tissue OBOL:automatic midgut epithelium BTO:0005053 midgut epithelium OBOL:automatic An epithelium that is part of a hindgut [Automatically generated definition]. EHDAA2:0000782 EMAPA:16717 MA:0003206 epithelial tissue of hindgut hindgut epithelial tissue hindgut epithelium uberon UBERON:0003353 epithelium of hindgut An epithelium that is part of a hindgut [Automatically generated definition]. OBOL:automatic epithelial tissue of hindgut OBOL:automatic hindgut epithelial tissue OBOL:automatic hindgut epithelium OBOL:automatic An epithelium that is part of a rectum [Automatically generated definition]. CALOHA:TS-2066 EHDAA2:0001594 EMAPA:17898 FMA:17510 MA:0003219 VHOG:0001037 epithelial tissue of rectum rectal epithelium rectum epithelial tissue rectum epithelium uberon UBERON:0003354 epithelium of rectum An epithelium that is part of a rectum [Automatically generated definition]. OBOL:automatic epithelial tissue of rectum OBOL:automatic rectal epithelium FMA:17510 rectum epithelial tissue OBOL:automatic rectum epithelium OBOL:automatic An epithelium that is part of a right lung [Automatically generated definition]. EMAPA:17663 MA:0003132 epithelial tissue of right lung right lung epithelial tissue right lung epithelium uberon UBERON:0003364 epithelium of right lung An epithelium that is part of a right lung [Automatically generated definition]. OBOL:automatic epithelial tissue of right lung OBOL:automatic right lung epithelial tissue OBOL:automatic right lung epithelium OBOL:automatic An epithelium that is part of a left lung [Automatically generated definition]. EMAPA:17655 MA:0003131 epithelial tissue of left lung left lung epithelial tissue left lung epithelium uberon UBERON:0003365 epithelium of left lung An epithelium that is part of a left lung [Automatically generated definition]. OBOL:automatic epithelial tissue of left lung OBOL:automatic left lung epithelial tissue OBOL:automatic left lung epithelium OBOL:automatic An unilaminar epithelium that surrounds a pelvic appendage bud. UBERON:0005232 EHDAA2:0001034 EMAPA:16780 VHOG:0001048 hindlimb ectoderm hindlimb bud ectoderm hindlimb ectoderm lower limb bud ectoderm pelvic fin bud ectoderm uberon leg ectoderm UBERON:0003371 pelvic appendage bud ectoderm EHDAA2 EHDAA2 An unilaminar epithelium that surrounds a pelvic appendage bud. OBOL:automatic hindlimb ectoderm VHOG:0001048 hindlimb bud ectoderm EMAPA:16780 hindlimb bud ectoderm hindlimb ectoderm VHOG:0001048 lower limb bud ectoderm EHDAA2:0001034 pelvic fin bud ectoderm leg ectoderm OBOL:automatic An unilaminar epithelium that surrounds a pectoral appendage bud. UBERON:0005231 UBERON:0005663 EHDAA2:0002134 EMAPA:16407 VHOG:0001047 forelimb bud ectoderm forelimb ectoderm pectoral fin bud ectoderm upper limb bud ectoderm wing ectoderm uberon arm ectoderm UBERON:0003372 pectoral appendage bud ectoderm EHDAA2 EHDAA2 An unilaminar epithelium that surrounds a pectoral appendage bud. OBOL:automatic forelimb bud ectoderm EMAPA:16407 forelimb bud ectoderm forelimb ectoderm VHOG:0001047 pectoral fin bud ectoderm upper limb bud ectoderm EHDAA2:0002134 wing ectoderm Geisha:syn NCBITaxon:8782 arm ectoderm OBOL:automatic A portion of cardiac muscle tissue that is part of a right ventricle [Automatically generated definition]. EMAPA:17342 FMA:83452 VHOG:0001236 cardiac muscle tissue of right ventricle right ventricular cardiac muscle tissue uberon right ventricle cardiac muscle UBERON:0003381 cardiac muscle of right ventricle A portion of cardiac muscle tissue that is part of a right ventricle [Automatically generated definition]. OBOL:automatic cardiac muscle tissue of right ventricle FMA:83452 right ventricular cardiac muscle tissue GO:0003221 right ventricle cardiac muscle VHOG:0001236 A portion of cardiac muscle tissue that is part of a left ventricle [Automatically generated definition]. EMAPA:17339 FMA:83453 VHOG:0001234 cardiac muscle tissue of left ventricle left ventricular cardiac muscle tissue uberon left ventricle cardiac muscle UBERON:0003382 cardiac muscle of left ventricle A portion of cardiac muscle tissue that is part of a left ventricle [Automatically generated definition]. OBOL:automatic cardiac muscle tissue of left ventricle FMA:83453 left ventricular cardiac muscle tissue GO:0003220 left ventricle cardiac muscle VHOG:0001234 A portion of cardiac muscle tissue that is part of an interventricular septum [Automatically generated definition]. EHDAA2:0004158 EMAPA:17335 FMA:84084 VHOG:0000999 cardiac muscle of interventricular septum cardiac muscle tissue of interventricular septum interventricular septum cardiac muscle interventricular septum heart muscle interventricular septum myocardium uberon interventricular septum muscle UBERON:0003383 cardiac muscle tissue of interventricular septum A portion of cardiac muscle tissue that is part of an interventricular septum [Automatically generated definition]. OBOL:automatic cardiac muscle tissue of interventricular septum FMA:84084 interventricular septum cardiac muscle VHOG:0000999 interventricular septum heart muscle EHDAA2:0004158 interventricular septum myocardium VHOG:0000999 interventricular septum muscle A portion of skeletal muscle tissue that is part of a pharynx [Automatically generated definition]. EMAPA:18963 pharynx skeletal muscle pharynx skeletal muscle tissue skeletal muscle tissue of pharynx uberon UBERON:0003384 skeletal muscle tissue of pharynx A portion of skeletal muscle tissue that is part of a pharynx [Automatically generated definition]. OBOL:automatic pharynx skeletal muscle OBOL:automatic pharynx skeletal muscle tissue OBOL:automatic skeletal muscle tissue of pharynx OBOL:automatic any of the striated muscles that move the eye and include: superior rectus, inferior rectus, medial rectus, lateral rectus, superior oblique, inferior oblique, retractor bulbi Not clear if we need this and intra-ocular muscle. See issue #331. MA includes ciliary and iris smooth muscle EMAPA:18807 MA:0001268 ocular smooth muscle uberon UBERON:0003386 smooth muscle of eye any of the striated muscles that move the eye and include: superior rectus, inferior rectus, medial rectus, lateral rectus, superior oblique, inferior oblique, retractor bulbi MGI:cwg MP:0005247 ocular smooth muscle MA:0001268 A portion of smooth muscle tissue that is part of a trachea [Automatically generated definition]. UBERON:0004244 BTO:0001391 EMAPA:19192 FMA:262010 MA:0001863 NCIT:C49306 UMLS:C1710458 trachea smooth muscle tracheal smooth muscle uberon UBERON:0003387 smooth muscle of trachea A portion of smooth muscle tissue that is part of a trachea [Automatically generated definition]. OBOL:automatic UMLS:C1710458 ncithesaurus:Trachea_Smooth_Muscle_Tissue trachea smooth muscle MA:0001863 tracheal smooth muscle BTO:0001391 A cartilage element that is part of a respiratory system [Automatically generated definition]. EMAPA:18694 MA:0001818 apparatus respiratorius cartilage cartilage of apparatus respiratorius respiratory system cartilage uberon UBERON:0003406 cartilage of respiratory system A cartilage element that is part of a respiratory system [Automatically generated definition]. OBOL:automatic apparatus respiratorius cartilage OBOL:automatic cartilage of apparatus respiratorius OBOL:automatic respiratory system cartilage OBOL:automatic A gland that is part of a digestive tract [Automatically generated definition]. EMAPA:18815 MA:0003202 digestive tract gland gland of digestive tract gland of lower gastrointestinal tract gut gland lower gastrointestinal tract gland uberon UBERON:0003408 gland of digestive tract A gland that is part of a digestive tract [Automatically generated definition]. OBOL:automatic digestive tract gland OBOL:automatic gland of digestive tract OBOL:automatic gland of lower gastrointestinal tract OBOL:automatic gut gland MA:0003202 lower gastrointestinal tract gland OBOL:automatic Mesenchyme that is part of a pelvic appendage bud. Mesoderm part of pelvic fin bud.[TAO] EHDAA2:0001035 EMAPA:16781 TAO:0001386 ZFA:0001386 leg mesenchyme lower limb bud mesenchyme hindlimb bud mesenchyme mesoderm pelvic fin bud pelvic fin bud mesenchyme uberon UBERON:0003412 pelvic appendage bud mesenchyme Mesenchyme that is part of a pelvic appendage bud. OBOL:automatic Mesoderm part of pelvic fin bud.[TAO] 2012-08-14 TAO:0001386 TAO ZFIN:curator leg mesenchyme OBOL:automatic lower limb bud mesenchyme EHDAA2:0001035 hindlimb bud mesenchyme EMAPA:16781 mesoderm pelvic fin bud ZFA:0001386 pelvic fin bud mesenchyme Mesenchyme that is part of a pectoral appendage bud. Mesoderm that is part of the pectoral fin bud.[TAO] UBERON:0005703 EHDAA2:0002135 EHDAA:1703 EMAPA:16408 TAO:0000789 ZFA:0000789 arm mesenchyme forelimb bud mesenchyme mesoderm pectoral fin bud pectoral fin bud mesenchyme upper limb bud mesenchyme wing mesenchyme uberon UBERON:0003413 pectoral appendage bud mesenchyme Mesenchyme that is part of a pectoral appendage bud. OBOL:automatic Mesoderm that is part of the pectoral fin bud.[TAO] 2012-08-14 TAO:0000789 TAO ZFIN:curator arm mesenchyme OBOL:automatic forelimb bud mesenchyme EMAPA:16408 mesoderm pectoral fin bud ZFA:0000789 pectoral fin bud mesenchyme upper limb bud mesenchyme EHDAA2:0002135 wing mesenchyme OBOL:automatic An adipose tissue that is part of a dermis [Automatically generated definition]. MA:0000798 adipose tissue of dermis dermis fat tissue dermis fatty tissue fat tissue of dermis fatty tissue of dermis uberon UBERON:0003426 dermis adipose tissue An adipose tissue that is part of a dermis [Automatically generated definition]. OBOL:automatic adipose tissue of dermis OBOL:automatic dermis fat tissue OBOL:automatic dermis fatty tissue OBOL:automatic fat tissue of dermis OBOL:automatic fatty tissue of dermis OBOL:automatic A nerve that is part of an abdomen [Automatically generated definition]. MA:0000521 nerve of abdomen uberon UBERON:0003429 abdomen nerve A nerve that is part of an abdomen [Automatically generated definition]. OBOL:automatic nerve of abdomen OBOL:automatic A nerve that is part of a neck [Automatically generated definition]. EMAPA:37263 MA:0000588 neck (volume) nerve nerve of neck nerve of neck (volume) uberon UBERON:0003430 neck nerve A nerve that is part of a neck [Automatically generated definition]. OBOL:automatic EMAPA:37263 MA:th neck (volume) nerve OBOL:automatic nerve of neck OBOL:automatic nerve of neck (volume) OBOL:automatic Any nerve that innervates the iris. added for consistency with mouse ontologies. The term 'ciliary nerve' is usually used to denote either of the two nerves (with different origins) that innervate the iris, as well as ciliary muscles and cornea EMAPA:35449 MA:0001291 nerve of iris ciliary nerve uberon UBERON:0003438 iris nerve Any nerve that innervates the iris. UBERON:cjm nerve of iris OBOL:automatic A nerve that is part of the trunk region of the body (not to be confused with a nerve trunk). EMAPA:37264 MA:0000515 nerve of torso nerve of trunk torso nerve uberon trunk nerve UBERON:0003439 nerve of trunk region A nerve that is part of the trunk region of the body (not to be confused with a nerve trunk). EMAPA:37264 MA:th nerve of torso OBOL:automatic nerve of trunk OBOL:automatic torso nerve OBOL:automatic trunk nerve MA:0000515 A nerve that is located in a thoracic cavity [Automatically generated definition]. consider merging with thoracic nerve. In MA the only subclass is the phrenic nerve, which arises from a cervical nerve EMAPA:37267 MA:0000556 cavity of chest nerve cavity of thorax nerve chest cavity nerve nerve of cavity of chest nerve of cavity of thorax nerve of chest cavity nerve of pectoral cavity nerve of thoracic cavity pectoral cavity nerve uberon UBERON:0003443 thoracic cavity nerve A nerve that is located in a thoracic cavity [Automatically generated definition]. OBOL:automatic EMAPA:37267 MA:th cavity of chest nerve OBOL:automatic cavity of thorax nerve OBOL:automatic chest cavity nerve OBOL:automatic nerve of cavity of chest OBOL:automatic nerve of cavity of thorax OBOL:automatic nerve of chest cavity OBOL:automatic nerve of pectoral cavity OBOL:automatic nerve of thoracic cavity OBOL:automatic pectoral cavity nerve OBOL:automatic A nerve that is part of a pelvis [Automatically generated definition]. EMAPA:37269 MA:0000542 nerve of pelvis uberon UBERON:0003444 pelvis nerve A nerve that is part of a pelvis [Automatically generated definition]. OBOL:automatic EMAPA:37269 MA:th nerve of pelvis OBOL:automatic A bone that is part of a head [Automatically generated definition]. EMAPA:35996 MA:0000576 adult head bone adult head bone organ bone of adult head bone of head bone organ of adult head bone organ of head head bone organ uberon craniofacial bone UBERON:0003457 Different sources vary regarding which bones are craniofacial; e.g. hyoid bone head bone A bone that is part of a head [Automatically generated definition]. OBOL:automatic adult head bone OBOL:automatic adult head bone organ OBOL:automatic bone of adult head OBOL:automatic bone of head OBOL:automatic bone organ of adult head OBOL:automatic bone organ of head OBOL:automatic head bone organ OBOL:automatic craniofacial bone A bone that is part of a neck [Automatically generated definition]. EMAPA:37246 MA:0000584 OpenCyc:Mx4rvnpJSJwpEbGdrcN5Y29ycA bone of neck bone of neck (volume) bone organ of neck bone organ of neck (volume) neck (volume) bone neck (volume) bone organ neck bone organ uberon UBERON:0003458 neck bone A bone that is part of a neck [Automatically generated definition]. OBOL:automatic EMAPA:37246 MA:th bone of neck OBOL:automatic bone of neck (volume) OBOL:automatic bone organ of neck OBOL:automatic bone organ of neck (volume) OBOL:automatic neck (volume) bone OBOL:automatic neck (volume) bone organ OBOL:automatic neck bone organ OBOL:automatic A bone that is part of a facial skeleton [Automatically generated definition]. test whether 'facial bone' is an exact synonym EMAPA:19019 EMAPA:35924 MA:0001482 MA:0003159 NCIT:C63706 UMLS:C0015455 bone of facial skeleton facial bone facial skeleton bone uberon bone of viscerocranium viscerocranium bone UBERON:0003462 facial bone MA A bone that is part of a facial skeleton [Automatically generated definition]. OBOL:automatic UMLS:C0015455 ncithesaurus:Facial_Bone bone of facial skeleton OBOL:automatic facial bone EMAPA:19019 facial skeleton bone OBOL:automatic bone of viscerocranium OBOL:automatic viscerocranium bone OBOL:automatic A bone that is part of a trunk [Automatically generated definition]. EMAPA:36583 MA:0000512 bone of torso bone of trunk bone organ of torso bone organ of trunk torso bone torso bone organ trunk bone organ uberon UBERON:0003463 trunk bone A bone that is part of a trunk [Automatically generated definition]. OBOL:automatic bone of torso OBOL:automatic bone of trunk OBOL:automatic bone organ of torso OBOL:automatic bone organ of trunk OBOL:automatic torso bone OBOL:automatic torso bone organ OBOL:automatic trunk bone organ OBOL:automatic The ureteral branches of renal artery are small branches which supply the ureter. ureteric artery EMAPA:37676 FMA:70491 MA:0002074 uberon UBERON:0003468 ureteric segment of renal artery FMA FMA The ureteral branches of renal artery are small branches which supply the ureter. ureteric artery MA:0002074 EMAPA:37676 MA:th An artery that is part of a respiratory system [Automatically generated definition]. EMAPA:37569 MA:0001804 uberon UBERON:0003469 respiratory system artery An artery that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37569 MA:th The Iinferior labial artery (inferior labial branch of facial artery) arises near the angle of the mouth; it passes upward and forward beneath the Triangularis and, penetrating the Orbicularis oris, runs in a tortuous course along the edge of the lower lip between this muscle and the mucous membrane. It supplies the labial glands, the mucous membrane, and the muscles of the lower lip; and anastomoses with the artery of the opposite side, and with the mental branch of the inferior alveolar artery. EMAPA:37429 FMA:49567 MA:0001916 arteria labialis inferior inferior labial artery inferior labial branch of facial artery ramus labialis inferior (arteria facialis) ramus labialis inferior arteriae facialis uberon UBERON:0003471 artery of lower lip FMA The Iinferior labial artery (inferior labial branch of facial artery) arises near the angle of the mouth; it passes upward and forward beneath the Triangularis and, penetrating the Orbicularis oris, runs in a tortuous course along the edge of the lower lip between this muscle and the mucous membrane. It supplies the labial glands, the mucous membrane, and the muscles of the lower lip; and anastomoses with the artery of the opposite side, and with the mental branch of the inferior alveolar artery. EMAPA:37429 MA:th arteria labialis inferior inferior labial artery FMA:49567 inferior labial branch of facial artery FMA:49567 ramus labialis inferior (arteria facialis) FMA:TA ramus labialis inferior arteriae facialis An artery that is part of a thoracic cavity[cjm]. in MA, aorta is classified here - but this is problematic because the abdominal aorta is not in the thoracic cavity EMAPA:37241 MA:0001902 MESH:D013895 uberon thoracic artery UBERON:0003473 thoracic cavity artery An artery that is part of a thoracic cavity[cjm]. in MA, aorta is classified here - but this is problematic because the abdominal aorta is not in the thoracic cavity MA EMAPA:37241 MA:th thoracic artery MESH:A07.231.114.891 A vein that is part of a ureter [Automatically generated definition]. EMAPA:37679 MA:0002250 ureter vein vein of ureter uberon UBERON:0003475 ureteric vein A vein that is part of a ureter [Automatically generated definition]. OBOL:automatic EMAPA:37679 MA:th ureter vein OBOL:automatic vein of ureter OBOL:automatic A vein that is part of a respiratory system [Automatically generated definition]. EMAPA:37584 MA:0001809 MA:0001810 apparatus respiratorius vein respiratory system vein vein of apparatus respiratorius vein of respiratory system uberon UBERON:0003476 respiratory system venous blood vessel A vein that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37584 MA:th apparatus respiratorius vein OBOL:automatic respiratory system vein OBOL:automatic vein of apparatus respiratorius OBOL:automatic vein of respiratory system OBOL:automatic The inferior labial vein is the vein receiving blood from the lower lip. EMAPA:37202 FMA:52541 MA:0002253 inferior labial vein lower lip vein vena labialis inferior uberon venae labiales inferiores UBERON:0003478 vein of lower lip The inferior labial vein is the vein receiving blood from the lower lip. EMAPA:37202 MA:th inferior labial vein FMA:52541 lower lip vein OBOL:automatic vena labialis inferior venae labiales inferiores A vein that is part of a thoracic cavity [Automatically generated definition]. EMAPA:37242 MA:0001903 cavity of chest vein cavity of thorax vein chest cavity vein pectoral cavity vein vein of cavity of chest vein of cavity of thorax vein of chest cavity vein of pectoral cavity vein of thoracic cavity uberon UBERON:0003479 thoracic cavity vein A vein that is part of a thoracic cavity [Automatically generated definition]. OBOL:automatic EMAPA:37242 MA:th cavity of chest vein OBOL:automatic cavity of thorax vein OBOL:automatic chest cavity vein OBOL:automatic pectoral cavity vein OBOL:automatic vein of cavity of chest OBOL:automatic vein of cavity of thorax OBOL:automatic vein of chest cavity OBOL:automatic vein of pectoral cavity OBOL:automatic vein of thoracic cavity OBOL:automatic An endothelium of capillary that is part of a respiratory system [Automatically generated definition]. EMAPA:37575 MA:0001808 apparatus respiratorius blood capillary endothelium apparatus respiratorius capillary endothelium apparatus respiratorius capillary vessel endothelium apparatus respiratorius endothelium of blood capillary apparatus respiratorius endothelium of capillary apparatus respiratorius endothelium of capillary vessel blood capillary endothelium of apparatus respiratorius blood capillary endothelium of respiratory system capillary endothelium of apparatus respiratorius capillary endothelium of respiratory system capillary vessel endothelium of apparatus respiratorius capillary vessel endothelium of respiratory system endothelium of blood capillary of apparatus respiratorius endothelium of blood capillary of respiratory system endothelium of capillary of apparatus respiratorius endothelium of capillary of respiratory system endothelium of capillary vessel of apparatus respiratorius endothelium of capillary vessel of respiratory system respiratory system blood capillary endothelium respiratory system capillary vessel endothelium respiratory system endothelium of blood capillary respiratory system endothelium of capillary respiratory system endothelium of capillary vessel uberon UBERON:0003489 respiratory system capillary endothelium true An endothelium of capillary that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37575 MA:th apparatus respiratorius blood capillary endothelium OBOL:automatic apparatus respiratorius capillary endothelium OBOL:automatic apparatus respiratorius capillary vessel endothelium OBOL:automatic apparatus respiratorius endothelium of blood capillary OBOL:automatic apparatus respiratorius endothelium of capillary OBOL:automatic apparatus respiratorius endothelium of capillary vessel OBOL:automatic blood capillary endothelium of apparatus respiratorius OBOL:automatic blood capillary endothelium of respiratory system OBOL:automatic capillary endothelium of apparatus respiratorius OBOL:automatic capillary endothelium of respiratory system OBOL:automatic capillary vessel endothelium of apparatus respiratorius OBOL:automatic capillary vessel endothelium of respiratory system OBOL:automatic endothelium of blood capillary of apparatus respiratorius OBOL:automatic endothelium of blood capillary of respiratory system OBOL:automatic endothelium of capillary of apparatus respiratorius OBOL:automatic endothelium of capillary of respiratory system OBOL:automatic endothelium of capillary vessel of apparatus respiratorius OBOL:automatic endothelium of capillary vessel of respiratory system OBOL:automatic respiratory system blood capillary endothelium OBOL:automatic respiratory system capillary vessel endothelium OBOL:automatic respiratory system endothelium of blood capillary OBOL:automatic respiratory system endothelium of capillary OBOL:automatic respiratory system endothelium of capillary vessel OBOL:automatic A venule that is part of a respiratory system [Automatically generated definition]. EMAPA:37587 MA:0001813 apparatus respiratorius venule venule of apparatus respiratorius venule of respiratory system uberon UBERON:0003494 respiratory system venule A venule that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37587 MA:th apparatus respiratorius venule OBOL:automatic venule of apparatus respiratorius OBOL:automatic venule of respiratory system OBOL:automatic An arteriole that is part of a respiratory system [Automatically generated definition]. EMAPA:37568 MA:0001803 uberon UBERON:0003495 respiratory system arteriole true An arteriole that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37568 MA:th A blood vessel that is part of a head [Automatically generated definition]. EMAPA:36610 MA:0000575 adult head blood vessel blood vessel of adult head blood vessel of head uberon UBERON:0003496 head blood vessel true A blood vessel that is part of a head [Automatically generated definition]. OBOL:automatic adult head blood vessel OBOL:automatic blood vessel of adult head OBOL:automatic blood vessel of head OBOL:automatic A blood vessel that is part of an abdomen [Automatically generated definition]. MA:0000518 blood vessel of abdomen uberon UBERON:0003497 abdomen blood vessel UBERON:0012254 A blood vessel that is part of an abdomen [Automatically generated definition]. OBOL:automatic blood vessel of abdomen OBOL:automatic UBERON:0012254 abdominal aorta artery A blood vessel that is part of a heart [Automatically generated definition]. EMAPA:35397 MA:0002483 blood vessel of heart uberon cardiac blood vessel UBERON:0003498 heart blood vessel A blood vessel that is part of a heart [Automatically generated definition]. OBOL:automatic blood vessel of heart OBOL:automatic cardiac blood vessel EMAPA:35397 A blood vessel that is part of a brain [Automatically generated definition]. EMAPA:35182 MA:0002769 blood vessel of brain uberon UBERON:0003499 brain blood vessel A blood vessel that is part of a brain [Automatically generated definition]. OBOL:automatic blood vessel of brain OBOL:automatic A blood vessel that is part of a cornea [Automatically generated definition]. follow up on tracker item EMAPA:36611 MA:0001241 blood vessel of cornea cornea blood vessel uberon UBERON:0003500 corneal blood vessel A blood vessel that is part of a cornea [Automatically generated definition]. blood vessel of cornea OBOL:automatic cornea blood vessel OBOL:automatic A blood vessel that is part of a retina [Automatically generated definition]. EMAPA:36520 GAID:509 MA:0001317 MESH:D012171 XAO:0004153 blood vessel of inner layer of eyeball blood vessel of retina blood vessel of tunica interna of eyeball inner layer of eyeball blood vessel retinal blood vessel tunica interna of eyeball blood vessel uberon UBERON:0003501 retina blood vessel A blood vessel that is part of a retina [Automatically generated definition]. OBOL:automatic blood vessel of inner layer of eyeball OBOL:automatic blood vessel of retina OBOL:automatic blood vessel of tunica interna of eyeball OBOL:automatic inner layer of eyeball blood vessel OBOL:automatic retinal blood vessel OBOL:automatic tunica interna of eyeball blood vessel OBOL:automatic A blood vessel that is part of a neck [Automatically generated definition]. EMAPA:37236 MA:0000583 blood vessel of neck blood vessel of neck (volume) neck (volume) blood vessel uberon UBERON:0003502 neck blood vessel A blood vessel that is part of a neck [Automatically generated definition]. OBOL:automatic EMAPA:37236 MA:th blood vessel of neck OBOL:automatic blood vessel of neck (volume) OBOL:automatic neck (volume) blood vessel OBOL:automatic A blood vessel that is part of a respiratory system [Automatically generated definition]. EMAPA:35731 EMAPA:35995 MA:0001799 apparatus respiratorius blood vessel blood vessel of apparatus respiratorius blood vessel of respiratory system uberon UBERON:0003504 respiratory system blood vessel A blood vessel that is part of a respiratory system [Automatically generated definition]. OBOL:automatic apparatus respiratorius blood vessel OBOL:automatic blood vessel of apparatus respiratorius OBOL:automatic blood vessel of respiratory system OBOL:automatic A blood vessel that is part of a trachea. UBERON:0003525 EMAPA:35874 MA:0001852 blood vessel of trachea uberon UBERON:0003505 trachea blood vessel A blood vessel that is part of a trachea. OBOL:automatic blood vessel of trachea OBOL:automatic A blood vessel that is part of the arterial system. Includes artery, arteriole and aorta. EMAPA:35144 MA:0000061 uberon UBERON:0003509 only in MA - supertype of artery, arteriole, aorta. arterial blood vessel A blood vessel that is part of the arterial system. Includes artery, arteriole and aorta. A blood vessel that is part of a iris [Automatically generated definition]. EMAPA:37387 MA:0001290 ZFA:0005568 blood vessel of iris uberon UBERON:0003511 iris blood vessel A blood vessel that is part of a iris [Automatically generated definition]. OBOL:automatic EMAPA:37387 MA:th blood vessel of iris OBOL:automatic A blood vessel that is part of a lung [Automatically generated definition]. EMAPA:32867 MA:0002457 blood vessel of lung uberon pulmonary vascular element UBERON:0003512 lung blood vessel A blood vessel that is part of a lung [Automatically generated definition]. OBOL:automatic blood vessel of lung OBOL:automatic pulmonary vascular element EMAPA:32867 A blood vessel that is part of a trunk [Automatically generated definition]. EMAPA:37237 MA:0000511 blood vessel of torso blood vessel of trunk torso blood vessel uberon UBERON:0003513 trunk blood vessel A blood vessel that is part of a trunk [Automatically generated definition]. OBOL:automatic EMAPA:37237 MA:th blood vessel of torso OBOL:automatic blood vessel of trunk OBOL:automatic torso blood vessel OBOL:automatic A blood vessel that is part of a kidney [Automatically generated definition]. EMAPA:28457 MA:0001682 TAO:0005306 ZFA:0005306 blood vessel of kidney renal blood vessel uberon UBERON:0003517 kidney blood vessel A blood vessel that is part of a kidney [Automatically generated definition]. OBOL:automatic blood vessel of kidney OBOL:automatic renal blood vessel OBOL:automatic A blood vessel that is part of a thoracic cavity [Automatically generated definition]. EMAPA:37240 MA:0000554 blood vessel of cavity of chest blood vessel of cavity of thorax blood vessel of chest cavity blood vessel of pectoral cavity blood vessel of thoracic cavity cavity of chest blood vessel cavity of thorax blood vessel chest cavity blood vessel pectoral cavity blood vessel uberon UBERON:0003519 thoracic cavity blood vessel A blood vessel that is part of a thoracic cavity [Automatically generated definition]. OBOL:automatic EMAPA:37240 MA:th blood vessel of cavity of chest OBOL:automatic blood vessel of cavity of thorax OBOL:automatic blood vessel of chest cavity OBOL:automatic blood vessel of pectoral cavity OBOL:automatic blood vessel of thoracic cavity OBOL:automatic cavity of chest blood vessel OBOL:automatic cavity of thorax blood vessel OBOL:automatic chest cavity blood vessel OBOL:automatic pectoral cavity blood vessel OBOL:automatic A blood vessel that is part of a pelvis [Automatically generated definition]. EMAPA:37244 MA:0000531 blood vessel of pelvis uberon UBERON:0003520 pelvis blood vessel A blood vessel that is part of a pelvis [Automatically generated definition]. OBOL:automatic EMAPA:37244 MA:th blood vessel of pelvis OBOL:automatic A capillary that is part of a respiratory system [Automatically generated definition]. EMAPA:37574 MA:0001807 apparatus respiratorius blood capillary apparatus respiratorius capillary apparatus respiratorius capillary vessel blood capillary of apparatus respiratorius blood capillary of respiratory system capillary of apparatus respiratorius capillary of respiratory system capillary vessel of apparatus respiratorius capillary vessel of respiratory system respiratory system blood capillary respiratory system capillary vessel uberon UBERON:0003526 respiratory system capillary A capillary that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37574 MA:th apparatus respiratorius blood capillary OBOL:automatic apparatus respiratorius capillary OBOL:automatic apparatus respiratorius capillary vessel OBOL:automatic blood capillary of apparatus respiratorius OBOL:automatic blood capillary of respiratory system OBOL:automatic capillary of apparatus respiratorius OBOL:automatic capillary of respiratory system OBOL:automatic capillary vessel of apparatus respiratorius OBOL:automatic capillary vessel of respiratory system OBOL:automatic respiratory system blood capillary OBOL:automatic respiratory system capillary vessel OBOL:automatic A capillary that is part of a kidney [Automatically generated definition]. EMAPA:31443 MA:0002586 blood capillary of kidney capillary of kidney capillary vessel of kidney kidney blood capillary kidney capillary vessel renal capillary uberon UBERON:0003527 kidney capillary A capillary that is part of a kidney [Automatically generated definition]. OBOL:automatic blood capillary of kidney OBOL:automatic capillary of kidney OBOL:automatic capillary vessel of kidney OBOL:automatic kidney blood capillary OBOL:automatic kidney capillary vessel OBOL:automatic renal capillary OBOL:automatic A gray matter that is part of a brain [Automatically generated definition]. EMAPA:35184 MA:0000810 NCIT:C49333 UMLS:C1707348 brain grey matter brain grey substance gray matter of brain grey matter of brain grey substance of brain uberon UBERON:0003528 brain gray matter A gray matter that is part of a brain [Automatically generated definition]. OBOL:automatic UMLS:C1707348 ncithesaurus:Cerebral_Gray_Matter brain grey matter MA:0000810 brain grey substance OBOL:automatic gray matter of brain OBOL:automatic grey matter of brain OBOL:automatic grey substance of brain OBOL:automatic A portion of connective tissue that is part of a head [Automatically generated definition]. EMAPA:16098 MA:0000577 adult head connective tissue adult head portion of connective tissue adult head textus connectivus connective tissue of adult head connective tissue of head head portion of connective tissue head textus connectivus portion of connective tissue of adult head portion of connective tissue of head textus connectivus of adult head textus connectivus of head uberon UBERON:0003566 head connective tissue A portion of connective tissue that is part of a head [Automatically generated definition]. OBOL:automatic adult head connective tissue OBOL:automatic adult head portion of connective tissue OBOL:automatic adult head textus connectivus OBOL:automatic connective tissue of adult head OBOL:automatic connective tissue of head OBOL:automatic head portion of connective tissue OBOL:automatic head textus connectivus OBOL:automatic portion of connective tissue of adult head OBOL:automatic portion of connective tissue of head OBOL:automatic textus connectivus of adult head OBOL:automatic textus connectivus of head OBOL:automatic A portion of connective tissue that is part of an abdomen [Automatically generated definition]. MA:0000519 abdomen portion of connective tissue abdomen textus connectivus connective tissue of abdomen portion of connective tissue of abdomen textus connectivus of abdomen uberon UBERON:0003567 abdomen connective tissue A portion of connective tissue that is part of an abdomen [Automatically generated definition]. OBOL:automatic abdomen portion of connective tissue OBOL:automatic abdomen textus connectivus OBOL:automatic connective tissue of abdomen OBOL:automatic portion of connective tissue of abdomen OBOL:automatic textus connectivus of abdomen OBOL:automatic A portion of connective tissue that is part of a neck [Automatically generated definition]. EMAPA:37250 MA:0000585 connective tissue of neck connective tissue of neck (volume) neck (volume) connective tissue neck (volume) portion of connective tissue neck (volume) textus connectivus neck portion of connective tissue neck textus connectivus portion of connective tissue of neck portion of connective tissue of neck (volume) textus connectivus of neck textus connectivus of neck (volume) uberon UBERON:0003568 neck connective tissue A portion of connective tissue that is part of a neck [Automatically generated definition]. OBOL:automatic EMAPA:37250 MA:th connective tissue of neck OBOL:automatic connective tissue of neck (volume) OBOL:automatic neck (volume) connective tissue OBOL:automatic neck (volume) portion of connective tissue OBOL:automatic neck (volume) textus connectivus OBOL:automatic neck portion of connective tissue OBOL:automatic neck textus connectivus OBOL:automatic portion of connective tissue of neck OBOL:automatic portion of connective tissue of neck (volume) OBOL:automatic textus connectivus of neck OBOL:automatic textus connectivus of neck (volume) OBOL:automatic A portion of connective tissue that is part of a respiratory system [Automatically generated definition]. EMAPA:35968 EMAPA:35977 MA:0001814 apparatus respiratorius connective tissue apparatus respiratorius portion of connective tissue apparatus respiratorius textus connectivus connective tissue of apparatus respiratorius connective tissue of respiratory system portion of connective tissue of apparatus respiratorius portion of connective tissue of respiratory system respiratory system portion of connective tissue respiratory system textus connectivus textus connectivus of apparatus respiratorius textus connectivus of respiratory system uberon UBERON:0003570 respiratory system connective tissue A portion of connective tissue that is part of a respiratory system [Automatically generated definition]. OBOL:automatic apparatus respiratorius connective tissue OBOL:automatic apparatus respiratorius portion of connective tissue OBOL:automatic apparatus respiratorius textus connectivus OBOL:automatic connective tissue of apparatus respiratorius OBOL:automatic connective tissue of respiratory system OBOL:automatic portion of connective tissue of apparatus respiratorius OBOL:automatic portion of connective tissue of respiratory system OBOL:automatic respiratory system portion of connective tissue OBOL:automatic respiratory system textus connectivus OBOL:automatic textus connectivus of apparatus respiratorius OBOL:automatic textus connectivus of respiratory system OBOL:automatic A portion of connective tissue that is part of a trachea. EMAPA:35876 MA:0001853 connective tissue of trachea connective tissue of windpipe uberon UBERON:0003571 trachea connective tissue A portion of connective tissue that is part of a trachea. OBOL:automatic connective tissue of trachea OBOL:automatic connective tissue of windpipe OBOL:automatic A portion of connective tissue that is part of a lower respiratory tract [Automatically generated definition]. EMAPA:37548 MA:0002409 connective tissue of lower respiratory tract lower respiratory tract portion of connective tissue lower respiratory tract textus connectivus portion of connective tissue of lower respiratory tract textus connectivus of lower respiratory tract uberon UBERON:0003580 lower respiratory tract connective tissue A portion of connective tissue that is part of a lower respiratory tract [Automatically generated definition]. OBOL:automatic EMAPA:37548 MA:th connective tissue of lower respiratory tract OBOL:automatic lower respiratory tract portion of connective tissue OBOL:automatic lower respiratory tract textus connectivus OBOL:automatic portion of connective tissue of lower respiratory tract OBOL:automatic textus connectivus of lower respiratory tract OBOL:automatic A portion of connective tissue that is part of a larynx [Automatically generated definition]. EMAPA:35471 MA:0001754 NCIT:C49245 UMLS:C1708651 connective tissue of larynx larynx portion of connective tissue larynx textus connectivus portion of connective tissue of larynx textus connectivus of larynx uberon laryngeal connective tissue UBERON:0003583 larynx connective tissue A portion of connective tissue that is part of a larynx [Automatically generated definition]. OBOL:automatic UMLS:C1708651 ncithesaurus:Laryngeal_Connective_Tissue connective tissue of larynx OBOL:automatic larynx portion of connective tissue OBOL:automatic larynx textus connectivus OBOL:automatic portion of connective tissue of larynx OBOL:automatic textus connectivus of larynx OBOL:automatic laryngeal connective tissue EMAPA:35471 A portion of connective tissue that is part of a dermis [Automatically generated definition]. EMAPA:36509 MA:0000799 connective tissue of dermis dermis portion of connective tissue dermis textus connectivus portion of connective tissue of dermis textus connectivus of dermis uberon UBERON:0003585 dermis connective tissue A portion of connective tissue that is part of a dermis [Automatically generated definition]. OBOL:automatic connective tissue of dermis OBOL:automatic dermis portion of connective tissue OBOL:automatic dermis textus connectivus OBOL:automatic portion of connective tissue of dermis OBOL:automatic textus connectivus of dermis OBOL:automatic A portion of connective tissue that is part of a trunk [Automatically generated definition]. EMAPA:37252 MA:0000513 connective tissue of torso connective tissue of trunk portion of connective tissue of torso portion of connective tissue of trunk textus connectivus of torso textus connectivus of trunk torso connective tissue torso portion of connective tissue torso textus connectivus trunk portion of connective tissue trunk textus connectivus uberon UBERON:0003586 trunk connective tissue A portion of connective tissue that is part of a trunk [Automatically generated definition]. OBOL:automatic EMAPA:37252 MA:th connective tissue of torso OBOL:automatic connective tissue of trunk OBOL:automatic portion of connective tissue of torso OBOL:automatic portion of connective tissue of trunk OBOL:automatic textus connectivus of torso OBOL:automatic textus connectivus of trunk OBOL:automatic torso connective tissue OBOL:automatic torso portion of connective tissue OBOL:automatic torso textus connectivus OBOL:automatic trunk portion of connective tissue OBOL:automatic trunk textus connectivus OBOL:automatic A portion of connective tissue that is part of a bronchus [Automatically generated definition]. EMAPA:32690 EMAPA:35193 MA:0001831 NCIT:C49210 UMLS:C1707052 bronchi connective tissue bronchi portion of connective tissue bronchi textus connectivus bronchial trunk connective tissue bronchial trunk portion of connective tissue bronchial trunk textus connectivus bronchus portion of connective tissue bronchus textus connectivus connective tissue of bronchi connective tissue of bronchial trunk connective tissue of bronchus portion of connective tissue of bronchi portion of connective tissue of bronchial trunk portion of connective tissue of bronchus textus connectivus of bronchi textus connectivus of bronchial trunk textus connectivus of bronchus uberon bronchial connective tissue bronchial mesenchyme UBERON:0003592 bronchus connective tissue A portion of connective tissue that is part of a bronchus [Automatically generated definition]. OBOL:automatic UMLS:C1707052 ncithesaurus:Bronchus_Connective_Tissue bronchi connective tissue OBOL:automatic bronchi portion of connective tissue OBOL:automatic bronchi textus connectivus OBOL:automatic bronchial trunk connective tissue OBOL:automatic bronchial trunk portion of connective tissue OBOL:automatic bronchial trunk textus connectivus OBOL:automatic bronchus portion of connective tissue OBOL:automatic bronchus textus connectivus OBOL:automatic connective tissue of bronchi OBOL:automatic connective tissue of bronchial trunk OBOL:automatic connective tissue of bronchus OBOL:automatic portion of connective tissue of bronchi OBOL:automatic portion of connective tissue of bronchial trunk OBOL:automatic portion of connective tissue of bronchus OBOL:automatic textus connectivus of bronchi OBOL:automatic textus connectivus of bronchial trunk OBOL:automatic textus connectivus of bronchus OBOL:automatic bronchial connective tissue EMAPA:35193 bronchial mesenchyme EMAPA:32690 A portion of connective tissue that is part of a thoracic cavity [Automatically generated definition]. EMAPA:37255 MA:0000555 cavity of chest connective tissue cavity of chest portion of connective tissue cavity of chest textus connectivus cavity of thorax connective tissue cavity of thorax portion of connective tissue cavity of thorax textus connectivus chest cavity connective tissue chest cavity portion of connective tissue chest cavity textus connectivus connective tissue of cavity of chest connective tissue of cavity of thorax connective tissue of chest cavity connective tissue of pectoral cavity connective tissue of thoracic cavity pectoral cavity connective tissue pectoral cavity portion of connective tissue pectoral cavity textus connectivus portion of connective tissue of cavity of chest portion of connective tissue of cavity of thorax portion of connective tissue of chest cavity portion of connective tissue of pectoral cavity portion of connective tissue of thoracic cavity textus connectivus of cavity of chest textus connectivus of cavity of thorax textus connectivus of chest cavity textus connectivus of pectoral cavity textus connectivus of thoracic cavity thoracic cavity portion of connective tissue thoracic cavity textus connectivus uberon UBERON:0003593 thoracic cavity connective tissue A portion of connective tissue that is part of a thoracic cavity [Automatically generated definition]. OBOL:automatic EMAPA:37255 MA:th cavity of chest connective tissue OBOL:automatic cavity of chest portion of connective tissue OBOL:automatic cavity of chest textus connectivus OBOL:automatic cavity of thorax connective tissue OBOL:automatic cavity of thorax portion of connective tissue OBOL:automatic cavity of thorax textus connectivus OBOL:automatic chest cavity connective tissue OBOL:automatic chest cavity portion of connective tissue OBOL:automatic chest cavity textus connectivus OBOL:automatic connective tissue of cavity of chest OBOL:automatic connective tissue of cavity of thorax OBOL:automatic connective tissue of chest cavity OBOL:automatic connective tissue of pectoral cavity OBOL:automatic connective tissue of thoracic cavity OBOL:automatic pectoral cavity connective tissue OBOL:automatic pectoral cavity portion of connective tissue OBOL:automatic pectoral cavity textus connectivus OBOL:automatic portion of connective tissue of cavity of chest OBOL:automatic portion of connective tissue of cavity of thorax OBOL:automatic portion of connective tissue of chest cavity OBOL:automatic portion of connective tissue of pectoral cavity OBOL:automatic portion of connective tissue of thoracic cavity OBOL:automatic textus connectivus of cavity of chest OBOL:automatic textus connectivus of cavity of thorax OBOL:automatic textus connectivus of chest cavity OBOL:automatic textus connectivus of pectoral cavity OBOL:automatic textus connectivus of thoracic cavity OBOL:automatic thoracic cavity portion of connective tissue OBOL:automatic thoracic cavity textus connectivus OBOL:automatic A portion of connective tissue that is part of a pelvis [Automatically generated definition]. EMAPA:37257 MA:0000533 connective tissue of pelvis pelvis portion of connective tissue pelvis textus connectivus portion of connective tissue of pelvis textus connectivus of pelvis uberon UBERON:0003594 pelvis connective tissue A portion of connective tissue that is part of a pelvis [Automatically generated definition]. OBOL:automatic EMAPA:37257 MA:th connective tissue of pelvis OBOL:automatic pelvis portion of connective tissue OBOL:automatic pelvis textus connectivus OBOL:automatic portion of connective tissue of pelvis OBOL:automatic textus connectivus of pelvis OBOL:automatic A cartilage that is part of a neck [Automatically generated definition]. EMAPA:37251 MA:0000586 cartilage of neck cartilage of neck (volume) neck (volume) cartilage uberon UBERON:0003601 neck cartilage A cartilage that is part of a neck [Automatically generated definition]. OBOL:automatic EMAPA:37251 MA:th cartilage of neck OBOL:automatic cartilage of neck (volume) OBOL:automatic neck (volume) cartilage OBOL:automatic A cartilage that is part of a lower respiratory tract [Automatically generated definition]. EMAPA:37547 MA:0001819 NCIT:C49256 UMLS:C1708759 cartilage of lower respiratory tract uberon UBERON:0003603 lower respiratory tract cartilage A cartilage that is part of a lower respiratory tract [Automatically generated definition]. OBOL:automatic EMAPA:37547 MA:th UMLS:C1708759 ncithesaurus:Lower_Respiratory_Tract_Cartilage cartilage of lower respiratory tract OBOL:automatic the ring-shaped cartilaginous structures that support the trachea check whether to classify as part of splanchoncranium in mammals the rings are incomplete, in avians the rings are complete. EMAPA:18699 EMAPA:35875 FMA:7434 MA:0001857 NCIT:C49304 UMLS:C1710456 cartilage of trachea cartilage of windpipe cartilaginous ring of trachea cartilaginous trachea cartilage cartilago trachealis tracheal cartilage windpipe cartilage uberon cartilage of the trachea cartilagines tracheales ring of the trachea trachea ring tracheal ring UBERON:0003604 trachea cartilage the ring-shaped cartilaginous structures that support the trachea J:97123 MGI:smb MP:0003120 UMLS:C1710456 ncithesaurus:Trachea_Cartilage cartilage of trachea OBOL:automatic cartilage of windpipe OBOL:automatic cartilaginous ring of trachea EMAPA:18699 cartilaginous trachea cartilage OBOL:automatic cartilago trachealis FMA:7434 tracheal cartilage FMA:7434 windpipe cartilage OBOL:automatic cartilage of the trachea cartilagines tracheales ring of the trachea tracheal ring A skin gland that is part of a camera-type eye [Automatically generated definition]. EMAPA:37530 MA:0002451 camera-type eye skin gland camera-type eye skin glands camera-type eye skin glands set skin gland of camera-type eye skin gland of vertebrate eye skin glands of camera-type eye skin glands of vertebrate eye skin glands set of camera-type eye skin glands set of vertebrate eye vertebrate eye skin gland vertebrate eye skin glands vertebrate eye skin glands set uberon UBERON:0003605 eye skin gland A skin gland that is part of a camera-type eye [Automatically generated definition]. OBOL:automatic EMAPA:37530 MA:th camera-type eye skin gland OBOL:automatic camera-type eye skin glands OBOL:automatic camera-type eye skin glands set OBOL:automatic skin gland of camera-type eye OBOL:automatic skin gland of vertebrate eye OBOL:automatic skin glands of camera-type eye OBOL:automatic skin glands of vertebrate eye OBOL:automatic skin glands set of camera-type eye OBOL:automatic skin glands set of vertebrate eye OBOL:automatic vertebrate eye skin gland OBOL:automatic vertebrate eye skin glands OBOL:automatic vertebrate eye skin glands set OBOL:automatic The dense connective tissue which contains predominantly elastic fibers and is found in the tunica media of the aorta wall. MA:0002859 adult aorta elastic connective tissue adult aorta elastic tissue adult aorta textus connectivus elasticus aorta elastic connective tissue aorta elastic lamina aorta elastic laminae aorta textus connectivus elasticus dorsal aorta elastic connective tissue dorsal aorta elastic tissue dorsal aorta textus connectivus elasticus elastic connective tissue of adult aorta elastic connective tissue of aorta elastic connective tissue of dorsal aorta elastic connective tissue of trunk of aortic tree elastic tissue of adult aorta elastic tissue of aorta elastic tissue of dorsal aorta elastic tissue of trunk of aortic tree textus connectivus elasticus of adult aorta textus connectivus elasticus of aorta textus connectivus elasticus of dorsal aorta textus connectivus elasticus of trunk of aortic tree trunk of aortic tree elastic connective tissue trunk of aortic tree elastic tissue trunk of aortic tree textus connectivus elasticus uberon UBERON:0003609 aorta elastic tissue The dense connective tissue which contains predominantly elastic fibers and is found in the tunica media of the aorta wall. MP:0009862 adult aorta elastic connective tissue OBOL:automatic adult aorta elastic tissue OBOL:automatic adult aorta textus connectivus elasticus OBOL:automatic aorta elastic connective tissue OBOL:automatic aorta elastic lamina MP:0009862 aorta elastic laminae MP:0009862 aorta textus connectivus elasticus OBOL:automatic dorsal aorta elastic connective tissue OBOL:automatic dorsal aorta elastic tissue OBOL:automatic dorsal aorta textus connectivus elasticus OBOL:automatic elastic connective tissue of adult aorta OBOL:automatic elastic connective tissue of aorta OBOL:automatic elastic connective tissue of dorsal aorta OBOL:automatic elastic connective tissue of trunk of aortic tree OBOL:automatic elastic tissue of adult aorta OBOL:automatic elastic tissue of aorta OBOL:automatic elastic tissue of dorsal aorta OBOL:automatic elastic tissue of trunk of aortic tree OBOL:automatic textus connectivus elasticus of adult aorta OBOL:automatic textus connectivus elasticus of aorta OBOL:automatic textus connectivus elasticus of dorsal aorta OBOL:automatic textus connectivus elasticus of trunk of aortic tree OBOL:automatic trunk of aortic tree elastic connective tissue OBOL:automatic trunk of aortic tree elastic tissue OBOL:automatic trunk of aortic tree textus connectivus elasticus OBOL:automatic The type of heart connective tissue found in the endocardial layer that consists mainly of elastic fibers. MA:0002858 cardiac elastic tissue elastic connective tissue of heart elastic tissue of heart heart elastic connective tissue heart textus connectivus elasticus textus connectivus elasticus of heart uberon UBERON:0003610 heart elastic tissue The type of heart connective tissue found in the endocardial layer that consists mainly of elastic fibers. MP:0009863 cardiac elastic tissue MP:0009863 elastic connective tissue of heart OBOL:automatic elastic tissue of heart OBOL:automatic heart elastic connective tissue OBOL:automatic heart textus connectivus elasticus OBOL:automatic textus connectivus elasticus of heart OBOL:automatic An elastic tissue that is part of a respiratory system [Automatically generated definition]. EMAPA:37579 MA:0001820 apparatus respiratorius elastic connective tissue apparatus respiratorius elastic tissue apparatus respiratorius textus connectivus elasticus elastic connective tissue of apparatus respiratorius elastic connective tissue of respiratory system elastic tissue of apparatus respiratorius elastic tissue of respiratory system respiratory system elastic connective tissue respiratory system textus connectivus elasticus textus connectivus elasticus of apparatus respiratorius textus connectivus elasticus of respiratory system uberon UBERON:0003611 respiratory system elastic tissue An elastic tissue that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37579 MA:th apparatus respiratorius elastic connective tissue OBOL:automatic apparatus respiratorius elastic tissue OBOL:automatic apparatus respiratorius textus connectivus elasticus OBOL:automatic elastic connective tissue of apparatus respiratorius OBOL:automatic elastic connective tissue of respiratory system OBOL:automatic elastic tissue of apparatus respiratorius OBOL:automatic elastic tissue of respiratory system OBOL:automatic respiratory system elastic connective tissue OBOL:automatic respiratory system textus connectivus elasticus OBOL:automatic textus connectivus elasticus of apparatus respiratorius OBOL:automatic textus connectivus elasticus of respiratory system OBOL:automatic An elastic tissue that is part of a circulatory system [Automatically generated definition]. MA:0002857 cardiovascular system elastic connective tissue cardiovascular system textus connectivus elasticus circulatory system elastic connective tissue circulatory system elastic tissue circulatory system textus connectivus elasticus elastic connective tissue of cardiovascular system elastic connective tissue of circulatory system elastic tissue of cardiovascular system elastic tissue of circulatory system textus connectivus elasticus of cardiovascular system textus connectivus elasticus of circulatory system uberon UBERON:0003613 cardiovascular system elastic tissue An elastic tissue that is part of a circulatory system [Automatically generated definition]. OBOL:automatic cardiovascular system elastic connective tissue OBOL:automatic cardiovascular system textus connectivus elasticus OBOL:automatic circulatory system elastic connective tissue OBOL:automatic circulatory system elastic tissue OBOL:automatic circulatory system textus connectivus elasticus OBOL:automatic elastic connective tissue of cardiovascular system OBOL:automatic elastic connective tissue of circulatory system OBOL:automatic elastic tissue of cardiovascular system OBOL:automatic elastic tissue of circulatory system OBOL:automatic textus connectivus elasticus of cardiovascular system OBOL:automatic textus connectivus elasticus of circulatory system OBOL:automatic Elastic tissue layer that lines a blood vessel layer. elastic lamina elastic laminae EMAPA:36300 MA:0002856 blood vessel elastic connective tissue blood vessel textus connectivus elasticus elastic connective tissue of blood vessel elastic tissue of blood vessel textus connectivus elasticus of blood vessel vascular elastic lamina vascular elastic laminae vascular elastic tissue uberon UBERON:0003614 blood vessel elastic tissue Elastic tissue layer that lines a blood vessel layer. elastic lamina MP:0006083 elastic laminae MP:0006083 blood vessel elastic connective tissue OBOL:automatic blood vessel textus connectivus elasticus OBOL:automatic elastic connective tissue of blood vessel OBOL:automatic elastic tissue of blood vessel OBOL:automatic textus connectivus elasticus of blood vessel OBOL:automatic vascular elastic lamina vascular elastic laminae vascular elastic tissue MP:0006083 Elastic tissue that is part of a lung [Automatically generated definition]. MA:0002860 elastic connective tissue of lung elastic tissue of lung lung elastic connective tissue lung textus connectivus elasticus textus connectivus elasticus of lung pulmonary elastic fiber uberon UBERON:0003615 lung elastic tissue Elastic tissue that is part of a lung [Automatically generated definition]. OBOL:automatic elastic connective tissue of lung OBOL:automatic elastic tissue of lung OBOL:automatic lung elastic connective tissue OBOL:automatic lung textus connectivus elasticus OBOL:automatic textus connectivus elasticus of lung OBOL:automatic pulmonary elastic fiber An elastic tissue that is part of a bronchus [Automatically generated definition]. MA:0001838 NCIT:C49211 UMLS:C1707053 bronchi elastic connective tissue bronchi elastic tissue bronchi textus connectivus elasticus bronchial trunk elastic connective tissue bronchial trunk elastic tissue bronchial trunk textus connectivus elasticus bronchus elastic connective tissue bronchus textus connectivus elasticus elastic connective tissue of bronchi elastic connective tissue of bronchial trunk elastic connective tissue of bronchus elastic tissue of bronchi elastic tissue of bronchial trunk elastic tissue of bronchus textus connectivus elasticus of bronchi textus connectivus elasticus of bronchial trunk textus connectivus elasticus of bronchus uberon UBERON:0003616 bronchus elastic tissue An elastic tissue that is part of a bronchus [Automatically generated definition]. OBOL:automatic UMLS:C1707053 ncithesaurus:Bronchus_Elastic_Tissue bronchi elastic connective tissue OBOL:automatic bronchi elastic tissue OBOL:automatic bronchi textus connectivus elasticus OBOL:automatic bronchial trunk elastic connective tissue OBOL:automatic bronchial trunk elastic tissue OBOL:automatic bronchial trunk textus connectivus elasticus OBOL:automatic bronchus elastic connective tissue OBOL:automatic bronchus textus connectivus elasticus OBOL:automatic elastic connective tissue of bronchi OBOL:automatic elastic connective tissue of bronchial trunk OBOL:automatic elastic connective tissue of bronchus OBOL:automatic elastic tissue of bronchi OBOL:automatic elastic tissue of bronchial trunk OBOL:automatic elastic tissue of bronchus OBOL:automatic textus connectivus elasticus of bronchi OBOL:automatic textus connectivus elasticus of bronchial trunk OBOL:automatic textus connectivus elasticus of bronchus OBOL:automatic An elastic tissue that is part of a trachea [Automatically generated definition]. MA:0001861 cartilaginous trachea elastic connective tissue cartilaginous trachea elastic tissue cartilaginous trachea textus connectivus elasticus elastic connective tissue of cartilaginous trachea elastic connective tissue of vertebrate trachea elastic connective tissue of windpipe elastic tissue of cartilaginous trachea elastic tissue of vertebrate trachea elastic tissue of windpipe textus connectivus elasticus of cartilaginous trachea textus connectivus elasticus of vertebrate trachea textus connectivus elasticus of windpipe vertebrate trachea elastic connective tissue vertebrate trachea elastic tissue vertebrate trachea textus connectivus elasticus windpipe elastic connective tissue windpipe elastic tissue windpipe textus connectivus elasticus uberon UBERON:0003617 trachea elastic tissue An elastic tissue that is part of a trachea [Automatically generated definition]. OBOL:automatic cartilaginous trachea elastic connective tissue OBOL:automatic cartilaginous trachea elastic tissue OBOL:automatic cartilaginous trachea textus connectivus elasticus OBOL:automatic elastic connective tissue of cartilaginous trachea OBOL:automatic elastic connective tissue of vertebrate trachea OBOL:automatic elastic connective tissue of windpipe OBOL:automatic elastic tissue of cartilaginous trachea OBOL:automatic elastic tissue of vertebrate trachea OBOL:automatic elastic tissue of windpipe OBOL:automatic textus connectivus elasticus of cartilaginous trachea OBOL:automatic textus connectivus elasticus of vertebrate trachea OBOL:automatic textus connectivus elasticus of windpipe OBOL:automatic vertebrate trachea elastic connective tissue OBOL:automatic vertebrate trachea elastic tissue OBOL:automatic vertebrate trachea textus connectivus elasticus OBOL:automatic windpipe elastic connective tissue OBOL:automatic windpipe elastic tissue OBOL:automatic windpipe textus connectivus elasticus OBOL:automatic The middle layer of the aorta wall, containing the smooth muscle layer and elastic fibers. EMAPA:35138 FMA:74433 MA:0002903 adult aorta tunica media dorsal aorta tunica media trunk of aortic tree tunica media tunica media of adult aorta tunica media of aorta tunica media of dorsal aorta tunica media of trunk of aortic tree uberon UBERON:0003618 aorta tunica media The middle layer of the aorta wall, containing the smooth muscle layer and elastic fibers. MP:0009873 adult aorta tunica media OBOL:automatic dorsal aorta tunica media OBOL:automatic trunk of aortic tree tunica media OBOL:automatic tunica media of adult aorta OBOL:automatic tunica media of aorta OBOL:automatic tunica media of dorsal aorta OBOL:automatic tunica media of trunk of aortic tree OBOL:automatic The innermost layer of the aorta, containing the endothelium and an inner elastic membrane. BTO:0005553 EMAPA:35137 FMA:74419 MA:0002904 adult aorta tunica intima dorsal aorta tunica intima trunk of aortic tree tunica intima tunica intima of adult aorta tunica intima of aorta tunica intima of dorsal aorta tunica intima of trunk of aortic tree uberon UBERON:0003619 aorta tunica intima The innermost layer of the aorta, containing the endothelium and an inner elastic membrane. MP:0009872 adult aorta tunica intima OBOL:automatic dorsal aorta tunica intima OBOL:automatic trunk of aortic tree tunica intima OBOL:automatic tunica intima of adult aorta OBOL:automatic tunica intima of aorta OBOL:automatic tunica intima of dorsal aorta OBOL:automatic tunica intima of trunk of aortic tree OBOL:automatic An arterial blood vessel that is part of a respiratory system [Automatically generated definition]. EMAPA:37565 MA:0001800 uberon UBERON:0003643 respiratory system arterial blood vessel An arterial blood vessel that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37565 MA:th An arterial blood vessel that is part of a kidney [Automatically generated definition]. EMAPA:31436 MA:0002578 uberon kidney arterial system UBERON:0003644 kidney arterial blood vessel An arterial blood vessel that is part of a kidney [Automatically generated definition]. OBOL:automatic kidney arterial system EMAPA:31436 The part of the ventral body cavity that is within the abdomen proper (excluding the pelvic cavity). in FMA this contains the pelvic cavity, but this is inconsistent with the concept of abdominopelvic cavity EFO:0000213 EMAPA:36505 FMA:12266 GAID:17 MA:0003057 MESH:A01.047.025 NCIT:C12664 OpenCyc:Mx4rvZR1TJwpEbGdrcN5Y29ycA UMLS:C0230168 galen:AbdominalCavity cavity of abdominal compartment cavity of compartment of abdomen space of abdominal compartment uberon cavitas abdominis UBERON:0003684 abdominal cavity The part of the ventral body cavity that is within the abdomen proper (excluding the pelvic cavity). UBERON:cjm in FMA this contains the pelvic cavity, but this is inconsistent with the concept of abdominopelvic cavity FMA UMLS:C0230168 ncithesaurus:Abdominal_Cavity cavity of abdominal compartment FMA:12266 cavity of compartment of abdomen FMA:12266 space of abdominal compartment FMA:12266 cavitas abdominis cavitas abdominis GAID:17 In anatomy, in the occipital bone, the foramen magnum is one of the several oval or circular apertures in the base of the skull, through which the medulla oblongata (an extension of the spinal cord) enters and exits the skull vault. Apart from the transmission of the medulla oblongata and its membranes, the foramen magnum transmits the Spinal Accessory nerve, vertebral arteries, the anterior and posterior spinal arteries, the membrana tectoria and alar ligaments. [WP,unvetted]. Foramen in the occipital region of neurocranium to allow passage of spinal cord.[TAO] AAO:0010826 EMAPA:37868 FMA:75306 GAID:228 MESH:D005539 NCIT:C12495 OpenCyc:Mx4rwOm-FpwpEbGdrcN5Y29ycA TAO:0002045 UMLS:C0016519 ZFA:0005387 uberon UBERON:0003687 Design pattern notes: check whether this fits the foramen design pattern foramen magnum In anatomy, in the occipital bone, the foramen magnum is one of the several oval or circular apertures in the base of the skull, through which the medulla oblongata (an extension of the spinal cord) enters and exits the skull vault. Apart from the transmission of the medulla oblongata and its membranes, the foramen magnum transmits the Spinal Accessory nerve, vertebral arteries, the anterior and posterior spinal arteries, the membrana tectoria and alar ligaments. [WP,unvetted]. Foramen in the occipital region of neurocranium to allow passage of spinal cord.[TAO] 2012-08-14 TAO:0002045 TAO TAO:wd EMAPA:37868 MA:th UMLS:C0016519 ncithesaurus:Foramen_Magnum The tissues that surround the organs that are present within the abdominal cavity. The abdominal wall tissue is composed of layers of fat, parietal peritoneum, fascia, and muscles. EMAPA:37064 FMA:10429 FMA:259054 GAID:26 MESH:A01.047.050 NCIT:C77608 UMLS:C0836916 paries abdominalis wall of abdomen wall of abdomen proper uberon abdominal wall proper layers of the abdominal wall paries abdominalis UBERON:0003697 abdominal wall The tissues that surround the organs that are present within the abdominal cavity. The abdominal wall tissue is composed of layers of fat, parietal peritoneum, fascia, and muscles. ncithesaurus:Abdominal_Wall EMAPA:37064 MA:th UMLS:C0836916 ncithesaurus:Abdominal_Wall paries abdominalis wall of abdomen FMA:259054 wall of abdomen proper FMA:10429 abdominal wall proper FMA:10429 layers of the abdominal wall paries abdominalis A vein arising from the splenic trabecular vein in the hilum of the spleen that drains into the portal vein. EMAPA:37226 FMA:14331 GAID:541 MA:0002164 MESH:D013162 NCIT:C33608 OpenCyc:Mx4rwCt0eZwpEbGdrcN5Y29ycA UMLS:C0038001 galen:SplenicVein vena splenica uberon lienal vein vena lienalis UBERON:0003713 splenic vein A vein arising from the splenic trabecular vein in the hilum of the spleen that drains into the portal vein. ncithesaurus:Splenic_Vein EMAPA:37226 MA:th UMLS:C0038001 ncithesaurus:Splenic_Vein vena splenica FMA:14331 FMA:TA lienal vein MA:0002164 vena lienalis Portion of tissue in the nervous system which consists of neurons and glial cells, and may also contain parts of the vasculature. One of the four types of tissue in traditional classifications. Cells forming the brain, spinal cord and peripheral nervous system.[AAO] FMA definition includes vasculature AAO:0000325 AEO:0000123 EHDAA2:0003123 FMA:9642 GAID:609 MESH:D009417 NCIT:C13052 OpenCyc:Mx4rVmfYCsQ_QdeM_bFAeS8NRQ UMLS:C0027757 nerve tissue nervous tissue portion of neural tissue uberon UBERON:0003714 neural tissue Portion of tissue in the nervous system which consists of neurons and glial cells, and may also contain parts of the vasculature. FMA:9642 One of the four types of tissue in traditional classifications. Cells forming the brain, spinal cord and peripheral nervous system.[AAO] 2012-06-20 AAO:0000325 AAO AAO:LAP FMA definition includes vasculature FMA UMLS:C0027757 ncithesaurus:Nervous_Tissue nerve tissue FMA:9642 nervous tissue FMA:9642 portion of neural tissue FMA:9642 The major nerves supplying sympathetic innervation to the abdomen, including the greater, lesser, and lowest (or smallest) splanchnic nerves that are formed by preganglionic fibers from the spinal cord which pass through the paravertebral ganglia and then to the celiac ganglia and plexuses and the lumbar splanchnic nerves carry fibers which pass through the lumbar paravertebral ganglia to the mesenteric and hypogastric ganglia. All carry sympathetic fibers except for the pelvic splanchnic nerves, which carry parasympathetic fibers BAMS:spn EMAPA:37959 FMA:5883 GAID:800 MESH:D013153 uberon splanchnic nerves visceral nerve UBERON:0003715 splanchnic nerve The major nerves supplying sympathetic innervation to the abdomen, including the greater, lesser, and lowest (or smallest) splanchnic nerves that are formed by preganglionic fibers from the spinal cord which pass through the paravertebral ganglia and then to the celiac ganglia and plexuses and the lumbar splanchnic nerves carry fibers which pass through the lumbar paravertebral ganglia to the mesenteric and hypogastric ganglia. MP:0008318 EMAPA:37959 MA:th splanchnic nerves BAMS:spn visceral nerve A branch of the vagus nerve that supplies motor function and sensation to the larynx (voice box). It travels within the endoneurium. It is the nerve of the 6th Branchial Arch. Branch of the vagus nerve that separates from the vagus well postcranially, then continues anteriorly to innervate the larynx[AAO:0010754]. recurrent nerve AAO:0010754 FMA:6246 GAID:804 MESH:D012009 VHOG:0001347 nervus laryngeus recurrens recurrent laryngeal nerve from vagus nerve vagus X nerve recurrent laryngeal branch uberon inferior laryngeal nerve ramus recurrens UBERON:0003716 recurrent laryngeal nerve Wikipedia A branch of the vagus nerve that supplies motor function and sensation to the larynx (voice box). It travels within the endoneurium. It is the nerve of the 6th Branchial Arch. Branch of the vagus nerve that separates from the vagus well postcranially, then continues anteriorly to innervate the larynx[AAO:0010754]. AAO:0010754 recurrent nerve nervus laryngeus recurrens vagus X nerve recurrent laryngeal branch VHOG:0001347 inferior laryngeal nerve GAID:804 ramus recurrens AAO:0010754 A mucous membrane that lines the mouth. this is defined as any mucous membrane of the mouth - including palate, lips, uvula, etc. ncit split mouth/oral mucosa into lip and buccal. In future we may split into masticatory/keratinized (gingiva + hard palate) vs lining/non-keratinized (lips, cheeks, floor of mouth, soft palate). FMA distinguishes between mucosa of mouth and region of mouth (the latter including the buccal mucosa) the mucous membrane epithelium of the mouth. It can be divided into three categories: masticatory, lining, and specialized[Wikipedia:Oral_mucosa]. BTO:0002860 CALOHA:TS-0716 EMAPA:26937 FMA:59660 GAID:951 MA:0002794 MESH:D009061 NCIT:C77637 UMLS:C0026639 mouth mucosa mouth mucous membrane mouth organ mucosa mucosa of mouth mucous membrane of mouth oral mucous membrane oral part of viscerocranial mucosa tunica mucosa oris uberon buccal mucosa mucosal lining of mouth oral mucosa tunica mucosa oris UBERON:0003729 mouth mucosa A mucous membrane that lines the mouth. the mucous membrane epithelium of the mouth. It can be divided into three categories: masticatory, lining, and specialized[Wikipedia:Oral_mucosa]. UMLS:C0026639 ncithesaurus:Oral_Mucosa mouth mucosa FMA:59660 mouth mucous membrane OBOL:accepted mouth organ mucosa OBOL:accepted mucosa of mouth OBOL:accepted mucous membrane of mouth FMA:59660 oral part of viscerocranial mucosa FMA:59660 tunica mucosa oris FMA:59660 FMA:TA buccal mucosa GAID:951 mucosal lining of mouth MA:0002794 oral mucosa GAID:951 tunica mucosa oris A nerve that is part of a thorax [Automatically generated definition]. EMAPA:37265 MA:0000562 MESH:D013900 nerve of thorax thoracic segment nerve thorax nerve uberon upper body nerve UBERON:0003824 nerve of thoracic segment A nerve that is part of a thorax [Automatically generated definition]. OBOL:automatic EMAPA:37265 MA:th nerve of thorax OBOL:automatic thoracic segment nerve MA:0000562 thorax nerve OBOL:automatic upper body nerve MA:0000562 A nerve that is part of an abdominal segment of trunk [Automatically generated definition]. EMAPA:37061 MA:0000528 abdominal segment nerve uberon UBERON:0003825 nerve of abdominal segment A nerve that is part of an abdominal segment of trunk [Automatically generated definition]. OBOL:automatic EMAPA:37061 MA:th abdominal segment nerve MA:0000528 A bone that is part of a thorax [Automatically generated definition]. EMAPA:37247 MA:0000559 bone of thorax bone organ of thorax thorax bone thorax bone organ uberon upper body bone UBERON:0003827 thoracic segment bone A bone that is part of a thorax [Automatically generated definition]. OBOL:automatic EMAPA:37247 MA:th bone of thorax OBOL:automatic bone organ of thorax OBOL:automatic thorax bone OBOL:automatic thorax bone organ OBOL:automatic upper body bone MA:0000559 A bone that is part of an abdominal segment of trunk [Automatically generated definition]. EMAPA:37058 MA:0000525 abdominal segment of trunk bone abdominal segment of trunk bone organ bone of abdominal segment of trunk bone organ of abdominal segment of trunk uberon UBERON:0003828 abdominal segment bone A bone that is part of an abdominal segment of trunk [Automatically generated definition]. OBOL:automatic EMAPA:37058 MA:th abdominal segment of trunk bone OBOL:automatic abdominal segment of trunk bone organ OBOL:automatic bone of abdominal segment of trunk OBOL:automatic bone organ of abdominal segment of trunk OBOL:automatic Any muscle tissue that is part of the urethra. EMAPA:37787 MA:0002649 uberon urethral muscle layer UBERON:0003829 urethra muscle tissue Any muscle tissue that is part of the urethra. UBERON:cjm EMAPA:37787 MA:th urethral muscle layer MA:0002649 Any muscle organ that is part of a thorax [Automatically generated definition]. MA:0000561 thoracic segment muscle muscle organ of thorax thorax muscle organ uberon upper body muscle UBERON:0003830 thoracic segment muscle prolog Any muscle organ that is part of a thorax [Automatically generated definition]. OBOL:automatic muscle organ of thorax OBOL:automatic thorax muscle organ OBOL:automatic upper body muscle MA:0000561 Any muscle organ that is part of a respiratory system [Automatically generated definition]. EMAPA:35733 MA:0001828 apparatus respiratorius muscle organ muscle organ of apparatus respiratorius muscle organ of respiratory system respiratory system muscle organ uberon UBERON:0003831 respiratory system muscle Any muscle organ that is part of a respiratory system [Automatically generated definition]. OBOL:automatic apparatus respiratorius muscle organ OBOL:automatic muscle organ of apparatus respiratorius OBOL:automatic muscle organ of respiratory system OBOL:automatic respiratory system muscle organ OBOL:automatic A muscle organ that is part of an abdominal segment of trunk [Automatically generated definition]. EMAPA:37060 MA:0000527 abdominal segment of trunk muscle organ muscle organ of abdominal segment of trunk uberon UBERON:0003833 abdominal segment muscle A muscle organ that is part of an abdominal segment of trunk [Automatically generated definition]. OBOL:automatic EMAPA:37060 MA:th abdominal segment of trunk muscle organ OBOL:automatic muscle organ of abdominal segment of trunk OBOL:automatic A blood vessel that is part of a thorax [Automatically generated definition]. EMAPA:37238 MA:0000558 blood vessel of thorax thorax blood vessel uberon upper body blood vessel UBERON:0003834 thoracic segment blood vessel A blood vessel that is part of a thorax [Automatically generated definition]. OBOL:automatic EMAPA:37238 MA:th blood vessel of thorax OBOL:automatic thorax blood vessel OBOL:automatic upper body blood vessel MA:0000558 A blood vessel that is part of an abdominal segment of trunk [Automatically generated definition]. EMAPA:37057 MA:0000524 abdominal segment of trunk blood vessel blood vessel of abdominal segment of trunk uberon UBERON:0003835 abdominal segment blood vessel A blood vessel that is part of an abdominal segment of trunk [Automatically generated definition]. OBOL:automatic EMAPA:37057 MA:th abdominal segment of trunk blood vessel OBOL:automatic blood vessel of abdominal segment of trunk OBOL:automatic A skin of body that is part of an abdominal segment of trunk [Automatically generated definition]. EMAPA:37063 FMA:264898 MA:0000530 abdominal segment of trunk skin skin of abdominal segment of trunk uberon UBERON:0003836 abdominal segment skin A skin of body that is part of an abdominal segment of trunk [Automatically generated definition]. OBOL:automatic EMAPA:37063 MA:th abdominal segment of trunk skin OBOL:automatic skin of abdominal segment of trunk OBOL:automatic A portion of connective tissue that is part of a thorax [Automatically generated definition]. EMAPA:37253 MA:0000560 connective tissue of thorax portion of connective tissue of thorax textus connectivus of thorax thorax connective tissue thorax portion of connective tissue thorax textus connectivus uberon upper body connective tissue UBERON:0003837 thoracic segment connective tissue A portion of connective tissue that is part of a thorax [Automatically generated definition]. OBOL:automatic EMAPA:37253 MA:th connective tissue of thorax OBOL:automatic portion of connective tissue of thorax OBOL:automatic textus connectivus of thorax OBOL:automatic thorax connective tissue OBOL:automatic thorax portion of connective tissue OBOL:automatic thorax textus connectivus OBOL:automatic upper body connective tissue MA:0000560 A portion of connective tissue that is part of an abdominal segment of trunk [Automatically generated definition]. EMAPA:37059 MA:0000526 abdominal segment of trunk connective tissue abdominal segment of trunk portion of connective tissue abdominal segment of trunk textus connectivus connective tissue of abdominal segment of trunk portion of connective tissue of abdominal segment of trunk textus connectivus of abdominal segment of trunk uberon UBERON:0003838 abdominal segment connective tissue A portion of connective tissue that is part of an abdominal segment of trunk [Automatically generated definition]. OBOL:automatic EMAPA:37059 MA:th abdominal segment of trunk connective tissue OBOL:automatic abdominal segment of trunk portion of connective tissue OBOL:automatic abdominal segment of trunk textus connectivus OBOL:automatic connective tissue of abdominal segment of trunk OBOL:automatic portion of connective tissue of abdominal segment of trunk OBOL:automatic textus connectivus of abdominal segment of trunk OBOL:automatic An anatomical space that surrounded_by a neural tube. (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] UBERON:0005713 AAO:0011073 EHDAA2:0001269 EHDAA:2889 EHDAA:914 EMAPA:16167 VHOG:0001119 XAO:0000252 cavity of neural tube lumen of neural tube neural tube neural lumen prosencoel uberon central lumen neural lumen neurocoel UBERON:0003842 neural tube lumen An anatomical space that surrounded_by a neural tube. OBOL:automatic (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] 2012-09-17 VHOG:0001119 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 cavity of neural tube lumen of neural tube neural tube neural lumen EHDAA2:0001269 neural lumen EHDAA:2889 neurocoel VHOG:0001119 In medicine, gonadal vein refers to the blood vessel that carrying blood away from the gonad (testis, ovary) toward the heart. Females : ovarian vein Males : testicular vein [WP,unvetted]. EHDAA2:0000719 EHDAA:8703 OpenCyc:Mx4rvlWYh5wpEbGdrcN5Y29ycA VHOG:0001340 gonad vein gonada vein vein of gonad vein of gonada uberon UBERON:0003848 gonadal vein In medicine, gonadal vein refers to the blood vessel that carrying blood away from the gonad (testis, ovary) toward the heart. Females : ovarian vein Males : testicular vein [WP,unvetted]. gonad vein OBOL:automatic gonada vein OBOL:automatic vein of gonad OBOL:automatic vein of gonada OBOL:automatic A neural crest that has_potential_to_developmentally_contribute_to a midbrain. We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] EFO:0003591 EHDAA2:0001101 EHDAA:360 TAO:0000935 VHOG:0000796 ZFA:0000935 mesencephalic neural crest neural crest midbrain uberon UBERON:0003849 mesencephalic neural crest ZFA A neural crest that has_potential_to_developmentally_contribute_to a midbrain. OBOL:automatic We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] 2012-09-17 VHOG:0000796 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 mesencephalic neural crest ZFA:0000935 neural crest midbrain ZFA:0000935 A neural crest that has_potential_to_developmentally_contribute_to a hindbrain. Cranial neural crest that is part of the hindbrain.[TAO] We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] EHDAA2:0001628 EHDAA:362 EMAPA:35747 TAO:0007063 VHOG:0001210 ZFA:0007063 neural crest hindbrain rhombencephalic neural crest uberon rhombomere neural crest UBERON:0003852 rhombencephalon neural crest ZFA A neural crest that has_potential_to_developmentally_contribute_to a hindbrain. OBOL:automatic Cranial neural crest that is part of the hindbrain.[TAO] 2012-08-14 TAO:0007063 TAO ZFIN:curator We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] 2012-09-17 VHOG:0001210 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 neural crest hindbrain ZFA:0007063 rhombencephalic neural crest ZFA:0007063 rhombomere neural crest EMAPA:35747 A neural crest that has_potential_to_developmentally_contribute_to a spinal cord. We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...)[well established][VHOG] EHDAA:696 EMAPA:16163 EMAPA:16881 VHOG:0001006 neural crest spinal cord uberon spinal neural crest UBERON:0003853 spinal cord neural crest A neural crest that has_potential_to_developmentally_contribute_to a spinal cord. OBOL:automatic We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...)[well established][VHOG] 2012-09-17 VHOG:0001006 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 neural crest spinal cord VHOG:0001006 spinal neural crest VHOG:0001006 A neural plate that develops_from a future spinal cord. Neural plate that is part of the spinal cord. [Bgee_curator][VHOG] (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...)[well established][VHOG] FMA:312957 TAO:0007021 VHOG:0000439 ZFA:0007021 neural plate of spinal cord uberon UBERON:0003854 spinal cord neural plate ZFA A neural plate that develops_from a future spinal cord. OBOL:automatic Neural plate that is part of the spinal cord. [Bgee_curator][VHOG] 2012-09-17 VHOG:0000439 VHOG (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...)[well established][VHOG] 2012-09-17 VHOG:0000439 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 neural plate of spinal cord OBOL:automatic Mesenchyme that is part of a developing gonad [Automatically generated definition]. EHDAA:5012 EMAPA:16858 EMAPA:17385 VHOG:0001090 gonada mesenchyme mesenchyme of gonad mesenchyme of gonada uberon UBERON:0003855 gonad mesenchyme Mesenchyme that is part of a developing gonad [Automatically generated definition]. OBOL:automatic gonada mesenchyme OBOL:automatic mesenchyme of gonad OBOL:automatic mesenchyme of gonada OBOL:automatic A presumptive structure that has the potential to develop into a ganglion. uberon UBERON:0003869 presumptive ganglion A presumptive structure that has the potential to develop into a ganglion. OBOL:automatic An anatomical cavity that has the potential to develop into a coelemic cavity lumen. uberon body cavity precursor UBERON:0003886 future coelemic cavity lumen An anatomical cavity that has the potential to develop into a coelemic cavity lumen. OBOL:automatic The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults (...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG] EHDAA:251 EMAPA:16088 NCIT:C34195 UMLS:C1512940 VHOG:0000316 somatic coelom uberon UBERON:0003887 intraembryonic coelom Wikipedia The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom MGI:anna MP:0012187 (...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG] 2012-09-17 VHOG:0000316 VHOG ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.166 UMLS:C1512940 ncithesaurus:Intraembryonic_Coelom somatic coelom Initial section of the oviduct through which the ova pass from the ovary to the uterus Homologous to appendix testis salpinges salpinx CALOHA:TS-0732 EHDAA2:0000504 EMAPA:18984 EMAPA:35660 EV:0100112 FMA:18245 GAID:365 MA:0000385 MESH:D005187 NCIT:C12403 OpenCyc:Mx4rvViVeZwpEbGdrcN5Y29ycA UMLS:C0015560 galen:FallopianTube mammalian oviduct uterine tube (sensu Mammalia) uberon fallopian tubes female paramesonephric duct paramesonephric duct of female tuba uterina UBERON:0003889 fallopian tube FMA-abduced-lr Initial section of the oviduct through which the ova pass from the ovary to the uterus MGI:smb MP:0003574 Homologous to appendix testis salpinges UMLS:C0015560 ncithesaurus:Fallopian_Tube mammalian oviduct female paramesonephric duct EHDAA2:0000504 paramesonephric duct of female EMAPA:35660 tuba uterina paired ducts of the embryo that run down the lateral sides of the urogenital ridge and terminate at the mullerian eminence in the primitive urogenital sinus. In the female, they will develop to form the fallopian tubes, uterus, and the upper portion of the vagina; in the male, they are lost. These ducts are made of tissue of mesodermal origin[WP]. develops either by lengthwise splitting of the archinephric duct (in chondrichthyans and some amphibians) or by a elongated invagination of the coelomic epithelium (other vertebrates) In males, the oviducts regress. The cranial end of the oviduct maintains an opening into the coelom (which primitively may have been the anteriormost coelomic funnels connecting the nephrocoel with the coelom). This opening is the ostium tubae[USM]. Either of the paired embryonic ducts developing into the uterine tubes, uterus, and vagina in the female and becoming largely obliterated in the male. [TFD][VHOG] Transient developmental organ which gives rise to oviducts in female (documented to persist in some male frogs).[AAO] In females, the archinephric (mesonephric) ducts tend to function only within the urinary systems. The muellerian duct arises embryologically next to the archinephric (wolffian) duct. In males, the muellerian duct regresses if it appears at all, but in females, the muellerian ducts become the oviducts of the reproductive system.[well established][VHOG] Sertoli cells secrete anti-Mullerian hormone (AMH) inducing the demise of this duct UBERON:0005318 AAO:0010141 EHDAA2:0004048 EMAPA:27665 GAID:1309 MESH:A16.254.570 NCIT:C13260 RETIRED_EHDAA2:0001399 UMLS:C0026732 VHOG:0001199 XAO:0000330 Muellerian duct Müllerian duct ductus paramesonephricus paramesonephric duct early paramesonephric duct uberon UBERON:0003890 Mullerian duct Wikipedia paired ducts of the embryo that run down the lateral sides of the urogenital ridge and terminate at the mullerian eminence in the primitive urogenital sinus. In the female, they will develop to form the fallopian tubes, uterus, and the upper portion of the vagina; in the male, they are lost. These ducts are made of tissue of mesodermal origin[WP]. develops either by lengthwise splitting of the archinephric duct (in chondrichthyans and some amphibians) or by a elongated invagination of the coelomic epithelium (other vertebrates) In males, the oviducts regress. The cranial end of the oviduct maintains an opening into the coelom (which primitively may have been the anteriormost coelomic funnels connecting the nephrocoel with the coelom). This opening is the ostium tubae[USM]. GO:0061205 Either of the paired embryonic ducts developing into the uterine tubes, uterus, and vagina in the female and becoming largely obliterated in the male. [TFD][VHOG] 2012-09-17 VHOG:0001199 VHOG Transient developmental organ which gives rise to oviducts in female (documented to persist in some male frogs).[AAO] 2012-06-20 AAO:0010141 AAO AAO:RED In females, the archinephric (mesonephric) ducts tend to function only within the urinary systems. The muellerian duct arises embryologically next to the archinephric (wolffian) duct. In males, the muellerian duct regresses if it appears at all, but in females, the muellerian ducts become the oviducts of the reproductive system.[well established][VHOG] 2012-09-17 VHOG:0001199 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.559 UMLS:C0026732 ncithesaurus:Mullerian_Duct paramesonephric duct EMAPA:27665 early paramesonephric duct EHDAA2:0004048 One of the skeletal muscles of the head and neck, spine, and ribs. EHDAA:5982 EMAPA:18167 MA:0003153 RETIRED_EHDAA2:0000160 TAO:0001954 uberon UBERON:0003897 axial muscle One of the skeletal muscles of the head and neck, spine, and ribs. HP:0003327 A portion of skeletal muscle tissue in the trunk. skeletal muscle of torso skeletal muscle tissue of torso skeletal muscle tissue of trunk torso skeletal muscle torso skeletal muscle tissue trunk skeletal muscle trunk skeletal muscle tissue uberon UBERON:0003898 skeletal muscle tissue of trunk A portion of skeletal muscle tissue in the trunk. skeletal muscle of torso OBOL:automatic skeletal muscle tissue of torso OBOL:automatic skeletal muscle tissue of trunk OBOL:automatic torso skeletal muscle OBOL:automatic torso skeletal muscle tissue OBOL:automatic trunk skeletal muscle OBOL:automatic trunk skeletal muscle tissue OBOL:automatic The part of the retina that contains neurons and photoreceptor cells[GO]. (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] AAO:0011095 BTO:0000929 CALOHA:TS-0685 EHDAA2:0001253 EHDAA:4763 EMAPA:17171 EMAPA:18590 FMA:58628 MA:0000277 NCIT:C33166 TAO:0000046 UMLS:C1518263 VHOG:0000535 XAO:0003216 ZFA:0000046 neural layer of retina neural retina neuroretina stratum nervosum (retina) stratum nervosum retinae uberon neural retinal epithelium UBERON:0003902 retinal neural layer Bgee:AN The part of the retina that contains neurons and photoreceptor cells[GO]. GO:0003407 (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] 2012-09-17 VHOG:0000535 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 UMLS:C1518263 ncithesaurus:Neural_Retina neural layer of retina FMA:58628 neural retina XAO:0003216 ZFA:0000046 neuroretina ZFA:0000046 stratum nervosum (retina) FMA:58628 stratum nervosum retinae FMA:58628 FMA:TA neural retinal epithelium MA:000027 Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system. contrast with a multi-tissue tube, which has as parts both epithelium, connective tissue, possibly muscle layers AEO:0000114 EHDAA2:0003114 FBbt:00007474 epithelial or endothelial tube uberon UBERON:0003914 epithelial tube Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system. GO:0060562 Any endothelium that has the quality of being cylindrical [Automatically generated definition]. uberon UBERON:0003915 endothelial tube Any endothelium that has the quality of being cylindrical [Automatically generated definition]. OBOL:automatic Kidney mesenchyme is the tissue made up of loosely connected mesenchymal cells in the kidney[GO]. check this mesenchyme of kidney uberon UBERON:0003918 kidney mesenchyme Kidney mesenchyme is the tissue made up of loosely connected mesenchymal cells in the kidney[GO]. GO:0072074 A blood vessel that carries blood from the capillaries toward the heart EMAPA:35932 FMA:86188 MA:0000066 segment of venous tree organ venous tree organ segment uberon UBERON:0003920 Compare to: vein venous blood vessel A blood vessel that carries blood from the capillaries toward the heart segment of venous tree organ FMA:86188 venous tree organ segment FMA:86188 A duct that is part of a digestive system [Automatically generated definition]. TAO:0005162 ZFA:0005162 duct of digestive system duct of gastrointestinal system gastrointestinal system duct uberon UBERON:0003928 digestive system duct A duct that is part of a digestive system [Automatically generated definition]. OBOL:automatic duct of digestive system OBOL:automatic duct of gastrointestinal system OBOL:automatic gastrointestinal system duct OBOL:automatic An epithelium that lines the lumen of the digestive tract. Epithelium lining the lumen of the gut.[TAO] BTO:0000956 EHDAA2:0004567 EMAPA:32928 MA:0003201 NCIT:C12963 TAO:0005123 UMLS:C0836205 XAO:0003200 ZFA:0005123 digestive tract epithelial tissue epithelial tissue of digestive tract epithelial tissue of gut epithelium of digestive tract epithelium of gut gastrodermis gut epithelial tissue gut epithelium uberon alimentary tract epithelium UBERON:0003929 digestive tract epithelium An epithelium that lines the lumen of the digestive tract. Epithelium lining the lumen of the gut.[TAO] 2012-08-14 TAO:0005123 TAO ZFIN:curator UMLS:C0836205 ncithesaurus:Gut_Epithelium digestive tract epithelial tissue OBOL:automatic epithelial tissue of digestive tract OBOL:automatic epithelial tissue of gut OBOL:automatic epithelium of digestive tract OBOL:automatic epithelium of gut OBOL:automatic gastrodermis BGEE:ANN NCBITaxon:6073 gut epithelial tissue OBOL:automatic gut epithelium EHDAA2:0004567 MA:0003201 ZFA:0005123 alimentary tract epithelium OBOL:automatic A cartilage element of chondrocranium. Example: neurocranial trabecula. EFO:0003690 TAO:0001461 ZFA:0001461 cartilage of chondrocranium cartilaginous element of chondrocranium chondrocranium cartilage neurocranium cartilage uberon UBERON:0003932 cartilage element of chondrocranium A cartilage element of chondrocranium. Example: neurocranial trabecula. cartilage of chondrocranium OBOL:accepted cartilaginous element of chondrocranium OBOL:accepted chondrocranium cartilage ZFA:0001461 neurocranium cartilage ZFA:0001461 A cartilage element that is part of the cranial skeleton. Cartilage which is part of the cranium.