Becky Steck Christopher Park John F. O’Toole Matthias Kretzler Sean Mooney Anthony Huffman Asiyah Yu Lin Fred Dowd Hong Yu Hong Yu Jennifer Schaub Jie Zheng Long Tran Qingliang Leon Li Suyuan Peng Yongqun "Oliver" He (YH) 3-15-2024 OPMI is a biomedical ontology in the area of precision medicine and its related investigations. It is community-driven and developed by following the OBO Foundry ontology development principles. OWL-DL OPMI subject: Precision medicine and related investigations OPMI: Ontology of Precision Medicine and Investigation http://creativecommons.org/licenses/by/4.0/ Vision Release: 1.0.166 BFO OWL specification label 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. Really of interest to developers only BFO OWL specification label BFO OWL specification label BFO CLIF specification label Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 Person:Alan Ruttenberg Really of interest to developers only BFO CLIF specification label BFO CLIF specification label editor preferred label editor preferred label editor preferred term editor preferred term editor preferred term~editor preferred label The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) 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 example example of usage 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. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> example of usage example of usage has curation status PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot OBI_0000281 has curation status has curation status definition definition textual definition English language definitions of what NCI means by the concept. These are limited to 1024 characters. They may also include information about the definition's source and attribution in a form that can easily be interpreted by software. 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. 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 definition textual definition editor note 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. PERSON:Daniel Schober GROUP:OBI:<http://purl.obfoundry.org/obo/obi> GROUP:OBI:<http://purl.obofoundry.org/obo/obi> IAO:0000116 uberon editor_note 1 editor_note editor note editor note definition editor term editor 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 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. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition editor definition editor term editor term editor alternative term An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> alternative term alternative term definition source 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 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> definition source definition source 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 An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg IAO:0000232 uberon curator_notes 1 curator_notes curator note curator note curator notes term tracker item term tracker item the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ 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. 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 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. The 'tracker item' can associate a tracker with a specific ontology term. term tracker item ontology term requester 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 imported from For external terms/classes, the ontology from which the term was imported PERSON:Alan Ruttenberg PERSON:Melanie Courtot GROUP:OBI:<http://purl.obolibrary.org/obo/obi> imported from imported from expand expression to expand expression to expand assertion 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 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 elucidation elucidation has associated axiom(nl) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom associated with a term expressed using natural language has associated axiom(nl) has associated axiom(nl) has associated axiom(fol) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom expressed in first order logic using CLIF syntax has associated axiom(fol) has associated axiom(fol) C3829466 NCIT_C106180 term_mapping_to_UMLS term_mapping_to_NCIT A property created to allow the source NICHD to assign a parent to each concept with the intent of creating a hierarchy that includes only terms in which they are the contributing source. A11 Conceptual Entity Has_NICHD_Parent Has_NICHD_Parent Has_NICHD_Parent true NHC0 code code code The semantic type describes the sort of thing or category to which a concept belongs in the context of the UMLS semantic network. P106 Conceptual Entity Semantic Type Semantic_Type In general, applying semantic types aids in allowing users (or computer programs) to draw conclusions about concepts by virtue of the categories to which they have been assigned. We use a set of semantic types developed for the UMLS Metathesaurus. There are currently 134 semantic types in the UMLS. Semantic_Type Semantic_Type Provides an alternative Preferred Name for use in some NCI systems. P107 Conceptual Entity Display Name Display_Name Display Name Display_Name Display_Name The word or phrase that NCI uses by preference to refer to the concept. P108 Conceptual Entity Preferred Name Preferred_Name Preferred Name Preferred Term Preferred_Name Preferred_Name Concept Unique Identifiers, or CUIs, are concept numbers assigned by the National Library of Medicine (NLM). If a concept in any NCI-maintained knowledgebase exists in the NLM Unified Medical Language System (UMLS), NCI includes the NLM CUI among the information we provide about the concept. P207 Conceptual Entity UMLS CUI UMLS_CUI UMLS_CUI UMLS_CUI Contains a Concept Unique Identifier for those concepts that appear in NCI Metathesaurus but not in the NLM UMLS. P208 Conceptual Entity NCI Metathesaurus CUI NCI_META_CUI NCI_META_CUI NCI_META_CUI An NCI Thesaurus property used to indicate the standing of a concept in relation to currently accepted classifications and concepts. In NCI Thesaurus concept status subtype indicates concepts with unusual and problematic characteristics that should be evaluated by people and/or programs before those concept are used. P310 Conceptual Entity Concept Status Concept_Status Concept_Status Concept_Status This property is used to indicate when a non-EVS entity has contributed to, and has a stake in, a concept. This is used where such entities, within or outside NCI, have indicated the need to be able to track their own concepts. A single concept can have multiple instances of this property if multiple entities have such a defined stake. P322 Conceptual Entity Contributing Source Contributing_Source Contributing_Source Contributing_Source English language definitions of what a source other than NCI means by the concept. These are limited to 1024 characters. They include information about the definition's source in a form that can easily be interpreted by software. P325 Conceptual Entity [source] Definition ALT_DEFINITION ALT_DEFINITION ALT_DEFINITION true A retired unique concept identifier created and stored as Concept Name by legacy EVS software. Use of these values was long discouraged, but continued as late as 2009 when creation of new values ceased and Concept Name was retired. Legacy values are intended solely to help resolve and update earlier coding. P366 Conceptual Entity Legacy Concept Name Legacy Concept Name Legacy_Concept_Name P371 Conceptual Entity NICHD_Hierarchy_Term NICHD NICHD_Hierarchy_Term NICHD_Hierarchy_Term Design notes are notations made by NCI vocabulary curators. They are intended to provide supplemental, unstructured information to the user or additional insight about the concept. P98 Conceptual Entity DesignNote DesignNote DesignNote DesignNote has_MedDRA_id ISA alternative term An alternative term used by the ISA tools project (http://isa-tools.org). Requested by Alejandra Gonzalez-Beltran https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891&atid=886178 Person: Alejandra Gonzalez-Beltran Person: Philippe Rocca-Serra ISA tools project (http://isa-tools.org) ISA alternative term NIAID GSCID-BRC alternative term An alternative term used by the National Institute of Allergy and Infectious Diseases (NIAID) Genomic Sequencing Centers for Infectious Diseases (GSCID) and Bioinformatics Resource Centers (BRC). PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group NIAID GSCID-BRC alternative term IEDB alternative term An alternative term used by the IEDB. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IEDB alternative term A subproperty of seeAlso that represents a NCIT identifier mapped to the specified term Oliver He term mapping to NCIT ID A subproperty of seeAlso that represents a UMLS CUI identifier mapped to the specified term Oliver He term mapping to UMLS CUI An annotation property that refers to a code defined by NCIT NCIT code alternative term in Chinese 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 temporal interpretation https://oborel.github.io/obo-relations/temporal-semantics/ https://code.google.com/p/obo-relations/wiki/ROAndTime https://github.com/oborel/obo-relations/wiki/ROAndTime tooth SubClassOf 'never in taxon' value 'Aves' x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL. Chris Mungall ?X DisjointWith RO_0002162 some ?Y never in taxon An assertion that holds between an ontology class and an organism taxon class, which is intepreted to yield some relationship between instances of the ontology class and the taxon. taxonomic class assertion S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T. RO:0002174 uberon dubious_for_taxon 1 1 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 time to resolve. Example: metencephalon in teleost dubious_for_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 RO:0002175 applicable for taxon uberon present_in_taxon 1 1 present_in_taxon present_in_taxon An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL. logical macro assertion https://github.com/oborel/obo-relations/wiki/ShortcutRelations A logical macro assertion whose domain is an IRI for a class The domain for this class can be considered to be owl:Class, but we cannot assert this in OWL2-DL logical macro assertion on a class A logical macro assertion whose domain is an IRI for a property logical macro assertion on a 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 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 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 1 external_definition This annotation property may be replaced with an annotation property from an external ontology such as IAO external_definition A textual description of an axiom loss in this ontology compared to an external ontology. UBPROP:0000002 uberon axiom_lost_from_external_ontology 1 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 Notes on the homology status of this class. UBPROP:0000003 uberon homology_notes 1 homology_notes This annotation property may be replaced with an annotation property from an external ontology such as IAO homology_notes 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 1 has_relational_adjective has_relational_adjective Notes on the how instances of this class vary across species. UBPROP:0000008 uberon taxon_notes 1 taxon_notes taxon_notes 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 1 structure_notes structure_notes 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 1 development_notes development_notes 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 1 external_ontology_notes external_ontology_notes 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 1 terminology_notes terminology_notes A metadata relation between a class and its taxonomic rank (eg species, family) ncbi_taxonomy has_rank 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 1 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. An entity primarily responsible for making the content of the resource. 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 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. An account of the content of the resource. 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. A reference to a resource from which the present resource is derived. Source Source 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 Mark Miller 2018-05-11T13:47:29Z has_alternative_id has_broad_synonym database_cross_reference Fully qualified synonym, contains the string, term type, source, and an optional source code if appropriate. Each subfield is deliniated to facilitate interpretation by software. FULL_SYN Synonym with Source Data has exact synonym has_exact_synonym has_narrow_synonym has_obo_namespace has_related_synonym Used to associate the concept defining a particular terminology subset with concepts that belong to this subset. Concept_In_Subset in subset in_subset shorthand label label label uberon foaf-depicted_by 1 foaf-depicted_by depicted_by 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ 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 uberon 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ 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 uberon has_part has_part has part has part bearer of bearer_of http://purl.obolibrary.org/obo/omrse.owl is bearer of is_bearer_of 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 http://purl.obolibrary.org/obo/ro.owl [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]) 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 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]) 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 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 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 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 occurs_in unfolds in unfolds_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 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 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 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 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 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 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 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 Near the outer surface of the organism. Thus, skin is superficial to the muscle layer. BSPO:0000108 uberon superficial_to superficial_to superficial_to 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 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 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 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 has measurement unit label This document is about information artifacts and their representations A (currently) primitive relation that relates an information artifact to an entity. 