[TAO] TAO:0001458 ZFA:0001458 cartilage of cranium cranium cartilage uberon cranial cartilages UBERON:0003933 cranial cartilage A cartilage element that is part of the cranial skeleton. ZFA:0001458 Cartilage which is part of the cranium.[TAO] 2012-08-14 TAO:0001458 TAO ZFIN:curator cartilage of cranium OBOL:automatic cranium cartilage OBOL:automatic cranial cartilages ZFA:0001458 Any of the organized aggregations of cells that function as secretory or excretory organs and are associated with reproduction. MA:0001751 genitalia gland gland of genitalia gland of reproductive system reproductive gland reproductive system gland sex gland uberon UBERON:0003937 reproductive gland Any of the organized aggregations of cells that function as secretory or excretory organs and are associated with reproduction. MP:0000653 genitalia gland OBOL:automatic gland of genitalia MP:0000653 gland of reproductive system OBOL:automatic reproductive gland MA:0001751 reproductive system gland OBOL:automatic sex gland MP:0000653 The sensory system for the sense of touch and pain. The neural tissue involved in the transmission of sensory signals MP defines this in a may more appropriate to somatosensory cortex UBERON:0014511 EMAPA:37954 somatic sensory system somatosensory system system for detection of somatic senses uberon UBERON:0003942 somatic sensory system The sensory system for the sense of touch and pain. NIFSTD:nlx_anat_090818 The neural tissue involved in the transmission of sensory signals MP:0000959 MP defines this in a may more appropriate to somatosensory cortex MP EMAPA:37954 MA:th somatosensory system NIFSTD:nlx_anat_090818 The slender connective tissue fiber in the extracellular matrix of skin tissue that is composed of microfibrils and amorphous elastin and is characterized by great elasticity EMAPA:37841 cutaneous elastic fiber dermal elastic fiber uberon UBERON:0003967 cutaneous elastic tissue The slender connective tissue fiber in the extracellular matrix of skin tissue that is composed of microfibrils and amorphous elastin and is characterized by great elasticity MP:0008418 EMAPA:37841 MA:th cutaneous elastic fiber MP:0008418 dermal elastic fiber MP:0008418 The internal feminine genital organs, including the ovaries, uterine tubes, uterus, uterine cervix, and vagina. BTO:0003099 FMA:45654 female internal genitalia internal female genital organ internal genitalia of female reproductive system uberon organa genitalia feminina interna UBERON:0003975 TODO: Relabel. Make distinct organ class. See https://github.com/obophenotype/uberon/issues/547 internal female genitalia The internal feminine genital organs, including the ovaries, uterine tubes, uterus, uterine cervix, and vagina. MP:0009209 female internal genitalia FMA:45654 internal female genital organ BTO:0003099 internal genitalia of female reproductive system OBOL:automatic organa genitalia feminina interna BTO:0003099 valvular EHDAA2:0004046 EHDAA:1892 EHDAA:4406 FMA:67611 OpenCyc:Mx4rvqiwE5wpEbGdrcN5Y29ycA galen:Valve anatomical valve uberon UBERON:0003978 valve anatomical valve FMA:67611 A conical pouch formed from the upper and left angle of the right ventricle in the chordate heart, from which the pulmonary artery arises[WP]. the anteriosuperior, smooth-walled portion of the cavity of the right ventricle, beginning at the supraventricular crest and terminates in the pulmonary trunk[MP]. Receives blood from the left atrium and becomes the median truncus arteriosus.[AAO] Kardong says absent in adult tetrapods, check AAO we use the term CA for the anterior chamber if it is composed of cardiac muscle, contractile, and contains conal valves internally AAO:0010250 uberon UBERON:0003983 conus arteriosus A conical pouch formed from the upper and left angle of the right ventricle in the chordate heart, from which the pulmonary artery arises[WP]. the anteriosuperior, smooth-walled portion of the cavity of the right ventricle, beginning at the supraventricular crest and terminates in the pulmonary trunk[MP]. MP:0009464 Receives blood from the left atrium and becomes the median truncus arteriosus.[AAO] 2012-06-20 AAO:0010250 AAO AAO:BJB we use the term CA for the anterior chamber if it is composed of cardiac muscle, contractile, and contains conal valves internally ISBN10:0073040584 The funnel-like expansion of the abdominal extremity of the uterine tube[MP] The third part of the uterine tube is the infundibulum. It terminates with the ostium of Fallopian tube, surrounded by fimbriae, one of which is attached to the ovary[Wikipedia:Infundibulum_of_uterine_tube]. infundibulum EMAPA:29897 FMA:18307 infundibulum of oviduct infundibulum of uterine tube infundibulum of fallopian tube uberon infundibulum tubae uterinae UBERON:0003984 uterine tube infundibulum FMA The funnel-like expansion of the abdominal extremity of the uterine tube[MP] MP:0009466 The third part of the uterine tube is the infundibulum. It terminates with the ostium of Fallopian tube, surrounded by fimbriae, one of which is attached to the ovary[Wikipedia:Infundibulum_of_uterine_tube]. infundibulum infundibulum of oviduct FMA:18307 infundibulum of uterine tube FMA:18307 infundibulum of fallopian tube FMA:18307 infundibulum tubae uterinae The connection between the embryo proper and extraembryonic tissues uberon UBERON:0004015 embryonic-extraembryonic boundary The connection between the embryo proper and extraembryonic tissues MP:0003890 A transitional population of migrating mesenchymal cells that derive from somites and that will become dermal cells. Not to be confused with 'dermatome segment of skin'. AAO:0011028 AEO:0001017 EHDAA2_RETIRED:0003428 EHDAA:1719 EHDAA:1725 EHDAA:1731 EHDAA:1737 EMAPA:32838 FMA:295656 NCIT:C61572 UMLS:C0180383 XAO:0000220 cutis plate dermatomal mesenchyme uberon epimere mesoderm mesenchyma dermatomiale UBERON:0004016 dermatome AEO EHDAA2-abduced A transitional population of migrating mesenchymal cells that derive from somites and that will become dermal cells. AEO:0001017 AEO:JB UMLS:C0180383 ncithesaurus:Dermatome cutis plate dermatomal mesenchyme mesenchyma dermatomiale The single layer of epithelial cells that lines the early neural tube and develops into the nervous system and into the neural crest cells As the cells adjacent to the lumen continue to divide, the migrating cells form a second layer around the original neural tube. This layer becomes progressively thicker as more cells are added to it from the germinal neuroepithelium. This new layer is called the mantle (or intermediate) zone, and the germinal epithelium is now called the ventricular zone (and, later, the ependyma)[NCBIBook:NBK10047] germinal neuroepithelial layer germinal neuroepithelium original neural tube uberon UBERON:0004022 germinal neuroepithelium NCBIBook:NBK10047 The single layer of epithelial cells that lines the early neural tube and develops into the nervous system and into the neural crest cells MP:0004261 germinal neuroepithelial layer germinal neuroepithelium NCBIBook:NBK10047 original neural tube NCBIBook:NBK10047 The layer of undifferentiated, proliferating cells that line the neural tube lumen that is the immediate transformation of the germinal neuroepithelium consider merging with 'ventricular zone'; note that the MA class probably does not belong here, as this is an embryonic structure The layer of undifferentiated, proliferating cells that line the neural tube lumen ependymal layer EMAPA:17152 EMAPA:35362 EMAPA_RETIRED:16783 MA:0003193 neural tube ependymal layer neural tube ventricular germinal zone neural tube ventricular zone neural tube ependymal zone uberon UBERON:0004060 neural tube ventricular layer NCBIBook:NBK10047 NCBIBook:NBK10047 The layer of undifferentiated, proliferating cells that line the neural tube lumen that is the immediate transformation of the germinal neuroepithelium MP:0009689 The layer of undifferentiated, proliferating cells that line the neural tube lumen MP:0009689 ependymal layer NCBIBook:NBK10047 neural tube ependymal layer NCBIBook:NBK10047 neural tube ventricular germinal zone NCBIBook:NBK10047 neural tube ventricular zone MP:0009689 neural tube ependymal zone MP:0009689 The layer of glia and differentiating neurons that forms as a second layer around the germinal neuroepithium; as this develops it comes to lie between the ventricular and marginal layers and includes the basal and alar plates. Develops into neurons and glia forming a gray matter layer. EMAPA:17148 EMAPA:35360 neural tube intermediate zone uberon future brain marginal layer UBERON:0004061 neural tube mantle layer NCBIBook:NBK10047 by division NCBIBook:NBK10047 The layer of glia and differentiating neurons that forms as a second layer around the germinal neuroepithium; as this develops it comes to lie between the ventricular and marginal layers and includes the basal and alar plates. Develops into neurons and glia forming a gray matter layer. MP:0009690 neural tube intermediate zone MP:0009690 future brain marginal layer EMAPA:35360 The outermost layer of the neural tube that consists of axons from the developing mantle layer and will form the white matter EMAPA:17151 neural tube marginal zone uberon brain marginal zone UBERON:0004062 neural tube marginal layer forms from axons The outermost layer of the neural tube that consists of axons from the developing mantle layer and will form the white matter MP:0009691 neural tube marginal zone MP:0009691 The region of the mantle layer of the neural tube that lies ventral to the sulcus limitans and contains primarily motor neurons and interneurons. AAO:0010561 EFO:0001904 NCIT:C34111 UMLS:C1511061 basal plate basal plate of neural tube spinal cord basal plate uberon motor part of neural tube ventral part of neural tube UBERON:0004064 neural tube basal plate Shh Swenson The region of the mantle layer of the neural tube that lies ventral to the sulcus limitans and contains primarily motor neurons and interneurons. MP:0009693 UMLS:C1511061 ncithesaurus:Basal_Plate basal plate of neural tube spinal cord basal plate MP:0009693 Any of the veins that carries deoxygenated blood from a part of the body into the right atrium of the heart. AAO:0010215 BTO:0001438 EMAPA:18415 FMA:321896 GAID:547 MA:0000068 MESH:D014684 NCIT:C12817 OpenCyc:Mx4rkJQ4U6gEEdudWQACs5b6Bw UMLS:C0042460 uberon caval vein venae cavae UBERON:0004087 vena cava Any of the veins that carries deoxygenated blood from a part of the body into the right atrium of the heart. UMLS:C0042460 ncithesaurus:Vena_Cava venae cavae The subdivision of the face that includes the eye (eyeball plus adnexa such as eyelids) and the orbit of the skull and associated parts of the face such as the eyebrows, if present note the FMA class is more narrow though, and is more like eye + muscles + vasculature. The FMA also has FMA:72951 orbital part of eye in HP covers eyelid, eyebrow. FMA:260119 content of orbital part of eye eye region orbital part of face uberon ocular and peri-ocular region ocular region orbital content orbital part of eye UBERON:0004088 orbital region The subdivision of the face that includes the eye (eyeball plus adnexa such as eyelids) and the orbit of the skull and associated parts of the face such as the eyebrows, if present in HP covers eyelid, eyebrow. HP:0000284 content of orbital part of eye FMA:260119 eye region orbital part of face orbital content FMA:260119 orbital part of eye FMA:72951 2 2 Any tube, opening or passage that connects two distinct anatomical spaces. FMA has both conduit and conduit space. In EHDAA2 this is a surface feature AEO:0000080 EHDAA2:0003080 FMA:242873 foramen foramina uberon opening ostia ostium UBERON:0004111 anatomical conduit Any tube, opening or passage that connects two distinct anatomical spaces. FMA has both conduit and conduit space. In EHDAA2 this is a surface feature FMA foramen EHDAA2:0003080 foramina ostia A vasculature that is part of a iris [Automatically generated definition]. ZFA:0005568 iris blood vessels iris vascular network iris vasculature vascular network of iris uberon UBERON:0004118 vasculature of iris A vasculature that is part of a iris [Automatically generated definition]. OBOL:automatic iris blood vessels ZFA:0005568 iris vascular network OBOL:automatic vascular network of iris OBOL:automatic An anatomical structure that develops (entirely or partially) from the endoderm. Grouping term for query purposes uberon UBERON:0004119 endoderm-derived structure An anatomical structure that develops (entirely or partially) from the endoderm. An anatomical structure that develops (entirely or partially) from the mesoderm. Grouping term for query purposes FBbt:00025998 mesodermal derivative uberon UBERON:0004120 mesoderm-derived structure An anatomical structure that develops (entirely or partially) from the mesoderm. mesodermal derivative FBbt:00025998 An anatomical structure that develops (entirely or partially) from the ectoderm. Grouping term for query purposes FBbt:00025990 ectodermal deriviative uberon UBERON:0004121 ectoderm-derived structure An anatomical structure that develops (entirely or partially) from the ectoderm. ectodermal deriviative FBbt:00025990 Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction. Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction.[AAO] relationship type change: differentiates_from intermediate mesoderm (AAO:0010575) CHANGED TO: develops_from intermediate mesoderm (UBERON:0003064)[AAO] Kidneys and gonads (of vertebrates) develop from adjacent tissues, and after the excretory or urinary ducts have developed, the reproductive system usually taps into them or their derivatives.[well established][VHOG] genitourinary urogenital AAO:0000624 BILA:0000122 BTO:0003091 EFO:0003864 EHDAA:1013 EMAPA:16367 EV:0100094 FMA:280610 GAID:362 MESH:D014566 NCIT:C12810 OpenCyc:Mx4rQRpVMgAKEdyHxgDggVfs8g UMLS:C0042066 VHOG:0000286 XAO:0000140 galen:GenitoUrinarySystem urogenital system uberon GU tract UG tract Urogenitalsystem genito-urinary system genitourinary tract urogenital tract UBERON:0004122 genitourinary system Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction. VHOG:0000286 Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction.[AAO] 2012-06-20 AAO:0000624 AAO AAO:EJS relationship type change: differentiates_from intermediate mesoderm (AAO:0010575) CHANGED TO: develops_from intermediate mesoderm (UBERON:0003064)[AAO] 2012-06-20 AAO:0000624 AAO Kidneys and gonads (of vertebrates) develop from adjacent tissues, and after the excretory or urinary ducts have developed, the reproductive system usually taps into them or their derivatives.[well established][VHOG] 2012-09-17 VHOG:0000286 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.633 UMLS:C0042066 ncithesaurus:Genitourinary_System Urogenitalsystem BTO:0003091 genito-urinary system FMA:280610 urogenital tract BTO:0003091 The optic vesicle is the evagination of neurectoderm that precedes formation of the optic cup[GO]. Portion of tissue that is comprised of neuroepitheium which has pinched off from the anterior neural keel and will form the optic cup[ZFA]. (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles.[well established][VHOG] AAO:0011039 EHDAA2:0001320 EMAPA:16540 FMA:293357 NCIT:C34236 TAO:0000050 UMLS:C0231106 VHOG:0000165 XAO:0000228 ZFA:0000050 uberon evagination eye vesicle ocular vesicle optic vesicles UBERON:0004128 Genes: Six3, Pax6, Rx1 are expressed together in the tip of the neural plate [ISBN:9780878932504 "Developmental Biology"]. Development notes: During subsequent develop- ment, the optic vesicle invaginates and becomes a two-layered structure with an inner neural retina and outer retinal pigment epithelium. As soon as the developing optic vesicle makes contact with the overlying ectoderm, it induces the ectoderm to thicken and form the lens placode [PMID:16496288] optic vesicle ZFA GO-def ZFA The optic vesicle is the evagination of neurectoderm that precedes formation of the optic cup[GO]. Portion of tissue that is comprised of neuroepitheium which has pinched off from the anterior neural keel and will form the optic cup[ZFA]. GO:0003404 (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles.[well established][VHOG] 2012-09-17 VHOG:0000165 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 UMLS:C0231106 ncithesaurus:Optic_Vesicle eye vesicle XAO:0000228 ocular vesicle VHOG:0000165 optic vesicles ZFA:0000050 . salivary nucleus uberon UBERON:0004133 salivatory nucleus . GO:0021751 salivary nucleus GO:0021751 The first recognizable structure derived from the heart field TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO (In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side.[well established][VHOG] EHDAA2:0000215 EMAPA:16106 VHOG:0000975 myocardial plate uberon cardiac crescent cardiogenic crescent heart rudiment UBERON:0004139 cardiogenic plate The first recognizable structure derived from the heart field GO:0003142 (In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side.[well established][VHOG] 2012-09-17 VHOG:0000975 VHOG PMID:15611355 Gittenberger-de Groot AC, Bartelings MM, Deruiter MC, Poelmann RE, Basics of cardiac development for the understanding of congenital heart malformations. Pediatric Research (2005) myocardial plate EHDAA2:0000215 cardiac crescent EMAPA:16106 cardiogenic crescent GO:0003142 A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle. this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138] XAO:0004185 first heart field primary heart field uberon FHF PHF heart field UBERON:0004140 primary heart field GO:0003128 BGEE:ann A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle. GO:0003138 GOC:mtg_heart GOC:rl this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138] GO first heart field XAO:0004185 primary heart field XAO:0004185 FHF XAO:0004185 PHF XAO:0004185 heart field XAO:0004185 An epithelial tube that will give rise to the mature heart. the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube. AAO:0010411 EFO:0003526 EMAPA:32685 NCIT:C34161 TAO:0000360 XAO:0000337 ZFA:0000360 embryonic heart tube endocardial heart tube endocardial tube uberon UBERON:0004141 heart tube ZFA-modified An epithelial tube that will give rise to the mature heart. GO:0003143 GOC:mtg_heart the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube. MP:0012700 embryonic heart tube GO:0003143 endocardial heart tube MP:0012700 endocardial tube XAO:0000337 The outflow tract septum is a partition in the outflow tract uberon UBERON:0004142 outflow tract septum The outflow tract septum is a partition in the outflow tract GO:0003148 The outflow tract is the portion of the heart through which blood flows into the arteries Depending on the species, attached at the cardiac outflow are described the conus arteriosus, the truncus arteriosus and, or the bulbus arteriosus. At the distal limit of these outflow structures, but lying outside the pericardial cavity, is the ventral aorta[PMID:20735616] EHDAA2:0001351 EHDAA:464 EHDAA:798 EMAPA:16346 MA:0000100 VHOG:0000670 XAO:0004139 cardiac outflow tract heart outflow tract uberon arterial (outflow) pole UBERON:0004145 outflow tract The outflow tract is the portion of the heart through which blood flows into the arteries GO:0003151 cardiac outflow tract arterial (outflow) pole Vein of heart that drains the myocardium EHDAA2:0004507 EMAPA:37137 FMA:12846 NCIT:C12878 NCIT:C12882 UMLS:C0226654 UMLS:C0226737 ZFA:0005814 galen:CoronaryVein cardiac vein coronary vein heart vein vein of heart uberon coronary vein UBERON:0004148 cardiac vein FMA Vein of heart that drains the myocardium EMAPA:37137 MA:th UMLS:C0226654 ncithesaurus:Cardiac_Vein UMLS:C0226737 ncithesaurus:Coronary_Vein cardiac vein FMA:12846 coronary vein ZFA:0005814 heart vein OBOL:automatic vein of heart OBOL:automatic coronary vein A cardiac chamber surrounds an enclosed cavity within the heart FMA:7095 OpenCyc:Mx4rmexpjPdAEduAAAAOpmP6tw chamber of heart heart chamber uberon UBERON:0004151 generic enough to cover FBbt:00003156 heart chamber but this is a cavity. GO defines it as the cavity. TODO - move subclasses. Note this also includes sinus venosus cardiac chamber A cardiac chamber surrounds an enclosed cavity within the heart GO:0003205 The internal genitalia are the internal sex organs such as the uterine tube, the uterus and the vagina in female mammals, and the testis, seminal vesicle, ejaculatory duct and prostate in male mammals FMA:45652 internal genitalia internal genitals uberon internal reproductive organ internal sex organ UBERON:0004175 TODO: make a subdivision of reproductive system. Relabel. See https://github.com/obophenotype/uberon/issues/547 internal genitalia The internal genitalia are the internal sex organs such as the uterine tube, the uterus and the vagina in female mammals, and the testis, seminal vesicle, ejaculatory duct and prostate in male mammals GO:0035260 The external genitalia are the outer sex organs, such as the penis or vulva in mammals FMA:45643 external genitalia uberon external reproductive organ external sex organ UBERON:0004176 TODO: make a subdivision of reproductive system. Relabel. See https://github.com/obophenotype/uberon/issues/547 external genitalia The external genitalia are the outer sex organs, such as the penis or vulva in mammals GO:0035261 Organ that is part of the hematopoietic system. consider splitting out lymph organ, compare with lymph node the organs in which the formed elements of the blood and lymph are produced[http://encyclopedia2.thefreedictionary.com/Hematopoietic+Organs]. the FMA class 'lymphoid organ' is a general anatomical term BTO:0004605 EMAPA:37665 FMA:7143 MA:0000747 haematological system organ haemopoietic system organ hematopoeitic organ hematopoietic system organ organ of haematological system organ of haemopoietic system organ of hematopoietic system organ of organa haemopoietica organa haemopoietica organ hematopoeitic or lymphoid organ lymph organ lymphoid organ uberon UBERON:0004177 hemopoietic organ Organ that is part of the hematopoietic system. GOC:Obol the organs in which the formed elements of the blood and lymph are produced[http://encyclopedia2.thefreedictionary.com/Hematopoietic+Organs]. the FMA class 'lymphoid organ' is a general anatomical term FMA EMAPA:37665 MA:th haematological system organ OBOL:automatic haemopoietic system organ OBOL:automatic hematopoietic system organ OBOL:automatic organ of haematological system OBOL:automatic organ of haemopoietic system OBOL:automatic organ of hematopoietic system OBOL:automatic organ of organa haemopoietica OBOL:automatic organa haemopoietica organ OBOL:automatic lymph organ MA:0000747 lymphoid organ BTO:0004605 FMA:7143 the nonstriated, involuntary muscle tissue located in the wall of the aorta BTO:0001685 CALOHA:TS-0048 EFO:0002775 EMAPA:35135 MA:0000702 NCIT:C49191 UMLS:C1706825 aorta non-striated muscle aorta smooth muscle aortic smooth muscle uberon UBERON:0004178 aorta smooth muscle tissue the nonstriated, involuntary muscle tissue located in the wall of the aorta MGI:csmith MP:0009865 UMLS:C1706825 ncithesaurus:Aorta_Smooth_Muscle_Tissue aorta non-striated muscle OBOL:automatic aorta smooth muscle OBOL:automatic aortic smooth muscle BTO:0001685 A portions of the gut that is derived from endoderm. EMAPA:32930 endodermal gut gut endoderm uberon UBERON:0004185 endodermal part of digestive tract A portions of the gut that is derived from endoderm. GO:0061031 gut endoderm EMAPA:32930 A nerve that is part of a back [Automatically generated definition]. EMAPA:37268 MA:0000497 nerve of back uberon UBERON:0004215 back nerve A nerve that is part of a back [Automatically generated definition]. OBOL:automatic EMAPA:37268 MA:th nerve of back OBOL:automatic A portion of smooth muscle tissue that is part of a urethra [Automatically generated definition]. EMAPA:36630 FMA:76909 MA:0001691 muscle layer of urethra muscular coat of urethra muscular layer of urethra smooth muscle of urethra smooth muscle tissue of urethra tunica muscularis urethrae urethra smooth muscle tissue uberon urethral smooth muscle UBERON:0004219 urethra smooth muscle layer A portion of smooth muscle tissue that is part of a urethra [Automatically generated definition]. OBOL:automatic muscle layer of urethra FMA:76909 muscular coat of urethra FMA:76909 muscular layer of urethra FMA:76909 smooth muscle of urethra OBOL:automatic smooth muscle tissue of urethra OBOL:automatic tunica muscularis urethrae FMA:TA urethra smooth muscle tissue OBOL:automatic urethral smooth muscle MA:0001691 A portion of smooth muscle tissue that is part of a large intestine [Automatically generated definition]. MA class may specifically mean muscle layer, but we treat as the sum of smooth muscle in both muscle layer and muscularis mucosa EMAPA:35469 MA:0001547 involuntary muscle of large intestine large intestine involuntary muscle large intestine non-striated muscle large intestine smooth muscle tissue non-striated muscle of large intestine smooth muscle of large intestine smooth muscle tissue of large intestine uberon UBERON:0004220 large intestine smooth muscle MA consider merging A portion of smooth muscle tissue that is part of a large intestine [Automatically generated definition]. OBOL:automatic MA class may specifically mean muscle layer, but we treat as the sum of smooth muscle in both muscle layer and muscularis mucosa MA involuntary muscle of large intestine OBOL:automatic large intestine involuntary muscle OBOL:automatic large intestine non-striated muscle OBOL:automatic large intestine smooth muscle tissue OBOL:automatic non-striated muscle of large intestine OBOL:automatic smooth muscle of large intestine OBOL:automatic smooth muscle tissue of large intestine OBOL:automatic A portion of smooth muscle tissue that is part of a intestine [Automatically generated definition]. MA class may specifically mean muscle layer, but we treat as the sum of smooth muscle in both muscle layer and muscularis mucosa BTO:0000643 EMAPA:35441 EMAPA:35443 MA:0001539 NCIT:C49243 UMLS:C1708547 bowel involuntary muscle bowel non-striated muscle bowel smooth muscle bowel smooth muscle tissue intestine involuntary muscle intestine non-striated muscle intestine smooth muscle tissue involuntary muscle of bowel involuntary muscle of intestine non-striated muscle of bowel non-striated muscle of intestine smooth muscle of bowel smooth muscle of intestine smooth muscle tissue of bowel smooth muscle tissue of intestine uberon intestinal muscularis intestinal smooth muscle UBERON:0004221 intestine smooth muscle consider merging A portion of smooth muscle tissue that is part of a intestine [Automatically generated definition]. OBOL:automatic MA class may specifically mean muscle layer, but we treat as the sum of smooth muscle in both muscle layer and muscularis mucosa MA UMLS:C1708547 ncithesaurus:Intestinal_Smooth_Muscle_Tissue bowel involuntary muscle OBOL:automatic bowel non-striated muscle OBOL:automatic bowel smooth muscle OBOL:automatic bowel smooth muscle tissue OBOL:automatic intestine involuntary muscle OBOL:automatic intestine non-striated muscle OBOL:automatic intestine smooth muscle tissue OBOL:automatic involuntary muscle of bowel OBOL:automatic involuntary muscle of intestine OBOL:automatic non-striated muscle of bowel OBOL:automatic non-striated muscle of intestine OBOL:automatic smooth muscle of bowel OBOL:automatic smooth muscle of intestine OBOL:automatic smooth muscle tissue of bowel OBOL:automatic smooth muscle tissue of intestine OBOL:automatic intestinal muscularis EMAPA:35441 intestinal smooth muscle BTO:0000643 A portion of smooth muscle tissue that is part of a stomach [Automatically generated definition]. BTO:0001818 EMAPA:35823 MA:0001627 involuntary muscle of stomach involuntary muscle of ventriculus non-striated muscle of stomach non-striated muscle of ventriculus smooth muscle of stomach smooth muscle of ventriculus smooth muscle tissue of stomach smooth muscle tissue of ventriculus stomach involuntary muscle stomach non-striated muscle stomach smooth muscle tissue ventriculus involuntary muscle ventriculus non-striated muscle ventriculus smooth muscle ventriculus smooth muscle tissue uberon gastric muscle gastric smooth muscle stomach muscle UBERON:0004222 stomach smooth muscle A portion of smooth muscle tissue that is part of a stomach [Automatically generated definition]. OBOL:automatic involuntary muscle of stomach OBOL:automatic involuntary muscle of ventriculus OBOL:automatic non-striated muscle of stomach OBOL:automatic non-striated muscle of ventriculus OBOL:automatic smooth muscle of stomach OBOL:automatic smooth muscle of ventriculus OBOL:automatic smooth muscle tissue of stomach OBOL:automatic smooth muscle tissue of ventriculus OBOL:automatic stomach involuntary muscle OBOL:automatic stomach non-striated muscle OBOL:automatic stomach smooth muscle tissue OBOL:automatic ventriculus involuntary muscle OBOL:automatic ventriculus non-striated muscle OBOL:automatic ventriculus smooth muscle OBOL:automatic ventriculus smooth muscle tissue OBOL:automatic gastric muscle BTO:0001818 gastric smooth muscle MA:0001627 stomach muscle BTO:0001818 A portion of smooth muscle tissue that is part of a vagina [Automatically generated definition]. BTO:0004999 EMAPA:30997 MA:0001733 involuntary muscle of vagina non-striated muscle of vagina smooth muscle of vagina smooth muscle tissue of vagina vagina involuntary muscle vagina non-striated muscle vagina smooth muscle tissue vaginal smooth muscle uberon vagina smooth muscle UBERON:0004223 vagina smooth muscle A portion of smooth muscle tissue that is part of a vagina [Automatically generated definition]. OBOL:automatic involuntary muscle of vagina OBOL:automatic non-striated muscle of vagina OBOL:automatic smooth muscle of vagina OBOL:automatic smooth muscle tissue of vagina OBOL:automatic vagina involuntary muscle OBOL:automatic vagina non-striated muscle OBOL:automatic vagina smooth muscle tissue OBOL:automatic vaginal smooth muscle BTO:0004999 vagina smooth muscle BTO:0004999 A portion of smooth muscle tissue that is part of a respiratory system [Automatically generated definition]. BTO:0001660 EMAPA:35734 MA:0001830 respiratory smooth muscle smooth muscle of respiratory system uberon airway smooth muscle airway smooth muscle cell UBERON:0004225 respiratory system smooth muscle A portion of smooth muscle tissue that is part of a respiratory system [Automatically generated definition]. OBOL:automatic respiratory smooth muscle BTO:0001660 smooth muscle of respiratory system OBOL:automatic airway smooth muscle BTO:0001660 airway smooth muscle cell BTO:0001660 A portion of smooth muscle tissue that is part of a digestive system [Automatically generated definition]. EMAPA:35117 MA:0001523 smooth muscle tissue of gastrointestinal system uberon UBERON:0004226 gastrointestinal system smooth muscle A portion of smooth muscle tissue that is part of a digestive system [Automatically generated definition]. OBOL:automatic smooth muscle tissue of gastrointestinal system OBOL:automatic the smooth muscle tissue surrounding the urothelium of the kidney pelvis EMAPA:28120 FMA:262022 MA:0002631 kidney pelvis smooth muscle renal pelvis smooth muscle smooth muscle tissue of renal pelvis uberon pelvic smooth muscle UBERON:0004227 kidney pelvis smooth muscle the smooth muscle tissue surrounding the urothelium of the kidney pelvis MGI:csmith MP:0011335 kidney pelvis smooth muscle EMAPA:28120 renal pelvis smooth muscle EMAPA:28120 smooth muscle tissue of renal pelvis FMA:262022 pelvic smooth muscle EMAPA:28120 A portion of smooth muscle tissue that is part of a urinary bladder [Automatically generated definition]. BTO:0001849 CALOHA:TS-1087 EMAPA:37791 MA:0001697 bladder involuntary muscle bladder non-striated muscle bladder smooth muscle bladder smooth muscle tissue involuntary muscle of bladder involuntary muscle of urinary bladder non-striated muscle of bladder non-striated muscle of urinary bladder smooth muscle of bladder smooth muscle of urinary bladder smooth muscle tissue of bladder smooth muscle tissue of urinary bladder urinary bladder involuntary muscle urinary bladder muscle urinary bladder non-striated muscle urinary bladder smooth muscle tissue uberon smooth muscle layer of bladder UBERON:0004228 urinary bladder smooth muscle A portion of smooth muscle tissue that is part of a urinary bladder [Automatically generated definition]. OBOL:automatic EMAPA:37791 MA:th bladder involuntary muscle OBOL:automatic bladder non-striated muscle OBOL:automatic bladder smooth muscle OBOL:automatic bladder smooth muscle tissue OBOL:automatic involuntary muscle of bladder OBOL:automatic involuntary muscle of urinary bladder OBOL:automatic non-striated muscle of bladder OBOL:automatic non-striated muscle of urinary bladder OBOL:automatic smooth muscle of bladder OBOL:automatic smooth muscle of urinary bladder OBOL:automatic smooth muscle tissue of bladder OBOL:automatic smooth muscle tissue of urinary bladder OBOL:automatic urinary bladder involuntary muscle OBOL:automatic urinary bladder muscle MA:0001697 urinary bladder non-striated muscle OBOL:automatic urinary bladder smooth muscle tissue OBOL:automatic A portion of smooth muscle tissue that is part of a neck of urinary bladder [Automatically generated definition]. EMAPA:30123 FMA:67990 MA:0001699 bladder neck involuntary muscle bladder neck non-striated muscle bladder neck smooth muscle bladder neck smooth muscle tissue involuntary muscle of bladder neck involuntary muscle of neck of bladder involuntary muscle of neck of urinary bladder involuntary muscle of urinary bladder neck involuntary muscle of vesical neck neck of bladder involuntary muscle neck of bladder non-striated muscle neck of bladder smooth muscle neck of bladder smooth muscle tissue neck of urinary bladder involuntary muscle neck of urinary bladder non-striated muscle neck of urinary bladder smooth muscle neck of urinary bladder smooth muscle tissue non-striated muscle of bladder neck non-striated muscle of neck of bladder non-striated muscle of neck of urinary bladder non-striated muscle of urinary bladder neck non-striated muscle of vesical neck smooth muscle of bladder neck smooth muscle of neck of bladder smooth muscle of neck of urinary bladder smooth muscle of urinary bladder neck smooth muscle of vesical neck smooth muscle tissue of bladder neck smooth muscle tissue of neck of bladder smooth muscle tissue of neck of urinary bladder smooth muscle tissue of urinary bladder neck smooth muscle tissue of vesical neck trigonal muscle trigonal muscle of urinary bladder urinary bladder neck involuntary muscle urinary bladder neck muscle urinary bladder neck non-striated muscle urinary bladder neck smooth muscle tissue vesical neck involuntary muscle vesical neck non-striated muscle vesical neck smooth muscle vesical neck smooth muscle tissue uberon UBERON:0004230 urinary bladder neck smooth muscle A portion of smooth muscle tissue that is part of a neck of urinary bladder [Automatically generated definition]. OBOL:automatic bladder neck involuntary muscle OBOL:automatic bladder neck non-striated muscle OBOL:automatic bladder neck smooth muscle OBOL:automatic bladder neck smooth muscle tissue OBOL:automatic involuntary muscle of bladder neck OBOL:automatic involuntary muscle of neck of bladder OBOL:automatic involuntary muscle of neck of urinary bladder OBOL:automatic involuntary muscle of urinary bladder neck OBOL:automatic involuntary muscle of vesical neck OBOL:automatic neck of bladder involuntary muscle OBOL:automatic neck of bladder non-striated muscle OBOL:automatic neck of bladder smooth muscle OBOL:automatic neck of bladder smooth muscle tissue OBOL:automatic neck of urinary bladder involuntary muscle OBOL:automatic neck of urinary bladder non-striated muscle OBOL:automatic neck of urinary bladder smooth muscle OBOL:automatic neck of urinary bladder smooth muscle tissue OBOL:automatic non-striated muscle of bladder neck OBOL:automatic non-striated muscle of neck of bladder OBOL:automatic non-striated muscle of neck of urinary bladder OBOL:automatic non-striated muscle of urinary bladder neck OBOL:automatic non-striated muscle of vesical neck OBOL:automatic smooth muscle of bladder neck OBOL:automatic smooth muscle of neck of bladder OBOL:automatic smooth muscle of neck of urinary bladder OBOL:automatic smooth muscle of urinary bladder neck OBOL:automatic smooth muscle of vesical neck OBOL:automatic smooth muscle tissue of bladder neck OBOL:automatic smooth muscle tissue of neck of bladder OBOL:automatic smooth muscle tissue of neck of urinary bladder OBOL:automatic smooth muscle tissue of urinary bladder neck OBOL:automatic smooth muscle tissue of vesical neck OBOL:automatic trigonal muscle FMA:67990 trigonal muscle of urinary bladder FMA:67990 urinary bladder neck involuntary muscle OBOL:automatic urinary bladder neck muscle MA:0001699 urinary bladder neck non-striated muscle OBOL:automatic urinary bladder neck smooth muscle tissue OBOL:automatic vesical neck involuntary muscle OBOL:automatic vesical neck non-striated muscle OBOL:automatic vesical neck smooth muscle OBOL:automatic vesical neck smooth muscle tissue OBOL:automatic A portion of smooth muscle tissue that is part of an anal region [Automatically generated definition]. EMAPA:37394 MA:0001532 anal part of perineum involuntary muscle anal part of perineum non-striated muscle anal part of perineum smooth muscle anal part of perineum smooth muscle tissue anal region involuntary muscle anal region non-striated muscle anal region smooth muscle tissue anal triangle involuntary muscle anal triangle non-striated muscle anal triangle smooth muscle anal triangle smooth muscle tissue involuntary muscle of anal part of perineum involuntary muscle of anal region involuntary muscle of anal triangle non-striated muscle of anal part of perineum non-striated muscle of anal region non-striated muscle of anal triangle smooth muscle of anal part of perineum smooth muscle of anal region smooth muscle of anal triangle smooth muscle tissue of anal part of perineum smooth muscle tissue of anal region smooth muscle tissue of anal triangle uberon UBERON:0004231 anal region smooth muscle A portion of smooth muscle tissue that is part of an anal region [Automatically generated definition]. OBOL:automatic EMAPA:37394 MA:th anal part of perineum involuntary muscle OBOL:automatic anal part of perineum non-striated muscle OBOL:automatic anal part of perineum smooth muscle OBOL:automatic anal part of perineum smooth muscle tissue OBOL:automatic anal region involuntary muscle OBOL:automatic anal region non-striated muscle OBOL:automatic anal region smooth muscle tissue OBOL:automatic anal triangle involuntary muscle OBOL:automatic anal triangle non-striated muscle OBOL:automatic anal triangle smooth muscle OBOL:automatic anal triangle smooth muscle tissue OBOL:automatic involuntary muscle of anal part of perineum OBOL:automatic involuntary muscle of anal region OBOL:automatic involuntary muscle of anal triangle OBOL:automatic non-striated muscle of anal part of perineum OBOL:automatic non-striated muscle of anal region OBOL:automatic non-striated muscle of anal triangle OBOL:automatic smooth muscle of anal part of perineum OBOL:automatic smooth muscle of anal region OBOL:automatic smooth muscle of anal triangle OBOL:automatic smooth muscle tissue of anal part of perineum OBOL:automatic smooth muscle tissue of anal region OBOL:automatic smooth muscle tissue of anal triangle OBOL:automatic A portion of smooth muscle tissue that is part of a lower respiratory tract [Automatically generated definition]. EMAPA:35520 MA:0002410 involuntary muscle of lower respiratory tract lower respiratory tract involuntary muscle lower respiratory tract non-striated muscle lower respiratory tract smooth muscle tissue non-striated muscle of lower respiratory tract smooth muscle of lower respiratory tract smooth muscle tissue of lower respiratory tract uberon UBERON:0004233 lower respiratory tract smooth muscle A portion of smooth muscle tissue that is part of a lower respiratory tract [Automatically generated definition]. OBOL:automatic involuntary muscle of lower respiratory tract OBOL:automatic lower respiratory tract involuntary muscle OBOL:automatic lower respiratory tract non-striated muscle OBOL:automatic lower respiratory tract smooth muscle tissue OBOL:automatic non-striated muscle of lower respiratory tract OBOL:automatic smooth muscle of lower respiratory tract OBOL:automatic smooth muscle tissue of lower respiratory tract OBOL:automatic A portion of smooth muscle tissue that is part of a iris [Automatically generated definition]. see notes for muscle of iris. BTO:0000655 EMAPA:35448 FMA:312338 MA:0001270 involuntary muscle of iris iridial smooth muscle iris involuntary muscle iris non-striated muscle iris smooth muscle tissue non-striated muscle of iris smooth muscle of iris smooth muscle tissue of iris uberon UBERON:0004234 iris smooth muscle MA A portion of smooth muscle tissue that is part of a iris [Automatically generated definition]. OBOL:automatic involuntary muscle of iris OBOL:automatic iridial smooth muscle iris involuntary muscle OBOL:automatic iris non-striated muscle OBOL:automatic iris smooth muscle tissue OBOL:automatic non-striated muscle of iris OBOL:automatic smooth muscle of iris OBOL:automatic smooth muscle tissue of iris OBOL:automatic A portion of smooth muscle tissue that is part of an arteriole [Automatically generated definition]. EMAPA:36287 FMA:312251 MA:0000706 uberon UBERON:0004236 arteriole smooth muscle A portion of smooth muscle tissue that is part of an arteriole [Automatically generated definition]. OBOL:automatic smooth muscle found within, and composing the majority of the wall of blood vessels. Vascular smooth muscle contracts or relaxes to both change the volume of blood vessels and the local blood pressure, a mechanism that is responsible for the redistribution of the blood within the body to areas where it is needed (i.e. areas with temporarily enhanced oxygen consumption). Thus the main function of vascular smooth muscle tonus is to regulate the caliber of the blood vessels in the body. Excessive vasoconstriction leads to hypertension, while excessive vasodilation as in shock leads to hypotension. UBERON:0010508 BTO:0001431 CALOHA:TS-1107 EMAPA:35177 MA:0000710 MESH:D009131 NCIT:C33853 TAO:0005321 UMLS:C1519956 ZFA:0005321 blood vessel involuntary muscle blood vessel non-striated muscle blood vessel smooth muscle tissue involuntary muscle of blood vessel non-striated muscle of blood vessel smooth muscle of blood vessel smooth muscle tissue of blood vessel vascular smooth muscle vascular smooth muscle tissue uberon UBERON:0004237 blood vessel smooth muscle smooth muscle found within, and composing the majority of the wall of blood vessels. UMLS:C1519956 ncithesaurus:Vascular_Smooth_Muscle_Tissue blood vessel involuntary muscle OBOL:automatic blood vessel non-striated muscle OBOL:automatic blood vessel smooth muscle tissue OBOL:automatic involuntary muscle of blood vessel OBOL:automatic non-striated muscle of blood vessel OBOL:automatic smooth muscle of blood vessel OBOL:automatic smooth muscle tissue of blood vessel OBOL:automatic vascular smooth muscle ZFA:0005321 A portion of smooth muscle tissue that is part of a bronchus [Automatically generated definition]. BTO:0004401 EMAPA:35195 MA:0001840 NCIT:C49213 UMLS:C1707055 bronchi involuntary muscle bronchi non-striated muscle bronchi smooth muscle bronchi smooth muscle tissue bronchial trunk involuntary muscle bronchial trunk non-striated muscle bronchial trunk smooth muscle bronchial trunk smooth muscle tissue bronchus involuntary muscle bronchus non-striated muscle bronchus smooth muscle tissue involuntary muscle of bronchi involuntary muscle of bronchial trunk involuntary muscle of bronchus non-striated muscle of bronchi non-striated muscle of bronchial trunk non-striated muscle of bronchus smooth muscle of bronchi smooth muscle of bronchial trunk smooth muscle of bronchus smooth muscle tissue of bronchi smooth muscle tissue of bronchial trunk smooth muscle tissue of bronchus uberon bronchial smooth muscle UBERON:0004242 bronchus smooth muscle A portion of smooth muscle tissue that is part of a bronchus [Automatically generated definition]. OBOL:automatic UMLS:C1707055 ncithesaurus:Bronchus_Smooth_Muscle_Tissue bronchi involuntary muscle OBOL:automatic bronchi non-striated muscle OBOL:automatic bronchi smooth muscle OBOL:automatic bronchi smooth muscle tissue OBOL:automatic bronchial trunk involuntary muscle OBOL:automatic bronchial trunk non-striated muscle OBOL:automatic bronchial trunk smooth muscle OBOL:automatic bronchial trunk smooth muscle tissue OBOL:automatic bronchus involuntary muscle OBOL:automatic bronchus non-striated muscle OBOL:automatic bronchus smooth muscle tissue OBOL:automatic involuntary muscle of bronchi OBOL:automatic involuntary muscle of bronchial trunk OBOL:automatic involuntary muscle of bronchus OBOL:automatic non-striated muscle of bronchi OBOL:automatic non-striated muscle of bronchial trunk OBOL:automatic non-striated muscle of bronchus OBOL:automatic smooth muscle of bronchi OBOL:automatic smooth muscle of bronchial trunk OBOL:automatic smooth muscle of bronchus OBOL:automatic smooth muscle tissue of bronchi OBOL:automatic smooth muscle tissue of bronchial trunk OBOL:automatic smooth muscle tissue of bronchus OBOL:automatic bronchial smooth muscle EMAPA:35195 A portion of smooth muscle tissue that is part of a fallopian tube [Automatically generated definition]. EMAPA:29046 MA:0001721 fallopian tube involuntary muscle fallopian tube non-striated muscle fallopian tube smooth muscle fallopian tube smooth muscle tissue involuntary muscle of fallopian tube non-striated muscle of fallopian tube smooth muscle of fallopian tube smooth muscle tissue of fallopian tube uberon UBERON:0004245 oviduct smooth muscle A portion of smooth muscle tissue that is part of a fallopian tube [Automatically generated definition]. OBOL:automatic fallopian tube involuntary muscle OBOL:automatic fallopian tube non-striated muscle OBOL:automatic fallopian tube smooth muscle OBOL:automatic fallopian tube smooth muscle tissue OBOL:automatic involuntary muscle of fallopian tube OBOL:automatic non-striated muscle of fallopian tube OBOL:automatic smooth muscle of fallopian tube OBOL:automatic smooth muscle tissue of fallopian tube OBOL:automatic A portion of smooth muscle tissue that is part of a outflow tract [Automatically generated definition]. EMAPA:37708 MA:0000492 involuntary muscle of outflow tract non-striated muscle of outflow tract outflow tract involuntary muscle outflow tract non-striated muscle outflow tract smooth muscle tissue smooth muscle of outflow tract smooth muscle tissue of outflow tract uberon UBERON:0004246 outflow tract smooth muscle A portion of smooth muscle tissue that is part of a outflow tract [Automatically generated definition]. OBOL:automatic EMAPA:37708 MA:th involuntary muscle of outflow tract OBOL:automatic non-striated muscle of outflow tract OBOL:automatic outflow tract involuntary muscle OBOL:automatic outflow tract non-striated muscle OBOL:automatic outflow tract smooth muscle tissue OBOL:automatic smooth muscle of outflow tract OBOL:automatic smooth muscle tissue of outflow tract OBOL:automatic A bone that is part of the dorsal region of an animal. this class may be obsoleted. See: https://github.com/obophenotype/mouse-anatomy-ontology/issues/93 https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern EMAPA:37248 MA:0000494 uberon back bone bone of back dorsal region bone UBERON:0004247 bone of dorsum A bone that is part of the dorsal region of an animal. EMAPA:37248 MA:th back bone MA:0000494 bone of back OBOL:automatic dorsal region bone Any muscle organ that is part of a skin of body [Automatically generated definition]. review as part of general integumentary system review - part of skin, or more generally, integumental system in MA, the only skin muscle is arrector pili. The only integumental muscle is panniculus carnosus. In EMAPA, the arrector pili only UBERON:0015797 EMAPA:18187 EMAPA:35776 MA:0002710 MA:0003139 integumental system muscle muscle of integumental system muscle organ of skin skin muscle organ uberon UBERON:0004253 skin muscle Any muscle organ that is part of a skin of body [Automatically generated definition]. OBOL:automatic in MA, the only skin muscle is arrector pili. The only integumental muscle is panniculus carnosus. In EMAPA, the arrector pili only MA integumental system muscle MA:0003139 muscle of integumental system EMAPA:18187 muscle organ of skin OBOL:automatic skin muscle organ OBOL:automatic A blood vessel that is part of a back [Automatically generated definition]. EMAPA:37243 MA:0000493 blood vessel of back uberon UBERON:0004258 back blood vessel A blood vessel that is part of a back [Automatically generated definition]. OBOL:automatic EMAPA:37243 MA:th blood vessel of back OBOL:automatic A myocardium that is part of a outflow tract [Automatically generated definition]. (...) (theme) is how the vertebrate cardiovascular system differs from that of the presumptive evolutionary chordate ancestor. (...) At best we can tell there are two essential new ingredients: (1) vertebrates all have a continuous endothelial lining to the heart and vessels and (2) vertebrates have developed a second chamber in the heart, one designed for generating high systemic blood pressure.[uncertain][VHOG] EHDAA2:0001358 EMAPA:35623 MA:0000489 VHOG:0000603 cardiac muscle of outflow tract heart muscle of outflow tract heart myocardium of outflow tract muscle of heart of outflow tract myocardium of outflow tract outflow tract cardiac muscle outflow tract heart muscle outflow tract heart myocardium outflow tract muscle of heart uberon UBERON:0004265 outflow tract myocardium A myocardium that is part of a outflow tract [Automatically generated definition]. OBOL:automatic (...) (theme) is how the vertebrate cardiovascular system differs from that of the presumptive evolutionary chordate ancestor. (...) At best we can tell there are two essential new ingredients: (1) vertebrates all have a continuous endothelial lining to the heart and vessels and (2) vertebrates have developed a second chamber in the heart, one designed for generating high systemic blood pressure.[uncertain][VHOG] 2012-09-17 VHOG:0000603 VHOG PMID:9187138 Fishman MC, Chien KR, Fashioning the vertebrate heart: earliest embryonic decisions. Development (1997) cardiac muscle of outflow tract OBOL:automatic heart muscle of outflow tract OBOL:automatic heart myocardium of outflow tract OBOL:automatic muscle of heart of outflow tract OBOL:automatic myocardium of outflow tract OBOL:automatic outflow tract cardiac muscle OBOL:automatic outflow tract heart muscle OBOL:automatic outflow tract heart myocardium OBOL:automatic outflow tract muscle of heart OBOL:automatic A portion of connective tissue that is part of a back [Automatically generated definition]. EMAPA:37256 MA:0000495 uberon mesenchyne of back UBERON:0004267 back connective tissue A portion of connective tissue that is part of a back [Automatically generated definition]. OBOL:automatic EMAPA:37256 MA:th mesenchyne of back OBOL:automatic A muscle that is part of the eye region. AAO:0000156 EMAPA:35335 MA:0000271 OpenCyc:Mx8Ngx4rwKSh9pwpEbGdrcN5Y29ycB4rvViTvpwpEbGdrcN5Y29ycB4rvYA8cJwpEbGdrcN5Y29ycA uberon UBERON:0004277 eye muscle MA A muscle that is part of the eye region. OBOL:automatic Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body. Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO] skeletal AEO:0000168 EHDAA2:0001843 EHDAA:5047 EMAPA:17213 FMA:23875 GAID:177 MA:0003006 MAT:0000032 MESH:D012863 MIAA:0000032 OpenCyc:Mx4rvVi1rpwpEbGdrcN5Y29ycA VSAO:0000026 XAO:0004053 galen:Skeleton set of all bones set of bones of body uberon UBERON:0004288 skeleton https://github.com/obophenotype/uberon/wiki/The-skeletal-system Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body. VSAO:0000026 Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO] 2012-08-14 VSAO:0000026 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 The bilaminar epithelium formed from the myotome and dermatome. Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis. Within the dermomyotome there is also a medio-lateral difference. The central region makes dermis, the mesenchymal connective tissue of the back skin. The medial region (closest to neural tube) makes epaxial muscle, and the lateral region (furthest from neural tube) makes hypaxial muscle[http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A66768]. Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis.[TAO] Portion of somites that gives rise to dermis and muscles.[AAO] all but the sclerotome of a mesodermal somite; the primordium of skeletal muscle and, perhaps, of the dermis. Thus, representatives of the agnathan vertebrates, chondrichthyans, and sarcopterygians all have a layer of undifferentiated cells external to the embryonic myotome. In the amniotes, this external cell layer is the dermomyotome. The simplest interpretation of the similar position, morphology, and lack of myosin labeling is that a dermomyotome epithelium is a shared, ancestral vertebrate characteristic.[well established][VHOG] AAO:0010572 AEO:0000214 EHDAA2:0003259 EMAPA:31109 FMA:295654 NCIT:C34140 TAO:0001513 UMLS:C1511786 VHOG:0000676 ZFA:0001513 uberon dermamyotome dermomyotomes UBERON:0004290 dermomyotome AEO AEO EHDAA2 ZFA The bilaminar epithelium formed from the myotome and dermatome. AEO:0000214 Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis. Within the dermomyotome there is also a medio-lateral difference. The central region makes dermis, the mesenchymal connective tissue of the back skin. The medial region (closest to neural tube) makes epaxial muscle, and the lateral region (furthest from neural tube) makes hypaxial muscle[http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A66768]. Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis.[TAO] 2012-08-14 TAO:0001513 TAO ZFIN:curator Portion of somites that gives rise to dermis and muscles.[AAO] 2012-06-20 AAO:0010572 AAO AAO:EJS all but the sclerotome of a mesodermal somite; the primordium of skeletal muscle and, perhaps, of the dermis. Thus, representatives of the agnathan vertebrates, chondrichthyans, and sarcopterygians all have a layer of undifferentiated cells external to the embryonic myotome. In the amniotes, this external cell layer is the dermomyotome. The simplest interpretation of the similar position, morphology, and lack of myosin labeling is that a dermomyotome epithelium is a shared, ancestral vertebrate characteristic.[well established][VHOG] 2012-09-17 VHOG:0000676 VHOG DOI:10.1111/j.1525-142X.2006.05079.x Devoto SH, Stoiber W, Hammond CL, Steinbacher P, Haslett JR, Barresi MJF, Patterson SE, Adiarte EG and Hughes SM, Generality of vertebrate developmental patterns: evidence for a dermomyotome in fish. Evolution and Development (2006) UMLS:C1511786 ncithesaurus:Dermomyotome dermamyotome VHOG:0000676 dermomyotomes VHOG:0000676 A cone-like structure that is formed when myocardial progenitor cells of the heart field fuse at the midline. The heart rudiment is the first structure of the heart tube. The migrating myocardial precursors of the heart rudiment form a cone like structure between 19.5hpf and 22hpf, and eventually telescope out into the primitive heart tube at 24hpf. Stainier 2001.[TAO] TAO:0000115 ZFA:0000115 heart cone rudimentary heart uberon UBERON:0004291 heart rudiment A cone-like structure that is formed when myocardial progenitor cells of the heart field fuse at the midline. The heart rudiment is the first structure of the heart tube. GO:0003313 The migrating myocardial precursors of the heart rudiment form a cone like structure between 19.5hpf and 22hpf, and eventually telescope out into the primitive heart tube at 24hpf. Stainier 2001.[TAO] 2012-08-14 TAO:0000115 TAO ZFIN:curator heart cone GO:0003313 rudimentary heart ZFA:0000115 A blood vessel smooth muscle that is part of a respiratory system [Automatically generated definition]. EMAPA:37573 MA:0001806 smooth muscle tissue of blood vessel of respiratory system uberon UBERON:0004297 respiratory system blood vessel smooth muscle A blood vessel smooth muscle that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37573 MA:th smooth muscle tissue of blood vessel of respiratory system OBOL:automatic The primitive streak is a structure that forms during the early stages of avian, reptilian and mammalian embryonic development[WP]. the midline ridge of the embryonic epiblast that later develops into mesoderm and endoderm[MP] (...) the blastopore equivalent of chordates (germ ring in fish, marginal zone/blastopore lip in frog and node/primitive streak in chick and mouse) (...) (reference 1); Indeed, the primitive streak has been considered the homologue of the blastopore since the 1870s (reference 2).[well established][VHOG] VHOG includes a very broad grouping here based on http://www.ncbi.nlm.nih.gov/pubmed/9609826 EHDAA2:0001525 EHDAA:185 EMAPA:16072 FMA:293110 NCIT:C28402 UMLS:C0033153 VHOG:0001202 primitive streak - blastopore - germ ring uberon UBERON:0004341 primitive streak EHDAA2 The primitive streak is a structure that forms during the early stages of avian, reptilian and mammalian embryonic development[WP]. the midline ridge of the embryonic epiblast that later develops into mesoderm and endoderm[MP] MP:0002231 (...) the blastopore equivalent of chordates (germ ring in fish, marginal zone/blastopore lip in frog and node/primitive streak in chick and mouse) (...) (reference 1); Indeed, the primitive streak has been considered the homologue of the blastopore since the 1870s (reference 2).[well established][VHOG] 2012-09-17 VHOG:0001202 VHOG PMID:9609826 Wu LH, Lengyel JA, Role of caudal in hindgut specification and gastrulation suggests homology between Drosophila amnioproctodeal invagination and vertebrate blastopore. Development (1998), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.139 VHOG includes a very broad grouping here based on http://www.ncbi.nlm.nih.gov/pubmed/9609826 VHOG UMLS:C0033153 ncithesaurus:Primitive_Streak primitive streak - blastopore - germ ring VHOG:0001202 The embryonic structure that gives rise to the corneal ectoderm EHDAA:938 EMAPA:16322 RETIRED_EHDAA2:0001308 VHOG:0001296 uberon UBERON:0004348 optic eminence The embryonic structure that gives rise to the corneal ectoderm MP:0006305 multilayered ectodermal region at the distal tip of a limb or fin bud necessary for the proper development of the underlying mesenchyme[MP,modified]. Along with the zone of polarizing activity, it is a crucial organizing region during limb development[WP]. note that media, dorsal fins etc have AERs. Distal ectodermal thickening which forms along the anterior-posterior limb axis. Signaling from this region influences proximal-distal patterning of the limb. Structure is missing in some lineages (salamanders, Eleutherodactylus coqui) however morphologically their indistinct distal ectoderm may still be involved in signaling.[AAO] Proliferative region that is part of the developing fin fold or fin.[TAO] relationship loss: subclass proliferative region (TAO:0000098)[TAO] The AER of tetrapods regresses after specification of skeletal progenitors, the AER of teleosts form an elongating fin fold maintaining mesenchyme in plastic proliferating state; maintaining expression of A-P axis genes; interacting with D-V proteins. Genes: AER induced by Fgf10 in mesenchyme. AER secretes Fgf8, which stimulates mitosis in the mesenchyme causing Fgf10 production - positive feedback loop AAO:0010760 EMAPA:32744 NCIT:C34109 TAO:0002146 UMLS:C1516037 XAO:0004121 ZFA:0001702 apical epidermal ridge uberon AER crista ectodermalis apicalis UBERON:0004356 apical ectodermal ridge multilayered ectodermal region at the distal tip of a limb or fin bud necessary for the proper development of the underlying mesenchyme[MP,modified]. Along with the zone of polarizing activity, it is a crucial organizing region during limb development[WP]. MP:0001676 Distal ectodermal thickening which forms along the anterior-posterior limb axis. Signaling from this region influences proximal-distal patterning of the limb. Structure is missing in some lineages (salamanders, Eleutherodactylus coqui) however morphologically their indistinct distal ectoderm may still be involved in signaling.[AAO] 2012-06-20 AAO:0010760 AAO AAO:EJS Proliferative region that is part of the developing fin fold or fin.[TAO] 2012-08-14 TAO:0002146 TAO ZFIN:curator relationship loss: subclass proliferative region (TAO:0000098)[TAO] 2012-08-14 TAO:0002146 TAO The AER of tetrapods regresses after specification of skeletal progenitors, the AER of teleosts form an elongating fin fold UMLS:C1516037 ncithesaurus:Apical_Ectodermal_Ridge apical epidermal ridge XAO:0004121 AER MP:0001676 crista ectodermalis apicalis An outgrowth on the lateral trunk of the embryo that develops into a limb or paired fin. The limb/fin bud is divided into ectoderm and mesenchyme[cjm, modified from MP]. The tetrapod limb is derived from a posterior part of the fin endoskeleton of elasmobranchs and basal bony fish, the so-called metapterygium, a series of endoskeletal elements that is the first to form in the developing paired fins. (...) In addition, there is an independent endoskeletal element called the protopterygium that develops anterior to the metapterygium in many basal fishes (e.g., the bichir and sturgeon). Teleosts have lost the metapterygium whereas the sarcopterygians, on the other hand, have lost the protopterygium. Sarcopterygians thus develop all their endoskeletal structures from the metapterygium and consequently the tetrapod limb skeleton is derived from the metapterygium.[uncertain][VHOG] VHOG:0001258 limb - fin bud paired appendage bud paired limb/fin bud uberon UBERON:0004357 Genes: In limb buds of chick and mouse, Shh expression is activated as soon as there is a morphological bud, whereas in S. canicula fin buds, consistent with reported data in other cartilaginous fishes, Shh is transcribed late in fin development[PMID:17187056] paired limb/fin bud An outgrowth on the lateral trunk of the embryo that develops into a limb or paired fin. The limb/fin bud is divided into ectoderm and mesenchyme[cjm, modified from MP]. ISBN:9780878932504 MP:0005650 The tetrapod limb is derived from a posterior part of the fin endoskeleton of elasmobranchs and basal bony fish, the so-called metapterygium, a series of endoskeletal elements that is the first to form in the developing paired fins. (...) In addition, there is an independent endoskeletal element called the protopterygium that develops anterior to the metapterygium in many basal fishes (e.g., the bichir and sturgeon). Teleosts have lost the metapterygium whereas the sarcopterygians, on the other hand, have lost the protopterygium. Sarcopterygians thus develop all their endoskeletal structures from the metapterygium and consequently the tetrapod limb skeleton is derived from the metapterygium.[uncertain][VHOG] 2012-09-17 VHOG:0001258 VHOG DOI:10.1002/jez.1100 Wagner GP, Chiu C, The tetrapod limb: A hypothesis on its origin. J Exp Zool (Mol Dev Evol) (2001) limb - fin bud VHOG:0001258 paired limb/fin bud VHOG:0001258 The first of the series of pharyngeal arches that develop into jaw bones or their homologs, and their associated nerves and arteries The first of the series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO] the first arch which contributes to development of mastication muscles, maxilla, mandible, incus, malleus, Meckel's cartilage, trigeminal nerve, and maxillary artery A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] 1 AAO:0010364 CALOHA:TS-2089 EHDAA2:0000006 EHDAA:573 EMAPA:16118 FMA:293019 MFMO:0000095 NCIT:C34175 TAO:0001595 UMLS:C1517197 VHOG:0000296 XAO:0000097 ZFA:0001612 1st pharyngeal arch branchial arch 1 first branchial arch first pharyngeal arch first visceral arch mandibular arch visceral arch 1 uberon 1st arch 1st visceral arch arcus pharyngeus primus UBERON:0004362 pharyngeal arch 1 The first of the series of pharyngeal arches that develop into jaw bones or their homologs, and their associated nerves and arteries The first of the series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO] 2012-06-20 AAO:0010364 AAO XAO:EJS the first arch which contributes to development of mastication muscles, maxilla, mandible, incus, malleus, Meckel's cartilage, trigeminal nerve, and maxillary artery MP:0006337,MGI:smb A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] 2012-09-17 VHOG:0000296 VHOG DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005) UMLS:C1517197 ncithesaurus:First_Pharyngeal_Arch branchial arch 1 first branchial arch first visceral arch visceral arch 1 1st arch EHDAA2:0000006 1st visceral arch VHOG:0000296 arcus pharyngeus primus One of a series of paired embryological vascular structures formed within a pharyngeal arch; in the adult, some of these vessels give rise to the great vessels[MP] add specific artery derivatives Do not confuse with arch of aorta. Paired vessels arching from the ventral to the dorsal aorta through the pharyngeal arches. [TFD][VHOG] When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG] Number varies - Lampreys have 8, hagfishes 15; only up to 6 appear in embryonic development in most gnathostome fishes and all tetrapods The third, fourth, and sixth arches, along with the seventh intersegmental arteries and the left dorsal aorta, are the primary contributors to the normal aortic arch and its major thoracic branches UBERON:0004342 AAO:0010414 EFO:0003695 EHDAA2:0000186 EHDAA:398 EHDAA:7327 EMAPA:16684 NCIT:C32123 TAO:0005004 UMLS:C0003489 VHOG:0000122 XAO:0000341 ZFA:0005004 PAA aortic arch aortic arches branchial aortic arches branchial arch artery embryonic aortic arch artery pharyngeal arch artery uberon a. arcuum pharyngeorum aortic arch artery arteriae arcuum pharyngeorum branchial aortic arches pharyngeal arch arteries pharyngeal arch artery UBERON:0004363 pharyngeal arch artery ZFA One of a series of paired embryological vascular structures formed within a pharyngeal arch; in the adult, some of these vessels give rise to the great vessels[MP] MP:0002672 Paired vessels arching from the ventral to the dorsal aorta through the pharyngeal arches. [TFD][VHOG] 2012-09-17 VHOG:0000122 VHOG When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG] 2012-09-17 VHOG:0000122 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620 UMLS:C0003489 ncithesaurus:Aortic_Arch PAA MP:0002672 aortic arch ZFA:0005004 aortic arches ZFA:0005004 branchial aortic arches ZFIN:ZDB-PUB-080512-6 branchial arch artery EMAPA:16684 embryonic aortic arch artery EMAPA:16684 MP:0002672 pharyngeal arch artery MP:0002672 a. arcuum pharyngeorum aortic arch artery EMAPA:16684 arteriae arcuum pharyngeorum branchial aortic arches ZFA:0005004,ZFIN:ZDB-PUB-080512-6 pharyngeal arch arteries pharyngeal arch artery VHOG:0000122 A transparent homogeneous acellular layer, 6 to 9 um thick, lying between the basal lamina of the outer layer of stratified epithelium and the substantia propria of the cornea; it is considered to be a basement membrane. Acellular anatomical structure that is the zone of collagen fibers adjacent the basement membrane of the corneal epithelium.[TAO] Compared to terrestial animals, the cornea of zebrafish is relatively flat. It consists of nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals FMA:58273 MA:0001240 NCIT:C32226 TAO:0002155 UMLS:C0229127 ZFA:0001684 Bowman's anterior elastic lamina Bowman's layer Bowman's membrane anterior elastic lamina anterior limiting lamina anterior limiting lamina of cornea lamina limitans anterior (cornea) lamina limitans anterior corneae uberon Reichert's membrane anterior limiting membrane UBERON:0004370 anterior limiting lamina of cornea A transparent homogeneous acellular layer, 6 to 9 um thick, lying between the basal lamina of the outer layer of stratified epithelium and the substantia propria of the cornea; it is considered to be a basement membrane. ncithesaurus:Bowman_s_Membrane Acellular anatomical structure that is the zone of collagen fibers adjacent the basement membrane of the corneal epithelium.[TAO] 2012-08-14 TAO:0002155 TAO ZFIN:ZDB-PUB-061010-3 UMLS:C0229127 ncithesaurus:Bowman_s_Membrane Bowman's anterior elastic lamina FMA:58273 Bowman's layer FMA:58273 Bowman's membrane FMA:58273 anterior elastic lamina ZFA:0001684 anterior limiting lamina MA:0001240 anterior limiting lamina of cornea FMA:58273 lamina limitans anterior (cornea) FMA:58273 lamina limitans anterior corneae FMA:58273 FMA:TA Reichert's membrane anterior limiting membrane ZFA:0001684 A bone that is part of an appendage [Automatically generated definition]. appendage bone bone of appendage bone of free segment of appendicular skeleton uberon UBERON:0004375 bone of free limb or fin A bone that is part of an appendage [Automatically generated definition]. OBOL:automatic An embryo at the neurula stage. UBERON:0007013 BILA:0000061 BTO:0001766 NCIT:C34229 UMLS:C1518306 neurula uberon UBERON:0004455 neurula embryo An embryo at the neurula stage. UMLS:C1518306 ncithesaurus:Neurula neurula BTO:0001766 Sum of all sensory systems in an organism. note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs FMA:78499 sense organ system uberon UBERON:0004456 entire sense organ system Sum of all sensory systems in an organism. sense organ system FMA:78499 Any collection of skeletal muscles that is part of a head [Automatically generated definition]. EMAPA:18171 FMA:71287 head musculature muscle group of head muscles of head musculi capitis set of muscles of head uberon UBERON:0004461 This class is restricted to skeletal muscles that attach to the cranial skeleton. This seems to be consistent with FMA and EMAPA usage. Note that by definition this excludes invertebrate head musculature. It corresponds to the individual muscle organ term UBERON:0002376 skeletal musculature of head Any collection of skeletal muscles that is part of a head [Automatically generated definition]. OBOL:automatic head musculature FMA:71287 muscle group of head FMA:71287 muscles of head FMA:71287 musculi capitis FMA:71287 FMA:TA set of muscles of head FMA:71287 Any collection of muscles that is part of a thorax [Automatically generated definition]. BTO and FMA do not mean precisely the same thing here. BTO thorax muscle is a pectoral muscle or diaphragm BTO:0000508 EMAPA:37260 FMA:71293 muscle group of thorax muscles of thorax musculi thoracis set of muscles of thorax thoracic musculature uberon UBERON:0004464 musculature of thorax Any collection of muscles that is part of a thorax [Automatically generated definition]. OBOL:automatic BTO and FMA do not mean precisely the same thing here. BTO thorax muscle is a pectoral muscle or diaphragm BTO EMAPA:37260 MA:th muscle group of thorax FMA:71293 muscles of thorax FMA:71293 musculi thoracis FMA:71293 FMA:TA set of muscles of thorax FMA:71293 thoracic musculature FMA:71293 Any collection of muscles that is part of a neck [Automatically generated definition]. AAO:0000091 EMAPA:36050 FMA:71290 MESH:D009334 cervical muscles muscle group of neck muscles of neck musculi cervicis musculi colli neck musculature set of muscles of neck uberon UBERON:0004465 musculature of neck Any collection of muscles that is part of a neck [Automatically generated definition]. OBOL:automatic cervical muscles AAO:0000091 muscle group of neck FMA:71290 muscles of neck FMA:71290 musculi cervicis FMA:71290 FMA:TA musculi colli FMA:71290 FMA:TA neck musculature FMA:71290 set of muscles of neck FMA:71290 Any collection of muscles that is part of a back [Automatically generated definition]. FMA:71291 muscle group of back muscles of back musculi dorsi set of muscles of back uberon UBERON:0004469 musculature of back Any collection of muscles that is part of a back [Automatically generated definition]. OBOL:automatic muscle group of back FMA:71291 muscles of back FMA:71291 musculi dorsi FMA:71291 FMA:TA set of muscles of back FMA:71291 Any collection of muscles that is part of a pelvic girdle [Automatically generated definition]. we merge two FMA classes here UBERON:0004485 UBERON:0005633 AAO:0000427 EHDAA2:0001429 EMAPA:18184 FMA:50205 FMA:50248 muscle group of pelvic girdle muscle group of pelvis pelvic girdle muscle system pelvic girdle muscles pelvic girdle musculature set of muscles of pelvic girdle uberon muscular system of pelvis set of muscles of pelvis UBERON:0004470 musculature of pelvic girdle Any collection of muscles that is part of a pelvic girdle [Automatically generated definition]. OBOL:automatic we merge two FMA classes here FMA muscle group of pelvic girdle FMA:50205 muscle group of pelvis FMA:50248 pelvic girdle muscle system EHDAA2:0001429 pelvic girdle muscles AAO:0000427 pelvic girdle musculature FMA:50205 set of muscles of pelvic girdle FMA:50205 muscular system of pelvis FMA:50248 set of muscles of pelvis FMA:50248 A subdivision of the musculature of the body in the pectoral girdle region. Includes pectoral and shoulder muscles. AAO:0000423 EMAPA:37857 FMA:33519 muscle group of pectoral girdle pectoral girdle muscles pectoral girdle musculature set of muscles of pectoral girdle uberon UBERON:0004471 musculature of pectoral girdle A subdivision of the musculature of the body in the pectoral girdle region. Includes pectoral and shoulder muscles. EMAPA:37857 MA:th muscle group of pectoral girdle FMA:33519 pectoral girdle muscles AAO:0000423 pectoral girdle musculature FMA:33519 set of muscles of pectoral girdle FMA:33519 Any collection of muscles that is part of a face. originally created to reflect the distinction drawn in FMA between a facial muscle and the entire musculature of the face. However, naming both does not serve any particular purpose FMA:71288 entire facial musculature facial muscles muscle group of face musculi faciei uberon set of facial muscles set of muscles of face UBERON:0004473 musculature of face Any collection of muscles that is part of a face. OBOL:automatic entire facial musculature facial muscles FMA:71288 muscle group of face FMA:71288 musculi faciei FMA:71288 FMA:TA set of facial muscles FMA:71288 set of muscles of face FMA:71288 The collection of muscles that are part of the larynx. currently defined by location rather than attachment FMA:264611 FMA:46616 MESH:D007821 laryngeal muscles laryngeal muscles set muscle group of larynx set of laryngeal muscles set of muscles of larynx uberon UBERON:0004478 musculature of larynx The collection of muscles that are part of the larynx. laryngeal muscles FMA:46616 laryngeal muscles set FMA:46616 muscle group of larynx FMA:46616 set of laryngeal muscles FMA:46616 set of muscles of larynx FMA:264611 Any collection of muscles that is part of a trunk [Automatically generated definition]. currently defined by location rather than attachment AAO:0011572 EFO:0003531 FMA:50187 muscle group of trunk set of muscles of trunk uberon muscular system of trunk UBERON:0004479 musculature of trunk Any collection of muscles that is part of a trunk [Automatically generated definition]. OBOL:automatic muscle group of trunk FMA:50187 set of muscles of trunk FMA:50187 muscular system of trunk FMA:50187 A portion of cardiac muscle tissue that is part of a cardiac septum [Automatically generated definition]. FMA:226279 cardiac septum cardiac muscle tissue cardiac septum heart muscle cardiac septum muscle cardiac septum myocardium uberon UBERON:0004492 cardiac muscle tissue of cardiac septum A portion of cardiac muscle tissue that is part of a cardiac septum [Automatically generated definition]. OBOL:automatic cardiac septum cardiac muscle tissue cardiac septum heart muscle cardiac septum muscle cardiac septum myocardium A portion of cardiac muscle tissue that is part of a myocardium [Automatically generated definition]. Note placement of MA class based on parthood relationship EMAPA:32688 FMA:261726 MA:0002441 uberon UBERON:0004493 cardiac muscle tissue of myocardium MA A portion of cardiac muscle tissue that is part of a myocardium [Automatically generated definition]. OBOL:automatic A vasculature that is part of a muscle organ [Automatically generated definition]. FMA:87123 muscular organ vasculature uberon UBERON:0004521 vasculature of muscle organ A vasculature that is part of a muscle organ [Automatically generated definition]. OBOL:automatic muscular organ vasculature FMA:87123 A vasculature that is part of a musculoskeletal system [Automatically generated definition]. FMA:239607 uberon UBERON:0004522 vasculature of musculoskeletal system A vasculature that is part of a musculoskeletal system [Automatically generated definition]. OBOL:automatic Anatomical system that has as its parts the heart and blood vessels. we treat cardiovascular as part of circulatory system, with the latter including other kinds of circulation, including lymph. The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG] AAO:0011001 BILA:0000016 BTO:0000088 CALOHA:TS-1297 EFO:0000791 EHDAA2:0000216 EHDAA:394 EMAPA:16104 EMAPA:16370 EV:0100017 FMA:7161 GAID:467 MA:0000010 MAT:0000016 MESH:D002319 MIAA:0000016 NCIT:C12686 OpenCyc:Mx4rvVjzG5wpEbGdrcN5Y29ycA TAO:0000010 UMLS:C0007226 VHOG:0000302 WikipediaCategory:Cardiovascular_system XAO:0000100 XAO:0001010 ZFA:0000010 uberon CV system Herz und Gefaesssystem UBERON:0004535 cardiovascular system Anatomical system that has as its parts the heart and blood vessels. BTO:0000088 The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG] 2012-09-17 VHOG:0000302 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.451 UMLS:C0007226 ncithesaurus:Cardiovascular_System CV system BTO:0000088 Herz und Gefaesssystem BTO:0000088 A vascular network consisting of blood vessels. TAO:0001079 ZFA:0001079 blood vascular network set of blood vessels uberon blood system blood vessel system blood vessels UBERON:0004537 blood vasculature A vascular network consisting of blood vessels. blood vessels TAO:0001079 A kidney that is part of a left side of organism [Automatically generated definition]. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EMAPA:36589 FMA:7205 MA:0001655 NCIT:C34006 UMLS:C0227614 uberon UBERON:0004538 left kidney A kidney that is part of a left side of organism [Automatically generated definition]. OBOL:automatic UMLS:C0227614 ncithesaurus:Left_Kidney A kidney that is part of a right side of organism [Automatically generated definition]. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EMAPA:36590 FMA:7204 MA:0001683 NCIT:C34005 UMLS:C0227613 uberon UBERON:0004539 right kidney A kidney that is part of a right side of organism [Automatically generated definition]. OBOL:automatic UMLS:C0227613 ncithesaurus:Right_Kidney An eye that is part of a left side of organism [Automatically generated definition]. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EMAPA:37362 FMA:12515 MA:0002949 NCIT:C119334 left eyeball left orbital part of face left orbital region uberon UBERON:0004548 left eye An eye that is part of a left side of organism [Automatically generated definition]. OBOL:automatic EMAPA:37362 MA:th left eyeball FMA:12515 left orbital part of face FMA:54450 left orbital region FMA:54450 An eye that is part of a right side of organism [Automatically generated definition]. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EMAPA:37363 FMA:12514 MA:0002950 NCIT:C119333 right eyeball right orbital part of face right orbital region uberon UBERON:0004549 right eye An eye that is part of a right side of organism [Automatically generated definition]. OBOL:automatic EMAPA:37363 MA:th right eyeball FMA:12514 right orbital part of face FMA:54449 right orbital region FMA:54449 The part of the arterial system which carries oxygenated blood away from the heart to the body, and returns deoxygenated blood back to the heart. FMA:45623 systemic arterial circulatory system uberon UBERON:0004571 systemic arterial system MA-inferred The part of the arterial system which carries oxygenated blood away from the heart to the body, and returns deoxygenated blood back to the heart. systemic arterial circulatory system FMA:45623 The part of the cardiovascular system consisting of all arteries. The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] BTO:0004690 EHDAA2:0000143 EHDAA:396 EMAPA:16201 EMAPA:16371 MA:0002719 VHOG:0000273 uberon UBERON:0004572 arterial system MA The part of the cardiovascular system consisting of all arteries. The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] 2012-09-17 VHOG:0000273 VHOG DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2005) An artery of the systemic circulation, which is the part of the cardiovascular system which carries oxygenated blood away from the heart, to the body, and returns deoxygenated blood back to the heart. EMAPA:37126 FMA:66464 systemic arterial subtree uberon UBERON:0004573 systemic artery An artery of the systemic circulation, which is the part of the cardiovascular system which carries oxygenated blood away from the heart, to the body, and returns deoxygenated blood back to the heart. EMAPA:37126 MA:th systemic arterial subtree FMA:66464 The part of the venous system that drains the general body tissues[Kardong] In human anatomy, the systemic venous system refers to veins that drain into the right atrium without passing through two vascular beds (i.e. they originate from a set of capillaries and do not pass through a second set of capillaries before reaching the right side of the heart). The term systemic venous system is often used to differentiate veins from veins that drain the pulmonary system (the pulmonary venous system) and veins that drain the digestive tract (the portal venous system). Large veins that are considered part of the systemic venous system are the: Superior vena cava; Inferior vena cava[WP] Subdivision of cardiovascular system which has as its parts the right side of heart, the superior vena cava and the inferior vena cava[FMA] The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] FMA:45626 systemic venous circulatory system uberon UBERON:0004581 systemic venous system The part of the venous system that drains the general body tissues[Kardong] ISBN10:0073040584 In human anatomy, the systemic venous system refers to veins that drain into the right atrium without passing through two vascular beds (i.e. they originate from a set of capillaries and do not pass through a second set of capillaries before reaching the right side of the heart). The term systemic venous system is often used to differentiate veins from veins that drain the pulmonary system (the pulmonary venous system) and veins that drain the digestive tract (the portal venous system). Large veins that are considered part of the systemic venous system are the: Superior vena cava; Inferior vena cava[WP] Subdivision of cardiovascular system which has as its parts the right side of heart, the superior vena cava and the inferior vena cava[FMA] FMA FMA:45626 The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] 2012-09-17 VHOG:0000277 VHOG DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2005) systemic venous circulatory system FMA:45626 The part of the cardiovascular system consisting of all venous vessels. In vertebrates with a double circulation, this can be divided into systemic and pulmonary portions. The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] BTO:0004692 EHDAA2:0002171 EHDAA:486 EMAPA:16240 MA:0002720 NCIT:C33858 UMLS:C1267406 VHOG:0000277 vein system uberon UBERON:0004582 venous system MA The part of the cardiovascular system consisting of all venous vessels. In vertebrates with a double circulation, this can be divided into systemic and pulmonary portions. The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] 2012-09-17 VHOG:0000277 VHOG DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2005) UMLS:C1267406 ncithesaurus:Venous_System An endothelium that lines the blood vasculature. Other endothelia may line lymph vessels, the heart BTO:0000766 CALOHA:TS-2155 EMAPA:35176 MA:0000709 NCIT:C53395 TAO:0005257 UMLS:C1706972 ZFA:0005257 uberon UBERON:0004638 blood vessel endothelium An endothelium that lines the blood vasculature. Other endothelia may line lymph vessels, the heart UMLS:C1706972 ncithesaurus:Blood_Vessel_Endothelium An anatomical wall that is part of an aorta, enclosing the luminal space. EMAPA:35139 FMA:14156 MA:0002901 aortic wall wall of aorta uberon UBERON:0004663 aorta wall An anatomical wall that is part of an aorta, enclosing the luminal space. aortic wall FMA:14156 wall of aorta FMA:14156 the outermost layer of the aorta wall, containing connective tissue and collagen and elastic fibers EMAPA:35136 FMA:14283 MA:0002902 tunica adventitia of aorta uberon UBERON:0004664 aorta tunica adventitia the outermost layer of the aorta wall, containing connective tissue and collagen and elastic fibers ISBN:0-683-40008-8 MP:0009871 tunica adventitia of aorta FMA:14283 The membranous portion of the wall between the two lower chambers of the heart The membranous septum is the upper part of ventricular septum[GO:0003149]. UBERON:0004143 membranous septum ventricle membranous septum ventricular membranous septum EHDAA2:0004596 EMAPA:18246 FMA:7135 MA:0002939 VHOG:0000927 cardiac ventricular membranous septum membranous interventricular septum membranous part interventricular septum membranous part of interventricular septum membranous portion of interventricular septum pars membranacea (septi interventricularis) pars membranacea septi interventricularis uberon membranous interventricular septum UBERON:0004666 interventricular septum membranous part Wikipedia The membranous portion of the wall between the two lower chambers of the heart MP:0008823 The membranous septum is the upper part of ventricular septum[GO:0003149]. GO:0003149 membranous septum GO:0003149 ventricle membranous septum VT:0000018 ventricular membranous septum MP:0008823 cardiac ventricular membranous septum membranous interventricular septum FMA:7135 membranous part interventricular septum VHOG:0000927 membranous part of interventricular septum FMA:7135 membranous portion of interventricular septum FMA:7135 pars membranacea (septi interventricularis) FMA:7135 pars membranacea septi interventricularis FMA:7135 FMA:TA membranous interventricular septum MA:0002939 The muscular portion of the wall between the two lower chambers of the heart The muscular septum is the lower part of the ventricular septum[GO] UBERON:0004144 muscular septum EHDAA2:0000885 EHDAA:2607 EMAPA:18247 FMA:7134 MA:0002940 RETIRED_EHDAA2:0000888 cardiac ventricular muscular septum muscular interventricular septum muscular part interventricular septum muscular part of interventricular septum pars muscularis (septi interventricularis) pars muscularis septi interventricularis septum membranaceum ventricular muscular septum uberon muscular interventricular septum UBERON:0004667 interventricular septum muscular part The muscular portion of the wall between the two lower chambers of the heart The muscular septum is the lower part of the ventricular septum[GO] GO:0003150 muscular septum GO:0003150 cardiac ventricular muscular septum muscular interventricular septum FMA:7134 muscular part of interventricular septum FMA:7134 pars muscularis (septi interventricularis) FMA:7134 pars muscularis septi interventricularis FMA:7134 FMA:TA septum membranaceum muscular interventricular septum MA:0002940 The raphe nuclei are thin plates of cells in and immediately adjacent to the sagittal plane. BAMS:RA EMAPA:35721 FMA:84017 MA:0003147 MESH:A08.186.211.132.659.632 NCIT:C97335 TAO:0001429 UMLS:C0034671 ZFA:0001429 nuclei raphes raphe nuclei raphe nuclei set uberon nuclei raphes raphe cluster raphe nucleus raphe of mesenchephalon set of raphe nuclei UBERON:0004684 we treat NR obscurus, NR magnus etc as parts of the raphe nuclei. This is consistent with treatment in FMA, where the class is 'set of raphe nuclei' raphe nuclei GO Wikipedia The raphe nuclei are thin plates of cells in and immediately adjacent to the sagittal plane. NIFSTD:nlx_anat_20090205 UMLS:C0034671 ncithesaurus:Raphe_Nuclei nuclei raphes FMA:84017 FMA:TA raphe nuclei FMA:84017 raphe nuclei NIFSTD:nlx_anat_20090205 raphe nuclei set FMA:84017 nuclei raphes raphe cluster raphe nucleus ZFA:0001429 raphe of mesenchephalon BAMS:RA set of raphe nuclei FMA:84017 The costocervical trunk arises from the upper and back part of the subclavian artery, behind the scalenus anterior on the right side, and medial to that muscle on the left side. Passing backward, it splits into the deep cervical artery and the supreme intercostal artery (or the Highest intercostal artery), which descends behind the pleura in front of the necks of the first and second ribs, and anastomoses with the first aortic intercostal (3rd posterior intercostal artery). As it crosses the neck of the first rib it lies medial to the anterior division of the first thoracic nerve, and lateral to the first thoracic ganglion of the sympathetic trunk. In the first intercostal space, it gives off a branch which is distributed in a manner similar to the distribution of the aortic intercostals. The branch for the second intercostal space usually joins with one from the highest aortic intercostal artery. This branch is not constant, but is more commonly found on the right side; when absent, its place is supplied by an intercostal branch from the aorta. Each intercostal gives off a posterior branch which goes to the posterior vertebral muscles, and sends a small spinal branch through the corresponding intervertebral foramen to the medulla spinalis and its membranes. [WP,unvetted]. EMAPA:37496 FMA:10636 MA:0001939 costocervical trunk trunk of costocervical artery uberon truncus costocervicalis UBERON:0004688 costo-cervical trunk The costocervical trunk arises from the upper and back part of the subclavian artery, behind the scalenus anterior on the right side, and medial to that muscle on the left side. Passing backward, it splits into the deep cervical artery and the supreme intercostal artery (or the Highest intercostal artery), which descends behind the pleura in front of the necks of the first and second ribs, and anastomoses with the first aortic intercostal (3rd posterior intercostal artery). As it crosses the neck of the first rib it lies medial to the anterior division of the first thoracic nerve, and lateral to the first thoracic ganglion of the sympathetic trunk. In the first intercostal space, it gives off a branch which is distributed in a manner similar to the distribution of the aortic intercostals. The branch for the second intercostal space usually joins with one from the highest aortic intercostal artery. This branch is not constant, but is more commonly found on the right side; when absent, its place is supplied by an intercostal branch from the aorta. Each intercostal gives off a posterior branch which goes to the posterior vertebral muscles, and sends a small spinal branch through the corresponding intervertebral foramen to the medulla spinalis and its membranes. [WP,unvetted]. EMAPA:37496 MA:th costocervical trunk FMA:10636 trunk of costocervical artery FMA:10636 truncus costocervicalis A portion of smooth muscle tissue that is part of an arterial system [Automatically generated definition]. EMAPA:36503 MA:0000704 uberon UBERON:0004695 arterial system smooth muscle A portion of smooth muscle tissue that is part of an arterial system [Automatically generated definition]. OBOL:automatic A portion of smooth muscle tissue that is part of a venous system [Automatically generated definition]. EMAPA:36613 MA:0000715 uberon UBERON:0004696 venous system smooth muscle A portion of smooth muscle tissue that is part of a venous system [Automatically generated definition]. OBOL:automatic An endothelium that is part of a vena cava [Automatically generated definition]. EMAPA:37800 MA:0000713 NCIT:C49318 UMLS:C1710623 uberon UBERON:0004698 vena cava endothelium An endothelium that is part of a vena cava [Automatically generated definition]. OBOL:automatic EMAPA:37800 MA:th UMLS:C1710623 ncithesaurus:Vena_Cava_Endothelium An endothelium that is part of a outflow tract [Automatically generated definition]. It is assumed that during evolution, a circulatory system composed of the heart and endothelial tubular system first formed in vertebrates, medial smooth muscle then appeared for regulation of the system, and innervation of the muscle tissue took place. This sequence of development assumed for phylogenesis is actually realized in the ontogenetic processes.[well established][VHOG] MA:0000490 VHOG:0001524 uberon UBERON:0004699 outflow tract endothelium An endothelium that is part of a outflow tract [Automatically generated definition]. OBOL:automatic It is assumed that during evolution, a circulatory system composed of the heart and endothelial tubular system first formed in vertebrates, medial smooth muscle then appeared for regulation of the system, and innervation of the muscle tissue took place. This sequence of development assumed for phylogenesis is actually realized in the ontogenetic processes.[well established][VHOG] 2012-09-17 VHOG:0001524 VHOG DOI:10.1254/jjp.87.253 Shigei T, Tsuru H, Ishikawa N, Yoshioka K, Absence of endothelium in invertebrate blood vessels: significance of endothelium and sympathetic nerve/medial smooth muscle in the vertebrate vascular system. Japanese Journal of Pharmacology (2001) An endothelium that is part of an arterial system [Automatically generated definition]. EMAPA:35145 MA:0000703 NCIT:C49329 UMLS:C1706849 uberon UBERON:0004700 arterial system endothelium An endothelium that is part of an arterial system [Automatically generated definition]. OBOL:automatic UMLS:C1706849 ncithesaurus:Arterial_System_Endothelium An endothelium that is part of a venous system [Automatically generated definition]. EMAPA:35907 MA:0000714 NCIT:C49320 UMLS:C1710626 uberon UBERON:0004701 venous system endothelium An endothelium that is part of a venous system [Automatically generated definition]. OBOL:automatic UMLS:C1710626 ncithesaurus:Venous_System_Endothelium A blood vessel endothelium that is part of a respiratory system [Automatically generated definition]. EMAPA:35732 MA:0001805 uberon UBERON:0004702 respiratory system blood vessel endothelium A blood vessel endothelium that is part of a respiratory system [Automatically generated definition]. OBOL:automatic a transient fetal dilation of the distal (or cranial) heart tube located where the arterial trunk joins the ventral roots of the aortic arches TODO - check relationship to bulbus arteriosus A pear shaped chamber that functions as a capacitor, maintaining continuous blood flow into the gill arches. The bulbus arteriosus has three distinct layers. Hu et al. 2000.[TAO] EHDAA2:0000197 EHDAA:438 EHDAA:768 EMAPA:16333 FMA:70300 NCIT:C34114 UMLS:C1284055 primitive right ventricle endocardium uberon UBERON:0004706 bulbus cordis a transient fetal dilation of the distal (or cranial) heart tube located where the arterial trunk joins the ventral roots of the aortic arches ISBN:0-683-40008-8 MP:0010568 A pear shaped chamber that functions as a capacitor, maintaining continuous blood flow into the gill arches. The bulbus arteriosus has three distinct layers. Hu et al. 2000.[TAO] 2012-08-14 TAO:0000173 TAO ZFIN:curator UMLS:C1284055 ncithesaurus:Bulbus_Cordis primitive right ventricle endocardium EHDAA2:0000197 JB:def An appendage that is part of an appendage girdle complex. this class is the union of the classes limb, pectoral fin and pelvic fin. UBERON:0009872 VSAO:0000067 girdle-associated appendage limb or fin limb/fin pectoral or pelvic appendage pelvic/pectoral appendage jointed paired lateral appendage paired appendage uberon UBERON:0004708 paired limb/fin VSAO VSAO definitional An appendage that is part of an appendage girdle complex. UBERON:cjm girdle-associated appendage limb or fin limb/fin pectoral or pelvic appendage pelvic/pectoral appendage jointed paired lateral appendage paired appendage VSAO:0000067 Paired appendage that consists of the posterior appendicular skeleton and associated soft and hard tissues, but excludes the pelvic girdle and its associated soft and hard tissues. UBERON:0009876 posterior appendage VSAO:0000126 hindlimb/pelvic fin pelvic appendage pelvic limb/fin posterior limb/fin posterior paired appendage uberon UBERON:0004709 pelvic appendage definitional lexical Paired appendage that consists of the posterior appendicular skeleton and associated soft and hard tissues, but excludes the pelvic girdle and its associated soft and hard tissues. VSAO:0000150 hindlimb/pelvic fin pelvic appendage VSAO:0000126 pelvic limb/fin posterior paired appendage VSAO:0000126 Paired appendage that consists of the anterior appendicular skeleton and associated soft and hard tissues, but excludes the pectoral girdle and its associated soft and hard tissues. While the skeletons of teleost pectoral fins and tetrapod forelimbs are homologous at the level of endoskeletal radials, teleosts and tetrapods do not share homologous skeletal elements at the level of 'individuated' pro-, meso-, and metapterygia. Among osteichthyans, only basal actinopterygians retain the full complement of elements present in non-osteichthyan gnathostomes.[uncertain][VHOG] UBERON:0009875 anterior appendage VHOG:0001753 VSAO:0000125 anterior limb/fin anterior paired appendage forelimb - pectoral fin forelimb or pectoral fin forelimb/pectoral fin pectoral limb/fin uberon UBERON:0004710 pectoral appendage definitional lexical Paired appendage that consists of the anterior appendicular skeleton and associated soft and hard tissues, but excludes the pectoral girdle and its associated soft and hard tissues. VSAO:0000150-modified While the skeletons of teleost pectoral fins and tetrapod forelimbs are homologous at the level of endoskeletal radials, teleosts and tetrapods do not share homologous skeletal elements at the level of 'individuated' pro-, meso-, and metapterygia. Among osteichthyans, only basal actinopterygians retain the full complement of elements present in non-osteichthyan gnathostomes.[uncertain][VHOG] 2012-09-17 VHOG:0001753 VHOG DOI:10.1002/jmor.10264 Davis MC, Shubin NH, Force A, Pectoral fin and girdle development in the basal actinopterygians Polyodon spathula and Acipenser transmontanus. Journal of Morphology (2004) anterior limb/fin anterior paired appendage VSAO:0000148 forelimb - pectoral fin VHOG:0001753 forelimb or pectoral fin forelimb/pectoral fin pectoral limb/fin The jugular veins are veins that bring deoxygenated blood from the head back to the heart via the superior vena cava. BTO:0001744 CALOHA:TS-0497 EMAPA:18638 GAID:536 MA:0002154 MESH:D007601 NCIT:C12738 UMLS:C0022427 uberon jugular vena jugularis UBERON:0004711 jugular vein The jugular veins are veins that bring deoxygenated blood from the head back to the heart via the superior vena cava. UMLS:C0022427 ncithesaurus:Jugular_Vein vena jugularis BTO:0001744 The embryo and its adnexa (appendages or adjunct parts) or associated membranes (i.e. the products of conception) The conceptus includes all structures that develop from the zygote, both embryonic and extraembryonic. It includes the embryo as well as the embryonic part of the placenta and its associated membranes - amnion, chorion (gestational sac), and yolk sac[WP]. EHDAA2 places this as a subtype of organism. This leads to the inference that a conceptus is an embryo (if an embryo is defined as an organism at embryo stage), which eliminates the embryonic + extra-embryonic = conceptus AEO:0000194 BTO:0003834 EHDAA2:0000001 EHDAA2:0003235 EMAPA:36040 NCIT:C34131 UMLS:C1516779 embryo plus adnexa uberon UBERON:0004716 conceptus The embryo and its adnexa (appendages or adjunct parts) or associated membranes (i.e. the products of conception) The conceptus includes all structures that develop from the zygote, both embryonic and extraembryonic. It includes the embryo as well as the embryonic part of the placenta and its associated membranes - amnion, chorion (gestational sac), and yolk sac[WP]. BTO:0003834 UMLS:C1516779 ncithesaurus:Conceptus A transverse unitary subdivision of the neural tube that shares a common dorsoventral structure (floor, basal, alar, and roof plates), but each having differential molecular identities and fates; they comprise the secondary prosencephalon, diencephalon (prosomeres), the midbrain (mesomeres), and the hindbrain (rhombomeres). We take the definition of neuromere from Puelles et al, although the existence of mesomeres and prosomeres may not be widely accepted A metameric segment of the central nervous system.[ZFA] Melissa Haendel 2009-06-18T09:00:04Z TAO:0001328 ZFA:0001328 neural tube metameric segment neural tube segment neuromere neuromeres uberon neural metamere neural segment UBERON:0004731 neuromere A transverse unitary subdivision of the neural tube that shares a common dorsoventral structure (floor, basal, alar, and roof plates), but each having differential molecular identities and fates; they comprise the secondary prosencephalon, diencephalon (prosomeres), the midbrain (mesomeres), and the hindbrain (rhombomeres). A metameric segment of the central nervous system.[ZFA] 2012-08-14 TAO:0001328 TAO ZFIN:curator neural tube metameric segment neuromeres TAO:0001328 Any segmental subdivision of a nervous system. Includes metameric developmental segments, such as vertebrates neuromeres. revisit this after CARO is revised and/or we have defined metameric segment; note that with the additional of an A/P axis constraint this corresponds to what Richter at al call a neuromere (PMID:21062451) FBbt:00005140 uberon neuromere UBERON:0004732 segmental subdivision of nervous system Any segmental subdivision of a nervous system. Includes metameric developmental segments, such as vertebrates neuromeres. FBbt:00005140 neuromere FBbt:00005140 An organ subunit that is part of a hindbrain [Automatically generated definition]. FMA:61998 hindbrain segment segment of hindbrain uberon UBERON:0004733 segmental subdivision of hindbrain An organ subunit that is part of a hindbrain [Automatically generated definition]. OBOL:automatic hindbrain segment FMA:61998 segment of hindbrain FMA:61998 Organism at the gastrula stage. We explicitly merge the NCITA terms here UBERON:0007012 BILA:0000060 BTO:0001403 FBbt:00005317 FMA:293108 GAID:1302 MESH:A16.254.412 MIAA:0000179 NCIT:C34057 NCIT:C34058 UMLS:C0017199 UMLS:C1284022 gastrula embryo uberon blastocystis trilaminaris tri-laminar disc tri-laminar disk trilaminar blastocyst trilaminar blastoderm trilaminar disc trilaminar disk trilaminar germ UBERON:0004734 gastrula Organism at the gastrula stage. We explicitly merge the NCITA terms here NCIT UMLS:C0017199 ncithesaurus:Gastrula UMLS:C1284022 ncithesaurus:Trilaminar_Embryonic_Disc gastrula embryo BILA:0000060 blastocystis trilaminaris tri-laminar disc tri-laminar disk trilaminar blastocyst trilaminar blastoderm trilaminar disc trilaminar disk trilaminar germ A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO] A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO] EMAPA:37744 MA:0003047 VSAO:0000015 XAO:0004038 ZFA:0005619 uberon UBERON:0004755 Four classes of mineralized tissues are found in vertebrates: bone, cartilage, dentine, and enamel. We think of cartilage and bone as skeletal tissues and of enamel and dentine as dental tissues, but enamel and dentine arose evolutionarily together with bone as skeletal tissues in the dermal skeleton (exoskeleton) of early vertebrates. Scales and teeth of sharks are examples of dermal skeletal elements that are still composed of the three ancient components-enamel, dentine, and bone. Cartilage, on the other hand, provided the basis for the second vertebrate skeletal system, the endoskeleton (Smith and Hall, 1990; Hall, 1998a,b). some invertebrate skeletal tissues have surprisingly bone-like features. Examples include chondrocytes interconnected by cell processes in cephalopod cartilages (Cole and Hall, 2004a,b), and the calcium phosphate layer in the shells of brachiopods (Rodland et al., 2003). However, neither bone nor mineralized cartilage have been found in invertebrates. Editors notes: TODO - develops_from skeletal tissue VSAO A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO] GO_REF:0000034 PSPUB:0000170 VSAO:0000015 A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO] 2012-08-14 VSAO:0000015 taken from version of VSAO used in TAO and used directly in Uberon VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 PSPUB:0000170 EMAPA:37744 MA:th dermis-derived entity that is made of skeletal tissue. dermal element uberon UBERON:0004756 dermal skeletal element dermis-derived entity that is made of skeletal tissue. dermal element VSAO:curator A gland that is part of an anal canal [Automatically generated definition]. EMAPA:27221 EMAPA:27233 EMAPA:27543 FMA:15720 FMA:15724 NCIT:C32068 UMLS:C0162322 gland of anal canal uberon anal gland anal sac gland of anus rectal gland UBERON:0004760 gland of anal canal A gland that is part of an anal canal [Automatically generated definition]. OBOL:automatic UMLS:C0162322 ncithesaurus:Anal_Gland gland of anal canal OBOL:automatic anal sac The primitive cartilagionous skeletal structure of the fetal skull that grows to envelop the rapidly growing embyonic brain. In humans, the chondrocranium begins forming at 28 days from mesenchymal condensations and is fully formed between week 7 and 9 of fetal development. While the majority of the chondrocranium is succeeded by the bony skull in most higher vertebrates, some components do persist into adulthood.[1] In Cartilagious fishes and Agnathans, the chondrocranium persist throughout life.[2] Embryologically, the chondrocranium represent the basal cranial structure, and lay the base for the formation of the endocranium in higher vertebrates[WP]. in contrast to chondrocranium, this structure is entirely cartiliginous. In Chondricthyes this is the same as the neurocranium. FMA:76621 is an undefined fetal structure, so we assume the correct placement is here. Note that this is distinct from MA:0000317 which is the uberon:neurocranium (the part of the cranium that encloses the brain) AAO:0000094 AAO:0010153 EHDAA:6031 FMA:76621 NCIT:C34121 UMLS:C1516496 XAO:0003059 cartilaginous chondocranium cartiligionous skeletal structure of skull uberon cartilaginous skull chondocranium embryonic chondocranium neurocranium UBERON:0004761 cartilaginous neurocranium FMA PMC1571569 The primitive cartilagionous skeletal structure of the fetal skull that grows to envelop the rapidly growing embyonic brain. In humans, the chondrocranium begins forming at 28 days from mesenchymal condensations and is fully formed between week 7 and 9 of fetal development. While the majority of the chondrocranium is succeeded by the bony skull in most higher vertebrates, some components do persist into adulthood.[1] In Cartilagious fishes and Agnathans, the chondrocranium persist throughout life.[2] Embryologically, the chondrocranium represent the basal cranial structure, and lay the base for the formation of the endocranium in higher vertebrates[WP]. in contrast to chondrocranium, this structure is entirely cartiliginous. In Chondricthyes this is the same as the neurocranium. FMA:76621 is an undefined fetal structure, so we assume the correct placement is here. Note that this is distinct from MA:0000317 which is the uberon:neurocranium (the part of the cranium that encloses the brain) FMA UMLS:C1516496 ncithesaurus:Chondrocranium chondocranium neurocranium Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO] Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO] AAO:0011129 TAO:0001890 VSAO:0000128 XAO:0004012 ZFA:0005494 galen:SkeletalStructure uberon UBERON:0004765 skeletal element VSAO Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO] 2012-08-14 VSAO:0000128 VSAO PSPUB:0000170 Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO] 2012-08-14 TAO:0001890 TAO TAO:VSAO_workshop A bone that is part of a cranium. here cranium = skull - mandible cranium bone uberon UBERON:0004766 cranial bone A bone that is part of a cranium. UBERON:automatic cranium bone UBERON:automatic Any bone that is part of the lower jaw skeleton. This includes (when present): the dentary/mandible, the articular, the splenial, the suprangular Do not manually classify under here - bones are automatically classified lower jaw bone uberon UBERON:0004768 bone of lower jaw Any bone that is part of the lower jaw skeleton. This includes (when present): the dentary/mandible, the articular, the splenial, the suprangular Anatomical system that consists of all the joints of the body. EMAPA:35150 FMA:23878 MA:0003007 VSAO:0000181 joint system set of all joints of body uberon set of all joints set of joints of body UBERON:0004770 articular system FMA Anatomical system that consists of all the joints of the body. VSAO:0000181 joint system FMA:23878 set of all joints of body FMA:23878 set of joints of body FMA:23878 A submucosa that is part of a respiratory system [Automatically generated definition]. EMAPA:37578 MA:0001822 apparatus respiratorius submucosa submucosa of apparatus respiratorius submucosa of respiratory system uberon UBERON:0004777 respiratory system submucosa A submucosa that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37578 MA:th apparatus respiratorius submucosa OBOL:automatic submucosa of apparatus respiratorius OBOL:automatic submucosa of respiratory system OBOL:automatic A submucosa that is part of a larynx [Automatically generated definition]. EMAPA:35474 FMA:321584 MA:0002728 submucosa of larynx uberon laryngeal submucosa UBERON:0004778 larynx submucosa A submucosa that is part of a larynx [Automatically generated definition]. OBOL:automatic submucosa of larynx OBOL:automatic laryngeal submucosa EMAPA:35474 A serous membrane that is part of a digestive system [Automatically generated definition]. EMAPA:37592 MA:0001522 digestive system serosa digestive system serous membrane gastrointestinal system serous membrane serosa of digestive system serosa of gastrointestinal system serous membrane of digestive system serous membrane of gastrointestinal system uberon UBERON:0004782 gastrointestinal system serosa A serous membrane that is part of a digestive system [Automatically generated definition]. OBOL:automatic EMAPA:37592 MA:th digestive system serosa OBOL:automatic digestive system serous membrane OBOL:automatic gastrointestinal system serous membrane OBOL:automatic serosa of digestive system OBOL:automatic serosa of gastrointestinal system OBOL:automatic serous membrane of digestive system OBOL:automatic serous membrane of gastrointestinal system OBOL:automatic An anatomical wall that is part of a cardiac ventricle [Automatically generated definition]. FMA:13884 MA:0002791 NCIT:C119295 anatomical wall of cardiac ventricle anatomical wall of heart ventricle anatomical wall of lower chamber of heart anatomical wall of ventricle of heart cardiac ventricle anatomical wall cardiac ventricle wall heart ventricle anatomical wall lower chamber of heart anatomical wall lower chamber of heart wall ventricle of heart anatomical wall ventricle of heart wall ventricular wall wall of cardiac ventricle wall of heart ventricle wall of lower chamber of heart wall of ventricle of heart uberon wall of ventricle UBERON:0004784 heart ventricle wall An anatomical wall that is part of a cardiac ventricle [Automatically generated definition]. OBOL:automatic anatomical wall of cardiac ventricle OBOL:automatic anatomical wall of heart ventricle OBOL:automatic anatomical wall of lower chamber of heart OBOL:automatic anatomical wall of ventricle of heart OBOL:automatic cardiac ventricle anatomical wall OBOL:automatic cardiac ventricle wall OBOL:automatic heart ventricle anatomical wall OBOL:automatic lower chamber of heart anatomical wall OBOL:automatic lower chamber of heart wall OBOL:automatic ventricle of heart anatomical wall OBOL:automatic ventricle of heart wall OBOL:automatic ventricular wall FMA:13884 wall of cardiac ventricle OBOL:automatic wall of heart ventricle OBOL:automatic wall of lower chamber of heart OBOL:automatic wall of ventricle of heart OBOL:automatic wall of ventricle MA:0002791 the mucous membrane lining the respiratory tract TODO - split respiratory tract mucosa from respiratory system mucosa BTO:0000973 EMAPA:18334 EMAPA:37577 FMA:302092 GAID:304 MA:0001827 MESH:D020545 apparatus respiratorius mucosa apparatus respiratorius mucosa of organ apparatus respiratorius mucous membrane mucosa of apparatus respiratorius mucosa of organ of apparatus respiratorius mucosa of organ of respiratory system mucosa of respiratory system mucous membrane of apparatus respiratorius mucous membrane of respiratory system respiratory system mucosa of organ respiratory system mucous membrane uberon laryngeal mucous membrane respiratory mucosa respiratory tract mucosa UBERON:0004785 respiratory system mucosa the mucous membrane lining the respiratory tract MESH:A04.760 MGI:cwg MP:0002277 EMAPA:37577 MA:th apparatus respiratorius mucosa OBOL:automatic apparatus respiratorius mucosa of organ OBOL:automatic apparatus respiratorius mucous membrane OBOL:automatic mucosa of apparatus respiratorius OBOL:automatic mucosa of organ of apparatus respiratorius OBOL:automatic mucosa of organ of respiratory system OBOL:automatic mucosa of respiratory system OBOL:automatic mucous membrane of apparatus respiratorius OBOL:automatic mucous membrane of respiratory system OBOL:automatic respiratory system mucosa of organ OBOL:automatic respiratory system mucous membrane OBOL:automatic laryngeal mucous membrane EMAPA:18334 respiratory mucosa BTO:0000973 A mucosa that is part of a gastrointestinal system. BTO:0000546 BTO:0005568 EMAPA:36591 MA:0001521 digestive tract mucosa gut mucosa gut mucuous membrane mucosa of gut uberon UBERON:0004786 The gut mucosa of amphioxus has insulin-secreting cells. http://www.ncbi.nlm.nih.gov/pubmed/16417468 gastrointestinal system mucosa BTO-modified A mucosa that is part of a gastrointestinal system. OBOL:automatic digestive tract mucosa gut mucosa BTO:0000546 gut mucuous membrane mucosa of gut A mucous gland that is part of a larynx [Automatically generated definition]. EMAPA:37631 MA:0001767 mucous gland of larynx uberon UBERON:0004789 larynx mucous gland A mucous gland that is part of a larynx [Automatically generated definition]. OBOL:automatic EMAPA:37631 MA:th mucous gland of larynx OBOL:automatic A mucous gland that is part of the skin. See comments for 'skin mucus' EMAPA:35775 MA:0000148 mucous gland of entire skin mucous gland of skin of body skin mucus gland skin of body mucous gland uberon UBERON:0004790 skin mucous gland A mucous gland that is part of the skin. mucous gland of entire skin OBOL:automatic mucous gland of skin of body OBOL:automatic skin mucus gland OBOL:automatic skin of body mucous gland OBOL:automatic Any of the tissue layers that comprise a blood vessel. Examples: tunica media, tunica adventitia. EMAPA:36296 MA:0002854 uberon UBERON:0004797 blood vessel layer Any of the tissue layers that comprise a blood vessel. Examples: tunica media, tunica adventitia. An epithelium that is part of a uterine cervix [Automatically generated definition]. The epithelium of the cervix is varied. The ectocervix (more distal, by the vagina) is composed of nonkeratinized stratified squamous epithelium. The endocervix (more proximal, within the uterus) is composed of simple columnar epithelium BTO:0000241 CALOHA:TS-0137 EFO:0001913 EMAPA:29929 MA:0001724 NCIT:C49218 UMLS:C1711358 cervical canal epithelial tissue cervical canal epithelium cervical epithelium cervix epithelial tissue epithelium of cervix uberon UBERON:0004801 cervix epithelium An epithelium that is part of a uterine cervix [Automatically generated definition]. OBOL:automatic The epithelium of the cervix is varied. The ectocervix (more distal, by the vagina) is composed of nonkeratinized stratified squamous epithelium. The endocervix (more proximal, within the uterus) is composed of simple columnar epithelium UMLS:C1711358 ncithesaurus:Cervix_Epithelium cervical canal epithelial tissue OBOL:automatic cervical canal epithelium OBOL:automatic cervical epithelium BTO:0000241 cervix epithelial tissue OBOL:automatic epithelium of cervix OBOL:automatic the pseudostratified ciliated epithelium that lines much of the conducting portion of the airway, including part of the nasal cavity and larynx, the trachea, and bronchi BTO:0000419 CALOHA:TS-0023 EMAPA:32827 MA:0001480 VHOG:0000981 epithelial tissue of respiratory tract epithelium of respiratory tract respiratory tract epithelial tissue uberon airway epithelium respiratory epithelium UBERON:0004802 respiratory tract epithelium the pseudostratified ciliated epithelium that lines much of the conducting portion of the airway, including part of the nasal cavity and larynx, the trachea, and bronchi ISBN:0-683-40008-8 MGI:anna MP:0010942 epithelial tissue of respiratory tract OBOL:automatic epithelium of respiratory tract OBOL:automatic respiratory tract epithelial tissue OBOL:automatic airway epithelium BTO:0000419 respiratory epithelium BTO:0000419 An epithelium that is part of a oviduct [Automatically generated definition]. in FMA, epithelium of uterine tube is a subclass of ciliated columnar epithelium. MA introduces subtypes: ciliated columnar and cuboidal. We map the FMA type according to its relationships, not its label BTO:0002402 CALOHA:TS-1316 EMAPA:29043 MA:0001718 epithelial tissue of oviduct epithelium of fallopian tube epithelium of oviduct epithelium of uterine tube oviduct epithelial tissue uberon columnar epithelium of the fallopian tube columnar epithelium of the oviduct fallopian tube epithelium UBERON:0004804 oviduct epithelium An epithelium that is part of a oviduct [Automatically generated definition]. OBOL:automatic in FMA, epithelium of uterine tube is a subclass of ciliated columnar epithelium. MA introduces subtypes: ciliated columnar and cuboidal. We map the FMA type according to its relationships, not its label FMA epithelial tissue of oviduct OBOL:automatic epithelium of fallopian tube OBOL:automatic epithelium of oviduct OBOL:automatic epithelium of uterine tube FMA:62016 oviduct epithelial tissue OBOL:automatic columnar epithelium of the fallopian tube BTO:0002402 columnar epithelium of the oviduct BTO:0002402 fallopian tube epithelium BTO:0002402 An epithelium that is part of a respiratory system [Automatically generated definition]. CALOHA:TS-0023 EMAPA:32826 MA:0001823 VHOG:0000981 apparatus respiratorius epithelial tissue apparatus respiratorius epithelium epithelial tissue of apparatus respiratorius epithelial tissue of respiratory system epithelium of apparatus respiratorius epithelium of respiratory system respiratory system epithelial tissue uberon UBERON:0004807 respiratory system epithelium An epithelium that is part of a respiratory system [Automatically generated definition]. OBOL:automatic apparatus respiratorius epithelial tissue OBOL:automatic apparatus respiratorius epithelium OBOL:automatic epithelial tissue of apparatus respiratorius OBOL:automatic epithelial tissue of respiratory system OBOL:automatic epithelium of apparatus respiratorius OBOL:automatic epithelium of respiratory system OBOL:automatic respiratory system epithelial tissue OBOL:automatic An epithelium that is part of a digestive system [Automatically generated definition]. EMAPA:32683 MA:0001520 digestive system epithelial tissue digestive system epithelium epithelial tissue of digestive system epithelial tissue of gastrointestinal system epithelium of digestive system epithelium of gastrointestinal system gastrointestinal system epithelial tissue uberon UBERON:0004808 gastrointestinal system epithelium An epithelium that is part of a digestive system [Automatically generated definition]. OBOL:automatic digestive system epithelial tissue OBOL:automatic digestive system epithelium OBOL:automatic epithelial tissue of digestive system OBOL:automatic epithelial tissue of gastrointestinal system OBOL:automatic epithelium of digestive system OBOL:automatic epithelium of gastrointestinal system OBOL:automatic gastrointestinal system epithelial tissue OBOL:automatic An epithelium that is part of an endometrium [Automatically generated definition]. In rodents and primates, the uterine epithelium (the endometrium) is eroded away so that maternal blood comes into direct contact with the trophoblast surface (called haemochorial) EMAPA:35307 MA:0002731 endometrium epithelial tissue epithelial tissue of endometrium epithelium of endometrium epithelium of tunica mucosa of endometrium uberon uterine epithelium UBERON:0004811 endometrium epithelium An epithelium that is part of an endometrium [Automatically generated definition]. OBOL:automatic In rodents and primates, the uterine epithelium (the endometrium) is eroded away so that maternal blood comes into direct contact with the trophoblast surface (called haemochorial) endometrium epithelial tissue OBOL:automatic epithelial tissue of endometrium OBOL:automatic epithelium of endometrium OBOL:automatic epithelium of tunica mucosa of endometrium OBOL:automatic uterine epithelium An epithelium that is part of a upper respiratory tract [Automatically generated definition]. EMAPA:35894 MA:0001912 epithelial tissue of upper respiratory tract epithelium of upper respiratory tract upper respiratory tract epithelial tissue uberon UBERON:0004814 upper respiratory tract epithelium An epithelium that is part of a upper respiratory tract [Automatically generated definition]. OBOL:automatic epithelial tissue of upper respiratory tract OBOL:automatic epithelium of upper respiratory tract OBOL:automatic upper respiratory tract epithelial tissue OBOL:automatic An epithelium that is part of a lower respiratory tract [Automatically generated definition]. EMAPA:37549 MA:0001481 epithelial tissue of lower respiratory tract epithelium of lower respiratory tract lower respiratory tract epithelial tissue uberon UBERON:0004815 lower respiratory tract epithelium An epithelium that is part of a lower respiratory tract [Automatically generated definition]. OBOL:automatic EMAPA:37549 MA:th epithelial tissue of lower respiratory tract OBOL:automatic epithelium of lower respiratory tract OBOL:automatic lower respiratory tract epithelial tissue OBOL:automatic An epithelium that is part of a larynx [Automatically generated definition]. composed of squamous epithelium in the upper larynx and ciliated columnar epithelium in the lower larynx [ISBN:0-397-51047-0] EHDAA2:0004065 EMAPA:35472 MA:0001765 NCIT:C49247 UMLS:C0751258 epithelial tissue of larynx epithelium of larynx laryngeal epithelium larynx epithelial tissue uberon UBERON:0004816 larynx epithelium An epithelium that is part of a larynx [Automatically generated definition]. OBOL:automatic UMLS:C0751258 ncithesaurus:Laryngeal_Epithelium epithelial tissue of larynx OBOL:automatic epithelium of larynx OBOL:automatic laryngeal epithelium OBOL:automatic larynx epithelial tissue OBOL:automatic the cellular avascular layer of the kidney luminar surfaces BTO:0000059 CALOHA:TS-0505 EMAPA:35457 MA:0002846 epithelial tissue of kidney epithelium of kidney kidney epithelial tissue uberon renal epithelium UBERON:0004819 kidney epithelium the cellular avascular layer of the kidney luminar surfaces MGI:csmith MP:0004967 epithelial tissue of kidney OBOL:automatic epithelium of kidney OBOL:automatic kidney epithelial tissue OBOL:automatic renal epithelium EMAPA:35457 A portion of skeletal muscle tissue that is part of a urethra [Automatically generated definition]. EMAPA:37788 MA:0001690 skeletal muscle of urethra skeletal muscle tissue of urethra urethra skeletal muscle tissue uberon urethra skeletal muscle urethral skeletal muscle UBERON:0004829 urethra skeletal muscle tissue A portion of skeletal muscle tissue that is part of a urethra [Automatically generated definition]. OBOL:automatic EMAPA:37788 MA:th skeletal muscle of urethra OBOL:automatic skeletal muscle tissue of urethra OBOL:automatic urethra skeletal muscle tissue OBOL:automatic urethra skeletal muscle MA:0001690 urethral skeletal muscle MA:0001690 A portion of skeletal muscle tissue that is part of a respiratory system [Automatically generated definition]. EMAPA:37583 MA:0001829 respiratory system skeletal muscle tissue skeletal muscle of apparatus respiratorius skeletal muscle of respiratory system skeletal muscle tissue of apparatus respiratorius skeletal muscle tissue of respiratory system uberon UBERON:0004830 respiratory system skeletal muscle A portion of skeletal muscle tissue that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37583 MA:th respiratory system skeletal muscle tissue OBOL:automatic skeletal muscle of apparatus respiratorius OBOL:automatic skeletal muscle of respiratory system OBOL:automatic skeletal muscle tissue of apparatus respiratorius OBOL:automatic skeletal muscle tissue of respiratory system OBOL:automatic A portion of skeletal muscle tissue that is part of an anal region [Automatically generated definition]. EMAPA:37393 MA:0001530 anal part of perineum skeletal muscle anal part of perineum skeletal muscle tissue anal region skeletal muscle tissue anal triangle skeletal muscle anal triangle skeletal muscle tissue skeletal muscle of anal part of perineum skeletal muscle of anal region skeletal muscle of anal triangle skeletal muscle tissue of anal part of perineum skeletal muscle tissue of anal region skeletal muscle tissue of anal triangle uberon UBERON:0004832 anal region skeletal muscle A portion of skeletal muscle tissue that is part of an anal region [Automatically generated definition]. OBOL:automatic EMAPA:37393 MA:th anal part of perineum skeletal muscle OBOL:automatic anal part of perineum skeletal muscle tissue OBOL:automatic anal region skeletal muscle tissue OBOL:automatic anal triangle skeletal muscle OBOL:automatic anal triangle skeletal muscle tissue OBOL:automatic skeletal muscle of anal part of perineum OBOL:automatic skeletal muscle of anal region OBOL:automatic skeletal muscle of anal triangle OBOL:automatic skeletal muscle tissue of anal part of perineum OBOL:automatic skeletal muscle tissue of anal region OBOL:automatic skeletal muscle tissue of anal triangle OBOL:automatic A portion of skeletal muscle tissue that is part of a lip [Automatically generated definition]. this class is derived from MA. Consider re-modeling this as being a muscle that acts on the lips. See: http://en.wikipedia.org/wiki/Lip#Muscles_acting_on_the_lips EMAPA:37642 MA:0001578 lip skeletal muscle tissue skeletal muscle of lip skeletal muscle tissue of lip uberon UBERON:0004833 lip skeletal muscle A portion of skeletal muscle tissue that is part of a lip [Automatically generated definition]. OBOL:automatic EMAPA:37642 MA:th lip skeletal muscle tissue OBOL:automatic skeletal muscle of lip OBOL:automatic skeletal muscle tissue of lip OBOL:automatic An endothelium of artery that is part of a respiratory system [Automatically generated definition]. EMAPA:37566 MA:0001801 apparatus respiratorius arterial endothelium apparatus respiratorius artery endothelium apparatus respiratorius endothelium of artery arterial endothelium of apparatus respiratorius arterial endothelium of respiratory system artery endothelium of apparatus respiratorius artery endothelium of respiratory system endothelium of artery of apparatus respiratorius endothelium of artery of respiratory system respiratory system artery endothelium respiratory system endothelium of artery uberon UBERON:0004848 respiratory system arterial endothelium true An endothelium of artery that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37566 MA:th apparatus respiratorius arterial endothelium OBOL:automatic apparatus respiratorius artery endothelium OBOL:automatic apparatus respiratorius endothelium of artery OBOL:automatic arterial endothelium of apparatus respiratorius OBOL:automatic arterial endothelium of respiratory system OBOL:automatic artery endothelium of apparatus respiratorius OBOL:automatic artery endothelium of respiratory system OBOL:automatic endothelium of artery of apparatus respiratorius OBOL:automatic endothelium of artery of respiratory system OBOL:automatic respiratory system artery endothelium OBOL:automatic respiratory system endothelium of artery OBOL:automatic An endothelium of vein that is part of a respiratory system [Automatically generated definition]. EMAPA:37585 MA:0001811 apparatus respiratorius endothelium of vein apparatus respiratorius vein endothelium apparatus respiratorius venous endothelium endothelium of vein of apparatus respiratorius endothelium of vein of respiratory system respiratory system endothelium of vein respiratory system vein endothelium vein endothelium of apparatus respiratorius vein endothelium of respiratory system venous endothelium of apparatus respiratorius venous endothelium of respiratory system uberon UBERON:0004849 respiratory system venous endothelium An endothelium of vein that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37585 MA:th apparatus respiratorius endothelium of vein OBOL:automatic apparatus respiratorius vein endothelium OBOL:automatic apparatus respiratorius venous endothelium OBOL:automatic endothelium of vein of apparatus respiratorius OBOL:automatic endothelium of vein of respiratory system OBOL:automatic respiratory system endothelium of vein OBOL:automatic respiratory system vein endothelium OBOL:automatic vein endothelium of apparatus respiratorius OBOL:automatic vein endothelium of respiratory system OBOL:automatic venous endothelium of apparatus respiratorius OBOL:automatic venous endothelium of respiratory system OBOL:automatic the thin layer of flat cells that line the aorta and form a barrier between circulating blood in the lumen and the rest of the vessel wall BTO:0000394 CALOHA:TS-0047 EFO:0002597 EMAPA:35134 MA:0000701 NCIT:C49190 UMLS:C1706824 adult aorta endothelium endothelium of adult aorta endothelium of aorta endothelium of trunk of aortic tree endothelium of trunk of systemic arterial tree trunk of aortic tree endothelium trunk of systemic arterial tree endothelium uberon aortic endothelium UBERON:0004851 aorta endothelium the thin layer of flat cells that line the aorta and form a barrier between circulating blood in the lumen and the rest of the vessel wall MGI:csmith MP:0009864 UMLS:C1706824 ncithesaurus:Aorta_Endothelium adult aorta endothelium OBOL:automatic endothelium of adult aorta OBOL:automatic endothelium of aorta OBOL:automatic endothelium of trunk of aortic tree OBOL:automatic endothelium of trunk of systemic arterial tree OBOL:automatic trunk of aortic tree endothelium OBOL:automatic trunk of systemic arterial tree endothelium OBOL:automatic aortic endothelium BTO:0000394 An endothelium that is part of the cardiovascular system. consider merging with 'endothelium' Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG] BTO:0001853 EMAPA:35201 GAID:519 MA:0000717 MESH:D004730 NCIT:C13053 TAO:0002171 UMLS:C0014261 VHOG:0001217 XAO:0000356 ZFA:0001639 uberon endothelia vascular endothelia UBERON:0004852 cardiovascular system endothelium An endothelium that is part of the cardiovascular system. Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG] 2012-09-17 VHOG:0001217 VHOG ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207 UMLS:C0014261 ncithesaurus:Vascular_Endothelium endothelia ZFA:0001639 vascular endothelia XAO:0000356 A connective tissue that surrounds a skeletal muscle tissue. EMAPA:37743 MA:0002868 connective tissue of skeletal muscle connective tissue of skeletal muscle tissue portion of connective tissue of skeletal muscle portion of connective tissue of skeletal muscle tissue skeletal muscle portion of connective tissue skeletal muscle textus connectivus skeletal muscle tissue connective tissue skeletal muscle tissue portion of connective tissue skeletal muscle tissue textus connectivus textus connectivus of skeletal muscle textus connectivus of skeletal muscle tissue uberon skeletal muscle interstitial tissue skeletal muscle interstitum UBERON:0004857 skeletal muscle connective tissue A connective tissue that surrounds a skeletal muscle tissue. OBOL:automatic EMAPA:37743 MA:th connective tissue of skeletal muscle OBOL:automatic connective tissue of skeletal muscle tissue OBOL:automatic portion of connective tissue of skeletal muscle OBOL:automatic portion of connective tissue of skeletal muscle tissue OBOL:automatic skeletal muscle portion of connective tissue OBOL:automatic skeletal muscle textus connectivus OBOL:automatic skeletal muscle tissue connective tissue OBOL:automatic skeletal muscle tissue portion of connective tissue OBOL:automatic skeletal muscle tissue textus connectivus OBOL:automatic textus connectivus of skeletal muscle OBOL:automatic textus connectivus of skeletal muscle tissue OBOL:automatic skeletal muscle interstitial tissue MA:0002868 skeletal muscle interstitum MA:0002868 A gland that is part of a eye. The eye is a compound unit which depending on the species may consist of an eyeballs plus associated ducts and integumentary structures. Eye glands therefore include the various types of lacrimal gland, the various types of apocrine and sebaceous glands associated with the eyelid. EMAPA:35334 MA:0000267 eye-associated gland gland of eye uberon UBERON:0004859 Examples: harderian gland, accessory lacrimal gland, gland of Moll, gland of Zeis, nictitating membrane glands eye gland A gland that is part of a eye. The eye is a compound unit which depending on the species may consist of an eyeballs plus associated ducts and integumentary structures. Eye glands therefore include the various types of lacrimal gland, the various types of apocrine and sebaceous glands associated with the eyelid. eye-associated gland gland of eye OBOL:automatic A vasculature that is part of a retina [Automatically generated definition]. FMA:76552 MESH:D012171 XAO:0004153 retina vasculature retina vasculature of camera-type eye retinal blood vessels retinal blood vessels set retinal vasculature set of blood vessels of retina set of retinal blood vessels vasa sanguinea retinae uberon UBERON:0004864 vasculature of retina A vasculature that is part of a retina [Automatically generated definition]. OBOL:automatic retina vasculature GO:0061298 retina vasculature of camera-type eye GO:0061298 retinal blood vessels FMA:76552 retinal blood vessels set FMA:76552 retinal vasculature OBOL:automatic set of blood vessels of retina OBOL:automatic set of retinal blood vessels FMA:76552 vasa sanguinea retinae FMA:76552 FMA:TA Layer of lateral plate mesoderm that forms the circulatory system and future gut wall - overlies endoderm[WP]. We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors visceral mesoderm AAO:0011102 BILA:0000044 FMA:295568 XAO:0000276 inner layer of lateral plate mesoderm uberon splanchnic mesoderm UBERON:0004872 splanchnic layer of lateral plate mesoderm Layer of lateral plate mesoderm that forms the circulatory system and future gut wall - overlies endoderm[WP]. We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors BILA visceral mesoderm BILA:0000044 splanchnic mesoderm ISBN:9780878932504 A structure created during embryogenesis when the lateral mesoderm splits into two layers - the inner (or splanchnic) layer adheres to the endoderm, and with it forms the splanchnopleure[WP]. TODO - check relationship to LPM EHDAA2:0001903 EHDAA:383 EMAPA:16181 FMA:295564 NCIT:C34303 UMLS:C1519472 VHOG:0000558 uberon ventral splanchnic mesoderm UBERON:0004873 splanchnopleure EHDAA2 A structure created during embryogenesis when the lateral mesoderm splits into two layers - the inner (or splanchnic) layer adheres to the endoderm, and with it forms the splanchnopleure[WP]. UMLS:C1519472 ncithesaurus:Splanchnopleure ventral splanchnic mesoderm A structure created during embryogenesis when the lateral mesoderm splits into two layers - the outer (or somatic) layer becomes applied to the inner surface of the ectoderm, and with it forms the somatopleure.[WP]. Gives rise to the paired appendages in jawed vertebrates. a persistent somatopleure through the redistribution and expansion of the lateral plate mesoderm is a synapomorphy for gnathostomes and a critical step in generating a novel developmental module with dramatic evolutionary potentia (Tulenko et al. 2012) http://burkelab.research.wesleyan.edu/current-projects/lamprey/ sources differ as to whether this is part-of or develops-from the LPM EHDAA2:0001847 EHDAA:381 EMAPA:16180 FMA:295566 NCIT:C34301 UMLS:C1519423 VHOG:0000557 uberon UBERON:0004874 somatopleure EHDAA2 A structure created during embryogenesis when the lateral mesoderm splits into two layers - the outer (or somatic) layer becomes applied to the inner surface of the ectoderm, and with it forms the somatopleure.[WP]. UMLS:C1519423 ncithesaurus:Somatopleure A portion of the urogenital ridge which is the source of much of the urinary system[WP]. FMA:72168 NCIT:C34219 UMLS:C1283944 uberon chorda nephrogenica UBERON:0004875 part_of or develops_from urogenital ridge? nephrogenic cord A portion of the urogenital ridge which is the source of much of the urinary system[WP]. UMLS:C1283944 ncithesaurus:Nephrogenic_Cord chorda nephrogenica One of of the pair of folds derived from the cloacal folds which give rise to a portion of the external genitalia; in male embryos they close over the urethral plate and fuse to form the spongy (penile) urethra and ventral aspect of the penis, not including the glans; failure of fusion of the urethral folds leads to hypospadias; in female embryos they fuse only anterior to the anus and form the labia minora[MP]. Less commonly, urogenital fold refers to the fold in the mesonephros which is the precursor of e.g. the suspensory ligament of the ovary. This is the case in older versions of Gray's anatomy[WP] EHDAA2:0004022 EMAPA:30888 FMA:321919 urethral fold urogenital fold uberon urogenital ridge UBERON:0004876 urogenital fold EHDAA2 Wikipedia EHDAA2 One of of the pair of folds derived from the cloacal folds which give rise to a portion of the external genitalia; in male embryos they close over the urethral plate and fuse to form the spongy (penile) urethra and ventral aspect of the penis, not including the glans; failure of fusion of the urethral folds leads to hypospadias; in female embryos they fuse only anterior to the anus and form the labia minora[MP]. MP:0011835 MP:anna urethral fold EMAPA:30888 urogenital fold EHDAA2:0004022 MP:0011835 urogenital ridge MP:0011835 The central region of trunk mesoderm. This tissue forms the notochord Notochord rudiment[ZFIN:ZDB-PUB-961014-576]. WP treats this as synonym of axial mesoderm. Induces neural tube. Gilbert: contains an anterior head process and the notochord. AAO:0000478 EFO:0003426 TAO:0000091 ZFA:0000091 axial chorda mesoderm chorda mesoderm dorsal mesoderm presumptive notochord uberon UBERON:0004880 chordamesoderm The central region of trunk mesoderm. This tissue forms the notochord Notochord rudiment[ZFIN:ZDB-PUB-961014-576]. ZFIN:ZDB-PUB-961014-576 axial chorda mesoderm ZFA:0000091 dorsal mesoderm presumptive notochord ZFA:0000091 The mass of tissue made up of mesenchymal cells in the lung. EMAPA:32866 lung-associated mesenchyme mesenchyme of lung pulmonary mesenchyme uberon UBERON:0004883 lung mesenchyme The mass of tissue made up of mesenchymal cells in the lung. GO:0060484 lung-associated mesenchyme GO:0060484 mesenchyme of lung OBOL:automatic pulmonary mesenchyme GO:0060484 The fetal urogenital sinus (from which the prostate derives) is a simple cylinder of stratified basal epithelium, surrounded by mesenchyme and positioned between the embryonic bladder and pelvic urethra we follow EHDAA2 in dividing the UGS into epithelium and lumen EHDAA2:0004061 EMAPA:31509 UGE epithelium of urogenital sinus uberon UBERON:0004902 urogenital sinus epithelium The fetal urogenital sinus (from which the prostate derives) is a simple cylinder of stratified basal epithelium, surrounded by mesenchyme and positioned between the embryonic bladder and pelvic urethra we follow EHDAA2 in dividing the UGS into epithelium and lumen EHDAA2 UGE epithelium of urogenital sinus OBOL:automatic A neuron projection bundle that connects the retina or its analog in the eye with the brain. This includes the vertebrate optic nerve (not truly a nerve) as well as analogous structures such as the Bolwig nerve in Drosophila optic nerve BTO:0000966 EV:0100351 FBbt:00001956 TADS:0000232 optic nerve (generic) uberon UBERON:0004904 for the vertebrate-specific structure, see UBERON:0000941 (cranial nerve II) neuron projection bundle connecting eye with brain A neuron projection bundle that connects the retina or its analog in the eye with the brain. This includes the vertebrate optic nerve (not truly a nerve) as well as analogous structures such as the Bolwig nerve in Drosophila optic nerve BTO:0000966 Anatomical cluster that connects two or more adjacent skeletal elements or hardened body parts. FBbt:00005811 joint uberon UBERON:0004905 articulation Anatomical cluster that connects two or more adjacent skeletal elements or hardened body parts. A portion of the gut that is derived from ectoderm. ectodermal gut gut ectoderm uberon UBERON:0004906 ectodermal part of digestive tract A portion of the gut that is derived from ectoderm. GO:0007439 gut ectoderm EMAPA:32930 The region of the digestive tract extending from the beginning of the intestines to the anus[GO - gut definition]. MA class was moved from here. See https://github.com/obophenotype/uberon/issues/509 WP: small intestine, large intestine, anus. Anal canal not part of LGIT according to FMA, but anus is considered part of LGIT according to WP. Duodenum overlaps both U/L gut FMA:49179 NCIT:C33010 UMLS:C0226875 galen:LowerGastrointestinalTract lower GI tract lower gastrointestinal tract uberon UBERON:0004907 lower digestive tract The region of the digestive tract extending from the beginning of the intestines to the anus[GO - gut definition]. MA class was moved from here. See https://github.com/obophenotype/uberon/issues/509 MA WP: small intestine, large intestine, anus. Anal canal not part of LGIT according to FMA, but anus is considered part of LGIT according to WP. Duodenum overlaps both U/L FMA gut GO:0048565 UMLS:C0226875 ncithesaurus:Lower_Gastrointestinal_Tract An epithelium surrounding a gonad. after reasoning this should subsume the more specific germinal epithelium classes. We include the fly structure here although it is not clear if the sheath is an epithelium or a multi-tissue structure that includes epithelium as parts EHDAA:4032 EHDAA:5931 FBbt:00004859 NCIT:C32676 UMLS:C1517534 gonad epithelium gonadal epithelium uberon gonadal sheath UBERON:0004909 epithelium of gonad An epithelium surrounding a gonad. OBOL:automatic UMLS:C1517534 ncithesaurus:Germinal_Epithelium gonad epithelium OBOL:automatic gonadal epithelium OBOL:automatic gonadal sheath FBbt:00004859 An epithelium surrounding an ovary. after reasoning this should subsume the more specific germinal epithelium classes. We include the fly structure here although it is not clear if the sheath is an epithelium or a multi-tissue structure that includes epithelium as parts BTO:0003661 FBbt:00004896 ovarian epithelium ovary epithelium ovarian sheath uberon UBERON:0004911 epithelium of female gonad An epithelium surrounding an ovary. OBOL:automatic ovarian epithelium OBOL:automatic ovary epithelium OBOL:automatic ovarian sheath FBbt:00004896 A proximal-distal subdivision of the digestive tract. intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct. FBbt:00100315 FMA:71131 uberon alimentary system subdivision intestinal tract segment of intestinal tract subdivision of alimentary system UBERON:0004921 subdivision of digestive tract A proximal-distal subdivision of the digestive tract. alimentary system subdivision FMA:71131 subdivision of alimentary system FMA:71131 A part of a wall of an organ that forms a layer. FMA:82485 uberon UBERON:0004923 organ component layer A part of a wall of an organ that forms a layer. The tissue underlying the tunica mucosa of the pharynx. BTO:0002113 FMA:75144 pharyngeal submucosa pharynx submucosa tela submucosa pharyngea tela submucosa pharyngis uberon pharyngobasilar fascia submucous coat of pharynx submucous layer of pharynx UBERON:0004924 submucosa of pharynx The tissue underlying the tunica mucosa of the pharynx. BTO:0002113 pharyngeal submucosa FMA:75144 pharynx submucosa OBOL:automatic tela submucosa pharyngea FMA:75144 FMA:TA tela submucosa pharyngis BTO:0002113 submucous coat of pharynx BTO:0002113 submucous layer of pharynx BTO:0002113 A submucosa that is part of a sigmoid colon [Automatically generated definition]. FMA:15027 sigmoid colon submucosa uberon UBERON:0004932 submucosa of sigmoid colon A submucosa that is part of a sigmoid colon [Automatically generated definition]. OBOL:automatic sigmoid colon submucosa OBOL:automatic The submucous layer of the wall of the urinary bladder. BTO:0002117 EMAPA:32275 FMA:15929 bladder submucosa submucosa of bladder tela submucosa (vesica urinaria) tela submucosa vesicae tela submucosa vesicae urinariae urinary bladder submucosa uberon submucous layer of urinary bladder UBERON:0004943 submucosa of urinary bladder The submucous layer of the wall of the urinary bladder. BTO:0002117 bladder submucosa OBOL:automatic submucosa of bladder OBOL:automatic tela submucosa (vesica urinaria) FMA:15929 FMA:TA tela submucosa vesicae FMA:15929 FMA:TA tela submucosa vesicae urinariae BTO:0002117 urinary bladder submucosa OBOL:automatic submucous layer of urinary bladder BTO:0002117 A submucosa that is part of a neck of urinary bladder [Automatically generated definition]. EMAPA:32276 FMA:17851 bladder neck submucosa neck of bladder submucosa neck of urinary bladder submucosa submucosa of bladder neck submucosa of neck of bladder submucosa of urinary bladder neck submucosa of vesical neck urinary bladder neck submucosa vesical neck submucosa uberon UBERON:0004945 submucosa of neck of urinary bladder A submucosa that is part of a neck of urinary bladder [Automatically generated definition]. OBOL:automatic bladder neck submucosa OBOL:automatic neck of bladder submucosa OBOL:automatic neck of urinary bladder submucosa OBOL:automatic submucosa of bladder neck OBOL:automatic submucosa of neck of bladder OBOL:automatic submucosa of urinary bladder neck OBOL:automatic submucosa of vesical neck OBOL:automatic urinary bladder neck submucosa OBOL:automatic vesical neck submucosa OBOL:automatic A mucosa that is part of a ureter [Automatically generated definition]. FMA:15894 galen:MucousMembraneOfUreter mucosa of organ of ureter mucosal layer of ureter mucous membrane of ureter organ mucosa of ureter tunica mucosa (ureter) tunica mucosa ureteris ureter mucosa ureter mucosa of organ ureter mucous membrane ureter organ mucosa ureteral mucosa ureteric mucosa uberon UBERON:0004980 mucosa of ureter A mucosa that is part of a ureter [Automatically generated definition]. OBOL:automatic mucosa of organ of ureter OBOL:automatic mucosal layer of ureter FMA:15894 mucous membrane of ureter OBOL:automatic organ mucosa of ureter OBOL:automatic tunica mucosa (ureter) FMA:15894 tunica mucosa ureteris FMA:15894 FMA:TA ureter mucosa OBOL:automatic ureter mucosa of organ OBOL:automatic ureter mucous membrane OBOL:automatic ureter organ mucosa OBOL:automatic ureteral mucosa FMA:15894 ureteric mucosa FMA:15894 A mucosa that is part of a vagina [Automatically generated definition]. BTO:0005676 FMA:19975 mucosa of organ of vagina mucous membrane of vagina organ mucosa of vagina tunica mucosa vaginae vagina mucosa vagina mucosa of organ vagina mucous membrane vagina organ mucosa vaginal mucosa uberon UBERON:0004983 mucosa of vagina A mucosa that is part of a vagina [Automatically generated definition]. OBOL:automatic mucosa of organ of vagina OBOL:automatic mucous membrane of vagina OBOL:automatic organ mucosa of vagina OBOL:automatic tunica mucosa vaginae FMA:19975 FMA:TA vagina mucosa OBOL:automatic vagina mucosa of organ OBOL:automatic vagina mucous membrane OBOL:automatic vagina organ mucosa OBOL:automatic vaginal mucosa FMA:19975 A mucosa that is part of a sigmoid colon [Automatically generated definition]. FMA:15026 mucosa of organ of sigmoid colon mucous membrane of sigmoid colon organ mucosa of sigmoid colon sigmoid colon mucosa sigmoid colon mucosa of organ sigmoid colon mucous membrane sigmoid colon organ mucosa uberon UBERON:0004993 mucosa of sigmoid colon A mucosa that is part of a sigmoid colon [Automatically generated definition]. OBOL:automatic mucosa of organ of sigmoid colon OBOL:automatic mucous membrane of sigmoid colon OBOL:automatic organ mucosa of sigmoid colon OBOL:automatic sigmoid colon mucosa OBOL:automatic sigmoid colon mucosa of organ OBOL:automatic sigmoid colon mucous membrane OBOL:automatic sigmoid colon organ mucosa OBOL:automatic A mucosa that is part of a right ureter [Automatically generated definition]. FMA:17806 mucosa of organ of right ureter mucous membrane of right ureter organ mucosa of right ureter right ureter mucosa right ureter mucosa of organ right ureter mucous membrane right ureter organ mucosa right ureteral mucosa uberon UBERON:0005004 mucosa of right ureter A mucosa that is part of a right ureter [Automatically generated definition]. OBOL:automatic mucosa of organ of right ureter OBOL:automatic mucous membrane of right ureter OBOL:automatic organ mucosa of right ureter OBOL:automatic right ureter mucosa OBOL:automatic right ureter mucosa of organ OBOL:automatic right ureter mucous membrane OBOL:automatic right ureter organ mucosa OBOL:automatic right ureteral mucosa FMA:17806 A mucosa that is part of a left ureter [Automatically generated definition]. FMA:17807 left ureter mucosa left ureter mucosa of organ left ureter mucous membrane left ureter organ mucosa left ureteral mucosa mucosa of organ of left ureter mucous membrane of left ureter organ mucosa of left ureter uberon UBERON:0005005 mucosa of left ureter A mucosa that is part of a left ureter [Automatically generated definition]. OBOL:automatic left ureter mucosa OBOL:automatic left ureter mucosa of organ OBOL:automatic left ureter mucous membrane OBOL:automatic left ureter organ mucosa OBOL:automatic left ureteral mucosa FMA:17807 mucosa of organ of left ureter OBOL:automatic mucous membrane of left ureter OBOL:automatic organ mucosa of left ureter OBOL:automatic A mucosa that is part of a renal pelvis [Automatically generated definition]. FMA:17931 kidney pelvis mucosa kidney pelvis mucosa of organ kidney pelvis mucous membrane kidney pelvis organ mucosa mucosa of kidney pelvis mucosa of organ of kidney pelvis mucosa of organ of pelvis of ureter mucosa of organ of renal pelvis mucosa of pelvis of ureter mucous membrane of kidney pelvis mucous membrane of pelvis of ureter mucous membrane of renal pelvis organ mucosa of kidney pelvis organ mucosa of pelvis of ureter organ mucosa of renal pelvis pelvis of ureter mucosa pelvis of ureter mucosa of organ pelvis of ureter mucous membrane pelvis of ureter organ mucosa renal pelvic mucosa renal pelvis mucosa renal pelvis mucosa of organ renal pelvis mucous membrane renal pelvis organ mucosa tunica mucosa pelvis renalis uberon UBERON:0005006 mucosa of renal pelvis A mucosa that is part of a renal pelvis [Automatically generated definition]. OBOL:automatic kidney pelvis mucosa OBOL:automatic kidney pelvis mucosa of organ OBOL:automatic kidney pelvis mucous membrane OBOL:automatic kidney pelvis organ mucosa OBOL:automatic mucosa of kidney pelvis OBOL:automatic mucosa of organ of kidney pelvis OBOL:automatic mucosa of organ of pelvis of ureter OBOL:automatic mucosa of organ of renal pelvis OBOL:automatic mucosa of pelvis of ureter OBOL:automatic mucous membrane of kidney pelvis OBOL:automatic mucous membrane of pelvis of ureter OBOL:automatic mucous membrane of renal pelvis OBOL:automatic organ mucosa of kidney pelvis OBOL:automatic organ mucosa of pelvis of ureter OBOL:automatic organ mucosa of renal pelvis OBOL:automatic pelvis of ureter mucosa OBOL:automatic pelvis of ureter mucosa of organ OBOL:automatic pelvis of ureter mucous membrane OBOL:automatic pelvis of ureter organ mucosa OBOL:automatic renal pelvic mucosa FMA:17931 renal pelvis mucosa OBOL:automatic renal pelvis mucosa of organ OBOL:automatic renal pelvis mucous membrane OBOL:automatic renal pelvis organ mucosa OBOL:automatic tunica mucosa pelvis renalis FMA:17931 FMA:TA A mucosa that is part of a neck of urinary bladder [Automatically generated definition]. FMA:17846 bladder neck mucosa bladder neck mucosa of organ bladder neck mucous membrane bladder neck organ mucosa mucosa of bladder neck mucosa of neck of bladder mucosa of organ of bladder neck mucosa of organ of neck of bladder mucosa of organ of neck of urinary bladder mucosa of organ of urinary bladder neck mucosa of organ of vesical neck mucosa of urinary bladder neck mucosa of vesical neck mucous membrane of bladder neck mucous membrane of neck of bladder mucous membrane of neck of urinary bladder mucous membrane of urinary bladder neck mucous membrane of vesical neck neck of bladder mucosa neck of bladder mucosa of organ neck of bladder mucous membrane neck of bladder organ mucosa neck of urinary bladder mucosa neck of urinary bladder mucosa of organ neck of urinary bladder mucous membrane neck of urinary bladder organ mucosa organ mucosa of bladder neck organ mucosa of neck of bladder organ mucosa of neck of urinary bladder organ mucosa of urinary bladder neck organ mucosa of vesical neck urinary bladder neck mucosa urinary bladder neck mucosa of organ urinary bladder neck mucous membrane vesical neck mucosa vesical neck mucosa of organ vesical neck mucous membrane vesical neck organ mucosa uberon UBERON:0005010 mucosa of neck of urinary bladder A mucosa that is part of a neck of urinary bladder [Automatically generated definition]. OBOL:automatic bladder neck mucosa OBOL:automatic bladder neck mucosa of organ OBOL:automatic bladder neck mucous membrane OBOL:automatic bladder neck organ mucosa OBOL:automatic mucosa of bladder neck OBOL:automatic mucosa of neck of bladder OBOL:automatic mucosa of organ of bladder neck OBOL:automatic mucosa of organ of neck of bladder OBOL:automatic mucosa of organ of neck of urinary bladder OBOL:automatic mucosa of organ of urinary bladder neck OBOL:automatic mucosa of organ of vesical neck OBOL:automatic mucosa of urinary bladder neck OBOL:automatic mucosa of vesical neck OBOL:automatic mucous membrane of bladder neck OBOL:automatic mucous membrane of neck of bladder OBOL:automatic mucous membrane of neck of urinary bladder OBOL:automatic mucous membrane of urinary bladder neck OBOL:automatic mucous membrane of vesical neck OBOL:automatic neck of bladder mucosa OBOL:automatic neck of bladder mucosa of organ OBOL:automatic neck of bladder mucous membrane OBOL:automatic neck of bladder organ mucosa OBOL:automatic neck of urinary bladder mucosa OBOL:automatic neck of urinary bladder mucosa of organ OBOL:automatic neck of urinary bladder mucous membrane OBOL:automatic neck of urinary bladder organ mucosa OBOL:automatic organ mucosa of bladder neck OBOL:automatic organ mucosa of neck of bladder OBOL:automatic organ mucosa of neck of urinary bladder OBOL:automatic organ mucosa of urinary bladder neck OBOL:automatic organ mucosa of vesical neck OBOL:automatic urinary bladder neck mucosa OBOL:automatic urinary bladder neck mucosa of organ OBOL:automatic urinary bladder neck mucous membrane OBOL:automatic vesical neck mucosa OBOL:automatic vesical neck mucosa of organ OBOL:automatic vesical neck mucous membrane OBOL:automatic vesical neck organ mucosa OBOL:automatic A mucosa that is part of a right uterine tube [Automatically generated definition]. FMA:18452 mucosa of organ of right fallopian tube mucosa of organ of right oviduct mucosa of organ of right uterine tube mucosa of right fallopian tube mucosa of right oviduct mucous membrane of right fallopian tube mucous membrane of right oviduct mucous membrane of right uterine tube organ mucosa of right fallopian tube organ mucosa of right oviduct organ mucosa of right uterine tube right fallopian tube mucosa right fallopian tube mucosa of organ right fallopian tube mucous membrane right fallopian tube organ mucosa right oviduct mucosa right oviduct mucosa of organ right oviduct mucous membrane right oviduct organ mucosa right uterine tube mucosa right uterine tube mucosa of organ right uterine tube mucous membrane right uterine tube organ mucosa uberon UBERON:0005011 mucosa of right uterine tube A mucosa that is part of a right uterine tube [Automatically generated definition]. OBOL:automatic mucosa of organ of right fallopian tube OBOL:automatic mucosa of organ of right oviduct OBOL:automatic mucosa of organ of right uterine tube OBOL:automatic mucosa of right fallopian tube OBOL:automatic mucosa of right oviduct OBOL:automatic mucous membrane of right fallopian tube OBOL:automatic mucous membrane of right oviduct OBOL:automatic mucous membrane of right uterine tube OBOL:automatic organ mucosa of right fallopian tube OBOL:automatic organ mucosa of right oviduct OBOL:automatic organ mucosa of right uterine tube OBOL:automatic right fallopian tube mucosa OBOL:automatic right fallopian tube mucosa of organ OBOL:automatic right fallopian tube mucous membrane OBOL:automatic right fallopian tube organ mucosa OBOL:automatic right oviduct mucosa OBOL:automatic right oviduct mucosa of organ OBOL:automatic right oviduct mucous membrane OBOL:automatic right oviduct organ mucosa OBOL:automatic right uterine tube mucosa OBOL:automatic right uterine tube mucosa of organ OBOL:automatic right uterine tube mucous membrane OBOL:automatic right uterine tube organ mucosa OBOL:automatic A mucosa that is part of a left uterine tube [Automatically generated definition]. FMA:18453 left fallopian tube mucosa left fallopian tube mucosa of organ left fallopian tube mucous membrane left fallopian tube organ mucosa left oviduct mucosa left oviduct mucosa of organ left oviduct mucous membrane left oviduct organ mucosa left uterine tube mucosa left uterine tube mucosa of organ left uterine tube mucous membrane left uterine tube organ mucosa mucosa of left fallopian tube mucosa of left oviduct mucosa of organ of left fallopian tube mucosa of organ of left oviduct mucosa of organ of left uterine tube mucous membrane of left fallopian tube mucous membrane of left oviduct mucous membrane of left uterine tube organ mucosa of left fallopian tube organ mucosa of left oviduct organ mucosa of left uterine tube uberon UBERON:0005012 mucosa of left uterine tube A mucosa that is part of a left uterine tube [Automatically generated definition]. OBOL:automatic left fallopian tube mucosa OBOL:automatic left fallopian tube mucosa of organ OBOL:automatic left fallopian tube mucous membrane OBOL:automatic left fallopian tube organ mucosa OBOL:automatic left oviduct mucosa OBOL:automatic left oviduct mucosa of organ OBOL:automatic left oviduct mucous membrane OBOL:automatic left oviduct organ mucosa OBOL:automatic left uterine tube mucosa OBOL:automatic left uterine tube mucosa of organ OBOL:automatic left uterine tube mucous membrane OBOL:automatic left uterine tube organ mucosa OBOL:automatic mucosa of left fallopian tube OBOL:automatic mucosa of left oviduct OBOL:automatic mucosa of organ of left fallopian tube OBOL:automatic mucosa of organ of left oviduct OBOL:automatic mucosa of organ of left uterine tube OBOL:automatic mucous membrane of left fallopian tube OBOL:automatic mucous membrane of left oviduct OBOL:automatic mucous membrane of left uterine tube OBOL:automatic organ mucosa of left fallopian tube OBOL:automatic organ mucosa of left oviduct OBOL:automatic organ mucosa of left uterine tube OBOL:automatic A mucosa that is part of a female urethra [Automatically generated definition]. FMA:239940 female urethra mucosa female urethra mucosa of organ female urethra mucous membrane female urethra organ mucosa mucosa of organ of female urethra mucous membrane of female urethra organ mucosa of female urethra uberon UBERON:0005014 mucosa of female urethra A mucosa that is part of a female urethra [Automatically generated definition]. OBOL:automatic female urethra mucosa OBOL:automatic female urethra mucosa of organ OBOL:automatic female urethra mucous membrane OBOL:automatic female urethra organ mucosa OBOL:automatic mucosa of organ of female urethra OBOL:automatic mucous membrane of female urethra OBOL:automatic organ mucosa of female urethra OBOL:automatic A mucosa that is part of a lower lip [Automatically generated definition]. FMA:59833 NCIT:C12225 UMLS:C0226939 lower labial mucosa lower lip mucosa lower lip mucosa of organ lower lip mucous membrane lower lip organ mucosa mucosa of organ of lower lip mucous membrane of lower lip organ mucosa of lower lip uberon UBERON:0005032 mucosa of lower lip A mucosa that is part of a lower lip [Automatically generated definition]. OBOL:automatic UMLS:C0226939 ncithesaurus:Mucosa_of_the_Lower_Lip lower labial mucosa UBERON:cjm lower lip mucosa OBOL:automatic lower lip mucosa of organ OBOL:automatic lower lip mucous membrane OBOL:automatic lower lip organ mucosa OBOL:automatic mucosa of organ of lower lip OBOL:automatic mucous membrane of lower lip OBOL:automatic organ mucosa of lower lip OBOL:automatic A mucosa that is part of a fallopian tube [Automatically generated definition]. FMA:18319 fallopian tube mucosa fallopian tube mucosa of organ fallopian tube mucous membrane fallopian tube organ mucosa mucosa of fallopian tube mucosa of organ of fallopian tube mucosa of organ of uterine tube mucosa of oviduct mucous membrane of fallopian tube mucous membrane of uterine tube organ mucosa of fallopian tube organ mucosa of uterine tube tunica mucosa tubae uterinae uterine tubal mucosa uterine tube mucosa uterine tube mucosa of organ uterine tube mucous membrane uterine tube organ mucosa uberon UBERON:0005048 mucosa of uterine tube A mucosa that is part of a fallopian tube [Automatically generated definition]. OBOL:automatic fallopian tube mucosa OBOL:automatic fallopian tube mucosa of organ OBOL:automatic fallopian tube mucous membrane OBOL:automatic fallopian tube organ mucosa OBOL:automatic mucosa of fallopian tube OBOL:automatic mucosa of organ of fallopian tube OBOL:automatic mucosa of organ of uterine tube OBOL:automatic mucosa of oviduct FMA:18319 mucous membrane of fallopian tube OBOL:automatic mucous membrane of uterine tube OBOL:automatic organ mucosa of fallopian tube OBOL:automatic organ mucosa of uterine tube OBOL:automatic tunica mucosa tubae uterinae FMA:18319 FMA:TA uterine tubal mucosa FMA:18319 uterine tube mucosa OBOL:automatic uterine tube mucosa of organ OBOL:automatic uterine tube mucous membrane OBOL:automatic uterine tube organ mucosa OBOL:automatic A mucosa that is part of a uterine tube infundibulum [Automatically generated definition]. FMA:18357 mucosa of infundibulum of fallopian tube mucosa of infundibulum of oviduct mucosa of organ of uterine tube infundibulum mucosa of uterine tube infundibulum mucous membrane of uterine tube infundibulum organ mucosa of uterine tube infundibulum uterine tube infundibulum mucosa uterine tube infundibulum mucosa of organ uterine tube infundibulum mucous membrane uterine tube infundibulum organ mucosa uberon UBERON:0005049 mucosa of infundibulum of uterine tube A mucosa that is part of a uterine tube infundibulum [Automatically generated definition]. OBOL:automatic mucosa of infundibulum of fallopian tube FMA:18357 mucosa of infundibulum of oviduct FMA:18357 mucosa of organ of uterine tube infundibulum OBOL:automatic mucosa of uterine tube infundibulum OBOL:automatic mucous membrane of uterine tube infundibulum OBOL:automatic organ mucosa of uterine tube infundibulum OBOL:automatic uterine tube infundibulum mucosa OBOL:automatic uterine tube infundibulum mucosa of organ OBOL:automatic uterine tube infundibulum mucous membrane OBOL:automatic uterine tube infundibulum organ mucosa OBOL:automatic An external genitalia that is part of a female reproductive system [Automatically generated definition]. in eutherians, this is known as the vulva in and composed of the mons pubis, the labia majora and minora, the clitoris, the vestibule of the vagina and its glands, and the opening of the urethra and of the vagina [MP:0003126] BTO:0003100 EMAPA:30984 FMA:45649 galen:FemaleExternalGenitalia external female genital organ external genitalia of female reproductive system female external genitalia uberon organa genitalia feminina externa UBERON:0005056 TODO: Relabel. Make distinct organ class. See https://github.com/obophenotype/uberon/issues/547 external female genitalia An external genitalia that is part of a female reproductive system [Automatically generated definition]. OBOL:automatic external female genital organ BTO:0003100 external genitalia of female reproductive system OBOL:automatic female external genitalia FMA:45649 organa genitalia feminina externa BTO:0003100 A gland that is part of a hemolymphoid system [Automatically generated definition]. hemopoietic or lymphoid organ EMAPA:18766 MA:0002962 hemopoietic or lymphoid gland uberon haemolymphoid system gland UBERON:0005058 hemolymphoid system gland A gland that is part of a hemolymphoid system [Automatically generated definition]. OBOL:automatic hemopoietic or lymphoid organ GO:0048534 hemopoietic or lymphoid gland haemolymphoid system gland EMAPA:18766 The median dorsal longitudinal groove formed in the embryo by the neural plate after the appearance of the neural folds. The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove]. AAO:0011071 EMAPA:35594 FMA:295624 NCIT:C34224 UMLS:C0814992 XAO:0000248 uberon UBERON:0005061 neural groove The median dorsal longitudinal groove formed in the embryo by the neural plate after the appearance of the neural folds. GO:0001842 The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove]. UMLS:C0814992 ncithesaurus:Neural_Groove One of the two elevated edges of the neural groove[GO,MP]. In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold]. EHDAA2:0001249 FMA:295618 NCIT:C34223 UMLS:C0814993 XAO:0004087 medullary fold uberon UBERON:0005062 neural fold One of the two elevated edges of the neural groove[GO,MP]. GO:0001842 MP:0011256 In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold]. UMLS:C0814993 ncithesaurus:Neural_Fold medullary fold MP:0011256 A solid rod of neurectoderm derived from the neural keel. The neural rod is roughly circular in cross section. Neural rod formation occurs during primary neurulation in teleosts[GO]. An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube[ZFIN]. An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO] EFO:0003498 TAO:0000133 ZFA:0000133 uberon neural tube rod UBERON:0005068 neural rod A solid rod of neurectoderm derived from the neural keel. The neural rod is roughly circular in cross section. Neural rod formation occurs during primary neurulation in teleosts[GO]. An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube[ZFIN]. GO:0014024 ZFA:0000133 An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000133 TAO ZFIN:curator neural tube rod GO:0014027 An anatomical boundary that adjacent_to a hindbrain and adjacent_to a spinal cord. hindbrain-spinal cord boundary region uberon UBERON:0005076 hindbrain-spinal cord boundary An anatomical boundary that adjacent_to a hindbrain and adjacent_to a spinal cord. OBOL:automatic The portion of the ureteric bud tube that contributes to the morphogenesis of the metanephros[GO]. uberon UBERON:0005080 metanephric ureteric bud The portion of the ureteric bud tube that contributes to the morphogenesis of the metanephros[GO]. GO:0035502 The portion of the ureteric bud that contributes to the morphogenesis of the ureter. The ureter ureteric bud is the initial structure that forms the ureter[GO]. uberon UBERON:0005081 ureter ureteric bud The portion of the ureteric bud that contributes to the morphogenesis of the ureter. The ureter ureteric bud is the initial structure that forms the ureter[GO]. GO:0035503 A hole in a tube[GO]. AEO:0000078 EHDAA2:0004618 RETIRED_EHDAA2:0003078 uberon UBERON:0005082 tube lumen A hole in a tube[GO]. GO:0060609 An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm[GO] consder adding placodal ectoderm as a distinct class? Also place placodal ectoderm as develops_from ectoderm; need to check taxon-appropriateness With the exception of the adenohypophysis, homologues of the nonneurogenic placodes (e.g. placodes giving rise to the teeth, hair follicles and lens), appear to be lacking in invertebrate chordates. in GO, covers optic, otic, olfactory, mammary, hair, tooth, sebaceous - and also insect structures AEO:0000218 uberon epithelial placode UBERON:0005085 ectodermal placode An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm[GO] GO:0060788 in GO, covers optic, otic, olfactory, mammary, hair, tooth, sebaceous - and also insect structures GO epithelial placode AEO:0000112 Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO]. in some organisms such as drosophila, muscles can be single cells. This class groups together all discrete muscle elements, from multicellular muscle organs in vertebrates, to individual single-cell muscles in drisophila EMAPA:32715 FBbt:00005073 FMA:30316 musculus uberon muscle muscle element UBERON:0005090 muscle structure Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO]. GO:0061061 musculus FMA:30316 . class added for consistency with GO - consider merging with kidney mesenchyme. uberon kidney anlage UBERON:0005095 kidney rudiment GO . GO:0072003 kidney anlage GOC:mtg_kidney_jan10 An epithelium that is part of a mesonephros [Automatically generated definition]. uberon UBERON:0005103 mesonephric epithelium An epithelium that is part of a mesonephros [Automatically generated definition]. OBOL:automatic A metanephric tubule is an epithelial tube that is part of the metanephros[GO]. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes.[well established][VHOG] VHOG:0001526 uberon UBERON:0005106 metanephric tubule A metanephric tubule is an epithelial tube that is part of the metanephros[GO]. GO:0072173 The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes.[well established][VHOG] 2012-09-17 VHOG:0001526 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.543 An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure[GO]. uberon UBERON:0005108 metanephric epithelium An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure[GO]. GO:0072207 Any smooth muscle tissue that is part of a metanephros. uberon UBERON:0005109 metanephric smooth muscle tissue Any smooth muscle tissue that is part of a metanephros. GO:0072208 The metanephric capsule is the tough fibrous layer surrounding the metanephros, covered in a thick layer of perinephric adipose tissue. It provides some protection from trauma and damage[GO]. UBERON:0005112 uberon UBERON:0005137 metanephric capsule The metanephric capsule is the tough fibrous layer surrounding the metanephros, covered in a thick layer of perinephric adipose tissue. It provides some protection from trauma and damage[GO]. GO:0072213 A bud is a protrusion that forms from an epithelial sheet by localized folding. BTO:0001639 uberon UBERON:0005153 epithelial bud A bud is a protrusion that forms from an epithelial sheet by localized folding. GO:0060572 Any anatomical structure that is part of the reproductive system. reproductive system element reproductive system structure uberon UBERON:0005156 reproductive structure Any anatomical structure that is part of the reproductive system. An epithelial sheet bent on a linear axis. uberon UBERON:0005157 epithelial fold An epithelial sheet bent on a linear axis. GO:0060571 A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part. we go with the FMA classification rather than the CARO one. FMA def: 'Anatomical cluster which has as direct parts cell parts from two or more cells.' AAO:0011000 CARO:0001000 FBbt:00007060 FMA:83115 multi-cell-component structure multi-cell-part structure uberon cell part cluster UBERON:0005162 multi cell part structure FMA A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part. CARO:0001000 we go with the FMA classification rather than the CARO one. FMA def: 'Anatomical cluster which has as direct parts cell parts from two or more cells.' CARO FMA multi-cell-component structure CARO:0001000 multi-cell-part structure CARO:0001000 cell part cluster FMA:83115 An organ or element that is in the abdomen. Examples: spleen, intestine, kidney, abdominal mammary gland. MA:0000522 abdomen organ uberon UBERON:0005172 abdomen element An organ or element that is in the abdomen. Examples: spleen, intestine, kidney, abdominal mammary gland. abdomen organ MA:0000522 An organ or element that is part of the adbominal segment of the organism. This region can be further subdivided into the abdominal cavity and the pelvic region. EMAPA:37062 MA:0000529 abdominal segment organ uberon UBERON:0005173 abdominal segment element An organ or element that is part of the adbominal segment of the organism. This region can be further subdivided into the abdominal cavity and the pelvic region. EMAPA:37062 MA:th abdominal segment organ MA:0000529 An organ or element that part of the dorsum of the organism. Examples: spinal cord, vertebrae, muscles of back. EMAPA:37274 MA:0001901 back organ dorsal region organ uberon UBERON:0005174 dorsal region element An organ or element that part of the dorsum of the organism. Examples: spinal cord, vertebrae, muscles of back. EMAPA:37274 MA:th back organ MA:0001901 An organ or element that part of the trunk region. The trunk region can be further subdividied into thoracic (including chest and thoracic cavity) and abdominal (including abdomen and pelbis) regions. EMAPA:37270 MA:0000516 trunk organ uberon UBERON:0005177 trunk region element An organ or element that part of the trunk region. The trunk region can be further subdividied into thoracic (including chest and thoracic cavity) and abdominal (including abdomen and pelbis) regions. EMAPA:37270 MA:th trunk organ MA:0000516 An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli. EMAPA:37273 MA:0000557 thoracic cavity organ uberon UBERON:0005178 thoracic cavity element An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli. EMAPA:37273 MA:th thoracic cavity organ MA:0000557 An organ or element that is part of the pelvic region. Examples: reproductive organs (in some organisms), urinary bladder, bones of the pelvis. EMAPA:37275 MA:0000543 pelvic element pelvis organ pelvis region organ uberon UBERON:0005179 pelvic region element An organ or element that is part of the pelvic region. Examples: reproductive organs (in some organisms), urinary bladder, bones of the pelvis. EMAPA:37275 MA:th pelvis organ MA:0000543 An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions. EMAPA:37271 MA:0000563 uberon upper body organ UBERON:0005181 thoracic segment organ An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions. EMAPA:37271 MA:th upper body organ MA:0000563 A vein that is part of a thorax [Automatically generated definition]. EMAPA:37197 MA:0002235 NCIT:C53142 UMLS:C0226629 uberon UBERON:0005194 thoracic vein A vein that is part of a thorax [Automatically generated definition]. OBOL:automatic EMAPA:37197 MA:th UMLS:C0226629 ncithesaurus:Thoracic_Vein A gland that is part of a larynx submucosa [Automatically generated definition]. EMAPA:35475 MA:0002729 uberon laryngeal submucosa gland UBERON:0005204 larynx submucosa gland A gland that is part of a larynx submucosa [Automatically generated definition]. OBOL:automatic laryngeal submucosa gland EMAPA:35475 An external ectoderm that is part of a optic eminence [Automatically generated definition]. EMAPA:16539 RETIRED_EHDAA2:0001311 VHOG:0000520 uberon UBERON:0005216 optic eminence surface ectoderm true An external ectoderm that is part of a optic eminence [Automatically generated definition]. OBOL:automatic An ectoderm that is part of a optic eminence [Automatically generated definition]. EHDAA:940 EMAPA:16539 RETIRED_EHDAA2:0001309 VHOG:0001105 uberon UBERON:0005234 optic eminence ectoderm An ectoderm that is part of a optic eminence [Automatically generated definition]. OBOL:automatic The ventral half of the developing neural tube that is the metencephalon. [Chordate_evolution_and_the_origin_of_craniates:_An_old_brain_in_a_new_head._AnaT_Rec_(New_Anat)_(2000)_261(3):_111-125, See_Butler_AB][VHOG] EHDAA2:0001154 EMAPA:17078 VHOG:0000320 metencephalon basal plate uberon UBERON:0005239 basal plate metencephalon The ventral half of the developing neural tube that is the metencephalon. [Chordate_evolution_and_the_origin_of_craniates:_An_old_brain_in_a_new_head._AnaT_Rec_(New_Anat)_(2000)_261(3):_111-125, See_Butler_AB][VHOG] 2012-09-17 VHOG:0000320 VHOG metencephalon basal plate EHDAA2:0001154 An endocardium that is part of a interventricular septum [Automatically generated definition]. TODO - split? EHDAA2:0000886 EHDAA2:0000887 FMA:83584 VHOG:0000615 endocardium of interventricular septum uberon interventricular septum endocardial tissue UBERON:0005243 interventricular septum endocardium An endocardium that is part of a interventricular septum [Automatically generated definition]. OBOL:automatic endocardium of interventricular septum FMA:83584 interventricular septum endocardial tissue VHOG:0000615 A myocardium that is part of a bulbus cordis [Automatically generated definition]. EMAPA:36488 VHOG:0000609 uberon bulbus cordis cardiac muscle UBERON:0005248 bulbus cordis myocardium A myocardium that is part of a bulbus cordis [Automatically generated definition]. OBOL:automatic bulbus cordis cardiac muscle VHOG:0000609 A renal pelvis that is part of a metanephros. The ureteric bud itself forms the collecting tubules and the ureter that drain the adult kidney. This type of kidney, called the metanephros, occurs in all adult amniotes.[well established][VHOG] VHOG:0000945 metanephros pelvis uberon UBERON:0005249 metanephric renal pelvis A renal pelvis that is part of a metanephros. OBOL:automatic The ureteric bud itself forms the collecting tubules and the ureter that drain the adult kidney. This type of kidney, called the metanephros, occurs in all adult amniotes.[well established][VHOG] 2012-09-17 VHOG:0000945 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.639 metanephros pelvis VHOG:0000945 A gland that is part of a stomodeum. check this VHOG:0000658 stomatodaeum gland uberon UBERON:0005250 stomatodeum gland A gland that is part of a stomodeum. OBOL:automatic stomatodaeum gland VHOG:0000658 Portion of primordial embryonic connective tissue of the developing head, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to head connective tissue, bone and musculature in conjunction with cranial neural crest cells. Mesoderm that will give rise, along with cranial neural crest cells, to connective tissue, bone and musculature in the head. (Source: BioGlossary, www.Biology-Text.com)[TAO] EFO:0003492 EHDAA2:0000732 EHDAA:179 EMAPA:16098 EMAPA_RETIRED:16269 FMA:76622 TAO:0000113 VHOG:0000332 ZFA:0000113 cephalic mesenchyme uberon cranial mesenchyme desmocranium UBERON:0005253 head mesenchyme EHDAA2 Portion of primordial embryonic connective tissue of the developing head, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to head connective tissue, bone and musculature in conjunction with cranial neural crest cells. ISBN:0683400088 MP:0011260 Mesoderm that will give rise, along with cranial neural crest cells, to connective tissue, bone and musculature in the head. (Source: BioGlossary, www.Biology-Text.com)[TAO] 2012-08-14 TAO:0000113 TAO ZFIN:curator cephalic mesenchyme MP:0011260 cranial mesenchyme MGI:anna desmocranium FMA:76622 Mesenchyme that is part of a developing trunk. EFO:0003485 EHDAA2:0002092 EHDAA:377 EMAPA:16177 TAO:0000081 VHOG:0000281 ZFA:0000081 uberon trunk and cervical mesenchyme UBERON:0005256 trunk mesenchyme EHDAA2 Mesenchyme that is part of a developing trunk. OBOL:automatic trunk and cervical mesenchyme EHDAA2:0002092 The posterior part of the developing vertebrate hindbrain or the corresponding part of the adult brain composed of the medulla oblongata and a portion of the fourth ventricle; as well as the glossopharyngeal nerve (CN IX), vagus nerve (CN X), accessory nerve (CN XI), hypoglossal nerve (CN XII), and a portion of the vestibulocochlear nerve (CN VIII).[BTO,WP]. The posterior of the two brain vesicles formed by specialization of the rhombencephalon in the developing embryo, it comprises the medulla oblongata. [TFD][VHOG] The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG] the terms metencephalon and myelencephalon are only meaningful in mammals and birds - Neuroanatomy of the Zebrafish Brain. Note that its not clear if this refers to the developing medulla oblongata - MA (adult) has two distinct classes BTO:0000758 CALOHA:TS-0607 CALOHA:TS-2365 DHBA:10662 EHDAA2:0001207 EHDAA:5526 EMAPA:17082 HBA:9512 MA:0000205 VHOG:0000456 uberon myelencephalon (medulla oblongata) UBERON:0005290 myelencephalon definitional The posterior part of the developing vertebrate hindbrain or the corresponding part of the adult brain composed of the medulla oblongata and a portion of the fourth ventricle; as well as the glossopharyngeal nerve (CN IX), vagus nerve (CN X), accessory nerve (CN XI), hypoglossal nerve (CN XII), and a portion of the vestibulocochlear nerve (CN VIII).[BTO,WP]. BTO:0000758 The posterior of the two brain vesicles formed by specialization of the rhombencephalon in the developing embryo, it comprises the medulla oblongata. [TFD][VHOG] 2012-09-17 VHOG:0000456 VHOG The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000456 VHOG ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.381-382, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500 myelencephalon (medulla oblongata) DHBA:10662 A portion of tissue that is part of an embryo. CALOHA:TS-2100 portion of embryonic tissue uberon developing tissue UBERON:0005291 embryonic tissue A portion of tissue that is part of an embryo. OBOL:automatic portion of embryonic tissue OBOL:automatic Portion of tissue that is contiguous with the embryo and is comprised of portions of tissue or cells that will not contribute to the embryo. BTO:0003360 CALOHA:TS-2119 EFO:0001406 MAT:0000061 MIAA:0000061 extra-embryonic tissue uberon UBERON:0005292 extraembryonic tissue Portion of tissue that is contiguous with the embryo and is comprised of portions of tissue or cells that will not contribute to the embryo. The endothelial lining of the endocardium. FMA:83596 endocardium endothelium endothelium of endocardium uberon UBERON:0005316 endocardial endothelium The endothelial lining of the endocardium. UBERON:cjm endocardium endothelium FMA:83596 endothelium of endocardium FMA:83596 An pulmonary artery endothelium is an epithelium that lines the pulmonary artery[GO]. BTO:0000137 pulmonary artery endothelial tube uberon UBERON:0005317 pulmonary artery endothelium An pulmonary artery endothelium is an epithelium that lines the pulmonary artery[GO]. GO:0061155 pulmonary artery endothelial tube GO:0061155 . uberon UBERON:0005321 mesonephric smooth muscle tissue . GO:0061214 Mesonephric mesenchyme is the tissue made up of loosely connected mesenchymal cells in the mesonephros[GO]. AAO:0011062 EHDAA2:0001132 EMAPA:16745 XAO:0000291 uberon UBERON:0005323 mesonephric mesenchyme Mesonephric mesenchyme is the tissue made up of loosely connected mesenchymal cells in the mesonephros[GO]. GO:0061219 A ventricular outflow tract is a portion of either the left ventricle or right ventricle of the heart through which blood passes in order to enter the great arteries. The right ventricular outflow tract (RVOT) is an infundibular extension of the ventricular cavity which connects to the pulmonary artery. The left ventricular outflow tract (LVOT), which connects to the aorta, is nearly indistinguishable from the rest of the ventricle[WP]. FMA:13225 XAO:0004140 heart ventricle outflow tract outflow part of ventricle ventricular outflow tract uberon UBERON:0005337 outflow tract of ventricle A ventricular outflow tract is a portion of either the left ventricle or right ventricle of the heart through which blood passes in order to enter the great arteries. The right ventricular outflow tract (RVOT) is an infundibular extension of the ventricular cavity which connects to the pulmonary artery. The left ventricular outflow tract (LVOT), which connects to the aorta, is nearly indistinguishable from the rest of the ventricle[WP]. heart ventricle outflow tract MP:0010224 ventricular outflow tract An outflow tract that is part of a aorta. merge with LVOT? EHDAA2:0001353 EMAPA:17329 MA:0000101 VHOG:0001394 uberon UBERON:0005338 outflow tract aortic component An outflow tract that is part of a aorta. OBOL:automatic merge with RVOT? EHDAA2:0001359 EHDAA:4401 EMAPA:17330 MA:0000102 VHOG:0001395 uberon UBERON:0005339 outflow tract pulmonary component the group of sensory neuron cell bodies associated with the vagus nerve gX EMAPA:16798 FMA:53472 MA:0001081 TAO:0007067 VHOG:0000684 ZFA:0007067 ganglion of vagus nerve right glossopharyngeal ganglion vagal ganglion vagus ganglion vagus neural ganglion uberon vagus X UBERON:0005362 vagus X ganglion ZFA the group of sensory neuron cell bodies associated with the vagus nerve ISBN:0-683-40008-8 MP:0001100 gX ZFA:0007067 ganglion of vagus nerve FMA:53472 right glossopharyngeal ganglion FMA:53472 vagal ganglion ZFA:0007067 vagus neural ganglion FMA:53472 vagus X EMAPA:16798 An epithelium that lines the nasal cavity. this class may in future be split into the embryonic precursor of the oronasal membrane and the structure that is part of the mucosa in the developed organism CALOHA:TS-0656 EHDAA2:0001227 EHDAA:6803 EMAPA:17605 FMA:63140 MA:0001324 NCIT:C49261 UMLS:C1709151 VHOG:0000501 nasal epithelium uberon nasal mucosa UBERON:0005384 nasal cavity epithelium An epithelium that lines the nasal cavity. UMLS:C1709151 ncithesaurus:Nasal_Cavity_Epithelium nasal epithelium FMA:63140 nasal mucosa MA:0001324 An array of photoreceptors and any supporting cells found in an eye. FBbt:00004200 light-sensitive tissue uberon UBERON:0005388 photoreceptor array An array of photoreceptors and any supporting cells found in an eye. A transparent structure that is part of a visual sense organ, the function of which is to direct or focus light onto a photoreceptor array. directing or focusing light onto light receptors lens uberon UBERON:0005389 transparent eye structure A transparent structure that is part of a visual sense organ, the function of which is to direct or focus light onto a photoreceptor array. One of: the common carotid artery, or its branches, the external and internal carotid arteries. This is a generic grouping class that is the superclass of the trunks/branches of the common carotid artery. Note that AOs vary widely in how they divide up and generalize arteries Artery originating at the junction of the first two aortic arches and supplying the anterior brain. Kimmel et al, 1995.