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. 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 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 relates a process to a time-measurement-datum that represents the duration of the process Person:Alan Ruttenberg is duration of An adverse event has a participant quality, such as a hyperkalemia AE has a participatn quality blood potassium increased. an object property that represents a relation between a process and a quality, in which the process has a participant that has the quality. This is a shortcut relation of the following full version: 'has participant' some (participant 'has quality' ) in: process 'has participant' some (participant 'has quality' some quality) Yongqun He has participant quality a 'occurs in' relation that is applied at the adverse event setting and indicates where an adverse event occurs in. Yongqun He adverse event occurs in AE occurs in a specific 'preceded by' object property that has a domain of an adverse event. Yongqun He adverse event preceded by provides_service_consumer_with The provides_service_consumer_with relation links the service to its primary process it provides for the consumer (as opposed to secondary processual parts of a service process such as payment or documentation). For example, a 'DNA sequencing service' provides_service_consumer_with 'DNA sequencing' as the essential process performed by the provider for the client. A relation between a service and the primary processual part of the service that is performed by the provider for the consumer. provides_service_consumer_with is_supported_by_data The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA. The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process OBI OBI Philly 2011 workshop is_supported_by_data has_specified_input has_specified_input see is_input_of example_of_usage 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. The inverse property of is_specified_input_of 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. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Coutot has_specified_input 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 has_specified_output has_specified_output 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. The inverse property of is_specified_output_of PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Courtot has_specified_output 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 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 has organization member has value specification A relation between an information content entity and a value specification that specifies its value. PERSON: James A. Overton OBI has value specification BFO relation takes precedence. We anticipate BFO 2.0 including and defining this relation. When it does, we will obsolete this property and declare it equivalent to the BFO 2.0 relation. is-aggregate-of true A kidney biopsy protocol is executed in a kidney biopsy process. A shortcut relation that is concretized and realized in some process. Jie Zheng, Oliver He executed in A 'has part' object property that has the range of a textual question Oliver He has question form generated by An object property that indicates a relation between a question and an answer has answer to question has answer An object property that represents a relation between a form and a question where the question sets up an exclusion criterion. Specifically, when the answer to the question is Yes, the candidate becomes ineligible for the participation of a study. Fred Dowd, Oliver He has exclusion question An object property that represents a relation between a form and a question where the question sets up an inclusion criterion. Specifically, when the answer to the question is Yes, then the candidate fulfills a criterion for being eligible for participating in a study. Note that there might be other criteria that the candidate also need to meet in order to be fully eligible. Meanwhile, if the answer is No, the candidate may still be eligible depending on the other restriction. Fred Dowd, Oliver He has inclusion question has process quality An object property that represents a relation between a person with a biological sex and a process where the person has a specific susceptbility to a process Anthony Huffman, Oliver He has sex-specific susceptibility to An object property that represents a relation between a person with a biological sex and a process where the person has an increased susceptbility to a process compared to corresponding male population Anthony Huffman, Oliver He has increased susceptibility compared to male to Male has increased susceptibility to death due to COVID-19 infection compared to female. Note that in this case, the male can mean one single male individual. however, the female here means the whole female population. It is reported that the ratio of deaths in COVID-19 infected males to females is 1·21:1 in high-income countries, but 2·8:1 in low-income countries (Reference: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8023692/). An object property that represents a relation between a person with a biological sex and a process where the person has an increased susceptbility to a process compared to corresponding female population Anthony Huffman, Oliver He has increased susceptibility compared to female to An object property that represents a relation between a person with a biological sex and a process where the person has an increased susceptbility to a process compared to the whole population with all sexes included Anthony Huffman, Oliver He has increased sex-specific susceptibility compared to sex baseline to A care_site has a care_site_id (OMOP: http://ohdsi.github.io/CommonDataModel/cdm54.html#CARE_SITE) An object property that represents a relation between an entity and its corresponding identifier that is owned by the entity. Oliver He, Long Tran has identifier A patient was admitted to the hospital from home or a long-term care facility. An object property that represents a relation between a patient and a site from which the patient was admitted. Long Tran, Oliver He http://ohdsi.github.io/CommonDataModel/cdm54.html#VISIT_OCCURRENCE admitted from After a visit, a person was discharged to home or a long-term care site. Typically this applies only to visits that have a length of stay of a day or more. An object property that represents a relation between a patient and a site to which the patient was discharged after a visit. http://ohdsi.github.io/CommonDataModel/cdm54.html#VISIT_OCCURRENCE discharged to An admission diagnosis status has the content of adimission diagnosis (as an information content entity). An object property that represents a relation between a status and an information content entity where the status has its content information defined by the information content entity. Oliver He, Long Tran has status content inheres in this fragility inheres in this vase this fragility is a characteristic of this vase this red color inheres in this apple this red color is a characteristic of this apple a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. 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 at all times' inheres_in http://purl.obolibrary.org/obo/ro.owl Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. characteristic of inheres in bearer of this apple is bearer of this red color this vase is bearer of this fragility Inverse of characteristic_of 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 bearer_of is bearer of bearer of bearer_of has characteristic is 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 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://purl.obolibrary.org/obo/ro.owl http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant has_participant concretizes 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. http://purl.obolibrary.org/obo/obi.owl It is recommended to not use this if possible in OMRSE. According to OntoBee this relation has been obsoleted and replaced with 'concretization of at all times'. As of Dec. 2, 2013 iao-main still uses this relation. 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 this apple has quality this red color a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. has_quality has quality this person has role this investigator role (more colloquially: this person has this role of investigator) a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence 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. has_role has role 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 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 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 file:/Users/michaelashburner/Desktop/gaz/gaz.oboInOwl uberon located_in located_in located in located_in located_in (type level) RO:0002002 uberon has_boundary has_boundary has boundary 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. bounding layer of David Osumi-Sutherland <= Primitive instance level timing relation between events before or simultaneous with Relation between occurrents, shares start and end boundaries. David Osumi-Sutherland RO:0002082 coincides_with is_equal_to uberon simultaneous_with simultaneous_with t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) simultaneous with simultaneous_with 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 David Osumi-Sutherland ends_at_start_of meets X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) immediately precedes David Osumi-Sutherland io X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) starts during David Osumi-Sutherland d during X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) happens during David Osumi-Sutherland o overlaps X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). ends during x overlaps y if and only if there exists some z such that x has part z and z part of y http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) overlaps 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 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. 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 RO:0002202 uberon develops_from develops_from develops_from RO:0002203 uberon develops_into develops_into 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 regulates regulates (processual) 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) 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)) capable of part of '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 has active participant 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 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 surrounded_by 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 inverse of surrounded by inverse of surrounded_by Chris Mungall RO:0002221 uberon surrounds surrounds surrounds surrounds Chris Mungall 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. temporally related to Relation between occurrents, shares a start boundary with. RO:0002223 uberon starts starts 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 Relation between occurrents, shares an end boundary with. RO:0002229 finishes uberon ends ends ends 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 p has direct input c iff 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 RO:0002254 uberon has_developmental_contribution_from has_developmental_contribution_from has developmental contribution from 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. 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 RO:0002258 uberon developmentally_preceded_by developmentally_preceded_by developmentally preceded by RO:0002285 uberon developmentally_replaces developmentally_replaces developmentally_replaces 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 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 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 Chris Mungall This is a grouping relation that collects relations used for the purpose of connecting structure and function functionally related to inverse of enables Chris Mungall enabled by inverse of regulates Chris Mungall regulated by (processual) 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 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 input of inverse of has output Chris Mungall output of Chris Mungall formed as result of x has the potential to develop into y iff x develops into y or if x is capable of developing into y RO:0002387 uberon has_potential_to_develop_into has_potential_to_develop_into has potential to develop into 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 RO:0002433 uberon contributes_to_morphology_of contributes_to_morphology_of contributes to morphology of '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 UBREL:0000002 RO:0002473 uberon composed_primarily_of composed_primarily_of composed primarily of Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s. BFO:0000068 RO:0002488 begins_to_exist_during uberon existence_starts_during existence_starts_during existence starts during Relation between continuant and occurrent, such that c comes into existence at the start of p. RO:0002489 uberon existence_starts_with existence_starts_with existence starts with 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. BFO:0000069 RO:0002492 ceases_to_exist_during uberon existence_ends_during existence_ends_during existence ends during Relation between continuant and occurrent, such that c ceases to exist at the end of p. RO:0002493 uberon existence_ends_with existence_ends_with existence ends with RO:0002494 transforms from uberon transformation_of transformation_of transformation of RO:0002495 direct_transformation_of immediately transforms from uberon immediate_transformation_of immediate_transformation_of immediate transformation of RO:0002496 uberon existence_starts_during_or_after existence_starts_during_or_after existence starts during or after RO:0002497 uberon existence_ends_during_or_before existence_ends_during_or_before 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 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 A coral reef environment is determined by a particular coral reef s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s. The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future Chris Mungall determined by (system to material entity) Chris Mungall Pier Buttigieg RO:0002507 uberon has_material_contribution_from has_material_contribution_from determined by has material contribution from inverse of determined by Chris Mungall determines (material entity to system) determines s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w. Chris Mungall determined by part of A relation between a subdivision of an organism and the single subdivision of skeleton that provides structural support for that subdivision. RO:0002551 uberon has sekeletal support has supporting framework has_skeleton has_skeleton has skeleton Chris Mungall causally influenced by (material entity to material entity) causally influenced by 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 RO:0002572 uberon luminal_space_of luminal_space_of luminal space of 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 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 Inverse of 'causal agent in' 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. related via dependence to RO:0003000 uberon produces produces produces RO:0003001 uberon produced_by produced_by produced_by carries uberon channel_for channel for x is a conduit for y iff y passes through the lumen of x. uberon conduit_for conduit for uberon existence_starts_and_ends_during existence starts and ends during X in_central_side Y <=> if Y is subdivided into left and right portions around some median divisor, all parts of X are closer to the median divisor than the outermost lateral sides. uberon in_central_side_of in_central_side_of https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern 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 http://purl.org/obo/owl/relationship OBO_REL:0000007 relationship has_proper_part has_proper_part has measurement value The data type "last 4 digits of social security number" has digit number of 4. A data property that represents a relation between a data type and a number of integer digits that the data type has. Oliver He has digit number quality measured by year entity Entity entity Julius Caesar Verdi’s Requiem the Second World War your body mass index 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 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 An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) entity continuant Continuant continuant 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. 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 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] continuant occurrent 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 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 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 process 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] process disposition Disposition an atom of element X has the disposition to decay to an atom of element Y certain people have a predisposition to colon cancer children are innately disposed to categorize objects in certain ways. the cell wall is disposed to filter chemicals in endocytosis and exocytosis 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. 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]) (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] disposition realizable RealizableEntity 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 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. 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] realizable entity quality 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] quality sdc SpecificallyDependentContinuant specifically dependent continuant 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 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]) 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. (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] specifically dependent continuant 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 fiat object fiat object part 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 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 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]) object 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 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 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 material MaterialEntity material entity 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] material entity 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 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 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 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 Material anatomical entity that is a member of an individual species or is a viral or viroid particle. organism or virus or viroid A cardiovascular drug that tends to raise reduced blood pressure. Wikipedia:Antihypotensive_agent chebi_ontology antihypotensive agents pressor pressors vasopressor agens vasopressor agent CHEBI:137431 antihypotensive agent peptide Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc. peptide Any member of the group of substituted penams containing two methyl substituents at position 2, a carboxylate substituent at position 3 and a carboxamido group at position 6. 0 C9H11N2O4SR 243.26000 243.04395 [H][C@]12SC(C)(C)[C@@H](N1C(=O)[C@H]2NC([*])=O)C(O)=O CHEBI:14742 CHEBI:25869 CHEBI:7961 CiteXplore:12833570 CiteXplore:1502708 CiteXplore:16033609 CiteXplore:7798534 KEGG COMPOUND:C00395 KEGG:C00395 PMID:11851248 PMID:12833570 PMID:1502708 PMID:16033609 PMID:7061385 PMID:7798534 Wikipedia:Penicillin Penicillin penicillin penicillins chebi_ontology C9H11N2O4SR [H][C@]12SC(C)(C)[C@@H](N1C(=O)[C@H]2NC([*])=O)C(O)=O penicillins CHEBI:17334 penicillin A class of beta-lactam antibiotics differing from the penicillins in having a 6-membered, rather than a 5-membered, side ring. A class of beta-lactam antibiotics differing from the penicillins in having a 6-membered, rather than a 5-membered, side ring. Although cephalosporins are among the most commonly used antibiotics in the treatment of routine infections, and their use is increasing over time, they can cause a range of hypersensitivity reactions, from mild, delayed-onset cutaneous reactions to life-threatening anaphylaxis in patients with immunoglobulin E (IgE)-mediated allergy. 0 C7H5NO3SR2 183.18500 182.99901 [H][C@]12SCC([*])=C(N1C(=O)[C@H]2[*])C(O)=O CHEBI:3538 CiteXplore:12833570 CiteXplore:6762896 KEGG COMPOUND:C00875 KEGG:C00875 PMID:10069359 PMID:11936371 PMID:12833570 PMID:24269048 PMID:3320614 PMID:6762896 PMID:8426246 Wikipedia:Cephalosporin Cephalosporin chebi_ontology C7H5NO3SR2 [H][C@]12SCC([*])=C(N1C(=O)[C@H]2[*])C(O)=O cephalosphorin cephalosphorins cephalosporins CHEBI:23066 cephalosporin 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 cyclic amide cyclic amides CHEBI:23443 cyclic amide 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 CHEBI:24531 heterocyclic antibiotic A cyclic compound having as ring members atoms of carbon and at least of one other element. chebi_ontology organic heterocycle organic heterocyclic compounds CHEBI:24532 organic heterocyclic compound Hydroxides are chemical compounds containing a hydroxy group or salts containing hydroxide (OH(-)). chebi_ontology CHEBI:24651 hydroxides A compound which contains oxygen, at least one other element, and at least one hydrogen bound to oxygen, and which produces a conjugate base by loss of positive hydrogen ion(s) (hydrons). oxoacid oxoacids oxacids oxiacids oxo acid oxy-acids oxyacids CHEBI:24833 oxoacid Cyclic amides of amino carboxylic acids, having a 1-azacycloalkan-2-one structure, or analogues having unsaturation or heteroatoms replacing one or more carbon atoms of the ring. lactam lactams chebi_ontology Laktam Laktame lactams CHEBI:24995 lactam Any polyatomic entity that is an electrically neutral entity consisting of more than one atom. molecule chebi_ontology Molekuel molecula molecules neutral molecular compounds CHEBI:25367 molecule chebi_ontology organonitrogen heterocyclic antibiotics CHEBI:25558 organonitrogen heterocyclic antibiotic oxygen molecular entity chebi_ontology oxygen molecular entities CHEBI:25806 oxygen molecular entity chebi_ontology CHEBI:25865 penicillanic acids sulfur molecular entity sulfur molecular entities CHEBI:26835 sulfur molecular entity chebi_ontology heterobicyclic compounds organic heterobicyclic compounds CHEBI:27171 organic heterobicyclic compound An organonitrogen heterocyclic antibiotic that contains a beta-lactam ring. CHEBI:10427 CHEBI:22844 KEGG:C03438 PMID:19254642 PMID:22594007 Wikipedia:Beta-lactam_antibiotic chebi_ontology beta-Lactam antibiotics beta-lactam antibiotics CHEBI:27933 beta-lactam antibiotic An amide is a derivative of an oxoacid RkE(=O)l(OH)m (l =/= 0) in which an acidic hydroxy group has been replaced by an amino or substituted amino group. CHEBI:22473 CHEBI:2633 KEGG COMPOUND:C00241 KEGG:C00241 Amide amides chebi_ontology CHEBI:32988 amide atom A chemical entity constituting the smallest component of an element having the chemical properties of the element. atom An organosulfur compound is a compound containing at least one carbon-sulfur bond. CHEBI:23010 CHEBI:25714 Wikipedia:Organosulfur_compounds organosulfur compound chebi_ontology organosulfur compounds CHEBI:33261 organosulfur compound A heteroorganic entity is an organic molecular entity in which carbon atoms or organic groups are bonded directly to one or more heteroatoms. chebi_ontology heteroorganic entities organoelement compounds CHEBI:33285 heteroorganic entity pnictogen molecular entity pnictogen molecular entities CHEBI:33302 pnictogen molecular entity Any p-block molecular entity containing a chalcogen. chalcogen molecular entity chebi_ontology chalcogen compounds chalcogen molecular entities CHEBI:33304 chalcogen molecular entity A carbon oxoacid acid carrying at least one -C(=O)OH group and having the structure RC(=O)OH, where R is any any monovalent functional group. Carboxylic acids are the most common type of organic acid. An oxoacid acid carrying at least one -C(=O)OH group and having the structure RC(=O)OH, where R is any any monovalent functional group. Carboxylic acids are the most common type of organic acid. 0 CHO2R 45.01740 44.99765 OC([*])=O CHEBI:13428 CHEBI:13627 CHEBI:23027 CiteXplore:17147560 CiteXplore:18433345 PMID:17147560 PMID:18433345 Wikipedia:Carboxylic_acid carboxylic acid carboxylic acids chebi_ontology CHO2R Carbonsaeure Carbonsaeuren Karbonsaeure OC([*])=O RC(=O)OH acide carboxylique acides carboxyliques acido carboxilico acidos carboxilicos CHEBI:33575 carboxylic acid A molecular entity containing one or more atoms from any of groups 1, 2, 13, 14, 15, 16, 17, and 18 of the periodic table. chebi_ontology main group compounds main group molecular entities CHEBI:33579 main group molecular entity carbon group molecular entity carbon group molecular entities CHEBI:33582 carbon group molecular entity Any molecule that consists of a series of atoms joined together to form a ring. Wikipedia:Cyclic_compound chebi_ontology cyclic compounds CHEBI:33595 cyclic compound hydrogen compounds hydrogen molecular entities CHEBI:33608 hydrogen molecular entity A molecule that features two fused rings. bicyclic compounds CHEBI:33636 bicyclic compound A polycyclic compound in which at least one of the rings contains at least one non-carbon atom. heteropolycyclic compounds chebi_ontology polyheterocyclic compounds CHEBI:33671 heteropolycyclic compound A bicyclic compound in which at least one of the rings contains at least one skeletal heteroatom. heterobicyclic compounds chebi_ontology CHEBI:33672 heterobicyclic compound An s-block molecular entity is a molecular entity containing one or more atoms of an s-block element. s-block molecular entity s-block compounds s-block molecular entities CHEBI:33674 s-block molecular entity A main group molecular entity that contains one or more atoms of a p-block element. A p-block molecular entity is a molecular entity containing one or more atoms of a p-block element. chebi_ontology p-block compounds p-block molecular entities p-block molecular entitiy CHEBI:33675 p-block molecular entity nucleic acid A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid. nucleic acid Any organic molecule that consists of atoms connected in the form of a ring. chebi_ontology organic cyclic compounds CHEBI:33832 organic cyclic compound macromolecule A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. polymer macromolecule Any heteroorganic entity containing at least one carbon-nitrogen bond. organonitrogen compounds chebi_ontology organonitrogens CHEBI:35352 organonitrogen compound chebi_ontology carbon oxoacids oxoacids of carbon CHEBI:35605 carbon oxoacid A beta-lactam is a lactam in which the amide bond is contained within a four-membered ring, which includes the amide nitrogen and the carbonyl carbon. A lactam in which the amide bond is contained within a four-membered ring, which includes the amide nitrogen and the carbonyl carbon. 