[TAO] AAO:0010217 BTO:0000168 CALOHA:TS-0116 EFO:0000818 EHDAA:6385 EMAPA:18609 EV:0100379 FMA:70504 GAID:478 MA:0001925 MAT:0000501 MESH:D002339 NCIT:C12687 OpenCyc:Mx4rvg7rcJwpEbGdrcN5Y29ycA TAO:0000097 UMLS:C0007272 VHOG:0000266 ZFA:0000097 galen:CarotidArtery carotid carotid artery subdivision of common carotid artery uberon common carotid arterial subdivision UBERON:0005396 carotid artery segment FMA One of: the common carotid artery, or its branches, the external and internal carotid arteries. Artery originating at the junction of the first two aortic arches and supplying the anterior brain. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000097 TAO ZFIN:curator UMLS:C0007272 ncithesaurus:Carotid_Artery carotid AAO:0010217 carotid artery MA:0001925 subdivision of common carotid artery FMA:70504 common carotid arterial subdivision FMA:70504 A sex gland that is part of a female reproductive system. BTO:0000254 MA:0000383 uberon UBERON:0005398 female reproductive gland A sex gland that is part of a female reproductive system. OBOL:automatic The part of the digestive system that excludes the hepatobiliary system. the decision to split digestive and gastrointestinal in this way may be revisited. As it currently stands, this class more closely aligns what MA calls the alimentary system The system that includes the esophagus, stomach, small and large intestine, anus, liver, biliary tract, and pancreas[ncithesaurus:Gastrointestinal_System]. All metazoans (with degenerate exceptions) have some sort of digestive cavity with a means of entrance to and exit from it.[well established][VHOG] that many anatomy ontologies consider this synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class. We have one entity that is part of both gastrointestinal and hepatobiliary systems: hepatopancreatic ampulla. BTO:0000058 CALOHA:TS-0407 EHDAA2:0000110 EHDAA:514 EMAPA:16246 EV:0100056 FMA:71132 GAID:294 MA:0000323 MESH:A03.492 NCIT:C12378 UMLS:C0012240 VHOG:0000412 galen:GastrointestinalTract uberon GI tract alimentary system alimentary tract gastro-intestinal system gastroenterological system gastrointestinal (GI) tract gastrointestinal system gastrointestinal tract UBERON:0005409 alimentary part of gastrointestinal system The part of the digestive system that excludes the hepatobiliary system. The system that includes the esophagus, stomach, small and large intestine, anus, liver, biliary tract, and pancreas[ncithesaurus:Gastrointestinal_System]. ncithesaurus:Gastrointestinal_System All metazoans (with degenerate exceptions) have some sort of digestive cavity with a means of entrance to and exit from it.[well established][VHOG] 2012-09-17 VHOG:0000412 VHOG ISBN:978-0721676685 Sherwood Romer A and Parsons T, Vertebrate body (1977) p.3 that many anatomy ontologies consider this synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class. We have one entity that is part of both gastrointestinal and hepatobiliary systems: hepatopancreatic ampulla. MA UMLS:C0012240 ncithesaurus:Gastrointestinal_System GI tract GAID:294 alimentary system MA:0000323 alimentary tract MA:0000323 gastro-intestinal system FMA:71132 gastroenterological system UBERON:cjm gastrointestinal (GI) tract GAID:294 gastrointestinal system FMA:71132 gastrointestinal tract FMA:71132 A limb bud that develops into a forelimb or pectoral fin. Fin bud that develops into the pectoral fin.[TAO] While the skeletons of teleost pectoral fins and tetrapod forelimbs are homologous at the level of endoskeletal radials, teleosts and tetrapods do not share homologous skeletal elements at the level of 'individuated' pro-, meso-, and metapterygia. Among osteichthyans, only basal actinopterygians retain the full complement of elements present in non-osteichthyan gnathostomes.[uncertain][VHOG] EFO:0003430 TAO:0000141 VHOG:0001754 VHOG_RETIRED:0001259 ZFA:0000141 forelimb - pectoral fin bud uberon pectoral fin bud pectoral fin buds UBERON:0005419 at this time we have no need to name a more specific 'pectoral fin bud' class, but we may in future pectoral appendage bud A limb bud that develops into a forelimb or pectoral fin. OBOL:automatic Fin bud that develops into the pectoral fin.[TAO] 2012-08-14 TAO:0000141 TAO ZFIN:curator While the skeletons of teleost pectoral fins and tetrapod forelimbs are homologous at the level of endoskeletal radials, teleosts and tetrapods do not share homologous skeletal elements at the level of 'individuated' pro-, meso-, and metapterygia. Among osteichthyans, only basal actinopterygians retain the full complement of elements present in non-osteichthyan gnathostomes.[uncertain][VHOG] 2012-09-17 VHOG:0001754 VHOG DOI:10.1002/jmor.10264 Davis MC, Shubin NH, Force A, Pectoral fin and girdle development in the basal actinopterygians Polyodon spathula and Acipenser transmontanus. Journal of Morphology (2004) forelimb - pectoral fin bud VHOG:0001754 pectoral fin bud TAO:0000141 pectoral fin buds TAO:0000141 A limb bud that develops into a hindlimb or pelvic fin. Fin bud that develops into the pelvic fin.[TAO] Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] EFO:0003469 TAO:0001384 VHOG:0001260 ZFA:0001384 hindlimb/pelvic fin bud uberon pelvic fin bud pelvic fin buds UBERON:0005420 at this time we have no need to name a more specific 'pelvic fin bud' class, but we may in future pelvic appendage bud A limb bud that develops into a hindlimb or pelvic fin. OBOL:automatic Fin bud that develops into the pelvic fin.[TAO] 2012-08-14 TAO:0001384 TAO ZFIN:curator Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] 2012-09-17 VHOG:0001260 VHOG ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268 hindlimb/pelvic fin bud VHOG:0001260 pelvic fin bud TAO:0001384 pelvic fin buds ZFA:0001384 An apical ectodermal ridge that is part of a pectoral appendage bud. An ectodermal thickening at the end of the forelimb bud in the developing embryo. [TFD][VHOG] Apical ectodermal ridge that is part of the pectoral fin bud.[TAO] Pectoral and pelvic fins are homologous to the tetrapod fore and hindlimb, respectively. (...) The zebrafish AER [apical ectodermal ridge] is an apical ectodermal thickening at the distal tip of the fin bud and consists of wedge-shaped cells of the basal stratum. The AER is observed only transiently, and from 36 hpf onwards the cells of this region form the apical fold (AF), which consists of a dorsal and a ventral layer of cylindrically-shaped ectodermal cells extending from the anterior to the posterior fin margin. Despite the change in shape, the AF still carries out the same functions as the AER. Indeed, although the AER receives its name from its characteristic shape, being composed of a pseudostratified ectoderm in the chicken and a polystratified ectoderm in the mouse, this independence of AER morphology from its function is also observed in tetrapods. The AF also expresses similar molecular markers to the tetrapod AER, suggesting that it fulfills similar functions in the fin as the AER does in tetrapod limbs.[well established][VHOG] EFO:0003487 EHDAA2:0000138 EMAPA:16778 TAO:0000085 TAO:0000736 VHOG:0001064 ZFA:0000085 AER forelimb apical ectodermal ridge forelimb apical ectodermal ridge pectoral fin bud upper limb bud apical ectodermal ridge wing AER wing apical ectodermal ridge uberon aer pectoral fin apical ectodermal ridge pectoral fin apical fold pectoral fin UBERON:0005421 pectoral appendage apical ectodermal ridge EHDAA2 An apical ectodermal ridge that is part of a pectoral appendage bud. OBOL:automatic An ectodermal thickening at the end of the forelimb bud in the developing embryo. [TFD][VHOG] 2012-09-17 VHOG:0001064 VHOG Apical ectodermal ridge that is part of the pectoral fin bud.[TAO] 2012-08-14 TAO:0000085 TAO ZFIN:curator Pectoral and pelvic fins are homologous to the tetrapod fore and hindlimb, respectively. (...) The zebrafish AER [apical ectodermal ridge] is an apical ectodermal thickening at the distal tip of the fin bud and consists of wedge-shaped cells of the basal stratum. The AER is observed only transiently, and from 36 hpf onwards the cells of this region form the apical fold (AF), which consists of a dorsal and a ventral layer of cylindrically-shaped ectodermal cells extending from the anterior to the posterior fin margin. Despite the change in shape, the AF still carries out the same functions as the AER. Indeed, although the AER receives its name from its characteristic shape, being composed of a pseudostratified ectoderm in the chicken and a polystratified ectoderm in the mouse, this independence of AER morphology from its function is also observed in tetrapods. The AF also expresses similar molecular markers to the tetrapod AER, suggesting that it fulfills similar functions in the fin as the AER does in tetrapod limbs.[well established][VHOG] 2012-09-17 VHOG:0001064 VHOG AER forelimb VHOG:0001064 apical ectodermal ridge forelimb VHOG:0001064 apical ectodermal ridge pectoral fin bud ZFA:0000085 upper limb bud apical ectodermal ridge EHDAA2:0000138 wing AER Giesha:syn wing apical ectodermal ridge aer pectoral fin TAO:0000085 apical ectodermal ridge pectoral fin TAO:0000085 apical fold pectoral fin TAO:0000085 An apical ectodermal ridge that is part of a pelvic appendage bud. An ectodermal thickening at the end of the hindlimb bud in the developing embryo. [TFD][VHOG] Apical ectodermal ridge that is part of the pelvic fin bud.[TAO] Pectoral and pelvic fins are homologous to the tetrapod fore and hindlimb, respectively. (...) The zebrafish AER [apical ectodermal ridge] is an apical ectodermal thickening at the distal tip of the fin bud and consists of wedge-shaped cells of the basal stratum. The AER is observed only transiently, and from 36 hpf onwards the cells of this region form the apical fold (AF), which consists of a dorsal and a ventral layer of cylindrically-shaped ectodermal cells extending from the anterior to the posterior fin margin. Despite the change in shape, the AF still carries out the same functions as the AER. Indeed, although the AER receives its name from its characteristic shape, being composed of a pseudostratified ectoderm in the chicken and a polystratified ectoderm in the mouse, this independence of AER morphology from its function is also observed in tetrapods. The AF also expresses similar molecular markers to the tetrapod AER, suggesting that it fulfills similar functions in the fin as the AER does in tetrapod limbs.[well established][VHOG] EFO:0003681 EHDAA2:0003194 EMAPA:16892 TAO:0001385 VHOG:0001066 ZFA:0001385 apical ectodermal ridge hind limb apical ectodermal ridge hindlimb lower lmb bud apical ectodermal ridge uberon AER hindlimb apical ectodermal ridge pelvic fin bud leg AER UBERON:0005422 pelvic appendage apical ectodermal ridge EHDAA2 An apical ectodermal ridge that is part of a pelvic appendage bud. OBOL:automatic An ectodermal thickening at the end of the hindlimb bud in the developing embryo. [TFD][VHOG] 2012-09-17 VHOG:0001066 VHOG Apical ectodermal ridge that is part of the pelvic fin bud.[TAO] 2012-08-14 TAO:0001385 TAO ZIFIN:curator Pectoral and pelvic fins are homologous to the tetrapod fore and hindlimb, respectively. (...) The zebrafish AER [apical ectodermal ridge] is an apical ectodermal thickening at the distal tip of the fin bud and consists of wedge-shaped cells of the basal stratum. The AER is observed only transiently, and from 36 hpf onwards the cells of this region form the apical fold (AF), which consists of a dorsal and a ventral layer of cylindrically-shaped ectodermal cells extending from the anterior to the posterior fin margin. Despite the change in shape, the AF still carries out the same functions as the AER. Indeed, although the AER receives its name from its characteristic shape, being composed of a pseudostratified ectoderm in the chicken and a polystratified ectoderm in the mouse, this independence of AER morphology from its function is also observed in tetrapods. The AF also expresses similar molecular markers to the tetrapod AER, suggesting that it fulfills similar functions in the fin as the AER does in tetrapod limbs.[well established][VHOG] 2012-09-17 VHOG:0001066 VHOG apical ectodermal ridge hind limb VHOG:0001066 apical ectodermal ridge hindlimb VHOG:0001066 lower lmb bud apical ectodermal ridge EHDAA2:0003194 AER hindlimb VHOG:0001066 apical ectodermal ridge pelvic fin bud TAO:0001385 AEO:0000125 CALOHA:TS-2122 EHDAA2:0003125 FBbt:00007006 FMA:292313 MIAA:0000019 uberon developing structure developmental structure developmental tissue UBERON:0005423 developing anatomical structure developmental tissue MIAA:0000019 Portion of tissue that is the inner layer of the optic cup and will become the neural retina. (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] EHDAA2:0001304 EMAPA:16675 TAO:0001071 VHOG:0000490 ZFA:0001071 future neural retina future retinal neural layer inner layer optic cup optic cup inner layer presumptive retinas uberon future NR future neural epithelium future neural layer presumptive retina UBERON:0005425 presumptive neural retina Portion of tissue that is the inner layer of the optic cup and will become the neural retina. ZFIN:curator (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] 2012-09-17 VHOG:0000490 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 inner layer optic cup ZFA:0001071 optic cup inner layer EHDAA2:0001304 presumptive retinas ZFA:0001071 future neural epithelium EMAPA:16675 future neural layer EMAPA:16675 presumptive retina TAO:0001071 Portion of tissue that gives rise to the lens. A vesicle formed from the lens pit of the embryo, developing into the crystalline lens. [TFD][VHOG] (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG] the lens of zebrafish (and other teleosts) forms from delamination of cells from the lens placode; thus, there is no formation of a hollow lens vesicle, in contrast to the situation in mammals and birds (Glass and Dahm, 2004) [PMID:16496288] The lens of the zebrafish forms by delamination of lens placodal cells and not through invagination. This results in a solid spherical mass as opposed to a hollow lens vesicle. Detachment of the solid lens vesicle of zebrafish at 24b26 hpf is accomplished in part by apoptosis, similar to mammals EHDAA2:0000983 EHDAA:4737 EMAPA:17163 TAO:0002205 VHOG:0001163 ZFA:0001679 hollow lens vesicle solid lens vesicle uberon immature lens lens mass presumptive lens UBERON:0005426 lens vesicle Portion of tissue that gives rise to the lens. ZFIN:curator A vesicle formed from the lens pit of the embryo, developing into the crystalline lens. [TFD][VHOG] 2012-09-17 VHOG:0001163 VHOG (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG] 2012-09-17 VHOG:0001163 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 the lens of zebrafish (and other teleosts) forms from delamination of cells from the lens placode; thus, there is no formation of a hollow lens vesicle, in contrast to the situation in mammals and birds (Glass and Dahm, 2004) [PMID:16496288] The lens of the zebrafish forms by delamination of lens placodal cells and not through invagination. This results in a solid spherical mass as opposed to a hollow lens vesicle. Detachment of the solid lens vesicle of zebrafish at 24b26 hpf is accomplished in part by apoptosis, similar to mammals ZFA hollow lens vesicle solid lens vesicle ZFA:0001679 immature lens ZFA:0001679 lens mass ZFA:0001679,ZFIN:ZDB-PUB-091023-49 presumptive lens ZFA:0001679 Portion of tissue that is part of the eye and gives rise to the mature, fully layered cornea. TAO:0002188 ZFA:0001688 uberon UBERON:0005427 corneal primordium ZFA Obol ZFA Portion of tissue that is part of the eye and gives rise to the mature, fully layered cornea. ZFIN:ZDB-PUB-061010-3 Vagal neural crest is adjacent to the first seven somites gives rise to both ganglionic and ectomesenchymal derivatives[ZFA]. Vagal neural crest is adjacent to the first seven somites gives rise to both ganglionic and ectomesenchymal derivatives.[TAO] We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] In chicken fate mapping studies it was found to originate from neural crest residing between Somite 1-7 (S1-7); In mouse it is considered to be derived from rhombencephalic (post otic) neural crest cells and trunk neural crest cells (anterior to S5) EHDAA2:0002156 EHDAA:669 TAO:0000818 VHOG:0001208 XAO:0004191 ZFA:0000818 VNC uberon enteric neural crest post-otic neural crest UBERON:0005428 vagal neural crest Vagal neural crest is adjacent to the first seven somites gives rise to both ganglionic and ectomesenchymal derivatives[ZFA]. ZFIN:curator Vagal neural crest is adjacent to the first seven somites gives rise to both ganglionic and ectomesenchymal derivatives.[TAO] 2012-08-14 TAO:0000818 TAO ZFIN:curator We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] 2012-09-17 VHOG:0001208 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 In chicken fate mapping studies it was found to originate from neural crest residing between Somite 1-7 (S1-7); In mouse it is considered to be derived from rhombencephalic (post otic) neural crest cells and trunk neural crest cells (anterior to S5) filemaps.com VNC XAO:0004191 post-otic neural crest ZFA:0000818 The dilated structure that is lined by endothelial cells and located at the arterial pole of the heart just above (distal to) the truncus arteriosus in mammalian embryos; it is the primordial vascular channel from which the aortic arches (and eventually the dorsal aortae) arise; the aortic sac is homologous to the ventral aorta of gill-bearing vertebrates the merged ventral aortae of the embryo which supplies blood to the aortic arches[TMD][http://medical-dictionary.thefreedictionary.com/aortic+sac]. EHDAA2:0004145 EHDAA:9826 EMAPA:36461 FMA:71008 RETIRED_EHDAA2:0000133 saccus aorticus uberon UBERON:0005432 aortic sac EHDAA2 EHDAA2 The dilated structure that is lined by endothelial cells and located at the arterial pole of the heart just above (distal to) the truncus arteriosus in mammalian embryos; it is the primordial vascular channel from which the aortic arches (and eventually the dorsal aortae) arise; the aortic sac is homologous to the ventral aorta of gill-bearing vertebrates MP:0012510 the merged ventral aortae of the embryo which supplies blood to the aortic arches[TMD][http://medical-dictionary.thefreedictionary.com/aortic+sac]. saccus aorticus The jugular foramen is a large aperture in the base of the skull. It is located behind the carotid canal and is formed in front by the petrous portion of the temporal, and behind by the occipital; it is generally larger on the right than on the left side Large foramen that houses the glossopharyngeal and vagus nerves and is located inside the condyloid fossa.[AAO] One of a pair of openings between the lateral part of the occipital bone and the petrous part of the temporal bones in the skull. The foramen contains the inferior petrosal sinus; the transverse sinus; some meningeal branches of the occipital and ascending pharyngeal arteries; and the glossopharyngeal, vagus, and accessory nerves. [Free_Online_Medical_Dictionary] relationship loss: subclass braincase and otic capsule opening (AAO:0000051)[AAO] AAO:0000249 EHDAA2:0000893 EHDAA:10631 EMAPA:18713 FMA:56432 NCIT:C12496 UMLS:C0222712 VHOG:0001113 Posterior lacerate foramen uberon foramen jugulare UBERON:0005456 jugular foramen The jugular foramen is a large aperture in the base of the skull. It is located behind the carotid canal and is formed in front by the petrous portion of the temporal, and behind by the occipital; it is generally larger on the right than on the left side Large foramen that houses the glossopharyngeal and vagus nerves and is located inside the condyloid fossa.[AAO] 2012-06-20 AAO:0000249 AAO AAO:LAP One of a pair of openings between the lateral part of the occipital bone and the petrous part of the temporal bones in the skull. The foramen contains the inferior petrosal sinus; the transverse sinus; some meningeal branches of the occipital and ascending pharyngeal arteries; and the glossopharyngeal, vagus, and accessory nerves. [Free_Online_Medical_Dictionary] 2012-09-17 VHOG:0001113 VHOG relationship loss: subclass braincase and otic capsule opening (AAO:0000051)[AAO] 2012-06-20 AAO:0000249 AAO UMLS:C0222712 ncithesaurus:Jugular_Foramen Posterior lacerate foramen FMA:56432 foramen jugulare A longitudinal groove in the neural tube wall that divides the neural tube into dorsal (alar) and ventral (basal) halves (dorsal receives input from sensory neurons, ventral effects motor functions); stretches from the mesencephalon caudad[TMD]. sulcus limitans BAMS:slim BAMS:slm neural tube lateral wall sulcus limitans uberon UBERON:0005478 sulcus limitans of neural tube EHDAA2 A longitudinal groove in the neural tube wall that divides the neural tube into dorsal (alar) and ventral (basal) halves (dorsal receives input from sensory neurons, ventral effects motor functions); stretches from the mesencephalon caudad[TMD]. neural tube lateral wall sulcus limitans EHDAA2:0001265 Cranial neural crest which gives rise to the glossopharyngeal ganglion. EHDAA2:0000714 EHDAA:660 TAO:0007066 ZFA:0007066 uberon UBERON:0005491 glossopharyngeal neural crest Cranial neural crest which gives rise to the glossopharyngeal ganglion. ZFA:0007066 Portion of tissue on the side of the lumen of the neural tube. EHDAA2:0001257 EHDAA:2873 EHDAA:912 EMAPA:16166 TAO:0001435 VHOG:0000513 ZFA:0001435 lateral wall neural tube uberon UBERON:0005496 neural tube lateral wall Portion of tissue on the side of the lumen of the neural tube. ZFA:0001435 lateral wall neural tube ZFA:0001435 todo - epidermis? todo - track down EHDAA2 class in new release In the early gastrula of vertebrates, factors from the organizer (e.g. noggin, chordin, and follistatin in Xenopus) antagonize the epidermalizing factor bone morphogenetic protein 4 (BMP4), thus dividing the epiblast into neuroectoderm. In Drosophila, decapentaplegic, the homologue of BMP4, interacts similarly with the protein short gastrulation, the homologue of chordin. Thus, a comparable molecular mechanism for distinguishing non-neural ectoderm from neural ectoderm was probably present in the common ancestor of all bilaterally symmetrical animals.[well established][VHOG] After gastrulation, neural crest cells are specified at the border of the neural plate and the non-neural ectoderm. EFO:0003643 EHDAA:257 EMAPA:16074 RETIRED_EHDAA2:0001273 TAO:0001178 VHOG:0001372 XAO:0004091 ZFA:0001178 non neural ectoderm epidermal ectoderm epithelial ectoderm uberon surface ectoderm ventral ectoderm UBERON:0005497 Gene notes: One of the first genes to be expressed in nonneural ectoderm in amphioxus is BMP2/4 (Panopoulou et al. 1998). BMP2/4 homologues appear to have a very ancient role in distinguishing neural from nonneural ectoderm; in Drosophila as well as in amphioxus and vertebrates, BMP2/4 homologues are expressed in nonneural ectoderm and function in distinguishing neural from nonneural ectoderm (Francois & Bier, 1995 ; Sasai et al. 1995 ; Wilson & Hemmati-Brivanlou, 1995; Panopoulou et al. 1998). A change in level of BMP2/4 from very high in nonneural ectoderm to low in neural ectoderm appears to be a key factor in development of neural crest (Baker & Bronner-Fraser,1997a,1997b;Erickson&Reedy,1998;Marchantet al.1998 ;Selleck et al. 1998). non-neural ectoderm ZFA In the early gastrula of vertebrates, factors from the organizer (e.g. noggin, chordin, and follistatin in Xenopus) antagonize the epidermalizing factor bone morphogenetic protein 4 (BMP4), thus dividing the epiblast into neuroectoderm. In Drosophila, decapentaplegic, the homologue of BMP4, interacts similarly with the protein short gastrulation, the homologue of chordin. Thus, a comparable molecular mechanism for distinguishing non-neural ectoderm from neural ectoderm was probably present in the common ancestor of all bilaterally symmetrical animals.[well established][VHOG] 2012-09-17 VHOG:0001372 VHOG DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999) non neural ectoderm ZFA:0001178 epidermal ectoderm epithelial ectoderm surface ectoderm ventral ectoderm ZFA:0001178 Multi-tissue structure that arises from the heart rudiment and will become the heart tube. EHDAA2:0001512 EHDAA:424 EHDAA:436 EMAPA:16215 FMA:321916 TAO:0000149 ZFA:0000149 primitive heart tube early primitive heart tube uberon UBERON:0005498 primitive heart tube ZFA Multi-tissue structure that arises from the heart rudiment and will become the heart tube. ZFA:0000149 primitive heart tube EMAPA:16215 early primitive heart tube EMAPA:16208 A neural tube lateral wall that is part of a rhombomere. EMAPA:32819 EMAPA:35364 uberon future hindbrain lateral wall UBERON:0005501 rhombomere lateral wall A neural tube lateral wall that is part of a rhombomere. OBOL:automatic future hindbrain lateral wall EMAPA:35364 Cranial neural crest which gives rise to the trigeminal ganglion. todo - compare ZFA and EHDAA2 representation We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] EFO:0003484 EHDAA2:0002083 EHDAA:667 EMAPA:16170 TAO:0000080 VHOG:0000269 ZFA:0000080 uberon UBERON:0005563 trigeminal neural crest ZFA EHDAA2 Cranial neural crest which gives rise to the trigeminal ganglion. ZFA:0000080 We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] 2012-09-17 VHOG:0000269 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 Portion of tissue that gives rise to the immature gonad. Immature reproductive tissue that has not undergone final maturation into either testis or ovary.[TAO] this is a very broad grouping class EFO:0003651 EHDAA:5927 EMAPA:17204 RETIRED_EHDAA2:0002148 TAO:0001262 WBbt:0008366 ZFA:0001262 future gonad gonadal primordium primitive gonad undifferentiated gonad uberon immature gonad UBERON:0005564 gonad primordium Obol ZFA Portion of tissue that gives rise to the immature gonad. ZFA:0001262 Immature reproductive tissue that has not undergone final maturation into either testis or ovary.[TAO] 2012-08-14 TAO:0001262 TAO ZFIN:curator future gonad gonadal primordium ZFA:0001262 primitive gonad undifferentiated gonad ZFA:0001262 immature gonad Cranial neural crest that gives rise to the facio-acoustic ganglion. We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] EHDAA2:0000492 EHDAA:658 EMAPA:16312 TAO:0000762 VHOG:0000268 ZFA:0000762 facio acoustic neural crest uberon UBERON:0005565 facio-acoustic neural crest EHDAA2 EHDAA2 Cranial neural crest that gives rise to the facio-acoustic ganglion. ZFA:0000762 We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] 2012-09-17 VHOG:0000268 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 facio acoustic neural crest ZFA:0000762 Somite located in the head region, caudal to the otic vesicle in humans this includes somites 1-4 They provide the epaxial and hypaxial muscles of the neck, the pharyngeal and laryngeal muscles that develop in the caudal branchial arches and the musculature of the tongue. Despite their localisation in the head, myogenic precursors from occipital somites essentially follow the trunk programmes (E. H. Walters and S. D., unpublished). during evolution, have been secondarily incorporated into the head (Gans and Northcutt, 1983) EHDAA2 has both 'head somite' and 'head somite group', with part_of and develops_from for latter EHDAA2:0003437 EMAPA:16172 XAO:0000313 occipital somite uberon cranial somite UBERON:0005594 head somite EHDAA2 EHDAA2 Somite located in the head region, caudal to the otic vesicle They provide the epaxial and hypaxial muscles of the neck, the pharyngeal and laryngeal muscles that develop in the caudal branchial arches and the musculature of the tongue. Despite their localisation in the head, myogenic precursors from occipital somites essentially follow the trunk programmes (E. H. Walters and S. D., unpublished). during evolution, have been secondarily incorporated into the head (Gans and Northcutt, 1983) EHDAA2 has both 'head somite' and 'head somite group', with part_of and develops_from for latter EHDAA2 occipital somite XAO:0000313 cranial somite XAO:0000313 A pair of lateral diverticula just over the liver rudiment representing the primordia of the lungs, formed by the floor of the foregut just anterior to the liver diverticulum. UBERON:3010717 AAO:0011059 EFO:0002578 EMAPA:36007 XAO:0001002 uberon lateral diverticula lung diverticulum lung endoderm UBERON:0005597 lung primordium XAO XAO A pair of lateral diverticula just over the liver rudiment representing the primordia of the lungs, formed by the floor of the foregut just anterior to the liver diverticulum. XAO:0001002 lateral diverticula XAO:0001002 lung diverticulum AAO:3010717 lung endoderm EFO:0002578 A somite that is part of a trunk. AAO:0010385 EHDAA2:0003438 EMAPA:16184 XAO:0000314 uberon UBERON:0005598 trunk somite A somite that is part of a trunk. OBOL:automatic Any of the three veins including the common, external and internal iliac veins. EHDAA2:0000811 EMAPA:37151 MA:0002142 MESH:D007084 NCIT:C12734 UMLS:C0020888 uberon pelvic vein UBERON:0005610 iliac vein Any of the three veins including the common, external and internal iliac veins. ncithesaurus:Iliac_Vein EMAPA:37151 MA:th UMLS:C0020888 ncithesaurus:Iliac_Vein A study of embryos shows that in all vertebrates six arterial arches link the ventral aorta with a pair of lateral dorsal aortae on each side of the body. The latter unite posteriorly to form a single median dorsal aorta wich takes blood to the body.[well established][VHOG] Contributes to the arch of aorta in humans EHDAA2:0000936 EHDAA:404 EMAPA:16205 MA:0000478 VHOG:0000484 uberon UBERON:0005613 left dorsal aorta A study of embryos shows that in all vertebrates six arterial arches link the ventral aorta with a pair of lateral dorsal aortae on each side of the body. The latter unite posteriorly to form a single median dorsal aorta wich takes blood to the body.[well established][VHOG] 2012-09-17 VHOG:0000484 VHOG ISBN:978-0174480198 Roberts MBV, Biology: a functional approach (1986) p.572 Contributes to the arch of aorta in humans A layer of cuboidal epithelial cells bounded anteriorly by the capsule of the lens and posteriorly by the lens cortex. Cells of the subcapsular epithelium (or anterior lens cells) are mitotically active. In adult individuals they only cover the anterior 'hemisphere' of the lens. As they divide, cells gradually move towards the equator of the lens where they tranform into lens fibres. The apical part of the gradually elongating cell extends between the subcapsular epithelium and adjacent lens fibres towards the anterior pole of the lens. The basal part extends towards the posterior pole. The nucleus remains close to the equatorial plane of the lens - http://www.lab.anhb.uwa.edu.au/mb140/corepages/eye/eye.htm lens epithelium EHDAA2:0000984 EHDAA:9059 EMAPA:17304 EMAPA:17839 FMA:70612 MA:0001302 NCIT:C33641 RETIRED_EHDAA2:0000976 UMLS:C1182652 VHOG:0001425 lens subcapsular epithelium subcapsular lens epithelium uberon anterior epithelium of lens vesicle anterior surface of lens UBERON:0005614 lens anterior epithelium A layer of cuboidal epithelial cells bounded anteriorly by the capsule of the lens and posteriorly by the lens cortex. UMLS:C1182652 ncithesaurus:Subcapsular_Epithelium_of_the_Lens lens subcapsular epithelium subcapsular lens epithelium FMA:70612 anterior epithelium of lens vesicle EMAPA:17304 anterior surface of lens FMA:58889 Arteries which arise from the abdominal aorta and distribute to most of the intestines. includes posterior and anterior mesenteric arteries, which branch from the dorsal aorta (see Kardong), and superior and inferior mesenteric arteries BTO:0000779 EHDAA2:0001123 EHDAA:4343 EMAPA:17312 MA:0002003 MESH:D008638 NCIT:C52975 UMLS:C0025465 VHOG:0001117 XAO:0000370 uberon UBERON:0005616 mesenteric artery Arteries which arise from the abdominal aorta and distribute to most of the intestines. MESH:A07.231.114.565 UMLS:C0025465 ncithesaurus:Mesenteric_Artery A vein that returns blood from the intestines. In humans the inferior mesenteric vein empties into the splenic vein, the superior mesenteric vein joins the splenic vein to form the portal vein BTO:0002781 EHDAA:4442 EMAPA:17348 MA:0002177 MESH:D008642 NCIT:C53055 RETIRED_EHDAA2:0001125 UMLS:C0025473 uberon intestinal vein UBERON:0005617 mesenteric vein A vein that returns blood from the intestines. MESH:A07.231.908.670.385 UMLS:C0025473 ncithesaurus:Mesenteric_Vein intestinal vein A study of embryos shows that in all vertebrates six arterial arches link the ventral aorta with a pair of lateral dorsal aortae on each side of the body. The latter unite posteriorly to form a single median dorsal aorta wich takes blood to the body.[well established][VHOG] Normally regresses in humans EHDAA2:0001720 EHDAA:406 EMAPA:16206 MA:0000479 VHOG:0000485 uberon UBERON:0005622 right dorsal aorta A study of embryos shows that in all vertebrates six arterial arches link the ventral aorta with a pair of lateral dorsal aortae on each side of the body. The latter unite posteriorly to form a single median dorsal aorta wich takes blood to the body.[well established][VHOG] 2012-09-17 VHOG:0000485 VHOG ISBN:978-0174480198 Roberts MBV, Biology: a functional approach (1986) p.572 Normally regresses in humans An epithelium that is part of a anterior chamber of eyeball. EHDAA2:0000130 uberon UBERON:0005638 anterior chamber epithelium An epithelium that is part of a anterior chamber of eyeball. OBOL:automatic An epithelium that is part of a lens vesicle. EHDAA2:0000987 EMAPA:17165 VHOG:0000532 uberon UBERON:0005656 lens vesicle epithelium An epithelium that is part of a lens vesicle. OBOL:automatic An ectoderm that is part of a pharyngeal arch 2. In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] EHDAA2:0000055 EMAPA:16277 EMAPA:16397 EMAPA:16398 RETIRED_EHDAA2:0000064 VHOG:0001062 2nd pharyngeal arch ectoderm uberon UBERON:0005660 2nd arch ectoderm An ectoderm that is part of a pharyngeal arch 2. OBOL:automatic In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] 2012-09-17 VHOG:0001062 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) 2nd pharyngeal arch ectoderm VHOG:0001062 An ectoderm that is part of a pharyngeal arch 4. In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] EHDAA2:0004032 EMAPA:16762 EMAPA:16764 EMAPA:16768 RETIRED_EHDAA2:0000094 VHOG:0001095 4th pharyngeal arch ectoderm uberon UBERON:0005662 4th arch ectoderm An ectoderm that is part of a pharyngeal arch 4. OBOL:automatic In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] 2012-09-17 VHOG:0001095 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) 4th pharyngeal arch ectoderm VHOG:0001095 An endoderm that is part of a pharyngeal arch 2. In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] EHDAA2:0000061 EMAPA:16274 EMAPA:16276 EMAPA:16278 RETIRED_EHDAA2:0000065 VHOG:0001108 2nd pharyngeal arch endoderm uberon UBERON:0005664 2nd arch endoderm An endoderm that is part of a pharyngeal arch 2. OBOL:automatic In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] 2012-09-17 VHOG:0001108 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) 2nd pharyngeal arch endoderm VHOG:0001108 An endoderm that is part of a pharyngeal arch 4. In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] EHDAA2:0004033 EMAPA:16765 EMAPA:16767 EMAPA:16769 RETIRED_EHDAA2:0000095 VHOG:0001092 4th pharyngeal arch endoderm uberon UBERON:0005666 4th arch endoderm An endoderm that is part of a pharyngeal arch 4. OBOL:automatic In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] 2012-09-17 VHOG:0001092 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) 4th pharyngeal arch endoderm VHOG:0001092 An endothelium that is part of a right lung. EHDAA2:0001755 uberon UBERON:0005672 right lung endothelium An endothelium that is part of a right lung. OBOL:automatic An endothelium that is part of a left lung. EHDAA2:0000961 uberon UBERON:0005673 left lung endothelium An endothelium that is part of a left lung. OBOL:automatic An anatomical cavity that is part of a lens vesicle. (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG] cavity of lens lens cavity EHDAA2:0000986 EMAPA:17164 VHOG:0000531 cavity of lens vesicle uberon UBERON:0005688 lens vesicle cavity An anatomical cavity that is part of a lens vesicle. OBOL:automatic (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG] 2012-09-17 VHOG:0000531 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 lens cavity EHDAA2:0000986 cavity of lens vesicle EMAPA:17164 Mesenchyme that is part of a pharyngeal arch 2. In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] EHDAA2:0000066 EHDAA:625 EMAPA:16279 FMA:295698 VHOG:0001102 2nd pharyngeal arch mesenchyme uberon 2nd branchial arch mesenchyme pharyngeal arch 2 mesenchyme UBERON:0005689 2nd arch mesenchyme Mesenchyme that is part of a pharyngeal arch 2. OBOL:automatic In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] 2012-09-17 VHOG:0001102 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) 2nd pharyngeal arch mesenchyme VHOG:0001102 Mesenchyme that is part of a pharyngeal arch 4. In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] EHDAA2:0000096 EHDAA:1677 EMAPA:16770 FMA:295702 VHOG:0001052 4th pharyngeal arch mesenchyme uberon 4th branchial arch mesenchyme pharyngeal arch 4 mesenchyme UBERON:0005691 4th arch mesenchyme Mesenchyme that is part of a pharyngeal arch 4. OBOL:automatic In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] 2012-09-17 VHOG:0001052 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) 4th pharyngeal arch mesenchyme VHOG:0001052 Mesenchyme that is part of a optic eminence. EHDAA:942 EMAPA:16324 RETIRED_EHDAA2:0001310 VHOG:0001073 uberon UBERON:0005702 optic eminence mesenchyme Mesenchyme that is part of a optic eminence. OBOL:automatic A venous system that is part of a hindbrain. EHDAA2:0000776 EMAPA:18632 VHOG:0001322 uberon rhombencephalon venous system UBERON:0005720 hindbrain venous system A venous system that is part of a hindbrain. OBOL:automatic rhombencephalon venous system VHOG:0001322 A mesoderm that has the potential to develop into a pronephros. Portion of tissue that consists of the mesenchymal precursor to the pronephric kidney and that begins to separate from the intermediate mesoderm at NF stage 21 and epithelializes by NF stage 30.[AAO] AAO:0011090 EFO:0003479 TAO:0000067 VHOG:0001239 XAO:0000264 ZFA:0000067 uberon pronephric anlage pronephric bulge pronephric mesenchyme pronephric primordium UBERON:0005721 the intermediate mesoderm of the chick embryo acquires its ability to form kidneys through its interactions with the paraxial mesoderm [ISBN:9780878932504 "Developmental Biology", http://www.ncbi.nlm.nih.gov/pubmed/10720431 "Signals from trunk paraxial mesoderm induce pronephros formation in chick intermediate mesoderm"]. These interactions induce the expression of TFs including Lim1, Pax2 and Pax6 that cause the intermediate mesoderm to form the kidney pronephric mesoderm ZFA Bgee:AN A mesoderm that has the potential to develop into a pronephros. OBOL:automatic Portion of tissue that consists of the mesenchymal precursor to the pronephric kidney and that begins to separate from the intermediate mesoderm at NF stage 21 and epithelializes by NF stage 30.[AAO] 2012-06-20 AAO:0011090 AAO XAO:curator pronephric anlage XAO:0000264 pronephric bulge XAO:0000264 pronephric mesenchyme XAO:0000264 pronephric primordium XAO:0000264 BILA:0000139 uberon UBERON:0005726 chemosensory system A limb/fin field that has the potential to develop into a pectoral appendage bud mesenchyme. Embryonic region that develops into the pectoral fin bud.[TAO] TAO:0001453 ZFA:0001453 pectoral appendage field of lateral plate mesoderm pectoral fin field uberon UBERON:0005729 pectoral appendage field A limb/fin field that has the potential to develop into a pectoral appendage bud mesenchyme. OBOL:automatic Embryonic region that develops into the pectoral fin bud.[TAO] 2012-08-14 TAO:0001453 TAO ZFIN:curator pectoral fin field ZFA:0001453 A limb/fin field that has the potential to develop into a pelvic appendage bud mesenchyme. Embryonic region that develops into the pelvic fin bud.[TAO] TAO:0001454 ZFA:0001454 pelvic appendage field of lateral plate mesoderm pelvic fin field uberon UBERON:0005730 pelvic appendage field A limb/fin field that has the potential to develop into a pelvic appendage bud mesenchyme. OBOL:automatic Embryonic region that develops into the pelvic fin bud.[TAO] 2012-08-14 TAO:0001454 TAO ZFIN:curator pelvic fin field ZFA:0001454 A ring of cells capable of forming a limb or paired fin[Gilbert,modified]. we represent the field as being a part of the LPM (consistent with ZFA, Gilbert). As a consequence, the relationship between limb bud (with is ectoderm+mesenchyme) stands in a weaker has_developmental_contribution_from relation to the field - TODO implement this. limb/fin field of lateral plate mesoderm paired limb/fin field uberon UBERON:0005732 paired limb/fin field ISBN:9780878932504 ZFA-inferred A ring of cells capable of forming a limb or paired fin[Gilbert,modified]. ISBN:9780878932504 The outermost layer of a blood vessel, composed mainly of fibrous tissue. TODO - note terminological problems. WP says tunica external layer of blood vessel. FMA says tunica externa = adventitia, and is FMA adventitia covers other kinds of vessels. Here we opt for a lengthier name that attempts to disambiguate. There is no precise FMA equivalent, as FMA has tunica externa of arteries, veins, genital ducts etc as siblings The outermost layer of a blood vessel, surrounding the tunica media. It is mainly composed of collagen. The collagen serves to anchor the blood vessel to nearby organs, giving it stability[Wikipedia:Tunica_externa_%28vessels%29]. BTO:0002010 EMAPA:36299 NCIT:C33818 UMLS:C0225342 adventitia externa tunica adventitia tunica adventitia of vessel uberon external coat tunica adventitia vasorum tunica externa vasorum UBERON:0005734 tunica adventitia of blood vessel cjm The outermost layer of a blood vessel, composed mainly of fibrous tissue. ISBN10:0073040584 The outermost layer of a blood vessel, surrounding the tunica media. It is mainly composed of collagen. The collagen serves to anchor the blood vessel to nearby organs, giving it stability[Wikipedia:Tunica_externa_%28vessels%29]. UMLS:C0225342 ncithesaurus:Tunica_Adventitia adventitia externa tunica adventitia tunica adventitia of vessel external coat tunica adventitia vasorum tunica externa vasorum A tunica intima that is part of a artery. EMAPA:36293 EV:0100028 FMA:14272 galen:IntimaOfArtery arterial intima tunica interna (intima)(arteriae) uberon UBERON:0005740 tunica intima of artery A tunica intima that is part of a artery. OBOL:automatic arterial intima EV:0100028 tunica interna (intima)(arteriae) FMA:14272 An outermost connective tissue covering of an organ, vessel, or other structure[WP]. BTO:0002010 FMA:45635 tunica advetitia tunica externa uberon UBERON:0005742 adventitia An outermost connective tissue covering of an organ, vessel, or other structure[WP]. tunica advetitia tunica externa FMA:45635 Anatomical space that is an opening in a bone, usually for passage of blood vessels or nerves. in FMA and ZFA this is a conduit space, not a conduit. Note there may be some additional disambiguation required: foramen is used loosely in the sense of any opening (e.g. foramen primum). FMA appears to use cranial conduit (undefined) in the sense of any foramen of the skull (includes mental foramen, which is not in the cranium proper). foramen AAO:0010438 TAO:0001736 VHOG:0001760 ZFA:0005386 foramens@fr foramina@fr uberon UBERON:0005744 bone foramen Anatomical space that is an opening in a bone, usually for passage of blood vessels or nerves. TAO:curator in FMA and ZFA this is a conduit space, not a conduit. Note there may be some additional disambiguation required: foramen is used loosely in the sense of any opening (e.g. foramen primum). FMA appears to use cranial conduit (undefined) in the sense of any foramen of the skull (includes mental foramen, which is not in the cranium proper). FMA foramen ZFA:0005386 foramens@fr TAO:0001736 foramina@fr TAO:0001736 The metanephros develops from the most caudal part of the nephrogenic cord that is itself derived from the intermediate plate mesoderm. caudal portion of nephrogenic cord caudal region of nephrogenic cord rear part of nephrogenic cord rear portion of nephrogenic cord uberon UBERON:0005753 caudal part of nephrogenic cord The metanephros develops from the most caudal part of the nephrogenic cord that is itself derived from the intermediate plate mesoderm. caudal portion of nephrogenic cord OBOL:automatic caudal region of nephrogenic cord OBOL:automatic rear part of nephrogenic cord OBOL:automatic rear portion of nephrogenic cord The initial renal anlage that develops from the most rostral part of the nephrogenic cord is termed the pronephros. uberon UBERON:0005754 rostral part of nephrogenic cord The initial renal anlage that develops from the most rostral part of the nephrogenic cord is termed the pronephros. A acellular anatomical structure that is the bounding layer of a anatomical structure. FMA:63871 uberon UBERON:0005764 acellular membrane A acellular anatomical structure that is the bounding layer of a anatomical structure. OBOL:automatic An acellular membrane that is part of the epithelium, lies adjacent to the epithelial cells, and is the fusion of the the basal lamina and the reticular lamina. this class represents a continuous sheet of basement membrane which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal membrane' represents a portion of substance on the scale of a single cell. AAO:0010596 FMA:63872 GAID:915 NCIT:C13191 UMLS:C0004799 basement membrane of connective tissue membrana basalis uberon basement membrane UBERON:0005769 basement membrane of epithelium FMA An acellular membrane that is part of the epithelium, lies adjacent to the epithelial cells, and is the fusion of the the basal lamina and the reticular lamina. UMLS:C0004799 ncithesaurus:Basement_Membrane basement membrane of connective tissue FMA:63872 membrana basalis basement membrane FMA:63872 Nephric tubules (nephrons) form embryonically along the nephric ridge. The ridge comprises three regions; anterior, middle and posterior. The functional kidney uses nephrons from only one or two regions of the ridge. A pronephric kidney uses only the nephrons from the anterior region of the ridge. A mesonephric kidney uses only the middle region, a metanephric kidney uses only the posterior region and an opisthonephric kidney uses the middle and posterior regions. TODO - check ridge vs cord vs nephrogenic cord vs blastema EHDAA2:0001242 EHDAA:1015 EMAPA:16368 VHOG:0001240 uberon nephric cord UBERON:0005792 nephric ridge Nephric tubules (nephrons) form embryonically along the nephric ridge. The ridge comprises three regions; anterior, middle and posterior. The functional kidney uses nephrons from only one or two regions of the ridge. A pronephric kidney uses only the nephrons from the anterior region of the ridge. A mesonephric kidney uses only the middle region, a metanephric kidney uses only the posterior region and an opisthonephric kidney uses the middle and posterior regions. nephric cord VHOG:0001240 FMA:72173 fetal uterus uberon UBERON:0005795 embryonic uterus fetal uterus FMA:72173 Any portion of the aorta including the ascending and descending aorta, and aortic arch or a portion of the aortic orifice of the left ventricle. FMA:13087 NCIT:C34027 UMLS:C0506947 aortic section uberon aortic segment portion of aorta segment of aorta UBERON:0005800 section of aorta Any portion of the aorta including the ascending and descending aorta, and aortic arch or a portion of the aortic orifice of the left ventricle. ncithesaurus:Aortic_Segment UMLS:C0506947 ncithesaurus:Aortic_Segment aortic segment FMA:13087 segment of aorta FMA:13087 The dorsal aorta is a blood vessel in a single-pass circulatory system that carries oxygenated blood from the gills to the rest of the body. In a single-pass circulatory system blood passes once through the heart to supply the body once. Each primitive aorta receives anteriorly a vein 'the vitelline vein' from the yolk-sac, and is prolonged backward on the lateral aspect of the notochord under the name of the dorsal aorta. The dorsal aortae give branches to the yolk-sac, and are continued backward through the body-stalk as the umbilical arteries to the villi of the chorion. The two dorsal aortae combine to become the descending aorta in later development[WP]. Principal unpaired, median artery of the trunk, leading from the paired roots (radices) of the dorsal aorta to the caudal artery. Kimmel et al, 1995.[TAO] The artery in vertebrate embryos that transports blood from the aortic arches to the trunk and limbs. In adult fish it is a major artery that carries oxygenated blood from the efferent branchial arteries to branches that supply the body organ. In adult tetrapods it arises from the systemic arch relationship loss: part_of axial vasculature (TAO:0001073)[TAO] When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG] AAO:0011029 BTO:0004673 EHDAA:402 EMAPA:18606 TAO:0000014 VHOG:0000264 XAO:0000051 ZFA:0000014 DA aorta dorsalis uberon aortae dorsales dorsal aorta root dorsal aortae dorsal aortic root dorsal aortæ UBERON:0005805 dorsal aorta The dorsal aorta is a blood vessel in a single-pass circulatory system that carries oxygenated blood from the gills to the rest of the body. In a single-pass circulatory system blood passes once through the heart to supply the body once. GO:0035907 Each primitive aorta receives anteriorly a vein 'the vitelline vein' from the yolk-sac, and is prolonged backward on the lateral aspect of the notochord under the name of the dorsal aorta. The dorsal aortae give branches to the yolk-sac, and are continued backward through the body-stalk as the umbilical arteries to the villi of the chorion. The two dorsal aortae combine to become the descending aorta in later development[WP]. Principal unpaired, median artery of the trunk, leading from the paired roots (radices) of the dorsal aorta to the caudal artery. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000014 TAO ZFIN:curator The artery in vertebrate embryos that transports blood from the aortic arches to the trunk and limbs. In adult fish it is a major artery that carries oxygenated blood from the efferent branchial arteries to branches that supply the body organ. In adult tetrapods it arises from the systemic arch BTO:0004673 relationship loss: part_of axial vasculature (TAO:0001073)[TAO] 2012-08-14 TAO:0000014 TAO When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG] 2012-09-17 VHOG:0000264 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620 DA ZFA:0000014 aorta dorsalis XAO:0000051 aortae dorsales dorsal aorta root VHOG:0000264 dorsal aortae dorsal aortic root VHOG:0000264 dorsal aortæ A delimited region of dense mesenchyme within looser mesenchyme. AEO:0000148 EHDAA2_RETIRED:0003148 EHDAA:8979 mesenchyme condensation uberon UBERON:0005856 developing mesenchymal condensation AEO cjm A delimited region of dense mesenchyme within looser mesenchyme. AEO:0000148 mesenchyme condensation EMAPA:25351 Cell condensation that is an aggregation of mesenchymal cells that are committed to differentiate into chondroblasts and chondrocytes. isa cell condensation in VSAO; has_part chondroblast in AEO AEO:0000147 EHDAA2_RETIRED:0003147 EMAPA:32731 VSAO:0000092 XAO:0004022 cartilage condensation cartilagenous condensation chondrogenic condensation uberon UBERON:0005863 cartilaginous condensation AEO AEO Cell condensation that is an aggregation of mesenchymal cells that are committed to differentiate into chondroblasts and chondrocytes. GO:curator isa cell condensation in VSAO; has_part chondroblast in AEO VSAO cartilage condensation EMAPA:25353 cartilagenous condensation EHDAA2:0003147 chondrogenic condensation VSAO:0000092 A delimited region of dense mesenchyme within looser mesenchyme whose cells are committed to become chondroblasts. A closely packed aggregation of mesenchymal cells just prior to their differentiation into embryonic cartilage. AEO:0000150 EHDAA2:0003150 EMAPA:32736 pre-chondrogenic condensation precartilage condensation precartilagenous condensation prechondrogenic condensation uberon UBERON:0005866 pre-cartilage condensation AEO AEO A delimited region of dense mesenchyme within looser mesenchyme whose cells are committed to become chondroblasts. AEO:0000150 AEO:JB A closely packed aggregation of mesenchymal cells just prior to their differentiation into embryonic cartilage. the paired ventral prominences formed by bifurcation of the first pharyngeal arches in the embryo; the two prominences unite ventrally and fuse to form the mandible and lower lip check develops_from EHDAA2:0001061 EHDAA:5871 EMAPA:17355 FMA:293051 NCIT:C34204 UMLS:C1512982 uberon mandibular process mandibular swelling prominentia mandibularis UBERON:0005867 mandibular prominence the paired ventral prominences formed by bifurcation of the first pharyngeal arches in the embryo; the two prominences unite ventrally and fuse to form the mandible and lower lip ISBN:0-683-40008-8 MP:0010939 UMLS:C1512982 ncithesaurus:Mandibular_Prominence mandibular process mandibular swelling prominentia mandibularis An indentation of the olfactory placode which ends when the pits hollows out to form the nasopharynx[GO]. we represent the relationship as develops from, though in fact the pit is formed as an indentation in the placode By the upgrowth of the surrounding parts the olfactory areas are converted into pits, the nasal pits or olfactory pits, which indent the fronto-nasal process and divide it into a medial and two lateral nasal processes[Wikipedia:Nasal_pit]. AAO:0011068 EFO:0003496 EHDAA2:0001295 EHDAA:4772 EMAPA:16800 FMA:295840 XAO:0000275 XAO:0004073 nasal pit uberon UBERON:0005870 olfactory pit EHDAA2 EMAPA EHDAA2 XAO:0000275 nasal pit An indentation of the olfactory placode which ends when the pits hollows out to form the nasopharynx[GO]. GO:0060166 By the upgrowth of the surrounding parts the olfactory areas are converted into pits, the nasal pits or olfactory pits, which indent the fronto-nasal process and divide it into a medial and two lateral nasal processes[Wikipedia:Nasal_pit]. nasal pit XAO:0000275 Anatomical cluster that is located in the posterior region of the cranium and forms the margin of the foramen magnum and occipital condyles. TODO - check An anatomical cluster that is located in the posterior region of the neurocranium and forms the margin of the foramen margin and occipital condyles.[AAO] Anatomical cluster that is located in the posterior region of the cranium and forms the margin of the foramen magnum and occiptal condyle.[TAO] AAO:0010199 BTO:0004675 FMA:49187 TAO:0001414 XAO:0003173 ZFA:0001414 basicranial region occipital part of head occipital region of head uberon back of head UBERON:0005902 occipital region Anatomical cluster that is located in the posterior region of the cranium and forms the margin of the foramen magnum and occipital condyles. TAO:0001414 UBERONREF:0000007 An anatomical cluster that is located in the posterior region of the neurocranium and forms the margin of the foramen margin and occipital condyles.[AAO] 2012-06-20 AAO:0010199 AAO AAO:EJS Anatomical cluster that is located in the posterior region of the cranium and forms the margin of the foramen magnum and occiptal condyle.[TAO] 2012-08-14 TAO:0001414 TAO TAO:MAH basicranial region ZFA:0001414 occipital part of head FMA:49187 occipital region of head FMA:49187 back of head FMA:49187 Organ with organ cavity, which has as parts a serous membrane and a serous cavity . Examples: pleural sac, pericardial sac, tendon sheath, bursa.[FMA] EMAPA:16060 FMA:9689 MA:0000005 uberon UBERON:0005906 See notes for serous membrane serous sac Organ with organ cavity, which has as parts a serous membrane and a serous cavity . Examples: pleural sac, pericardial sac, tendon sheath, bursa.[FMA] FMA:9689 Epithelium that derives from the endoderm. Examples: urothelium, transitional epithelium of ureter, epithelium of prostatic gland.[FMA] FMA:69065 endoderm-derived epithelium endoepithelium uberon UBERON:0005911 endo-epithelium Epithelium that derives from the endoderm. Examples: urothelium, transitional epithelium of ureter, epithelium of prostatic gland.[FMA] FMA:69065 FMA:10483 bone organ zone uberon UBERON:0005913 zone of bone organ FMA bone organ zone FMA:10483 Subdivision of skeleton which consists of cranial skeleton, set of all vertebrae, set of all ribs and sternum[FMA, modified]. Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO] AAO:0000963 EMAPA:17214 EMAPA:18043 MA:0000308 NCIT:C32172 UMLS:C0222645 VSAO:0000056 XAO:0004011 uberon skeleton axiale UBERON:0005944 axial skeleton plus cranial skeleton http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton Subdivision of skeleton which consists of cranial skeleton, set of all vertebrae, set of all ribs and sternum[FMA, modified]. FMA:71221 VSAO:0000056 Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO] 2012-08-14 VSAO:0000056 VSAO PSPUB:0000170 UMLS:C0222645 ncithesaurus:Axial_Skeleton skeleton axiale Anteriosuperior, smooth-walled portion of the cavity of the right ventricle, beginning at the supraventricular crest and terminating in the pulmonary trunk infundibulum EMAPA:37926 FMA:7216 NCIT:C61368 UMLS:C1881209 RVOT conus arteriosus (infundibulum) infundibulum of right ventricle outflow tract of right ventricle pulmonary conus right ventricle pulmonary outflow tract right ventricular outflow tract uberon arterial cone conus arteriosus pulmonary cone pulmonary conus UBERON:0005953 outflow part of right ventricle Anteriosuperior, smooth-walled portion of the cavity of the right ventricle, beginning at the supraventricular crest and terminating in the pulmonary trunk MP:0010428 infundibulum EMAPA:37926 MA:th UMLS:C1881209 ncithesaurus:Infundibulum RVOT MP:0010428 conus arteriosus (infundibulum) FMA:7216 infundibulum of right ventricle FMA:7216 infundibulum of right ventricle MP:0010428 outflow tract of right ventricle FMA:7216 pulmonary conus FMA:7216 right ventricle pulmonary outflow tract MP:0010428 right ventricular outflow tract MP:0010428 arterial cone MP:0010428 conus arteriosus MP:0010428 pulmonary cone MP:0010428 pulmonary conus MP:0010428 Anterosuperior fibrous portion of the left ventricle that connects to the ascending aorta. EMAPA:37925 FMA:9473 LVOT Sibson vestibule aortic vestibule heart left ventricle outflow tract left ventricular outflow left ventricular outflow tract outflow tract of left ventricle vestibulum aortae uberon UBERON:0005956 outflow part of left ventricle Anterosuperior fibrous portion of the left ventricle that connects to the ascending aorta. MP:0010429 EMAPA:37925 MA:th LVOT MP:0010429 Sibson vestibule MP:0010429 aortic vestibule FMA:9473 aortic vestibule MP:0010429 heart left ventricle outflow tract MP:0010429 left ventricular outflow FMA:9473 left ventricular outflow tract HP:0011103 outflow tract of left ventricle FMA:9473 vestibulum aortae FMA:9473 FMA:TA The laminar structure of the heart uberon UBERON:0005983 heart layer The laminar structure of the heart MP:0010545 Any of the arteries or veins that supply blood to the heart or return blood from the heart muscles to the circulation TODO - change relation from part_of MESH:D003331 uberon UBERON:0005985 coronary vessel Any of the arteries or veins that supply blood to the heart or return blood from the heart muscles to the circulation MP:0010551 Anatomical structure embedded in or located in the integument that is part of the integumental system. Examples: hair, follicles, skin glands, claws, nails, feathers. add subclasses based on resolution of CARO tracker item. Also check: adnexal gland. Note that MP implicitly includes hypodermis. the tissue or structures associated with or embedded in the skin such as hair and hair follicles, sweat glands, sebaceous glands and claws or nails[MP:0010678] EMAPA:37883 body hair or bristle uberon adnexae cutis skin adnexa skin adnexal structure skin appendage UBERON:0006003 integumentary adnexa Anatomical structure embedded in or located in the integument that is part of the integumental system. Examples: hair, follicles, skin glands, claws, nails, feathers. the tissue or structures associated with or embedded in the skin such as hair and hair follicles, sweat glands, sebaceous glands and claws or nails[MP:0010678] MP:0010678 EMAPA:37883 MA:th body hair or bristle GO:GO adnexae cutis skin adnexa skin appendage uberon UBERON:0006056 posterior surface of head The mesonephric capsule is the tough fibrous layer surrounding the mesonephros, covered in a thick layer of perinephric adipose tissue. uberon UBERON:0006170 mesonephric capsule The mesonephric capsule is the tough fibrous layer surrounding the mesonephros, covered in a thick layer of perinephric adipose tissue. GO:0061285 GOC:mtg_kidney_jan10 The spiral septum that separates the truncus arteriosus into a ventral pulmonary trunk and the dorsal aorta[MP]. The aorticopulmonary septum is developmentally formed from neural crest, specifically the cardiac neural crest, and actively separates the aorta and pulmonary arteries and fuses with the interventricular septum within the heart during development. The actual mechanism of septation of the outflow tract is poorly understood, but is recognized as a dynamic process with contributions from contractile, hemodynamic, and extracellular matrix interactions. UBERON:0005999 CALOHA:TS-2409 EHDAA2:0000136 EHDAA:2592 EMAPA:16827 VHOG:0000502 aortico-pulmonary septum aorticopulmonary septum septum aorticopulmonale uberon aortic septum spiral septum UBERON:0006207 aortico-pulmonary spiral septum Wikipedia The spiral septum that separates the truncus arteriosus into a ventral pulmonary trunk and the dorsal aorta[MP]. The aorticopulmonary septum is developmentally formed from neural crest, specifically the cardiac neural crest, and actively separates the aorta and pulmonary arteries and fuses with the interventricular septum within the heart during development. The actual mechanism of septation of the outflow tract is poorly understood, but is recognized as a dynamic process with contributions from contractile, hemodynamic, and extracellular matrix interactions. MP:0010650 aortico-pulmonary septum aorticopulmonary septum septum aorticopulmonale aortic septum spiral septum The thin bilaminar membrane derived from the prechordal plate that is devoid of mesoderm and formed by the apposition of the stomodeal ectoderm with the foregut endoderm; after the embryonic head fold has evolved it lies at the caudal limit of the stomodeum, forming a septum between the primitive mouth and pharynx; the membrane eventually disappears, and thus a communication is established between the mouth and the future pharynx. EHDAA2:0000189 EHDAA:536 EMAPA:16259 FMA:313607 VHOG:0000380 uberon oral membrane oral plate oropharyngeal membrane pharyngeal membrane UBERON:0006211 buccopharyngeal membrane EHDAA2 The thin bilaminar membrane derived from the prechordal plate that is devoid of mesoderm and formed by the apposition of the stomodeal ectoderm with the foregut endoderm; after the embryonic head fold has evolved it lies at the caudal limit of the stomodeum, forming a septum between the primitive mouth and pharynx; the membrane eventually disappears, and thus a communication is established between the mouth and the future pharynx. MP:0012521 oral membrane MP:0012521 oral plate MP:0012521 oropharyngeal membrane pharyngeal membrane MP:0012521 The membrane that covers the embryonic cloaca, formed by the union of proctodeal (anal pit) ectoderm and cloacal endoderm, with no intervening mesoderm; the urorectal septum joins the cloacal membrane and divides it into an anal membrane and a urogenital membrane; the point where the urorectal septum intersects the cloacal membrane is the future site of the perineal body; proliferation of mesoderm and ectoderm around the cloacal membrane produces primordial tissues of the external genitalia in both sexes: the genital tubercle, genital folds, and genital swellings. A membrane that separates the proctodeum and the hindgut in the early embryo. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.497, see_Kardong_KV][VHOG] In mammals, the cloaca exists as an embryonic structure that undergoes septation to become distinct urethral, anal, and genital orifices.[well established][VHOG] EHDAA2:0000257 EHDAA:214 EHDAA:2933 EMAPA:16832 FMA:295525 NCIT:C34128 UMLS:C0231056 VHOG:0001198 embryonic cloacal membrane uberon membrana cloacalis UBERON:0006217 cloacal membrane Wikipedia The membrane that covers the embryonic cloaca, formed by the union of proctodeal (anal pit) ectoderm and cloacal endoderm, with no intervening mesoderm; the urorectal septum joins the cloacal membrane and divides it into an anal membrane and a urogenital membrane; the point where the urorectal septum intersects the cloacal membrane is the future site of the perineal body; proliferation of mesoderm and ectoderm around the cloacal membrane produces primordial tissues of the external genitalia in both sexes: the genital tubercle, genital folds, and genital swellings. MP:0011837 MP:anna A membrane that separates the proctodeum and the hindgut in the early embryo. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.497, see_Kardong_KV][VHOG] 2012-09-17 VHOG:0001198 VHOG In mammals, the cloaca exists as an embryonic structure that undergoes septation to become distinct urethral, anal, and genital orifices.[well established][VHOG] 2012-09-17 VHOG:0001198 VHOG PMID:11830557 De Santa Barbara P, Roberts DJ, Tail gut endoderm and gut/genitourinary/tail development: a new tissue-specific role for Hoxa13. Development (2002) UMLS:C0231056 ncithesaurus:Cloacal_Membrane membrana cloacalis EHDAA:1477 EMAPA:16660 RETIRED_EHDAA2:0000496 VHOG:0000715 uberon facio-acoustic preganglion complex UBERON:0006232 facio-acoustic VII-VIII preganglion complex EHDAA2 facio-acoustic preganglion complex EMAPA:16660 An anatomical junctions that overlaps the foregut and midgut. Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[well established][VHOG] EHDAA2:0000569 EHDAA:526 EMAPA:16363 VHOG:0000291 uberon UBERON:0006235 foregut-midgut junction An anatomical junctions that overlaps the foregut and midgut. OBOL:automatic Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[well established][VHOG] 2012-09-17 VHOG:0000291 VHOG ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 The embryonic precursor of the brain. The embryonic precursor of the brain and the set of mature brain structures that derive from it (CUMBO) BAMS:Enc BTO:0004726 EFO:0003431 EHDAA:300 EHDAA:830 EMAPA:16089 FMA:312967 RETIRED_EHDAA2:0000591 TAO:0000146 ZFA:0000146 brain rudiment presumptive brain encephalon uberon embryonic brain UBERON:0006238 future brain The embryonic precursor of the brain. NIFSTD:nlx_94995 The embryonic precursor of the brain and the set of mature brain structures that derive from it (CUMBO) brain rudiment TAO:0000146 presumptive brain ZFA:0000146 encephalon NIFSTD:nlx_94995 embryonic brain BTO:0004726 EFO:0003438 EHDAA2:0000674 EHDAA:898 EMAPA:16092 EMAPA:16755 TAO:0000417 ZFA:0000417 presumptive spinal cord presumptive spinal cord neural keel presumptive spinal cord neural plate presumptive spinal cord neural rod uberon UBERON:0006241 future spinal cord EHDAA2 presumptive spinal cord ZFA:0000417 presumptive spinal cord neural keel TAO:0000417 presumptive spinal cord neural plate TAO:0000417 presumptive spinal cord neural rod TAO:0000417 An anatomical junctions that overlaps the mouth and foregut. EHDAA:534 EMAPA:16258 RETIRED_EHDAA2:0001205 VHOG:0000592 uberon UBERON:0006264 mouth-foregut junction An anatomical junctions that overlaps the mouth and foregut. OBOL:automatic The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. TODO - check ordering; awaiting confirmation from JB The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG] EHDAA2:0001278 EHDAA:264 EMAPA:16101 NCIT:C34231 UMLS:C1518429 VHOG:0001212 uberon UBERON:0006267 notochordal plate EHDAA2 EHDAA2 The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. VHOG:0001212 The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG] 2012-09-17 VHOG:0001212 VHOG UMLS:C1518429 ncithesaurus:Notochordal_Plate A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot EHDAA2:0001279 EHDAA:224 EMAPA:16102 FMA:293135 NCIT:C34232 UMLS:C1518430 VHOG:0001213 uberon chordamesoderm presumptive notochord UBERON:0006268 The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus. notochordal process EHDAA2 A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot UMLS:C1518430 ncithesaurus:Notochordal_Process the pair of depressions of thickened otic placode epithelium, that further develops into the otic vesicles A depression appearing in each otic placode, marking the beginnning of embryonic development of the internal ear. [TFD][VHOG] UBERON:0009123 EHDAA2:0001336 EHDAA:929 EMAPA:16536 FMA:302911 NCIT:C34238 VHOG:0001147 otic cup uberon UBERON:0006273 otic pit EHDAA2 the pair of depressions of thickened otic placode epithelium, that further develops into the otic vesicles ISBN:0-683-40008-8 MP:0011172 A depression appearing in each otic placode, marking the beginnning of embryonic development of the internal ear. [TFD][VHOG] 2012-09-17 VHOG:0001147 VHOG otic cup NCBIBook:NBK53175 Multi-tissue structure that is part of the heart tube and will become the cardiac ventricle. UBERON:0010226 embryonic ventricle EHDAA2:0001531 EMAPA:16350 FMA:71006 NCIT:C34160 TAO:0002231 ZFA:0001719 early heart ventricle embryonic heart ventricle future heart ventricle presumptive cardiac ventricle heart tube primitive ventricle primitive ventricle of heart primordial cardiac ventricle primordial ventricle uberon UBERON:0006283 The embryonic ventricle or primitive ventricle of the developing heart gives rise to the trabeculated parts of the left and right ventricles. In contrast, the smooth parts of the left and right ventricles originate from the embryological bulbus cordis. The primitive ventricle becomes divided by a septum, the septum inferius or ventricular septum, which grows upward from the lower part of the ventricle, its position being indicated on the surface of the heart by a furrow. Its dorsal part increases more rapidly than its ventral portion, and fuses with the dorsal part of the septum intermedium. For a time an interventricular foramen exists above its ventral portion, but this foramen is ultimately closed by the fusion of the aortic septum with the ventricular septum[WP] future cardiac ventricle ZFA EMAPA Multi-tissue structure that is part of the heart tube and will become the cardiac ventricle. ZFA:0001719 presumptive cardiac ventricle heart tube ZFA:0001719 primitive ventricle EHDAA2:0001531 primitive ventricle of heart EMAPA:16350 primordial cardiac ventricle FMA:71006 primordial ventricle FMA:71006 EHDAA:924 EMAPA:16663 RETIRED_EHDAA2:0002089 trigeminal V preganglion uberon trigeminal preganglion UBERON:0006304 See: https://github.com/obophenotype/mouse-anatomy-ontology/issues/13 and https://github.com/obophenotype/uberon/issues/693 -- consider merging into trigeminal ganglion, as this complicates the model future trigeminal ganglion EHDAA2 trigeminal V preganglion EMAPA:16663 trigeminal preganglion EMAPA:16663 A segment of the eyeball that is filled with refractive media BTO:0002085 EMAPA:37529 FMA:58071 MA:0002459 NCIT:C32301 UMLS:C0459556 eye chamber eyeball chamber uberon chamber of eye UBERON:0006311 chamber of eyeball A segment of the eyeball that is filled with refractive media EMAPA:37529 MA:th UMLS:C0459556 ncithesaurus:Chamber_of_the_Eye eye chamber MA:0002459 eyeball chamber FMA:58071 chamber of eye BTO:0002085 Body substance in a liquid or semi-solid state in the eyeball which serves to refract light. ocular refraction MA:0001911 uberon UBERON:0006312 ocular refractive media Body substance in a liquid or semi-solid state in the eyeball which serves to refract light. Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not. fluid EMAPA:37441 FMA:280556 GAID:266 MESH:D001826 galen:BodyFluid body fluid uberon UBERON:0006314 bodily fluid Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not. MESH:A12.207 EMAPA:37441 MA:th body fluid GAID:266 A nucleus of brain that is part of a brainstem. EMAPA:32790 MA:0000821 uberon brain stem nucleus UBERON:0006331 brainstem nucleus A nucleus of brain that is part of a brainstem. OBOL:automatic brain stem nucleus EMAPA:32790 2 2 An artery that connects two larger arteries. EMAPA:18598 MA:0001938 NCIT:C52851 UMLS:C1707451 uberon UBERON:0006347 Grouping for anterior and posterior communicating artery An artery that connects two larger arteries. ncithesaurus:Communicating_Artery UMLS:C1707451 ncithesaurus:Communicating_Artery inferred from artery EMAPA:18646 MA:0002227 uberon UBERON:0006355 superior vesical vein true MA A portion of organism substance that secreted_by a zone of skin. MA:0002537 skin fluid/secretion uberon skin fluid skin substance UBERON:0006535 skin secretion A portion of organism substance that secreted_by a zone of skin. OBOL:automatic skin fluid/secretion MA:0002537 A portion of organism substance that is secreted by a female reproductive gland. MA:0002510 female reproductive system fluid/secretion uberon female reproductive system fluid female reproductive system secretion UBERON:0006537 female reproductive gland secretion A portion of organism substance that is secreted by a female reproductive gland. UBERON:cjm female reproductive system fluid/secretion MA:0002510 A portion of organism substance that secreted_by a respiratory system. EMAPA:36550 MA:0002533 NCIT:C13722 UMLS:C1514899 uberon respiratory system fluid respiratory system secretion UBERON:0006538 respiratory system fluid/secretion A portion of organism substance that secreted_by a respiratory system. OBOL:automatic UMLS:C1514899 ncithesaurus:Respiratory_System_Fluid_or_Secretion A vasculature that is part of a kidney. EMAPA:28457 TAO:0005305 ZFA:0005305 uberon UBERON:0006544 kidney vasculature A vasculature that is part of a kidney. OBOL:automatic A tube in the kidney that collect and transport urine. in ZFA this is defined as part of mesonephros TAO:0005289 ZFA:0005289 uberon UBERON:0006553 renal duct A tube in the kidney that collect and transport urine. ZFIN:ZDB-PUB-071029-9 in ZFA this is defined as part of mesonephros ZFA A tube that is part of a excretory system. uberon UBERON:0006555 excretory tube A tube that is part of a excretory system. OBOL:automatic The pharynx is the part of the digestive system immediately posterior to the mouth[GO]. currently this is an extremely generic class, encompassing both protostomes and deuterostomes. branchial pharyngeal FBbt:00005380 MAT:0000049 MIAA:0000049 uberon anterior part of foregut pharyngeal tube UBERON:0006562 pharynx The pharynx is the part of the digestive system immediately posterior to the mouth[GO]. GO:0060465 Tunica media of artery which is continuous with the myocardium of right ventricle.[FMA] FMA:85030 uberon UBERON:0006563 tunica media of pulmonary trunk Tunica media of artery which is continuous with the myocardium of right ventricle.[FMA] FMA:85030 FMA:FMA A urethral meatus that is part of a female urethra[Automatically generated definition]. The external urethral orifice (urinary meatus) is the external opening of the urethra, from which urine is ejected during urination. It is placed about 2.5 cm behind the glans clitoridis and immediately in front of that of the vagina; it usually assumes the form of a short, sagittal cleft with slightly raised margins. To its left and right are the openings of the Skene's ducts. EMAPA:36453 FMA:85266 MA:0002639 external orifice of female urethra external urethral orifice (female) female urethral meatus ostium urethrae externum (urethra feminina) urethral meatus of clitoral urethra uberon distal urethral opening of female urethral opening of clitoral urethra UBERON:0006565 female urethral meatus A urethral meatus that is part of a female urethra[Automatically generated definition]. OBOL:automatic The external urethral orifice (urinary meatus) is the external opening of the urethra, from which urine is ejected during urination. It is placed about 2.5 cm behind the glans clitoridis and immediately in front of that of the vagina; it usually assumes the form of a short, sagittal cleft with slightly raised margins. To its left and right are the openings of the Skene's ducts. external orifice of female urethra FMA:85266 external urethral orifice (female) FMA:85266 female urethral meatus FMA:85266 ostium urethrae externum (urethra feminina) FMA:85266 FMA:TA urethral meatus of clitoral urethra EMAPA:36453 distal urethral opening of female EMAPA:36453 urethral opening of clitoral urethra EMAPA:36453 A myocardium that is part of a left ventricle of a heart. Myocardium of ventricle which is continuous with the tunica media of aorta. EMAPA:17339 FMA:9558 MA:0002983 left ventricular myocardium myocardium of left ventricle uberon UBERON:0006566 left ventricle myocardium A myocardium that is part of a left ventricle of a heart. Myocardium of ventricle which is continuous with the tunica media of aorta. FMA:9558 left ventricular myocardium FMA:9558 myocardium of left ventricle FMA:9558 A myocardium that is part of a right ventricle of a heart. Myocardium of ventricle which is continuous with the tunica media of the pulmonary trunk. EMAPA:17342 FMA:9535 MA:0002984 myocardium of right ventricle right ventricular myocardium uberon UBERON:0006567 right ventricle myocardium A myocardium that is part of a right ventricle of a heart. Myocardium of ventricle which is continuous with the tunica media of the pulmonary trunk. FMA:9535 myocardium of right ventricle FMA:9535 right ventricular myocardium FMA:9535 The pectinate line (anocutaneous line, dentate line, anorectal junction) is a line which divides the upper 2/3rds and lower 1/3rd of the anal canal. Developmentally, this line represents the hindgut-proctodeum junction. It is an important anatomical landmark, and several distinctions can be made based upon the location of a structure relative to this line: FMA also has FMA:29321 but it's not clear how this differs EMAPA:19159 FMA:75383 NCIT:C34245 UMLS:C0821671 linea pectinata canalis analis pectinate line of anal canal uberon Hilton's 'white line' dentate line linea anocutanea recto-anal junction site of anal membrane UBERON:0006574 pectinate line The pectinate line (anocutaneous line, dentate line, anorectal junction) is a line which divides the upper 2/3rds and lower 1/3rd of the anal canal. Developmentally, this line represents the hindgut-proctodeum junction. It is an important anatomical landmark, and several distinctions can be made based upon the location of a structure relative to this line: FMA also has FMA:29321 but it's not clear how this differs FMA UMLS:C0821671 ncithesaurus:Pectinate_Line linea pectinata canalis analis FMA:75383 FMA:TA pectinate line of anal canal FMA:75383 Hilton's 'white line' EMAPA:19159 dentate line linea anocutanea recto-anal junction site of anal membrane EMAPA:19159 Presumptive structure of the blastula that will develop into endoderm. AAO:0000471 EFO:0003437 TAO:0000416 ZFA:0000416 uberon UBERON:0006595 presumptive endoderm Presumptive structure of the blastula that will develop into endoderm. AAO:0000468 EFO:0003439 TAO:0000568 ZFA:0000568 future blood uberon UBERON:0006596 presumptive blood Portion of embryonic tissue determined by fate mapping to become a structure. Consider merging with anlage AAO:0000479 TAO:0001116 ZFA:0001116 future structure presumptive structures uberon UBERON:0006598 presumptive structure Portion of embryonic tissue determined by fate mapping to become a structure. GOC:CVS GOC:YMB ZFA:0001116 presumptive structures ZFA:0001116 Presumptive structure of the blastula that will develop into ectoderm. AAO:0000470 EFO:0003466 TAO:0001376 XAO:0004132 ZFA:0001376 uberon presumptive epidermis UBERON:0006601 presumptive ectoderm Presumptive structure of the blastula that will develop into ectoderm. presumptive epidermis ZFA:0001376 Presumptive structure of the blastula that will develop into mesoderm. AAO:0000476 EFO:0003467 TAO:0001377 ZFA:0001377 uberon UBERON:0006603 presumptive mesoderm Presumptive structure of the blastula that will develop into mesoderm. A muscle layer that is part of a fallopian tube. EMAPA:29046 FMA:18318 muscle layer of fallopian tube muscle layer of oviduct muscle layer of uterine tube muscular coat of uterine tube muscular layer of uterine tube muscularis of uterine tube tunica muscularis (Tuba uterina) tunica muscularis tubae uterinae uterine tubal muscularis uberon UBERON:0006642 muscle layer of oviduct A muscle layer that is part of a fallopian tube. OBOL:automatic muscle layer of fallopian tube FMA:18318 muscle layer of oviduct FMA:18318 muscle layer of uterine tube FMA:18318 muscular coat of uterine tube FMA:18318 muscular layer of uterine tube FMA:18318 muscularis of uterine tube FMA:18318 tunica muscularis (Tuba uterina) FMA:18318 tunica muscularis tubae uterinae FMA:18318 FMA:TA uterine tubal muscularis FMA:18318 EMAPA:30997 FMA:19976 muscular coat of vagina tunica muscularis vaginae vaginal muscularis uberon UBERON:0006652 muscular layer of vagina muscular coat of vagina FMA:19976 tunica muscularis vaginae FMA:19976 FMA:TA A region of muscle in many organs in the vertebrate body, adjacent to the submucosa membrane. It is responsible for gut movement such as peristalsis. currently this class conflates a generic layer of muscle and a specific layer found lining the digestive tract (the muscularis externa), typically composed of circular and longitudinal layers (although this varies) An outer layer of smooth muscle surrounding a hollow or tubular organ as the bladder, esophagus, large intestine, small intestine, stomach, ureter, uterus, and vagina that often consists of an inner layer of circular fibers serving to narrow the lumen of the organ and an outer layer of longitudinal fibers serving to shorten its length[BTO]. typically smooth muscle, but there may be exceptions - in the upper esophagus, part of the externa is skeletal muscle, rather than smooth muscle. BTO:0004838 UMLS:C0225358 muscular layer muscularis layer tunica muscularis uberon muscular coat muscularis muscularis externa muscularis propria transverse muscular fibers tunica externa tunica muscularis UBERON:0006660 muscular coat A region of muscle in many organs in the vertebrate body, adjacent to the submucosa membrane. It is responsible for gut movement such as peristalsis. An outer layer of smooth muscle surrounding a hollow or tubular organ as the bladder, esophagus, large intestine, small intestine, stomach, ureter, uterus, and vagina that often consists of an inner layer of circular fibers serving to narrow the lumen of the organ and an outer layer of longitudinal fibers serving to shorten its length[BTO]. BTO:0004838 UMLS:C0225358 ncithesaurus:Muscle_Layer muscular layer OBOL:automatic muscularis layer FMA:45634 tunica muscularis BTO:0004838 muscular coat muscularis externa BTO:0004838 muscularis propria transverse muscular fibers tunica externa BTO:0004838 tunica muscularis A valve that is part of a vein. FMA:68095 valve of vein uberon UBERON:0006675 venous valve A valve that is part of a vein. OBOL:automatic valve of vein FMA:68095 An anatomical boundary that adjacent_to a epithelium. FMA:70997 epithelium surface uberon UBERON:0006677 surface of epithelium An anatomical boundary that adjacent_to a epithelium. OBOL:automatic epithelium surface FMA:70997 the edge of the cornea where it joins the sclera; the limbus is a common site for the occurrence of corneal epithelial neoplasm EFO:0001403 EMAPA:37835 FMA:58342 GAID:896 MESH:D016850 ZFA:0005570 cornea limbus corneal limbus corneal-scleral limbus corneoscleral junction limbus corneae sclerocorneal junction sclerocorneal limbus uberon limbus corneae UBERON:0006761 This location has parts such as blood vessels etc. See PMC2868485, http://www.ncbi.nlm.nih.gov/pubmed/2695343 corneo-scleral junction the edge of the cornea where it joins the sclera; the limbus is a common site for the occurrence of corneal epithelial neoplasm MP:0013477 EMAPA:37835 MA:th corneal limbus FMA:58342 corneal limbus GAID:896 corneal-scleral limbus corneoscleral junction GAID:896 limbus corneae sclerocorneal junction FMA:58342 sclerocorneal limbus GAID:896 limbus corneae An epithelium that is composed primarily of secretory cells. consider splitting epithelium from epithelial tissue BTO:0002991 NCIT:C43370 NCIT:C45715 UMLS:C0682578 UMLS:C1708242 uberon UBERON:0006799 glandular epithelium An epithelium that is composed primarily of secretory cells. UMLS:C0682578 ncithesaurus:Glandular_Epithelium UMLS:C1708242 ncithesaurus:Glandular_Epithelial_Tissue Structural framework that provides support to the nasal sacs and ducts. AAO:0000320 FMA:60116 skeleton of nose uberon UBERON:0006813 nasal skeleton FMA FMA facial series Kardong-abduced Structural framework that provides support to the nasal sacs and ducts. AAO:0000320 skeleton of nose FMA:60116 An anatomical space that surrounded_by a trachea. FMA:7469 lumen of cartilaginous trachea tracheal lumen uberon UBERON:0006833 lumen of trachea An anatomical space that surrounded_by a trachea. OBOL:automatic lumen of cartilaginous trachea OBOL:automatic tracheal lumen FMA:7469 A furrow or an incomplete tube. AEO:0000161 EHDAA2_RETIRED:0003161 uberon groove UBERON:0006846 surface groove A furrow or an incomplete tube. AEO:0000161 AEO:JB groove AEO:0000161 A muscular coat that is part of a ureter. EMAPA:28811 FMA:15893 MA:0002654 muscular coat of ureter muscular layer of ureter muscularis of ureter tunica muscularis (ureter) tunica muscularis ureteris uberon ureteral smooth muscle layer UBERON:0006855 muscular coat of ureter FMA A muscular coat that is part of a ureter. OBOL:automatic muscular coat of ureter FMA:15893 muscular layer of ureter FMA:15893 muscularis of ureter FMA:15893 tunica muscularis (ureter) FMA:TA tunica muscularis ureteris FMA:TA ureteral smooth muscle layer EMAPA:28567 The distalmost portion of the digestive tract, derived from the hindgut, and terminating with the anus. this class is the superclass of 'rectum', which is currently reserved for the vertebrate structure. May be merged in future. FBbt:00005756 WBbt:0005773 rectum uberon rectal part of digestive tract terminal section of digestive tract UBERON:0006866 terminal part of digestive tract The distalmost portion of the digestive tract, derived from the hindgut, and terminating with the anus. rectum FBbt:00005756 A vasculature that is part of a organ. FMA:74612 organ vasculature set of blood vessels of organ uberon UBERON:0006876 vasculature of organ A vasculature that is part of a organ. OBOL:automatic organ vasculature FMA:74612 set of blood vessels of organ FMA:74612 A head mesenchyme that develops_from a mesoderm. merged in 'head mesoderm' from XAO/AAO and EFO here. Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme AAO:0011051 EFO:0003337 EFO:0003603 EHDAA2:0001118 EHDAA:655 EMAPA:16099 EMAPA_RETIRED:16270 FMA:293859 TAO:0000998 VHOG:0000185 XAO:0000053 ZFA:0000998 head mesenchyme derived from mesoderm head mesenchyme from head mesoderm head mesenchyme from mesoderm mesenchyme derived from head mesoderm mesenchyme from head mesoderm uberon cranial mesoderm head mesoderm UBERON:0006904 head mesenchyme from mesoderm ZFA EHDAA2 XAO A head mesenchyme that develops_from a mesoderm. OBOL:automatic head mesenchyme from head mesoderm EHDAA2:0001118 mesenchyme derived from head mesoderm EHDAA:1057 cranial mesoderm UBERON:0005280 head mesoderm AAO:0011051 UBERON:0005280 Mesenchyme that is part of a mandibular prominence. EHDAA2:0001062 EHDAA:5861 EHDAA:5873 EMAPA:17357 mesenchyme of mandibular process mesenchyme of mandibular prominence uberon UBERON:0006905 mandibular process mesenchyme Mesenchyme that is part of a mandibular prominence. OBOL:automatic mesenchyme of mandibular process EMAPA:17357 mesenchyme of mandibular prominence An anatomical space that surrounded_by a digestive tract. BTO:0000349 EMAPA:32908 FMA:45677 digestive tract lumen gut cavity gut lumen lumen of alimentary tract lumen of digestive tract lumen of gut uberon UBERON:0006909 lumen of digestive tract An anatomical space that surrounded_by a digestive tract. OBOL:automatic digestive tract lumen gut cavity BTO:0000349 gut lumen FMA:45677 lumen of alimentary tract lumen of digestive tract lumen of gut FMA:45677 An epithelium that is part of a lip. The thick, high squamous-stratified epithelium that covers the lips. It contains abundant melanocytes, many mucous cells and has well differentiated taste buds.[TAO] BTO:0004468 TAO:0005334 ZFA:0005334 uberon UBERON:0006913 lip epithelium An epithelium that is part of a lip. OBOL:automatic The thick, high squamous-stratified epithelium that covers the lips. It contains abundant melanocytes, many mucous cells and has well differentiated taste buds.[TAO] 2012-08-14 TAO:0005334 TAO ZFIN:ZDB-PUB-060921-12 An epithelium characterised by its most superficial layer consisting of squamous epithelial cells. FBbt:00007028 (squamous epithelium) A type of epithelium that is made up of flattened cells which are arranged with their long axes in the plane of the epithelium BTO:0002072 NCIT:C12848 UMLS:C0221909 uberon UBERON:0006914 squamous epithelium An epithelium characterised by its most superficial layer consisting of squamous epithelial cells. FBbt:00007028 (squamous epithelium) A type of epithelium that is made up of flattened cells which are arranged with their long axes in the plane of the epithelium FBbt UMLS:C0221909 ncithesaurus:Squamous_Epithelium Multilaminar epithelium which consists of more than one layer of squamous cells only one layer of which is in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, epithelium of wall of esophagus.[FMA] FMA:45563 NCIT:C13180 UMLS:C0836131 epithelium stratificatum squamosum uberon UBERON:0006915 stratified squamous epithelium Multilaminar epithelium which consists of more than one layer of squamous cells only one layer of which is in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, epithelium of wall of esophagus.[FMA] FMA:45563 UMLS:C0836131 ncithesaurus:Stratified_Squamous_Epithelium epithelium stratificatum squamosum FMA:45563 A squamous epithelium that is part of a stomach. EMAPA:35824 MA:0001611 uberon UBERON:0006921 stomach squamous epithelium A squamous epithelium that is part of a stomach. OBOL:automatic The squamous epithelium of the cervical portio is similar to that of the vagina, except that it is generally smooth and lacks rete pegs. Colposcopically, it appears featureless except for a fine network of vessels which is sometimes visible. The relative opacity and pale pink coloration of the squamous epithelium derives from its multi-layered histology and the location of its supporting vessels below the basement membrane. MA:0001725 NCIT:C49219 UMLS:C1707351 cervical squamous epithelium uberon UBERON:0006922 cervix squamous epithelium The squamous epithelium of the cervical portio is similar to that of the vagina, except that it is generally smooth and lacks rete pegs. Colposcopically, it appears featureless except for a fine network of vessels which is sometimes visible. The relative opacity and pale pink coloration of the squamous epithelium derives from its multi-layered histology and the location of its supporting vessels below the basement membrane. UMLS:C1707351 ncithesaurus:Cervix_Squamous_Epithelium A squamous epithelium that is part of a vagina. EMAPA:37794 MA:0001731 NCIT:C49314 UMLS:C1711259 vaginal squamous epithelium uberon UBERON:0006923 vagina squamous epithelium A squamous epithelium that is part of a vagina. OBOL:automatic EMAPA:37794 MA:th UMLS:C1711259 ncithesaurus:Vaginal_Squamous_Epithelium A glandular epithelium that lines the stomach. The stomach's glandular epithelium is characterized by the presence of gastric glands. we follow Kardong in treating the glandular epithelium as a distinct entity, and thus as an epithelium which has glands; FMA has 'epithelium of gastric gland', which is part of the gastric gland. EMAPA:17623 EMAPA:35814 FMA:63458 MA:0002784 epithelium of gastric gland uberon gastric gland epithelium UBERON:0006924 stomach glandular epithelium FMA A glandular epithelium that lines the stomach. The stomach's glandular epithelium is characterized by the presence of gastric glands. ISBN10:0073040584 epithelium of gastric gland FMA:63458 gastric gland epithelium FMA:63458 Any gland that is part of the digestive system. AAO:0000130 BTO:0000345 uberon digestive gland UBERON:0006925 digestive system gland Any gland that is part of the digestive system. UBERON:cjm digestive gland BTO:0000345 Simple columnar epithelium that constitutes the secretory part of a gland. Examples: epithelium of stomach, luminal epithelium of lactiferous duct.[FMA] FMA:64800 NCIT:C13182 UMLS:C0225337 uberon UBERON:0006929 glandular columnar epithelium Simple columnar epithelium that constitutes the secretory part of a gland. Examples: epithelium of stomach, luminal epithelium of lactiferous duct.[FMA] FMA:64800 UMLS:C0225337 ncithesaurus:Columnar_Epithelium stomach mucosa that is lined with glandular epithelium and part of a stomach glandular region. EMAPA:27167 MA:0001614 stomach glandular region glandular mucous membrane uberon UBERON:0006931 stomach glandular region mucosa stomach mucosa that is lined with glandular epithelium and part of a stomach glandular region. stomach glandular region glandular mucous membrane EMAPA:27167 Simple columnar epithelium made up of cells specialized to serve as sensory cells for the reception of external stimuli, as the sensory cells of the cochlea, vestibule, nasal mucosa, and tongue. note that the definition sourced from Dorlands say 'simple columnar', but FMA says atypical CALOHA:TS-0682 FMA:62410 uberon neuroepithelium UBERON:0006934 sensory epithelium Simple columnar epithelium made up of cells specialized to serve as sensory cells for the reception of external stimuli, as the sensory cells of the cochlea, vestibule, nasal mucosa, and tongue. BTO:0000314 note that the definition sourced from Dorlands say 'simple columnar', but FMA says atypical FMA neuroepithelium BTO:0000314 the epithelial cell layer containing the sensory hair cells and their associated sensory nerve terminals EMAPA:32883 MA:0001189 uberon UBERON:0006937 inner ear epithelium the epithelial cell layer containing the sensory hair cells and their associated sensory nerve terminals MGI:csmith MP:0003308 An epithelium that is part of a uterus. BTO:0003082 uberon uterus epithelium UBERON:0006955 uterine epithelium An epithelium that is part of a uterus. OBOL:automatic uterus epithelium BTO:0003082 The vascular cord is the primordial vasculature that will develop into blood vessels by the process of tubulogenesis[GO]. The vascular cord is composed of angioblast or vascular endothelial cells in a solid linear mass called a cord. The cord then undergoes tubulogenesis to form the lumen of the vessels[ZFA]. EFO:0003709 TAO:0005077 ZFA:0005077 uberon UBERON:0006965 vascular cord The vascular cord is the primordial vasculature that will develop into blood vessels by the process of tubulogenesis[GO]. The vascular cord is composed of angioblast or vascular endothelial cells in a solid linear mass called a cord. The cord then undergoes tubulogenesis to form the lumen of the vessels[ZFA]. GO:0072360 ZFA:0005077 A capillary that is part of the coronary system. ZFA:0005813 heart capillary uberon UBERON:0006966 coronary capillary A capillary that is part of the coronary system. heart capillary GO:0003248 A two dimensional anatomical structure that is the boundary between an anatomical structure and an anatomical substance, an anatomical space or the organism's environment. Examples include the surface of your skin, the surface of the lining of your gut; the surface of the endothelium of you aorta that is in contact with blood.n BILA:0000010 CARO:0001002 EHDAA2_RETIRED:0003192 FMA:24137 NCIT:C34022 UMLS:C1515977 uberon UBERON:0006984 Old definition: 'Non-material anatomical entity of two dimensions, that is demarcated by anatomical lines or points on the external or internal surfaces of anatomical structures.' Note, in the new definition, the space referred to is not necessarily an anatomical space. It may be the outside of an organism. anatomical surface via morphological boundary in CARO A two dimensional anatomical structure that is the boundary between an anatomical structure and an anatomical substance, an anatomical space or the organism's environment. Examples include the surface of your skin, the surface of the lining of your gut; the surface of the endothelium of you aorta that is in contact with blood.n CARO:0001002 UMLS:C1515977 ncithesaurus:Anatomic_Surface The splanchnic mesoderm in the cardiogenic region where the heart develops; it gives rise to endocardial heart tubes that fuse to form the primordial cardiac tube, the heart primordium[web]. Two migratory heart primordia that move ventrally during the course of neurulation, and then fuse[XAO]. consider FBbt:00005541 ! cardiogenic mesoderm review EHDAA2 placement AAO:0011021 BILA:0000051 EFO:0000315 EHDAA2:0000214 EHDAA:385 FMA:293143 VHOG:0001641 XAO:0000235 cardiogenic splanchnopleure uberon cardiac mesoderm cardiogenic mesoderm cardiogenic region heart primordia UBERON:0007005 cardiogenic splanchnic mesoderm The splanchnic mesoderm in the cardiogenic region where the heart develops; it gives rise to endocardial heart tubes that fuse to form the primordial cardiac tube, the heart primordium[web]. Two migratory heart primordia that move ventrally during the course of neurulation, and then fuse[XAO]. XAO:0000235 cardiogenic splanchnopleure EHDAA2:0000214 cardiac mesoderm XAO:0000235 cardiogenic mesoderm cardiogenic region heart primordia XAO:0000235 Organism at the cleavage stage. BILA:0000058 uberon UBERON:0007010 cleaving embryo Organism at the cleavage stage. OBOL:automatic A multicellular organism that is at the juvenile stage. Whole organism that is not fully grown or sexually mature.[TAO] juvenile BILA:0000076 TAO:0002047 juvenile organism juveniles uberon UBERON:0007021 sexually immature organism A multicellular organism that is at the juvenile stage. OBOL:automatic Whole organism that is not fully grown or sexually mature.[TAO] 2012-08-14 TAO:0002047 TAO TAO:wd juvenile organism BILA:0000076 juveniles TAO:0002047 A multicellular organism that existence_ends_with a post-juvenile adult stage and existence_starts_with a post-juvenile adult stage. Whole organism that is fully grown or sexually mature.[TAO] adult BILA:0000078 FBbt:00003004 HAO:0000087 NCIT:C17600 TAO:0002046 UMLS:C0001675 galen:Adult adults uberon UBERON:0007023 adult organism A multicellular organism that existence_ends_with a post-juvenile adult stage and existence_starts_with a post-juvenile adult stage. OBOL:automatic Whole organism that is fully grown or sexually mature.[TAO] 2012-08-14 TAO:0002046 TAO TAO:wd UMLS:C0001675 ncithesaurus:Adult adults TAO:0002046 The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis BILA:0000084 NCIT:C34268 UMLS:C1514442 future digestive tract future digestive tube future gut primitive gut uberon embryonic digestive tube primordial digestive tube primordial gut UBERON:0007026 presumptive gut The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis NCBIBook:NBK10107 UMLS:C1514442 ncithesaurus:Primordial_Gut BILA:0000142 uberon UBERON:0007037 mechanosensory system Cranial neural crest that migrates into the mandibular arch. TAO:0007064 XAO:0000024 ZFA:0007064 uberon UBERON:0007098 mandibular neural crest ZFA ZFA Cranial neural crest that migrates into the mandibular arch. ZFA:0007064 Cranial neural crest that migrates into the hyoid arch. TAO:0007065 XAO:0000025 ZFA:0007065 hyoid crest uberon UBERON:0007099 hyoid neural crest ZFA ZFA Cranial neural crest that migrates into the hyoid arch. ZFA:0007065 hyoid crest XAO:0000025 A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified]. note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis FBbt:00003154 SPD:0000130 TADS:0000147 dorsal tube heart uberon adult heart UBERON:0007100 Gene notes: Bmp, Nkx, Gata primary circulatory organ A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified]. GO:0007507 dorsal tube heart GO:0007507 adult heart FBbt:00003154 Ganglion which is located in the trunk. EFO:0000901 MAT:0000344 MIAA:0000344 TAO:0001573 ZFA:0001573 body ganglion trunk ganglia uberon UBERON:0007134 trunk ganglion Ganglion which is located in the trunk. ZFIN:curator body ganglion MAT:0000344 trunk ganglia ZFA:0001573 An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO] EFO:0003497 TAO:0000131 ZFA:0000131 uberon presumptive central nervous system UBERON:0007135 neural keel An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. ZFIN:ZDB-PUB-961014-576 An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000131 TAO ZFIN:curator presumptive central nervous system ZFA:0000131 An anatomical cavity that surrounded_by a midgut. EMAPA:18377 FMA:54366 midgut lumen uberon UBERON:0007147 lumen of midgut An anatomical cavity that surrounded_by a midgut. OBOL:automatic midgut lumen FMA:54366 An anatomical cavity that surrounded_by a hindgut. EMAPA:18396 FMA:54367 hindgut lumen uberon UBERON:0007148 lumen of hindgut An anatomical cavity that surrounded_by a hindgut. OBOL:automatic hindgut lumen FMA:54367 An anatomical cavity that surrounded_by a anal canal. EMAPA:18836 FMA:17357 anal canal lumen uberon UBERON:0007158 lumen of anal canal An anatomical cavity that surrounded_by a anal canal. OBOL:automatic anal canal lumen FMA:17357 An anatomical cavity that surrounded_by a colon. EMAPA:18945 FMA:18374 colon lumen uberon colonic lumen UBERON:0007159 lumen of colon An anatomical cavity that surrounded_by a colon. OBOL:automatic colon lumen FMA:18374 colonic lumen FMA:18374 A serous membrane that is part of a uterine tube infundibulum. EMAPA:29903 FMA:18324 serosa of infundibulum of fallopian tube serosa of infundibulum of oviduct uberon UBERON:0007181 serosa of infundibulum of uterine tube A serous membrane that is part of a uterine tube infundibulum. OBOL:automatic serosa of infundibulum of fallopian tube FMA:18324 serosa of infundibulum of oviduct FMA:18324 A muscle layer that is part of a uterine tube infundibulum. EMAPA:31264 FMA:18336 muscle layer of infundibulum of fallopian tube muscle layer of infundibulum of oviduct muscularis of infundibulum of uterine tube uberon UBERON:0007182 muscle layer of infundibulum of uterine tube A muscle layer that is part of a uterine tube infundibulum. OBOL:automatic muscle layer of infundibulum of fallopian tube FMA:18336 muscle layer of infundibulum of oviduct FMA:18336 muscularis of infundibulum of uterine tube FMA:18336 The structure from the trachea, bronchi, and bronchioles that forms the airways that supply air to the lungs. The lining of the tracheobronchial tree consists of ciliated columnar epithelial cells. UBERON:0004102 FMA:7393 NCIT:C117875 arbor tracheobronchialis uberon tracheobronchial system UBERON:0007196 tracheobronchial tree Wikipedia The structure from the trachea, bronchi, and bronchioles that forms the airways that supply air to the lungs. The lining of the tracheobronchial tree consists of ciliated columnar epithelial cells. arbor tracheobronchialis FMA:7393 FMA:TA tracheobronchial system HP:0005607 Mesenchyme that develops_from a cranial neural crest. EFO:0003572 EHDAA2:0000735 EMAPA:16169 EMAPA:16271 EMAPA_RETIRED:16271 TAO:0000787 ZFA:0000787 head mesenchyme from cranial neural crest head mesenchyme from neural crest head neural crest derived mesenchyme uberon UBERON:0007213 mesenchyme derived from head neural crest ZFA Mesenchyme that develops_from a cranial neural crest. OBOL:automatic head mesenchyme from neural crest EHDAA2:0000735 Mesenchyme that develops_from a trunk neural crest. EHDAA2:0002093 EMAPA:16182 TAO:0000999 ZFA:0000999 trunk mesenchyme from neural crest trunk neural crest derived mesenchyme uberon UBERON:0007214 mesenchyme derived from trunk neural crest Mesenchyme that develops_from a trunk neural crest. OBOL:automatic trunk mesenchyme from neural crest EHDAA2:0002093 relationship to Meckel's cartilage to be added Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG] EHDAA2:0000031 EHDAA:583 EMAPA:16382 VHOG:0000510 ventral pharyngeal arch 1 uberon ventral mandibular arch ventral visceral arch 1 UBERON:0007237 1st arch mandibular component EHDAA2 Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG] 2012-09-17 VHOG:0000510 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) ventral pharyngeal arch 1 VHOG:0000510 ventral mandibular arch VHOG:0000510 ventral visceral arch 1 VHOG:0000510 A tunica media that is part of a artery. EMAPA:36294 EV:0100029 FMA:14273 NCIT:C49321 UMLS:C1710627 arterial media tunica media (arteriae) uberon UBERON:0007239 tunica media of artery A tunica media that is part of a artery. OBOL:automatic UMLS:C1710627 ncithesaurus:Venous_System_Smooth_Muscle_Tissue arterial media EV:0100029 tunica media (arteriae) FMA:14273 A tunica adventitia that is part of a artery. EMAPA:36295 EV:0100030 FMA:14274 arterial adventitia tunica externa (adventitia)(arteriae) uberon UBERON:0007240 tunica adventitia of artery A tunica adventitia that is part of a artery. OBOL:automatic arterial adventitia EV:0100030 tunica externa (adventitia)(arteriae) FMA:14274 A tunica adventitia that is part of a vein. EMAPA:36310 EV:0100034 FMA:14355 tunica externa (adventitia)(venae) venous adventitia uberon UBERON:0007241 tunica adventitia of vein A tunica adventitia that is part of a vein. OBOL:automatic tunica externa (adventitia)(venae) FMA:14355 venous adventitia EV:0100034 A tunica intima that is part of a vein. EMAPA:36308 EV:0100032 FMA:14353 tunica interna (intima)(venae) venous intima uberon UBERON:0007242 tunica intima of vein A tunica intima that is part of a vein. OBOL:automatic tunica interna (intima)(venae) FMA:14353 venous intima EV:0100032 A tunica media that is part of a vein. EMAPA:36309 EV:0100033 FMA:14354 tunica media (venae) venous media uberon UBERON:0007243 tunica media of vein A tunica media that is part of a vein. OBOL:automatic tunica media (venae) FMA:14354 venous media EV:0100033 Gray matter of the central nervous system which is a collection of clustered nuclei. FMA:256381 FMA:84059 uberon cluster of neural nuclei neural nuclei nuclear complex UBERON:0007245 nuclear complex of neuraxis Gray matter of the central nervous system which is a collection of clustered nuclei. Any of the nuclei that comprise the superior olivary complex (superior olive). This includes both the primary nuclei such as the lateral and medial nuclei, as well as periolivary nuclei. this class exists largely for consistency with the FMA. It is defined trivially with respect to the SOC. The class may be removed in future. FMA:72246 superior olivary complex nucleus uberon UBERON:0007247 nucleus of superior olivary complex Any of the nuclei that comprise the superior olivary complex (superior olive). This includes both the primary nuclei such as the lateral and medial nuclei, as well as periolivary nuclei. superior olivary complex nucleus FMA:72246 A pre-cartilage condensation that is part of a trachea. EHDAA2:0002070 EHDAA:7082 uberon UBERON:0007267 trachea pre-cartilage rings A pre-cartilage condensation that is part of a trachea. OBOL:automatic Any collection of muscles that is part of a pectoral appendage. currently defined by location rather than attachment EFO:0003540 TAO:0000563 ZFA:0000563 pectoral fin muscle pectoral fin musculature uberon UBERON:0007269 pectoral appendage musculature Any collection of muscles that is part of a pectoral appendage. OBOL:automatic pectoral fin muscle ZFA:0000563 pectoral fin musculature ZFA:0000563 Any collection of muscles that is part of a pelvic appendage. currently defined by location rather than attachment Musculature that is part of the pelvic fin.[TAO] TAO:0000258 ZFA:0000258 pelvic fin musculature uberon UBERON:0007270 pelvic appendage musculature Any collection of muscles that is part of a pelvic appendage. OBOL:automatic Musculature that is part of the pelvic fin.[TAO] 2012-08-14 TAO:0000258 TAO TAO:curator pelvic fin musculature ZFA:0000258 Any collection of muscles that is part of an appendage. currently defined by location rather than attachment TAO:0000207 ZFA:0000207 fin musculature uberon UBERON:0007271 appendage musculature Any collection of muscles that is part of an appendage. OBOL:automatic fin musculature ZFA:0000207 Skeletal subdivision consisting of the anterior appendicular limb skeleton, excluding the pectoral girdle. VSAO:0005000 uberon cheiropterygium UBERON:0007272 pectoral appendage skeleton VSAO Skeletal subdivision consisting of the anterior appendicular limb skeleton, excluding the pectoral girdle. VSAO:0005000 VSAO:NI cheiropterygium VSAO:0005000 VSAO:NI The collection of all skeletal elements in a pelvic appendage region. uberon UBERON:0007273 pelvic appendage skeleton VSAO The collection of all skeletal elements in a pelvic appendage region. The rhombencephalon (or hindbrain) is a developmental categorization of portions of the central nervous system in vertebrates. The rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. In the human embryo eight rhombomeres can be distinguished, from caudal to rostral: Rh7-Rh1 and the isthmus (the most rostral rhombomere). A rare disease of the rhombencephalon, 'rhombencephalosynapsis' is characterized by a missing vermis resulting in a fused cerebellum. Patients generally present with cerebellar ataxia. The caudal rhombencephalon has been generally considered as the initiation site for neural tube closure. TODO - unify naming conventions The embryonic rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. Rhombomeres Rh7-Rh4 form the myelencephalon that will give the medulla oblongata. Rhombomeres Rh3-Rh1 form the metencephalon that will form the pons and the cerebellum[NPX:PDR]. BAMS:HB CALOHA:TS-2118 EFO:0003440 EHDAA2:0001630 FMA:295640 TAO:0000569 ZFA:0000569 presumptive rhombencephalon uberon embryonic rhombencephalon future hindbrain rhombencephalon UBERON:0007277 presumptive hindbrain XAO-abduced cjm The rhombencephalon (or hindbrain) is a developmental categorization of portions of the central nervous system in vertebrates. The rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. In the human embryo eight rhombomeres can be distinguished, from caudal to rostral: Rh7-Rh1 and the isthmus (the most rostral rhombomere). A rare disease of the rhombencephalon, 'rhombencephalosynapsis' is characterized by a missing vermis resulting in a fused cerebellum. Patients generally present with cerebellar ataxia. The caudal rhombencephalon has been generally considered as the initiation site for neural tube closure. The embryonic rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. Rhombomeres Rh7-Rh4 form the myelencephalon that will give the medulla oblongata. Rhombomeres Rh3-Rh1 form the metencephalon that will form the pons and the cerebellum[NPX:PDR]. NPX:PDR presumptive rhombencephalon ZFA:0000569 embryonic rhombencephalon CALOHA:TS-2118 future hindbrain rhombencephalon EHDAA2:0001630 A presumptive structure that has the potential to develop into a endocardium. Portion of tissue that is part of the heart tube and will become the endocardium.[TAO] TAO:0002233 ZFA:0001724 uberon UBERON:0007280 presumptive endocardium A presumptive structure that has the potential to develop into a endocardium. OBOL:automatic Portion of tissue that is part of the heart tube and will become the endocardium.[TAO] 2012-08-14 TAO:0002233 TAO ZFIN:curator Embryonic structure that gives rise to the midbrain hindbrain boundary. EFO:0003446 TAO:0001187 XAO:0004086 ZFA:0001187 presumptive MHB presumptive midbrain-hindbrain boundary uberon UBERON:0007281 presumptive midbrain hindbrain boundary ZFA Embryonic structure that gives rise to the midbrain hindbrain boundary. ZFA:0001187 presumptive MHB presumptive midbrain-hindbrain boundary ZFA:0001187 A presumptive structure that has the potential to develop into a presomitic mesoderm. EFO:0003421 TAO:0000053 ZFA:0000053 uberon presumptive segmental plates UBERON:0007282 presumptive segmental plate https://github.com/obophenotype/uberon/wiki/The-neural-crest EDHAA2 A presumptive structure that has the potential to develop into a presomitic mesoderm. OBOL:automatic presumptive segmental plates ZFA:0000053 A presumptive structure that has the potential to develop into a neural plate. consider merging Region of the gastrula which gives rise to the neural plate.[TAO] EFO:0003424 TAO:0000063 ZFA:0000063 prospective neuroectoderm prospective vegetal ectoderm uberon UBERON:0007284 presumptive neural plate A presumptive structure that has the potential to develop into a neural plate. OBOL:automatic Region of the gastrula which gives rise to the neural plate.[TAO] 2012-08-14 TAO:0000063 TAO ZFIN:curator prospective neuroectoderm ZFA:0000063 prospective vegetal ectoderm ZFA:0000063 The part of the blastula that has the potential to develop into a paraxial mesoderm. EFO:0003443 TAO:0000591 XAO:0004134 ZFA:0000591 future paraxial mesenchyme future paraxial mesoderm uberon UBERON:0007285 presumptive paraxial mesoderm The part of the blastula that has the potential to develop into a paraxial mesoderm. UBERON:cjm future paraxial mesenchyme UBERON:cjm A presumptive structure that has the potential to develop into a pronephric mesoderm. EFO:0003619 TAO:0001070 ZFA:0001070 nephron primordium uberon UBERON:0007297 presumptive pronephric mesoderm A presumptive structure that has the potential to develop into a pronephric mesoderm. OBOL:automatic nephron primordium ZFA:0001070 A blood vessel that is part of a pectoral appendage. TAO:0005301 ZFA:0005301 pectoral fin blood vessel uberon UBERON:0007300 pectoral appendage blood vessel A blood vessel that is part of a pectoral appendage. OBOL:automatic pectoral fin blood vessel ZFA:0005301 A blood vessel that is part of a limb/fin. TAO:0005299 ZFA:0005299 fin blood vessel limb blood vessel uberon UBERON:0007301 appendage blood vessel A blood vessel that is part of a limb/fin. OBOL:automatic fin blood vessel ZFA:0005299 limb blood vessel A vasculature that is part of a pectoral appendage. TAO:0005096 ZFA:0005096 pectoral fin vasculature uberon UBERON:0007302 pectoral appendage vasculature A vasculature that is part of a pectoral appendage. OBOL:automatic pectoral fin vasculature ZFA:0005096 A vasculature that is part of a chordate pharynx. TAO:0005003 ZFA:0005003 branchial vasculature uberon UBERON:0007303 pharyngeal vasculature A vasculature that is part of a chordate pharynx. OBOL:automatic branchial vasculature ZFA:0005003 A vasculature that is part of a limb/fin. TAO:0005095 ZFA:0005095 fin vasculature uberon UBERON:0007304 appendage vasculature A vasculature that is part of a limb/fin. OBOL:automatic fin vasculature ZFA:0005095 The epidermis is the entire outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species[GO]. this grouping class exists primarily to align with GO - see GO:0008544. BSA:0000073 BTO:0000313 FBbt:00004993 HAO:0000298 TADS:0000109 WBbt:0005733 epidermis epidermis (sensu Metazoa) outer epidermal layer outer epithelial layer uberon hypoderm hypodermis UBERON:0007376 outer epithelium The epidermis is the entire outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species[GO]. GO:0008544 epidermis GO:0008544 hypoderm BTO:0000313 hypodermis GO:0008544 WBbt:0005733 Portion of the dermis characterized by a well-arranged, plywood-like, collagenous network. Portion of the dermis characterized by a well-arranged, plywood-like, collagenous network. Le Guellec et al, 2004.[TAO] relationship loss: develops_from collagenous dermal stroma (TAO:0001186)[TAO] connective tissue in the skin is usually diffuse and irregular, although in some species collagen bundles are arranged in a distinct ordered layer in the dermis AAO:0010600 TAO:0001182 ZFA:0001182 dermal deep region stratum compactum uberon UBERON:0007377 stratum compactum of dermis Portion of the dermis characterized by a well-arranged, plywood-like, collagenous network. ISBN10:0073040584 ZFIN:ZDB-PUB-040726-12 Portion of the dermis characterized by a well-arranged, plywood-like, collagenous network. Le Guellec et al, 2004.[TAO] 2012-08-14 TAO:0001182 TAO ZFIN:curator relationship loss: develops_from collagenous dermal stroma (TAO:0001186)[TAO] 2012-08-14 TAO:0001182 TAO dermal deep region ZFA:0001182 stratum compactum AAO:0010600 Outermost layer of cells surrounding the embryo. Outermost monolayer of cells surrounding the embryo that become very flattened in the blastula and give rise to the periderm. Sometimes used synonymously with periderm. Kimmel et al, 1995.[TAO] relationship loss: develops_from superficial blastomere (TAO:0001484)[TAO] Originally this tissue is one cell layer thick but in most vertebrates it soon becomes a two layered structure. The outer layer gives rise to the periderm. EFO:0003425 TAO:0000086 ZFA:0000086 EVL enveloping layer uberon UBERON:0007383 enveloping layer of ectoderm Outermost layer of cells surrounding the embryo. Outermost monolayer of cells surrounding the embryo that become very flattened in the blastula and give rise to the periderm. Sometimes used synonymously with periderm. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000086 TAO ZFIN:curator relationship loss: develops_from superficial blastomere (TAO:0001484)[TAO] 2012-08-14 TAO:0000086 TAO EVL ZFA:0000086 enveloping layer ZFIN:ZDB-PUB-961014-576 A cartilage tissue that is part of a paired limb or fin. Cartilage which is part of one of the paired fins.[TAO] TAO:0001543 ZFA:0001543 uberon UBERON:0007389 paired limb/fin cartilage A cartilage tissue that is part of a paired limb or fin. Cartilage which is part of one of the paired fins.[TAO] 2012-08-14 TAO:0001543 TAO ZFIN:curator A cartilage tissue that is part of a pectoral appendage. Cartilage which is part of the pectoral fin.[TAO] TAO:0000257 ZFA:0000257 uberon pectoral fin cartilage UBERON:0007390 pectoral appendage cartilage tissue A cartilage tissue that is part of a pectoral appendage. OBOL:automatic Cartilage which is part of the pectoral fin.[TAO] 2012-08-14 TAO:0000257 TAO ZFIN:curator pectoral fin cartilage TAO:0000257 A cartilage tissue that is part of a pelvic appendage. Cartilage which is part of the pelvic fin.[TAO] TAO:0001459 ZFA:0001459 uberon pelvic fin cartilage UBERON:0007391 pelvic appendage cartilage tissue A cartilage tissue that is part of a pelvic appendage. OBOL:automatic Cartilage which is part of the pelvic fin.[TAO] 2012-08-14 TAO:0001459 TAO ZFIN:curator pelvic fin cartilage TAO:0001459 A nucleus of brain that spans a midbrain tegmentum. this class groups together any nuclei in the tegmentum region, possibly including disparate structures across species UBERON:0012277 FMA:258768 ZFA:0005577 tegmental nuclei tegmental nucleus uberon UBERON:0007414 nucleus of midbrain tegmentum A nucleus of brain that spans a midbrain tegmentum. OBOL:automatic tegmental nuclei tegmental nucleus ZFA:0005577 The space within an epithelial sphere. EHDAA2:0003079 AEO:0000079 cavity of vesicle uberon UBERON:0007473 lumen of epithelial sac The space within an epithelial sphere. AEO:JB cavity of vesicle AEO:0000079 An epithelial tube that is open at one end only. AEO:0000115 EHDAA2:0003115 uberon UBERON:0007499 epithelial sac AEO An epithelial tube that is open at one end only. AEO:JB UBERONREF:0000001 An epithelial tube open at both ends that allows fluid flow. AEO_RETIRED:0000116 RETIRED_EHDAA2:0003116 uberon UBERON:0007500 epithelial tube open at both ends AEO An epithelial tube open at both ends that allows fluid flow. AEO:JB UBERONREF:0000001 A closed epithelium with a lumen. EHDAA2:0003119 AEO:0000119 EHDAA2:0003119 uberon UBERON:0007503 epithelial vesicle AEO A closed epithelium with a lumen. AEO:JB Mesenchyme with little extracellular matrix. EHDAA2:0003146 AEO:0000146 EHDAA2:0003146 uberon UBERON:0007524 dense mesenchyme tissue AEO Mesenchyme with little extracellular matrix. AEO:JB Mesenchymal cells that are migrating. this class will be an important part of the NC reorganization EHDAA2:0003152 AEO:0000152 EHDAA2:0003152 uberon UBERON:0007530 migrating mesenchyme population Mesenchymal cells that are migrating. AEO:JB A ciliated columnar epithelium that is part of a oviduct. in FMA, epithelium of uterine tube is a subclass of ciliated columnar epithelium. MA introduces subtypes: ciliated columnar and cuboidal. We map the FMA type according to its relationships, not its label FMA:62016 MA:0001719 uberon epithelium of uterine tube uterine tube epithelium UBERON:0007589 ciliated columnar oviduct epithelium MA FMA A ciliated columnar epithelium that is part of a oviduct. OBOL:automatic in FMA, epithelium of uterine tube is a subclass of ciliated columnar epithelium. MA introduces subtypes: ciliated columnar and cuboidal. We map the FMA type according to its relationships, not its label FMA epithelium of uterine tube FMA:62016 uterine tube epithelium FMA:62016 A cuboidal epithelium that is part of a oviduct. MA:0001720 uberon UBERON:0007590 cuboidal oviduct epithelium MA A cuboidal epithelium that is part of a oviduct. OBOL:automatic Simple columnar epithelium in which the luminal side of the cells bears cilia. Examples: epithelium of trachea, epithelium of uterine tube.[FMA] In humans, Ciliated columnar epithelial cells are found mainly in the tracheal and bronchial regions of the pulmonary system and also in the fallopian tubes of the female reproductive system Ciliated columnar epithelium in the pulmonary system is interspersed with goblet cells that secrete mucous to form a mucosal layer apical to the epithelial layer. The rowing-like action of epithelial cilia work in tandem with goblet cells to propel mucus away from the lungs, preventing particulate matter from causing infection[http://www.bio.davidson.edu/people/kabernd/berndcv/lab/epithelialinfoweb/ciliated%20columnar%20epithelium.html] FMA:64798 uberon UBERON:0007592 ciliated columnar epithelium FMA Simple columnar epithelium in which the luminal side of the cells bears cilia. Examples: epithelium of trachea, epithelium of uterine tube.[FMA] FMA:64798 Epithelium bearing vibratile cilia on the free surface. uberon UBERON:0007601 ciliated epithelium Epithelium bearing vibratile cilia on the free surface. A thin, loose vascular connective tissue that makes up the membranes surrounding joints and the sheaths protecting tendons (particularly flexor tendons in the hands and feet) where they pass over bony prominences. Synovial tissue contains synovial cells, which secrete a viscous liquid called synovial fluid; this liquid contains protein and hyaluronic acid and serves as a lubricant and nutrient for the joint cartilage surfaces[BTO]. Synovial tissue can be found in tendons (tissues that connect muscle to bone), bursae (fluid-filled, cushioning sacs found in spaces between tendons, ligaments, and bones), and the cavity (hollow enclosed area) that separates the bones of a freely movable joint, such as the knee or elbow[BTO]. BTO:0001338 CALOHA:TS-0998 FMA:66762 synovium stratum synoviale synovial layer synovial membrane uberon synovial tissue UBERON:0007616 layer of synovial tissue BTO A thin, loose vascular connective tissue that makes up the membranes surrounding joints and the sheaths protecting tendons (particularly flexor tendons in the hands and feet) where they pass over bony prominences. Synovial tissue contains synovial cells, which secrete a viscous liquid called synovial fluid; this liquid contains protein and hyaluronic acid and serves as a lubricant and nutrient for the joint cartilage surfaces[BTO]. Synovial tissue can be found in tendons (tissues that connect muscle to bone), bursae (fluid-filled, cushioning sacs found in spaces between tendons, ligaments, and bones), and the cavity (hollow enclosed area) that separates the bones of a freely movable joint, such as the knee or elbow[BTO]. BTO:0001338 synovium CALOHA:TS-0998 stratum synoviale FMA:TA synovial layer FMA:66762 synovial membrane FMA:66762 synovial tissue BTO:0001338 An anatomical cavity that surrounded_by a synovial joint. FMA:11356 articular cavity (synovial joint) cavitas articularis (junctura synovialis) cavity of synovial joint uberon joint cavity synovial cavity UBERON:0007617 synovial cavity of joint An anatomical cavity that surrounded_by a synovial joint. OBOL:automatic articular cavity (synovial joint) FMA:11356 cavitas articularis (junctura synovialis) FMA:11356 cavity of synovial joint FMA:11356 joint cavity FMA:11356 synovial cavity FMA:11356 epithelial layer of the retina, ciliary body, or iris composed of cells containing pigment granules. GAID:907 MESH:D010857 uberon eye pigment epithelium UBERON:0007625 pigment epithelium of eye epithelial layer of the retina, ciliary body, or iris composed of cells containing pigment granules. MP:0005200 eye pigment epithelium MESH:A09.371.670 A neural nucleus that is part of a medulla oblongata. FMA:258772 uberon UBERON:0007635 nucleus of medulla oblongata A neural nucleus that is part of a medulla oblongata. OBOL:automatic The sensory trigeminal nerve nuclei are the largest of the cranial nerve nuclei, and extend through the whole of the midbrain, pons and medulla. There is also a distinct trigeminal motor nucleus that is medial to the chief sensory nucleus[WP]. in MA and FMA this is part of the pons / pontime tegmentum. We weaken this to overlaps to avoid inconsistency. In NIF this is a composite structure spanning multiple regions, which is more appropriate. BM:V CALOHA:TS-2077 DHBA:266441713 FMA:71248 HBA:9203 UMLS:C0040999 trigeminal nuclei uberon nuclei trigemini UBERON:0007641 trigeminal nuclear complex FMA FMA The sensory trigeminal nerve nuclei are the largest of the cranial nerve nuclei, and extend through the whole of the midbrain, pons and medulla. There is also a distinct trigeminal motor nucleus that is medial to the chief sensory nucleus[WP]. in MA and FMA this is part of the pons / pontime tegmentum. We weaken this to overlaps to avoid inconsistency. In NIF this is a composite structure spanning multiple regions, which is more appropriate. MA UMLS:C0040999 NIFSTD:birnlex_4096 trigeminal nuclei FMA:71248 nuclei trigemini 2 An anatomical structure that connects two structures junction FMA:5898 anatomical junction uberon UBERON:0007651 anatomical junction FMA An anatomical structure that connects two structures region of the embryo into the area in which the kidney rudiment will develop. uberon kidney anlage UBERON:0007687 kidney field region of the embryo into the area in which the kidney rudiment will develop. GO:0072004 GOC:mtg_kidney_jan10 kidney anlage GOC:mtg_kidney_jan10 Anlagen are populations of contiguous cells, typically arranged in one plane, that are morphologically indistinct, but that already correspond in extent to a later organ/tissue. field AEO:0000170 EFO:0001649 EHDAA2:0003170 FBbt:00005426 developmental field uberon future organ organ field UBERON:0007688 anlage FBbt AEO FBbt Anlagen are populations of contiguous cells, typically arranged in one plane, that are morphologically indistinct, but that already correspond in extent to a later organ/tissue. FBbt:00005426 JB:DEF . EFO:0003626 EHDAA2:0001457 EHDAA:962 EMAPA:32754 FMA:293087 TAO:0001104 ZFA:0001104 early pharyngeal arch endoderm uberon pharyngeal arch endoderm pharyngeal endoderm pharyngeal region endoderm UBERON:0007690 relation conflict: ZFA vs EHDAA2. Note EHDAA2 term renamed to 'early PA endoderm' early pharyngeal endoderm cjm . early pharyngeal arch endoderm EHDAA2:0001457 pharyngeal endoderm ZFA:0001104 pharyngeal region endoderm EHDAA2:0001456 The minute opening of a taste bud on the surface of the oral mucosa through which the gustatory hairs of the specialised neuroepithelial gustatory cells project. FMA:63589 NCIT:C33738 UMLS:C0226971 porus gustatorius taste pore uberon UBERON:0007691 gustatory pore FMA FMA The minute opening of a taste bud on the surface of the oral mucosa through which the gustatory hairs of the specialised neuroepithelial gustatory cells project. UMLS:C0226971 ncithesaurus:Taste_Pore porus gustatorius taste pore FMA:63589 A bone that is part of a reproductive organ. baculum uberon os penis/os clitoris UBERON:0007719 bone of reproductive organ A bone that is part of a reproductive organ. OBOL:automatic A gland that is part of a epidermis. FMA:59153 epidermal gland gland of epidermis uberon UBERON:0007771 epidermis gland A gland that is part of a epidermis. OBOL:automatic gland of epidermis FMA:59153 Any bodily fluid that has passed through a membrane such as the capillary wall, as a result of unbalanced hydrostatic and osmotic forces transudative characteristically low in protein and cellular content (unless there has been secondary concentration) FMA:12276 GAID:1195 MESH:D005122 ncithesaurus:Transudate uberon plasma ultrafiltrate UBERON:0007779 transudate Any bodily fluid that has passed through a membrane such as the capillary wall, as a result of unbalanced hydrostatic and osmotic forces Any fluid produced by a serous gland. serous fluid serosal fluid serous gland fluid uberon UBERON:0007794 secretion of serous gland Any fluid produced by a serous gland. UBERON:cjm serosal fluid Anatomical system that consists of all blood and lymph vessels. consider merging with vasculature The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System]. in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system BTO:0001085 CALOHA:TS-2053 EHDAA2:0004520 EMAPA:35905 MA:0002718 NCIT:C33854 UMLS:C0489903 uberon Gefaesssystem@de UBERON:0007798 vascular system MA Anatomical system that consists of all blood and lymph vessels. The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System]. ncithesaurus:Vascular_System in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system MA UMLS:C0489903 ncithesaurus:Vascular_System Gefaesssystem@de BTO:0001085 Adipose tissue that is located in the abdominal region. This includes any subcutaneous fat, visceral fat or encapsulated adipose tissue depots. CALOHA:TS-0002 EFO:0003771 uberon abdominal adipose tissue abdominal fat intra-abdominal fat UBERON:0007808 adipose tissue of abdominal region Adipose tissue that is located in the abdominal region. This includes any subcutaneous fat, visceral fat or encapsulated adipose tissue depots. CALOHA:paula MGI:csmith abdominal adipose tissue BTO:0004041 abdominal fat BTO:0004041 intra-abdominal fat BTO:0004041 The anteriormost subdivision of the body that includes the head, jaws, pharyngeal region and the neck (if present). In vertebrates this is the subdivision that includes the cervical vertebrae. CALOHA:TS-2356 EV:0100009 FMA:280881 MA:0000006 NCIT:C12418 UMLS:C0460004 WikipediaCategory:Head_and_neck galen:HeadAndNeck uberon cephalic area cephalic part of animal cephalic region head and neck head or neck UBERON:0007811 craniocervical region MA The anteriormost subdivision of the body that includes the head, jaws, pharyngeal region and the neck (if present). In vertebrates this is the subdivision that includes the cervical vertebrae. UMLS:C0460004 ncithesaurus:Head_and_Neck cephalic area cephalic part of animal cephalic region head and neck FMA:280881 An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). this encompasses non-skeletal tissue An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). There are only two instances of appendage girdle regions per organism.[VSAO] UBERON:0007824 girdle girdle region EMAPA:37854 FMA:24874 VSAO:0000303 uberon fin girdle fin girdle region limb girdle limb girdle region UBERON:0007823 appendage girdle region An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). UBERONREF:0000003 An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). There are only two instances of appendage girdle regions per organism.[VSAO] 2012-08-14 VSAO:0000303 VSAO EMAPA:37854 MA:th fin girdle fin girdle region limb girdle limb girdle region A bone that is part of a appendage girdle region. EMAPA:35379 MA:0000291 girdle bone uberon UBERON:0007828 girdle bone/zone A bone that is part of a appendage girdle region. OBOL:automatic girdle bone MA:0000291 A bone that is part of a pectoral girdle region. EMAPA:35669 MA:0000292 bone of pectoral girdle uberon UBERON:0007829 pectoral girdle bone MA A bone that is part of a pectoral girdle region. OBOL:automatic A bone element or fused bone that is part of pelvic girdle. check sacrum, coccyx (MA does NOT include these) typically the ilium, ischium and pubis. These can alternately be considered individual bones, or zones of a single fused bone EMAPA:18028 MA:0000293 NCIT:C33287 UMLS:C0030786 bone of pelvic girdle pelvic girdle bone uberon UBERON:0007830 pelvic girdle bone/zone MA A bone element or fused bone that is part of pelvic girdle. UMLS:C0030786 ncithesaurus:Pelvic_Bone pelvic girdle bone MA:0000293 A subdivision of a limb or fin skeleton consisting of bones which connects the upper limb or fin to the axial skeleton on each side. It consists of the clavicle and scapula in humans and, in those species with three bones in the pectoral girdle, the coracoid. Some mammalian species (e.g. the dog and the horse) have only the scapula. In humans, the only joints between the shoulder girdle and axial skeleton are the sternoclavicular joints on each side. No joint exists between each scapula and the rib cage; instead the muscular connection between the two permits relatively great mobility of the shoulder girdle in relation to the pelvic girdle. In those species having only the scapula, no joint exists between the forelimb and the thorax, the only attachment being muscular[WP]. Examples: There are only two instances, right and left pectoral girdle skeletons. Anatomical cluster of paired dermal and endochondral bones that attaches to the dorso-posterior part of the cranium, and support the radials and pectoral fin. It consists of two components: the primary pectoral girdle consisting of the endochondral coracoid, scapula and mesocoracoid bones, and the secondary pectoral girdle consisting of the dermal posttemporal, supracleithrum, cleithrum and poscleithrum(thra) bones.[TAO] Girdle skeleton consisting of a set of bones linking the axial series to the forelimb/fin skeleton and offering anchoring areas for forelimb/fin and caudal musculature.[VSAO] Skeletal structure immediately behind the head attached to the vertebral column by muscles and supporting the forelimbs.[AAO] The pectoral girdle is clearly of dual origin, composed of dermal as well as endochondral bones. The endochondral component, the scapulocoracoid, evolved by fusion or enlargment of several basal fin elements. (...) The dermal component of the shoulder girdle evolved from dermal bones of the body's surface. (...) Like endochondral bones, these dermal bones were passed along to tetrapods (...).[well established][VHOG] Note that the VSAO and many ontologies use the label 'pectoral girdle' to denote the skeletal region specifically. AAO:0000422 AAO:0000754 EFO:0000946 EHDAA2:0001420 FMA:24141 MAT:0000181 MIAA:0000181 NCIT:C33547 TAO:0000407 UMLS:C0427245 VHOG:0001156 VSAO:0000156 XAO:0003063 ZFA:0000407 skeletal parts of pectoral girdle skeleton of pectoral girdle uberon cingulum pectorale pectoral girdle scapular girdle UBERON:0007831 pectoral girdle skeleton A subdivision of a limb or fin skeleton consisting of bones which connects the upper limb or fin to the axial skeleton on each side. It consists of the clavicle and scapula in humans and, in those species with three bones in the pectoral girdle, the coracoid. Some mammalian species (e.g. the dog and the horse) have only the scapula. In humans, the only joints between the shoulder girdle and axial skeleton are the sternoclavicular joints on each side. No joint exists between each scapula and the rib cage; instead the muscular connection between the two permits relatively great mobility of the shoulder girdle in relation to the pelvic girdle. In those species having only the scapula, no joint exists between the forelimb and the thorax, the only attachment being muscular[WP]. Examples: There are only two instances, right and left pectoral girdle skeletons. Anatomical cluster of paired dermal and endochondral bones that attaches to the dorso-posterior part of the cranium, and support the radials and pectoral fin. It consists of two components: the primary pectoral girdle consisting of the endochondral coracoid, scapula and mesocoracoid bones, and the secondary pectoral girdle consisting of the dermal posttemporal, supracleithrum, cleithrum and poscleithrum(thra) bones.[TAO] 2012-08-14 TAO:0000407 TAO TAO:wd Girdle skeleton consisting of a set of bones linking the axial series to the forelimb/fin skeleton and offering anchoring areas for forelimb/fin and caudal musculature.[VSAO] 2012-08-14 VSAO:0000156 VSAO Skeletal structure immediately behind the head attached to the vertebral column by muscles and supporting the forelimbs.[AAO] 2012-06-20 AAO:0000422 AAO AAO:LAP The pectoral girdle is clearly of dual origin, composed of dermal as well as endochondral bones. The endochondral component, the scapulocoracoid, evolved by fusion or enlargment of several basal fin elements. (...) The dermal component of the shoulder girdle evolved from dermal bones of the body's surface. (...) Like endochondral bones, these dermal bones were passed along to tetrapods (...).[well established][VHOG] 2012-09-17 VHOG:0001156 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.336 and Figure 9.18 Note that the VSAO and many ontologies use the label 'pectoral girdle' to denote the skeletal region specifically. VSAO UMLS:C0427245 ncithesaurus:Shoulder_Girdle skeletal parts of pectoral girdle skeleton of pectoral girdle cingulum pectorale pectoral girdle VSAO:0000156 scapular girdle TAO:0000407 Skeletal subdivision consisting of a set of bones linking the axial series to the hindlimb zeugopodium and offering anchoring areas for hindlimb and caudal musculature. need to resolve whether this is a paired structure or a single belt (Paired in FMA - implicitly paired in VSAO) Anatomical cluster by which the hind limbs are supported and attached to the vertebral column.[AAO] Anatomical cluster that consists of the paired basipterygia which support the pelvic fin.[TAO] Girdle skeleton consisting of a set of bones linking the axial series to the hindlimb/fin skeleton and offering anchoring areas for hindlimb/fin and caudal musculature.[VSAO] The pelvic girdle is never joined by contributions of dermal bone. From its first appearance in placoderms, the pelvic girdle is exclusively endoskeletal. It arose from pterygiophores, perhaps several times, in support of the fin.[well established][VHOG] Note that the VSAO and many ontologies use the label 'pelvic girdle' to denote the skeletal region specifically. We place the EHDAA2 class here, note that this includes the pre-cartilage condensation as parts AAO:0000426 AAO:0000768 EFO:0000947 EHDAA2:0001426 EHDAA:7149 EHDAA:8324 EMAPA:18028 FMA:87592 MAT:0000182 MIAA:0000182 TAO:0000565 VHOG:0000305 VSAO:0000155 XAO:0003064 ZFA:0000565 galen:PelvicGirdle pelvic girdle skeleton skeletal parts of pelvic girdle skeleton of pelvic girdle uberon pelvic girdle UBERON:0007832 pelvic girdle skeleton Skeletal subdivision consisting of a set of bones linking the axial series to the hindlimb zeugopodium and offering anchoring areas for hindlimb and caudal musculature. VSAO:0000155 Anatomical cluster by which the hind limbs are supported and attached to the vertebral column.[AAO] 2012-06-20 AAO:0000426 AAO AAO:LAP Anatomical cluster that consists of the paired basipterygia which support the pelvic fin.[TAO] 2012-08-14 TAO:0000565 TAO TAO:wd Girdle skeleton consisting of a set of bones linking the axial series to the hindlimb/fin skeleton and offering anchoring areas for hindlimb/fin and caudal musculature.[VSAO] 2012-08-14 VSAO:0000155 VSAO The pelvic girdle is never joined by contributions of dermal bone. From its first appearance in placoderms, the pelvic girdle is exclusively endoskeletal. It arose from pterygiophores, perhaps several times, in support of the fin.[well established][VHOG] 2012-09-17 VHOG:0000305 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.333 Note that the VSAO and many ontologies use the label 'pelvic girdle' to denote the skeletal region specifically. We place the EHDAA2 class here, note that this includes the pre-cartilage condensation as parts VSAO pelvic girdle skeleton VSAO:0000155 skeletal parts of pelvic girdle skeleton of pelvic girdle pelvic girdle VSAO:0000155 Bone element that arises as a result of intramembranous ossification. Bone element that arises as a result of intramembranous ossification.[VSAO] Intramembranous bone that forms deep in the organism.[TAO] AEO:0000085 EHDAA2:0003085 TAO:0001645 VSAO:0000023 XAO:0004014 ZFA:0001636 uberon membrane bones UBERON:0007842 membrane bone VSAO Bone element that arises as a result of intramembranous ossification. GO_REF:0000034 VSAO:0000023 Bone element that arises as a result of intramembranous ossification.[VSAO] 2012-08-14 VSAO:0000023 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 PSPUB:0000170 Intramembranous bone that forms deep in the organism.[TAO] 2012-08-14 TAO:0001645 TAO TAO:wd membrane bones ZFA:0001636 Skeletal element that is composed of cartilage tissue and may be permanent or transient. TAO still mixes tissue and element AAO:0011130 CALOHA:TS-0118 EMAPA:32730 FMA:55107 VSAO:0000000 XAO:0004013 ZFA:0001501 cartilage organ cartilaginous element chondrogenic element uberon cartilage UBERON:0007844 cartilage element VSAO VSAO VSAO Skeletal element that is composed of cartilage tissue and may be permanent or transient. GO_REF:0000034 PSPUB:0000170 VSAO:0000000 TAO still mixes tissue and element TAO cartilage organ FMA:55107 cartilaginous element chondrogenic element VSAO:0000000 cartilage VSAO:0000000 Connective tissue, which consists of fibroblasts, the intercellular matrix of which contains a regular network of collagen and elastic fiber bundles. Examples: bone (tissue), cartilage (tissue), dense regular connective tissue. the connective tissue hierarchy largely follows FMA with definitions from VSAO. Note that in FMA, loose-CT is irregular-CT. This means regular-CT is necessarily equivalent to dense-regular-CT (assuming a JEPD classification). FMA:20103 uberon UBERON:0007845 regular connective tissue FMA Connective tissue, which consists of fibroblasts, the intercellular matrix of which contains a regular network of collagen and elastic fiber bundles. Examples: bone (tissue), cartilage (tissue), dense regular connective tissue. FMA:20103 Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts). Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts).[VSAO] Regular connective tissue, the intercellular matrix of which consists predominantly of collagen fiber bundles arranged in parallel arrays.[FMA] FMA:64781 NCIT:C33453 UMLS:C0225333 VSAO:0000050 XAO:0004030 dense fibrous connective tissue dense regular collagenous connective tissue dense regular collagenous tissue regular dense connective tissue typus regularis (textus connectivus collagenosus compactus) uberon UBERON:0007846 dense regular connective tissue FMA ncithesaurus Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts). GO_REF:0000034 PSPUB:0000170 VSAO:0000050 Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts).[VSAO] 2012-08-14 VSAO:0000050 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 PSPUB:0000170 Regular connective tissue, the intercellular matrix of which consists predominantly of collagen fiber bundles arranged in parallel arrays.[FMA] 2012-08-29 FMA:64781 FMA UMLS:C0225333 ncithesaurus:Regular_Dense_Connective_Tissue dense fibrous connective tissue FMA:64781 dense regular collagenous connective tissue FMA:64781 dense regular collagenous tissue FMA:64781 typus regularis (textus connectivus collagenosus compactus) FMA:64781 A bone that is part of a craniocervical region. EMAPA:37245 MA:0000569 head or neck bone uberon cranial bone UBERON:0007914 bone of craniocervical region MA MA A bone that is part of a craniocervical region. OBOL:automatic EMAPA:37245 MA:th head or neck bone MA:0000569 A skeletal joint that is part of a appendage girdle region. MA:0001505 girdle joint uberon UBERON:0008114 joint of girdle MA A skeletal joint that is part of a appendage girdle region. OBOL:automatic girdle joint OBOL:automatic A anatomical surface that is part of a cartilage element. FMA:76668 cartilage surface uberon UBERON:0008115 surface of cartilage A anatomical surface that is part of a cartilage element. OBOL:automatic cartilage surface FMA:76668 A bone that is hollow or contains many air cells, such as the mastoid process of the temporal bone[TMD]. subclasses of this should be checked for taxonomic consistency Skeletal pneumaticity is the presence of air spaces within bones. Skeletal pneumaticity exists only in synapsids and archosaurs. It is generally produced during development by excavation of bone by pneumatic diverticula (air sacs) from an air-filled space such as the lungs or nasal cavity. Pneumatization is highly variable between individuals, and bones not normally pneumatized can become pneumatized in pathological development. Pneumatization occurs in the skulls of mammals, crocodilians and birds among extant groups, as well as extinct archosaurs including the dinosaurs and pterosaurs. Pneumatic spaces include the paranasal sinuses and some of the mastoid cells[WP]. [Wikipedia:Skeletal_pneumaticity] FMA:7478 galen:PneumaticBone os pneumaticum pneumatic bone uberon hollow bone UBERON:0008193 pneumatized bone A bone that is hollow or contains many air cells, such as the mastoid process of the temporal bone[TMD]. os pneumaticum FMA:7478 pneumatic bone FMA:7478 Any muscle organ that is part of a pectoral girdle region. EMAPA has both non-skeletal and skeletal types, with the non-skeletal also including a chest muscle, so we place the skeletal class here as the most accurate EMAPA:17748 FMA:37347 muscle of pectoral girdle muscle of shoulder girdle pectoral girdle muscle uberon UBERON:0008196 muscle of pectoral girdle Any muscle organ that is part of a pectoral girdle region. OBOL:automatic EMAPA has both non-skeletal and skeletal types, with the non-skeletal also including a chest muscle, so we place the skeletal class here as the most accurate EMAPA muscle of shoulder girdle FMA:37347 pectoral girdle muscle FMA:37347 The part of the ventral body cavity that is within the pelvis. EMAPA:37235 FMA:9738 MA:0003089 space of pelvic compartment uberon cavitas pelvis UBERON:0008203 pelvic cavity The part of the ventral body cavity that is within the pelvis. UBERON:cjm EMAPA:37235 MA:th space of pelvic compartment FMA:9738 cavitas pelvis Musculature system of the pharyngeal and head regions. in MA this is restricted to skeletal muscles EMAPA:37259 MA:0000571 TAO:0000328 ZFA:0000328 head or neck muscle uberon head muscles head or neck muscle UBERON:0008229 craniocervical region musculature MA MA Musculature system of the pharyngeal and head regions. ZFA:0000328 ZFA:curator in MA this is restricted to skeletal muscles MA EMAPA:37259 MA:th head or neck muscle MA:0000571 head muscles ZFA:0000328 head or neck muscle MA:0000571 An endothelium that is part of a heart [Automatically generated definition]. this class includes any endothelia that are part of the heart. This might include the endocardial epithelia, as well as endothelia of vessels that are considered strictly part of the heart (e.g. outflow tract). As a grouping class, this may lack utility, and pending review this class may be obsoleted. For annotation consider a more specific class. BTO:0004293 uberon cardiac endothelium UBERON:0008307 heart endothelium An endothelium that is part of a heart [Automatically generated definition]. OBOL:automatic cardiac endothelium BTO:0004293 Any muscle organ that is part of an nose. FMA:73758 NCIT:C33158 UMLS:C0224219 muscle of nose uberon UBERON:0008522 nasal muscle FMA Any muscle organ that is part of an nose. OBOL:automatic UMLS:C0224219 ncithesaurus:Nasal_Muscle muscle of nose OBOL:automatic A transient embryonic complex that comprises the pharyngeal arches, bulges of tissues of mesoderm and neural crest derivation through which pass nerves and pharyngeal arch arteries. The arches are separated internally by pharyngeal pouches, evaginations of foregut endoderm, and externally by pharyngeal clefts, invaginations of surface ectoderm. The development of the system ends when the stucture it contributes to are forming, which may include (depending on species) the thymus, thyroid, parathyroids, maxilla, mandible, aortic arch, cardiac outflow tract, external and middle ear[GO,modified]. Currently defined in a vertebrate specific manner. The arch system has origins in basal deuterostomes, consider generalizing EHDAA2:0000187 FMA:293041 NCIT:C34248 UMLS:C1519038 embryonic pharyngeal complex pharyngeal apparatus pharyngeal system uberon pharyngeal arch complex pharyngeal arch region pharyngeal arches and clefts pharyngeal complex UBERON:0008814 pharyngeal arch system A transient embryonic complex that comprises the pharyngeal arches, bulges of tissues of mesoderm and neural crest derivation through which pass nerves and pharyngeal arch arteries. The arches are separated internally by pharyngeal pouches, evaginations of foregut endoderm, and externally by pharyngeal clefts, invaginations of surface ectoderm. The development of the system ends when the stucture it contributes to are forming, which may include (depending on species) the thymus, thyroid, parathyroids, maxilla, mandible, aortic arch, cardiac outflow tract, external and middle ear[GO,modified]. GO:0060037 GOC:dph UMLS:C1519038 ncithesaurus:Pharyngeal_Apparatus pharyngeal system GO:0060037 pharyngeal arch region EHDAA2:0000187 A head that is part of a embryo. CALOHA:TS-0246 FBbt:00000155 FMA:293011 uberon UBERON:0008816 embryonic head A head that is part of a embryo. OBOL:automatic A brain that develops_from a neural tube. a reasoner should automatically classify all the vertebrate ontology brain classes here vertebrate brain uberon UBERON:0008823 neural tube derived brain ZFA FMA A brain that develops_from a neural tube. OBOL:automatic The smooth muscle layer of the stomach wall that functions to churn and mix food and gastric secretions as well as to move food along the digestive tract to the intestines the muscularis externa in the stomach differs from that of other GI organs in that it has three layers of smooth muscle instead of two FMA:14909 gastric muscularis muscle layer of stomach muscularis externa of stomach tunica muscularis (gaster) tunica muscularis gastris uberon UBERON:0008856 stomach muscularis externa MA-abduced The smooth muscle layer of the stomach wall that functions to churn and mix food and gastric secretions as well as to move food along the digestive tract to the intestines MP:0010779 the muscularis externa in the stomach differs from that of other GI organs in that it has three layers of smooth muscle instead of two WP gastric muscularis FMA:14909 muscle layer of stomach FMA:14909 muscularis externa of stomach FMA:14909 tunica muscularis (gaster) FMA:14909 Any skeletal muscle organ in the hypodermis / superficial fascia We follow MP and treat this as part of the hypodermis, although some sources may consider the hypodermis to be superficial to this UBERON:0010934 EMAPA:18188 MA:0003140 hypodermal muscle layer hypodermis muscle layer superficial fascia muscular layer panniculus carnosus uberon UBERON:0008876 hypodermis skeletal muscle layer MP-def Any skeletal muscle organ in the hypodermis / superficial fascia ISBN10:0123813611 MP:0011157 hypodermal muscle layer MP:0011157 hypodermis muscle layer MP:0011157 panniculus carnosus MP:0011157 The part of the cardiovascular system consisting of all pulmonary arteries and all pulmonary veins. Subdivision of cardiovascular system which has as its parts the pulmonary arterial and venous tree organs.[FMA] FMA:45621 pulmonary circulatory system pulmonary system uberon UBERON:0008886 pulmonary vascular system Obol The part of the cardiovascular system consisting of all pulmonary arteries and all pulmonary veins. ISBN10:0073040584 Subdivision of cardiovascular system which has as its parts the pulmonary arterial and venous tree organs.[FMA] FMA FMA:45621 pulmonary circulatory system FMA:45621 pulmonary system ISBN10:0073040584 Subdivision of endoskeleton derived from pharyngeal arches Anatomical cluster that is part of the cranium and consists of the jaws, hyoid and branchial arches.[TAO] Anatomical cluster that is part of the cranium and consists of the jaws, hyoid, and branchial arches.[AAO] The part of the skull derived from the embryonic pharyngeal arches. [Biology_Online][VHOG] The skull of ancestral tetrapods has the three basic components that we have been considering: (1) chondrocranium, (2) splanchnocranium, and (3) dermatocranium (reference 1); Each part of the skull arises from a separate phylogenetic source. The most ancient part is the splanchnocranium (visceral cranium), which first arose to support pharyngeal slits in protochordates (reference 2).[well established][VHOG] VSAO labels this term 'pharyngeal arch' (2012-06-01) - however, it clearly means pharyngeal arch skeleton. many sources define this as the part of the endoskeletal that is from pharyngeal arches - this would make it part-disjoint from dermatocranium. However, there are many bones in AOs that have part-paths to both AAO:0010157 TAO:0001216 VHOG:0000315 VSAO:0000149 XAO:0003176 ZFA:0001216 pharyngeal endoskeleton viscerocranium uberon branchial arch skeleton gill arch skeleton pharyngeal arch pharyngeal arch skeleton pharyngeal skeleton visceral cranium visceral skeletal system visceral skeleton UBERON:0008895 splanchnocranium redundant Grays Subdivision of endoskeleton derived from pharyngeal arches ISBN10:0073040584 Anatomical cluster that is part of the cranium and consists of the jaws, hyoid and branchial arches.[TAO] 2012-08-14 TAO:0001216 TAO ZFIN:curator Anatomical cluster that is part of the cranium and consists of the jaws, hyoid, and branchial arches.[AAO] 2012-06-20 AAO:0010157 AAO AAO:EJS The part of the skull derived from the embryonic pharyngeal arches. [Biology_Online][VHOG] 2012-09-17 VHOG:0000315 VHOG The skull of ancestral tetrapods has the three basic components that we have been considering: (1) chondrocranium, (2) splanchnocranium, and (3) dermatocranium (reference 1); Each part of the skull arises from a separate phylogenetic source. The most ancient part is the splanchnocranium (visceral cranium), which first arose to support pharyngeal slits in protochordates (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000315 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.242, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.235 VSAO labels this term 'pharyngeal arch' (2012-06-01) - however, it clearly means pharyngeal arch skeleton. VSAO pharyngeal endoskeleton viscerocranium VHOG:0000315 ZFA:0001216 pharyngeal arch VSAO:0000149 pharyngeal arch skeleton ZFA:0001216 pharyngeal skeleton ZFA:0001216 visceral cranium visceral skeletal system visceral skeleton UBERONREF:0000007 A pharyngeal arch that is posterior to the hyoid arch. i.e. any pharyngeal arch with a number 3 or higher. Posterior-most stream of cranial neural crest, which sub-divides during migration.[AAO] AAO:0010362 BTO:0002152 EFO:0003694 TAO:0001597 XAO:0000099 ZFA:0001613 branchial arch branchial arches branchial bar branchial bars gill arch gill arches 1-5 pharyngeal arch 3-7 visceral arches 3-7 uberon gill bar UBERON:0008896 post-hyoid pharyngeal arch A pharyngeal arch that is posterior to the hyoid arch. i.e. any pharyngeal arch with a number 3 or higher. Posterior-most stream of cranial neural crest, which sub-divides during migration.[AAO] 2012-06-20 AAO:0010362 AAO AAO:EJS branchial arch ZFA:0001613 branchial arches ZFA:0001613 branchial bar ZFA:0001613 branchial bars ZFA:0001613 gill arch ZFA:0001613 gill arches 1-5 ZFA:0001613 pharyngeal arch 3-7 ZFA:0001613 visceral arches 3-7 ZFA:0001613 gill bar Skeletal element that forms superficially in the organism, usually in association with the ectoderm[VSAO]. Intramembranous bone that forms superficially in the organism.[TAO] other AOs are not yet in sync with this classification AAO:0010769 TAO:0001590 VSAO:0000130 XAO:0004015 ZFA:0001590 uberon dermal bones UBERON:0008907 dermal bone wd VSAO VSAO Skeletal element that forms superficially in the organism, usually in association with the ectoderm[VSAO]. GO_REF:0000034 VSAO:0000130 Intramembranous bone that forms superficially in the organism.[TAO] 2012-08-14 TAO:0001590 TAO TAO:wd dermal bones ZFA:0001590 Bone element that is adjacent to the notochord. We go with the latest VSAO in making this a subtype of bone, and add a logical definition based on the textual definition in VSAO. We also include the subtyping under 'replacement bone', for consistency with ZFA Replacement bone that forms within the connective tissue surrounding the notochord.[TAO] AAO:0010777 TAO:0001639 VSAO:0000307 ZFA:0001629 perichordal bones uberon perichordal bone UBERON:0008909 perichordal bone not in VSAO ZFA Bone element that is adjacent to the notochord. GO_REF:0000034 VSAO:0000307 Replacement bone that forms within the connective tissue surrounding the notochord.[TAO] 2012-08-14 TAO:0001639 TAO TAO:wd perichordal bones ZFA:0001629 perichordal bone ZFA:0001629 EHDAA2:0004069 NCIT:C34283 UMLS:C1514898 uberon UBERON:0008947 respiratory primordium Obol UMLS:C1514898 ncithesaurus:Respiratory_Primordium System pertaining to blood vessels in the brain. UBERON:0005284 BTO:0003840 EFO:0003491 EMAPA:35186 FMA:242007 FMA:61935 TAO:0000099 ZFA:0000099 brain vasculature cerebrovascular system intracerebral vasculature uberon UBERON:0008998 vasculature of brain System pertaining to blood vessels in the brain. BTO:0003840 cerebrovascular system BTO:0003840 intracerebral vasculature FMA:61935 Any portion of tissue that surrounds a urethra. BTO:0005081 uberon UBERON:0009010 periurethral tissue Any portion of tissue that surrounds a urethra. UBERON:cjm An artery that supplies blood to the urinary bladder. EMAPA:37131 MA:0002078 arteria vesicali vesical arteries uberon UBERON:0009027 vesical artery An artery that supplies blood to the urinary bladder. EMAPA:37131 MA:th arteria vesicali vesical arteries Vein that drains left lung and returns blood to the heart. A vein that returns oxygenated blood from the left lung to the left atrium of the heart[ncithesaurus:Left_Pulmonary_Vein]. EMAPA:37165 MA:0002207 NCIT:C48946 UMLS:C0226670 uberon UBERON:0009030 left pulmonary vein Vein that drains left lung and returns blood to the heart. A vein that returns oxygenated blood from the left lung to the left atrium of the heart[ncithesaurus:Left_Pulmonary_Vein]. ncithesaurus:Left_Pulmonary_Vein EMAPA:37165 MA:th UMLS:C0226670 ncithesaurus:Left_Pulmonary_Vein Vein that drains right lung and returns blood to the heart. A vein that returns oxygenated blood from the right lung to the left atrium of the heart[ncithesaurus:Right_Pulmonary_Vein]. EMAPA:37379 MA:0002208 NCIT:C48947 UMLS:C0226669 uberon UBERON:0009032 right pulmonary vein Vein that drains right lung and returns blood to the heart. A vein that returns oxygenated blood from the right lung to the left atrium of the heart[ncithesaurus:Right_Pulmonary_Vein]. ncithesaurus:Right_Pulmonary_Vein EMAPA:37379 MA:th UMLS:C0226669 ncithesaurus:Right_Pulmonary_Vein An organism containing a developing embryo, fetus, or unborn offspring within the body. BTO:0004733 uberon gravid pregnant adult pregnant adult stage pregnant organism pregnant stage UBERON:0009097 gravid organism An organism containing a developing embryo, fetus, or unborn offspring within the body. BTO:0004733 gravid BTO:0004733 pregnant adult BTO:0004733 pregnant adult stage BTO:0004733 pregnant stage BTO:0004733 The uterus in pregnancy NCIT:C12406 UMLS:C1514389 ncithesaurus:Gravid_Uterus uberon womb UBERON:0009098 gravid uterus The uterus in pregnancy UMLS:C1514389 ncithesaurus:Pregnant_Uterus A gonad prior to differentiating into a definitive testis or ovary. EHDAA2:0000716 NCIT:C34192 UMLS:C1512703 uberon gonad rudiment UBERON:0009117 typically part of the embryo - however, in male tammar wallabies the gonads are indifferent at the neonatal stage[8827321] indifferent gonad A gonad prior to differentiating into a definitive testis or ovary. UMLS:C1512703 ncithesaurus:Indifferent_Gonad Rostralmost epibranchial placode. Associated with 1st branchial cleft. EHDAA2:0004206 TAO:0001295 XAO:0004211 ZFA:0001295 epibranchial placode 1 facial epibranchial placode facial placode uberon facial VII placode hyoid VII placode hyoid placode UBERON:0009124 Taxonomic equivalence to EHDAA2 class made on basis of shared development: gives rise to geniculate ganglion geniculate placode ZFA Rostralmost epibranchial placode. Associated with 1st branchial cleft. NCBIBook:NBK53175 epibranchial placode 1 EHDAA2:0004206 facial epibranchial placode XAO:0004211 facial placode ZFA:0001295 hyoid VII placode ISBN10:0471888893 hyoid placode ISBN10:0471888893 Epibranchial placode between geniculate and nodose. Associated with 2nd branchial cleft. EHDAA2:0004207 TAO:0001296 XAO:0004212 ZFA:0001296 epibranchial placode 2 glossopharyngeal IX placode glossopharyngeal epibranchial placode glossopharyngeal placode uberon UBERON:0009125 Taxonomic equivalence to EHDAA2 class made on basis of shared development: gives rise to glossopharyngeal ganglion petrosal placode ZFA Epibranchial placode between geniculate and nodose. Associated with 2nd branchial cleft. NCBIBook:NBK53175 epibranchial placode 2 EHDAA2:0004207 glossopharyngeal IX placode ISBN10:0471888893 glossopharyngeal epibranchial placode XAO:0004212 glossopharyngeal placode ISBN10:0471888893 ZFA:0001296 Cranial ganglion which develops from an epibranchial placode. TAO:0001555 ZFA:0001555 epibranchial ganglia uberon UBERON:0009127 Epibranchial ganglia orchestrate the development of the cranial neurogenic crest epibranchial ganglion ZFA NCBIBook:NBK53175 Cranial ganglion which develops from an epibranchial placode. ZFIN:curator epibranchial ganglia ZFA:0001555 A vein that is part of a craniocervical region. EHDAA2:0004542 craniocervical vein head and neck veins vein of head and neck uberon UBERON:0009141 craniocervical region vein A vein that is part of a craniocervical region. OBOL:automatic head and neck veins EHDAA2:0004542 Sum total of mesenchyme in the embryo. consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm) UBERON:0003313 EHDAA2:0001113 EHDAA:177 EMAPA:16097 uberon UBERON:0009142 entire embryonic mesenchyme EHDAA2 Sum total of mesenchyme in the embryo. EMAPA:16549 RETIRED_EHDAA2:0001454 pharyngeal region uberon UBERON:0009145 pharyngeal region of foregut EHDAA2 pharyngeal region EMAPA:16549 EHDAA2:0004021 uberon UBERON:0009196 indifferent external genitalia cjm A nephric duct is a tube that drains a primitive kidney[GO]. EMAPA:16577 uberon UBERON:0009201 pronephric duct or mesonephric duct nephric duct EHDAA2 A nephric duct is a tube that drains a primitive kidney[GO]. GO:0072176 Mesenchyme that is part of a otic placode. EHDAA2:0001340 EMAPA:16196 uberon UBERON:0009477 associated mesenchyme of otic placode Mesenchyme that is part of a otic placode. OBOL:automatic An ectoderm that is part of a buccopharyngeal membrane. EHDAA2:0000190 EMAPA:16260 uberon UBERON:0009479 ectoderm of buccopharyngeal membrane An ectoderm that is part of a buccopharyngeal membrane. OBOL:automatic An endoderm that is part of a buccopharyngeal membrane. EHDAA2:0000191 EMAPA:16261 uberon UBERON:0009480 endoderm of buccopharyngeal membrane An endoderm that is part of a buccopharyngeal membrane. OBOL:automatic Mesenchyme that is part of a foregut-midgut junction. EHDAA2:0000570 EMAPA:16364 uberon UBERON:0009482 associated mesenchyme of foregut-midgut junction Mesenchyme that is part of a foregut-midgut junction. OBOL:automatic A portion of mesenchymal tissue associated with an individual pharyngeal arch. this represents a part of the entire arch mesenchyme (UBERON:0010046), and is therefore a superclass of the individual arch mesenchyme classes. Alternate definition: primordial embryonic connective tissue associated with the branchial arches, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to facial and cranial nerve-associated structures. EMAPA:32755 FMA:295694 branchial arch mesenchyme pharyngeal arch mesenchyme uberon UBERON:0009494 pharyngeal arch mesenchymal region EHDAA2 cjm A portion of mesenchymal tissue associated with an individual pharyngeal arch. this represents a part of the entire arch mesenchyme (UBERON:0010046), and is therefore a superclass of the individual arch mesenchyme classes. Alternate definition: primordial embryonic connective tissue associated with the branchial arches, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to facial and cranial nerve-associated structures. MP:0011262 branchial arch mesenchyme MP:0011262 pharyngeal arch mesenchyme An epithelium that is part of a foregut-midgut junction. EHDAA2:0000573 EMAPA:16564 uberon UBERON:0009497 epithelium of foregut-midgut junction EHDAA2 An epithelium that is part of a foregut-midgut junction. OBOL:automatic Anatomical region that surrounds the otic vesicle. EHDAA2:0001343 EMAPA:16670 XAO:0004474 otocyst associated mesenchyme otocyst mesenchyme uberon periotic region UBERON:0009500 periotic mesenchyme XAO EHDAA2 Anatomical region that surrounds the otic vesicle. XAO:0004474 XAO:curators otocyst associated mesenchyme EHDAA2:0001343 otocyst mesenchyme EMAPA:16670 periotic region XAO:0004474 Mesenchyme that is part of a developing hindgut. EHDAA2:0000780 EMAPA:16716 hindgut associated mesenchyme uberon UBERON:0009503 mesenchyme of hindgut Mesenchyme that is part of a developing hindgut. OBOL:automatic hindgut associated mesenchyme EHDAA2:0000780 Mesenchyme that is part of a developing trachea. EHDAA2:0002067 EMAPA:16854 trachea associated mesenchyme uberon UBERON:0009505 mesenchyme of trachea EHDAA2 Mesenchyme that is part of a developing trachea. OBOL:automatic trachea associated mesenchyme EHDAA2:0002067 An endoderm that is part of a anal region. EHDAA2:0004020 EMAPA:17177 uberon UBERON:0009521 anal membrane endodermal component An endoderm that is part of a anal region. OBOL:automatic An endoderm that is part of a foregut-midgut junction. EHDAA2:0000572 EMAPA:18403 uberon UBERON:0009550 endoderm of foregut-midgut junction An endoderm that is part of a foregut-midgut junction. OBOL:automatic A submucosa that is part of a intestine. FMA:15696 submucosa of intestine uberon UBERON:0009566 intestinal submucosa FMA A submucosa that is part of a intestine. OBOL:automatic submucosa of intestine FMA:15696 FMA:25054 region of trunk trunk subdivision uberon UBERON:0009569 subdivision of trunk region of trunk FMA:25054 trunk subdivision FMA:25054 A sulcus limitans of neural tube that is part of a future spinal cord. EHDAA2:0001265 EMAPA:17584 VHOG:0001548 spinal cord lateral wall sulcus limitans uberon UBERON:0009570 spinal cord sulcus limitans A sulcus limitans of neural tube that is part of a future spinal cord. OBOL:automatic spinal cord lateral wall sulcus limitans EHDAA2:0001265 A sulcus limitans of neural tube that is part of a future medulla oblongata. EHDAA2:0001100 EMAPA:17561 uberon UBERON:0009576 medulla oblongata sulcus limitans EHDAA2 A sulcus limitans of neural tube that is part of a future medulla oblongata. OBOL:automatic A sulcus limitans of neural tube that is part of a future metencephalon. EHDAA2:0001161 EMAPA:17567 uberon UBERON:0009577 metencephalon sulcus limitans A sulcus limitans of neural tube that is part of a future metencephalon. OBOL:automatic A sulcus limitans of neural tube that is part of a future myelencephalon. EHDAA2:0001945 uberon UBERON:0009578 myelencephalon sulcus limitans A sulcus limitans of neural tube that is part of a future myelencephalon. OBOL:automatic EHDAA2:0001172 EMAPA:16977 VHOG:0000910 mantle layer lateral wall midbrain midbrain lateral wall mantle layer uberon mantle layer lateral wall mesencephalon UBERON:0009581 midbrain mantle layer mantle layer lateral wall midbrain VHOG:0000910 mantle layer lateral wall mesencephalon VHOG:0000910 EMAPA:17580 VHOG:0000911 mantle layer lateral wall spinal cord spinal cord lateral wall mantle layer uberon UBERON:0009583 spinal cord mantle layer mantle layer lateral wall spinal cord VHOG:0000911 Mesenchyme that is part of a 1st arch mandibular component. UBERON:0010043 EHDAA2:0000034 EMAPA:16385 mesenchymal region of mandibular component of first pharyngeal arch mesenchyme of mandibular component uberon mandibular component mesenchyme mandibular mesenchyme UBERON:0009584 1st arch mandibular mesenchyme EMAPA Mesenchyme that is part of a 1st arch mandibular component. OBOL:automatic mesenchymal region of mandibular component of first pharyngeal arch mesenchyme of mandibular component EMAPA:16385 Mesenchyme that is part of a developing left lung. EHDAA2:0000944 EMAPA:16730 EMAPA:17654 left lung mesenchyme uberon UBERON:0009602 left lung associated mesenchyme Mesenchyme that is part of a developing left lung. OBOL:automatic left lung mesenchyme EMAPA:17654 Mesenchyme that is part of a developing right lung. EHDAA2:0001739 EMAPA:17662 right lung mesenchyme uberon UBERON:0009603 right lung associated mesenchyme Mesenchyme that is part of a developing right lung. OBOL:automatic right lung mesenchyme EMAPA:17662 A neural plate that develops_from a presumptive midbrain. TAO:0007019 ZFA:0007019 uberon UBERON:0009611 midbrain neural plate ZFA ZFA A neural plate that develops_from a presumptive midbrain. OBOL:automatic A neural plate that develops_from a presumptive hindbrain. TAO:0007022 ZFA:0007022 uberon UBERON:0009614 hindbrain neural plate ZFA ZFA A neural plate that develops_from a presumptive hindbrain. OBOL:automatic TODO - developmental relationships for lines TAO:0007044 ZFA:0007044 MHB neural plate midbrain-hindbrain boundary neural plate uberon UBERON:0009615 midbrain hindbrain boundary neural plate ZFA https://github.com/obophenotype/uberon/issues/438 Bgee:AN MHB neural plate midbrain-hindbrain boundary neural plate ZFA:0007044 A presumptive structure that has the potential to develop into a midbrain. TODO - unify naming conventions BAMS:MES EFO:0003432 EHDAA2:0000615 EMAPA:16140 TAO:0000148 ZFA:0000148 presumptive mesencephalon uberon early midbrain future midbrain mesencephalon UBERON:0009616 presumptive midbrain ZFA ZFA A presumptive structure that has the potential to develop into a midbrain. OBOL:automatic presumptive mesencephalon ZFA:0000148 early midbrain future midbrain mesencephalon EHDAA2:0000615 Bilateral mesenchymal mesoderm parallel and immediately adjacent to the neural tube/notochord; it generates a subset of extra-ocular, and other head, muscles. A major contributor to neurocranium [PMID:16313393] EHDAA2:0000736 EHDAA:364 EMAPA:16171 cephalic paraxial mesenchyme cephalic paraxial mesoderm cranial paraxial mesenchyme cranial paraxial mesoderm head paraxial mesenchyme uberon somitomere somitomeric mesoderm UBERON:0009617 head paraxial mesoderm Bilateral mesenchymal mesoderm parallel and immediately adjacent to the neural tube/notochord; it generates a subset of extra-ocular, and other head, muscles. cephalic paraxial mesenchyme cephalic paraxial mesoderm cranial paraxial mesenchyme cranial paraxial mesoderm head paraxial mesenchyme EHDAA2:0000736 EHDAA2:0002094 trunk and cervical paraxial mesenchyme uberon trunk paraxial mesenchyme UBERON:0009618 trunk paraxial mesoderm trunk and cervical paraxial mesenchyme EHDAA2:0002094 trunk paraxial mesenchyme EMAPA:35878 MA:0001859 uberon UBERON:0009644 trachea non-cartilage connective tissue MA A basement membrane that is part of a bronchus. MA classifies as type of connective tissue: https://github.com/obophenotype/mouse-anatomy-ontology/issues/108 EMAPA:37809 MA:0001832 NCIT:C49208 UMLS:C1707051 bronchial basement membrane uberon UBERON:0009652 bronchus basement membrane true A basement membrane that is part of a bronchus. OBOL:automatic MA classifies as type of connective tissue: https://github.com/obophenotype/mouse-anatomy-ontology/issues/108 MA EMAPA:37809 MA:th UMLS:C1707051 ncithesaurus:Bronchus_Basement_Membrane bronchial basement membrane A basement membrane that is part of a trachea. EMAPA:37552 MA:0001854 NCIT:C49302 UMLS:C1710455 uberon UBERON:0009653 trachea basement membrane true MA-modified A basement membrane that is part of a trachea. OBOL:automatic EMAPA:37552 MA:th UMLS:C1710455 ncithesaurus:Trachea_Basement_Membrane EMAPA:37092 MA:0001987 NCIT:C52947 UMLS:C1708633 labial artery uberon UBERON:0009657 artery of lip EMAPA:37092 MA:th UMLS:C1708633 ncithesaurus:Labial_Artery labial artery MA:0001987 Nucleus located in the midbrain. TAO:0002209 ZFA:0001665 uberon UBERON:0009661 midbrain nucleus Nucleus located in the midbrain. ZFIN:curator Nucleus located within the hindbrain. TAO:0002177 ZFA:0001658 uberon UBERON:0009662 hindbrain nucleus Nucleus located within the hindbrain. ZFIN:curator An anatomical space that surrounded_by a embryonic cloaca. EHDAA2:0004586 uberon UBERON:0009669 embryonic cloacal lumen An anatomical space that surrounded_by a embryonic cloaca. OBOL:automatic An anatomical space that surrounded_by a rectum. EHDAA2:0004587 EMAPA:18388 FMA:14598 lumen of rectum uberon UBERON:0009670 rectal lumen cjm EHDAA2 An anatomical space that surrounded_by a rectum. OBOL:automatic lumen of rectum FMA:14598 Any endocardium that is part of the right ventricle of the heart. Endocardium of ventricle which is continuous tricuspid valve, pulmonary valve and with the tunica intima of the pulmonary trunk. EHDAA2:0002188 EMAPA:17341 FMA:9536 NCIT:C102343 VHOG:0001235 right ventricle endocardium right ventricular endocardium uberon endocardial lining of right ventricle right ventricle endocardial tissue UBERON:0009712 endocardium of right ventricle EHDAA2 FMA Any endocardium that is part of the right ventricle of the heart. Endocardium of ventricle which is continuous tricuspid valve, pulmonary valve and with the tunica intima of the pulmonary trunk. FMA:9536 right ventricle endocardium VHOG:0001235 right ventricular endocardium FMA:9536 endocardial lining of right ventricle EMAPA:17341 right ventricle endocardial tissue VHOG:0001235 Any endocardium that is part of the left ventricle of the heart. Endocardium of ventricle which is continuous with mitral valve, aortic valve, atrioventricular septum and the tunica intima of the aorta. EHDAA2:0002182 EMAPA:17338 FMA:9559 VHOG:0001233 left ventricle endocardium left ventricular endocardium uberon endocardial lining of left ventricle left ventricle endocardial tissue UBERON:0009713 endocardium of left ventricle FMA Any endocardium that is part of the left ventricle of the heart. Endocardium of ventricle which is continuous with mitral valve, aortic valve, atrioventricular septum and the tunica intima of the aorta. FMA:9559 left ventricle endocardium VHOG:0001233 left ventricular endocardium FMA:9559 endocardial lining of left ventricle EMAPA:17338 left ventricle endocardial tissue VHOG:0001233 An anatomical cavity that surrounded_by a stomodeum. lumen of stomatodaeum lumen of stomodeum stomatodeal cavity uberon UBERON:0009715 stomodeal lumen An anatomical cavity that surrounded_by a stomodeum. OBOL:automatic EHDAA2:0004621 EMAPA:32754 FMA:293087 uberon pharyngeal arch endoderm UBERON:0009722 entire pharyngeal arch endoderm pharyngeal arch endoderm EHDAA2:0004621 The embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the developing cardiac structures decide whether to merge with cardiac mesoderm. In EHDAA2 this lasts CS12->unbounded, includes mesenchyme of individual components as parts EHDAA2:0004162 EMAPA:36438 heart mesenchyme uberon UBERON:0009751 cardiac mesenchyme The embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the developing cardiac structures MP:0011264 heart mesenchyme EMAPA:36438 A ganglion that is part of a abdominal segment of trunk. uberon UBERON:0009758 abdominal ganglion A ganglion that is part of a abdominal segment of trunk. OBOL:automatic The many-lobed berry cluster of cells that is the terminous of a gland where the secretion is produced is acinar in form. acinar acinus FMA:55588 uberon acini UBERON:0009842 glandular acinus The many-lobed berry cluster of cells that is the terminous of a gland where the secretion is produced is acinar in form. acinus FMA:55588 acini An anatomical space that surrounded_by a primitive urogenital sinus. EHDAA2:0002142 uberon UBERON:0009844 urogenital sinus lumen EHDAA2 An anatomical space that surrounded_by a primitive urogenital sinus. OBOL:automatic Mesenchyme that surrounds primitive urogenital sinus. Androgen receptor (AR) activation releases instructive signals from UGM that acts on UGS epithelium (UGE) to stimulate cell proliferation, form prostate ductal progenitors (prostatic buds), and regulate cell adhesion dynamics to permit prostatic bud outgrowth EMAPA:31500 UGM uberon UBERON:0009845 urogenital sinus mesenchyme Mesenchyme that surrounds primitive urogenital sinus. OBOL:automatic UGM An epithelium that is part of a embryonic cloaca. cloacal epithelium EHDAA2:0004585 uberon UBERON:0009846 embryonic cloacal epithelium EHDAA2 An epithelium that is part of a embryonic cloaca. OBOL:automatic cloacal epithelium EHDAA2:0004585 Branch or outpocketing of the digestive tract. FBbt:00100316 uberon diverticulum of gut intestinal pouch UBERON:0009854 digestive tract diverticulum Branch or outpocketing of the digestive tract. diverticulum of gut FBbt:00100316 galen:Diverticulum pouch uberon diverticulum UBERON:0009856 sac A division of the stomach. The stomach can be divided based on mucosal histology (glandular epithelium and gastric glands) and the relative position and type of gastric gland. We follow Kardong in defining stomach regions by gland, but we also include 'body of stomach'. In future we may want to have different partitions of the stomach UBERON:0009034 EMAPA:35821 FMA:14558 MA:0002561 gastric zone region of stomach section of stomach uberon UBERON:0009870 zone of stomach A division of the stomach. The stomach can be divided based on mucosal histology (glandular epithelium and gastric glands) and the relative position and type of gastric gland. ISBN10:0073040584 gastric zone FMA:14558 EFO:0003704 TAO:0005041 ZFA:0005041 ALPM uberon UBERON:0009881 anterior lateral plate mesoderm ZFA ALPM ZFA:0005041 A specific region of the lateral mesoderm that will form the majority of the mesodermal component of the right ventricle, arterial pole (outflow tract) and venous pole (inflow tract). extra-cardiac population of mesodermal progenitors that gives rise to the right ventricle and outflow tract[PMID:17276708]. In general, the two studies in chick concluded that the contribution of the SHF was to the outflow tract, whereas the mouse work suggested that the second lineage contributed more broadly to the heart, including the outflow tract and much or all of the right ventricle [11-14]. These different conclusions may represent differences in the experimental approaches used or may represent bona fide differences in the contribution of the second lineage to the hearts of birds compared to mammals [11]. Alternatively, the secondary/anterior heart fields described in the chick may represent a subset of a broader field that makes a more substantial contribution to the heart, as the mouse studies suggested in mouse has left ventricular identity[PMID:22855565] XAO:0004186 anterior heart field anterior/second heart field second heart field uberon SHF UBERON:0009889 secondary heart field GO:0003129 A specific region of the lateral mesoderm that will form the majority of the mesodermal component of the right ventricle, arterial pole (outflow tract) and venous pole (inflow tract). GO:0003139 GOC:mtg_heart GOC:rl extra-cardiac population of mesodermal progenitors that gives rise to the right ventricle and outflow tract[PMID:17276708]. In general, the two studies in chick concluded that the contribution of the SHF was to the outflow tract, whereas the mouse work suggested that the second lineage contributed more broadly to the heart, including the outflow tract and much or all of the right ventricle [11-14]. These different conclusions may represent differences in the experimental approaches used or may represent bona fide differences in the contribution of the second lineage to the hearts of birds compared to mammals [11]. Alternatively, the secondary/anterior heart fields described in the chick may represent a subset of a broader field that makes a more substantial contribution to the heart, as the mouse studies suggested anterior heart field anterior/second heart field Geisha:syn NCBITaxon:8782 second heart field XAO:0004186 SHF XAO:0004186 Mesenchyme that is part of a developing face. EMAPA:35337 FMA:302884 face mesenchyme mesenchyme of face uberon UBERON:0009891 facial mesenchyme Mesenchyme that is part of a developing face. OBOL:automatic An anatomical wall that is part of a ureter. FMA:15888 ureteral wall uberon UBERON:0009916 wall of ureter An anatomical wall that is part of a ureter. OBOL:automatic ureteral wall FMA:15888 The smooth muscle tissue surrounding the epithelium of the ureter EMAPA:28811 ureteral smooth muscle ureteral smooth muscle layer uberon UBERON:0009919 ureter smooth muscle The smooth muscle tissue surrounding the epithelium of the ureter MP:0011426 ureteral smooth muscle MP:0011426 ureteral smooth muscle layer EMAPA:28844 EHDAA2:0001315 EHDAA:1122 uberon UBERON:0009920 optic neural crest EHDAA2 A multicellular organism that existence_starts_with a post-embryonic stage. MA:0002405 postnatal organism TS28 mouse post-hatching organism post-natal organism postnatal mouse uberon UBERON:0009953 post-embryonic organism A multicellular organism that existence_starts_with a post-embryonic stage. OBOL:automatic TS28 mouse MA:0002405 post-hatching organism post-natal organism postnatal mouse MA:0002405 Cranial ectodermal placode with potential to develop into a component of the nervous system, such as nerves or ganglia. Includes: trigeminal, otic, lateral line and epibranchial placodes. While some sensory placodes (otic and olfactory) may have homologues in basal chordates (Wada et al., 1998), the so-called neurogenenic placodes (trigeminal, otic, lateral line and epibranchial placodes) appear to have emerged at a later time (Shimeld and Holland, 2000) EFO:0003460 TAO:0001309 XAO:0004620 ZFA:0001309 neurogenic placodes uberon placodae neurogenicae UBERON:0009955 neurogenic placode cjm Cranial ectodermal placode with potential to develop into a component of the nervous system, such as nerves or ganglia. While some sensory placodes (otic and olfactory) may have homologues in basal chordates (Wada et al., 1998), the so-called neurogenenic placodes (trigeminal, otic, lateral line and epibranchial placodes) appear to have emerged at a later time (Shimeld and Holland, 2000) NCBIBook:NBK53171 neurogenic placodes ZFA:0001309 placodae neurogenicae A anatomical space that is enclosed by a urinary bladder. EHDAA2:0004058 FMA:15924 galen:UrinaryBladderCavity bladder cavity cavity of urinary bladder lumen of urinary bladder urinary bladder lumen uberon UBERON:0009958 bladder lumen FMA FMA EHDAA2 A anatomical space that is enclosed by a urinary bladder. OBOL:automatic bladder cavity FMA:15924 cavity of urinary bladder FMA:15924 lumen of urinary bladder FMA:15924 urinary bladder lumen FMA:15924 The junction between the ureter and the renal pelvis of the kidney EMAPA:37782 FMA:15898 MA:0003021 NCIT:C106203 pelviureteric junction pelvoureteric junction uberon UBERON:0009972 ureteropelvic junction MP The junction between the ureter and the renal pelvis of the kidney MP:0011487 EMAPA:37782 MA:th pelviureteric junction FMA:15898 The valve-like structure found at the site of entry of the ureter into the urinary bladder, normally displays an oblique angulation through the detrusor to avoid reflux of urine up the ureters and the kidney EMAPA:37783 FMA:15899 MA:0003020 NCIT:C106202 vesico-ureteral junction vesico-ureteric junction vesicoureteric junction uberon UBERON:0009973 ureterovesical junction MP The valve-like structure found at the site of entry of the ureter into the urinary bladder, normally displays an oblique angulation through the detrusor to avoid reflux of urine up the ureters and the kidney MP:0011488 EMAPA:37783 MA:th vesico-ureteral junction MA:0003020 An anatomical structure that has more than one cell as a part. CARO:0010000 FBbt:00100313 multicellular structure uberon UBERON:0010000 multicellular anatomical structure CARO An anatomical structure that has more than one cell as a part. CARO:0010000 multicellular structure FBbt:00100313 A small cluster of cells of various types which form a discrete structure, largely delimited by a morphological boundary and whose components work together to make the whole structure capable of a specific function. CARO:0010001 FBbt:00007229 uberon UBERON:0010001 Examples include arthropod sensilla. cell cluster organ CARO CARO FBbt A small cluster of cells of various types which form a discrete structure, largely delimited by a morphological boundary and whose components work together to make the whole structure capable of a specific function. CARO:0010001 Mesenchyme that is part of a pharyngeal arch 6. EHDAA2:0004076 EMAPA:32765 FMA:318209 6th pharyngeal arch mesenchyme uberon 6th branchial arch mesenchyme pharyngeal arch 6 mesenchyme UBERON:0010031 6th arch mesenchyme Mesenchyme that is part of a pharyngeal arch 6. OBOL:automatic An organ of the digestive tract that is capable of retaining and storing food This is a very broad functionally defined grouping class that collects disparate structures from insects to vertebrates BSA:0000123 TADS:0000172 TGMA:0001041 uberon UBERON:0010039 food storage organ An organ of the digestive tract that is capable of retaining and storing food Mesenchyme that is part of a pharyngeal arch 1. EMAPA:16128 mesenchyme of 1st arch uberon UBERON:0010042 1st arch mesenchyme Mesenchyme that is part of a pharyngeal arch 1. OBOL:automatic mesenchyme of 1st arch EMAPA:16128 The sum total of mesenchymal tissue in the pharyngeal arch region. Pharyngeal mesenchyme is undifferentiated, loose connective tissue derived mostly from mesoderm, and also contains ectodermally derived neural crest cells. EHDAA2:0001459 EMAPA:16550 XAO:0004524 associated mesenchyme of pharyngeal region entire branchial arch associated mesenchyme pharyngeal arch associated mesenchyme uberon UBERON:0010046 entire pharyngeal arch associated mesenchyme EHDAA2 EHDAA2 cjm The sum total of mesenchymal tissue in the pharyngeal arch region. Pharyngeal mesenchyme is undifferentiated, loose connective tissue derived mostly from mesoderm, and also contains ectodermally derived neural crest cells. XAO:0004524 associated mesenchyme of pharyngeal region EMAPA:16550 entire branchial arch associated mesenchyme pharyngeal arch associated mesenchyme EHDAA2:0001459 Gland of the epithelium lining the oral cavity. The most common are the salivary glands. Note that Kardong classifies lacrimal glands here. EHDAA2 includes pituitary primordium, as this develops from oral mucosa UBERON:0003293 EHDAA2:0001327 EHDAA:2181 EMAPA:16572 EMAPA:16723 VHOG:0000652 buccal gland uberon gland of oral opening gland of oral region mouth gland oral cavity gland oral region gland UBERON:0010047 oral gland Gland of the epithelium lining the oral cavity. The most common are the salivary glands. ISBN10:0073040584 Note that Kardong classifies lacrimal glands here. EHDAA2 includes pituitary primordium, as this develops from oral mucosa EHDAA2 An epithelium consisting of cuboidal epithelial cells. TODO - coordinate with CL, add cuboidal cell in NCIT this is glandular NCIT:C32415 UMLS:C0682577 uberon UBERON:0010077 cuboidal epithelium An epithelium consisting of cuboidal epithelial cells. in NCIT this is glandular NCIT UMLS:C0682577 ncithesaurus:Cuboidal_Epithelium Mesenchyme that has the potential to develop into a dermis. check development EHDAA2:0000598 uberon UBERON:0010083 future dermis EHDAA2 EHDAA2 XAO Mesenchyme that has the potential to develop into a dermis. OBOL:automatic A developing anatomical structure that has the potential to develop into a metencephalon. EHDAA2:0000623 uberon UBERON:0010092 future metencephalon A developing anatomical structure that has the potential to develop into a metencephalon. OBOL:automatic A developing anatomical structure that has the potential to develop into a myelencephalon. EHDAA2:0000640 uberon UBERON:0010096 future myelencephalon A developing anatomical structure that has the potential to develop into a myelencephalon. OBOL:automatic A gray matter that has the potential to develop into a facial nucleus. EHDAA2:0004639 uberon UBERON:0010123 future facial nucleus A gray matter that has the potential to develop into a facial nucleus. OBOL:automatic A gray matter that has the potential to develop into a superior salivatory nucleus. EHDAA2:0004644 uberon UBERON:0010125 future superior salivatory nucleus A gray matter that has the potential to develop into a superior salivatory nucleus. OBOL:automatic Any portion of cardiac muscle tissue that is part of the conducting system of heart or the Purkinje fibers. EHDAA2:0004528 FMA:83378 specialized conducting tissue of heart specialized muscle tissue of heart uberon UBERON:0010131 conducting tissue of heart Any portion of cardiac muscle tissue that is part of the conducting system of heart or the Purkinje fibers. specialized conducting tissue of heart FMA:83378 specialized muscle tissue of heart FMA:83378 any of the organized aggregations of cells that function as secretory or excretory organs and that release hormones in response to neural stimuli MA:0000720 neuroendocrine system gland uberon UBERON:0010133 neuroendocrine gland any of the organized aggregations of cells that function as secretory or excretory organs and that release hormones in response to neural stimuli ISBN:0-683-40008-8 MP:0000631 A mucous secretion that is produced by glands in the epidermis. uberon epidermal mucus skin mucous UBERON:0010152 skin mucus A mucous secretion that is produced by glands in the epidermis. epidermal mucus BTO:0005082 An anatomical cavity that surrounded_by a blood vessel. FMA:312610 blood vessel lumen uberon UBERON:0010161 lumen of blood vessel An anatomical cavity that surrounded_by a blood vessel. OBOL:automatic An urethral gland that is part of a female urethra. EMAPA:29653 FMA:21444 female urethra gland gland of female urethra urethral gland (female) uberon UBERON:0010187 female urethral gland An urethral gland that is part of a female urethra. OBOL:automatic urethral gland (female) FMA:21444 A roughly circular bulge in a surface. requires review AEO:0000205 EHDAA2:0003250 FMA:82506 uberon UBERON:0010188 protuberance EHDAA2 A roughly circular bulge in a surface. EHDAA2:0003250 the paired arterial structures of the embryo that supplies each developing somite via efferent segmental arteries; the dorsal aortae articulate with the umbilical arteries, which return mixed blood to the villi of the chorion for reoxygenation EHDAA2:0000410 EMAPA:18606 MA:0000476 paired dorsal aortae uberon UBERON:0010190 pair of dorsal aortae EHDAA2 EHDAA2 the paired arterial structures of the embryo that supplies each developing somite via efferent segmental arteries; the dorsal aortae articulate with the umbilical arteries, which return mixed blood to the villi of the chorion for reoxygenation ISBN:0-914294-08-3 MP:0004787 paired dorsal aortae EHDAA2:0000410 EHDAA2:0004512 uberon UBERON:0010191 aortic system Wikipedia One of the laterally paired arteries that supply the gonads. gonadal artery uberon UBERON:0010192 genital artery One of the laterally paired arteries that supply the gonads. ISBN10:0073040584 An anatomical boundary that corresponds to some physical discontinuity. CARO:0001004 uberon UBERON:0010199 One might argue that all boundaries are actually fiat in the sense that there must be some fiat element at a fine enough scale of granularity. This ontology choses to ignore this issue as below the level of granularity relevant to anatomy. (DOS121102) bona-fide anatomical boundary CARO An anatomical boundary that corresponds to some physical discontinuity. CARO:0001004 Apparatus located between the lungs and the buccal cavity. This apparatus is composed of a pair of arytenoid cartilages that are supported by the cricoid ring. check this. See also https://github.com/obophenotype/uberon/wiki/The-axial-skeleton AAO:0000267 EHDAA2:0000904 laryngeal cartilage system uberon UBERON:0010212 laryngeal apparatus EHDAA2 Apparatus located between the lungs and the buccal cavity. This apparatus is composed of a pair of arytenoid cartilages that are supported by the cricoid ring. AAO:0000267 laryngeal cartilage system EHDAA2:0000904 uberon UBERON:0010213 laryngeal pre-cartilage condensation EHDAA2-abstracted EHDAA2-abstracted EHDAA2:0004085 uberon UBERON:0010221 Many sources say: thyroid cartilage from arch 4 other laryngeal cartilage (cricoid/arytenoid) from 6? laryngeal associated mesenchyme EHDAA2 EHDAA2 Wikipedia Wikipedia Wikipedia The core globe-shaped component of the camera-type eye. See notes for camera-type eye FMA:12513 MIAA:0000283 VHOG:0001616 bulbus oculi eye globe eyeball uberon eye globe UBERON:0010230 eyeball of camera-type eye FMA The core globe-shaped component of the camera-type eye. UBERON:cjm eye globe VHOG:0001616 eyeball FMA:12513 eye globe HP:0100886 MIAA:0000283 Mesenchyme that develops_from a neural crest and is part of a 1st arch mandibular mesenchyme. EHDAA2:0000037 uberon UBERON:0010252 1st arch mandibular mesenchyme from neural crest inferred Mesenchyme that develops_from a neural crest and is part of a 1st arch mandibular mesenchyme. OBOL:automatic Mesenchyme that develops_from a neural crest and is part of a 2nd arch mesenchyme. EHDAA2:0000068 EMAPA:16281 neural crest derived arch 2 mesenchyme pharyngeal arch 2 mesenchyme from neural crest uberon branchial arch 2 mesenchyme from neural crest UBERON:0010254 2nd arch mesenchyme from neural crest Mesenchyme that develops_from a neural crest and is part of a 2nd arch mesenchyme. OBOL:automatic Mesenchyme that develops_from a neural crest and is part of a 4th arch mesenchyme. In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] EHDAA2:0000098 EMAPA:16772 VHOG:0000580 4th pharyngeal arch mesenchyme derived from neural crest mesenchyme derived from neural crest of mesenchyme of 4th arch neural crest derived arch 4 mesenchyme pharyngeal arch 4 mesenchyme from neural crest uberon branchial arch 4 mesenchyme from neural crest UBERON:0010256 4th arch mesenchyme from neural crest Mesenchyme that develops_from a neural crest and is part of a 4th arch mesenchyme. OBOL:automatic In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] 2012-09-17 VHOG:0000580 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) 4th pharyngeal arch mesenchyme derived from neural crest VHOG:0000580 mesenchyme derived from neural crest of mesenchyme of 4th arch EMAPA:16772 Mesenchyme that develops_from a neural crest and is part of a 6th arch mesenchyme. EHDAA2:0004077 neural crest derived arch 6 mesenchyme pharyngeal arch 6 mesenchyme from neural crest uberon branchial arch 6 mesenchyme from neural crest UBERON:0010257 6th arch mesenchyme from neural crest Mesenchyme that develops_from a neural crest and is part of a 6th arch mesenchyme. OBOL:automatic Mesenchyme that develops_from a rhombencephalon neural crest. EHDAA2:0004423 uberon UBERON:0010258 mesenchyme from rhombencephalic neural crest Mesenchyme that develops_from a rhombencephalon neural crest. OBOL:automatic Mesenchyme that develops_from a neural crest and is part of a 1st arch mesenchyme. EMAPA:16129 mesenchyme derived from neural crest of mesenchyme of 1st arch neural crest derived arch 1 mesenchyme pharyngeal arch 1 mesenchyme from neural crest uberon branchial arch 1 mesenchyme from neural crest UBERON:0010259 1st arch mesenchyme from neural crest Mesenchyme that develops_from a neural crest and is part of a 1st arch mesenchyme. OBOL:automatic mesenchyme derived from neural crest of mesenchyme of 1st arch EMAPA:16129 Portion of tissue that is dorsolateral to the floor plate and part of the midbrain. DHBA:12322 EFO:0003567 EHDAA2:0004375 TAO:0000761 ZFA:0000761 basal plate midbrain basal plate midbrain region uberon UBERON:0010285 midbrain basal plate EHDAA2 EHDAA2 ZFA Portion of tissue that is dorsolateral to the floor plate and part of the midbrain. ZFA:0000761 basal plate midbrain TAO:0000761 basal plate midbrain region ZFA:0000761 Portion of neural tube that gives rise to the midbrain. we follow ZFA in temporally dividing midbrain NT from presumptive midbrain, but in future this may be collapsed TAO:0007039 ZFA:0007039 uberon UBERON:0010286 midbrain neural tube ZFA Portion of neural tube that gives rise to the midbrain. ZFA:0007039 . uberon UBERON:0010291 layer of sclera cjm . An endothelium that is part of a sclera. uberon UBERON:0010294 scleral endothelium Wikipedia An endothelium that is part of a sclera. OBOL:automatic Mesenchyme surrounding the developing optic cup which develops into the sclera. The mesenchyme surrounding the developing optic cup differentiates into the sclera, the dense fibrous coat of the eye.. http://www.ncbi.nlm.nih.gov/pubmed/16496288 uberon UBERON:0010299 scleral mesenchyme Mesenchyme surrounding the developing optic cup which develops into the sclera. An epithelium that is part of a extraembryonic structure. extra-embryonic epithelium uberon UBERON:0010303 extraembryonic epithelium An epithelium that is part of a extraembryonic structure. OBOL:automatic Stratified squamous epithelium is a stratified squamous epithelium, the cells of which synthesizes but does not accumulate keratin. Examples: epithelium of vagina, epithelium of wall of esophagus. FMA:45569 epithelium stratificatum squamosum noncornificatum nonkeratinizing stratified squamous epithelium stratified squamous non-keratinized epithelium stratified squamous nonkeratinizing epithelium uberon UBERON:0010304 non-keratinized stratified squamous epithelium FMA Stratified squamous epithelium is a stratified squamous epithelium, the cells of which synthesizes but does not accumulate keratin. Examples: epithelium of vagina, epithelium of wall of esophagus. FMA:45569 epithelium stratificatum squamosum noncornificatum FMA:45569 nonkeratinizing stratified squamous epithelium FMA:45569 stratified squamous non-keratinized epithelium stratified squamous nonkeratinizing epithelium Developing anatomical structure that develops into the eyeball and associated structures. Multi-tissue structure that consists of the structures that develop into the retina and lens.