0 C3H2NOR3 68.054 68.01364 C1(C(N(*)C1*)=O)* CHEBI:10426 CHEBI:13203 CHEBI:22845 KEGG COMPOUND:C01866 KEGG:C01866 Wikipedia:Beta-lactam beta-Lactam beta-lactam chebi_ontology a beta-lactam beta-lactams CHEBI:35627 beta-lactam Natural and synthetic antibiotics containing the 4-thia-1-azabicyclo[3.2.0]heptan-7-one structure, generally assumed to have the 5R configuration unless otherwise specified. penams chebi_ontology CHEBI:35992 penams Any molecular entity consisting of more than one atom. chebi_ontology polyatomic entities CHEBI:36357 polyatomic entity pseudoketone pseudoketones pseudoketones CHEBI:36585 pseudoketone Any compound containing the carbonyl group, C=O. The term is commonly used in the restricted sense of aldehydes and ketones, although it actually includes carboxylic acids and derivatives. carbonyl compounds chebi_ontology CHEBI:36586 carbonyl compound Organic compounds containing an oxygen atom, =O, doubly bonded to carbon or another element. oxo compounds organic oxo compounds CHEBI:36587 organic oxo compound A cyclic compound in which a carbonyl group in a ring is bonded to one or two skeletal heteroatoms. cyclic pseudoketones CHEBI:36588 cyclic pseudoketone An organochalcogen compound is a compound containing at least one carbon-chalcogen bond. organochalcogen compound chebi_ontology organochalcogen compounds CHEBI:36962 organochalcogen compound An organochalcogen compound containing at least one carbon-oxygen bond. CiteXplore:17586126 PMID:17586126 organooxygen compound chebi_ontology organooxygen compounds CHEBI:36963 organooxygen compound A molecular entity consisting of two or more chemical elements. chemical compound heteroatomic molecular entities CHEBI:37577 heteroatomic molecular entity An amide of a carboxylic acid, having the structure RC(=O)NR2. The term is used as a suffix in systematic name formation to denote the -C(=O)NH2 group including its carbon atom. 0 CNOR3 42.01680 41.99799 [*]C(=O)N([*])[*] CHEBI:35354 CHEBI:35355 carboxamides chebi_ontology carboxamides primary carboxamide CHEBI:37622 carboxamide Any organonitrogen compound containing a cyclic component with nitrogen and at least one other element as ring member atoms. chebi_ontology heterocyclic organonitrogen compounds organonitrogen heterocyclic compounds CHEBI:38101 organonitrogen heterocyclic compound chebi_ontology heterocyclic organosulfur compounds organosulfur heterocyclic compounds CHEBI:38106 organosulfur heterocyclic compound CHEBI:25429 CHEBI:38075 chebi_ontology organic heteropolycyclic compounds CHEBI:38166 organic heteropolycyclic compound chebi_ontology cephems CHEBI:38311 cephem Any molecular entity that contains carbon. CHEBI:25700 CHEBI:33244 chebi_ontology organic compounds organic entity organic molecular entities CHEBI:50860 organic molecular entity CHEBI:25556 CHEBI:7594 KEGG COMPOUND:C06061 KEGG:C06061 chebi_ontology Nitrogenous compounds nitrogen compounds nitrogen molecular entities CHEBI:51143 nitrogen molecular entity A cyclic compound having as ring members atoms of at least two different elements. Heterocyclic compound chebi_ontology compuesto heterociclico compuestos heterociclicos heterocycle heterocyclic compounds CHEBI:5686 heterocyclic compound Any molecule that consists of at least one carbon atom as part of the electrically neutral entity. chebi_ontology organic compound organic compounds organic molecules CHEBI:72695 organic molecule 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. cell cell cultured cell A cell in vitro that is or has been maintained or propagated as part of a cell culture. cultured cell 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 A quantitative or qualitative value which is the result of an act of assessing a morphological or physiological state or property in a single individual or sample or a group of individuals or samples, based on direct observation or experimental manipulation. clinical measurement Any value resulting from the quantification of a morphological or physiological parameter pertaining to the heart and/or blood vessels. cardiovascular measurement The number of contractions of the cardiac ventricles per unit of time. heart rate Measurement of the pressure, or force per area, exerted by circulating blood against the walls of the blood vessels. The pressure is dependent on the energy of the heart action, elasticity of the vessel walls and volume and viscosity of the blood. Not4Curation blood pressure measurement The maximum arterial pressure within the cardiac cycle, i.e. at the point at which the heart is in its maximal state of contraction. This is the time when the blood is forced from the ventricles of the heart into the pulmonary artery and the aorta. systolic blood pressure The minimum arterial pressure within the cardiac cycle, usually at the point at which the heart is in a state of relaxation and expansion. This is the time when the ventricles fill with blood. diastolic blood pressure The minimum pressure in the heart left ventricle, usually at the point at which the heart is in a state of relaxation and expansion and the ventricles fill with blood. left ventricular diastolic blood pressure Measurement of the pressure within the heart left ventricle at the point of maximal contraction, when the blood is forced from the left ventricle into the aorta. left ventricular systolic blood pressure A blood pressure measurement which has been normalized or adjusted by a mathematical process or computation. Blood pressure is the pressure, or force per area, exerted by circulating blood against the walls of the blood vessels. The pressure is dependent on the energy of the heart action, elasticity of the vessel walls and volume and viscosity of the blood. Not4Curation calculated blood pressure The average blood pressure within an artery over a specified period of time. It is often calculated using the formula of one third systolic pressure plus two thirds diastolic pressure, or alternatively, using the formula diastolic pressure plus 1/3 of the difference between systolic pressure and diastolic pressure (i.e. 1/3 pulse pressure). mean arterial blood pressure A calculated value for the difference between the systolic blood pressure and the diastolic blood pressure at a given point in time when measured in an isolated organ or vessel under conditions where perfusion pressure or flow can be controlled. developed blood pressure The level of heat in an organism. body temperature A measurement of the physical form or structure of the heart, the chambered, muscular organ in vertebrates that pumps blood received from the veins into the arteries, thereby maintaining the flow of blood through the entire circulatory system. This is the term which was just "heart measurement". Since it was under body morphological measurement it seemed to clearly refer to a morphological measurement. I made this term more specific so that another term for "heart measurement" could be added to the ontology above it which would also be a parent to other non-morphological heart-related terms. JRS 2-15-2012. heart morphological measurement The heaviness of the heart (the central cardiac muscle which maintains the circulation of the blood) or the degree to which it is drawn to the earth by gravity. heart weight A calculated measurement of the difference between the systolic pressure and the diastolic pressure in the heart left ventricle at a given point in time in an isolated organ or vessel under conditions where perfusion pressure or flow can be controlled. left ventricular developed pressure Measurement of the structure or forms of the entire body or parts of the body of an organism. anthropometric measurement morphometry body morphological measurement A quantification of a parameter of the chemical composition of blood. blood molecular composition measurement blood chemistry measurement mshimoyama 2010-12-13T10:32:58Z A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of one or more of the various, specific types of leukocytes present in a sample of blood for which a total white blood cell count was taken, usually 1 cubic mm of peripheral venous blood. calculated blood differential WBC count calculated blood differential leukocyte count calculated differential white blood cell count The amount of hemoglobin in a specific volume of blood, expressed as grams per deciliter of whole blood in humans. blood haemoglobin level blood hemoglobin level The number of white blood cells in a specified volume of blood. leukocyte count white corpuscle count white blood cell count Any measurement involving the amount, composition or type of protein, the complex organic compounds containing carbon, hydrogen, oxygen, nitrogen, and sulfur consisting of alpha-amino acids joined by peptide linkages, in blood. blood protein measurement The number of platelets (thrombocytes) in a specified volume of blood, usually expressed as platelets per cubic millimeter of whole blood. platelet count A measurement of the blood, it's contents, cells or other factors contained within the blood. blood measurement A value resulting from the quantification of a morphological or physiological parameter of blood cells, i.e. cells native to the circulation, including those of erythroid, lymphoid, myeloid and monocytic lineages. A cell is a membrane-enclosed protoplasmic mass constituting the smallest structural unit of an organism that is capable of independent functioning. blood cell measurement The level of urea in the blood in terms of nitrogen content; converted to urea concentration by multiplying by 60/28 or 2.14. Urea is the chief nitrogenous end product of protein metabolism in whole blood. Urea is formed in the liver from amino acids and from ammonia compounds and can be found in urine, blood, and lymph. BUN level blood urea nitrogen level Any value resulting from the quantification of a morphological or physiological parameter of a blood-derived lipid, any of a structurally diverse group of organic compounds found in blood that are insoluble in water but soluble innonpolar solvents that, among other biological functions, serve as a source of fuel and are an important constituent of cell structure. blood lipid measurement Measurement of the entire amount of cholesterol, a eukaryotic sterol that in higher animals is the precursor of bile acids and steroid hormones and a key constituent of cell membranes, without taking into account any association with other molecules such as lipoproteins, in a specified volume of blood, the fluid that circulates through the heart, arteries, capillaries and veins carrying nutrients and oxygen to the body tissues and metabolites away from them. blood TC level blood total cholesterol level Measurement of the amount of cholesterol, a eukaryotic sterol that in higher animals is the precursor of bile acids and steroid hormones and a key constituent of cell membranes, carried in high-density lipoprotein (HDL) molecules in a specified volume of blood, the fluid that circulates through the heart, arteries, capillaries and veins carrying nutrients and oxygen to the body tissues and metabolites away from them. HDL is the smallest of the major lipoprotein particles, complex molecules that consist of a protein membrane surrounding a core of lipids. The HDL class of lipoproteins, specifically the subtypes of HDL2 and HDL3, have densities between 1.063 and 1.210 g/ml. blood HDL level blood HDL-C Values for density ranges of the lipoprotein classes are approximate. The classes may be defined differently by different researchers, in part because class definitions depend on the number of subclasses into which the lipoprotein fractions are divided. blood high density lipoprotein cholesterol level Measurement of the amount of cholesterol, a eukaryotic sterol that in higher animals is the precursor of bile acids and steroid hormones and a key constituent of cell membranes, carried in low-density lipoprotein (LDL) molecules in a specified volume of blood, the fluid that circulates through the heart, arteries, capillaries and veins carrying nutrients and oxygen to the body tissues and metabolites away from them. LDL constitute a class of relatively large, heterogeneous lipoprotein particles, complex molecules that consist of a protein membrane surrounding a core of lipids. The LDL class of lipoproteins has a density between 1.019 and 1.063 g/ml. In some animal species, such as canine and rodents, this may overlap with the HDL1 class and be designated LDL/HDL1. blood LDL level blood LDL-C level Values for density ranges of the lipoprotein classes are approximate. The classes may be defined differently by different researchers, in part because class definitions depend on the number of subclasses into which the lipoprotein fractions are divided. blood low density lipoprotein cholesterol level Measurement of the total amount of all proteins, the complex organic compounds containing carbon, hydrogen, oxygen, nitrogen, and sulfur consisting of alpha-amino acids joined by peptide linkages, found in a specific volume of plasma, the fibrinogen-containing fluid portion of the blood in which the particulate components are suspended. plasma total protein level A quantification of one or more mineral salts found in the blood in the form of electrically charged ions. blood electrolyte measurement Any quantitation of the catalytic effect exerted by an enzyme in a specified sample of blood. An enzyme is a protein that catalyzes chemical reactions of other substances without itself being destroyed or altered upon completion of the reaction(s). Not4Curation blood enzyme activity level A measurement of the physical form and structure of an organ. This is the term which used to be just "organ measurement". Since it was under body morphological measurement, it clearly referred to a morphological measurement. Because a term for organ measurement was needed that was not morphological, and since this one already had annotations, I changed the term while keeping the ID and location in the ontology the same. JRS 2-15-2012. organ morphological measurement The weight of the heart after removal from the body but without desiccation. heart wet weight The weight of the heart after desiccation. heart dry weight The weight of the lower left chamber of the heart, which pumps oxygenated blood through the aorta into the systemic arteries, after removal from the body and separation from the rest of the heart but without desiccation. heart left ventricle wet weight The weight of the lower right chamber of the heart, which pumps venous blood through the pulmonary trunk and arteries to the capillaries of the lung, after removal from the body and separation from the rest of the heart but without desiccation. heart right ventricle wet weight calculated heart weight A calculated value in which the weight of the heart, the chambered, muscular organ in vertebrates that pumps blood received from the veins into the arteries, thereby maintaining the flow of blood through the entire circulatory system, is divided by the total weight of the body, and the result presented as a ratio, fraction, quotient or percentage, thus normalizing it to body weight and, by extension, to the size of the organism. heart weight to body weight ratio A calculated value in which the weight of the heart, the chambered, muscular organ in vertebrates that pumps blood received from the veins into the arteries, thereby maintaining the flow of blood through the entire circulatory system, is presented as percentage of the total weight of the body, thus normalizing it to body weight. heart weight as percentage of body weight The weight of the aorta, the main trunk from which the arterial system proceeds. Weight is the heaviness or degree to which a body is drawn to the earth by gravity. aorta weight Any quantification of a morphological or physiological parameter of one or more blood vessels, the network of muscular tubes that carry blood through the body. blood vessel measurement renal/urinary measurement The weight of one or both kidneys, the organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes. kidney weight The weight of the right kidney, the organ which lies on the right side of the body from the perspective of the subject and functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes, after removal from the body but without desiccation. right kidney wet weight The weight of the left kidney, the organ which lies on the left side of the body from the perspective of the subject and functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes, after removal from the body but without desiccation. left kidney wet weight The weight of a single kidney, the organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes, after removal from the body but without desiccation. individual kidney wet weight single kidney wet weight The weight of both kidneys, the organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes, after removal from the body but without desiccation. both kidneys wet weight Measurement of the physical form or structure of one or both kidneys, the organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes. kidney morphological measurement mshimoyama 2009-12-17T08:17:35Z A calculated value which compares the weight of the right ventricle, the lower chamber of the right side of the heart, which pumps venous blood through the pulmonary trunk and arteries to the capillaries of the lung, with the weight of the left ventricle, the lower chamber of the left side of the heart, which pumps oxygenated blood out through the aorta to all the tissues of the body, and presents it as a ratio. heart right ventricle weight to left ventricle weight ratio mshimoyama 2009-12-17T08:22:51Z The number of granulocytes (polymorphonuclear leukocytes) in a specified volume of blood, usually 1 cubic millimeter. blood granulocyte count mshimoyama 2009-12-17T10:21:58Z The amount of lipoproteins, any of a group of conjugated proteins that have at least one lipid component, in a specific volume of blood. blood lipoprotein level mshimoyama 2009-12-17T11:00:47Z Measurement of the amount of creatinine in a specified sample of urine, the fluid waste product excreted by the kidneys. Creatinine is a nitrogenous compound formed in muscle as the end product of creatine metabolism. Blood and urine tests for creatinine are used as diagnostic indicators of kidney function and muscle mass. urine creatinine level mshimoyama 2010-06-24T01:24:08Z Any measurement of the physical form or structure of the skeletal, smooth and/or heart muscles of the body. muscle morphological measurement mshimoyama 2009-12-17T11:01:46Z The amount of albumin in a specified volume of urine. Urine albumin levels which are above normal but not detectable with routine protein testing are referred to as microalbuminuria. urine microalbumin level urine albumin level RNigam 2010-05-17T01:48:45Z A calculated measurement in which the weight after removal from the body but without desiccation of both kidneys, the paired organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes, is divided by the total weight of the body and presented as a percentage, thus normalizing it to body weight. both kidneys wet weight as percentage of body weight RNigam 2010-05-25T04:01:05Z Any measurement that has been normalized, adjusted or derived by a mathematical process or computation, of the weight of one or both kidneys, the paired organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes. Not4Curation calculated kidney weight RNigam 2010-05-25T04:11:18Z The weight of one or both kidneys, the organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes, after removal from the body but without desiccation. kidney wet weight RNigam 2010-05-25T04:11:36Z The weight after desiccation of one or both kidneys, the organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes. kidney dry weight mshimoyama 2010-06-10T09:05:26Z The length of a line which crosses a transverse view of a blood vessel, passing through its center and ending on either side at either the inner surface or outer surface of the blood vessel wall. blood vessel diameter mshimoyama 2010-06-10T09:06:25Z Percentage of blood pumped out of the left ventricle with each heart beat. heart left ventricle ejection fraction ejection fraction mshimoyama 2010-06-10T09:08:28Z Volume of blood left in a ventricle at end of contraction. end-systolic volume mshimoyama 2010-06-10T09:38:29Z Any measurement of the movement of blood through the heart and blood vessels. blood flow measurement circulation measurement mshimoyama 2010-06-10T09:38:42Z The volume of blood flowing through a vessel or organ per unit of time. blood flow rate mshimoyama 2010-06-10T09:51:29Z The volume of blood pumped from the right or left ventricle per minute, also used to calculate - stroke volume X heart rate. cardiac output measurement mshimoyama 2010-06-10T09:56:23Z The volume of blood flowing through an artery per unit time. arterial blood flow rate mshimoyama 2010-06-10T09:56:38Z The volume of blood passing through a vein per unit time. venous blood flow rate mshimoyama 2010-06-10T10:04:04Z Movement of blood along the solid wall of a vessel, often represented by the Hagen-Poiseuille equation. vessel shear stress measurement mshimoyama 2010-06-10T10:51:43Z in vitro vessel shear stress mshimoyama 2010-06-10T10:52:06Z in vivo vessel shear stress mshimoyama 2010-06-10T11:20:31Z The time needed for plasma to form a fibrin clot after the addition of calcium and a phospholipid reagent. It is used to evaluate the intrinsic clotting system. activated partial thromboplastin time mshimoyama 2010-06-10T02:02:16Z vasodilation measurement blood vessel dilation measurement mshimoyama 2010-06-10T02:02:34Z lumen diameter at maximum dilation expressed as percent of baseline mshimoyama 2010-06-10T02:34:30Z vasoconstriction measurement blood vessel constriction measurement mshimoyama 2010-06-10T02:35:20Z lumen diameter at maximum constriction expressed as percent of baseline mshimoyama 2010-06-10T02:41:52Z Resistance to blood flow by blood vessels throughout the body, the degree to which the blood vessels impede the flow of blood, often calculated as SVR equal to the difference between mean arterial blood pressure(MAP) and central venous pressure(CVP) divided by cardiac output(CO). systemic vascular resistance (SVR) mshimoyama 2010-06-10T03:56:38Z Volume of blood in ventricle immediately before a contraction. end-diastolic volume mshimoyama 2010-06-11T01:32:10Z Volume of blood pumped from one ventricle of the heart with each beat, calculated by subtracting the volume of blood in the ventricle at the end of a beat (end-systolic volume) from the volume of blood just prior to the beat (end-diastolic volume). stroke volume mshimoyama 2010-06-17T10:30:36Z Any quantification of a morphological or physiological parameter of one or more cells. A cell is a membrane-enclosed protoplasmic mass constituting the smallest structural unit of an organism that is capable of independent functioning. cell measurement mshimoyama 2010-06-17T10:30:50Z Number of cells of muscular tissue in the heart in a specified sample size. cardiomyocyte count mshimoyama 2010-06-17T10:33:11Z The enumeration, i.e. measurement of the total number, of the specialized liner cells that form an interface between the circulating blood and the rest of the vessel wall in a specified sample of blood vessel, any one of the network of muscular tubes that carry blood through the body. blood vessel endothelial cell number vascular endothelial cell count blood vessel endothelial cell count mshimoyama 2010-06-17T10:36:15Z Any measurement of components of the Electrical conduction system of the heart.The electrical conduction system of the heart transmits signals generated usually by the sinoatrial node to cause contraction of the heart muscle. heart electrical conduction measurement mshimoyama 2010-06-17T10:39:30Z Interval between an R wave and the next R wave of successive heart beats, inverse of the heart rate. RR_Interval RR interval mshimoyama 2010-06-17T10:40:52Z Time between the beginning of the P wave to the beginning of the QRS complex, reflects the time the electrical impulse takes to travel from the sinus node through the AVE node and entering the ventricles, used as an estimate of AV node function. PR_Interval PR interval mshimoyama 2010-06-17T10:43:21Z The time between the J point ( the point at which the QRS complex finishes and the ST segment begins) to the end of the T wave. ST_Interval ST interval mshimoyama 2010-06-17T10:45:44Z An interval measured from the onset of the QRS wave complex to the offset of the T wave. QT_Interval QT interval mshimoyama 2010-06-17T10:53:08Z heart wall thickness mshimoyama 2010-06-17T10:54:17Z The depth of the wall of the aorta, the main trunk from which the arterial system proceeds. aortic wall thickness aorta wall thickness mshimoyama 2010-06-17T11:13:15Z The thickness or depth of the dorsal/posterior wall of the heart. The dorsal wall is the portion of the heart muscle which is closest to the spine and farthest from the chest wall of the organism. heart dorsal wall thickness heart posterior wall thickness mshimoyama 2010-06-17T11:15:28Z The thickness or depth (i.e. the measurement of the two-dimensional extent of the distance between the inner and outer surfaces) of the dorsal/posterior wall of the left ventricle of the heart. The dorsal wall is the portion of the muscle enclosing the ventricle which is closest to the spine and farthest from the chest wall of the organism. The left ventricle is the lower chamber of the left side of the heart, which pumps oxygenated blood out through the aorta to all the tissues of the body. heart left ventricle dorsal wall thickness Note that "left" in this context refers to the perspective of the organism, not that of the observer. heart left ventricle posterior wall thickness mshimoyama 2010-06-17T11:15:42Z The thickness or depth of the dorsal/posterior wall of the right ventricle of the heart. The dorsal wall is the portion of the muscle enclosing the ventricle which is closest to the spine and farthest from the chest wall of the organism. heart right ventricle dorsal wall thickness heart right ventricle posterior wall thickness mshimoyama 2010-06-17T12:26:05Z Any measurement of urine, the fluid waste product excreted by the kidneys, or its components. urine measurement mshimoyama 2010-06-17T12:27:01Z Measure of the concentration of particles in the urine. urine density urine specific gravity mshimoyama 2010-06-17T12:38:44Z The magnitude of the P wave, the initial deflection of the cardiac cycle representing excitation of the atria as presented in an electrocardiogram. P wave amplitude mshimoyama 2010-06-17T12:39:11Z The time from start to finish of the P wave , in the electrocardiograph illustrating the initial deflection of the cardiac cycle, representing the excitation of the atria. P wave duration mshimoyama 2010-06-17T12:39:35Z The distance to the lowest part of the Q wave which shows the initial downward deflection related to the initial phase of depolarization of the ventricular myocardium and the depolarization of the interventricular septum as measured by electrocardiograph. Q wave depth mshimoyama 2010-06-17T12:39:55Z The time from start to finish of the Q wave which illustrates the initial downward deflection related to the initial phase of depolarization of the ventricular myocardium and the depolarization of the interventricular septum as measured by an electrocardiograph. Q wave duration mshimoyama 2010-06-17T12:40:13Z The time from start to finish of the QRS interval as calculated from a set of measurements taken from the beginning of the QRS complex to the end of the QRS complex representing the time it takes for ventricles to depolarize. QRS duration mshimoyama 2010-06-17T12:40:30Z The magnitude of the portion of the electrocardiograph comprising the Q, R, and S waves which together represent ventricular depolarization. QRS amplitude mshimoyama 2010-06-17T12:40:52Z QT interval corrected for heart rate calculated by the QT interval divided by the square root of the interval from one QRS complex to the onset of the next QRS complex measured in seconds. QTC interval mshimoyama 2010-06-17T12:41:09Z The magnitude of the R wave, which is the initial upward deflection of the QRS complex following the Q wave representing early depolarization of the ventricles as illustrated by an electrocardiograph. R wave amplitude mshimoyama 2010-06-17T12:41:26Z The time from start to finish of the R wave, the initial upward deflection of the QRS complex following the