[TAO] TAO:0002201 ZFA:0001678 future eye uberon UBERON:0010312 immature eye definitional Developing anatomical structure that develops into the eyeball and associated structures. ZFA:0001678 Multi-tissue structure that consists of the structures that develop into the retina and lens.[TAO] 2012-08-14 TAO:0002201 TAO ZFIN:curator An anatomical structure that develops from the neural crest. Grouping term for query purposes uberon UBERON:0010313 neural crest-derived structure An anatomical structure that develops from the neural crest. An anatomical structure that has some part that develops from the neural crest. Grouping term for query purposes uberon UBERON:0010314 structure with developmental contribution from neural crest An anatomical structure that has some part that develops from the neural crest. uberon UBERON:0010316 germ layer / neural crest A skeletal element that is part of a orbital region. uberon eye skeleton ocular skeleton skeletal element of orbital region UBERON:0010321 skeletal element of eye region A skeletal element that is part of a orbital region. OBOL:automatic Skeletal subdivision of the head including skull (cranium plus mandible), pharyngeal and/or hyoid apparatus. we use 'cranial skeletal system', so that we can include the skull, which has joints/sutures as parts (recall, we follow FMA in distinguishing between the skeleton and skeletal system - only the latter includes joints) that the cranial skeleton includes the pharyngeal arch skeleton. It is thus more inclusive that the cranium itself, and extends beyond the head in tetrapods. The AAO class called 'skull' belongs here, as it includes the whole splanchnocranium Bony structure that encases the central nervous system and the primary sense organs of sight, olfaction, hearing, and equilibrium.[AAO] Skeletal system which is part of the skull, including the splanchnocranium, chondrocranium, and dermatocranium.[TAO] AAO:0000109 AAO:0000971 AAO:0010185 TAO:0000737 VSAO:0000049 XAO:0003075 ZFA:0000737 cranial skeleton osteocranium uberon cranium UBERON:0010323 cranial skeletal system Skeletal subdivision of the head including skull (cranium plus mandible), pharyngeal and/or hyoid apparatus. GO_REF:0000034 PSPUB:0000170 VSAO:0000049 Bony structure that encases the central nervous system and the primary sense organs of sight, olfaction, hearing, and equilibrium.[AAO] 2012-06-20 AAO:0000109 AAO AAO:LAP Skeletal system which is part of the skull, including the splanchnocranium, chondrocranium, and dermatocranium.[TAO] 2012-08-14 TAO:0000737 TAO ZFIN:curator cranium ZFA:0000737 Mesenchyme that is part of a limb/fin bud. uberon UBERON:0010329 paired limb/fin bud mesenchyme Mesenchyme that is part of a limb/fin bud. OBOL:automatic Mesenchyme that develops_from a neural crest and is part of a mandibular process mesenchyme. EHDAA2:0004603 uberon UBERON:0010336 mandibular process mesenchyme from neural crest EHDAA2 Mesenchyme that develops_from a neural crest and is part of a mandibular process mesenchyme. OBOL:automatic Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a mandibular process mesenchyme. EHDAA2:0004604 uberon UBERON:0010337 mandibular process mesenchyme from head mesenchyme EHDAA2 Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a mandibular process mesenchyme. OBOL:automatic Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch mandibular mesenchyme. EHDAA2:0000036 uberon UBERON:0010339 1st arch mandibular mesenchyme from head mesenchyme Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch mandibular mesenchyme. OBOL:automatic Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch mesenchyme. EMAPA:16130 mesenchyme derived from head mesoderm of mesenchyme of 1st arch uberon UBERON:0010341 1st arch mesenchyme from head mesenchyme Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch mesenchyme. OBOL:automatic mesenchyme derived from head mesoderm of mesenchyme of 1st arch EMAPA:16130 Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 2nd arch mesenchyme. EHDAA2:0000067 EMAPA:16280 head mesenchyme derived arch 2 mesenchyme mesenchyme derived from head mesoderm of mesenchyme of 2nd arch pharyngeal arch 2 mesenchyme from head mesenchyme uberon branchial arch 2 mesenchyme from head mesenchyme UBERON:0010343 2nd arch mesenchyme from head mesenchyme Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 2nd arch mesenchyme. OBOL:automatic mesenchyme derived from head mesoderm of mesenchyme of 2nd arch EMAPA:16280 Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 4th arch mesenchyme. EHDAA2:0000097 EMAPA:16771 head mesenchyme derived arch 4 mesenchyme mesenchyme derived from head mesoderm of mesenchyme of 4th arch pharyngeal arch 4 mesenchyme from head mesenchyme uberon branchial arch 4 mesenchyme from head mesenchyme UBERON:0010345 4th arch mesenchyme from head mesenchyme Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 4th arch mesenchyme. OBOL:automatic mesenchyme derived from head mesoderm of mesenchyme of 4th arch EMAPA:16771 Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 6th arch mesenchyme. EHDAA2:0004078 head mesenchyme derived arch 6 mesenchyme pharyngeal arch 6 mesenchyme from head mesenchyme uberon branchial arch 6 mesenchyme from head mesenchyme UBERON:0010347 6th arch mesenchyme from head mesenchyme Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 6th arch mesenchyme. OBOL:automatic Mesenchyme that develops_from a neural crest and is part of a entire pharyngeal arch associated mesenchyme. arch mesenchyme from neural crest branchial arch mesenchyme from neural crest neural crest derived arch mesenchyme uberon UBERON:0010359 Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme pharyngeal arch mesenchyme from neural crest Mesenchyme that develops_from a neural crest and is part of a entire pharyngeal arch associated mesenchyme. OBOL:automatic Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a entire pharyngeal arch associated mesenchyme. arch mesenchyme from head mesenchyme branchial arch mesenchyme from head mesenchyme head mesenchyme derived arch mesenchyme uberon UBERON:0010360 Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme pharyngeal arch mesenchyme from head mesenchyme Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a entire pharyngeal arch associated mesenchyme. OBOL:automatic Skeletal subdivision that undergoes indirect development and includes elements that develop as a replacement or substitution of other elements or tissues. An endoskeleton is an internal support structure of an animal, composed of mineralized tissue. Endoskeleton develops within the skin or in the deeper body tissues. The vertebrate is basically an endoskeleton made up of two types of tissues (bone and cartilage). During early embryonic development the endoskeleton is composed of notochord and cartilage. The notochord in most vertebrates is replaced by vertebral column and cartilage is replaced by bone in most adults. In three phyla and one subclass of animals, endoskeletons of various complexity are found: Chordata, Echinodermata, Porifera, and Coleoidea. An endoskeleton may function purely for support (as in the case of sponges), but often serves as an attachment site for muscle and a mechanism for transmitting muscular forces. A true endoskeleton is derived from mesodermal tissue. Such a skeleton is present in echinoderms and chordates. The poriferan 'skeleton' consists of microscopic calcareous or siliceous spicules or a spongin network. The Coleoidae do not have a true endoskeleton in the evolutionary sense; here, a mollusk exoskeleton evolved into several sorts of internal structure, the 'cuttlebone' of cuttlefish being the best-known version. Yet they do have cartilaginous tissue in their body, even if it is not mineralized, especially in the head, where it forms a primitive cranium. The endoskeleton gives shape,support and protection to the body and provides a mean of locomotion.[Wikipedia:Endoskeleton]t VSAO:0000037 XAO:0004026 replacement skeleton uberon UBERON:0010362 endoskeleton VSAO Skeletal subdivision that undergoes indirect development and includes elements that develop as a replacement or substitution of other elements or tissues. GO_REF:0000034 PSPUB:0000170 VSAO:0000037 An endoskeleton is an internal support structure of an animal, composed of mineralized tissue. Endoskeleton develops within the skin or in the deeper body tissues. The vertebrate is basically an endoskeleton made up of two types of tissues (bone and cartilage). During early embryonic development the endoskeleton is composed of notochord and cartilage. The notochord in most vertebrates is replaced by vertebral column and cartilage is replaced by bone in most adults. In three phyla and one subclass of animals, endoskeletons of various complexity are found: Chordata, Echinodermata, Porifera, and Coleoidea. An endoskeleton may function purely for support (as in the case of sponges), but often serves as an attachment site for muscle and a mechanism for transmitting muscular forces. A true endoskeleton is derived from mesodermal tissue. Such a skeleton is present in echinoderms and chordates. The poriferan 'skeleton' consists of microscopic calcareous or siliceous spicules or a spongin network. The Coleoidae do not have a true endoskeleton in the evolutionary sense; here, a mollusk exoskeleton evolved into several sorts of internal structure, the 'cuttlebone' of cuttlefish being the best-known version. Yet they do have cartilaginous tissue in their body, even if it is not mineralized, especially in the head, where it forms a primitive cranium. The endoskeleton gives shape,support and protection to the body and provides a mean of locomotion.[Wikipedia:Endoskeleton]t replacement skeleton VSAO:curator A skeletal element that has the potential to participate in endochondral ossification, and may participate in intramembranous ossification. VSAO:0000139 XAO:0004017 ZFA:0005620 endochondral replacement element uberon UBERON:0010363 endochondral element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern VSAO A skeletal element that has the potential to participate in endochondral ossification, and may participate in intramembranous ossification. GO_REF:0000034 PSPUB:0000170 VSAO:0000139 endochondral replacement element VSAO:0000139 Skeletal subdivision that undergoes direct development and includes elements that either develop in association with the basement membrane of the ectoderm or are homologous with such elements; includes dermatocranium, components of the appendicular skeleton, teeth and tooth-like elements of the oropharynx, and integumentary elements. exoskeleton VSAO:0000035 XAO:0004025 uberon dermal skeletal system dermoskeleton desmoskeleton UBERON:0010364 This ontology covers metazoa, so we do not use exoskeleton as primary label, as in VSAO dermal skeleton VSAO Skeletal subdivision that undergoes direct development and includes elements that either develop in association with the basement membrane of the ectoderm or are homologous with such elements; includes dermatocranium, components of the appendicular skeleton, teeth and tooth-like elements of the oropharynx, and integumentary elements. GO_REF:0000034 PSPUB:0000170 VSAO:0000035 exoskeleton VSAO:curator dermal skeletal system VSAO:curator dermoskeleton VSAO:curator desmoskeleton VSAO:curator Epithelium composed of cells that develops from the ectoderm[FMA,modified]. FMA:69064 ectoderm-derived epithelium uberon UBERON:0010371 ecto-epithelium Epithelium composed of cells that develops from the ectoderm[FMA,modified]. FMA:69064 Mesenchyme that develops_from a somatopleure. the way this class is defined also includes extraembryonic mesenchyme such as the amniotic mesenchyme; in future this may be restricted to embryonic derivatives EHDAA2:0001120 uberon UBERON:0010377 mesenchyme from somatopleure EHDAA2 EHDAA2 Mesenchyme that develops_from a somatopleure. OBOL:automatic Mesenchyme that develops_from a splanchnopleure. EHDAA2:0001122 uberon UBERON:0010378 mesenchyme from splanchnopleure EHDAA2 EHDAA2 Mesenchyme that develops_from a splanchnopleure. OBOL:automatic An organ cavity that is part of a urethra. FMA:19709 urethral lumen uberon UBERON:0010390 lumen of urethra An organ cavity that is part of a urethra. OBOL:automatic urethral lumen FMA:19709 The integrated unit (of the eye) that consists of the conjunctiva, the corneal surface, and the ocular mucosal adnexa including the lid margins and the meibomian gland openings, the lacrimal glands and the lacrimal drainage system, all which are critical to maintain ocular surface integrity and provide protection from external antigens and pathogenic microorganisms. EMAPA:35336 MA:0002486 eye surface eye surface region ocular surface uberon UBERON:0010409 ocular surface region The integrated unit (of the eye) that consists of the conjunctiva, the corneal surface, and the ocular mucosal adnexa including the lid margins and the meibomian gland openings, the lacrimal glands and the lacrimal drainage system, all which are critical to maintain ocular surface integrity and provide protection from external antigens and pathogenic microorganisms. MP:0013754 eye surface MA:0002486 An orifice that is part of a lower urinary tract. EMAPA:35965 MA:0002867 urethral orifice uberon UBERON:0010418 urethral opening An orifice that is part of a lower urinary tract. OBOL:automatic urethral orifice OBOL:automatic The ciliary processes are formed by the inward folding of the various layers of the choroid, i.e. , the choroid proper and the lamina basalis, and are received between corresponding foldings of the suspensory ligament of the lens. FMA:76551 ciliary processes ciliary processes set processus ciliares set of ciliary processes uberon ciliary process processus ciliares UBERON:0010427 ciliary processes The ciliary processes are formed by the inward folding of the various layers of the choroid, i.e. , the choroid proper and the lamina basalis, and are received between corresponding foldings of the suspensory ligament of the lens. ciliary processes FMA:76551 ciliary processes set FMA:76551 processus ciliares FMA:TA set of ciliary processes FMA:76551 ciliary process processus ciliares A bone that is shaped as a broad flat plate and composed of two thin layers of compact tissue enclosing between them a variable quantity of cancellous tissue, which is the location of red bone marrow. In an adult mammal, most red blood cells are formed in flat bones Flat bones are those bones which are found where the principal requirement is either extensive protection or the provision of broad surfaces for muscular attachment FMA:7476 NCIT:C32616 UMLS:C0222649 galen:FlatBone uberon os planum UBERON:0010428 Examples: cranium, the ilium, sternum, rib cage, the sacrum and the scapula; the occipital, parietal, frontal, nasal, lacrimal, vomer, scapula, os coxC&, sternum, and ribs flat bone FMA A bone that is shaped as a broad flat plate and composed of two thin layers of compact tissue enclosing between them a variable quantity of cancellous tissue, which is the location of red bone marrow. UMLS:C0222649 ncithesaurus:Flat_Bone os planum A simple columnar epithelium that looks stratified but is not, because its cells are arranged with their nuclei at different levels. Pseudostratified epithelia function in secretion or absorption. If a specimen looks stratified but has cilia, then it is a pseudostratified ciliated epithelium, since stratified epithelia do not have cilia. glandular in NCIT; we consider the two NCIT terms synonymous FMA:45572 NCIT:C33419 NCIT:C49316 UMLS:C0836138 UMLS:C1514590 uberon UBERON:0010498 pseudostratified columnar epithelium FMA A simple columnar epithelium that looks stratified but is not, because its cells are arranged with their nuclei at different levels. glandular in NCIT; we consider the two NCIT terms synonymous NCIT UMLS:C0836138 ncithesaurus:Pseudostratified_Columnar_Epithelium UMLS:C1514590 ncithesaurus:Pseudostratified_Epithelium Epithelium composed of a single layer of cells, appearing as layered because the column-shaped cells vary in height so the nuclei are at different levels. The basal portions of all the cells are in contact with the basement membrane. It lines the respiratory system and the male reproductive tract. The cilia in the respiratory tract are motile, while the stereocilia in the male reproductive tract are immobile. FMA:13146 NCIT:C13181 UMLS:C0506992 epithelium pseudostratificatum columnare ciliatum (trachea et bronchi) uberon UBERON:0010499 pseudostratified ciliated columnar epithelium Epithelium composed of a single layer of cells, appearing as layered because the column-shaped cells vary in height so the nuclei are at different levels. The basal portions of all the cells are in contact with the basement membrane. It lines the respiratory system and the male reproductive tract. The cilia in the respiratory tract are motile, while the stereocilia in the male reproductive tract are immobile. NCIT:NCIT UMLS:C0506992 ncithesaurus:Pseudostratified_Columnar_Ciliated_Epithelium epithelium pseudostratificatum columnare ciliatum (trachea et bronchi) FMA:13146 Skeletal element that forms as a replacement or substitution of another element or tissue. VSAO:0000135 XAO:0004016 ZFA:0005624 uberon UBERON:0010522 replacement element VSAO cjm Skeletal element that forms as a replacement or substitution of another element or tissue. GO_REF:0000034 PSPUB:0000170 VSAO:0000135 A vessel of the microcirculature, lying between the arterioles and venules; includes capillaries (blood and lymphatic), metarterioles and arteriovenous anastomoses. MESH:A07.231.432 TAO:0005251 ZFA:0005251 uberon microcirculatory vessels UBERON:0010523 microcirculatory vessel ZFA A vessel of the microcirculature, lying between the arterioles and venules; includes capillaries (blood and lymphatic), metarterioles and arteriovenous anastomoses. MESH:A07.231.432 ZFA:0005251 microcirculatory vessels TAO:0005251 An organ cavity that surrounded_by a bone. FMA:24021 bone organ cavity uberon UBERON:0010527 cavity of bone organ An organ cavity that surrounded_by a bone. OBOL:automatic bone organ cavity FMA:24021 FMA:24028 air space of bone uberon UBERON:0010528 pneumatic cavity of bone FMA air space of bone FMA:24028 An organism subdivision that includes both an appendage and its associated girdle region. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO] Anatomical group that consists of the soft and skeletal tissues of the appendicular region of the body and the appendage proper.[VSAO] It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO] note that the FMA uses the term 'limb' to refer to the entire appendage complex (free limb plus girdle region) haendel 2012-04-23T10:46:51Z EMAPA:37858 FMA:7182 VSAO:0000214 appendage complex appendage-girdle complex appendage/girdle complex girdle plus limb or fin uberon limb UBERON:0010707 appendage girdle complex An organism subdivision that includes both an appendage and its associated girdle region. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). Anatomical group that consists of the soft and skeletal tissues of the appendicular region of the body and the appendage proper.[VSAO] 2012-08-14 VSAO:0000214 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO] 2012-09-06 VSAO:0000214 VSAO Curator note that the FMA uses the term 'limb' to refer to the entire appendage complex (free limb plus girdle region) FMA EMAPA:37858 MA:th appendage complex appendage-girdle complex appendage/girdle complex VSAO:0000214 girdle plus limb or fin limb FMA:7182 Appendage girdle complex that when present, encompasses the pectoral appendicular skeleton and the pectoral girdle. Appendage girdle complex that when present, encompasses the pectoral appendage and half of the pectoral girdle.[VSAO] note that the FMA uses the terms 'upper limb' and 'lower limb' to refer to the entire appendage complex (free limb plus girdle region) EMAPA:37860 FMA:7183 VSAO:0000213 pectoral appendage/girdle complex pectoral girdle plus anterior limb or fin pectoral girdle plus pectoral limb or fin uberon upper limb upper limb and pectoral girdle upper limb and shoulder UBERON:0010708 pectoral complex Appendage girdle complex that when present, encompasses the pectoral appendicular skeleton and the pectoral girdle. VSAO:0000213 Appendage girdle complex that when present, encompasses the pectoral appendage and half of the pectoral girdle.[VSAO] 2012-08-14 VSAO:0000213 VSAO VSAO:MAH note that the FMA uses the terms 'upper limb' and 'lower limb' to refer to the entire appendage complex (free limb plus girdle region) FMA EMAPA:37860 MA:th pectoral appendage/girdle complex VSAO:0000213 pectoral girdle plus anterior limb or fin pectoral girdle plus pectoral limb or fin upper limb FMA:7183 upper limb and pectoral girdle upper limb and shoulder Appendage girdle complex that when present, encompasses the pelvic appendicular skeleton and the pelvic girdle. Appendage girdle complex that when present, encompasses the pelvic appendage and the pelvic girdle.[VSAO] note that the FMA uses the terms 'upper limb' and 'lower limb' to refer to the entire appendage complex (free limb plus girdle region). Note the MA class 'hindlimb' may also belong here EMAPA:37863 FMA:7184 VSAO:0000215 pelvic appendage/girdle complex pelvic girdle plus pelvic limb or fin pelvic girdle plus posterior limb or fin uberon lower limb lower limb and pelvic girdle lower limb and pelvis UBERON:0010709 pelvic complex Appendage girdle complex that when present, encompasses the pelvic appendicular skeleton and the pelvic girdle. VSAO:0000215 Appendage girdle complex that when present, encompasses the pelvic appendage and the pelvic girdle.[VSAO] 2012-08-14 VSAO:0000215 VSAO VSAO:MAH note that the FMA uses the terms 'upper limb' and 'lower limb' to refer to the entire appendage complex (free limb plus girdle region). Note the MA class 'hindlimb' may also belong here FMA EMAPA:37863 MA:th pelvic appendage/girdle complex VSAO:0000215 pelvic girdle plus pelvic limb or fin pelvic girdle plus posterior limb or fin lower limb FMA:7184 lower limb and pelvic girdle lower limb and pelvis The subdivision of the skeleton of either the pectoral or pelvic girdle. Skeletal subdivision that is part of the appendage girdle region.[VSAO] relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: part_of subdivision of skeleton (UBERON:0010912)[VSAO] relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: proximally_connected_to subdivision of skeleton (UBERON:0010912)[VSAO] AAO:0010686 VSAO:0000302 skeleton of girdle uberon UBERON:0010719 girdle skeleton The subdivision of the skeleton of either the pectoral or pelvic girdle. Skeletal subdivision that is part of the appendage girdle region.[VSAO] 2012-08-14 VSAO:0000302 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: part_of subdivision of skeleton (UBERON:0010912)[VSAO] 2012-08-14 VSAO:0000302 VSAO relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: proximally_connected_to subdivision of skeleton (UBERON:0010912)[VSAO] 2012-08-14 VSAO:0000302 VSAO A bone that is part of an appendage girdle complex (i.e. any bone in a limb, fin or girdle). EMAPA:35494 MA:0000688 uberon bone of extended limb/fin region limb bone UBERON:0010740 bone of appendage girdle complex UBERONREF:0000003 A bone that is part of an appendage girdle complex (i.e. any bone in a limb, fin or girdle). UBERONREF:0000003 bone of extended limb/fin region UBERONREF:0000003 limb bone MA:0000688 UBERONREF:0000003 A bone that is part of a pectoral complex. Examples: scapula, manus phalanx, any carpal bone, any bone of the pectoral fin. considering adding pectoral and pelvic complex skeleton classes note that the MA class includes girdle parts so it belongs here; EMAPA:32623 EMAPA:35933 MA:0000612 wing bone uberon bone of forelimb or pectoral fin or pectoral girdle forelimb bone UBERON:0010741 bone of pectoral complex A bone that is part of a pectoral complex. Examples: scapula, manus phalanx, any carpal bone, any bone of the pectoral fin. UBERONREF:0000003 note that the MA class includes girdle parts so it belongs here; MA wing bone UBERONREF:0000003 bone of forelimb or pectoral fin or pectoral girdle UBERONREF:0000003 forelimb bone MA:0000612 UBERONREF:0000003 A bone that is part of a pelvic complex. Examples: pubis, ischium, fot phalanx, any tarsal bone, any bone of the pelvic fin or girdle. the MA class called 'hindlimb bone' belongs here, as it includes bones in the pelvic girdle EMAPA:32633 EMAPA:35934 MA:0000660 uberon hindlimb bone UBERON:0010742 bone of pelvic complex MA A bone that is part of a pelvic complex. Examples: pubis, ischium, fot phalanx, any tarsal bone, any bone of the pelvic fin or girdle. UBERONREF:0000003 the MA class called 'hindlimb bone' belongs here, as it includes bones in the pelvic girdle MA hindlimb bone MA:0000660 UBERONREF:0000003 Muscles of the pelvic girdle, hindlimb or pelvic fin. Muscles of the pelvic girdle, thigh, leg (crus), and foot (pes).[AAO] AAO:0000218 EMAPA:32634 FMA:9622 MA:0000663 pelvic complex muscle pelvic girdle and hind limb muscles pelvic girdle or hind limb muscle pelvic girdle or posterior limb muscle uberon lower limb muscle muscle of lower limb muscle of pelvic girdle and leg UBERON:0010890 pelvic complex muscle prolog Muscles of the pelvic girdle, hindlimb or pelvic fin. Muscles of the pelvic girdle, thigh, leg (crus), and foot (pes).[AAO] 2012-06-20 AAO:0000218 AAO AAO:EJS pelvic girdle and hind limb muscles AAO:0000218 pelvic girdle or hind limb muscle pelvic girdle or posterior limb muscle lower limb muscle FMA:9622 muscle of lower limb FMA:9622 A muscle of a pectoral girdle, pectoral fin or anterior limb. the MA class belongs here, based on its current child classes Muscles of the pectoral girdle, arm, forearm, and hand (brachium, antebrachium, manus respectively).[AAO] AAO:0010687 EMAPA:32624 FMA:9621 MA:0000615 pectoral complex muscle pectoral girdle and fore limb muscles muscle of pectoral girdle and wing muscle of upper limb upper limb muscle uberon muscle of pectoral girdle and limb UBERON:0010891 pectoral complex muscle prolog A muscle of a pectoral girdle, pectoral fin or anterior limb. Muscles of the pectoral girdle, arm, forearm, and hand (brachium, antebrachium, manus respectively).[AAO] 2012-06-20 AAO:0010687 AAO AAO:EJS pectoral girdle and fore limb muscles AAO:0010687 muscle of pectoral girdle and wing NCBITaxon:8782 muscle of upper limb FMA:9621 upper limb muscle FMA:9621 Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints. Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO] FMA:23879 VSAO:0000042 skeletal subdivision uberon subdivision of skeleton (in vivo) UBERON:0010912 subdivision of skeleton cjm UBERONREF:0000003 VSAO Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints. UBERONREF:0000003 Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO] 2012-08-14 VSAO:0000042 incorrect VSAO VSAO:curator skeletal subdivision VSAO:0000042 subdivision of skeleton (in vivo) FMA:23879 Any muscle organ that is part of either the head or the neck. NCIT:C32716 UMLS:C0448281 muscle of head or neck uberon muscle of head and neck UBERON:0010959 craniocervical muscle prolog Any muscle organ that is part of either the head or the neck. UMLS:C0448281 ncithesaurus:Head_and_Neck_Muscle A cartilage element that is part of a splanchnocranium. EFO:0003689 TAO:0001460 ZFA:0001460 pharyngeal arch cartilages splanchnocranium cartilage uberon UBERON:0011004 pharyngeal arch cartilage ZFA ZFA A cartilage element that is part of a splanchnocranium. OBOL:automatic pharyngeal arch cartilages ZFA:0001460 splanchnocranium cartilage ZFA:0001460 A skeleton of pelvic girdle that is part of a right pelvic girdle region. FMA:87593 uberon UBERON:0011090 skeleton of right pelvic girdle A skeleton of pelvic girdle that is part of a right pelvic girdle region. OBOL:automatic A skeleton of pelvic girdle that is part of a left pelvic girdle region. FMA:87594 uberon UBERON:0011091 skeleton of left pelvic girdle A skeleton of pelvic girdle that is part of a left pelvic girdle region. OBOL:automatic A pelvic girdle region that is in the right side of a multicellular organism. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern FMA:16582 right pelvic girdle uberon UBERON:0011092 right pelvic girdle region A pelvic girdle region that is in the right side of a multicellular organism. OBOL:automatic right pelvic girdle FMA:16582 A pelvic girdle region that is in the left side of a multicellular organism. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern FMA:16583 left pelvic girdle uberon UBERON:0011093 left pelvic girdle region A pelvic girdle region that is in the left side of a multicellular organism. OBOL:automatic left pelvic girdle FMA:16583 A synovial joint that is part of a pelvic girdle region. FMA:35173 NCIT:C32890 UMLS:C0827002 joint of pelvic girdle pelvic girdle joint uberon UBERON:0011107 synovial joint of pelvic girdle A synovial joint that is part of a pelvic girdle region. OBOL:automatic UMLS:C0827002 ncithesaurus:Joint_of_the_Pelvic_Girdle pelvic girdle joint FMA:35173 A synovial joint that is part of a pectoral girdle region. in FMA, these are part of the bony pectoral girdle FMA:35243 joint of shoulder girdle pectoral girdle joint uberon UBERON:0011108 synovial joint of pectoral girdle A synovial joint that is part of a pectoral girdle region. OBOL:automatic in FMA, these are part of the bony pectoral girdle FMA pectoral girdle joint FMA:35243 A skeletal joint that connects a laryngeal cartilage. FMA:55100 joint of larynx laryngeal articulation uberon UBERON:0011120 laryngeal joint FMA A skeletal joint that connects a laryngeal cartilage. OBOL:automatic joint of larynx FMA:55100 laryngeal articulation FMA:55100 Joint in which the articulating bones or cartilages are connected by ligaments or fibrocartilage without an intervening synovial cavity. Examples: sagittal suture, inferior tibiofibular syndesmosis, costochondral joint, pubic symphysis. FMA:7491 solid joint uberon UBERON:0011134 nonsynovial joint FMA Joint in which the articulating bones or cartilages are connected by ligaments or fibrocartilage without an intervening synovial cavity. Examples: sagittal suture, inferior tibiofibular syndesmosis, costochondral joint, pubic symphysis. FMA:7491 solid joint FMA:7491 Subdivision of the skeletal system which consists of the axial skeleton plus associated joints. FMA:7483 uberon UBERON:0011137 axial skeletal system http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton FMA Subdivision of the skeletal system which consists of the axial skeleton plus associated joints. Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints. axial skeletal system FMA:302077 post-cranial axial skeletal system uberon UBERON:0011138 postcranial axial skeletal system http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton FMA cjm Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints. axial skeletal system Subdivision of urinary system which consists of the kidney and the ureters. FMA:45658 NCIT:C61107 galen:UpperUrinaryTract uberon UBERON:0011143 upper urinary tract FMA FMA-abduced-lr Subdivision of urinary system which consists of the kidney and the ureters. FMA:45658 Gland of the lamina epithelialis mucosae which perforate the lamina muscularis, with their adenomeres located in the submucosal connective tissue. BTO:0003751 EMAPA:37970 uberon UBERON:0011148 submucosal gland perforates Gland of the lamina epithelialis mucosae which perforate the lamina muscularis, with their adenomeres located in the submucosal connective tissue. BTO:0003751 EMAPA:37970 MA:th Subdivision of skull that consists of the facial bones. EHDAA2:0002206 EHDAA:8361 EMAPA:18022 FMA:53673 MA:0000318 facial skeleton uberon facial bone ossa facialia ossa faciei viscerocranium UBERON:0011156 facial skeleton FMA FMA Subdivision of skull that consists of the facial bones. MP:0005274 facial skeleton FMA:53673 facial bone MA:0000318 ossa facialia ossa faciei viscerocranium MA:0000318 The skull can be divided into two: the neurocranium and the facial skeleton FMA:54964 skull subdivision subdivision of skull uberon UBERON:0011158 primary subdivision of skull FMA The skull can be divided into two: the neurocranium and the facial skeleton skull subdivision FMA:54964 subdivision of skull FMA:54964 uberon UBERON:0011159 primary subdivision of cranial skeletal system FMA A bone that is part of a neurocranium [Automatically generated definition]. EMAPA:35238 MA:0001478 chondrocranium bone uberon UBERON:0011164 neurocranium bone A bone that is part of a neurocranium [Automatically generated definition]. OBOL:automatic chondrocranium bone MA:0001478 A muscle layer that is part of a large intestine. FMA:14971 NCIT:C32927 UMLS:C0734205 muscular coat of large intestine muscular layer of large intestine muscularis externa of large intestine tunica muscularis intestini crassi uberon UBERON:0011198 muscle layer of large intestine FMA A muscle layer that is part of a large intestine. OBOL:automatic UMLS:C0734205 ncithesaurus:Large_Intestinal_Muscular_Coat muscular coat of large intestine FMA:14971 muscular layer of large intestine FMA:14971 muscularis externa of large intestine FMA:14971 tunica muscularis intestini crassi FMA:TA A multi cell part structure that is part of a central nervous system. FMA:83143 cell part cluster of neuraxis neuraxis layer uberon UBERON:0011215 central nervous system cell part cluster A multi cell part structure that is part of a central nervous system. OBOL:automatic cell part cluster of neuraxis FMA:83143 neuraxis layer FMA:83143 A subdivision of an anatomical system. FBbt:00007330 FMA:67509 uberon UBERON:0011216 organ system subdivision FBbt FBbt A subdivision of an anatomical system. Muscles within the eye (bulbus oculi).[AAO] AAO:0010038 EMAPA:18808 FMA:49150 intrinsic muscle of eyeball intrinsic ocular muscle uberon UBERON:0011222 intra-ocular muscle EMAPA Muscles within the eye (bulbus oculi).[AAO] 2012-06-20 AAO:0010038 AAO AAO:EJS intrinsic ocular muscle EMAPA:18808 Synovial sac which surrounds parts of one or more tendons. Examples: synovial tendon sheath of manual digit 2, radial bursa. synovium BTO:0001823 FMA:40878 uberon UBERON:0011233 Alternate def: A synovial sheath is a layer of a tendon sheath containing tendons in the hand and foot. They lie internal to the fibrous tendon sheaths. An example is the common synovial sheath for the flexor tendons. [Wikipedia:Synovial_sheath] synovial membrane of synovial tendon sheath Synovial sac which surrounds parts of one or more tendons. Examples: synovial tendon sheath of manual digit 2, radial bursa. FMA:45087 synovium BTO:0001823 FMA:40877 uberon UBERON:0011234 fibrous membrane of synovial tendon sheath Subdivision of the skeletal system which consists of the appendicular skeleton plus associated joints. Skeletal system which consists of the appendicular skeleton plus associated joints.[VSAO] FMA:7484 VHOG:0001666 VSAO:0000306 uberon UBERON:0011249 appendicular skeletal system https://github.com/obophenotype/uberon/wiki/Appendages-and-the-appendicular-skeleton Subdivision of the skeletal system which consists of the appendicular skeleton plus associated joints. Skeletal system which consists of the appendicular skeleton plus associated joints.[VSAO] 2012-08-14 VSAO:0000306 VSAO The part of the trunk that is in the dorsum[cjm]. In humans, the subdivision of trunk which is demarcated from the trunk proper by the external surface of the posterolateral part of the rib cage, the anterior surface of the thoracic vertebral column and the posterior axillary lines, the external surface of the posterior abdominal wall; together with the trunk proper, it constitutes the trunk[FMA] EMAPA:35162 FMA:25056 MA:0000020 back of trunk dorsal part of trunk dorsum of trunk trunk back uberon UBERON:0011270 dorsal trunk FMA FMA The part of the trunk that is in the dorsum[cjm]. UBERONREF:0000006 back of trunk FMA:25056 dorsum of trunk FMA:25056 trunk back FMA:25056 compare with 'stratum basale of epidermis'. This class is the source for many adult structures - see WP2062. See also: 'enveloping layer of ectoderm' EHDAA2:0001845 uberon basal cell layer of skin outer epithelium of body UBERON:0011272 embryonic skin basal layer EHDAA2 EHDAA2 EHDAA2 outer epithelium of body Wikipathways:WP2062 The submucous layer of the wall of the uterine tube. BTO:0002116 submucosa of fallopian tube tela submucosa tubae uterinae uberon submucous layer of uterine tube uterine submucosa UBERON:0011298 submucosa of uterine tube The submucous layer of the wall of the uterine tube. BTO:0002116 tela submucosa tubae uterinae BTO:0002116 submucous layer of uterine tube BTO:0002116 A blood vasculature that is part of a head. Blood vessel part of cranial vasculature.[TAO] TAO:0005297 ZFA:0005297 cranial blood vessel set of blood vessels of head uberon cranial blood vessels UBERON:0011362 cranial blood vasculature A blood vasculature that is part of a head. OBOL:automatic Blood vessel part of cranial vasculature.[TAO] 2012-08-14 TAO:0005297 TAO ZFIN:curator cranial blood vessel ZFA:0005297 cranial blood vessels TAO:0005297 FMA:54364 cavity of digestive tract cavity of gastrointestinal tract gastrointestinal tract lumen lumen of gastrointestinal tract uberon UBERON:0011565 lumen of gastrointestinal system gastrointestinal tract lumen FMA:54364 lumen of gastrointestinal tract FMA:54364 A tube lumen that is part of a mesonephric duct. EHDAA2:0001244 nephric duct lumen uberon cavity of nephric duct UBERON:0011574 mesonephric duct lumen A tube lumen that is part of a mesonephric duct. OBOL:automatic nephric duct lumen EHDAA2:0001244 The collection of all skeletal elements in an individual limb or fin. Skeletal subdivision that is part of the paired limb/fin.[VSAO] VSAO:0000301 limb/fin skeleton skeletal parts of limb/fin skeleton of limb/fin uberon UBERON:0011582 paired limb/fin skeleton ISBN:9780878932504 The collection of all skeletal elements in an individual limb or fin. Skeletal subdivision that is part of the paired limb/fin.[VSAO] 2012-08-14 VSAO:0000301 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 limb/fin skeleton VSAO:0000301 Anatomical structure that is an aggregation of similar cells from which cartilages and bones form, and from which chondrogenesis and osteogenesis are initiated during repair and/or regeneration. (Hall and Miyake 1995). consider obsoleting, coordinate with VSAO VSAO:0000006 XAO:0004021 uberon UBERON:0011585 cell condensation VSAO Anatomical structure that is an aggregation of similar cells from which cartilages and bones form, and from which chondrogenesis and osteogenesis are initiated during repair and/or regeneration. (Hall and Miyake 1995). GO_REF:0000034 PSPUB:0000170 VSAO:0000006 A subdivision of the head that corresponds to the jaw skeleton, containing both soft tissue, skeleton and teeth (when present). The jaw region is divided into upper and lower regions. EMAPA:32905 NCIT:C114916 uberon UBERON:0011595 jaw region http://eol.org/collections/11578 EMAPA FMA-abduced ZFA-abduced A subdivision of the head that corresponds to the jaw skeleton, containing both soft tissue, skeleton and teeth (when present). The jaw region is divided into upper and lower regions. EHDAA2:0001020 lower jaw future lip uberon UBERON:0011596 future lower lip EHDAA2 lower jaw future lip EHDAA2:0001020 An epithelium that develops_from a ectoderm and is part of a oral epithelium. EHDAA2:0004137 uberon UBERON:0011642 oral epithelium from ectoderm EHDAA2 EHDAA2 An epithelium that develops_from a ectoderm and is part of a oral epithelium. OBOL:automatic AAO:0000247 EFO:0003511 TAO:0000236 XAO:0003269 ZFA:0000236 mandibular muscle mandibular muscles uberon UBERON:0011648 jaw muscle mandibular muscle TAO:0000236 mandibular muscles TAO:0000236 A major subdivision of an organism that divides an organism along its main body axis (typically anterio-posterior axis). In vertebrates, this is based on the vertebral column. Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem axial subdivision of organism uberon body segment main body segment UBERON:0011676 subdivision of organism along main body axis A major subdivision of an organism that divides an organism along its main body axis (typically anterio-posterior axis). In vertebrates, this is based on the vertebral column. A cardiovascular system that is part of a conceptus. EHDAA2:0000216 FMA:305965 NCIT:C34148 conceptus cardiovascular system uberon embryonic circulatory system fetal circulatory system UBERON:0011695 embryonic cardiovascular system A cardiovascular system that is part of a conceptus. OBOL:automatic The left nerve is longer than the right, because it crosses under the arch of the aorta at the ligamentum arteriosum.[WP] EMAPA:25350 FMA:14469 MA:0001107 left recurrent laryngeal branch left recurrent laryngeal nerve vagus X nerve left recurrent laryngeal branch uberon UBERON:0011766 left recurrent laryngeal nerve left recurrent laryngeal branch EMAPA:25350 left recurrent laryngeal nerve FMA:14469 vagus X nerve left recurrent laryngeal branch MA:0001107 EMAPA:17275 FMA:14468 MA:0001108 right recurrent laryngeal branch right recurrent laryngeal nerve vagus X nerve right recurrent laryngeal branch uberon UBERON:0011767 right recurrent laryngeal nerve right recurrent laryngeal branch EMAPA:17275 right recurrent laryngeal nerve FMA:14468 vagus X nerve right recurrent laryngeal branch MA:0001108 An anatomical space that is part of a bone of lower jaw. AAO:0000273 uberon UBERON:0011772 lower jaw opening An anatomical space that is part of a bone of lower jaw. OBOL:automatic A cranial nerve nucleus that is associated with a vagus nerve. FMA:54573 nucleus of Xth nerve nucleus of vagal X nerve nucleus of vagal nerve nucleus of vagus nerve tenth cranial nerve nucleus vagal X nucleus vagal nucleus vagus nucleus uberon nodosal nucleus UBERON:0011775 vagus nerve nucleus A cranial nerve nucleus that is associated with a vagus nerve. OBOL:automatic nucleus of vagus nerve FMA:54573 tenth cranial nerve nucleus FMA:54573 vagal X nucleus vagal nucleus vagus nucleus nodosal nucleus A neural nucleus that is part of the spinal cord. FMA:77011 spinal cord nucleus uberon UBERON:0011777 nucleus of spinal cord A neural nucleus that is part of the spinal cord. spinal cord nucleus FMA:77011 A nerve that is part of a head. uberon cephalic nerve head nerve UBERON:0011779 nerve of head region A nerve that is part of a head. OBOL:automatic Ectodermal placode that does not develop into a component of the nervous system. uberon UBERON:0011814 non-neurogenic ectodermal placode cjm Ectodermal placode that does not develop into a component of the nervous system. Connective tissue, which consists of a population of connective tissue cells, the intercellular matrix of which contains an irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, mucoid tissue, connective tissue of peritoneum, connective tissue of fibrous pericardium. FMA:20107 uberon UBERON:0011821 irregular connective tissue FMA Connective tissue, which consists of a population of connective tissue cells, the intercellular matrix of which contains an irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, mucoid tissue, connective tissue of peritoneum, connective tissue of fibrous pericardium. FMA:20107 Irregular connective tissue is an irregular connective tissue, the intercellular matrix of which contains a dense irregular network of collagen and elastic fiber bundles. Examples: connective tissue of peritoneum, connective tissue of fibrous pericardium. Tissue characterized by a thick, random arrangement of collagen and elastin fibers with very few cells. The majority of the cells are fibroblasts, but mast cells and macrophages may also be seen. It is found in the dermis, periosteum, perichondrium, capsules of organs and sheaths of nerves and muscles[NCIT] FMA:20109 NCIT:C32882 UMLS:C0738366 irregular dense connective tissue typus irregularis (textus connectivus collagenosus compactus) uberon UBERON:0011822 dense irregular connective tissue FMA Irregular connective tissue is an irregular connective tissue, the intercellular matrix of which contains a dense irregular network of collagen and elastic fiber bundles. Examples: connective tissue of peritoneum, connective tissue of fibrous pericardium. FMA:20109 Tissue characterized by a thick, random arrangement of collagen and elastin fibers with very few cells. The majority of the cells are fibroblasts, but mast cells and macrophages may also be seen. It is found in the dermis, periosteum, perichondrium, capsules of organs and sheaths of nerves and muscles[NCIT] 2012-08-29 ncithesaurus:Irregular_Dense_Connective_Tissue NCIT UMLS:C0738366 ncithesaurus:Irregular_Dense_Connective_Tissue typus irregularis (textus connectivus collagenosus compactus) FMA:20109 Dense connective tissue is mainly composed of collagen type I. Crowded between the collagen fibers are rows of fibroblasts, fiber-forming cells, that manufacture the fibers. Dense connective tissue forms strong, rope-like structures such as tendons and ligaments. Tendons attach skeletal muscles to bones; ligaments connect bones to bones at joints. Ligaments are more stretchy and contain more elastic fibers than tendons. Dense connective tissue also make up the lower layers of the skin (dermis), where it is arranged in sheets our OWL definition states that this is differentiated from other connective tissue types by virtue of the fact that the collage fiber component predominates, as opposed to cells and fluid. Connective tissue in which the fibrous component predominates. The cells, ground substance, and tissue fluid represent a minor component[NCIT] AAO:0000121 NCIT:C32450 UMLS:C1511770 uberon UBERON:0011823 dense connective tissue Dense connective tissue is mainly composed of collagen type I. Crowded between the collagen fibers are rows of fibroblasts, fiber-forming cells, that manufacture the fibers. Dense connective tissue forms strong, rope-like structures such as tendons and ligaments. Tendons attach skeletal muscles to bones; ligaments connect bones to bones at joints. Ligaments are more stretchy and contain more elastic fibers than tendons. Dense connective tissue also make up the lower layers of the skin (dermis), where it is arranged in sheets Connective tissue in which the fibrous component predominates. The cells, ground substance, and tissue fluid represent a minor component[NCIT] 2012-08-29 ncithesaurus:Dense_Connective_Tissue NCIT UMLS:C1511770 ncithesaurus:Dense_Connective_Tissue FMA:75634 uberon UBERON:0011824 fibrous connective tissue FMA Irregular connective tissue, the intercellular matrix of which contains a sparse irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, neuroglial tissue, mucoid tissue. FMA:19783 NCIT:C33007 UMLS:C1253917 textus connectivus collagenosus laxus textus connectivus laxus uberon UBERON:0011825 loose connective tissue FMA Irregular connective tissue, the intercellular matrix of which contains a sparse irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, neuroglial tissue, mucoid tissue. FMA:19783 UMLS:C1253917 ncithesaurus:Loose_Connective_Tissue textus connectivus collagenosus laxus FMA:19783 FMA:TA textus connectivus laxus FMA:19783 FMA:TA An acinus that is part of a exocrine gland. exocrine gland acinus uberon UBERON:0011858 acinus of exocrine gland An acinus that is part of a exocrine gland. OBOL:automatic the FMA class specifically refers to ureter FMA:63212 MESH:D024022 NCIT:C32339 NIF_Subcellular:sao7547390221 uberon UBERON:0011860 collection of collagen fibrils ZFA the FMA class specifically refers to ureter FMA The connective tissue bundles in the extracellular matrix of aorta tissue that are composed of collagen, and play a role in tissue strength and elasticity uberon UBERON:0011861 aorta collagen fibril The connective tissue bundles in the extracellular matrix of aorta tissue that are composed of collagen, and play a role in tissue strength and elasticity MP:0011640 The connective tissue bundles in the extracellular matrix of pulmonary tissue that are composed of collagen, and play a role in tissue strength and elasticity uberon UBERON:0011862 pulmonary collagen fibril The connective tissue bundles in the extracellular matrix of pulmonary tissue that are composed of collagen, and play a role in tissue strength and elasticity MP:0011641 The connective tissue bundles in the extracellular matrix of bone tissue that are composed of collagen, and play a role in tissue strength and elasticity uberon UBERON:0011863 bone collagen fibril The connective tissue bundles in the extracellular matrix of bone tissue that are composed of collagen, and play a role in tissue strength and elasticity MP:0011642 The connective tissue bundles in the extracellular matrix of tendon tissue that are composed of collagen, and play a role in tissue strength and elasticity uberon UBERON:0011864 tendon collagen fibril The connective tissue bundles in the extracellular matrix of tendon tissue that are composed of collagen, and play a role in tissue strength and elasticity MP:0011643 Front (ventral) portion of the vascular, pigmentary, or middle coat of the eye, including the ciliary body and the iris. EMAPA:37417 Haller tunica vascula anterior part of uveal tract anterior uveal tract anterior vascular layer of the eyeball anterior vascular tunic of the eye tunica vasculosa bulbosa ventral uveal tract uberon ciliary body and iris vasculosa oculi UBERON:0011892 anterior uvea ZFA MP lexical Front (ventral) portion of the vascular, pigmentary, or middle coat of the eye, including the ciliary body and the iris. MP:0005194 EMAPA:37417 MA:th Haller tunica vascula MP:0005194 tunica vasculosa bulbosa MP:0005194 vasculosa oculi MP:0005194 A organ cavity that is part of a vagina. FMA:19982 vaginal lumen uberon UBERON:0011894 lumen of vagina A organ cavity that is part of a vagina. OBOL:automatic vaginal lumen FMA:19982 Epimysium is a layer of connective tissue which ensheaths the entire muscle. It is composed of dense irregular connective tissue. It is continuous with fascia and other connective tissue wrappings of muscle including the endomysium, and perimysium. It is also continuous with tendons where it becomes thicker and collagenous. The Epimysium also protects muscles from friction against other muscles and bones FMA:9726 NCIT:C32527 UMLS:C0504096 fascia of muscle organ uberon epimysia UBERON:0011899 epimysium FMA FMA Epimysium is a layer of connective tissue which ensheaths the entire muscle. It is composed of dense irregular connective tissue. It is continuous with fascia and other connective tissue wrappings of muscle including the endomysium, and perimysium. It is also continuous with tendons where it becomes thicker and collagenous. UMLS:C0504096 ncithesaurus:Epimysium fascia of muscle organ FMA:9726 epimysia A region of the stomach that is lined with glandular epithelium. as currently defined, this would include the cardiac antrum; however, the intent may be to exclude the cardiac glands and in mice for this to be part of the region distal to the margo plicatus EMAPA:17623 MA:0001613 NCIT:C77661 UMLS:C0227197 uberon glandular stomach UBERON:0011953 stomach glandular region A region of the stomach that is lined with glandular epithelium. UMLS:C0227197 ncithesaurus:Glandular_Stomach The aggregate of the coelemic cavity lumen plus the membranes that line the lumen. EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining. coelomic EHDAA2:0004731 enterocoelom haemocoelom schizocoelom uberon coelem coelomic cavity UBERON:0011997 coelom EHDAA2 The aggregate of the coelemic cavity lumen plus the membranes that line the lumen. UBERON:cjm enterocoelom NCBITaxon:33511 coelomic cavity EHDAA2:0004731 The cavity within a myotome The central cavity within the mesoderm is the paired primary or embryonic coelom. Parts of the embryonic coelom often become enclosed in the mesoderm, forming a myocoel within the epimere, a nephrocoel within the mesomere, and simple coelom (body cavity) within the lateral plate mesoderm.[well established][VHOG] EMAPA:31134 VHOG:0001283 uberon UBERON:0012054 myocoele The cavity within a myotome The central cavity within the mesoderm is the paired primary or embryonic coelom. Parts of the embryonic coelom often become enclosed in the mesoderm, forming a myocoel within the epimere, a nephrocoel within the mesomere, and simple coelom (body cavity) within the lateral plate mesoderm.[well established][VHOG] 2012-09-17 VHOG:0001283 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.166 and Figure 5.6 Bone that forms as a replacement of another structural tissue. Bone that forms as a replacement of another structural tissue.[TAO] This class was introduced to be consistent with the ZFA hierarchy. The corresponding TAO term was obsoleted, and never introduced into VSAO. Note that VSAO does have replacement element. AAO:0010768 TAO:0001637 ZFA:0001628 replacement bones uberon UBERON:0012075 replacement bone ZFA ZFA Bone that forms as a replacement of another structural tissue. ZFA:0001628 Bone that forms as a replacement of another structural tissue.[TAO] 2012-08-14 TAO:0001637 TAO TAO:wd This class was introduced to be consistent with the ZFA hierarchy. The corresponding TAO term was obsoleted, and never introduced into VSAO. Note that VSAO does have replacement element. ZFA replacement bones ZFA:0001628 An anatomical cavity that is part of a bronchus. FMA:62646 bronchial lumen lumen of bronchus uberon UBERON:0012082 bronchial lumen FMA FMA An anatomical cavity that is part of a bronchus. OBOL:automatic bronchial lumen FMA:62646 lumen of bronchus FMA:62646 Anatomical system that consists of the integumental system plus all mucosae and submucosae. uberon dermatological system UBERON:0012125 dermatological-muscosal system Anatomical system that consists of the integumental system plus all mucosae and submucosae. dermatological system OBI:MC A primordium that has the potential to develop into a stomach. EFO:0002580 NCIT:C34305 UMLS:C1514976 uberon stomach endoderm UBERON:0012172 stomach primordium A primordium that has the potential to develop into a stomach. OBOL:automatic UMLS:C1514976 ncithesaurus:Stomach_Primordium stomach endoderm EFO:0002580 EHDAA2:0000494 EMAPA:16794 VHOG:0000715 acousticofacial ganglion facio-acoustic ganglion facio-acoustic ganglion complex VII-VIII uberon facio-acoustic VII-VIII ganglion complex facio-acoustic ganglion complex UBERON:0012175 acoustico-facial VII-VIII ganglion complex cjm EHDAA2 cjm facio-acoustic ganglion complex VII-VIII EMAPA:16794 facio-acoustic VII-VIII ganglion complex VHOG:0000715 facio-acoustic ganglion complex EMAPA:16794 A zone of skin that is part of a craniocervical region. EMAPA:37276 MA:0000574 NCIT:C12294 UMLS:C1522650 uberon UBERON:0012180 head or neck skin A zone of skin that is part of a craniocervical region. OBOL:automatic EMAPA:37276 MA:th UMLS:C1522650 ncithesaurus:Skin_of_the_Scalp_and_Neck network of tubes that carries blood through the distensible musculomembranous organ that serves to collect and store urine excreted by the kidneys[MP] EMAPA:28679 bladder vasculature blood vessels of bladder set of urinary bladder blood vessels uberon blood vessel of bladder UBERON:0012239 urinary bladder vasculature EMAPA network of tubes that carries blood through the distensible musculomembranous organ that serves to collect and store urine excreted by the kidneys[MP] MP:MP blood vessels of bladder EMAPA:28679 blood vessel of bladder EMAPA:28679 external opening or orifice of the urethra through which urine and seminal fluid (in males only) leave the body; in males the meatus presents as a vertical slit normally positioned at the tip of glans penis; in females the meatus is located between the clitoris and the vagina in the vulvular vestibule of the female genitalia[MP]. EMAPA:37977 FMA:19650 external meatus of urethra external urethral orifice external urethral ostium external urinary meatus meatus urinarius orificium urethrae externum orificium urethræ externum urethral meatus uberon urinary meatus UBERON:0012240 urethral meatus external opening or orifice of the urethra through which urine and seminal fluid (in males only) leave the body; in males the meatus presents as a vertical slit normally positioned at the tip of glans penis; in females the meatus is located between the clitoris and the vagina in the vulvular vestibule of the female genitalia[MP]. MP:MP EMAPA:37977 MA:th external meatus of urethra FMA:19650 external urethral orifice FMA:19650 external urethral ostium FMA:19650 external urinary meatus FMA:19650 meatus urinarius orificium urethrae externum orificium urethræ externum urethral meatus FMA:19650 the usually crescent-shaped opening of the urinary bladder into the urethra, placed at the anteroinferior angle (apex) of the urinary bladder trigone FMA:85263 internal meatus of urethra internal urethral orifice of urinary bladder internal urethral ostium orificium urethrae internum ostium orificium internum ostium urethrae internum vesicourethral orifice uberon internal urethral ostium internal urinary meatus UBERON:0012242 internal urethral orifice the usually crescent-shaped opening of the urinary bladder into the urethra, placed at the anteroinferior angle (apex) of the urinary bladder trigone MGI:anna MP:0011782 internal meatus of urethra FMA:85263 internal urethral orifice of urinary bladder FMA:85263 internal urethral ostium FMA:85263 orificium urethrae internum MP:0011782 ostium orificium internum ostium urethrae internum vesicourethral orifice FMA:85263 internal urethral ostium MP:0011782 internal urinary meatus MP:0011782 mucus-secreting glands in the mucosa of the uterine cervix NCIT:C32296 UMLS:C2724437 glandulae cervicales uberon UBERON:0012247 cervical gland mucus-secreting glands in the mucosa of the uterine cervix UMLS:C2724437 ncithesaurus:Cervical_Gland glandulae cervicales FMA:TA Lining of the head of the uterus (cervix); contains large branched glands; does not undergo sloughing. BTO:0000411 uberon UBERON:0012248 cervical mucosa Lining of the head of the uterus (cervix); contains large branched glands; does not undergo sloughing. BTO:0000411 The part of the cervix uteri that protrudes into the vagina and is lined with stratified squamous epithelium. distinction between two FMA classes not clear - we merge them here UBERON:0010182 BTO:0001850 CALOHA:TS-1098 FMA:77056 FMA:86484 NCIT:C12310 UMLS:C0227829 ectocervix portio vaginalis portio vaginalis cervicis uterine ectocervix vaginal part of cervix uberon exocervix UBERON:0012249 ectocervix BTO The part of the cervix uteri that protrudes into the vagina and is lined with stratified squamous epithelium. BTO:0001850 distinction between two FMA classes not clear - we merge them here FMA UMLS:C0227829 ncithesaurus:Ectocervix ectocervix BTO:0001850 ectocervix FMA:86484 portio vaginalis portio vaginalis cervicis BTO:0001850 uterine ectocervix CALOHA:TS-1098 vaginal part of cervix FMA:77056 exocervix BTO:0001850 A glandular epithelium that is part of a uterine cervix. The 'glandular' or columnar epithelium of the cervix is located cephalad to the squamocolumnar junction. It covers a variable amount of the ectocervix and lines the endocervical canal. It is comprised of a single layer of mucin-secreting cells. The epithelium is thrown into longitudinal folds and invaginations that make up the so-called endocervical glands (they are not true glands). These infolding crypts and channels make the cytologic and colposcopic detection of neoplasia less reliable and more problematic. The complex architecture of the endocervical glands gives the columnar epithelium a papillary appearance through the colposcope and a grainy appearance upon gross visual inspection. The single cell layer allows the coloration of the underlying vasculature to be seen more easily. Therefore, the columnar epithelium appears more red in comparison with the more opaque squamous epithelium. NCIT:C54414 UMLS:C1707350 uberon cervix columnar epithelium UBERON:0012250 cervix glandular epithelium A glandular epithelium that is part of a uterine cervix. OBOL:automatic The 'glandular' or columnar epithelium of the cervix is located cephalad to the squamocolumnar junction. It covers a variable amount of the ectocervix and lines the endocervical canal. It is comprised of a single layer of mucin-secreting cells. The epithelium is thrown into longitudinal folds and invaginations that make up the so-called endocervical glands (they are not true glands). These infolding crypts and channels make the cytologic and colposcopic detection of neoplasia less reliable and more problematic. The complex architecture of the endocervical glands gives the columnar epithelium a papillary appearance through the colposcope and a grainy appearance upon gross visual inspection. The single cell layer allows the coloration of the underlying vasculature to be seen more easily. Therefore, the columnar epithelium appears more red in comparison with the more opaque squamous epithelium. UMLS:C1707350 ncithesaurus:Cervix_Columnar_Epithelium A epithelium that is part of a ectocervix. exocervical epithelium uberon UBERON:0012251 ectocervical epithelium A epithelium that is part of a ectocervix. OBOL:automatic The glandular epithelium that lines the endocervix. NCIT:C96180 endocervical glandular epithelium uberon UBERON:0012252 endocervical epithelium The glandular epithelium that lines the endocervix. ncithesaurus:Endocervical_Glandular_Epithelium Region of cervical epithelium where columnar epithelium of endocervic and the stratified non-keratinising squamous epithelium of the ectocervic meet squamocolumnar junction NCIT:C97148 squamo-columnar junction of uterine cervix squamocolumnar junction of uterine cervix uberon UBERON:0012253 Site of 90% of lower genital tract neoplasia. This junction is presumed, but not proven, to be the embryologic junction of the Müllerian and urogenital sinus epithelia. cervical squamo-columnar junction Region of cervical epithelium where columnar epithelium of endocervic and the stratified non-keratinising squamous epithelium of the ectocervic meet An artery that originates from the abdominal aorta abdominal artery artery of abdomen uberon UBERON:0012254 abdominal aorta artery An artery that originates from the abdominal aorta An epithelium that consists of columnar epithelial cells. Columnar epithelia are epithelial cells whose heights are at least four times their width. Columnar epithelia are divided into simple (or unilayered), and the rarer stratified (or multi-layered).[WP, modified] uberon UBERON:0012274 columnar epithelium An epithelium that consists of columnar epithelial cells. Columnar epithelia are epithelial cells whose heights are at least four times their width. Columnar epithelia are divided into simple (or unilayered), and the rarer stratified (or multi-layered).[WP, modified] Epithelium that derives from the mesoderm. [Automatically generated definition]. FMA:86452 mesoderm-derived epithelium mesoepithelium uberon UBERON:0012275 meso-epithelium Epithelium that derives from the mesoderm. [Automatically generated definition]. OBOL:automatic EMAPA:35308 FMA:86488 MA:0002732 glandular part of endometrium uterine glands uterine glands set uberon UBERON:0012276 endometrium glandular epithelium glandular part of endometrium FMA:86488 The nasal glands are the seromucous glands in the respiratory region of the nasal mucous membrane. The three major types of nasal glands are anterior serous glands, seromucous glands, and Bowman glands. nasal gland EMAPA:37871 FMA:321518 NCIT:C22725 UMLS:C1522269 glandula nasalis glandulae nasales uberon UBERON:0012278 gland of nasal mucosa The nasal glands are the seromucous glands in the respiratory region of the nasal mucous membrane. The three major types of nasal glands are anterior serous glands, seromucous glands, and Bowman glands. EMAPA:37871 MA:th UMLS:C1522269 ncithesaurus:Nose_Nasal_Cavity_Nasal_Gland_MMHCC glandula nasalis glandulae nasales One of the pair of mesenchymal swellings (folds) located on either side of the cloacal membrane during the indifferent stage of embryonic development; cranial to the cloacal membrane the folds unite to form the genital tubercle; caudally the folds are subdivided into urogenital folds anteriorly and anal folds posteriorly cloacal fold EHDAA2:0004009 uberon UBERON:0012292 We presume this is distinct from AAO:0001003, an external integumentary structure - check with amphibian anatomy ontology developers. AO notes: the text def states mesenchymal swelling, EHDAA2 splits into mesenchymal and epithelial parts embryonic cloacal fold EHDAA2 One of the pair of mesenchymal swellings (folds) located on either side of the cloacal membrane during the indifferent stage of embryonic development; cranial to the cloacal membrane the folds unite to form the genital tubercle; caudally the folds are subdivided into urogenital folds anteriorly and anal folds posteriorly MP:0011836 MP:anna cloacal fold EHDAA2:0004009 A mucosa that is part of a urethra. EMAPA:37912 FMA:76904 mucous membrane of urethra tunica mucosa urethrae urethral mucosa uberon UBERON:0012299 mucosa of urethra A mucosa that is part of a urethra. OBOL:automatic EMAPA:37912 MA:th mucous membrane of urethra FMA:76904 tunica mucosa urethrae FMA:TA urethral mucosa FMA:76904 One of five swellings formed during the development of the face FMA:293103 uberon embryonic facial process facial primordium primordium of face UBERON:0012314 embryonic facial prominence One of five swellings formed during the development of the face The median slit located inferior and posterior to the external urethral orifice in the female; the exit for menstrual flow and birth and the entrance for the penis during sexual intercourse; the size and appearance of the vaginal orifice varies inversely with that of the hymen (G. membrane), a thin fold of mucous membrane that surrounds the vaginal orifice introitus EMAPA:37983 FMA:19984 opening of vagina orifice of vagina ostium vaginae vagina opening vaginal orifice uberon introitus introitus of vagina vaginal introitus UBERON:0012317 vagina orifice The median slit located inferior and posterior to the external urethral orifice in the female; the exit for menstrual flow and birth and the entrance for the penis during sexual intercourse; the size and appearance of the vaginal orifice varies inversely with that of the hymen (G. membrane), a thin fold of mucous membrane that surrounds the vaginal orifice MGI:anna MGI:csmith MP:0001142 introitus FMA:19984 EMAPA:37983 MA:th orifice of vagina FMA:19984 ostium vaginae FMA:TA vagina opening MP:0001142 vaginal orifice FMA:19984 introitus FMA:19984 introitus of vagina MP:0001142 An artery of the neck EMAPA:37075 NCIT:C52850 UMLS:C1707349 uberon UBERON:0012320 cervical artery An artery of the neck EMAPA:37075 MA:th UMLS:C1707349 ncithesaurus:Cervical_Artery The deep cervical artery (Profunda cervicalis) is an artery of the neck. FMA:10659 uberon profunda cervicalis UBERON:0012321 deep cervical artery FMA The deep cervical artery (Profunda cervicalis) is an artery of the neck. profunda cervicalis A bone element that is part of a jaw region. Do not manually classify under here - bones are automatically classified EMAPA:35453 MA:0003130 jaw bone uberon UBERON:0012360 bone of jaw A bone element that is part of a jaw region. OBOL:automatic EHDAA2:0004588 uberon UBERON:0012361 internal anal region EHDAA2 A muscle layer that is part of an intestine. FMA:15697 intestinal muscularis propria muscularis externa of intestine uberon smooth muscle of intestine UBERON:0012367 muscle layer of intestine FMA A muscle layer that is part of an intestine. OBOL:automatic intestinal muscularis propria FMA:15697 muscularis externa of intestine FMA:15697 A muscular coat that is part of a urinary bladder. FMA:15930 NCIT:C32206 UMLS:C1288327 bladder muscular coat muscle layer of urinary bladder muscular coat of bladder muscular coat of urinary bladder muscular layer of bladder muscular layer of urinary bladder tunica musculari vesicae tunica muscularis (vesica urinaria) uberon UBERON:0012378 muscle layer of urinary bladder FMA A muscular coat that is part of a urinary bladder. OBOL:automatic UMLS:C1288327 ncithesaurus:Bladder_Muscular_Coat muscle layer of urinary bladder FMA:15930 muscular coat of bladder FMA:15930 muscular coat of urinary bladder FMA:15930 muscular layer of bladder FMA:15930 muscular layer of urinary bladder FMA:15930 tunica musculari vesicae FMA:TA tunica muscularis (vesica urinaria) FMA:TA EMAPA:37567 MA:0001802 uberon UBERON:0012416 respiratory system arterial smooth muscle EMAPA:37567 MA:th A smooth muscle tissue that is part of a respiratory system venous blood vessel. EMAPA:37586 MA:0001812 uberon UBERON:0012418 respiratory system venous smooth muscle A smooth muscle tissue that is part of a respiratory system venous blood vessel. OBOL:automatic EMAPA:37586 MA:th The sclera and cornea form the fibrous tunic of the bulb of the eye; the sclera is opaque, and constitutes the posterior five-sixths of the tunic; the cornea is transparent, and forms the anterior sixth. tunica fibrosa FMA:58102 fibrous layer of eyeball uberon corneosclera fibrous tunic UBERON:0012430 tunica fibrosa of eyeball FMA The sclera and cornea form the fibrous tunic of the bulb of the eye; the sclera is opaque, and constitutes the posterior five-sixths of the tunic; the cornea is transparent, and forms the anterior sixth. fibrous layer of eyeball FMA:58102 corneosclera fibrous tunic A anatomical space that is enclosed by a cloaca. the ZFA class belongs here as it is an anatomical space. See https://sourceforge.net/p/obo/zebrafish-anatomy-zfa-term-requests/102/ TAO:0000330 ZFA:0000330 cloaca lumen cloacal chamber uberon UBERON:0012463 cloacal lumen cjm A anatomical space that is enclosed by a cloaca. OBOL:automatic the ZFA class belongs here as it is an anatomical space. See https://sourceforge.net/p/obo/zebrafish-anatomy-zfa-term-requests/102/ ZFA cloaca lumen ZFA:0000330 cloacal chamber ZFA:0000330 The opening of the cloacal chamber to the outside of the organism. Birds maintain a single cloacal opening throughout their lives. cloacal opening uberon cloacal orifice vent UBERON:0012464 cloacal vent The opening of the cloacal chamber to the outside of the organism. Birds maintain a single cloacal opening throughout their lives. A anatomical space that is enclosed by a terminal part of digestive tract. includes the cloacal lumen, in species where this is present uberon UBERON:0012465 lumen of terminal part of digestive tract A anatomical space that is enclosed by a terminal part of digestive tract. OBOL:automatic EHDAA2:0000472 EMAPA:16054 VHOG:0000767 uberon extraembryonic cavities UBERON:0012466 extraembryonic cavity extraembryonic cavities EHDAA2:0000472 An anatomical space with no opening to another space or to the exterior. AEO:0000222 closed anatomical space uberon UBERON:0012467 enclosed anatomical space An anatomical space with no opening to another space or to the exterior. AEO:0000222 EHDAA2:0004589 uberon UBERON:0012469 external anal region EHDAA2 The collection of all skeletal elements in a pectoral complex - i.e. the combination of free limb or fin plus pectoral girdle. FMA:24139 uberon bones of upper limb ossa membri superioris pectoral complex skeleton set of bones of upper limb skeleton of anterior limb/fin and girdle upper limb skeleton UBERON:0012475 skeleton of pectoral complex FMA The collection of all skeletal elements in a pectoral complex - i.e. the combination of free limb or fin plus pectoral girdle. bones of upper limb FMA:24139 ossa membri superioris FMA:TA pectoral complex skeleton set of bones of upper limb FMA:24139 skeleton of anterior limb/fin and girdle upper limb skeleton FMA:24139 The collection of all skeletal elements in a pelvic complex - i.e. the combination of free limb or fin plus pelvic girdle. FMA:24140 uberon bones of lower limb lower limb skeleton ossa membri inferioris pelvic complex skeleton set of bones of lower limb skeleton of posterior limb/fin and girdle UBERON:0012476 skeleton of pelvic complex FMA The collection of all skeletal elements in a pelvic complex - i.e. the combination of free limb or fin plus pelvic girdle. bones of lower limb FMA:24140 lower limb skeleton FMA:24140 ossa membri inferioris FMA:TA pelvic complex skeleton set of bones of lower limb FMA:24140 skeleton of posterior limb/fin and girdle A gland that is part of a cloaca. uberon UBERON:0012478 cloacal gland A gland that is part of a cloaca. OBOL:automatic A mucosa that is part of a cloaca [Automatically generated definition]. UBERON:0003349 cloaca mucosa cloaca mucosa of organ cloaca mucous membrane cloaca organ mucosa cloacal mucous membrane mucosa of cloaca mucosa of organ of cloaca mucous membrane of cloaca organ mucosa of cloaca uberon UBERON:0012480 cloacal mucosa A mucosa that is part of a cloaca [Automatically generated definition]. OBOL:automatic An epithelium that is part of a cloaca. cloacal epithelium (cle) (syn: cloacal endoderm) (TS17-TS20): the cloacal epithelium is derived from endoderm and lines the cloacal cavity. It is marked by Shh and Cdh1 and lines the cloacal lumen. The cloacal epithelium gives rise to the urogenital sinus epithelium, hindgut epithelium and the urethral plate epithelium. EMAPA:27577 EMAPA:36070 ZFA:0005783 uberon cloacal endoderm UBERON:0012481 cloacal epithelium An epithelium that is part of a cloaca. cloacal epithelium (cle) (syn: cloacal endoderm) (TS17-TS20): the cloacal epithelium is derived from endoderm and lines the cloacal cavity. It is marked by Shh and Cdh1 and lines the cloacal lumen. The cloacal epithelium gives rise to the urogenital sinus epithelium, hindgut epithelium and the urethral plate epithelium. EMAPA:27577 cloacal endoderm EMAPA:27577 A submucosa that is part of a cloaca [Automatically generated definition]. cloaca submucosa cloacal submucosa uberon UBERON:0012482 submucosa of cloaca A submucosa that is part of a cloaca [Automatically generated definition]. OBOL:automatic A serous membrane that is part of a cloaca [Automatically generated definition]. cloaca serosa cloaca serous membrane cloacal serosa serous membrane of cloaca visceral peritoneum of cloaca uberon UBERON:0012483 serosa of cloaca A serous membrane that is part of a cloaca [Automatically generated definition]. OBOL:automatic A muscular coat that is part of a cloaca. muscularis externa of cloaca uberon smooth muscle of cloaca UBERON:0012486 muscle layer of cloaca A muscular coat that is part of a cloaca. OBOL:automatic A muscular coat that is part of a colon. EMAPA:27383 FMA:14986 MA:0003198 colonic muscularis propria muscular coat of colon muscular layer of colon muscularis externa of colon tunica muscularis coli uberon colon muscularis UBERON:0012489 muscle layer of colon A muscular coat that is part of a colon. OBOL:automatic colonic muscularis propria FMA:14986 muscular coat of colon FMA:14986 muscular layer of colon FMA:14986 muscularis externa of colon FMA:14986 tunica muscularis coli FMA:TA colon muscularis MA:0003198 A muscular coat that is part of a anal canal. FMA:15708 anal canal muscularis propria anal muscularis propria muscular coat of anal canal muscular layer of anal canal muscularis externa of anal canal muscularis propria of anal canal uberon UBERON:0012490 muscle layer of anal canal A muscular coat that is part of a anal canal. OBOL:automatic anal muscularis propria FMA:15708 muscularis propria of anal canal FMA:15708 A serous membrane that is part of a fallopian tube. FMA:18316 serosa of fallopian tube serosa of oviduct serous coat of uterine tube tunica serosa (tuba uterina) tunica serosa tubae uterinae uterine tubal serosa uterine tube serosa uberon UBERON:0012499 serosa of uterine tube A serous membrane that is part of a fallopian tube. OBOL:automatic serosa of fallopian tube FMA:18316 serosa of oviduct FMA:18316 serous coat of uterine tube FMA:18316 tunica serosa (tuba uterina) FMA:18316 tunica serosa tubae uterinae FMA:TA uterine tubal serosa FMA:18316 uterine tube serosa FMA:18316 A vein that is part of a abdomen. TODO mirror representation of abdominal aorta this class groups all veins that are in the abdomen. The term 'abdominal vein' may have specific meanings in different contexts. The lateral abdominal veins are present in fishes but usually merged or absent in tetrapods; in amphibians, the L&R abdominal veins merge into the ventral abdominal vein abdominal vein uberon UBERON:0013126 vein of abdomen A vein that is part of a abdomen. OBOL:automatic A vein that drains a lip. labial vein of face lip vein vena labialis uberon labial vein UBERON:0013136 vein of lip FMA A vein that drains a lip. OBOL:automatic lip vein OBOL:automatic vena labialis Any vein within the general circulation that transports blood back to the right atrium of the heart. FMA:66644 NCIT:C33719 UMLS:C0447117 systemic venous tree organ part uberon UBERON:0013140 systemic vein Any vein within the general circulation that transports blood back to the right atrium of the heart. ncithesaurus:Systemic_Vein UMLS:C0447117 ncithesaurus:Systemic_Vein systemic venous tree organ part FMA:66644 A gland that is part of a foregut-midgut junction. EHDAA2:0000574 EMAPA:17065 gland of foregut-midgut junction uberon UBERON:0013158 foregut-midgut junction gland A gland that is part of a foregut-midgut junction. OBOL:automatic gland of foregut-midgut junction EMAPA:17065 The secretory unit of a serous gland. The acinar portion is composed of serous secreting cells. FMA:86279 acinus of serous gland uberon UBERON:0013232 serous acinus The secretory unit of a serous gland. The acinar portion is composed of serous secreting cells. The precursor of the urethra In humans, the urethral groove is a temporary linear indentation on the underside (ventral side) of the male penis during embryonic development. It typically appears around 8 weeks of gestation and becomes closed into a normal male urethra by the 12th week sulcus urethralis primarius urethral groove urethral sulcus uberon UBERON:0013241 embryonic urethral groove Wikipedia The precursor of the urethra In humans, the urethral groove is a temporary linear indentation on the underside (ventral side) of the male penis during embryonic development. It typically appears around 8 weeks of gestation and becomes closed into a normal male urethra by the 12th week sulcus urethralis primarius Anatomical cavity that is the lumen of the skull and contains the brain. EMAPA:37497 FMA:9644 MA:0003061 NCIT:C77638 UMLS:C0230041 cavitas cranii uberon intracranial cavity intracranial space UBERON:0013411 cranial cavity Wikipedia Anatomical cavity that is the lumen of the skull and contains the brain. UBERON:cjm EMAPA:37497 MA:th UMLS:C0230041 ncithesaurus:Cranial_Cavity cavitas cranii FMA:9644 FMA:TA intracranial cavity intracranial space A blood vessel endothelium that is part of a lung [Automatically generated definition]. BTO:0004128 CALOHA:TS-0573 uberon respiratory endothelium UBERON:0013479 lung endothelium A blood vessel endothelium that is part of a lung [Automatically generated definition]. OBOL:automatic respiratory endothelium BTO:0004128 The space that surrounds an organism. external to organism outside of body uberon UBERON:0013514 space surrounding organism The space that surrounds an organism. A section through the tube or network of tubes that connects the ovaries to the outside of the body. FMA class may only represent the uterine portion FMA:18302 subdivision of oviduct subdivision of uterine tube uterine tube zone zone of uterine tube subdivision of fallopian tube uberon UBERON:0013515 subdivision of oviduct A section through the tube or network of tubes that connects the ovaries to the outside of the body. FMA class may only represent the uterine portion FMA subdivision of oviduct FMA:18302 uterine tube zone FMA:18302 zone of uterine tube FMA:18302 subdivision of fallopian tube FMA:18302 uberon UBERON:0013522 subdivision of tube The anatomical space that is enclosed by a stomach. Organ cavity which is bound by the internal surface of the wall of stomach. Examples: There is only one cavity of stomach[FMA:14585]. EMAPA:18395 FMA:14585 cavity of stomach uberon gastric cavity UBERON:0013525 stomach lumen FMA The anatomical space that is enclosed by a stomach. Organ cavity which is bound by the internal surface of the wall of stomach. Examples: There is only one cavity of stomach[FMA:14585]. FMA:14585 cavity of stomach FMA:14585 gastric cavity FMA:14585 A anatomical cavity that is part of a ear vesicle. EHDAA2:0004121 EMAPA:25363 lumen of otocyst uberon UBERON:0013526 otocyst lumen EHDAA2 EHDAA2 EHDAA2 A anatomical cavity that is part of a ear vesicle. OBOL:automatic lumen of otocyst EMAPA:25363 Anatomical space that is an opening in a bone of the skull. FMA:53165 foramen of skull cranial conduit cranial foramen uberon foramina of the skull UBERON:0013685 foramen of skull Anatomical space that is an opening in a bone of the skull. TAO:curator foramen of skull cranial conduit FMA:53165 foramina of the skull 2 2 An anatomical space which is the lumen of some anatomical conduit and connects two or more spaces together[FMA,modified]. FMA:9338 foramen space uberon UBERON:0013686 anatomical conduit space FMA An anatomical space which is the lumen of some anatomical conduit and connects two or more spaces together[FMA,modified]. FMA:9338 Vascular endothelium found in blood vessels of the blood-brain-barrier. BTO:0001852 BTO:0003248 CALOHA:TS-0092 uberon cerebromicrovascular endothelium UBERON:0013694 brain endothelium Vascular endothelium found in blood vessels of the blood-brain-barrier. CALOHA:TS-0092 cerebromicrovascular endothelium CALOHA:TS-0092 Vascular endothelium found in colon blood vessels. CALOHA:TS-0162 uberon colon endothelial cell colon endothelial cells colonic endothelial cell colonic endothelium colorectal endothelial cell colorectal endothelium UBERON:0013695 colon endothelium Vascular endothelium found in colon blood vessels. CALOHA:TS-0162 colon endothelial cell CALOHA:TS-0162 colon endothelial cells CALOHA:TS-0162 colonic endothelial cell CALOHA:TS-0162 colonic endothelium CALOHA:TS-0162 colorectal endothelial cell CALOHA:TS-0162 colorectal endothelium CALOHA:TS-0162 Musculature of the head and neck, spine, and ribs. EHDAA2:0000159 EMAPA:18166 uberon UBERON:0013700 axial musculature Musculature of the head and neck, spine, and ribs. HP:0003327 A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages. uberon UBERON:0013701 main body axis A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages. The region of the organism associated with the visceral organs. Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]. AEO:0000103 BTO:0001489 EMAPA:36031 FMA:231424 uberon body whole body UBERON:0013702 body proper AEO The region of the organism associated with the visceral organs. AEO:0000103 Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]. FMA:231424 body AEO:0000103 whole body BTO:0001489 A tubular passage that extends from the primitive pit into the head process during the early stages of embryonic development in mammals. It perforates the splanchnopleure layer so that the yolk sac and the amnion are connected temporarily. FMA:293127 NCIT:C34230 UMLS:C1518428 uberon chordal canal UBERON:0013704 notochordal canal A tubular passage that extends from the primitive pit into the head process during the early stages of embryonic development in mammals. It perforates the splanchnopleure layer so that the yolk sac and the amnion are connected temporarily. UMLS:C1518428 ncithesaurus:Notochordal_Canal Fluid contained within the notochordal canal notochord fluid portion of notochordal fluid uberon UBERON:0013727 Distinct feature of coelocanths notochordal fluid Fluid contained within the notochordal canal A organ component layer that is part of a integumental system. layer of skin skin layer uberon UBERON:0013754 integumentary system layer A organ component layer that is part of a integumental system. OBOL:automatic A blood that is part of a artery. FMA:83066 arterial blood blood in artery portion of arterial blood uberon UBERON:0013755 arterial blood A blood that is part of a artery. OBOL:automatic arterial blood FMA:83066 blood in artery FMA:83066 portion of arterial blood FMA:83066 A blood that is part of a vein. FMA:83067 blood in vein portion of venous blood venous blood uberon UBERON:0013756 venous blood A blood that is part of a vein. OBOL:automatic blood in vein FMA:83067 portion of venous blood FMA:83067 venous blood FMA:83067 A blood that is part of a capillary. FMA:263901 NCIT:C32212 blood in capillary portion of blood in capillary portion of capillary blood uberon UBERON:0013757 capillary blood A blood that is part of a capillary. OBOL:automatic portion of blood in capillary FMA:263901 One of two openings in the uterine cervix. FMA:20422 uberon cervical opening uterine cervix opening UBERON:0013758 cervical os One of two openings in the uterine cervix. Opening of uterine cervix into the vagina. The external orifice of the uterus (or ostium of uterus, or external os) is a small, depressed, somewhat circular aperture on the rounded extremity of the vaginal portion of the cervix. Through this aperture, the cervical cavity communicates with that of the vagina. The external orifice is bounded by two lips, an anterior and a posterior. The anterior is shorter and thicker, though it projects lower than the posterior because of the slope of the cervix. Normally, both lips are in contact with the posterior vaginal wall. Prior to pregnancy, the external orifice has a rounded shape when viewed through the vaginal canal (as through a speculum). Following parturition, the orifice takes on an appearance more like a transverse slit or is 'H-shaped'[Wikipedia:External_orifice_of_the_uterus]. FMA:76836 NCIT:C32491 UMLS:C1512165 external os of uterus ostium uteri uberon external os ostium of uterus UBERON:0013760 external cervical os Opening of uterine cervix into the vagina. The external orifice of the uterus (or ostium of uterus, or external os) is a small, depressed, somewhat circular aperture on the rounded extremity of the vaginal portion of the cervix. Through this aperture, the cervical cavity communicates with that of the vagina. The external orifice is bounded by two lips, an anterior and a posterior. The anterior is shorter and thicker, though it projects lower than the posterior because of the slope of the cervix. Normally, both lips are in contact with the posterior vaginal wall. Prior to pregnancy, the external orifice has a rounded shape when viewed through the vaginal canal (as through a speculum). Following parturition, the orifice takes on an appearance more like a transverse slit or is 'H-shaped'[Wikipedia:External_orifice_of_the_uterus]. UMLS:C1512165 ncithesaurus:Ectocervical_Os external os of uterus FMA:76836 ostium uteri FMA:TA external os ostium of uterus The cavity formed by the walls of the cervix. BTO:0002249 FMA:17746 lumen of cervix of uterus uberon canal of the cervix cavity of cervix cervical canal cervical canal of uterus endocervical endocervical canal endocervix UBERON:0013761 cervical cavity The cavity formed by the walls of the cervix. lumen of cervix of uterus FMA:17746 canal of the cervix cavity of cervix BTO:0002249 cervical canal cervical canal of uterus BTO:0002249 endocervical endocervical canal endocervical canal BTO:0002249 endocervix Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements. EMAPA:37843 digestive organ digestive system organ uberon UBERON:0013765 digestive system element Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements. EMAPA:37843 MA:th Great vessels is a term used to refer collectively to the large vessels that bring blood to and from the heart. great vessel EMAPA:36460 great vessel of thorax uberon UBERON:0013768 Groupings may vary - typically pulmonary vessels and aorta and vena cavae great vessel of heart Great vessels is a term used to refer collectively to the large vessels that bring blood to and from the heart. A organ cavity that is part of a uterus. EMAPA:36273 FMA:17745 cavity of uterus uterine cavity uterine space uberon UBERON:0013769 uterine lumen A organ cavity that is part of a uterus. OBOL:automatic cavity of uterus FMA:17745 uterine cavity FMA:17745 Mesenchyme that develops_from the neural crest[Automatically generated definition]. EMAPA:32735 FMA:293883 mesenchyme from neural crest neural crest derived mesenchyme neural crest mesenchyme uberon UBERON:0014387 mesenchyme derived from neural crest Mesenchyme that develops_from the neural crest[Automatically generated definition]. OBOL:automatic Any member of the network of tubes that return blood from the renal tissues to the systemic circulation. we follow MA and MP in distinguishing the venous blood vessel from the vein. The kidney cortex vein is not considered a renal vein, nor is the vasa recta EMAPA:31450 MA:0002591 kidney venous blood vessel venous blood vessel of kidney uberon kidney venous system UBERON:0014401 renal venous blood vessel Any member of the network of tubes that return blood from the renal tissues to the systemic circulation. MGI:csmith we follow MA and MP in distinguishing the venous blood vessel from the vein. The kidney cortex vein is not considered a renal vein, nor is the vasa recta MA kidney venous blood vessel MA:0002591 kidney venous system EMAPA:31450 Subcutaneous adipose tissue that is located in the abdominal region. CALOHA:TS-2406 abdominal subcutaneous adipose tissue subcutaneous abdominal fat subcutaneous fat of abdominal region uberon UBERON:0014455 subcutaneous abdominal adipose tissue Subcutaneous adipose tissue that is located in the abdominal region. CALOHA:paula MGI:csmith Subdivision of skeletal system that consists of all skeletal elements in the thoracic region of the trunk. In most vertebrates this is the rib cage and sternum. EHDAA2:0002013 FMA:77169 skeleton of thorax thoracic part of axial skeleton thoracic skeleton uberon UBERON:0014477 thoracic skeleton Subdivision of skeletal system that consists of all skeletal elements in the thoracic region of the trunk. In most vertebrates this is the rib cage and sternum. thoracic skeleton EHDAA2:0002013 A unilaminar epithelium that develops_from a ectoderm and is part of a anal region. EHDAA2:0004019 EMAPA:25040 uberon UBERON:0014703 anal membrane ectodermal component A unilaminar epithelium that develops_from a ectoderm and is part of a anal region. OBOL:automatic The secretory unit of a mucous gland. The acinar portion is composed of mucous secreting cells. FMA:86278 acinus of mucuous gland mucus acinus uberon UBERON:0014717 mucous acinus The secretory unit of a mucous gland. The acinar portion is composed of mucous secreting cells. A neuromere that is part of the presumptive midbrain mesomere midbrain segment segment of midbrain EHDAA2:0004352 FMA:61997 mesomere of nervous system neuromere of mesomere group uberon future mesencephalon mesomere group UBERON:0014776 midbrain neuromere A neuromere that is part of the presumptive midbrain mesomere group EHDAA2:0004352 A neuromere that is part of the presumptive spinal cord TAO:0001332 ZFA:0001332 spinal cord metameric segment spinal neuromeres uberon spinal cord segment UBERON:0014777 spinal neuromere A neuromere that is part of the presumptive spinal cord spinal neuromeres TAO:0001332 spinal cord segment TAO:0001332 Any muscle organ that is part of a cloaca. uberon UBERON:0014783 cloacal muscle Any muscle organ that is part of a cloaca. OBOL:automatic Any collection of muscles that is part of a pelvic complex. The pelvic complex comprises the pelvic girdle and the associated limb or fin. currently defined by location rather than attachment EMAPA:37864 FMA:71297 muscles of lower limb musculature of lower limb musculi membri inferioris uberon UBERON:0014792 musculature of pelvic complex Any collection of muscles that is part of a pelvic complex. The pelvic complex comprises the pelvic girdle and the associated limb or fin. OBOL:automatic EMAPA:37864 MA:th muscles of lower limb FMA:71297 musculature of lower limb FMA:71297 musculi membri inferioris FMA:TA Any collection of muscles that is part of a pectoral complex. The pectoral complex comprises the pectoral girdle and the associated limb or fin. currently defined by location rather than attachment EMAPA:37861 FMA:71296 muscles of upper limb musculature of upper limb musculi membri superioris set of muscles of upper limb upper limb musculature uberon UBERON:0014793 musculature of pectoral complex Any collection of muscles that is part of a pectoral complex. The pectoral complex comprises the pectoral girdle and the associated limb or fin. OBOL:automatic EMAPA:37861 MA:th muscles of upper limb FMA:71296 musculature of upper limb FMA:71296 musculi membri superioris FMA:TA set of muscles of upper limb FMA:71296 upper limb musculature FMA:71296 Any muscle organ that is part of a pectoral appendage (forelimb or pectoral fin). uberon UBERON:0014794 pectoral appendage muscle prolog Any muscle organ that is part of a pectoral appendage (forelimb or pectoral fin). OBOL:automatic Any muscle organ that is part of a pelvic appendage (hindlimb or pelvic fin). uberon UBERON:0014795 pelvic appendage muscle prolog Any muscle organ that is part of a pelvic appendage (hindlimb or pelvic fin). OBOL:automatic A muscle organ that consists of skeletal muscle tissue ensheathed in epimysium, that develops from myotome and that is innervated by some somatic motor neuron. Skeletal muscles are typically attached (via a tendon) to a bone but there are exceptions (e.g. intrinsic tongue muscles). skeletal muscle AAO:0011099 BTO:0001103 CALOHA:TS-0933 EFO:0000888 EHDAA:5035 EHDAA:5043 EHDAA:5978 EHDAA:5984 EMAPA:35988 EV:0100377 GAID:141 MA:0003148 MAT:0000302 MESH:D018482 MIAA:0000302 OpenCyc:Mx4rv2kf-5wpEbGdrcN5Y29ycA TAO:0005277 VHOG:0000319 XAO:0000174 ZFA:0005277 uberon UBERON:0014892 skeletal muscle organ A muscle organ that consists of skeletal muscle tissue ensheathed in epimysium, that develops from myotome and that is innervated by some somatic motor neuron. Skeletal muscles are typically attached (via a tendon) to a bone but there are exceptions (e.g. intrinsic tongue muscles). GOC:dos A portion of tissue that will develop into vasculature. EFO:0003708 TAO:0005076 ZFA:0005076 uberon UBERON:0014903 primordial vasculature A portion of tissue that will develop into vasculature. ZFA:0005076 ZFA:curator A gland that is typically found in or near the orbital region, in or around either the medial or lateral canthi, and is typically associated with secretions onto the eyeball or associated ducts. Includes the Harderian, nictitans and lacrimal glands. the only orbital gland found in anuran amphibians is either the Harderian or the lacrimal; if it is a lacrimal, then a progressive lateral migration of the lacrimal glands must occur through the amniotes[PMID:7559104] the only orbital gland found in anuran amphibians is the Harderian[PMID:8843648] ocular gland uberon orbital gland UBERON:0015152 gland of ocular region inferred A gland that is typically found in or near the orbital region, in or around either the medial or lateral canthi, and is typically associated with secretions onto the eyeball or associated ducts. Includes the Harderian, nictitans and lacrimal glands. An eye consisting of multiple light-sensing organs uberon UBERON:0015165 multi-unit eye An eye consisting of multiple light-sensing organs present on tentacular crown present on mantle edge in arcacean Bivalvia The eyes (optic cushions) on the oral surface of Asteroida (Echinodermata), close to the base of the terminal tentacles, are also composed of a number of simple ocelli - as many as 80-200 in certain species A blood vessel that is part of a endometrium. blood vessel of endometrium uberon UBERON:0015172 endometrial blood vessel A blood vessel that is part of a endometrium. OBOL:automatic A region of somite adjacent to presomitic mesoderm. TAO:0001462 XAO:0004074 ZFA:0001462 uberon inter-somited border intersomitic boundary intersomitic fissure intersomitic junction segmental border somite boundary UBERON:0015178 somite border A region of somite adjacent to presomitic mesoderm. intersomitic junction XAO:0004074 somite boundary ZFA:0001462 Epithelium located in the intersomitic region. XAO:0004077 intersomitic epithelium intersomitic membrane uberon UBERON:0015179 somite boundary epithelium Epithelium located in the intersomitic region. XAO:0004077 XAO:EJS intersomitic epithelium XAO:0004077 intersomitic membrane XAO:0004077 Any structure that is placed on one side of the left-right axis of a bilaterian. This class is primarily to implement taxon constraints. It may be removed in the future. uberon UBERON:0015212 lateral structure Any structure that is placed on one side of the left-right axis of a bilaterian. A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile. heart SPD:0000130 cardiac pump heart or heart like organ circulatory vessel uberon cardiac structure UBERON:0015228 circulatory organ A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile. A basement membrane of epithelium that is part of a respiratory system. EMAPA:37570 MA:0001815 uberon UBERON:0015329 respiratory system basement membrane MA A basement membrane of epithelium that is part of a respiratory system. OBOL:automatic EMAPA:37570 MA:th EMAPA:37597 MA:0002449 heart/pericardium uberon UBERON:0015410 heart plus pericardium MA EMAPA:37597 MA:th heart/pericardium MA:0002449 A mesenchyme that is part of a urethra. EMAPA:37786 MA:0002648 uberon UBERON:0015418 urethra mesenchymal layer A mesenchyme that is part of a urethra. OBOL:automatic EMAPA:37786 MA:th A valve that is part of a ureter. EMAPA:37781 MA:0002658 ureteral valve valve or ureter uberon UBERON:0015420 ureteral valve A valve that is part of a ureter. OBOL:automatic EMAPA:37781 MA:th ureteral valve MA:0002658 A epithelium that is part of a anal canal. EMAPA:18835 FMA:17511 anal canal epithelium epithelium of anal canal uberon UBERON:0015716 anal canal epithelium A epithelium that is part of a anal canal. OBOL:automatic anal canal epithelium FMA:17511 epithelium of anal canal FMA:17511 A smooth muscle tissue that is part of a hypodermis. FMA:77862 muscle layer in fatty layer of subcutaneous tissue stratum musculosum panniculi adiposi telae subcutaneae uberon UBERON:0015783 smooth muscle layer in fatty layer of subcutaneous tissue A smooth muscle tissue that is part of a hypodermis. OBOL:automatic muscle layer in fatty layer of subcutaneous tissue FMA:77862 stratum musculosum panniculi adiposi telae subcutaneae FMA:77862 FMA:TA Any anatomical conduit which is part of the upper respiratory tract Anatomical cluster which consists a segment of the upper respiratory tract[FMA:265132]. FMA:265132 uberon respiratory conduit UBERON:0015787 upper respiratory conduit Any anatomical conduit which is part of the upper respiratory tract Anatomical cluster which consists a segment of the upper respiratory tract[FMA:265132]. FMA:265132 respiratory conduit FMA:265132 An anatomical chamber that is part of the olfactory apparatus, consisting of cavity walls (nasal epithelium and mucosal layers) and the space bounded anteriorly by the nares and posteriorly by the choanae, when these structures are present. FMA:265136 uberon UBERON:0015788 olfactory apparatus chamber An anatomical chamber that is part of the olfactory apparatus, consisting of cavity walls (nasal epithelium and mucosal layers) and the space bounded anteriorly by the nares and posteriorly by the choanae, when these structures are present. see also, 'facial nerve muscle', which is not precisely equivalent. We include this grouping to accomodate the MA class, which includes masticatory muscle as a subtype; note the masticatory muscle is noy innervated by the facial nerve, unlike the facial muscles proper EMAPA:25133 MA:0000579 cranial/facial muscle uberon cranial-facial muscle cranio-facial muscle craniofacial muscle UBERON:0015789 cranial or facial muscle cranial/facial muscle MA:0000579 cranial-facial muscle EMAPA:25133 cranio-facial muscle EMAPA:25133 craniofacial muscle EMAPA:25133 A epithelium that is part of a ear. EMAPA:32800 MA:0003161 uberon UBERON:0015807 ear epithelium A epithelium that is part of a ear. OBOL:automatic A epithelium that is part of a camera-type eye. EMAPA:35957 MA:0003162 uberon UBERON:0015808 eye epithelium A epithelium that is part of a camera-type eye. OBOL:automatic A epithelium that is part of a foregut. EMAPA:32922 MA:0003204 uberon UBERON:0015833 foregut epithelium A epithelium that is part of a foregut. OBOL:automatic A capillary that is part of a lung. FMA:14121 capillary of lung uberon UBERON:0016405 pulmonary capillary A capillary that is part of a lung. OBOL:automatic capillary of lung FMA:14121 is the sensory system for the sense of hearing. Auditory system is general anatomical term in FMA EMAPA:36002 FMA:7192 MA:0002443 NCIT:C12889 OpenCyc:Mx4rvViwtJwpEbGdrcN5Y29ycA UMLS:C0587901 uberon UBERON:0016490 auditory system is the sensory system for the sense of hearing. NIFSTD:nlx_anat_090817 Auditory system is general anatomical term in FMA FMA UMLS:C0587901 ncithesaurus:Auditory_System Luminal space of the right ventricle of the heart. EMAPA:26047 FMA:9291 right ventricle lumen right ventricular cavity uberon UBERON:0016509 cavity of right ventricle Luminal space of the right ventricle of the heart. right ventricle lumen EMAPA:26047 right ventricular cavity FMA:FMA luminal space of the left ventricle of the heart. EMAPA:26038 FMA:9466 left ventricular cavity uberon UBERON:0016514 cavity of left ventricle luminal space of the left ventricle of the heart. left ventricular cavity FMA:FMA A epithelium that is part of a female urethra. EMAPA:30470 FMA:19774 female urethral epithelium urethral epithelium of female uberon UBERON:0016520 epithelium of female urethra A epithelium that is part of a female urethra. OBOL:automatic female urethral epithelium FMA:FMA urethral epithelium of female EMAPA:30470 The external part of the developing pharynx that is made of ectoderm. During vertebrate development, pockets form in pharyngeal ectoderm between the pharyngeal arches. UBERON:2001379 TAO:0001379 ZFA:0001379 uberon UBERON:0016545 pharyngeal ectoderm The external part of the developing pharynx that is made of ectoderm. During vertebrate development, pockets form in pharyngeal ectoderm between the pharyngeal arches. A layer of of the central nervous system that is part of gray matter. grey matter layer FMA:83142 CNS gray matter layer CNS grey matter layer gray matter layer of neuraxis grey matter layer of neuraxis uberon UBERON:0016548 central nervous system gray matter layer A layer of of the central nervous system that is part of gray matter. gray matter layer of neuraxis FMA:83142 mucus produced in the respiratory tract. NCIT:C93171 uberon UBERON:0016552 phlegm mucus produced in the respiratory tract. Any mucus produced by a mucosae of the respiratory system. This includes the mucus produced in the nasal cavity (nasal mucus) and mucus produced in the respiratory tract (phlegm). uberon UBERON:0016553 respiratory system mucus Any mucus produced by a mucosae of the respiratory system. This includes the mucus produced in the nasal cavity (nasal mucus) and mucus produced in the respiratory tract (phlegm). An roughly circular indentation in a surface. AEO:0000204 uberon UBERON:0016566 pit An roughly circular indentation in a surface. AEO:0000204 AEO:JB FMA:68861 rexed lamina uberon UBERON:0016570 lamina of gray matter of spinal cord rexed lamina FMA:68861 Primordium that develops into the central nervous system UBERON:3000469 future CNS presumptive central nervous system uberon UBERON:0016879 future central nervous system Primordium that develops into the central nervous system Primordium that develops into the nervous system UBERON:3000477 AAO:0000477 presumptive nervous system uberon UBERON:0016880 future nervous system Primordium that develops into the nervous system presumptive nervous system AAO:0000477 Epithelium lining the distalmost portion of the digestive tract. BTO:0005445 WBbt:0005800 rectum epithelium uberon UBERON:0016885 epithelium of terminal part of digestive tract Epithelium lining the distalmost portion of the digestive tract. rectum epithelium BTO:0005445 Any muscle tissue of the distalmost portion of the digestive tract. rectum muscle rectum muscle structure uberon UBERON:0016886 muscle tissue of terminal part of digestive tract Any muscle tissue of the distalmost portion of the digestive tract. The part of the conceptus that may be lost before birth or will be discarded at birth, or when the embryo becomes an independent organism. AEO:0000195 EHDAA2:0000003 EMAPA:16042 extra-embryonic component extraembryonic component uberon UBERON:0016887 entire extraembryonic component AEO AEO The part of the conceptus that may be lost before birth or will be discarded at birth, or when the embryo becomes an independent organism. AEO:0000195 AEO:JB extraembryonic component AEO:0000195 An embryonic anatomical entity that will turn into one or more other anatomical entities, perhaps with other anatomical entities, later in development. AEO:0000132 uberon UBERON:0016888 transitional anatomical structure AEO An embryonic anatomical entity that will turn into one or more other anatomical entities, perhaps with other anatomical entities, later in development. AEO:0000132 AEO:JB A mesenchyme-derived anatomical entity undergoing a transtion to become another structure. AEO:0001016 uberon UBERON:0017650 developing mesenchymal structure A mesenchyme-derived anatomical entity undergoing a transtion to become another structure. AEO:0001016 AEO:JB A viscus that is part of a abdomen. FMA:32413 FMA:67355 abdominal viscera abdominal viscera set set of abdominal viscera uberon UBERON:0017672 abdominal viscera A viscus that is part of a abdomen. OBOL:automatic abdominal viscera FMA:32413 abdominal viscera set FMA:32413 set of abdominal viscera FMA:32413 A muscle layer that is part of the rectum FMA:15035 muscular coat of rectum muscularis externa of rectum rectal muscularis propria tunica muscularis (rectum) tunica muscularis recti uberon UBERON:0018111 muscle layer of rectum A muscle layer that is part of the rectum muscular coat of rectum FMA:15035 muscularis externa of rectum FMA:15035 rectal muscularis propria FMA:15035 tunica muscularis (rectum) FMA:15035 tunica muscularis recti FMA:TA Any portion of smooth muscle tissue that is part of the rectum rectal smooth muscle tissue rectum smooth muscle smooth muscle of rectum uberon UBERON:0018112 rectum smooth muscle tissue Any portion of smooth muscle tissue that is part of the rectum A renal pelvis that is part of a left ureter. FMA:15579 pelvis of left ureter renal pelvis of left kidney uberon UBERON:0018115 left renal pelvis A renal pelvis that is part of a left ureter. OBOL:automatic pelvis of left ureter FMA:15579 renal pelvis of left kidney FMA:15579 A renal pelvis that is part of a right ureter. FMA:15578 pelvis of right kidney pelvis of right ureter uberon UBERON:0018116 right renal pelvis A renal pelvis that is part of a right ureter. OBOL:automatic pelvis of right kidney FMA:15578 pelvis of right ureter FMA:15578 A zone of skin that is part of a lower lip. FMA:24767 lower lip skin uberon UBERON:0018150 skin of lower lip A zone of skin that is part of a lower lip. OBOL:automatic lower lip skin FMA:24767 A boundary delimiting a rhombomere. rhombomere junction uberon UBERON:0018239 rhombomere boundary A boundary delimiting a rhombomere. GO:0021654 Added for consistency with MA EMAPA and EHDAA2. See https://github.com/obophenotype/mouse-anatomy-ontology/issues/104 EHDAA2:0001842 EMAPA:35578 MA:0000165 uberon UBERON:0018254 skeletal musculature MA Any portion of submucosa that lines the digestive tract. uberon UBERON:0018257 submucosa of digestive tract Any portion of submucosa that lines the digestive tract. Any organ component layer that consists of muscle tissue. NCITA class may refer to smooth muscle only FMA:45634 NCIT:C75444 uberon UBERON:0018260 layer of muscle tissue Any organ component layer that consists of muscle tissue. NCITA class may refer to smooth muscle only NCIT A muscular coat that is part of a digestive tract. responsible for gut movement, such as peristalsis tunica muscularis of digestive tract uberon muscular layer of digestive tract muscularis externa of digestive tract tunica externa of digestive tract UBERON:0018261 muscular coat of digestive tract A muscular coat that is part of a digestive tract. OBOL:automatic Foramen that allows the passge of the glossopharyngeal nerve (cranial nerve IX). UBERONTEMP:9ca0bda7-9111-4f59-bc72-5d47bc3d7d61 uberon UBERON:0018321 foramen for glossopharyngeal nerve Foramen that allows the passge of the glossopharyngeal nerve (cranial nerve IX). PHENOSCAPE:alex A Z-shaped canal running through the temporal bone from the internal acoustic meatus to the stylomastoid foramen. It is located within the middle ear region, according to its shape it is divided into three main segments: the labyrinthine, the tympanic, and the mastoidal segment . FMA:54952 canalis nervi facialis facial canal uberon fallopian canal UBERON:0018413 facial nerve canal A Z-shaped canal running through the temporal bone from the internal acoustic meatus to the stylomastoid foramen. It is located within the middle ear region, according to its shape it is divided into three main segments: the labyrinthine, the tympanic, and the mastoidal segment . canalis nervi facialis FMA:54952 FMA:TA facial canal FMA:54952 fallopian canal FMA:54952 The anatomical space within the intestine. see notes in inclusivity in class 'intestine' FMA:14586 TADS:0000495 WBbt:0005791 ZFA:0005807 intestinal lumen intestine lumen uberon gut lumen UBERON:0018543 lumen of intestine The anatomical space within the intestine. intestinal lumen FMA:14586 intestine lumen ZFA:0005807 gut lumen ZFA:0005807 Muscle innervated by the trigeminal nerve (Cranial Nerve V). MFMO:0000072 muscle innervated by the trigeminal nerve muscles innervated by the trigeminal nerve uberon UBERON:0018544 trigeminal nerve muscle Muscle innervated by the trigeminal nerve (Cranial Nerve V). MFMO:0000072 muscles innervated by the trigeminal nerve MFMO:0000072 FMA:83450 ventricular cardiac muscle tissue ventricular heart muscle uberon ventricular muscle UBERON:0018649 cardiac muscle tissue of ventricle ventricular cardiac muscle tissue ventricular heart muscle ventricular muscle the neck region of a bone organ. bone neck neck of bone uberon UBERON:0018664 neck of bone element https://github.com/obophenotype/uberon/wiki/Hidden-GCIs the neck region of a bone organ. An interconnected tubular multi-tissue structure that contains fluid that is actively transported around the heart. FMA:73747 ZFA:0005811 cardiac vasculature uberon UBERON:0018674 heart vasculature An interconnected tubular multi-tissue structure that contains fluid that is actively transported around the heart. ZFA:0005811 ZFA:CVS cardiac vasculature FMA:73747 A membranous sac in animals that serves as the receptacle of a liquid or contains gas. BTO:0000123 bladder uberon UBERON:0018707 bladder organ A membranous sac in animals that serves as the receptacle of a liquid or contains gas. BTO:0000123 bladder BTO:0000123 BTO:0002439 genital mucosa uberon UBERON:0019042 reproductive system mucosa genital mucosa BTO:0002439 Adipose tissue which is located throughout skeletal muscle and is responsible for the marbling seen in certain cuts of beef. In humans, excess accumulation of intramuscular fat is associated with insulin resistance and type 2 diabetes. BTO:0004043 uberon intramuscular fat UBERON:0019143 intramuscular adipose tissue Adipose tissue which is located throughout skeletal muscle and is responsible for the marbling seen in certain cuts of beef. In humans, excess accumulation of intramuscular fat is associated with insulin resistance and type 2 diabetes. BTO:0004043 intramuscular fat BTO:0004043 BTO:0004626 uberon carotid endothelium carotid epithelium UBERON:0019189 carotid artery endothelium carotid endothelium BTO:0004626 BTO:0004638 FMA:13119 bronchial gland bronchial mucous gland peribronchial gland uberon UBERON:0019190 mucous gland of lung bronchial gland FMA:13119 bronchial mucous gland FMA:13119 peribronchial gland BTO:0004638 Any region of epithelium that is part of a skin region. BTO:0004382 uberon UBERON:0019204 skin epithelium Any region of epithelium that is part of a skin region. The part of the eye that consists of both the retina and the optic choroid chorioretina choroid and retina retinachoroid retinachoroidal region uberon UBERON:0019207 chorioretinal region The part of the eye that consists of both the retina and the optic choroid UBERON:drseb DHBA:10654 FMA:268630 gray matter of the hindbrain uberon UBERON:0019263 gray matter of hindbrain gray matter of the hindbrain DHBA:HGM DHBA:10649 FMA:83913 uberon UBERON:0019267 gray matter of midbrain EMAPA:35952 MA:0003174 uberon UBERON:0019304 sensory organ epithelium EMAPA:35958 MA:0003171 uberon UBERON:0019306 nose epithelium An exocrine gland that is part of a integumental system. integumental exocrine gland integumental system exocrine gland uberon UBERON:0019319 exocrine gland of integumental system An exocrine gland that is part of a integumental system. GOC:dos integumental exocrine gland integumental system exocrine gland The spinal accessory nucleus lies within the cervical spinal cord (C1-C5) in the ventral horn. The nucleus ambiguus is classically said to provide the 'cranial component' of the accessory nerve. However, the very existence of this cranial component has been recently questioned and seen as contributing exclusively to the vagus nerve. The terminology continues to be used in describing both human anatomy, and that of other animals. EMAPA:37067 FMA:83965 MA:0001033 accessory neural nucleus uberon accessory nucleus of anterior column of spinal cord nucleus accessorius columnae anterioris medullae spinalis nucleus nervi accessorii nucleus of accessory nerve nucleus of the accessory nerve nucleus of the spinal accessory nerve spinal accessory nucleus UBERON:0020358 See also: http://en.wikipedia.org/wiki/Spinal_accessory_nucleus accessory XI nerve nucleus FMA The spinal accessory nucleus lies within the cervical spinal cord (C1-C5) in the ventral horn. The nucleus ambiguus is classically said to provide the 'cranial component' of the accessory nerve. However, the very existence of this cranial component has been recently questioned and seen as contributing exclusively to the vagus nerve. The terminology continues to be used in describing both human anatomy, and that of other animals. EMAPA:37067 MA:th accessory neural nucleus FMA:83965 accessory nucleus of anterior column of spinal cord NeuroNames:2003 nucleus accessorius columnae anterioris medullae spinalis NeuroNames:2003 nucleus nervi accessorii NeuroNames:2003 nucleus of accessory nerve NeuroNames:2003 nucleus of the accessory nerve NeuroNames:2003 nucleus of the spinal accessory nerve NeuroNames:2003 spinal accessory nucleus A blood vessel that supplies or drains an ear. EMAPA:37386 MA:0001226 uberon UBERON:0020550 auricular blood vessel A blood vessel that supplies or drains an ear. EMAPA:37386 MA:th FMA:58315 uberon surface of region of wall of eyeball UBERON:0022288 surface of eyeball surface of region of wall of eyeball FMA:58315 A portion of organism substance that is secreted by a reproductive gland. uberon genital fluid genital secretion reproductive system fluid reproductive system fluid/secretion reproductive system secretion UBERON:0022293 reproductive gland secretion A portion of organism substance that is secreted by a reproductive gland. UBERON:cjm Single layer of a laminar structure, identified by different density, arrangement or size of cells and processes arranged in flattened layers or lamina[CUMBO]. this is currently used to group some cellular layers that may not strictly conform to the CARO definition of cell-part layer. Consider genericisizing and introducing subtypes for cellular layer, fibrous layer and cell soma layer lamina layer uberon UBERON:0022303 nervous system cell part layer Single layer of a laminar structure, identified by different density, arrangement or size of cells and processes arranged in flattened layers or lamina[CUMBO]. NIFSTD:nlx_149357 lamina CUMBO:CUMBO layer CUMBO:CUMBO Serous membrane layer that is adjacent to and lines an organ. FMA:15860 visceral wall of serous membrane uberon UBERON:0022350 visceral serous membrane Serous membrane layer that is adjacent to and lines an organ. visceral wall of serous membrane FMA:15860 Serous membrane layer that lines to a body cavity. cavity lining FMA:15859 MA:0002448 parietal wall of serous membrane uberon UBERON:0022351 parietal serous membrane Serous membrane layer that lines to a body cavity. cavity lining MA:0002448 parietal wall of serous membrane FMA:15859 The layer of endometrial epithelium adjacent to the uterine cavity. FMA:86492 NCIT:C32189 pars basalis of endometrium stratum basalis of endometrium uberon UBERON:0022355 basal layer of endometrium The layer of endometrial epithelium adjacent to the uterine cavity. stratum basalis of endometrium FMA:86492 A specific region of the foregut into the area in which the lung will develop. lung field uberon UBERON:0022361 lung field A specific region of the foregut into the area in which the lung will develop. GOC:dph GOC:mtg_lung An embryonic or larval epithelium that is committed to form part of the nervous system. neurepithelium AEO:0001008 BTO:0000314 EHDAA2_RETIRED:0004654 FMA:64807 embryonic neuroepithelium neuroepithelium uberon UBERON:0034705 developing neuroepithelium An embryonic or larval epithelium that is committed to form part of the nervous system. AEO:0001008 AEO:JB neurepithelium BTO:0000314 embryonic neuroepithelium neuroepithelium AEO:0001008 An epithelium that is undergoing proliferation to provide large numbers of neuronal cells. AEO:0001009 uberon UBERON:0034706 proliferating neuroepithelium AEO An epithelium that is undergoing proliferation to provide large numbers of neuronal cells. AEO:0001009 A neuroepithelium some of whose cells are undergoing terminal differentiation to become neuronal cells. AEO:0001010 uberon UBERON:0034707 differentiating neuroepithelium AEO A neuroepithelium some of whose cells are undergoing terminal differentiation to become neuronal cells. AEO:0001010 DHBA:12694 EMAPA:32916 marginal zone of hindbrain uberon MZH UBERON:0034709 hindbrain marginal layer marginal zone of hindbrain DHBA:12694 MZH DHBA:12694 EHDAA2:0001267 EMAPA:17585 spinal cord lateral wall ventricular layer uberon UBERON:0034710 spinal cord ventricular layer EHDAA2 spinal cord lateral wall ventricular layer EHDAA2:0001267 Any of the cranial nerves, or their central nervous system analogs (the optic tract, the epiphyseal tract). These analogs are not true nerves, and are instead evaginated sensory afferents emanating from the brain uberon cranial nerve fiber bundle cranial nerve fiber tract cranial nerve or tract neuron projection bundle from brain UBERON:0034713 cranial neuron projection bundle Any of the cranial nerves, or their central nervous system analogs (the optic tract, the epiphyseal tract). These analogs are not true nerves, and are instead evaginated sensory afferents emanating from the brain ISBN10:0471888893 cranial nerve fiber bundle cranial nerve fiber tract cranial nerve or tract neuron projection bundle from brain A taste bud that is located external to the digestive tube, on the head or body, as found in species such as goldfish. uberon UBERON:0034717 integumental taste bud A taste bud that is located external to the digestive tube, on the head or body, as found in species such as goldfish. A taste bud that is located on a lip. uberon UBERON:0034719 lip taste bud A taste bud that is located on a lip. A taste bud that is located on the skin of the head. uberon UBERON:0034720 head taste bud A taste bud that is located on the skin of the head. A taste bud that is located in the pharynx. uberon UBERON:0034721 pharyngeal taste bud A taste bud that is located in the pharynx. A taste bud that is located on the skin of the trunk. uberon UBERON:0034726 trunk taste bud A taste bud that is located on the skin of the trunk. The autonomic nerve is a small nerve which carries postganglionic sympathetic and parasympathetic neurons from the zygomaticotemporal nerve; a branch of the maxillary nerve, to the lacrimal nerve; a branch of the ophthalmic nerve. These neurons derive from the superior cervical ganglion and the pterygopalatine ganglion respectively. They will travel to the lacrimal gland via the lacrimal nerve. Parasympathetic will induce lacrimation and vice versa. EMAPA:37957 FMA:5866 MESH:D017776 nervus visceralis visceral nerve uberon UBERON:0034728 autonomic nerve The autonomic nerve is a small nerve which carries postganglionic sympathetic and parasympathetic neurons from the zygomaticotemporal nerve; a branch of the maxillary nerve, to the lacrimal nerve; a branch of the ophthalmic nerve. These neurons derive from the superior cervical ganglion and the pterygopalatine ganglion respectively. They will travel to the lacrimal gland via the lacrimal nerve. Parasympathetic will induce lacrimation and vice versa. EMAPA:37957 MA:th nervus visceralis FMA:5866 visceral nerve FMA:5866 EMAPA:37958 uberon UBERON:0034729 sympathetic nerve EMAPA:37958 MA:th Any substance in the body or expelled from the body that is in a gaseous state. FMA:84580 gas in anatomical space portion of gas in anatomical space uberon UBERON:0034873 bodily gas Any substance in the body or expelled from the body that is in a gaseous state. portion of gas in anatomical space FMA:84580 Any portion of gas located in a part of the respiratory system that is composed primarily of air. FMA:84581 respiratory air respiratory system air uberon UBERON:0034874 air in respiratory system Any portion of gas located in a part of the respiratory system that is composed primarily of air. respiratory air FMA:84581 the area of axial mesoderm that develops into the prechordal plate prechordal mesenchyme uberon UBERON:0034878 prechordal mesoderm the area of axial mesoderm that develops into the prechordal plate MGI:anna lumen of gland uberon UBERON:0034905 gland lumen An multicellular anatomical structure that has subparts of multiple organs as a part. CARO:0020001 uberon anatomical cluster UBERON:0034921 multi organ part structure CARO An multicellular anatomical structure that has subparts of multiple organs as a part. CARO:0020001 anatomical cluster CARO:0020001 A cluster of cells, largely surrounded by a morphological boundary. CARO:0020002 FMA:62807 uberon UBERON:0034922 cell cluster CARO A cluster of cells, largely surrounded by a morphological boundary. CARO:0020002 A collection of anatomical structures that are alike in terms of their morphology or developmental origin. resolve if this should be a subclass of disconnected anatomical group. Some collections (e.g. the skeleton or skull) are arguably connected uberon UBERON:0034925 anatomical collection A collection of anatomical structures that are alike in terms of their morphology or developmental origin. Any organ component layer that consists of smooth muscle tissue. uberon UBERON:0034933 layer of smooth muscle tissue Any organ component layer that consists of smooth muscle tissue. FMA:55268 organ sector organ zonal region organ zone uberon organ region with floating fiat boundary UBERON:0034944 zone of organ organ sector FMA:55268 organ zone FMA:55268 organ region with floating fiat boundary FMA:55268 Any portion of gas located in a part of the respiratory system. respiratory gas respiratory system gas uberon UBERON:0034947 gas in respiratory system Any portion of gas located in a part of the respiratory system. NCIT:C25787 uberon duct epithelium ductal epithelium UBERON:0034969 epithelial layer of duct Mesenchyme that is part of a developing jaw [Automatically generated definition]. EMAPA:32907 EMAPA:35454 uberon UBERON:0034995 jaw mesenchyme Mesenchyme that is part of a developing jaw [Automatically generated definition]. OBOL:automatic EMAPA:32904 MA:0003220 uberon UBERON:0035037 jaw epithelium hemorrhoidal artery uberon UBERON:0035039 rectal artery Any material entity that is located in the digestive tract. This includes undigested food and liquid as well as unexcreted waste products. It also includes other entities such as ingested stones used to aid digestion. Any microbial cells or cell populations are also included. Note that we treat any material entity that is ingested as an anatomical structure by defintion, although this may be expanding the CARO usage somewhat digestive tract contents uberon ingested material entity UBERON:0035118 material entity in digestive tract Any material entity that is located in the digestive tract. This includes undigested food and liquid as well as unexcreted waste products. It also includes other entities such as ingested stones used to aid digestion. Any microbial cells or cell populations are also included. digestive tract contents Anatomical surface, which is the external surface of the whole body. Examples: There is only one body surface. FMA:61695 NCIT:C29667 surface of body uberon UBERON:0035159 entire surface of organism Anatomical surface, which is the external surface of the whole body. Examples: There is only one body surface. FMA:61695 surface of body FMA:61695 The organ of hearing located on the right side of the head. FMA:53641 NCIT:C81285 uberon UBERON:0035174 right ear The organ of hearing located on the right side of the head. ncithesaurus:Right_Ear The organ of hearing located on the left side of the head[ncit,modified]. FMA:53642 NCIT:C81259 uberon UBERON:0035295 left ear The organ of hearing located on the left side of the head[ncit,modified]. ncithesaurus:Left_Ear FMA:70505 NCIT:C32552 external carotid arterial subdivision subdivision of external carotid artery uberon UBERON:0035398 branch of external carotid artery external carotid arterial subdivision FMA:70505 subdivision of external carotid artery FMA:70505 FMA:15590 NCIT:C32895 facies posterior (Ren) facies posterior renis uberon UBERON:0035471 posterior surface of kidney facies posterior (Ren) FMA:15590 facies posterior renis FMA:15590 FMA:TA FMA:51797 ciliary vein uberon UBERON:0035546 uveal vein ciliary vein FMA:51797 uberon UBERON:0035548 colic artery The part of the circulatory system that lies within the subcutaneous tissue layers close to the surface of the skin. FMA:225275 superficial part of circulatory system superficial vasculature dermis vasculature hypodermis vasculature uberon skin vasculature subcutaneous vasculature vasculature of skin UBERON:0035549 vasculature of integument The part of the circulatory system that lies within the subcutaneous tissue layers close to the surface of the skin. vasculature of skin FMA:225275 Any of the veins carrying deoxygenated blood from the subcutaneous tissue layers. FMA:76719 NCIT:C33666 uberon superfical vein superficial veins superficial vessels UBERON:0035550 superficial vein Any of the veins carrying deoxygenated blood from the subcutaneous tissue layers. ncithesaurus:Superficial_Vein superfical vein superficial veins superficial vessels The part of the circulatory system that lies deep beneath the subcutaneous tissue layers away from the surface of the skin. deep part of circulatory system uberon UBERON:0035551 deep vasculature The part of the circulatory system that lies deep beneath the subcutaneous tissue layers away from the surface of the skin. A blood vessel carrying deoxygenated blood far beneath the skin usually accompanying an artery. FMA:76718 NCIT:C32444 uberon deep veins deep vessels UBERON:0035552 deep vein A blood vessel carrying deoxygenated blood far beneath the skin usually accompanying an artery. ncithesaurus:Deep_Vein deep veins deep vessels Any chamber of the left side of the heart FMA:7166 uberon UBERON:0035553 left cardiac chamber Any chamber of the left side of the heart Any chamber of the right side of the heart FMA:7165 uberon UBERON:0035554 right cardiac chamber Any chamber of the right side of the heart The parts of the orbital region that are outside of the the eyeball, including the lacrimal apparatus, the extraocular muscles and the eyelids, eyelashes, eyebrows and the conjunctiva FMA:76554 NCIT:C32574 adnexa oculi uberon accessory parts of orbital region accessory visual structures accessory visual structures set adnexal parts of orbital region appendage of eye appendages of the eye eye adnexa set of accessory visual structures structurae oculi accessoriae UBERON:0035639 ocular adnexa The parts of the orbital region that are outside of the the eyeball, including the lacrimal apparatus, the extraocular muscles and the eyelids, eyelashes, eyebrows and the conjunctiva HPO:pr UBERON:cjm adnexa oculi accessory visual structures accessory visual structures FMA:76554 accessory visual structures set FMA:76554 appendage of eye appendages of the eye set of accessory visual structures FMA:76554 structurae oculi accessoriae Any nerve that innervates the larynx. MESH:A08.800.050.050.925.450 uberon UBERON:0035642 laryngeal nerve Any nerve that innervates the larynx. UBERON:cjm EHDAA2:0004181 FMA:9464 cardiac chamber cavity heart cavity heart lumen uberon UBERON:0035763 cavity of cardiac chamber FMA cardiac chamber cavity FMA:9464 heart cavity FMA:9464 heart lumen EHDAA2:0004181 FMA:223208 NCIT:C12930 uberon UBERON:0035767 intrapulmonary bronchus The primordial mouth region of the developing head. FMA:293105 primitive mouth primordial mouth uberon UBERON:0035804 future mouth The primordial mouth region of the developing head. MP:0003119 primitive mouth FMA:293105 A muscle layer that is part of the sigmoid colon FMA:15028 muscularis externa of sigmoid colon muscularis propria of sigmoid colon sigmoid colon muscularis propria uberon sigmoideum muscularis tunica muscularis colon sigmoideum UBERON:0035805 muscle layer of sigmoid colon A muscle layer that is part of the sigmoid colon muscularis externa of sigmoid colon FMA:15028 FMA:12241 uberon UBERON:0035809 serous cavity The sum of epicardial and paracardial fat deposits. ZFA:0005765 uberon UBERON:0035814 pericardial fat The sum of epicardial and paracardial fat deposits. Any fat deposit surrounding a visceral organ. uberon UBERON:0035818 visceral fat Any fat deposit surrounding a visceral organ. UBERON:cjm The part of the ventral body cavity that is within the abdominal segment of the trunk, which encompasses the abdomen proper plus pelvic cavity. FMA:12267 cavitas abdominis et pelvis uberon UBERON:0035819 abdominopelvic cavity The part of the ventral body cavity that is within the abdominal segment of the trunk, which encompasses the abdomen proper plus pelvic cavity. UBERON:cjm cavitas abdominis et pelvis FMA:TA BTO:0004378 EMAPA:37987 FMA:67473 blood vessel wall uberon vascular wall UBERON:0035965 wall of blood vessel EMAPA:37987 MA:th blood vessel wall FMA:67473 vascular wall BTO:0004378 EHDAA2:0004070 uberon UBERON:0036072 respiratory primordium epithelium EHDAA2 EHDAA2:0004071 respiratory primordium associated mesenchyme uberon UBERON:0036073 respiratory primordium mesenchyme EHDAA2 respiratory primordium associated mesenchyme EHDAA2:0004071 An region of the mesoderm that includes anterior lateral mesoderm of the first heart field plus contiguous pharyngeal mesoderm that gives rise to second-heart-field-derived regions of the heart and branchiomeric muscles. uberon UBERON:0036146 cardiopharyngeal field An region of the mesoderm that includes anterior lateral mesoderm of the first heart field plus contiguous pharyngeal mesoderm that gives rise to second-heart-field-derived regions of the heart and branchiomeric muscles. BGEE:ann An anatomical junction that is between the sigmoid colon and rectum. NCIT:C54188 uberon rectosigmoid region UBERON:0036214 rectosigmoid junction An anatomical junction that is between the sigmoid colon and rectum. NCIT:C54188 rectosigmoid region NCIT:C54188 Material anatomical entity that forms the outermost boundary of an anatomical structure. AAO:0010270 AEO:0000154 ZFA:0005594 uberon UBERON:0036215 anatomical surface region Material anatomical entity that forms the outermost boundary of an anatomical structure. A bodily fluid that is located in the coelom. he coelomic fluid serves several functions; it acts as a hydroskeleton, it allows free movement and growth of internal organs, it serves for transport of gases, nutrients and waste products between different parts of the body, it allows storage of sperm and eggs during maturation and it acts as a reservoir for waste[https://en.wikipedia.org/wiki/Coelom#Coelomic_fluid] BTO:0001708 uberon UBERON:0036217 coelomic fluid A bodily fluid that is located in the coelom. Any gland that is part os the respiratory system. uberon UBERON:0036225 respiratory system gland Any gland that is part os the respiratory system. UBERON:cjm A notochord that has persisted beyond the embryonic stage. uberon UBERON:0036242 post-embryonic notochord A notochord that has persisted beyond the embryonic stage. UBERON:cjm Fluid that lines the vaginal walls that consists of multiple secretions that collect in the vagina from different glands. uberon vaginal discharge vaginal secretion UBERON:0036243 vaginal fluid Fluid that lines the vaginal walls that consists of multiple secretions that collect in the vagina from different glands. A transudate found in the serous sac. serous fluid FMA:20932 serous sac fluid uberon UBERON:0036244 secretion of serous membrane A transudate found in the serous sac. FMA:20932 serous fluid FMA:20932 FMA:53133 cranial orifice skull orifice uberon UBERON:0036253 orifice of skull cranial orifice FMA:53133 skull orifice FMA:53133 The zygomaticotemporal nerve or zygomaticotemporal branch (temporal branch) is derived from the maxillary branch of the trigeminal nerve (Cranial nerve V). It runs along the lateral wall of the orbit in a groove in the zygomatic bone, receives a branch of communication from the lacrimal, and passes through zygomaticotemporal foramen in the zygomatic bone to enter the temporal fossa. It ascends between the bone, and substance of the Temporalis muscle, pierces the temporal fascia about 2.5 cm. above the zygomatic arch, and is distributed to the skin of the side of the forehead, and communicates with the facial nerve and with the auriculotemporal branch of the mandibular nerve. As it pierces the temporal fascia, it gives off a slender twig, which runs between the two layers of the fascia to the lateral angle of the orbit. FMA:52972 ramus zygomaticotemporalis (Nervus zygomaticus) ramus zygomaticotemporalis nervus zygomatici zygomaticotemporal branch of zygomatic nerve uberon zygomaticotemporal zygomaticotemporal branch UBERON:0036264 zygomaticotemporal nerve The zygomaticotemporal nerve or zygomaticotemporal branch (temporal branch) is derived from the maxillary branch of the trigeminal nerve (Cranial nerve V). It runs along the lateral wall of the orbit in a groove in the zygomatic bone, receives a branch of communication from the lacrimal, and passes through zygomaticotemporal foramen in the zygomatic bone to enter the temporal fossa. It ascends between the bone, and substance of the Temporalis muscle, pierces the temporal fascia about 2.5 cm. above the zygomatic arch, and is distributed to the skin of the side of the forehead, and communicates with the facial nerve and with the auriculotemporal branch of the mandibular nerve. As it pierces the temporal fascia, it gives off a slender twig, which runs between the two layers of the fascia to the lateral angle of the orbit. ramus zygomaticotemporalis (Nervus zygomaticus) FMA:52972 ramus zygomaticotemporalis nervus zygomatici FMA:TA zygomaticotemporal branch of zygomatic nerve FMA:52972 zygomaticotemporal zygomaticotemporal branch uberon UBERON:0036268 pelvic vein Wall of ventricle which is continuous with the wall of aorta. FMA:9556 left ventricular wall pared del ventrC-culo izquierdo@es uberon UBERON:0036285 wall of left ventricle FMA FMA Wall of ventricle which is continuous with the wall of aorta. FMA:9556 left ventricular wall FMA:9556 pared del ventrC-culo izquierdo@es FMA:9556 Wall of ventricle which is continuous with the wall of pulmonary trunk. FMA:9533 pared del ventrC-culo derecho@es right ventricular wall uberon UBERON:0036286 wall of right ventricle FMA FMA Wall of ventricle which is continuous with the wall of pulmonary trunk. FMA:9533 pared del ventrC-culo derecho@es FMA:9533 right ventricular wall FMA:9533 FMA:9560 uberon UBERON:0036288 anterior wall of left ventricle Region of wall of right ventricle which is continuous with the lateral and septal walls of right ventricle. FMA:9553 uberon UBERON:0036289 anterior wall of right ventricle Region of wall of right ventricle which is continuous with the lateral and septal walls of right ventricle. FMA:9553 FMA:87177 uberon UBERON:0036290 myocardium of anterior wall of left ventricle FMA:260877 uberon UBERON:0036291 myocardium of anterior wall of right ventricle A mucosa that is part of a lip region [Automatically generated definition]. NCIT:C12226 labial mucosa uberon UBERON:0036294 mucosa of lip A mucosa that is part of a lip region [Automatically generated definition]. OBOL:automatic labial mucosa UBERON:cjm The upper tract of the renal system. The renal pelvis is the large cavity in the middle of each kidney. Urine drains from each kidney through a long tube called the ureter, into the bladder, where it is stored until it is passed from the body through the urethra. NCIT:C54419 renal pelvis and ureter renal pelvis plus ureter uberon UBERON:0036295 renal pelvis/ureter NCIT The upper tract of the renal system. The renal pelvis is the large cavity in the middle of each kidney. Urine drains from each kidney through a long tube called the ureter, into the bladder, where it is stored until it is passed from the body through the urethra. NCIT:C54419 uberon UBERON:0036302 vasculature of central nervous system plus retina FMA:259905 uberon UBERON:0036303 vasculature of central nervous system A zone of skin that is part of the face. eriks 2012-02-05T05:23:01Z EMAPA:36657 FMA:24758 NCIT:C33561 UMLS:C0222084 face skin uberon facial skin UBERON:1000021 skin of face A zone of skin that is part of the face. UBERON:EJS UMLS:C0222084 ncithesaurus:Skin_of_the_Face face skin EMAPA:36657 FMA:24758 Cartilage which is part of the axial skeleton. This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon teleost_anatomy_curators ZFA:0001457 uberon/phenoscape-anatomy postcranial axial cartilage Cartilage which is part of the axial skeleton. ZFIN:curator Non neural ectoderm that surrounds the presumptive neural plate and gives rise to neurogenic placodes. This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon teleost_anatomy_curators ZFA:0007013 uberon/phenoscape-anatomy preplacodal ectoderm Non neural ectoderm that surrounds the presumptive neural plate and gives rise to neurogenic placodes. ZFIN:curator Structures of the dermis, epidermis, glands and pigment cells recognizable on the external surfaces of the integument. This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon amphibian_anatomy_curators uberon/phenoscape-anatomy Not clear how this differs from parent class. See https://github.com/obophenotype/uberon/issues/1305 external integument structure Structures of the dermis, epidermis, glands and pigment cells recognizable on the external surfaces of the integument. AAO:EJS Dermal, epidermal, glandular and pigment structures of the external head integument. This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon amphibian_anatomy_curators uberon/phenoscape-anatomy head external integument structure Dermal, epidermal, glandular and pigment structures of the external head integument. AAO:EJS Dermal, epidermal, glandular and pigment structures of the body integument. This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon amphibian_anatomy_curators uberon/phenoscape-anatomy body external integument structure Dermal, epidermal, glandular and pigment structures of the body integument. AAO:EJS Blood vessels in respiratory skin. Modified from the original AAO source amphibian_anatomy_curators uberon/phenoscape-anatomy vasculature of respiratory integument Blood vessels in respiratory skin. AAO:EJS An anatomical surface that is part of a bone bone surface surface of bone length unit A unit which is a standard measure of the distance between two points. length unit mass unit A unit which is a standard measure of the amount of matter/energy of a physical object. mass unit time unit A unit which is a standard measure of the dimension in which events occur in sequence. time unit temperature unit A unit which is a standard measure of the average kinetic energy of the particles in a sample of matter. temperature unit substance unit A unit which is a standardised quantity of an element or compound with uniform composition. substance unit concentration unit A unit which represents a standard measurement of how much of a given substance there is mixed with another substance. concentration unit volume unit A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas. volume unit frequency unit A unit which is a standard measure of the number of repetitive actions in a particular time. frequency unit volumetric flow rate unit A unit which is a standard measure of the volume of fluid which passes through a given surface per unit time . volumetric flow rate unit rate unit A unit which represents a standard measurement occurrence of a process per unit time. rate unit vaccine A vaccine is a processed material with the function that when administered, it prevents or ameliorates a disorder in a target organism by inducing or modifying adaptive immune responses specific to the antigens in the vaccine. Many vaccines are developed to protect against infectious pathogens that causes infectious diseases. Many vaccines are also being developed against other diseases such as cancer, allergy, and autoimmune diseases. YH, BP, BS, MC, LC, XZ, RS a role that inheres in a prepared material entity that is designed to induce protection or treament for a diease or infection in vivo. vaccine MeSH: D014612 A bacterial vaccine that prevents against Escherichia coli infection. YH E. coli vaccine Escherichia coli vaccine MeSH: D022361 A bacterial vaccine that prevents Neisseria meningitidis infection. YH Meningococcal vaccine Neisseria meningitidis vaccine MeSH: D022401 A Mycobacterium vaccine that protects against Mycobacterium tuberculosis. YH tuberculosis vaccine Mycobacterium tuberculosis vaccine MeSH: D032581 a vaccine adjuvant that is formed as a mineral salt. SGS, YH mineral salt vaccine adjuvant CVX: 119 YH, SGS a vaccine adjuvant that contains microbial derived material. microbial derivative vaccine adjuvant CVX: 52 CVX: 83 an aluminum vaccine adjuvant that contains aluminum hydroxide. YH alum aluminum hydroxide vaccine adjuvant an aluminum vaccine adjuvant that is aluminum phosphate. YH, SGS Adju-Phos® Al(PO)4 aluminum phosphate vaccine adjuvant a mineral salt vaccine adjuvant composed of calcium phosphate. YH, SGS CaHPO4 calcium phosphate vaccine adjuvant an emulsion vaccine adjuvant that consists of a water-in-oil emulsion of aqueous antigen in paraffin (mineral) oil of low specific gravity and low viscosity. It is named after Jules T. Freund (1890-1960), Hungarian-born American immunologist. It is a water in oil emulsion. YH, SGS Freunds emulsified oil adjuvant is a Freund's emulsfied oil adjuvant that contains inactivated and dried mycobacteria, usually Mycobacterium tuberculosis (the pathogenic agent of tuberculosis). YH complete Freunds adjuvant a Freud's adjuvant that does not contain the mycobacterial components. YH incomplete Freunds adjuvant A microbial derivative vaccine adjuvant consisting of cholera toxin (CT) from Vibrio cholerae. YH, SGS CT cholera toxin A microbial derivative vaccine adjuvant that is the P40 particulate fraction isolated from Corynebacterium. YH, SGS PMID: 8447157 Corynebacterium-derived P40 vaccine adjuvant an adjuvant role that inheres in a vaccine component which is added as part of a vaccine and induces enhanced adaptive immune response to the vaccine antigen. YH The Latin "adjuvans" means to help, particularly to reach a goal. Adjuvant therapy for cancer is surgery followed by chemotherapy or radiation to help decrease the risk of the cancer recurring (coming back). An adjuvant is a substance that helps and enhances the pharmacological effect of a drug or increases the ability of an antigen to stimulate the immune system. vaccine adjuvant role A vaccine that targets against a bacterial disease. YH bacterial vaccine MeSH: D001428 a processed material that is output of the vaccine preparation and part of a vaccine. YH cardinal part of vaccine vaccine ingredient vaccine component A microbial derivative vaccine adjuvant made from bacterial lipopolysaccharide (LPS) of gram-negative bacteria. YH, SGS LPS vaccine adjuvant lipopolysaccharide vaccine adjuvant a synthetic vaccine adjuvant formulated to correspond to a component found in a water-soluble extract of cell walls of mycobacteria used in complete Freund's adjuvant (CFA). YH, SGS MDP PMID: 344799 muramyl dipeptide an emulsion vaccine adjuvant that contains an organic polymer with some antigenic epitopes which might be shared with other organic polymers acting as immunostimulators. YH, SGS squalene a synthetic vaccine adjuvant that is an emulsifier called Arlacel A. YH, SGS PMID: 2042393 arlacel A YH a montanide vaccine adjuvant that is Montanide 103. Montanide 103 a microbial derivitive vaccine adjuvant that contains components from killed Bordetella pertussis. The killed B. pertussis has a strong adjuvant effect on the diphtheria and tetanus toxoids in the DPT vaccines. YH Bordetella pertussis component vaccine adjuvant vaccine function is a function that inheres in a vaccine that induces protective immune response against a disease. It is realized in the immunization process in the host. PERSPN: Oliver He: There has been hot discussion about whether we use 'vaccine function' or 'vaccine role'. Vaccine role may not be the good term to use. Vaccine is designed to be 'vaccine', so it should be vaccine function. One special case is cowpox virus. The cowpox virus can be mixed with some liquid like water and used as a smallpox vaccine. In this case, people often say: the cowpox virus has a 'vaccine role'. However, the cowpox virus vaccine is a processed material of a mix of the virus with water. The virus is a virus, it is not a vaccine per se. Therefore, vaccine role may not be an accurate term. YH, MC, XZ, and AR vaccine function A synthetic vaccine adjuvant that is PCPP salt. SGS PCPP salt polyidi (carboxylatophenoxy) lphosphazene polyphosphazene PMID: 75551218 Adjumer a vaccine adjuvant that contains particles made up of concentric lipid membranes containing phospholipids and other lipids in a bilayer configuration separated by aqueous compartments. It is a relatively stable but non-covalently-bound complex of saponin adjuvant Quil-A, cholesterol and amphipathic antigen in a molar ratio of approximately 1:1:1. The spectrum of viral capsid antigens and non-viral amphipathic antigens of relevance for human vaccination, incorporated into ISCOMs, comprises influenza, measles, rabies, gp340 from EB-virus, gp120 from HIV, Plasmodium falciparum and Trypanosoma cruzi. Ref: http://www.vaccination.inoz.com/adjuvants.html. YH liposome-based vaccine adjuvant YH PMID: 18472194 IL-15 plasmid vaccine adjuvant a microbial derivative vaccine adjuvant that is derived from E. coli heat labile toxin LT. YH, SGS E. coli LT toxin derived vaccine adjuvant YL,YH Page 73, Chapter 6, Vaccine, 5th Edition. EXPERT CONSULT by Plotkin SA., et. al. 2008 a role inheres in a material entity, that has been added into a vaccine's formulation by the manufacture for a specific purpose. For example: adjuvant to enhance the effect of immunogen, perservatives, stablizers and those materials added for affecting PH and isotonicity. vaccine additive role preventive vaccine function Protective antigen is an antigen that stimulates protective immunity when used in vivo. YH protective antigen role YH E. coli O157:H7 subunit vaccine expressing Esps and Tir PMID: 14670317 YH E. coli vaccine using intimin polypeptide PMID: 14688094 PMID: 17258324 immunization is a processual entity that primes or modifies an adaptivie immune response to some antigens. YH, XZ, BP WEB: http://en.wikipedia.org/wiki/Immunization immunization Active immunization is an immunization process that entails the introduction of a foreign molecule into the body, which causes the body itself to generate adaptive immunity against the target. YH, XZ WEB: http://en.wikipedia.org/wiki/Immunization Active immunization entails the introduction of a foreign molecule into the body, which causes the body itself to generate immunity against the target. This immunity comes from the T cells and the B cells with their antibodies. Active immunization can occur naturally when a person comes in contact with, for example, a microbe. If the person has not yet come into contact with the microbe and has no pre-made antibodies for defense (like in passive immunization), the person becomes immunized. The immune system will eventually create antibodies and other defenses against the microbe. The next time, the immune response against this microbe can be very efficient; this is the case in many of the childhood infections that a person only contracts once, but then is immune. Artificial active immunization is where the microbe, or parts of it, are injected into the person before they are able to take it in naturally. If whole microbes are used, they are pre-treated, Attenuated vaccine. (Wikipedia) active immunization artificial active immunization is an active immunization that occurs when a person or animal is vaccinated with a specific vaccine. YH, XZ artificial active immunization WEB: http://en.wikipedia.org/wiki/Immunization vaccine immunization YH Ag85B and ESAT-6 fusion protein PMID: a synthetic vaccine adjuvant, adamantylamide dipeptide (AdDP) is the desmuramyl analog of MDP. YH, SGS AdDP PMID: 8375945 adamantylamide dipeptide vaccine adjuvant therapeutic vaccine function a vaccine component that is chemical substance added to vaccine and enhance and direct immune response to protective antigen. Many of vaccine adjuvants cause a range of serious side-effects. YH vaccine adjuvant immunization objective is the specification of an objective to achieve immunization. YH, XZ WEB: http://en.wikipedia.org/wiki/Immunization immunization objective vaccine preparation is a manufacturing process to produce a vaccine. YH, BP vaccine generation vaccine production vaccine preparation A bacterial vaccine that protects against Mycobacterium bacterial infection. YH, RR https://en.wikipedia.org/wiki/Mycobacterium Mycobacterium vaccine A bacterial vaccine that protects against Yersinia bacterial infection. YH, ZX Yersinia vaccine A vaccine that targets against a viral disease. YH viral vaccine MeSH: D014765 YH a role that inheres in a material entity that becomes an ingredient of a vaccine. vaccine component role An E. coli vaccine that uses subunit antigen type. E. coli subunit vaccine A bacteria vaccine that prevents against Yersinia pestis infection that causes plague. YH Plague vaccine Yersinia pestis vaccine MeSH: D010931; SNOMEDCT: 11866009; UMLS_CUI:C0032066 a Streptococcal vaccine that is used against S. pneumoniae infection, which causes pneumococcal diseases. YH pneumococcal vaccine WEB: http://www.who.int/vaccines/en/pneumococcus.shtml Streptococcus pneumoniae vaccine A viral vaccine that protects against infection with Pseudorabies virus. YH pseudorabies vaccine Pseudorabies virus vaccine MeSH: D022421 A particulate antigen delivery system, ISCOM is a vaccine adjuvant that consists of an assembly of antigens in multimeric form and presents an antigen to induce specific immunologic responses. The assembly is attached to a matrix with a built-in adjuvant, saponin. ISCOMs induce strong serum antibody responses, and are used as highly immunogenic forms of subunit vaccines. MeSH term: D20.215.894.860.449. YH The immunostimulating complex ISCOM A bacterial vaccine that prevents streptococcal infections. YH Streptococcus vaccine https://en.wikipedia.org/wiki/Streptococcus Streptococcal vaccine MeSH: D022541 A Y. pestis subunit vaccine that uses recombinant Y. pestis V antigen. PMID: 7622205. YH Recombinant Y. pestis V antigen vaccine PMID: 7622205 YH recombinant Y. pestis YopD protein vaccine PMID: 10024607 PMID: 8890210 a mineral salt vaccine adjuvant that is composed of aluminum salt. Aluminum vaccine adjuvant is a vaccine adjuvant that is composed of some aluminum compound. YH aluminum vaccine adjuvant YL PMID: 19608270 "XG is derived from Xanthomonas campestris, has a pentasaccharide repeating unit structure, and its terminus contains a mannose moiety which acts as a toll-like receptor 2 agonist." REF: Mucoadhesive liposomes for intranasal immunization with an avian influenza virus vaccine in chickens, by Chiou C. et al. Biomaterials, Volume 30, Issue 29, October 2009, Pages 5862-5868, ISSN 0142-9612, 10.1016/j.biomaterials.2009.06.046. (http://www.sciencedirect.com/science/article/pii/S0142961209006371) xanthan gum vaccine ajuvant a cytokine vaccine adjuvant that includes IL-12. IL-12 vaccine adjuvant is a vaccine adjuvant that contains IL-12. YH, ZX IL-12 vacince adjuvant an E. coli subunit vaccine that uses E. coli FimH adhesin protein as teh antigen, and uses the complete Freund's adjuvant (CFA) in the first vaccination and the incomplete Freund's adjuvant (IFA) in the boost vaccination. YH PubMed: http://www.ncbi.nlm.nih.gov/pubmed/9110982 E. coli FimH with CFA and then IFA VIOLIN Vaccine ID: 4330 A microbial derivative vaccine adjuvant compsed of CpG DNA. YH PMID: 12899580 CpG DNA vaccine adjuvant Ribi vaccine adjuvant is an emulsion vaccine adjuvant that is a stable oil-in-water emulsion. SGS http://www.sigmaaldrich.com/catalog/ProductDetail.do?D7=0&N5=SEARCH_CONCAT_PNO%7CBRAND_KEY&N4=M6661%7CSIGMA&N25=0&QS=ON&F=SPEC Ribi vaccine adjuvant a synthetic vaccine adjuvant named RC529 that is a lipid A mimetic. SGS PMID: 16204643 RC529 vaccine adjuvant An aluminum vaccine adjuvant that is aluminum potassium sulfate (AlK(SO4)2). ZX, SGS aluminum potassium sulfate adjuvant An aluminum hydroxide vaccine adjuvant that is a gel that is made by precipitation of aluminum hydroxide Al(OH)3 under alkaline conditions. ZX, SGS PMID: 7551218 Alhydrogel A microbial derivative vaccine adjuvant made of the B subunit of the cholera toxin from Vibrio cholerae. SGS CTB cholera toxin B subunit an aqueous formula of the synthetic vaccine adjuvant RC529. RC529-AF can be obtained from Corixa Corporation (Seattle, WA). Reference: PMID: 15308371 RC529 vaccine adjuvant in an aqueour formulation RC529-AF vaccine adjuvant A microbial derivative vaccine adjuvant derived from the lipopolysaccharide (LPS) of Salmonella minnesota R595. SGS 3-O-deacylated monophosphoryl lipid A vaccine adjuvant 3D-MLA PMID: 7551218 MPL vaccine adjuvant PMID: 10768940 A microbial derivative vaccine adjuvant that is a mutant form of LT containing a Ser-Lys substitution in position 63 which has been shown to be totally devoid of toxicity stable to protease treatment and able to act as mucosal adjuvant. LTK63 is an enzymatically inactive mutant of the heat-labile enterotoxin of Escherichia coli. It can be used as a potent mucosal adjuvant. SGS PMID: 9607006 LTK63 vaccine mutant PMID: 10790422; PMID: 17920733 A microbial derivative vaccine adjuvant derived from heat-killed Corynebacterium parvum. SGS PMID: 5483667 killed Corynebacterium parvum vaccine adjuvant PMID: 4596278; PMID: 7591056 Titermax Gold is an emulsion vaccine adjuvant which is a water-in-oil adjuvant with CRL-8300 (a block copolymer), squalene, and sorbitan monooleate. SGS It's a water-in-oil emulsion adjuvant. Reference: http://www.titermax.com/i_gold4.htm. Titermax Gold URL: http://www.titermax.com/i_gold4.htm a synthetic vaccine adjuvant that is dimethyldioctadecylammonium bromide (DDA), a lipophilic quaternary ammonium salt known as a good adjuvant when co-administered systemically or nasally with an antigen. SGS Dimethyl dioctadecyl ammonium bromide DDA vaccine adjuvant PMID: 1439129 A liposome-based vaccine adjuvant that have a positive surface charge. SGS cationic liposomal vaccine adjuvant DDA:TDB PMID: 19874860 SGS PMID: 7551218 a tenosactive compound vaccine adjuvant that contains purified extract from the bark of the South American tree Quillaja saponaria Molina. QuilA vaccine adjuvant A combination vaccine adjuvant comprised of monophosphoryl lipid A (MPL), QS21 and an oil in water emulsion. SGS monophosphoryl lipid A (MPL), QS21 and an oil in water emulsion. AS02 vaccine adjuvant PMID: 15780441; PMID: 15187142 AS04 is a combination vaccine adjuvant that is a combination of 50 μg of the immunoenhancer MPL (3-O-desacyl-4′-monophosphoryl lipid A) with 500 μg of aluminium salt. SGS PMID: 21527299 AS04 vaccine adjuvant VSA-3 is an emulsion vaccine adjuvant which is an emulsion plus DDA. Emulsigen D PMID:16187717 SGS VSA-3 a tensoactive compound vaccine adjuvant that is derived from saponin, a compound that is an immunostimulator found in the plant P. senega. saponin vaccine adjuvant A Montanide vaccine adjuvant that is formulated as water-in-oil emulsions and induces high antibody titers in several animal species. It is a vaccine adjuvant composed of metabolizable oil and a surfactant system designed to make a water-in-oil emulsion. It has been used since 1992 in more than 50 clinical trials related to therapeutic vaccines against various diseases such as cancer and malaria. YH, SGS Montanide ISA 720 VG WEB: http://www.seppic.com/human-health/vaccine-adjuvant/montanide-isa-720-@/view-1044-seproduit.html?menuid=,979,&lang=en Montanide ISA 720 PMID: 15752840 a montanide vaccine adjuvant that is a mineral oil adjuvant. Montanide incomplete Seppic adjuvant A montanide vaccine adjuvant that is a vaccine adjuvant composed of a light mineral oil and a surfactant system designed to make a water-in-oil emulsion. SGS WEB: http://www.seppic.com/human-health/vaccine-adjuvant/montanide-isa-51-@/view-1042-seproduit.html?menuid=,979,&lang=en Montanide ISA51 An emulsion vaccine adjuvant developed by Montanide (http://www.montanide.com/). YH, SS Montanide vaccine adjuvant YH, SS B subunit of E. coli heat-labile enterotoxin A microbial derivative vaccine adjuvant composed of the B subunit of E. coli heat-labile toxin. EtxB vaccine adjuvant A synthetic vaccine adjuvant with the tradename Polygen. YH, SS Polygen vaccine adjuvant URL: http://www.mvp-technologies.com/adjuvants/Polygen%20Final%20Technical%20Bulletin.pdf a role of host that contains vaccine. It is a role that inheres in an organism that is the target of a vaccine administration (vaccination process). YH, ZX vaccine host role A nonantigenic carbohydrate adjuvant, which enhances both humoral and cell-mediated immunity to oligopeptides in experimental animal models. SGS PMID: 7551218 Algal Glucan vaccine adjuvant A suspension of 1-2μm ovoids of immune stimulant gamma inulin (g-IN) in which alum is embedded as a carrier for protein or other anionic antigens. SGS PMID:1887671 Algammulin vaccine adjuvant a synthetic vaccine adjuvant that is Bay R1005 (N-(2-Deoxy-2-L-leucylamino β-D-glucopyranosyl)-N-octadecyldodecanoylamide hydroacetate ). SGS N-( 2-Deoxy-2-L-leucylamino-β-D-glucopyranosyl)-N-octadecyldodecanoylamide hydroacetate PMID: 7551218 BAY R1005 A synthetic vaccine adjuvant that is N, N-dioctadecyl-N′, N′-bis( 2-hydroxyethyl) propanediamine (Avridine). SGS CP20,96 N, N-dioctadecyl-N′, N′-bis( 2-hydroxyethyl) propanediamine PMID:7551218 Avridine a calcium phosphate vaccine adjuvant that is a gel prepared by precipitating soluable calcium and phosphate salts. SGS PMID: 7551218 calcium phosphate gel A microbial derivative vaccine adjuvant composed of the CTA1-DD fusion protein. CTA1-DD gene fusion protein PMID: 7551218 SGS Cholera toxin A1-subunit-ProteinA D-fragment fusion protein SGS A mineral salt vaccine adjuvant that is composed of Deoxycholic acid sodium salt (DOC) complexed with aluminum hydroxide. PMID:7551218 DOC/Alum Complex gamma inulin is a carbohydrate adjuvant that is a highly specific activator of the alternative pathway of complement in vitro and in vivo, and is composed of linear (unbranched) b-D-(2-1) polyfructofuranosyl-a-D-glucose. SGS PMID: 3265692; PMID: 7551218 gamma Inulin vaccine adjuvant Gerbu adjuvant is a combination vaccine adjuvant that is comprised of a mixture of GMDP, DDA, and Zinc L-proline salt complex (ZnPro8). SGS PMID: 7551218 PMID: 15953835 Gerbu vaccine adjuvant a cytokine vaccine adjuvant that includes GM-CSF. YH, SGS GM-CSF vaccine adjuvant A synthetic vaccine adjuvant containing GMDP, a higly effective primary adjuvant. SGS N-acetylglucosaminyl-(b1-4)-N-acetylmuramyl-L-alanyl-D-isoglutamine PMID: 7551218 GMDP an IFN-gamma vaccine adjuvant that is composed of recombinant hIFN-gamma. YH, SGS recombinant hIFN-gamma/Interferon-g vaccine adjuvant a cytokine vaccine adjuvant that includes IL-1b. YH, SGS interleukin-1b vaccine adjuvant a cytokine vaccine adjuvant that includes IL-2. YH, SGS interleukin-2 a cytokine vaccine adjuvant that includes IL-7. YH, SGS interleukin-7 a synthetic vaccine adjuvant loxoribine is a guanosine analog derivatized at position N7 and C8, and activates TLR-7. SGS 7-allyl-8-oxoguanosine PMID: 7551218 Loxoribine An emulsion vaccine adjuvant consisting of an oil (squalene)-in-water nano emulsion. PMID: 20488726 SGS MF59 MTP-PE liposomes are a liposome-based vaccine adjuvant that consists of liposomes containing the synthetic lipophilic analog of muramyl dipeptide, muramyl tripeptide phosphatidylethanolamine (MTP-PE). SGS MTP-PE PMID: 1431559 MTP-PE Liposomes a synthetic vaccine adjuvant made of murametide that has adjuvant activity similar to MDP. SGS Nac-Mur-L-Ala-D-Gln-OCH3 PMID: 7551218 Murametide a synthetic vaccine adjuvant called murapalmitine. SGS Nac-Mur-L-Thr-D-isoGIn-sn-glyceroI dipalmitoyl PMID: 7551218 Murapalmitine a synthetic adjuvant that is an MDP analog called D-Murapalmitine. SGS Nac-Mur-D-Ala-D-isoGln-sn-glycerol dipalmitoyl PMID: 7551218 D-Murapalmitine a synthetic vaccine adjuvant that is composed of neuraminidase-galactose oxidase (NAGO) a mixture of mixture of the two enzymes-neuraminidase and galactose oxidase. SGS Neuraminidase-galactose oxidase PMID: 7551218 NAGO a synthetic vaccine adjuvant consisting of multi-lamellar vesicles comprising a mixture of non-ionic surfactant (e.g., 1-monopalmitoyl-rac-glycerol), cholesterol and dicetyl phosphate used as a primary vaccine adjuvant for entrapped antigen. SGS NISV PMID: 7551218 non-ionic surfactant vesicles a synthetic vaccine adjuvant made from the emulsion polymerization of methyl methacrylate. SGS Polymethyl methacrylate PMID: 7551218 PMMA a synthetic vaccine adjuvant synthesized from stable protein phospholipid-calcium precipitates. SGS PMID: 7551218 protein cochleates a tensoactive compound vaccine adjuvant that is composed of extracts from the bark of the Quillaja saponaria Molina tree. SGS Stimulon™ QS-21 Adjuvant PMID: 7551218 QS-21 An aluminum vaccine adjuvant that is a synthetic oxyhydroxide of aluminum (aluminum hydroxide) prepared by acid-base precipitation. SGS PMID: 7551218 Rehydragel HPA An aluminum hydroxide vaccine adjuvant that is a low visosity aluminum hydroxide gel. SGS PMID: 7551218 Rehydragel LV a cytokine vaccine adjuvant that contains the 163-171 peptide of IL-1β. YH, SGS IL-1β 163-171 peptide Sclavo peptide Specon is an emulsion vaccine adjuvant that is a water-in-oil emulsion that is used as an adjuvant and has immunostimulating properties similar to Freund's complete adjuvant (FCA). SGS PMID: 1439130 Specol SPT is an emulsion vaccine adjuvant that is an emulsion of squalane (5%), Tween 80( 0.2%), Pluronic L121( 1.25%), phosphate-buffered saline pH 7.4, and antigen. SGS PMID: 7551218 SPT (Antigen Formulation) a synthetic vaccine adjuvant stearyl tyrosine is considered an "organic equivelant" of aluminum hydroxide. SGS PMID: 7551218 stearyl tyrosine a synthetic vaccine adjuvant called Theramide that is composed of N-acetylglucosaminyl-N-acetylinuramyl-L-Ala-D-isoGlu-L-Ala-dipalmitoxy propylamide (DTP-DPP). SGS PMID: 7551218 Theramide a synthetic vaccine adjuvant that is a copolymer (CRL1005), based on a 12 kDa polyoxypropylene (POP) core with 5% POE. SGS PMID: 10717336 CRL1005 Nanoemulsion vaccine adjuvant is an emulsion vaccine adjuvant and is made from non-toxic lipid droplets a few hundred nanometers in diameter and made from surfactants approved for human consumption and common food substances that are 'Generally Recognized as Safe' (GRAS) by the FDA. SGS http://nano.med.umich.edu/platforms/Nanoemulsions.html nanoemulsion vaccine adjuvant AS03 is an emusion vaccine adjuvant that contains α-tocopherol and squalene, two biodegradable polyprenyls, in an oil-in-water emulsion. SGS PMID: 21256188 AS03 SGS A microbial deriviative vaccine adjuvant that is a mutant form of E.coli heat-labile toxin. PMID: 11803061 LTR192G A microbial derivative vaccine adjuvant containing E. coli heat-labile toxin. SGS LT Oral Adjuvant LT-OA PMID: 7551218 E. coli heat-labile toxin, LT An aluminum vaccine adjuvant that is a a proprietary aluminum hydroxyphosphate sulfate formulation that is both physically and functionally distinct from traditional aluminum phosphate and aluminum hydroxide adjuvants. SGS AAHSA Merck Aluminum Adjuvant PMID: 17581283 amorphous aluminum hydroxyphosphate sulfate adjuvant (AAHSA) Matrix-S a synthetic vaccine adjuvant contiaing imiquimod a imidazoquinoline. SGS 1-(2-methypropyl)-IH-imidazo[4,5-c]quinolin-4-amine Aldara™ R-837 S26308 PMID: 7551218, PMID: 18566444 imiquimod vaccine adjuvant a synthetic vaccine adjuvant, resiquimod is a chemical analog of imiquimod. SGS PMID: 15068862 resiquimod vaccine adjuvant An emulsion vaccine adjuvant containing 2.5% squalene. SGS PMID:20193791 AF03 vaccine adjuvant A microbial derivative vaccine adjuvant composed of flagellin from gram-negative bacteria. SGS FliC PMID: 16428759, PMID: 21048152 Flagellin vaccine adjuvant a synthetic vaccine adjuvant containing Poly(I:C), a synthetic double stranded analog of RNA. SGS polyriboinosinic-polyribocytidylic acid WEB: http://en.wikipedia.org/wiki/Polyinosinic:polycytidylic_acid poly(I:C) vaccine adjuvant a particulate antigen delivery system that is a vaccine adjuvant comprising cholesterol, phospholipid and saponin but without antigen. SGS PMID: 19450632 ISCOMATRIX is identical to ISCOMs except that it does not contain antigen. Ref: PMID: 17336431. ISCOMATRIX vaccine adjuvant a tensoactive compound vaccine adjuvant that is made from highly purified saponins. SGS, YH WEB: http://www.isconova.com/products/abisco-research-reagent/abisco-100.aspx Abisco-100 vaccine adjuvant a particulate antigen delivery system that is albumin-heparin microparticles vaccine adjuvant that is prepared from albumin and heparin stabilized by cross-linking reaction with EDC. SGS PMID: 16734558 albumin-heparin microparticles vaccine adjuvant SmithKline Beecham adjuvant system 2 (AS-2) is a combination vaccine adjuvant and is based on the combination of Monophosphoryl Lipid A(MPL), QS21 (a purified fraction of Saponin extracted from Quillarja Saponaria), and a proprietary oil in water emulsion. SGS http://www.pasteur.fr/applications/euroconf/vaccins/vaccins-abs.html AS-2 vaccine adjuvant a cytokine vaccine adjuvant that includes B7-2. YH, SGS B7-2 vaccine adjuvant a synthetic vaccine adjuvant that is a local anaesthetic drug belonging to the amino amide group, and is used as a vaccine adjuvant in DNA vaccines. SGS PMID: 15246629, WEB: http://en.wikipedia.org/wiki/Bupivacaine Bupivacaine vaccine adjuvant SGS A liposome-based vaccine adjuvant that is composed of virus sized liposomes that contain a DNA plasmid. PMID: 19285425 cationic liposome-DNA complex JVRS-100 SGS 5-androsten-3β-ol-17-one DHA Dehydroepiandrosterone androstenolone prasterone transdehydroandrosterone PMID: 7551218 a synthetic vaccine adjuvant that is DHEA, which is relatively stable and can be directly incorporated into vaccine formulations. DHEA vaccine adjuvant a synthetic vaccine adjuvant that is PLGA, which has been used in the controlled delivery of peptide drugs. SGS PLGA PLGA microspheres Polyester poly (DL-lactide-co-glycolide) PMID: 15560948 DL-PGL (Polyester poly (DL-lactide-co-glycolide)) vaccine adjuvant a cytokine vaccine adjuvant that uses the adjuvant effect of cytokine IL-15. YH, SGS IL-15 vaccine adjuvant immunoliposomes containing antibodies to costimulatory molecules is a liposome-based vaccine adjuvant which is prepared from dehydration-rehydration vesicles (DRVs). SGS PMID: 7551218 immunoliposomes containing antibodies to costimulatory molecules A microbial derivative vaccine adjuvant that is a mutant form of heat-labile Escherichia coli enterotoxin (LT) that contains a substitution Ala → Arg in position 72 of the A subunit. SGS PMID: 9529328 LTK72 vaccine adjuvant A microbial derivative vaccine adjuvant containing MPL and squalene. SGS PMID: 12213399 MPL-SE vaccine adjuvant A microbial derived vaccine adjuvant made of E112K mC, a mutated CT created by substituting a single amino acid in the ADP-ribosyltransferase active centre, glutamate to lysine at position 112. SGS mCT PMID: 11251876: non-toxic mutant E112K of Cholera Toxin mCT-E112K a microbial derivative vaccine adjuvant that is derived from cholera toxin. YH, SGS cholera toxin derived vaccine adjuvant SAF-1 is a combination vaccine adjuvant that is composed of threonyl-MDP (0.05-1%) in an emulsion vehicle [5% squalane, 2.5% Pluronic® L121, 0.2% Polysorbate 80 and phosphate buffered saline (pH 7.4)]. SGS PMID: 7551218 SAF-1 vaccine adjuvant SGS A liposome-based vaccine adjuvant that includes the glycoproteins of Sendai virus. PMID: 7551218 Sendai Proteoliposomes, Sendai-containing Lipid Matrices a synthetic vaccine adjuvant that is threonyl muramyl dipeptide (TMDP). SGS N-acetyl muramyl-L-threonyl-D-isoglutamine Termurtide™ [thr1 ]-MDP PMID: 7551218 threonyl muramyl dipeptide (TMDP) vaccine adjuvant A microbial derivative vaccine adjuvant made of virus like particles (VLPS) containing the yeast retrotransposon Ty which has the amino acids 1-381 of the pI protein encoded. SGS Ty-VLPs PMID: 7551218 ty particles vaccine adjuvant YH, SGS a vaccine adjuvant that contains active cytokine compound. cytokine vaccine adjuvant YH, SGS a vaccine adjuvant that is composed of differnt compounds under more than one category. combination vaccine adjuvant emulsion vaccine adjuvant a vaccine adjuvant that serves as a particulate antigen delivery system. YH, SGS particulate antigen delivery system A vaccine aduvant that contains synthetic material. YH, SGS synthetic vaccine adjuvant a vaccine adjuvant that includes tensioactive material. Tensioactive materials, surfactants or active surface agents are chemical substances with a polar-non polar structure. These substances have a tendency to locate themselves at the surface creating an adsorbed monomolecular layer on the interface. YH, SGS tensioactive compound vaccine adjuvant WEB: http://www.citt.ufl.edu/team/sepulveda/html/en_tensioactivos.htm tensoactive compound vaccine adjuvant YH, SGS a vaccine adjuvant that is primarily composed of carbohydrates. carbohydrate vaccine adjuvant a cytokine vaccine adjuvant that includes IFN-gamma. YH, SGS IFN-gamma vaccine adjuvant The objective that intends to produce vaccine via the vaccine preparation process. YH vaccine target specification A vaccine that protects against Listeria monocytogenes. YH, RR Listeria monocytogenes vaccine A CpG DNA vaccine adjuvant that is a short, synthetic, unmethylated CpG oligodeoxynucleotide (CpG ODN) with immunostimulatory activity. Oliver He, Kallan Roan ISS 1018 CpG ODN ISS 1018 CpG oligodeoxynucleotide ISS-1018 https://www.cancer.gov/publications/dictionaries/cancer-drug/def/iss-1018-cpg-oligodeoxynucleotide https://www.drugbank.ca/drugs/DB05463 ISS 1018 is a short, synthetic, unmethylated CpG oligodeoxynucleotide (CpG ODN) with immunostimulatory activity. ISS 1018 signals through Toll-like receptor 9 (TLR9) to induce the production of immunoglobulin by B cells and interferon (IFN) -alpha, IFN-beta, interleukin-12 (IL-12), and tumor necrosis factor - alpha (TNF-alpha) by plasmacytoid dendritic cells (pDC). ISS 1018 CpG ODN promotes antigen presentation and co-stimulatory molecule expression. ISS 1018 is currently being investigated in combination with HBsAg vaccine as a prophylactic treatment for to prevent Hepatitis B in adults. It is also being investigated in combination with rituximab for treatment of b-cell or non-hodgkin's lymphoma. ISS 1018 CpG ODN vaccine adjuvant DrugBank Accession number: DB05463 RS, NF, YH S. pneumoniae CbpA Protein Vaccine violinID: 787 RS, NF, YH S. pneumoniae ClpP protein Vaccine violinID: 789 RS, NF, YH S. pneumoniae PspA Protein Vaccine violinID: 795 RS, NF, YH S. pneumoniae SrtA Protein Vaccine violinID: 798 RS, NF, YH N. meningitidis ExbB Protein Vaccine violinID: 947 RS, NF, YH L. monocytogenes DNA Vaccine encoding hly violinID: 1077 RS, NF, YH M. tuberculosis DNA vaccine ESAT-6 violinID: 3543 RS, NF, YH Psuedorabies DNA vaccine encoding IE180 protein violinID: 822 RS, NF, YH M. tuberculosis DNA Vaccine encoding KatG violinID: 1094 RS, NF, YH M. tuberculosis HBHA Protein Vaccine violinID: 1095 a protein from a bacterium YH, ZX bacterium protein YH, ZX G+ bacterium protein YH, ZX G- bacterium protein a protein from a virus YH, ZX virus protein a protein from a parasite YH, ZX parasite protein YH, ZX Yersinia pestis protein YH, ZX Francisella tularensis protein YH, ZX Ebola virus protein YH, ZX Clostridium botulinum protein YH, ZX Escherichia coli protein YH, ZX Human Immunodeficiency Virus protein YH, ZX Mycobacterium tuberculosis protein YH, ZX Haemophilus influenzae protein YH, ZX Shigella protein YH, ZX Neisseria meningitidis protein YH, ZX Streptococcus pneumoniae protein YH, ZX Influenza virus protein YH, ZX Measles virus protein YH, ZX Rabies virus protein YH, ZX Pseudorabies virus protein YH, ZX Toxoplasma gondii protein YH, ZX Herpes simplex virus type 1 and 2 protein YH, ZX Bordetella pertussis protein YH, ZX Vibrio cholerae protein YH, ZX Yersinia enterocolitica protein YH, ZX 16 VP35 expressed from alphavirus replicons induced a protective immune response in C57BL/6 mice when challenged with Ebola virus Zaire [PMID:11485406]. VP35 expressed from alphavirus replicons induced a protective immune response in C57BL/6 mice when challenged with Ebola virus Zaire [PubMed: 11485406]. VP35 from Zaire ebolavirus Protegen ID: 16; NCBI Gene GI: 911827; NCBI Protein GI: 10313992; NCBI Protein Accession: NP_066244; NCBITaxon: 186538 YH, ZX 44 MAb BA5 protected animals against plague, neutralized the Y. pestis type III secretion pathway and promoted opsonophagocytic clearance of bacteria in blood. LcrV residues 196-225 were necessary and sufficient for MAb BA5 binding. These results identify LcrV residues 196-225 as a linear epitope that is recognized by the murine immune system to confer plague protection [PMID:20005318]. MAb BA5 protected animals against plague, neutralized the Y. pestis type III secretion pathway and promoted opsonophagocytic clearance of bacteria in blood. LcrV residues 196-225 were necessary and sufficient for MAb BA5 binding. These results identify LcrV residues 196-225 as a linear epitope that is recognized by the murine immune system to confer plague protection [PubMed: 20005318]. LcrV from y. pestis CO92 Protegen ID: 44; NCBI Gene GI: 1172676; NCBI Protein GI: 16082719; NCBI Protein Accession: NP_395165; NCBITaxon: 214092 YH, ZX 45 An LcrV variant lacking amino acid residues 271 to 300 (rV10) elicited immune responses that protected mice against a lethal challenge with Y. pestis [PMID:16041032]. An LcrV variant lacking amino acid residues 271 to 300 (rV10) elicited immune responses that protected mice against a lethal challenge with Y. pestis [PubMed: 16041032]. LcrV from Y. pestis KIM 10 Protegen ID: 45; NCBI Gene GI: 1149310; NCBI Protein GI: 31795491; NCBI Protein Accession: NP_857946; NCBITaxon: 187410 YH, ZX 48 Study evaluated the humoral immune response of mice that survived lethal Y. pestis aerosol challenge after antibiotic treatment. Results indicated that one of the predominant antibody response of mice surviving pneumonic plague after treatment with antibiotics was to pla [PMID:10085037]. Study evaluated the humoral immune response of mice that survived lethal Y. pestis aerosol challenge after antibiotic treatment. Results indicated that one of the predominant antibody response of mice surviving pneumonic plague after treatment with antibiotics was to pla [PubMed: 10085037]. Pla Protegen ID: 48; NCBI Gene GI: 1172643; NCBI Protein GI: 16082686; NCBI Protein Accession: NP_395233; NCBITaxon: 214092 YH, ZX 49 The type III secretion apparatus encoded on the low-calcium response (LCR) virulence plasmid, pCD1 in strain KIM5, of Y. pestis is a conserved virulence mechanism that is absolutely required for virulence of Y. pestis. YscF is a surface localized protein required both to secrete Yops and to translocate toxins into eukaryotic cells. YscF polymerization is possibly required for a YscF needle to puncture eukaryotic cell membranes. It is also likely that YscF and its homologs function to provide a base that a translocon complex is built upon, or that YscF builds a conduit from the bacterium to the eukaryotic membrane - this suggestion seems more likely given that other proteins such as YopB, YopD, and LcrV are also required for translocation into eukaryotic cells. YscF is thought to be a surface-expressed protein in Y. pestis and is required for virulence. YscF has been found to function as a protective antigen against experimental plague infection [PMID:15978133]. The type III secretion apparatus encoded on the low-calcium response (LCR) virulence plasmid, pCD1 in strain KIM5, of Y. pestis is a conserved virulence mechanism that is absolutely required for virulence of Y. pestis. YscF is a surface localized protein required both to secrete Yops and to translocate toxins into eukaryotic cells. YscF polymerization is possibly required for a YscF needle to puncture eukaryotic cell membranes. It is also likely that YscF and its homologs function to provide a base that a translocon complex is built upon, or that YscF builds a conduit from the bacterium to the eukaryotic membrane - this suggestion seems more likely given that other proteins such as YopB, YopD, and LcrV are also required for translocation into eukaryotic cells. YscF is thought to be a surface-expressed protein in Y. pestis and is required for virulence. YscF has been found to function as a protective antigen against experimental plague infection [PubMed: 15978133]. YopD from Y. pestis CO92 Protegen ID: 49; NCBI Gene GI: 1172673; NCBI Protein GI: 16082716; NCBI Protein Accession: NP_395162; NCBITaxon: 214092 YH, ZX 448 Mice and rabbits were immunized with recombinant HCR/A1 (rHCR/A1) from the classical type A-Hall strain (ATCC 3502) (BoNT/A1) and rHCR/E from BoNT serotype E Beluga (BoNT/E(B)). The protection elicited by rHCR/A1 to BoNT/A1 and BoNT/A2 and by rHCR/E(B) to BoNT/E(A) indicate that immunization with receptor binding domains elicit protection within sub-serotypes of BoNT [PMID:16177380]. Mice and rabbits were immunized with recombinant HCR/A1 (rHCR/A1) from the classical type A-Hall strain (ATCC 3502) (BoNT/A1) and rHCR/E from BoNT serotype E Beluga (BoNT/E(B)). The protection elicited by rHCR/A1 to BoNT/A1 and BoNT/A2 and by rHCR/E(B) to BoNT/E(A) indicate that immunization with receptor binding domains elicit protection within sub-serotypes of BoNT [PubMed: 16177380]. BoNT/A1 from C. botulinum A str. Hall Protegen ID: 448; NCBI Gene GI: 5398487; NCBI Protein GI: 153936924; NCBI Protein Accession: YP_001386738; NCBITaxon: 441771 YH, ZX 449 The DNA replicon vaccine (pSCARSBHc) encoding the Hc domain of BoNT/B (BHc) induced better responses and protection against BoNT/B mouse challenge than conventional DNA vaccine. Recombinant SFV particle VRP-BHc protected mice from high-dose BoNT/B challenge [PMID:28869522]. The production of ciBoNT/B1 HP, ciBoNT/C1 HP, ciBoNT/E1 HP and ciBoNT/F1 HP suggest the ciBoNT HP vaccines exhibit superior potency after single vaccinations.[PMID:28869522] The DNA replicon vaccine (pSCARSBHc) encoding the Hc domain of BoNT/B (BHc) induced better responses and protection against BoNT/B mouse challenge than conventional DNA vaccine. Recombinant SFV particle VRP-BHc protected mice from high-dose BoNT/B challenge [PubMed: 19712769]. BoNT/B Protegen ID: 449; NCBI Gene GI: 6030102; NCBI Protein GI: 169834607; NCBI Protein Accession: YP_001693307; NCBITaxon: 498213 YH, ZX 104 The heterologous prime-boost strategy of live Salmonella vaccine expressing Mycobacterium tuberculosis fusion antigen Age5B-ESAT6 (esxA) from the chromosome followed by a systemic boost of antigen and adjuvant reduced the levels of M. tuberculosis bacteria in the lungs and spleen to the same extent as BCG. Additionally, this vaccination regimen was observed to be statistically equivalent in terms of protection to immunisation with BCG [PMID:16751377]. In a prophylactic vaccine model, immunization with the Mycobacterium tuberculosis protein ESAT-6 with LANAC adjuvant elicited significant protective immunity against aerosol challenge with virulent M. tuberculosis [PMID:16751377]. The heterologous prime-boost strategy of live Salmonella vaccine expressing Mycobacterium tuberculosis fusion antigen Age5B-ESAT6 (esxA) from the chromosome followed by a systemic boost of antigen and adjuvant reduced the levels of M. tuberculosis bacteria in the lungs and spleen to the same extent as BCG. Additionally, this vaccination regimen was observed to be statistically equivalent in terms of protection to immunisation with BCG [PubMed: 19755145]. EsxA Protegen ID: 104; NCBI Gene GI: 886209; NCBI Protein GI: 57117165; NCBI Protein Accession: NC_000962.2; NCBITaxon: 1773 YH, ZX 199 Mice immunized intranasally with recombinant Tir protein had a survival rate of 92.9% after challenge with EHEC 0157:H7 [PMID:26020530]. Immunization of calves with recombinant EHEC O157 EspA, intimin and Tir resulted in the generation of antibodies capable of cross-reacting with antigens from non-O157 EHEC serotypes, suggesting that immunization with these antigens may provide a degree of cross-protection against other EHEC serotypes [PMID:26020530] Tir Protegen ID: 199; NCBI Gene GI: 960860; NCBI Protein GI: 15804222; NCBI Protein Accession: NP_290261.1; NCBITaxon: 562 YH, ZX 93 Systemic immunization of calves with a combination of EspA, intimin-531, and H7 flagellin resulted in a significant reduction in shedding of EHEC O157 to levels predicted to significantly impact on EHEC O157 cattle-to-cattle transmission [PMID:26020530] EHEC strains produce intimin, an outer membrane adhesin encoded by the eae gene located in a chromosomal pathogenicity island termed the locus of enterocyte effacement [PubMed: 17258324]. Eae Protegen ID: 93; NCBI Gene GI: 960862; NCBI Protein GI: 15804220; NCBI Protein Accession: NP_290259; NCBITaxon: 155864 YH, ZX 263 FimH is a protective antigen [PMID:9110982] Of the vaccine preparations, Fusion, Fusion + CT, and FimH admixed with FliC and CT showed the best protection against UPEC (Asadi et al., 2016). FimH is a protective antigen [PubMed: 9110982] FimH from E. coli UTI89 Protegen ID: 263; NCBI Gene GI: 3992235; NCBI Protein GI: 91213965; NCBI Protein Accession: YP_543951; NCBITaxon: 364106 YH, ZX 121 The 10-kDa culture filtrate protein (CFP-10, esxB) and 6-kDa early secretory antigen of T cells (ESAT-6) are secreted in abundance by Mycobacterium tuberculosis. Study demonstrated that protective immunity is induced by CFP-10 DNA vaccination in C3H mice as measured by a CFU reduction in the lung and spleen 4 and 8 weeks after challenge with M. tuberculosis [PMID:18332205]. The 10-kDa culture filtrate protein (CFP-10, esxB) and 6-kDa early secretory antigen of T cells (ESAT-6) are secreted in abundance by Mycobacterium tuberculosis. Study demonstrated that protective immunity is induced by CFP-10 DNA vaccination in C3H mice as measured by a CFU reduction in the lung and spleen 4 and 8 weeks after challenge with M. tuberculosis [PubMed: 18332205]. EsxB Protegen ID: 121; NCBI Gene GI: 886194; NCBI Protein GI: 15611010; NCBI Protein Accession: NP_218391; NCBITaxon: 83332 YH, ZX 122 Researchers have developed DNA vaccines expressing M. tuberculosis antigen 85A (Ag85A, fbpA) and cytokine granulocyte macrophage colony stimulating factor (GM-CSF). The immune strategy of BCG-prime and DNA vaccine boost induced mice to generate efficient immune protection against M. tuberculosis challenge [PMID:19450898]. Researchers have developed DNA vaccines expressing M. tuberculosis antigen 85A (Ag85A, fbpA) and cytokine granulocyte macrophage colony stimulating factor (GM-CSF). The immune strategy of BCG-prime and DNA vaccine boost induced mice to generate efficient immune protection against M. tuberculosis challenge [PubMed: 19450898]. FbpA Protegen ID: 122; NCBI Gene GI: 886132; NCBI Protein GI: 15610940; NCBI Protein Accession: NC_000962.2; NCBITaxon: 1773 YH, ZX 280 Immunization with IutA protects against urinary tract colinization by E.coli CFT073 in the bladders of CBA/J mice [PMID:26729174]. We demonstrated for IutA, antigen-specific serum IgG represents a strong correlate of protection in vaccinated mice [PMID:26729174]. Immunization with IutA protects against urinary tract colinization by E.coli CFT073 in the bladders of CBA/J mice [PubMed: 19806177]. IutA Protegen ID: 280; NCBI Gene GI: 1039578; NCBI Protein GI: 26249458; NCBI Protein Accession: NP_755498; NCBITaxon: 199310 YH, ZX 281 Antibodies directed at the putative binding region of FimH (anti- s-FimH1-25) significantly reduced E. coli bladder infections in the experimental mouse model of urinary tract infections [PMID:9276729]. Antibodies directed at the putative binding region of FimH (anti- s-FimH1-25) significantly reduced E. coli bladder infections in the experimental mouse model of urinary tract infections [PubMed: 9276729]. FimH Protegen ID: 281; NCBI Gene GI: 948847; NCBI Protein GI: 16132141; NCBI Protein Accession: NP_418740; NCBITaxon: 511145 YH, ZX 282 Active immunization of BALB/c mice with IroN antigen in Freund's adjuvant protects mice from lethal challenge with ExPEC strain S26 [PMID:17145948]. Active immunization of BALB/c mice with IroN antigen in Freund's adjuvant protects mice from lethal challenge with ExPEC strain S26 [PubMed: 17145948 ]. IroN Protegen ID: 282; NCBI Gene GI: 7379404; NCBI Protein GI: 222104801; NCBI Protein Accession: YP_002539290; NCBITaxon: 562 YH, ZX 288 S. flexneri M90T is a colonisation-defective mutant with a transposon in fnr, which encodes a regulator of anaerobic metabolism. To establish whether FNR-mediated repression of spa32 and spa33 contributes to increased Shigella entry into cells in an anaerobic cabinet, recombinant M90T strains were constructed which contain spa32 and spa33 under the control of either their native promoters (M90Tp32/33) or promoters with disrupted FNR boxes (M90Tp#32/#33).The presence in M90T of spa32 and spa33 alleles that are not repressed by FNR led to IpaB secretion during anaerobic growth, and loss of the increased entry of Shigella into cells in an anaerobic cabinet [PMID:20436458]. S. flexneri M90T is a colonisation-defective mutant with a transposon in fnr, which encodes a regulator of anaerobic metabolism. To establish whether FNR-mediated repression of spa32 and spa33 contributes to increased Shigella entry into cells in an anaerobic cabinet, recombinant M90T strains were constructed which contain spa32 and spa33 under the control of either their native promoters (M90Tp32/33) or promoters with disrupted FNR boxes (M90Tp#32/#33).The presence in M90T of spa32 and spa33 alleles that are not repressed by FNR led to IpaB secretion during anaerobic growth, and loss of the increased entry of Shigella into cells in an anaerobic cabinet [PubMed: 20436458]. Spa32 Protegen ID: 288; NCBI Gene GI: 876502; NCBI Protein GI: 13449098; NCBI Protein Accession: NP_085314; NCBITaxon: 424718 YH, ZX 326 Oral immunization of mice with ZJ111/pcDNA3-SAG1 elicited specific humoral responses and stimulated proliferation of splenocytes (P<0.05). Mice immunized with ZJ111/pcDNA3-SAG1 displayed significant protection against an intraperitoneally challenge with 500 tachyzoite forms of T. gondii RH strain. Vaccination at 10(7) and 10(8)CFU per mice provided a 20% and 10% survival rate comparing 100% mortality of the non-immunized mice, exhibiting longer living time and better survival rate [PMID:18590785]. Oral immunization of mice with ZJ111/pcDNA3-SAG1 elicited specific humoral responses and stimulated proliferation of splenocytes (P<0.05). Mice immunized with ZJ111/pcDNA3-SAG1 displayed significant protection against an intraperitoneally challenge with 500 tachyzoite forms of T. gondii RH strain. Vaccination at 10(7) and 10(8)CFU per mice provided a 20% and 10% survival rate comparing 100% mortality of the non-immunized mice, exhibiting longer living time and better survival rate [PubMed: 18590785]. SAG1 Protegen ID: 326; NCBI Gene GI: 7900172; NCBI Protein GI: 237839159; NCBI Protein Accession: XP_002368877; NCBITaxon: 508771 YH, ZX 339 Modified yopD antigens were able to partially protect immunized mice at various levels against lethal challenge with Y. pestis KIM 1001 strain [PMID:18291562]. Modified yopD antigens were able to partially protect immunized mice at various levels against lethal challenge with Y. pestis KIM 1001 strain [PubMed: 18291562]. YopD from Y. pestis KIM 10 Protegen ID: 339; NCBI Gene GI: 1149313; NCBI Protein GI: 31795494; NCBI Protein Accession: NP_857949; NCBITaxon: 187410 YH, ZX 351 Study tested the efficacy of 2 proteins, Psn and a portion of LcrV in protecting mice against virulent Yersinia pestis challenge. Results show that the truncated LcrV protein delivered by RASV is sufficient to afford a full protective immune response in a mouse model of bubonic plague and the Psn protein afforded partial protection in a non-optimized system [PMID:17966435]. Study tested the efficacy of 2 proteins, Psn and a portion of LcrV in protecting mice against virulent Yersinia pestis challenge. Results show that the truncated LcrV protein delivered by RASV is sufficient to afford a full protective immune response in a mouse model of bubonic plague and the Psn protein afforded partial protection in a non-optimized system [PubMed: 17966435]. Psn Protegen ID: 351; NCBI Gene GI: 1147351; NCBI Protein GI: 22126288; NCBI Protein Accession: NP_669711; NCBITaxon: 187410 YH, ZX 352 Study evaluated the humoral immune response of mice that survived lethal Y. pestis aerosol challenge after antibiotic treatment. Results indicated that one of the predominant antibody response of mice surviving pneumonic plague after treatment with antibiotics was to yopH [PMID:10085037]. Study evaluated the humoral immune response of mice that survived lethal Y. pestis aerosol challenge after antibiotic treatment. Results indicated that one of the predominant antibody response of mice surviving pneumonic plague after treatment with antibiotics was to yopH [PubMed: 10085037]. YopH from Y. pestis CO92 Protegen ID: 352; NCBI Gene GI: 1172712; NCBI Protein GI: 16082755; NCBI Protein Accession: NP_395201; NCBITaxon: 214092 YH, ZX 378 Researchers constructed isogenic mutants of B. pertussis Tohama expressing the alleles ptxA1 or ptxA2 and prn1 or prn2 and compared the efficacies of an acellular pertussis vaccine against the mutants in a mouse model. While the vaccine was effective against all of the B. pertussis strains regardless of the allele expression pattern, the strain expressing ptxA1 and prn2 displayed a survival advantage over the other strains [PMID:20357056]. Researchers constructed isogenic mutants of B. pertussis Tohama expressing the alleles ptxA1 or ptxA2 and prn1 or prn2 and compared the efficacies of an acellular pertussis vaccine against the mutants in a mouse model. While the vaccine was effective against all of the B. pertussis strains regardless of the allele expression pattern, the strain expressing ptxA1 and prn2 displayed a survival advantage over the other strains [PubMed: 20357056]. Prn Protegen ID: 378; NCBI Gene GI: 2664290; NCBI Protein GI: 33592195; NCBI Protein Accession: NP_879839; NCBITaxon: 257313 YH, ZX 379 BALB/c mice were immunized with PTx vaccine on day 6 of life and then challenged with B. pertussis using the aerosol challenge model. These primed mice were significantly better protected against leukocytosis, weight loss, and proliferation of B. pertussis in the lungs following aerosol challenge than the nonprimed group. This protection correlated with levels of anti-PT antibody in serum present on the day of aerosol challenge [PMID:12117973]. BALB/c mice were immunized with PTx vaccine on day 6 of life and then challenged with B. pertussis using the aerosol challenge model. These primed mice were significantly better protected against leukocytosis, weight loss, and proliferation of B. pertussis in the lungs following aerosol challenge than the nonprimed group. This protection correlated with levels of anti-PT antibody in serum present on the day of aerosol challenge [PubMed: 12117973]. PtxA Protegen ID: 379; NCBI Gene GI: 2665068; NCBI Protein GI: 33594638; NCBI Protein Accession: NP_882282; NCBITaxon: 257313 YH, ZX 470 Mice immunized with rLm/iglC were protected against lethal challenge with F. tularensis LVS administered by the intranasal route, a route chosen to mimic airborne infection, and, most importantly, against aerosol challenge with the highly virulent Type A F. tularensis SchuS4 strain [PMID:19126421]. Mice immunized with rLm/iglC were protected against lethal challenge with F. tularensis LVS administered by the intranasal route, a route chosen to mimic airborne infection, and, most importantly, against aerosol challenge with the highly virulent Type A F. tularensis SchuS4 strain [PubMed: 19126421]. IglC1 Protegen ID: 470; NCBI Gene GI: 3191591; NCBI Protein GI: 56708413; NCBI Protein Accession: YP_170309; NCBITaxon: 177416 YH, ZX 472 Immunization with WbtI(G191V) protected mice against a relatively low-dose intraperitoneal challenge with LVS (F. tularensis subspecies holarctica live vaccine strain), but was less protective against a high-dose challenge [PMID:17768257]. Immunization with WbtI(G191V) protected mice against a relatively low-dose intraperitoneal challenge with LVS (F. tularensis subspecies holarctica live vaccine strain), but was less protective against a high-dose challenge [PubMed: 17768257]. WbtI Protegen ID: 472; NCBI Gene GI: 5522688; NCBI Protein GI: 156502002; NCBI Protein Accession: YP_001428067; NCBITaxon: 458234 YH, ZX 477 Anti-lpnA MAbs conferred significant, although not complete, protection of naïve C3H/HeN mice from lethal challenge with F. tularensis LVS when administered therapeutically [PMID:19176692]. Anti-lpnA MAbs conferred significant, although not complete, protection of nave C3H/HeN mice from lethal challenge with F. tularensis LVS when administered therapeutically [PubMed: 19176692]. LpnA Protegen ID: 477; NCBI Gene GI: 3191792; NCBI Protein GI: 56708002; NCBI Protein Accession: YP_169898; NCBITaxon: 177416 YH, ZX 485 Rabbit antibody prepared against P2 from one strain was cross-reactive with P2 isolated from the other two heterologous strains by Western blot. This antibody passively protected infant rats against type b Haemophilus infection caused by the homologous organism, but not against challenge by a strain with the heterologous 36,500 mol wt P2 protein [PMID:6603479]. Rabbit antibody prepared against P2 from one strain was cross-reactive with P2 isolated from the other two heterologous strains by Western blot. This antibody passively protected infant rats against type b Haemophilus infection caused by the homologous organism, but not against challenge by a strain with the heterologous 36,500 mol wt P2 protein [PubMed: 6603479]. OmpP2 Protegen ID: 485; NCBI Gene GI: 3429565; NCBI Protein GI: 68248747; NCBI Protein Accession: YP_247859; NCBITaxon: 281310 YH, ZX 501 BALB/c mice receiving a glycoprotein D1 (gD1, US5) DNA vaccine alone were 80% protected against a subsequent HSV-1 challenge. Results also indicate that the administration of NLX as an adjuvant improved protective immunity against HSV-1 [PMID:19174474]. BALB/c mice receiving a glycoprotein D1 (gD1, US5) DNA vaccine alone were 80% protected against a subsequent HSV-1 challenge. Results also indicate that the administration of NLX as an adjuvant improved protective immunity against HSV-1 [PubMed: 19174474]. US5 Protegen ID: 501; NCBI Gene GI: 2703406; NCBI Protein GI: 9629447; NCBI Protein Accession: NP_044668; NCBITaxon: 10298 YH, ZX 507 Protection against a lethal intraperitoneal challenge of HSV-1 (5 x 10(4) pfu) with gC or gE (US8) plasmid vaccination could be demonstrated if the inoculating dose of DNA was 250 microg. All mice immunized with vaccinia recombinants expressing either gC or gE survived HSV-1 challenge [PMID:9728527]. Protection against a lethal intraperitoneal challenge of HSV-1 (5 x 10(4) pfu) with gC or gE (US8) plasmid vaccination could be demonstrated if the inoculating dose of DNA was 250 microg. All mice immunized with vaccinia recombinants expressing either gC or gE survived HSV-1 challenge [PubMed: 9728527]. US8 Protegen ID: 507; NCBI Gene GI: 2703448; NCBI Protein GI: 9629449; NCBI Protein Accession: NP_044670; NCBITaxon: 10298 YH, ZX 524 A targeted fusion protein based on the CTA1-DD adjuvant and containing tandem repeats of the matrix protein 2 (M2e) ectodomain epitope derived from Influenza A virus (A/Puerto Rico/8/34(H1N1)), CTA1-3M2e-DD, confers strong protective immunity against a potentially lethal challenge infection with influenza virus in mice. The formulation was highly effective for mucosal immunizations and promoted high M2e-specific serum IgG and mucosal IgA antibody titers and an hitherto unknown anti-M2e CD4 T cell immunity [PMID:18243429]. A targeted fusion protein based on the CTA1-DD adjuvant and containing tandem repeats of the matrix protein 2 (M2e) ectodomain epitope derived from Influenza A virus (A/Puerto Rico/8/34(H1N1)), CTA1-3M2e-DD, confers strong protective immunity against a potentially lethal challenge infection with influenza virus in mice. The formulation was highly effective for mucosal immunizations and promoted high M2e-specific serum IgG and mucosal IgA antibody titers and an hitherto unknown anti-M2e CD4 T cell immunity [PubMed: 18243429]. M2 from Influenza A virus (A/Puerto Rico/8/34(H1N1)) Protegen ID: 524; NCBI Gene GI: 956528; NCBI Protein GI: 56583270; NCBI Protein Accession: NP_040979; NCBITaxon: 211044 YH, ZX 580 Lewis rats were immunized with recombinant vaccinia virus (VV) expressing various proteins of measles virus (MV). VVP (Phosphoprotein) -immunized rats were partially protected from MV challenge [PMID:1833505]. Lewis rats were immunized with recombinant vaccinia virus (VV) expressing various proteins of measles virus (MV). VVP (Phosphoprotein) -immunized rats were partially protected from MV challenge [PubMed: 1833505]. P phosphoprotein Protegen ID: 580; NCBI Gene GI: 1489805; NCBI Protein GI: 9626947; NCBI Protein Accession: NP_056919; NCBITaxon: 11234 YH, ZX 581 Lewis rats were immunized with recombinant vaccinia virus (VV) expressing various proteins of measles virus (MV). VVM (Matrix Protein) -immunized rats were partially protected from MV challenge [PMID:1833505]. Lewis rats were immunized with recombinant vaccinia virus (VV) expressing various proteins of measles virus (MV). VVM (Matrix Protein) -immunized rats were partially protected from MV challenge [PubMed: 1833505]. M matrix protein Protegen ID: 581; NCBI Gene GI: 1489803; NCBI Protein GI: 9626949; NCBI Protein Accession: NP_056921; NCBITaxon: 11234 YH, ZX 601 A total of 11 meningococcal proteins that are necessary for establishing systemic infection were expressed as recombinant antigens and assessed for their ability to protect mice against live bacterial challenge against N. meningitidis; ExbB, which is required for iron acquisition, elicited protective immunity [PMID:15964482]. A total of 11 meningococcal proteins that are necessary for establishing systemic infection were expressed as recombinant antigens and assessed for their ability to protect mice against live bacterial challenge against N. meningitidis; ExbB, which is required for iron acquisition, elicited protective immunity [PubMed: 15964482]. ExbB Protegen ID: 601; NCBI Gene GI: 903370; NCBI Protein GI: 15677575; NCBI Protein Accession: NP_274732; NCBITaxon: 122586 YH, ZX 607 Immunization with the pneumococcal proteins pneumolysin (Ply), choline binding protein A (CbpA), or pneumococcal surface protein A (PspA) elicits protective responses against invasive pneumococcal disease in animal models.[PMID:26245351] The protective effects a pneumolysin mutant (DeltaA146 Ply) against pneumococcal infections in mice was evaluated. Vaccinated mice were challenged with pneumococcal strain D39 at 1,500 times the LD50 (1.5 x 105 CFU) and the vaccinated mice survived significantly longer than control mice after challenge [PubMed: 20038538]. Ply Protegen ID: 607; NCBI Gene GI: 4441611; NCBI Protein GI: 116515376; NCBI Protein Accession: YP_817150; NCBITaxon: 373153 YH, ZX 608 The protective effects of ATP-dependent caseinolytic protease (ClpP) was evaluated. Vaccinated mice were intraperitoneally and/or intranasally challenged with different pneumococcal strains. In intraperitoneal challenge models with pneumococcal strain D39 (serotype 2), clpP elicited some protection in mice [PMID:20038538]. The protective effects of ATP-dependent caseinolytic protease (ClpP) was evaluated. Vaccinated mice were intraperitoneally and/or intranasally challenged with different pneumococcal strains. In intraperitoneal challenge models with pneumococcal strain D39 (serotype 2), clpP elicited some protection in mice [PubMed: 20038538]. ClpP Protegen ID: 608; NCBI Gene GI: 4441476; NCBI Protein GI: 116516216; NCBI Protein Accession: YP_816144; NCBITaxon: 373153 YH, ZX 613 Mice immunized with recombinant (r)PsrP(BR) had significantly less bacteria in their blood and improved survival versus controls following intranasal challenge [PMID:19627498]. Mice immunized with recombinant (r)PsrP(BR) had significantly less bacteria in their blood and improved survival versus controls following intranasal challenge [PubMed: 19627498]. PsrP Protegen ID: 613; NCBI Gene GI: 7329552; NCBI Protein GI: 221232510; NCBI Protein Accession: YP_002511663; NCBITaxon: 561276 YH, ZX 615 Intraperitoneal immunization with recombinant SrtA was found to have conferred to mice protection against S. pneumoniae intraperitoneal challenge and the passive transfer of immune serum before intraperitoneal challenge was also protective. Moreover, by using the intranasal challenge model, significant reduction of bacteremia when mice were intraperitoneally immunized with SrtA was observed, while a moderate decrease of lung infection was achieved by intranasal immunization, even though no influence on nasopharynx colonization was seen [PMID:19433540]. Intraperitoneal immunization with recombinant SrtA was found to have conferred to mice protection against S. pneumoniae intraperitoneal challenge and the passive transfer of immune serum before intraperitoneal challenge was also protective. Moreover, by using the intranasal challenge model, significant reduction of bacteremia when mice were intraperitoneally immunized with SrtA was observed, while a moderate decrease of lung infection was achieved by intranasal immunization, even though no influence on nasopharynx colonization was seen [PubMed: 19433540]. SrtA Protegen ID: 615; NCBI Gene GI: 4442999; NCBI Protein GI: 116515518; NCBI Protein Accession: YP_816547; NCBITaxon: 373153 YH, ZX 619 Mice were actively immunized with a fragment of choline binding protein A (CbpA; also known as PspC, Hic, and SpsA). CbpA was able to protect mice from intraperitoneal challenge with medium to very high doses of a highly virulent capsular type 2 pneumococcal strain, D39 [PMID:11553536]. Mice were actively immunized with a fragment of choline binding protein A (CbpA; also known as PspC, Hic, and SpsA). CbpA was able to protect mice from intraperitoneal challenge with medium to very high doses of a highly virulent capsular type 2 pneumococcal strain, D39 [PubMed: 11553536]. CbpA Protegen ID: 619; NCBI Gene GI: 4441159; NCBI Protein GI: 116515359; NCBI Protein Accession: YP_817402; NCBITaxon: 373153 YH, ZX 620 Groups of BALB/c mice immunized with choline binding protein PspA were challenged with either D39 or WCH16. PspA elicited protection by using moderate challenge doses of S. pneumoniae [PMID:17088353]. Groups of BALB/c mice immunized with choline binding protein PspA were challenged with either D39 or WCH16. PspA elicited protection by using moderate challenge doses of S. pneumoniae [PubMed: 17088353]. PspA Protegen ID: 620; NCBI Gene GI: 4441373; NCBI Protein GI: 116515876; NCBI Protein Accession: YP_815641; NCBITaxon: 373153 YH, ZX 648 Mice vaccinated intraperitoneally (i.p.) with 10^7 p.f.u. of a vaccinia virus recombinant expressing either the glycoprotein (rVac-G) or nucleoprotein (rVac-N) of rabies virus 3 weeks before challenge were protected against peripheral lethal infection [PMID:8207400]. Mice vaccinated intraperitoneally (i.p.) with 10^7 p.f.u. of a vaccinia virus recombinant expressing either the glycoprotein (rVac-G) or nucleoprotein (rVac-N) of rabies virus 3 weeks before challenge were protected against peripheral lethal infection [PubMed: 8207400]. RABVgp1 nucleoprotein N Protegen ID: 648; NCBI Gene GI: 1489853; NCBI Protein GI: 9627198; NCBI Protein Accession: NP_056793; NCBITaxon: 11292 YH, ZX 658 To examine the response by IE180 more closely, a vaccine trial in mice with a vector DNA construct that contains the gene encoding for IE180, designated pcDNAIE180 was conducted. Seven months after immunization with pcDNAIE180, an overall 25% of BALB/c, C3H/HeJ, and C57BL/6 mice receiving a lethal PrV challenge were protected [PMID:9586695]. To examine the response by IE180 more closely, a vaccine trial in mice with a vector DNA construct that contains the gene encoding for IE180, designated pcDNAIE180 was conducted. Seven months after immunization with pcDNAIE180, an overall 25% of BALB/c, C3H/HeJ, and C57BL/6 mice receiving a lethal PrV challenge were protected [PubMed: 9586695]. IE180 Protegen ID: 658; NCBI Gene GI: 2952540; NCBI Protein GI: 51557548; NCBI Protein Accession: YP_068382; NCBITaxon: 10345 YH, ZX 707 Study compared the handling of overlapping 24-mer peptides from HIV Nef either mixed or covalently linked in tandem in one protein. With adjuvant, overlapping peptides were capable of protecting Balb/c mice against lethal viral challenge with 3 × 108 plaque forming units of vv-nef, whereas the intact protein was less protective [PMID:19193636]. Study compared the handling of overlapping 24-mer peptides from HIV Nef either mixed or covalently linked in tandem in one protein. With adjuvant, overlapping peptides were capable of protecting Balb/c mice against lethal viral challenge with 3 108 plaque forming units of vv-nef, whereas the intact protein was less protective [PubMed: 19193636]. Nef Protegen ID: 707; NCBI Gene GI: 156110; NCBI Protein GI: 28872818; NCBI Protein Accession: NP_057857; NCBITaxon: 11676 YH, ZX 733 Antibodies generated against TcpF are protective against experimental V. cholerae infection in the infant mouse cholera model [PMID:16040956]. Antibodies generated against TcpF are protective against experimental V. cholerae infection in the infant mouse cholera model [PubMed: 16040956]. TcpF Protegen ID: 733; NCBI Gene GI: 2614504; NCBI Protein GI: 15640854; NCBI Protein Accession: NP_230485; NCBITaxon: 243277 YH, ZX 790 Mice actively immunized using a recombinant V antigen (rVagHis, encoded by lcrV gene) of Y. enterocolitica were completely protected against challenge with both, Y. enterocolitica 0:8 and Y. pseudotuberculosis serotype III [PMID:10089162]. Mice actively immunized using a recombinant V antigen (rVagHis, encoded by lcrV gene) of Y. enterocolitica were completely protected against challenge with both, Y. enterocolitica 0:8 and Y. pseudotuberculosis serotype III [PubMed: 10089162]. LcrV Protegen ID: 790; NCBI Gene GI: 1449458; NCBI Protein GI: 32470278; NCBI Protein Accession: NP_863514; NCBITaxon: 630 YH, ZX E. coli IutA protein vaccine VIOLIN Vaccine ID: 926 YH, ZX Y. enterocolititica Subunit V Antigen Protein Vaccine VIOLIN Vaccine ID: 896 A vaccine that protects against Yersinia enterocolitica. YH, ZX Yersinia enterocolitica Yersinia enterocolitica vaccine YH, ZX 51 Study evaluated the humoral immune response of mice that survived lethal Y. pestis aerosol challenge after antibiotic treatment. Results indicated that one of the predominant antibody response of mice surviving pneumonic plague after treatment with antibiotics was to yopH [PMID:10085037]. YopH from Y. pestis strain: CO92, biovar: Orientalis Protegen ID: 51; NCBI Gene GI: 1172712; NCBI Protein GI: 16082755; NCBI Protein Accession: NP_395201; NCBITaxon: 214092 YH, ZX 816 In a prophylactic vaccine model, immunization with the Mycobacterium tuberculosis protein ESAT-6 with LANAC adjuvant elicited significant protective immunity against aerosol challenge with virulent M. tuberculosis [PMID:16751377]. In a prophylactic vaccine model, immunization with the Mycobacterium tuberculosis protein ESAT-6 with LANAC adjuvant elicited significant protective immunity against aerosol challenge with virulent M. tuberculosis [PubMed: 16751377]. ESAT-6 Protegen ID: 816; NCBI Gene GI: 886209; NCBI Protein GI: 57117165; NCBI Protein Accession: YP_178023; NCBITaxon: 83332 YH, ZX 817 DNA vaccines encoding KatG antigen fused to TPA signal sequences evoked a significant protective response in mice aerogenically challenged with low doses of Mycobacterium tuberculosis Erdman 17 to 21 days after the final immunization [PMID:10456931]. DNA vaccines encoding KatG antigen fused to TPA signal sequences evoked a significant protective response in mice aerogenically challenged with low doses of Mycobacterium tuberculosis Erdman 17 to 21 days after the final immunization [PubMed: 10456931]. KatG Protegen ID: 817; NCBI Gene GI: 885638; NCBI Protein GI: 15609045; NCBI Protein Accession: NP_216424; NCBITaxon: 83332 YH, ZX 820 A selection of previously identified protective Mycobacterium tuberculosis DNA vaccines were re-formulated as proteins and administered with a Th1-inducing adjuvant to help stimulate the relevant immune responses necessary for protection. One candidate (Rv1806-1807) induced protection in the guinea pig aerosol infection model 30 days post-challenge on the basis of reducing the bacterial burden of M. tuberculosis in the lungs [PMID:16520093]. A selection of previously identified protective Mycobacterium tuberculosis DNA vaccines were re-formulated as proteins and administered with a Th1-inducing adjuvant to help stimulate the relevant immune responses necessary for protection. One candidate (Rv1806-1807) induced protection in the guinea pig aerosol infection model 30 days post-challenge on the basis of reducing the bacterial burden of M. tuberculosis in the lungs [PubMed: 16520093]. PPE31 Protegen ID: 820; NCBI Gene GI: 885072; NCBI Protein GI: 57116920; NCBI Protein Accession: YP_177653; NCBITaxon: 83332 YH, ZX 821 Purified preparations of HBHA were emulsified in a dimethyldioctadecylammonium bromide-monophosphoryl lipid A adjuvant and tested for the ability to reduce M. tuberculosis infection in the mouse aerosol challenge model for tuberculosis. The HBHA-containing vaccine gave a approximately 0.7-log reduction in CFU in both mouse lungs and spleens compared to adjuvant controls 28 days following challenge [PMID:15557600]. Purified preparations of HBHA were emulsified in a dimethyldioctadecylammonium bromide-monophosphoryl lipid A adjuvant and tested for the ability to reduce M. tuberculosis infection in the mouse aerosol challenge model for tuberculosis. The HBHA-containing vaccine gave a approximately 0.7-log reduction in CFU in both mouse lungs and spleens compared to adjuvant controls 28 days following challenge [PubMed: 15557600]. HBHA Protegen ID: 821; NCBI Gene GI: 5211814; NCBI Protein GI: 148660242; NCBI Protein Accession: YP_001281765; NCBITaxon: 25177 YH, ZX 842 In an attempt to generate a subunit vaccine in this experimental disease model, eukaryotic plasmid DNA expression vectors containing genes encoding either the wild-type or modified forms of recombinant listeriolysin O (hly) were generated and used for genetic vaccination of naive mice. Results of these studies indicate that the intramuscular immunization of mice with specifically designed plasmid DNA constructs encoding recombinant forms of listeriolysin O (hly) stimulates peptide-specific CD8+ immune T cells that exhibit in vitro cytotoxic activity. More importantly, such immunization can provide protective immunity against a subsequent challenge with viable L. monocytogenes [PMID:10384131]. In an attempt to generate a subunit vaccine in this experimental disease model, eukaryotic plasmid DNA expression vectors containing genes encoding either the wild-type or modified forms of recombinant listeriolysin O (hly) were generated and used for genetic vaccination of naive mice. Results of these studies indicate that the intramuscular immunization of mice with specifically designed plasmid DNA constructs encoding recombinant forms of listeriolysin O (hly) stimulates peptide-specific CD8+ immune T cells that exhibit in vitro cytotoxic activity. More importantly, such immunization can provide protective immunity against a subsequent challenge with viable L. monocytogenes [PubMed: 10384131]. Hly Protegen ID: 842; NCBI Gene GI: 987033; NCBI Protein GI: 16802248; NCBI Protein Accession: NP_463733; NCBITaxon: 169963 cervical carcinoma cervical carcinoma 宫颈癌 James Malone James Malone Bowel Bowel adult alimentary canal adult alimentary canal gut gut intestines intestines 成人消化道 肠(Bowel) 肠(intestines) 肠道 AAO:0000246 AAO:0000246 BTO:0000648 BTO:0000648 EHDAA:518 EHDAA:518 EV:0100071 EV:0100071 FMAID:7199 FMAID:7199 MA:0000328 MA:0000328 MAT:0000043 MAT:0000043 MFO:0003040 MFO:0003040 SAEL:55 SAEL:55 TADS:0000165 TADS:0000165 TAO:0001338 TAO:0001338 TGMA:0001819 TGMA:0001819 WBbt:0005772 WBbt:0005772 XAO:0000129 XAO:0000129 ZFA:0001338 ZFA:0001338 The fluid-feeding habit of adult mosquitoes is reflected in the structure and ultrastructure of the alimentary canal. The fluid-feeding habit of adult mosquitoes is reflected in the structure and ultrastructure of the alimentary canal. The tubular part of the alimentary canal that extends from the stomach to the anus. The tubular part of the alimentary canal that extends from the stomach to the anus. 从胃延伸到肛门的消化道的管状部分。 成年蚊子的摄食习惯反映在消化道的结构和超微结构上。 intestine intestine 肠(intestine) URI: http://www.ebi.ac.uk/cellline#intestine URI: http://www.ebi.ac.uk/cellline#intestine RIKEN Cell Bank example to be eventually removed The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job Person:Alan Ruttenberg failed exploratory term Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. metadata complete term created to ease viewing/sort terms for development purpose, and will not be included in a release PERSON:Alan Ruttenberg organizational term Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." ready for release 准备好发布 Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. metadata incomplete Nothing done yet beyond assigning a unique class ID and proposing a preferred term. uncurated All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. pending final vetting 待最后审批 Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes. PERSON: Alan Ruttenberg PERSON: Melanie Courtot core placeholder removed An editor note should explain what were the merged terms and the reason for the merge. terms merged This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. term imported This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. term split This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason. We expect to be able to mine these new reasons and add instances as required. other true Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. Alan Ruttenberg A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf universal A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. Alan Ruttenberg defined class A named class expression is a logical expression that is given a name. The name can be used in place of the expression. named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions Alan Ruttenberg named class expression Terms with this status should eventually replaced with a term from another ontology. Alan Ruttenberg group:OBI to be replaced with external ontology term A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. Alan Ruttenberg group:OBI requires discussion Transformation-ML Transformation-ML file describing parameter transformations used in a GvHD experiment. Transformation-ML is a format standard of a digital entity that is conformant with the Transformation-ML standard.(http://wiki.ficcs.org/ficcs/Transformation-ML?action=AttachFile&do=get&target=Transformation-ML_v1.0.26.pdf) person:Jennifer Fostel web-page:http://wiki.ficcs.org/ficcs/Transformation-ML?action=AttachFile&do=get&target=Transformation-ML_v1.0.26.pdf Transformation-ML ACS d06.acs, ACS1.0 data file of well D06 of plate 2 of part 1 of a GvHD experiment. ACS is a format standard of a digital entity that is conformant with the Analytical Cytometry Standard. (http://www.isac-net.org/content/view/607/150/) person:Jennifer Fostel web-page:http://www.isac-net.org/content/view/607/150/ ACS XML RDF/XML file, OWL file, Compensation-ML file, WSDL document, SVG document XML is a format standard of a digital entity that is conformant with the W3C Extensible Markup Language Recommendation.(http://www.w3.org/XML/) person:Jennifer Fostel web-page:http://www.w3.org/XML/ XML RDF A FOAF file, a SKOS file, an OWL file. RDF is a format standard of a digital entity that is conformant with the W3C Resource Description Framework RDF/XML Syntax specification.(http://www.w3.org/RDF/) person:Jennifer Fostel web-page:http://www.w3.org/RDF/ RDF zip MagicDraw MDZIP archive, Java JAR file. zip is a format standard of a digital entity that is conformant with the PKWARE .ZIP file format specification (http://www.pkware.com/index.php?option=com_content&task=view&id=59&Itemid=103/) person:Jennifer Fostel web-page:http://www.pkware.com/index.php?option=com_content&task=view&id=59&Itemid=103/ zip tar Example.tar file. tar is a format standard of a digital entity that is conformant with the tape archive file format as standardized by POSIX.1-1998, POSIX.1-2001, or any other tar format compliant with the GNU tar specification. (http://www.gnu.org/software/tar/manual/) person:Jennifer Fostel web-page:http://www.gnu.org/software/tar/manual/ tar FCS d01.fcs, FCS3 data file of well D06 of plate 2 of part 1 of a GvHD experiment. FCS is a format standard of a digital entity that is conformant with the Flow Cytometry Data File Standard.(http://www.fcspress.com/) person:Jennifer Fostel web-page:http://www.fcspress.com/ FCS Compensation-ML compfoo.xml, Compensation-ML file describing compensation used in a GvHD experiment Compensation-ML is a format standard of a digital entity that is conformant with the Compensation-ML standard. (http://wiki.ficcs.org/ficcs/Compensation-ML?action=AttachFile&do=get&target=Compensation-ML_v1.0.24.pdf) person:Jennifer Fostel web-page:http://wiki.ficcs.org/ficcs/Compensation-ML?action=AttachFile&do=get&target=Compensation-ML_v1.0.24.pdf Compensation-ML Gating-ML foogate.xml, Gating-ML file describing gates used in a GvHD experiment. Gating-ML is a format standard of a digital entity that is conformant with the Gating-ML standard. (http://www.flowcyt.org/gating/) person:Jennifer Fostel web-page:http://www.flowcyt.org/gating/ Gating-ML OWL OBI ontology file, Basic Formal Ontology file, BIRNLex file, BioPAX file. OWL is a format standard of a digital entity that is conformant with the W3C Web Ontology Language specification.(http://www.w3.org/2004/OWL/) person:Jennifer Fostel web-page:http://www.w3.org/2004/OWL/ OWL Affymetrix Affymetrix supplied microarray An organization which supplies technology, tools and protocols for use in high throughput applications Affymetrix Thermo Philippe Rocca-Serra Thermo Waters Philippe Rocca-Serra Waters BIO-RAD Philippe Rocca-Serra BIO-RAD GenePattern hierarchical clustering James Malone GenePattern hierarchical clustering Ambion Philippe Rocca-Serra Ambion Helicos Philippe Rocca-Serra Helicos Roche Philippe Rocca-Serra Roche Illumina Philippe Rocca-Serra Illumina GenePattern PCA GenePattern PCA GenePattern module SVM GenePattern module SVM is a GenePattern software module which is used to run a support vector machine data transformation. James Malone Ryan Brinkman GenePattern module SVM GenePattern k-nearest neighbors James Malone GenePattern k-nearest neighbors GenePattern LOOCV GenePattern LOOCV GenePattern k-means clustering James Malone GenePattern k-means clustering Agilent Philippe Rocca-Serra Agilent GenePattern module KMeansClustering GenePattern module KMeansClustering is a GenePattern software module which is used to perform a k Means clustering data transformation. James Malone PERSON: James Malone GenePattern module KMeansClustering GenePattern CART James Malone GenePattern CART GenePattern module CARTXValidation GenePattern module CARTXValidation is a GenePattern software module which uses a CART decision tree induction with a leave one out cross validation data transformations. GenePattern module CARTXValidation Li-Cor Philippe Rocca-Serra Li-Cor Bruker Corporation Philippe Rocca-Serra Bruker Corporation GenePattern module KNNXValidation GenePattern module KNNXValidation is a GenePattern software module which uses a k-nearest neighbours clustering with a leave one out cross validation data transformations. James Malone PERSON: James Malone GenePattern module KNNXValidation GenePattern module PeakMatch GenePattern module PeakMatch GenePattern module KNN GenePattern module KNN is a GenePattern software module which perform a k-nearest neighbors data transformation. James Malone GenePattern module KNN GenePattern module HierarchicalClustering GenePattern module HierarchicalClustering is a GenePattern software module which is used to perform a hierarchical clustering data transformation. James Malone PERSON: James Malone GenePattern module HierarchicalClustering GenePattern SVM James Malone GenePattern SVM Applied Biosystems Philippe Rocca-Serra Applied Biosystems GenePattern module PCA GenePattern module PCA is a GenePattern software module which is used to perform a principal components analysis dimensionality reduction data transformation. James Malone PERSON: James Malone GenePattern module PCA GenePattern peak matching James Malone Ryan Brinkman GenePattern peak matching Bruker Daltonics Philippe Rocca-Serra Bruker Daltonics GenePattern HeatMapViewer data visualization The GenePattern process of generating Heat Maps from clustered data. James Malone GenePattern HeatMapViewer data visualization GenePattern HierarchicalClusteringViewer data visualization The GenePattern process of generating hierarchical clustering visualization from clustered data. James Malone GenePattern HierarchicalClusteringViewer data visualization GenePattern module HeatMapViewer A GenePattern software module which is used to generate a heatmap view of data. James Malone GenePattern module HeatMapViewer GenePattern module HierarchicalClusteringViewer A GenePattern software module which is used to generate a view of data that has been hierarchically clustered. James Malone GenePattern module HierarchicalClusteringViewer Sysmex Corporation, Kobe, Japan WEB:http://www.sysmex.com/@2009/08/06 2009/09/28 Alan Ruttenberg. Fucoidan-use-case Sysmex Corporation, Kobe, Japan U.S. Food and Drug Administration FDA U.S. Food and Drug Administration right handed right handed ambidexterous ambidexterous left handed left handed Edingburgh handedness inventory The Edinburgh Handedness Inventory is a set of questions used to assess the dominance of a person's right or left hand in everyday activities. PERSON:Alan Ruttenberg PERSON:Jessica Turner PMID:5146491#Oldfield, R.C. (1971). The assessment and analysis of handedness: The Edinburgh inventory. Neuropsychologia, 9, 97-113 WEB:http://www.cse.yorku.ca/course_archive/2006-07/W/4441/EdinburghInventory.html Edingburgh handedness inventory eBioscience A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.ebioscience.com/@2011/04/11 eBioscience Cytopeia A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.cytopeia.com/@2011/04/11 Cytopeia Exalpha Biological A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.exalpha.com/@2011/04/11 Exalpha Biological Apogee Flow Systems A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.apogeeflow.com/@2011/04/11 Apogee Flow Systems Exbio Antibodies A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.exbio.cz/@2011/04/11 Exbio Antibodies Becton Dickinson (BD Biosciences) A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.bdbiosciences.com/@2011/04/11 Becton Dickinson (BD Biosciences) Dako Cytomation A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.dakousa.com/@2011/04/11 Dako Cytomation Millipore A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.guavatechnologies.com/@2011/04/11 Millipore Antigenix A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.antigenix.com/@2011/04/11 Antigenix Partec A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.partec.de/@2011/04/11 Partec Beckman Coulter A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.beckmancoulter.com/@2011/04/11 Beckman Coulter Advanced Instruments Inc. (AI Companies) A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.aicompanies.com/@2011/04/11 Advanced Instruments Inc. (AI Companies) Miltenyi Biotec A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.miltenyibiotec.com/@2011/04/11 Miltenyi Biotec AES Chemunex A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.aeschemunex.com/@2011/04/11 AES Chemunex Bentley Instruments A supplier of flow cytometry analyzers Karin Breuer WEB:http://bentleyinstruments.com/@2011/04/11 Bentley Instruments Invitrogen A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.invitrogen.com/@2011/04/11 Invitrogen Luminex A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.luminexcorp.com/@2011/04/11 Luminex CytoBuoy A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.cytobuoy.com/@2011/04/11 CytoBuoy Nimblegen An organization that focuses on manufacturing target enrichment probe pools for DNA sequencing. Person: Jie Zheng Nimblegen Pacific Biosciences An organization that supplies tools for studying the synthesis and regulation of DNA, RNA and protein. It developed a powerful technology platform called single molecule real-time (SMRT) technology which enables real-time analysis of biomolecules with single molecule resolution. Person: Jie Zheng Pacific Biosciences NanoString Technologies An organization that supplies life science tools for translational research and molecular diagnostics based on a novel digital molecular barcoding technology. The NanoString platform can provide simple, multiplexed digital profiling of single molecules. NanoString Technologies Thermo Fisher Scientific An organization that is an American multinational, biotechnology product development company, created in 2006 by the merger of Thermo Electron and Fisher Scientific. Chris Stoeckert, Helena Ellis https://en.wikipedia.org/wiki/Thermo_Fisher_Scientific NCI BBRB Thermo Fisher Scientific G1: Well differentiated A histologic grade according to AJCC 7th edition indicating that the tumor cells and the organization of the tumor tissue appear close to normal. Chris Stoeckert, Helena Ellis G1 https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet NCI BBRB G1: Well differentiated G2: Moderately differentiated A histologic grade according to AJCC 7th edition indicating that the tumor cells are moderately differentiated and reflect an intermediate grade. Chris Stoeckert, Helena Ellis G2 https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet NCI BBRB G2: Moderately differentiated G3: Poorly differentiated A histologic grade according to AJCC 7th edition indicating that the tumor cells are poorly differentiated and do not look like normal cells and tissue. Chris Stoeckert, Helena Ellis G3 https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet NCI BBRB G3: Poorly differentiated G4: Undifferentiated A histologic grade according to AJCC 7th edition indicating that the tumor cells are undifferentiated and do not look like normal cells and tissue. Chris Stoeckert, Helena Ellis G4 https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet NCI BBRB G4: Undifferentiated G1 (Fuhrman) A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are round, uniform, approximately 10um and that nucleoli are inconspicuous or absent. Chris Stoeckert, Helena Ellis Grade 1 NCI BBRB, OBI NCI BBRB G1 (Fuhrman) G2 (Fuhrman) A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are slightly irregular, approximately 15um and nucleoli are evident. Chris Stoeckert, Helena Ellis Grade 2 NCI BBRB, OBI NCI BBRB G2 (Fuhrman) G3 (Fuhrman) A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are very irregular, approximately 20um and nucleoli large and prominent. Chris Stoeckert, Helena Ellis Grade 3 NCI BBRB, OBI NCI BBRB G3 (Fuhrman) G4 (Fuhrman) A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei arei bizarre and multilobulated, 20um or greater and nucleoli are prominent and chromatin clumped. Chris Stoeckert, Helena Ellis Grade 4 NCI BBRB, OBI NCI BBRB G4 (Fuhrman) Low grade ovarian tumor A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is low grade. Chris Stoeckert, Helena Ellis Low grade NCI BBRB, OBI NCI BBRB Low grade ovarian tumor High grade ovarian tumor A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is high grade. Chris Stoeckert, Helena Ellis High grade NCI BBRB, OBI NCI BBRB High grade ovarian tumor G1 (WHO) A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is well differentiated. Chris Stoeckert, Helena Ellis G1 NCI BBRB, OBI NCI BBRB G1 (WHO) G2 (WHO) A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is moderately differentiated. Chris Stoeckert, Helena Ellis G2 NCI BBRB, OBI NCI BBRB G2 (WHO) G3 (WHO) A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is poorly differentiated. Chris Stoeckert, Helena Ellis G3 NCI BBRB, OBI NCI BBRB G3 (WHO) G4 (WHO) A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is undifferentiated. Chris Stoeckert, Helena Ellis G4 NCI BBRB, OBI NCI BBRB G4 (WHO) pT0 (colon) A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that there is no evidence of primary tumor. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ NCI BBRB pT0 (colon) pTis (colon) A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating carcinoma in situ (intraepithelial or invasion of lamina propria). Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ NCI BBRB pTis (colon) pT1 (colon) A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades submucosa. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ NCI BBRB pT1 (colon) pT2 (colon) A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades muscularis propria. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ NCI BBRB pT2 (colon) pT3 (colon) A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades subserosa or into non-peritionealized pericolic or perirectal tissues. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ NCI BBRB pT3 (colon) pT4a (colon) A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor perforates visceral peritoneum. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ NCI BBRB pT4a (colon) pT4b (colon) A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor directly invades other organs or structures. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ NCI BBRB pT4b (colon) pT0 (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that there is no evidence of primary tumor. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB pT0 (lung) pTis (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating carcinoma in situ. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB pTis (lung) pT1 (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 3 cm or less in greatest dimension, surrounded by lung or visceral pleura without bronchoscopic evidence of invasion more proximal than the lobar bronchus (i.e., not in the main bronchus). Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB pT1 (lung) pT1a (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 2 cm or less in greatest dimension. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB pT1a (lung) pT1b (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 2 cm but not more than 3 cm in greatest dimension. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB pT1b (lung) pT2 (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 7 cm or the tumor has any of the following features: involves main bronchus, 2 cm or more distal to the carina, invades visceral pleura, associated with atelectasis or obstructive pneumonitis that extends to the hilar region but does not involve the entire lung. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB pT2 (lung) pT2a (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 5 cm in greatest dimension. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB pT2a (lung) pT2b (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 5 cm but not more than 7 cm in greatest dimension. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB pT2b (lung) pT3 (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 7 cm or one that directly invades any of: parietal pleura, chest wall (including superior sulcus tumors), diaphragm, phrenic nerve, mediastinal pleura, parietal pericardiu or the tumor is in the main bronchus less than 2 cm distal to the carina but without involvement of the carina or there is associated atelectasis or obstructive pneumonitis of the entire lung or there is separate tumor nodule(s) in the same lobe as the primary. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB pT3 (lung) pT4 (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor of any size that invades any of the following: mediastinum, heart, great vessels, trachea, recurrent laryngeal nerve, esophagus, vertebral body, carina or there is separate tumor nodule(s) in a different ipsilateral lobe to that of the primary. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB pT4 (lung) pT0 (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that there is no evidence of primary tumor. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT0 (kidney) pT1 (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 7 cm or less in greatest dimension and limited to the kidney. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT1 (kidney) pT1a (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 4 cm or less. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT1a (kidney) pT1b (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 4 cm but not more than 7 cm. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT1b (kidney) pT2 (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm in greatest dimension and limited to the kidney. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT2 (kidney) pT2a (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm but not more than 10 cm. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT2a (kidney) pT2b (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 10 cm and limited to the kidney. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT2b (kidney) pT3 (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor extends into major veins or perinephric tissues but not into the ipsilateral adrenal gland and not beyond the Gerota fascia. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT3 (kidney) pT3a (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into the renal vein or its segmental (muscle containing) branches, or the tumor invades perirenal and/or renal sinus fat (peripelvic) fat but not beyond Gerota fascia. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT3a (kidney) pT3b (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava below diaphragm. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT3b (kidney) pT3c (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava above the diaphragm or Invades the wall of the vena cava. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT3c (kidney) pT4 (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor invades beyond Gerota fascia (including contiguous extension into the ipsilateral adrenal gland). Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT4 (kidney) pT0 (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that there is no evidence of primary tumor. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT0 (ovary) pT1 (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to the ovaries (one or both). Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT1 (ovary) pT1a (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one ovary; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT1a (ovary) pT1b (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to both ovaries; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT1b (ovary) pT1c (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one or both ovaries with capsule ruptured, tumor on ovarian surface, or malignant cells in ascites or peritoneal washings. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT1c (ovary) pT2 (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with pelvic extension. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT2 (ovary) pT2a (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension and/or implants on uterus and/or tube(s) and no malignant cells in ascites or peritoneal washings. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT2a (ovary) pT2b (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension to other pelvic tissues and no malignant cells in ascites or peritoneal washings. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT2b (ovary) pT2c (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has pelvic extension with malignant cells in ascites or peritoneal washings. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT2c (ovary) pT3 (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with microscopically confirmed peritoneal metastasis outside the pelvis and/or regional lymph node metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT3 (ovary) pT3a (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has microscopic peritoneal metastasis beyond pelvis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT3a (ovary) pT3b (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has macroscopic peritoneal, metastatasis beyond pelvis, 2 cm or less in greatest dimension. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT3b (ovary) pT3c (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has peritoneal metastasis beyond pelvis, more than 2 cm in greatest dimension and/or regional lymph node metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT3c (ovary) pN0 (colon) A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating no regional lymph node metastsis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ NCI BBRB pN0 (colon) pN1 (colon) A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1-3 regional lymph nodes. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ NCI BBRB pN1 (colon) pN1a (colon) A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1 regional lymph node. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ NCI BBRB pN1a (colon) pN1b (colon) A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 2-3 regional lymph nodes. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ NCI BBRB pN1b (colon) pN1c (colon) A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating tumor deposit(s), i.e., satellites in the subserosa, or in non-peritonealized pericolic or perirectal soft tissue without regional lymph node metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ NCI BBRB pN1c (colon) pN2 (colon) A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 or more regional lymph nodes. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ NCI BBRB pN2 (colon) pN2a (colon) A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 to 6 regional lymph nodes. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ NCI BBRB pN2a (colon) pN2b (colon) A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 7 or more regional lymph nodes. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ NCI BBRB pN2b (colon) pN0 (lung) A pathologic lymph node stage for lung according to AJCC 7th edition indicating no regional lymph node metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/ NCI BBRB pN0 (lung) pN1 (lung) A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral peribronchial and/or ipsilateral hilar lymph nodes and intrapulmonary nodes, including involvement by direct extension. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/ NCI BBRB pN1 (lung) pN2 (lung) A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral mediastinal and/or subcarinal lymph node(s). Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/ NCI BBRB pN2 (lung) pN3 (lung) A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in contralateral mediastinal, contralateral hilar, ipsilateral or contralateral scalene, or supraclavicular lymph node(s). Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/ NCI BBRB pN3 (lung) pN0 (kidney) A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is no regional lymph node metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_n/ NCI BBRB pN0 (kidney) pN1 (kidney) A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is regional lymph node metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_n/ NCI BBRB pN1 (kidney) pN0 (ovary) A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is no regional lymph node metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_n/ NCI BBRB pN0 (ovary) pN1 (ovary) A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is regional lymph node metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_n/ NCI BBRB pN1 (ovary) cM0 (colon) A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there are no symptoms or signs of distant metastasis. Chris Stoeckert, Helena Ellis https://en.wikipedia.org/wiki/Cancer_staging#Pathological_M_Categorization_.28cM_and_pM.29 NCI BBRB cM0 (colon) cM1 (colon) A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is clinical evidence of distant metastases by history, physical examination, imaging studies, or invasive procedures, but without microscopic evidence of the presumed distant metastases. Chris Stoeckert, Helena Ellis https://en.wikipedia.org/wiki/Cancer_staging#Pathological_M_Categorization_.28cM_and_pM.29 NCI BBRB cM1 (colon) cM1a (colon) A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ based on clinical assessment. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ NCI BBRB cM1a (colon) cM1b (colon) A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum based on clinical assessment. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ NCI BBRB cM1b (colon) pM1 (colon) A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is microscopic evidence confirming distant metastatic disease. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ NCI BBRB pM1 (colon) pM1a (colon) A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ and histologically confirmed. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ NCI BBRB pM1a (colon) pM1b (colon) A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum and histologically confirmed. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ NCI BBRB pM1b (colon) cM0 (lung) A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is no distant metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ NCI BBRB cM0 (lung) cM1 (lung) A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ NCI BBRB cM1 (lung) cM1a (lung) A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is based on clinical assessment and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ NCI BBRB cM1a (lung) cM1b (lung) A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases based on clinical assessment. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ NCI BBRB cM1b (lung) pM1 (lung) A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ NCI BBRB pM1 (lung) pM1a (lung) A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is histologically confirmed and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ NCI BBRB pM1a (lung) pM1b (lung) A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ NCI BBRB pM1b (lung) cM0 (kidney) A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is no distant metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/ NCI BBRB cM0 (kidney) cM1 (kidney) A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/ NCI BBRB cM1 (kidney) pM1 (kidney) A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/ NCI BBRB pM1 (kidney) cM0 (ovary) A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is no distant metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/ NCI BBRB cM0 (ovary) cM1 (ovary) A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis based on clinical assessment. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/ NCI BBRB cM1 (ovary) pM1 (ovary) A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis that is histologically confirmed. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/ NCI BBRB pM1 (ovary) Occult Carcinoma (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating a small carcinoma, either asymptomatic or giving rise to metastases without symptoms due to the primary carcinoma. Chris Stoeckert, Helena Ellis Occult Carcinoma http://www.medilexicon.com/dictionary/14371 NCI BBRB Occult Carcinoma (AJCC 7th) Stage 0 (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating a carcinoma in situ (or melanoma in situ for melanoma of the skin or germ cell neoplasia in situ for testicular germ cell tumors) and generally is considered to have no metastatic potential. Chris Stoeckert, Helena Ellis Stage 0 https://en.wikipedia.org/wiki/Cancer_staging NCI BBRB Stage 0 (AJCC 7th) Stage I (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating cancers that are smaller or less deeply invasive without regional disease or nodes. Chris Stoeckert, Helena Ellis Stage I https://en.wikipedia.org/wiki/Cancer_staging NCI BBRB Stage I (AJCC 7th) Stage IIA (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIB and IIC. Chris Stoeckert, Helena Ellis Stage IIA https://en.wikipedia.org/wiki/Cancer_staging NCI BBRB Stage IIA (AJCC 7th) Stage IIB (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIC. Chris Stoeckert, Helena Ellis Stage IIB https://en.wikipedia.org/wiki/Cancer_staging NCI BBRB Stage IIB (AJCC 7th) Stage IIC (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIB. Chris Stoeckert, Helena Ellis Stage IIC https://en.wikipedia.org/wiki/Cancer_staging NCI BBRB Stage IIC (AJCC 7th) Stage IIIA (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIB and IIIC. Chris Stoeckert, Helena Ellis Stage IIIA https://en.wikipedia.org/wiki/Cancer_staging NCI BBRB Stage IIIA (AJCC 7th) Stage IIIB (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIC. Chris Stoeckert, Helena Ellis Stage IIIB https://en.wikipedia.org/wiki/Cancer_staging NCI BBRB Stage IIIB (AJCC 7th) Stage IIIC (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIB. Chris Stoeckert, Helena Ellis Stage IIIC https://en.wikipedia.org/wiki/Cancer_staging NCI BBRB Stage IIIC (AJCC 7th) Stage IVA (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVB. Chris Stoeckert, Helena Ellis Stage IVA https://en.wikipedia.org/wiki/Cancer_staging NCI BBRB Stage IVA (AJCC 7th) Stage IVB (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVA. Chris Stoeckert, Helena Ellis Stage IVB https://en.wikipedia.org/wiki/Cancer_staging NCI BBRB Stage IVB (AJCC 7th) Stage IA (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating invasive carcinoma which can be diagnosed only by microscopy, with deepest invasion <5 mm and the largest extension <7 mm. Chris Stoeckert, Helena Ellis Stage IA https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IA (FIGO) Stage IA1 (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of <3.0 mm in depth and extension of <7.0 mm. Chris Stoeckert, Helena Ellis Stage IA1 https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IA1 (FIGO) Stage IA2 (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of >3.0 mm and not >5.0 mm with an extension of not >7.0 mm. Chris Stoeckert, Helena Ellis Stage IA2 https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IA2 (FIGO) Stage IB (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesions limited to the cervix uteri or pre-clinical cancers greater than stage IA Chris Stoeckert, Helena Ellis Stage IB https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IB (FIGO) Stage IB1 (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA <4.0 cm in greatest dimension. Chris Stoeckert, Helena Ellis Stage IB1 https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IB1 (FIGO) Stage IB2 (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA >4.0 cm in greatest dimension. Chris Stoeckert, Helena Ellis Stage IB2 https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IB2 (FIGO) Stage IIA (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion. Chris Stoeckert, Helena Ellis Stage IIA https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IIA (FIGO) Stage IIA1 (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion <4.0 cm in greatest dimension. Chris Stoeckert, Helena Ellis Stage IIA1 https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IIA1 (FIGO) Stage IIA2 (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion >4.0 cm in greatest dimension. Chris Stoeckert, Helena Ellis Stage IIA2 https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IIA2 (FIGO) Stage IIB (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina with obvious parametrial invasion. Chris Stoeckert, Helena Ellis Stage IIB https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IIB (FIGO) Stage IIIA (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating tumour involves lower third of the vagina, with no extension to the pelvic wall. Chris Stoeckert, Helena Ellis Stage IIIA https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IIIA (FIGO) Stage IIIB (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating extension to the pelvic wall and/or hydronephrosis or non-functioning kidney. Chris Stoeckert, Helena Ellis Stage IIIB https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IIIB (FIGO) Stage IVA (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread of the growth to adjacent organs. Chris Stoeckert, Helena Ellis Stage IVA https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IVA (FIGO) Stage IVB (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread to distant organs. Chris Stoeckert, Helena Ellis Stage IVB https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IVB (FIGO) Stage 1 (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1, N0, and M0. Chris Stoeckert, Helena Ellis Stage 1 https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 1 (FIGO) Stage 1A (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1a, N0, and M0. Chris Stoeckert, Helena Ellis Stage 1A https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 1A (FIGO) Stage 1B (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1b, N0, and M0. Chris Stoeckert, Helena Ellis Stage 1B https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 1B (FIGO) Stage 1C (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1c, N0, and M0. Chris Stoeckert, Helena Ellis Stage 1C https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 1C (FIGO) Stage 2 (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2, N0, and M0. Chris Stoeckert, Helena Ellis Stage 2 https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 2 (FIGO) Stage 2A (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2a, N0, and M0. Chris Stoeckert, Helena Ellis Stage 2A https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 2A (FIGO) Stage 2B (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2b, N0, and M0. Chris Stoeckert, Helena Ellis Stage 2B https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 2B (FIGO) Stage 2C (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2c, N0, and M0. Chris Stoeckert, Helena Ellis Stage 2C https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 2C (FIGO) Stage 3 (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3, N0, and M0) or (T3,3a,3b, NX, and M0). Chris Stoeckert, Helena Ellis Stage 3 https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 3 (FIGO) Stage 3A (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3a, N0, and M0 . Chris Stoeckert, Helena Ellis Stage 3A https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 3A (FIGO) Stage 3B (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3b, N0, and M0 . Chris Stoeckert, Helena Ellis Stage 3B https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 3B (FIGO) Stage 3C (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3c, N0,X and M0) or (any T, N1 and M0). Chris Stoeckert, Helena Ellis Stage 3C https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 3C (FIGO) Stage 4 (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of any T, any N, and M1. Chris Stoeckert, Helena Ellis Stage 4 https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 4 (FIGO) Stage Unknown (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T0, N0, and M0) or (T1,1a-1c,2,2a-2c, NX, and M0) or (TX, N0,X, M0). Chris Stoeckert, Helena Ellis Stage Unknown https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage Unknown (FIGO) 3: symptomatic in bed more than 50% of the day but not bed ridden An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and in bed for more than 50% of the day but is not bed ridden. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB 3: symptomatic in bed more than 50% of the day but not bed ridden 2: symptomatic but in bed less than 50% of the day An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is in bed for less than 50% of the day. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB 2: symptomatic but in bed less than 50% of the day 4: bed ridden An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and is bed ridden. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB 4: bed ridden 0: asymptomatic An Eastern Cooperative Oncology Group score value specification indicating a patient is asymptomatic. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB 0: asymptomatic 1: symptomatic but fully ambulatory An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is fully ambulatory. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB 1: symptomatic but fully ambulatory 100: asymptomatic A Karnofsky score vaue specification indicating that a patient is asymptomatic. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB 100: asymptomatic 80-90: symptomatic but fully ambulatory A Karnofsky score vaue specification indicating that a patient is symptomatic but fully ambulatory. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB 80-90: symptomatic but fully ambulatory 60-70: symptomatic but in bed less than 50% of the day A Karnofsky score vaue specification indicating that a patient is symptomatic but in bed less than 50% of the day. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB 60-70: symptomatic but in bed less than 50% of the day 40-50: symptomatic, in bed more than 50% of the day, but not bed ridden A Karnofsky score vaue specification indicating that a patient is symptomatic, in bed more than 50% of the day, but not bed ridden. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB 40-50: symptomatic, in bed more than 50% of the day, but not bed ridden ## Elucidation This is used when the statement/axiom is assumed to hold true 'eternally' ## How to interpret (informal) First the "atemporal" FOL is derived from the OWL using the standard interpretation. This axiom is temporalized by embedding the axiom within a for-all-times quantified sentence. The t argument is added to all instantiation predicates and predicates that use this relation. ## Example Class: nucleus SubClassOf: part_of some cell forall t : forall n : instance_of(n,Nucleus,t) implies exists c : instance_of(c,Cell,t) part_of(n,c,t) ## Notes This interpretation is *not* the same as an at-all-times relation axiom holds for all times meter A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second. m meter kilogram A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France. kg kilogram second A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom. s sec second centimeter A length unit which is equal to one hundredth of a meter or 10^[-2] m. cm centimeter millimeter A length unit which is equal to one thousandth of a meter or 10^[-3] m. mm millimeter micrometer A length unit which is equal to one millionth of a meter or 10^[-6] m. um micrometer nanometer A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m. nm nanometer angstrom A length unit which is equal to 10 [-10] m. angstrom gram A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg. g gram milligram A mass unit which is equal to one thousandth of a gram or 10^[-3] g. mg milligram microgram A mass unit which is equal to one millionth of a gram or 10^[-6] g. ug microgram nanogram A mass unit which is equal to one thousandth of one millionth of a gram or 10^[-9] g. ng nanogram picogram A mass unit which is equal to 10^[-12] g. pg picogram degree Celsius A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K. C degree C degree Celsius minute A time unit which is equal to 60 seconds. min minute hour A time unit which is equal to 3600 seconds or 60 minutes. h hr hour day A time unit which is equal to 24 hours. day week A time unit which is equal to 7 days. week month A time unit which is approximately equal to the length of time of one of cycle of the moon's phases which in science is taken to be equal to 30 days. month year A time unit which is equal to 12 months which is science is taken to be equal to 365.25 days. year micromole A substance unit equal to a millionth of a mol or 10^[-6] mol. umol micromole nanomole A substance unit equal to one thousandth of one millionth of a mole or 10^[-9] mol. nmol nanomole picomole A substance unit equal to 10^[-12] mol. pmol picomole molar A unit of concentration which expresses a concentration of 1 mole of solute per liter of solution (mol/L). M molar millimolar A unit of molarity which is equal to one thousandth of a molar or 10^[-3] M. mM millimolar micromolar A unit of molarity which is equal to one millionth of a molar or 10^[-6] M. uM micromolar nanomolar A unit of molarity which is equal to one thousandth of one millionth of a molar or 10^[-9] M. nM nanomolar picomolar A unit of molarity which is equal to 10^[-12] M. pM picomolar cubic centimeter A volume unit which is equal to one millionth of a cubic meter or 10^[-9] m^[3], or to 1 ml. cc cubic centimeter milliliter A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter. ml milliliter liter A volume unit which is equal to one thousandth of a cubic meter or 10^[-3] m^[3], or to 1 decimeter. L liter cubic decimeter A volume unit which is equal to one thousand of a cubic meter or 10^[-3] m^[3], or to 1 L. cubic decimeter microliter A volume unit which is equal to one millionth of a liter or 10^[-6] L. ul microliter nanoliter A volume unit which is equal to one thousandth of one millionth of a liter or 10^[-9] L. nl nanoliter picoliter A volume unit which is equal to 10^[-12] L. pl picoliter hertz A frequency unit which is equal to 1 complete cycle of a recurring phenomenon in 1 second. hertz mass percentage A dimensionless concentration unit which denotes the mass of a substance in a mixture as a percentage of the mass of the entire mixture. % w/w percent weight pr weight mass percentage mass volume percentage A dimensionless concentration unit which denotes the mass of the substance in a mixture as a percentage of the volume of the entire mixture. % w/v percent vol per vol mass volume percentage volume percentage A dimensionless concentration unit which denotes the volume of the solute in mL per 100 mL of the resulting solution. % v/v percent vol per vol volume percentage gram per liter A mass unit density which is equal to mass of an object in grams divided by the volume in liters. g per L g/L gram per liter milligram per milliliter A mass unit density which is equal to mass of an object in milligrams divided by the volume in milliliters. mg per ml mg/ml milligram per milliliter degree Fahrenheit A temperature unit which is equal to 5/9ths of a kelvin. Negative 40 degrees Fahrenheit is equal to negative 40 degrees Celsius. degree Fahrenheit pH A dimensionless concentration notation which denotes the acidity of a solution in terms of activity of hydrogen ions (H+). pH milliliter per liter A volume per unit volume unit which is equal to one millionth of a liter of solute in one liter of solution. ml per L ml/l milliliter per liter gram per deciliter A mass density unit which is equal to mass of an object in grams divided by the volume in deciliters. g/dl gram per deciliter colony forming unit per volume A concentration unit which a measure of viable bacterial numbers in a given volume. colony forming unit per volume microliters per minute A volumetric flow rate unit which is equal to one microliter volume through a given surface in one minute. microliters per minute count per nanomolar second A rate unit which is equal to one over one nanomolar second. count per nanomolar second count per molar second A rate unit which is equal to one over one molar second. count per molar second count per nanomolar A rate unit which is equal to one over one nanomolar. count per nanomolar count per molar A rate unit which is equal to one over one molar. count per molar microgram per liter A mass unit density which is equal to mass of an object in micrograms divided by the volume in liters. ng/ml ug/L microgram per liter Person:Alan Ruttenberg disposition Disposition the cell wall is disposed to filter chemicals in endocitosis and exocitosis the cell wall is disposed to filter chemicals in endocytosis and exocytosis 倾向 BFO 2参考：倾向存在于强度连续体中。只有一小部分触发事件才能实现较弱的倾向形式。这些形式出现在相当数量的类似案例中。 (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] 如果b是一个可实现的实体，那么对于存在b的所有t时刻，b s-依赖_于t时刻的一个物质实体。 （BFO2公理标签参考：[063-002]） an atom of element X has the disposition to decay to an atom of element Y certain people have a predisposition to colon cancer (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] children are innately disposed to categorize objects in certain ways. 某些人有结肠癌的倾向 b是倾向方式：b是可实现的实体； b的持有人是一些物质实体； b是这样的，如果它不复存在，那么它的持有人发生了物理变化； b的实现发生在且因为这个持有者处于一些特殊的物理环境中；这种实现是由于持有者的物理构成而发生的。 （BFO2公理标签参考：[062-002]） 倾向 细胞壁被设置为过滤内吞作用和胞吐作用中的化学物质 倾向 (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] 元素X的原子具有衰减到元素Y的原子的倾向 Disposition b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) disposition 孩子天生就倾向于以特定的方式对物体进行分类。 倾向 If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. disposition BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type [89 disposition (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) To say that each spatiotemporal region s temporally_projects_onto some temporal region t is to say that t is the temporal extension of s. (axiom label in BFO2 Reference: [080-003]) To say that spatiotemporal region s spatially_projects_onto spatial region r at t is to say that r is the spatial extent of s at t. (axiom label in BFO2 Reference: [081-003]) To say that each spatiotemporal region s temporally_projects_onto some temporal region t is to say that t is the temporal extension of s. (axiom label in BFO2 Reference: [080-003]) To say that spatiotemporal region s spatially_projects_onto spatial region r at t is to say that r is the spatial extent of s at t. (axiom label in BFO2 Reference: [081-003]) GROUP:OBI:<http://purl.obolibrary.org/obo/obi> For external terms/classes, the ontology from which the term was imported 引自 PERSON:Melanie Courtot imported from imported from 引自 imported from 外部术语/类，术语引入的本体 PERSON:Alan Ruttenberg 引自 A disposition of a pathogen becoming harmless or less virulent towards its host, when the pathogen is altered physically or genetically. This disposition is realized in the process of the pathogen-host interaction. It is host dependent, or host specific. YL, Y.H. attenuated disposition http://en.wikipedia.org/wiki/Attenuated_vaccine has_specified_input PERSON: Alan Ruttenberg 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. see is_input_of example_of_usage PERSON: Melanie Coutot PERSON: Larry Hunter has_specified_input A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. has_specified_input PERSON: Bjoern Peters has_specified_input has_specified_output PERSON: Melanie Courtot PERSON: Bjoern Peters A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. has_specified_output has_specified_output PERSON: Alan Ruttenberg has_specified_output PERSON: Larry Hunter this person has role this investigator role (more colloquially: this person has this role of investigator) RO:0000087 false A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence has_role has role protein has_role false has role has_role has_role chebi_ontology true MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z infer input from direct reg GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' enabling an MF enables its parts true GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' involved in BP From ligand activity to has_ligand This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to "... -> overlaps" If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. inferring direct reg edge from input to regulatory subfunction inferring direct neg reg edge from input to regulatory subfunction inferring direct positive reg edge from input to regulatory subfunction From has_ligand to ligand activity effector input is compound function input Input of effector is input of its parent MF if effector directly regulates X, its parent MF directly regulates X if effector directly positively regulates X, its parent MF directly positively regulates X if effector directly negatively regulates X, its parent MF directly negatively regulates X 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).