Q wave which represents early depolarization of the ventricles as illustrated in and electrocardiograph. R wave duration mshimoyama 2010-06-17T12:41:54Z The magnitude of the S wave, the downward deflection of the QRS complex following the R wave representing late depolarization of the ventricles as illustrated in an electrocardiograph. S wave amplitude mshimoyama 2010-06-17T12:42:07Z The time from start to finish of the S wave which is the downward deflection of the QRS complex following the R wave representing late depolarization as illustrated by an electrocardiograph. S wave duration mshimoyama 2010-06-17T12:42:27Z ST amplitude mshimoyama 2010-06-17T12:42:46Z ST slope mshimoyama 2010-06-17T12:43:04Z ST wave displacement mshimoyama 2010-06-17T12:43:21Z The magnitude of the T wave, the deflection following the QRS complex representing repolarization of the ventricles as illustrated by and electrocardiograph. T wave amplitude mshimoyama 2010-06-17T03:09:47Z An interval measured from the onset of the P wave in one PQRST wave complex to the onset of the P wave in the following PQRST wave complex. PP_Interval PP interval mshimoyama 2010-06-25T01:54:10Z The difference between systolic and diastolic blood pressures, i.e. the difference between the maximal arterial pressure and minimal arterial pressure during the cardiac cycle. pulse pressure mshimoyama 2010-08-04T10:37:40Z The count of the rhythmic contractions and expansions of an artery due to the surge of blood from the beat of the heart. pulse mshimoyama 2010-09-01T08:30:15Z Measurement of the physical form or structure of either the right or the left upper chamber of the heart that receives blood from the veins and forces it into a ventricle. heart atrium morphological measurement mshimoyama 2010-09-01T08:30:28Z The weight of the left atrium of the heart, the upper chamber on the left which empties into the lower chamber. Weight is the heaviness or degree to which a body is drawn toward the earth by gravity. left atrium weight mshimoyama 2010-09-01T08:30:45Z The weight of the right atrium, the upper right chamber of the heart which empties into the lower right chamber, i.e. the right ventricle. Weight is the heaviness or degree to which a body is drawn to the earth by gravity. right atrium weight mshimoyama 2010-09-01T08:30:56Z A measure of the capacity of the left heart atrium, the upper left chamber which empties into the lower heart chamber. left atrium volume mshimoyama 2010-09-01T08:31:06Z A measure of the three dimensional capacity of the right atrium of the heart, the upper right chamber which empties into the lower right chamber, i.e. the right ventricle. right atrium volume mshimoyama 2010-09-01T08:31:46Z Any measurement of the physical form or structure of one or both ventricles of the heart, that is, the lower chambers of the heart that pump blood away from the heart either to the lungs to be oxygenated or, once oxygenated, to the rest of the body. heart ventricle morphological measurement mshimoyama 2011-09-21T01:41:55Z A calculated measurement in which the weight after removal from the body but without desiccation of both kidneys, the paired organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes, is divided by the total weight of the body and presented as a ratio, fraction or quotient, thus normalizing it to body weight. both kidneys wet weight to body weight ratio mshimoyama 2010-11-12T09:44:31Z The amount of triglycerides in a specified volume of serum, the clear liquid that separates from blood after it has clotted completely, i.e. blood plasma from which fibrinogen has been removed. Triglycerides are any of a group of lipids that are esters formed from one molecule of glycerol and three molecules of one or more fatty acids, are widespread in adipose tissue, and commonly circulate in the blood in the form of lipoproteins. serum triglyceride level mshimoyama 2010-11-12T09:46:59Z Measurement of the entire amount of cholesterol, a eukaryotic sterol that in higher animals is the precursor of bile acids and steroid hormones and a key constituent of cell membranes, without taking into account any association with other molecules such as lipoproteins, in a specified volume of serum, the clear liquid that separates from blood after it has clotted completely, i.e. blood plasma from which fibrinogen has been removed. serum TC level serum total cholesterol level mshimoyama 2010-12-13T10:24:28Z The number of each type of leukocyte present in a specific volume of blood, usually 1 cubic millimeter. blood differential leukocyte count blood differential WBC count blood differential white blood cell count mshimoyama 2010-12-13T10:35:10Z A calculated measurement in which the number of all granulocytes (regardless of type) in a specified sample of blood is divided by the total number of white blood cells in the sample, and the result presented as a ratio, fraction, quotient or percentage. granulocyte count as percentage of total white blood cells granulocyte count to total WBC count ratio granulocyte count to total white blood cell count ratio granulocyte percentage blood granulocyte count to total leukocyte count ratio mshimoyama 2010-12-13T10:38:12Z A calculated measurement in which the number of eosinophil granulocytes is divided by the number of all white blood cells in a specified sample of peripheral venous blood, and the result presented as a ratio, fraction, quotient or percentage. An eosinophil is a granular leukocyte having a nucleus with two lobes connected by a thread of chromatin, and cytoplasm containing coarse, round granules of uniform size that stain readily with eosin and other acid dyes. eosinophil count as percentage of total white blood cells eosinophil count to total WBC count ratio eosinophil granulocyte percentage eosinophil percentage blood eosinophil count to total leukocyte count ratio mshimoyama 2010-12-13T10:39:37Z A calculated measurement in which the number of neutrophil granulocytes is divided by the number of all white blood cells in a specified sample of peripheral venous blood, and the result presented as a ratio, fraction, quotient or percentage. A neutrophil is, or is in the process of becoming, a granular leucocyte having a nucleus with three to five lobes connected by threads of chromatin, cytoplasm containing very fine granules, and which is readily stainable with neutral dyes. neutrophil granulocyte percentage neutrophil count as percentage of total white blood cells neutrophil count to total WBC count ratio neutrophil percentage polymorphonuclear cell percentage blood neutrophil count to total leukocyte count ratio mshimoyama 2010-12-13T10:45:39Z A calculated measurement in which the number of lymphocytes in a specified sample of blood is divided by the total number of white blood cells in the sample, and the result presented as a ratio, fraction, quotient or percentage. lymphocyte count as percentage of total white blood cells lymphocyte count to total WBC count ratio lymphocyte percentage blood lymphocyte count to total leukocyte count ratio mshimoyama 2010-12-13T11:30:05Z The complete or entire amount of bilirubin in a specified volume of serum, the clear liquid that separates from blood after it has clotted completely, i.e. blood plasma from which fibrinogen has been removed. Bilirubin is the bile pigment produced by breakdown of heme and reduction of biliverdin. total serum bilirubin level mshimoyama 2011-01-04T12:01:33Z The amount of carbonic acid dissolved in carbon dioxide and carbonate ion found in a specified volume of serum. serum bicarbonate level mshimoyama 2011-01-04T12:06:48Z The amount of chloride ions found in a specified volume of serum. serum chloride level mshimoyama 2011-01-04T02:41:58Z An estimation of the volume of blood filtered from the kidney glomerular capillaries into the Bowman's capsule per specified unit of time based on serum creatinine level, wieght and age of organism and other factors. blood glomerular filtration rate mshimoyama 2011-01-04T02:48:14Z blood glomerular filtration rate, Diet in Renal Disease Formula (MDRD) mshimoyama 2011-01-04T02:48:55Z A calculated measurement which estimates the glomerular filtration rate (GFR), that is, the volume of fluid filtered from the renal capillaries per unit time, based on the serum creatinine level and adjusted for gender. blood glomerular filtration rate, Chronic Kidney Disease Epidemiology Collaboration formula (CKE-EPI) mshimoyama 2011-01-04T02:50:15Z blood glomerular filtration rate, May Quadratic formula mshimoyama 2011-01-04T02:50:43Z blood glomerular filtration rate, Schwartz formula mshimoyama 2011-01-04T02:52:02Z Amount of potassium ions in a specified volume of serum. serum potassium level mshimoyama 2011-01-04T02:56:30Z The amount of sodium ions in a specified volume of serum. serum sodium level mshimoyama 2011-01-04T03:15:06Z The amount of calcium ions in a specified volume of serum. serum calcium level mshimoyama 2011-01-21T08:57:36Z Blood pressure measured in the pulmonary artery during diastole, that is, during dilation or relaxation of the heart ventricles. pulmonary arterial diastolic blood pressure mshimoyama 2011-01-21T08:58:00Z Blood pressure measured in the pulmonary artery during systole, that is, during contraction of the heart ventricles. pulmonary arterial systolic blood pressure mshimoyama 2011-01-21T09:42:17Z A calculated value in which the weight of the left ventricle, the lower chamber of the left side of the heart, which pumps oxygenated blood out through the aorta to all the tissues of the body, is divided by the total weight of the body and the result presented as a ratio, fraction, quotient or percentage, thus normalizing it to body weight and by extension to the size of the organism. heart left ventricle weight as a percentage of body weight LV mass/BW heart left ventricle weight to body weight ratio mshimoyama 2011-10-28T04:24:16Z The difference in mean arterial blood pressure between two points in time or two conditions expressed as the result of the subtraction in and of itself without comparison by ratio with another quantity. The term "absolute change" refers to the subtraction of one value from another, as opposed to a dissimilarity of two values expressed as a ratio or as a percentage. In this context it is not intended to necessarily imply the difference expressed as an absolute value |n|, that is, the numeric value of the difference without regard to its sign. absolute change in mean arterial blood pressure mshimoyama 2011-10-28T04:25:37Z Absolute difference in heart rate between two points in time or two conditions. The term "absolute change" refers to the subtraction of one value from another, as opposed to a dissimilarity of two values expressed as a ratio or as a percentage. In this context it is not intended to necessarily imply the difference expressed as an absolute value |n|, that is, the numeric value of the difference without regard to its sign. absolute change in heart rate mshimoyama 2011-10-28T04:29:17Z The number of glomeruli in all or part of a kidney. Glomeruli are the tufts of capillaries each situated within a Bowman's capsule at the end of a renal tubule in the vertebrate kidney that filter waste products from the blood and thus initiate urine formation. glomeruli count glomerulus count mshimoyama 2011-10-28T04:33:14Z heart left ventricle dry weight mshimoyama 2011-11-02T02:44:01Z The amount of phosphorus, measured as inorganic phosphate, in a specified sample of serum. serum inorganic phosphate level serum inorganic phosphorus level serum phosphorus level serum phosphate level mshimoyama 2011-11-02T02:45:05Z Measurement of the amount of glucose, the monosaccharide sugar, C6H12O6, occurring widely in plant and animal tissues which is one of the three dietary monosaccharides that are absorbed directly into the bloodstream during digestion, is the end product of carbohydrate metabolism, and is the chief source of energy for living organisms, in a specified volume of serum, the clear liquid that separates from blood after it has clotted completely, i.e. blood plasma from which fibrinogen has been removed. serum glucose level mshimoyama 2011-11-02T02:48:13Z The amount of albumin in a specified sample of serum, the clear liquid that separates from blood after it has clotted completely, i.e. blood plasma from which fibrinogen has been removed. serum albumin level mshimoyama 2011-11-02T04:10:11Z The amount of ezymatic activity of glutamic-pyruvate transaminase enzyme, commonly known as alanine transaminase or alanine aminotransferase (ALT), enzyme in a specified sample of serum. ALT catalyzes the reversible transamination between alanine and 2-oxoglutarate to generate pyruvate and glutamate. Serum ALT level is used as an enzymatic marker for liver disease or damage. serum alanine transaminase activity level serum glutamic-pyruvate transaminase activity level serum ALT activity level serum GPT activity level serum alanine aminotransferase activity level mshimoyama 2011-11-02T04:11:05Z Quantitation of the catalytic effect exerted by alkaline phosphatase (AP) in a specified sample of serum, the clear liquid that separates from blood after it has clotted completely, i.e. blood plasma from which fibrinogen has been removed. AP is an enzyme that catalyzes the cleavage of orthophosphate from orthophosphoric monoesters under alkaline conditions. serum alkaline phosphatase activity level mshimoyama 2011-11-02T04:18:08Z The amount of enzymatic activity of glutamic-oxaloacetic transaminase enzyme, commonly known as aspartate transaminase or aspartate aminotransferase (AST), in a specified sample of serum. AST catalyzes the reversible transfer of an amine group from l-glutamic acid to oxaloacetic acid, forming alpha-ketoglutaric acid and l-aspartic acid. Serum AST level is used as an enzymatic marker for liver disease or damage. serum aspartate transaminase activity level serum glutamic-oxaloacetic transaminase activity level SGOT activity level serum AST activity level serum GOT activity level serum aspartate aminotransferase activity level mshimoyama 2011-11-03T01:45:21Z urine protein level mshimoyama 2011-11-03T02:34:53Z Measurement of the pressure within the heart left ventricle at the end of systole, the period of contraction of the heart when the blood is forced from the ventricles into the pulmonary artery (right ventricle) and the aorta (left ventricle). left ventricular end-systolic blood pressure mshimoyama 2011-11-03T02:35:59Z The pressure in the heart left ventricle at the end of diastole, the period when the heart is in a state of relaxation and expansion and the ventricles fill with blood. left ventricular end-diastolic blood pressure mshimoyama 2011-11-03T02:36:40Z Calculated measurement of a difference in the maximum arterial blood pressure, that is the pressure at the point of maximal contraction of the heart, between two points in time or two conditions expressed as a number (positive or negative), not as a ratio or percentage relative to another quantity. The term "absolute change" refers to the subtraction of one value from another, as opposed to a dissimilarity of two values expressed as a ratio or as a percentage. In this context it is not intended to necessarily imply the difference expressed as an absolute value |n|, that is, the numeric value of the difference without regard to its sign. absolute change in systolic blood pressure mshimoyama 2011-11-03T02:36:56Z Calculated measurement of a difference in diastolic blood pressure between two points or two conditions expressed as a number (positive or negative), not as a ratio or percentage relative to another quantity. The diastolic pressure is the minimum arterial pressure within the cardiac cycle, usually at the point at which the heart is in a state of relaxation and expansion. This is the time when the ventricles fill with blood. The term "absolute change" refers to the subtraction of one value from another, as opposed to a dissimilarity of two values expressed as a ratio or as a percentage. In this context it is not intended to necessarily imply the difference expressed as an absolute value |n|, that is, the numeric value of the difference without regard to its sign. absolute change in diastolic blood pressure mshimoyama 2011-11-03T02:50:38Z A calculated measurement in which the weight after removal from the body but without desiccation of a single kidney, one of the paired organs which function to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes, is divided by the total weight of the body and presented as a ratio, fraction or quotient, thus normalizing it to body weight. individual kidney wet weight to body weight ratio single kidney wet weight to body weight ratio mshimoyama 2011-11-03T02:50:52Z A calculated measurement in which the weight after removal from the body but without desiccation of a single kidney, one of the paired organs which function to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes, is divided by the total weight of the body and presented as a percentage, thus normalizing it to body weight. individual kidney wet weight as percentage of body weight single kidney wet weight as percentage of body weight mshimoyama 2011-11-04T12:57:25Z heart right ventricle dry weight JSmith 2012-02-15T11:39:00Z Any measurement of components of the periodic tightening and loosening of the heart muscle. heart contractility measurement heart contraction measurement JSmith 2012-02-15T11:42:05Z Measure of the time from the relaxation of the heart muscle to the beginning of the tightening of the heart muscle during contraction. time to onset of heart contraction JSmith 2012-02-15T11:48:18Z Measurement of the time from the beginning of heart muscle contraction to the maximum contracted state. time to peak heart contraction JSmith 2012-02-15T11:56:51Z Pressure exerted by the heart muscle in its maximally contracted state. heart contraction pressure JSmith 2012-02-15T05:00:53Z Any measurement of a structural part of a system of the body that is composed of tissues and cells that enable it to perform a particular function. organ measurement JSmith 2012-02-15T05:06:19Z This is not the same term as the original "heart measurement". That term is now "heart morphological measurement". heart measurement JSmith 2012-02-15T05:11:39Z A measurement made on a fluid flowing out of the heart. heart effluent measurement JSmith 2012-02-15T05:14:44Z The volume of a fluid flowing out of the heart. heart effluent volume JSmith 2012-02-15T05:16:22Z The volume of a fluid flowing out of the heart during a specified amount of time. timed heart effluent volume JSmith 2012-02-15T05:21:20Z The amount of an enzyme in a specified volume of fluid flowing out of the heart. heart effluent enzyme level JSmith 2012-02-15T05:25:02Z The amount of lactate dehydrogenase activity measured in a specified volume of fluid flowing out of the heart. heart effluent LDH activity level heart effluent lactate dehydrogenase activity level JSmith 2012-02-15T05:45:18Z Measurement of a lesion in an organ. A lesion is a localized pathological change in structure of an organ or tissue due to injury or disease; especially one that is circumscribed and well defined. tissue damage measurement organ lesion measurement JSmith 2012-02-15T05:48:03Z A measurement of any lesion of the heart. A lesion is a localized pathological change in structure of an organ or tissue due to injury or disease; especially one that is circumscribed and well defined. heart lesion measurement JSmith 2012-02-15T05:50:09Z Measurement of an area of necrotic tissue resulting from a reduction or obstruction of the oxygen supplied to that tissue. infarction measurement JSmith 2012-02-15T05:58:36Z Measurement of an area of necrotic tissue in the heart resulting from a reduction or obstruction of the oxygen supply. myocardial infarction measurement heart infarction measurement JSmith 2012-02-15T06:09:00Z Measurement of an area of necrotic tissue in the left ventricle of the heart resulting from a reduction or obstruction of the oxygen supply to the heart. heart left ventricle infarction measurement JSmith 2012-02-15T06:11:07Z Measurement of the area, volume or weight of necrotic tissue resulting from a reduction or obstruction of the oxygen supplied to that tissue. infarction size JSmith 2012-02-15T06:14:35Z Measurement of the area, volume or weight of necrotic tissue in the heart resulting from a reduction or obstruction of the oxygen supply to the heart. heart infarction size JSmith 2012-02-15T06:18:51Z Measurement of the area, volume or weight of necrotic tissue in the heart left ventricle resulting from a reduction or obstruction of the oxygen supply to the heart. heart left ventricle infarction size JSmith 2012-02-15T06:27:35Z calculated heart left ventricle infarction size JSmith 2012-02-15T06:28:08Z heart left ventricle infarction size as percentage of total heart left ventricle size JSmith 2012-02-15T06:46:40Z The heaviness of one or both ventricles of the heart, that is, the lower chambers of the heart that pump blood away from the heart either to the lungs to be oxygenated or, once oxygenated, to the rest of the body, or the degree to which one or both ventricles of the heart are drawn toward the earth by gravity. heart ventricle weight JSmith 2012-02-21T02:50:48Z heart infarction weight JSmith 2012-02-21T03:02:09Z heart infarction area JSmith 2012-02-21T03:02:46Z heart left ventricle infarction weight JSmith 2012-02-21T03:03:35Z heart left ventricle infarction area JSmith 2012-02-21T03:04:15Z calculated heart left ventricle infarction area JSmith 2012-02-21T03:04:51Z calculated heart left ventricle infarction weight JSmith 2012-02-21T03:05:44Z heart left ventricle infarction weight as percentage of total heart left ventricle weight JSmith 2012-02-21T03:08:57Z calculated heart infarction weight JSmith 2012-03-09T04:05:52Z The difference in body temperature between two different points in time or between two different conditions. The term "absolute change" refers to the subtraction of one value from another, as opposed to a dissimilarity of two values expressed as a ratio or as a percentage. In this context it is not intended to necessarily imply the difference expressed as an absolute value |n|, that is, the numeric value of the difference without regard to its sign. absolute change in body temperature JSmith 2012-03-09T05:24:30Z Measurement of the amount of resistance in a blood vessel to the flow of blood or other fluid through it. blood vessel resistance measurement JSmith 2012-03-09T05:53:03Z Resistance to blood flow by blood vessels in the lung. pulmonary vascular resistance (PVR) JSmith 2012-03-09T05:57:02Z Measurement of vascular resistance in lung blood vessels calculated from other indirect measurements. calculated PVR calculated pulmonary vascular resistance JSmith 2012-03-09T06:00:03Z R_Flow100 calculated pulmonary vascular resistance normalized to body weight JSmith 2012-03-13T12:26:02Z Measurement made on the endothelial tissue or endothelial cells lining a blood vessel. blood vessel endothelium measurement JSmith 2012-03-13T12:29:04Z calculated blood vessel endothelium measurement JSmith 2012-03-13T12:31:07Z FAPGG metabolism-surface area product JSmith 2012-03-13T01:02:07Z methylene blue metabolism-surface area product without auto-oxidation JSmith 2012-03-13T01:03:47Z methylene blue metabolism-surface area product after auto-oxidation JSmith 2012-03-13T01:12:29Z Ratio of the methylene blue metabolism-surface area product without auto-oxidation to the FAPGG metabolism-surface area product. methylene blue to FAPGG metabolism-surface area product ratio JSmith 2012-03-13T04:15:39Z Any measurement of the energy produced by the active reduction in the diameter of a blood vessel, any one of the network of muscular tubes that carry blood through the body, resulting from contraction of the muscular wall of the vessel. blood vessel contractility measurement blood vessel contractile force measurement JSmith 2012-03-13T04:46:14Z Measurement of the highest achievable amount of energy produced by the active reduction in the diameter of a blood vessel, any one of the network of muscular tubes that carry blood through the body, resulting from contraction of the muscular wall of the vessel. blood vessel maximum contractility measurement blood vessel maximum contractile force JSmith 2012-03-13T04:47:52Z maximum contractile force per wet weight of vessel JSmith 2012-03-14T04:09:34Z Measurement of an organism's, organ's, tissue's or cell's capacity to respond, such as by a change in activity, state or condition, to a drug or other chemical stimulus. chemical response/sensitivity measurement JSmith 2012-03-14T04:16:11Z A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of the energy produced by the active reduction in the diameter of a blood vessel, any one of the network of muscular tubes that carry blood through the body, resulting from contraction of the muscular wall of the vessel. calculated blood vessel contractile force measurement JSmith 2012-03-14T04:17:28Z A calculated value for the concentration of phenylephrine (PE), the phenylethanolamine with IUPAC name (R)-3-[-1-hydroxy-2-(methylamino)ethyl]phenol and formula C9H13NO2 that acts as a selective alpha1-adrenergic receptor agonist, decongestant and vasoconstrictor, at which the energy produced by the active reduction in the diameter of a blood vessel in response to the application of PE is halfway between the baseline value and the highest achievable value of such PE-induced contractile energy. phenylephrine half maximal effective concentration (EC50) concentration of phenylephrine at which the force of blood vessel contraction is half the maximum value (EC50) JSmith 2012-03-14T04:17:54Z A calculated value for logarithm of the concentration of phenylephrine (PE), the phenylethanolamine with IUPAC name (R)-3-[-1-hydroxy-2-(methylamino)ethyl]phenol and formula C9H13NO2 that acts as a selective alpha1-adrenergic receptor agonist, decongestant and vasoconstrictor, at which the energy produced by the active reduction in the diameter of a blood vessel in response to the application of PE is halfway between the baseline value and the highest achievable value of such PE-induced contractile energy. The logarithm of the concentration is the exponent indicating the power to which 10 must be raised to obtain that concentration value. phenylephrine Log half maximal effective concentration (Log EC50) logarithm of the concentration of phenylephrine at which the force of blood vessel contraction is half the maximum value (Log EC50) JSmith 2012-03-14T04:21:12Z Measurement of the reduction in force during dilation of a blood vessel via calculations from direct measurements rather than expressing the direct measurements themselves. calculated blood vessel dilation force reduction measurement JSmith 2012-03-14T04:23:57Z A calculated value for the concentration of acetylcholine (ACh), the ester of acetic acid and choline with chemical formula CH3C=OO(CH2)2-N(+)-(CH3)3 and IUPAC name 2-acetoxy-N,N,N-trimethylethanaminium, which acts as a neurotransmitter, at which the energy exerted during the active expansion in the diameter of a blood vessel in response to the application of ACh is halfway between the highest value, that is the force at greatest constriction (often measured in a pre-constricted blood vessel), and the lowest achievable value of such contractile energy during ACh-induced relaxation of the vessel wall (i.e. the maximum effect of Ach which is the minimum contractile energy). acetylcholine half maximal effective concentration (EC50) concentration of acetylcholine at which the reduction in force during dilation of a blood vessel is half the maximum value (EC50) JSmith 2012-03-14T04:24:16Z A calculated value for logarithm of the concentration of acetylcholine (ACh), the ester of acetic acid and choline with chemical formula CH3C=OO(CH2)2-N(+)-(CH3)3 and IUPAC name 2-acetoxy-N,N,N-trimethylethanaminium, which acts as a neurotransmitter, at which the energy exerted during the active expansion in the diameter of a blood vessel in response to the application of ACh is halfway between the highest value, that is the force at greatest constriction (often measured in a pre-constricted blood vessel), and the lowest achievable value of such contractile energy during ACh-induced relaxation of the vessel wall (i.e. the maximum effect of Ach which is the minimum contractile energy). The logarithm of the concentration is the exponent indicating the power to which 10 must be raised to obtain that concentration value. acetylcholine Log half maximal effective concentration (Log EC50) logarithm of the concentration of acetylcholine at which the reduction in force during dilation of a blood vessel is half the maximum value (Log EC50) JSmith 2012-03-14T04:24:44Z A calculated value for the concentration of sodium nitroprusside (SNP), the red-colored inorganic salt with the formula Na2[Fe(CN)5NO]-2H2O used as a potent vasodilator, at which the energy exerted during the active expansion in the diameter of a blood vessel in response to the application of SNP is halfway between the highest value, that is the force at greatest constriction (often measured in a pre-constricted blood vessel), and the lowest achievable value of such contractile energy during SNP-induced relaxation of the vessel wall (i.e. the maximum effect of SNP which is the minimum contractile energy). sodium nitroprusside half maximal effective concentration (EC50) concentration of sodium nitroprusside at which the reduction in force during dilation of a blood vessel is half the maximum value (EC50) JSmith 2012-03-14T04:25:16Z A calculated value for logarithm of the concentration of sodium nitroprusside (SNP), the red-coloured inorganic salt with the formula Na2[Fe(CN)5NO]-2H2O used as a potent vasodilator, at which the energy exerted during the active expansion in the diameter of a blood vessel in response to the application of SNP is halfway between the highest value, that is the force at greatest constriction (often measured in a pre-constricted blood vessel), and the lowest achievable value of such contractile energy during SNP-induced relaxation of the vessel wall (i.e. the maximum effect of SNP which is the minimum contractile energy). sodium nitroprusside Log half maximal effective concentration (Log EC50) logarithm of the concentration of sodium nitroprusside at which the reduction in force during dilation of a blood vessel is half the maximum value (Log EC50) JSmith 2012-03-15T11:42:31Z maximum contractile force per wet weight of aorta JSmith 2012-03-15T11:48:29Z Measurement of the reduction in force during blood vessel dilation. blood vessel dilation force reduction measurement JSmith 2012-03-15T11:53:37Z blood vessel dilation expressed as percent of force at maximum constriction JSmith 2012-03-15T11:55:20Z acetylcholine-induced blood vessel dilation expressed as percent of phenylephrine-induced vasoconstriction acetylcholine-induced blood vessel dilation expressed as percent of force at maximum constriction JSmith 2012-03-15T11:59:59Z sodium nitroprusside-induced blood vessel dilation expressed as percent of phenylephrine-induced vasoconstriction sodium nitroprusside-induced blood vessel dilation expressed as percent of force at maximum constriction JSmith 2012-03-15T12:00:51Z hypoxia-induced blood vessel dilation expressed as percent of force at maximum constriction JSmith 2012-03-15T12:03:40Z slope measurement of phenylephrine-induced contraction slope measurement of drug-induced contraction slope measurement of chemical-induced contraction JSmith 2012-03-15T12:05:49Z fast-slope measurement of phenylephrine-induced contraction fast-slope measurement of drug-induced contraction fast-slope measurement of chemical-induced contraction JSmith 2012-03-15T12:06:21Z slow-slope measurement of phenylephrine-induced contraction slow-slope measurement of drug-induced contraction slow-slope measurement of chemical-induced contraction JSmith 2012-03-15T12:11:24Z Measurement of an organism's, organ's, tissue's or cell's capacity to respond, such as by a change in activity, state or condition, to acetylcholine (ACh), the ester of acetic acid and choline with chemical formula CH3C=OO(CH2)2-N(+)-(CH3)3 and IUPAC name 2-acetoxy-N,N,N-trimethylethanaminium, which acts as a neurotransmitter. acetylcholine response/sensitivity measurement JSmith 2012-03-15T12:12:47Z Measurement of an organism's, organ's, tissue's or cell's capacity to respond, such as by a change in activity, state or condition, to phenylephrine (PE), the phenylethanolamine with IUPAC name (R)-3-[-1-hydroxy-2-(methylamino)ethyl]phenol and formula C9H13NO2 that acts as a selective alpha1-adrenergic receptor agonist, decongestant and vasoconstrictor. phenylephrine response/sensitivity measurement JSmith 2012-03-15T12:13:21Z Measurement of an organism's, organ's, tissue's or cell's capacity to respond, such as by a change in activity, state or condition, to sodium nitroprusside (SNP), the red-colored inorganic salt with the formula Na2[Fe(CN)5NO]-2H2O used as a potent vasodilator. sodium nitroprusside response/sensitivity measurement JSmith 2012-03-20T04:21:00Z percent change in heart rate JSmith 2012-03-20T04:31:30Z Calculation of a difference between representations of blood pressure in a treated versus untreated state or over time, after the original values have been normalized or adjusted by a mathematical process or computation. Blood pressure is the pressure, or force per area, exerted by circulating blood against the walls of the blood vessels. The pressure is dependent on the energy of the heart action, elasticity of the vessel walls and volume and viscosity of the blood. change in calculated blood pressure JSmith 2012-03-20T04:31:52Z A calculated measurement of the difference in developed blood pressure between a treated state and a control state. Developed pressure is systolic minus diastolic pressure when measured in an isolated organ or vessel under conditions where perfusion pressure or flow can be controlled. change in developed blood pressure JSmith 2012-03-20T04:32:19Z A calculated measurement of the difference in developed blood pressure between a treated state and a control state, expressed as a percentage. Developed pressure is systolic minus diastolic pressure when measured in an isolated organ or vessel under conditions where perfusion pressure or flow can be controlled. percent change in developed blood pressure JSmith 2012-03-20T04:34:31Z Calculated measurement of a difference in the maximum arterial blood pressure, that is the pressure at the point of maximal contraction of the heart, between two points in time or two conditions. change in systolic blood pressure JSmith 2012-03-20T04:35:00Z The relative difference in the maximum arterial blood pressure, that is the pressure at the point of maximal contraction of the heart, between two points in time or two conditions expressed as a percentage. percent change in systolic blood pressure JSmith 2012-03-20T04:37:30Z change in arterial blood flow rate JSmith 2012-03-20T04:38:02Z percent change in arterial blood flow rate JSmith 2012-03-20T04:38:35Z The term "absolute change" refers to the subtraction of one value from another, as opposed to a dissimilarity of two values expressed as a ratio or as a percentage. In this context it is not intended to necessarily imply the difference expressed as an absolute value |n|, that is, the numeric value of the difference without regard to its sign. absolute change in arterial blood flow rate JSmith 2012-03-21T01:08:08Z A calculated measurement of the difference in developed pressure measured in the heart left ventricle between a treated state and a control state, expressed as a percentage. Developed pressure is systolic minus diastolic pressure when measured in an isolated organ or vessel under conditions where perfusion pressure or flow can be controlled. percent change in left ventricular developed pressure JSmith 2012-03-21T01:09:30Z A calculated measurement of the difference in developed pressure measured in the heart left ventricle between a treated state and a control state. Developed pressure is systolic minus diastolic pressure when measured in an isolated organ or vessel under conditions where perfusion pressure or flow can be controlled. change in left ventricular developed pressure JSmith 2012-03-21T01:13:41Z Difference in the pressure within the heart left ventricle at the point of maximal contraction, when the blood is forced from the left ventricle into the aorta, between two points in time or two conditions. change in left ventricular systolic blood pressure JSmith 2012-03-21T01:14:31Z The relative difference in the pressure within the heart left ventricle at the point of maximal contraction, when the blood is forced from the left ventricle into the aorta, between two points in time or two conditions expressed as a percentage. percent change in left ventricular systolic blood pressure JSmith 2012-03-30T07:52:39Z The activity level of LDH in effluent expressed relative to the weight of the heart; calculated as LDH activity divided by heart wet weight. heart effluent lactate dehydrogenase activity level normalized to heart weight JSmith 2012-06-07T11:37:18Z heart left ventricle weight JSmith 2012-06-07T11:38:49Z heart right ventricle weight JSmith 2012-06-07T12:01:20Z The average blood pressure within the pulmonary artery over a specified period of time, or technically over a complete cycle of one heartbeat. mean pulmonary artery (PA) pressure mean pulmonary arterial blood pressure JSmith 2012-06-07T02:24:23Z Measurement of blood pressure in the pulmonary artery. pulmonary artery (PA) blood pressure measurement pulmonary artery pressure pulmonary arterial blood pressure measurement JSmith 2012-06-26T11:34:46Z Measurement of an organ lesion which is or has the potential to become a tumor, that is, a neoplasm or new growth of tissue in which cell multiplication is more or less uncontrolled and progressive. Tumorous lesions include tumors, preneoplastic lesions, and hyperplastic lesions composed of histologically normal cells. organ tumorous lesion measurement JSmith 2012-06-26T11:46:40Z Measurement of an organ lesion which is not neoplastic in origin. A lesion is a localized pathological change in structure of an organ or tissue due to injury or disease; especially one that is circumscribed and well defined. Examples of non-tumorous lesions would include wounds, sores, ulcers, infarctions, etc. organ non-tumorous lesion measurement JSmith 2012-06-26T12:53:39Z Measurement of a heart lesion which is not neoplastic in origin. A lesion is a localized pathological change in structure of an organ or tissue due to injury or disease; especially one that is circumscribed and well defined. Examples of non-tumorous lesions would include wounds, sores, ulcers, infarctions, etc. heart non-tumorous lesion measurement JSmith 2012-06-26T01:22:44Z Measurement of a lesion of the heart which is or has the potential to become a tumor, that is, a neoplasm or new growth of tissue in which cell multiplication is more or less uncontrolled and progressive. Tumorous lesions include tumors, preneoplastic lesions, and hyperplastic lesions composed of histologically normal cells. heart tumorous lesion measurement JSmith 2012-07-11T10:34:14Z Any measurement, morphological or physiological, involving the kidney or any part thereof. Not4Curation kidney measurement JSmith 2012-07-11T10:38:08Z Renal blood flow (RBF) is the volume of blood delivered to or exiting from the kidneys per unit time. renal blood flow rate JSmith 2012-07-11T10:44:48Z Arterial renal blood flow (RBFa) is the volume of blood delivered to the kidneys per unit time via the renal arteries. renal arterial blood flow rate JSmith 2012-07-11T10:48:22Z Venous renal blood flow (RBFv) is the volume of blood exiting from the kidneys per unit time via the renal veins. renal venous blood flow rate JSmith 2012-07-11T12:08:49Z A calculated value in which the weight of the right ventricle, the lower chamber of the right side of the heart, which pumps venous blood through the pulmonary trunk and arteries to the capillaries of the lung, is divided by the total weight of the body and presented as a ratio thus normalizing it to body weight. heart right ventricle weight to body weight ratio JSmith 2012-07-11T12:09:38Z A calculated value in which the weight of the right ventricle, the lower chamber of the right side of the heart, which pumps venous blood through the pulmonary trunk and arteries to the capillaries of the lung, is presented as percentage of the total weight of the body thus normalizing it to body weight. heart right ventricle weight as a percentage of body weight JSmith 2012-07-18T04:24:26Z Any measurement of the physical form or structure of the left ventricle of the heart. The left ventricle is the lower chamber of the left side of the heart, which pumps oxygenated blood out through the aorta to all the tissues of the body. Note, "left" in this context refers to the perspective of the organism, not that of the nobserver. heart left ventricle morphological measurement JSmith 2012-07-18T04:30:51Z Any measurement of the physical form or structure of the right ventricle of the heart. The right ventricle is the lower chamber of the right side of the heart (from the perspective of the organism rather than the observer), which pumps venous blood through the pulmonary trunk and arteries to the capillaries of the lung. heart right ventricle morphological measurement JSmith 2012-07-26T10:04:12Z Measurement of a localized pathological change in structure of a blood vessel due to injury or disease; especially one that is circumscribed and well defined. blood vessel lesion measurement JSmith 2012-07-26T12:15:46Z A measurement of blood vessel diameter which has been normalized or adjusted by a mathematical process or computation. Not4Curation calculated blood vessel diameter measurement JSmith 2012-07-26T12:18:48Z blood vessel wall thickness JSmith 2012-07-26T12:20:54Z A measurement of the depth of the wall of a blood vessel which has been normalized or adjusted by a mathematical process or computation. Not4Curation calculated blood vessel wall thickness measurement JSmith 2012-07-26T12:23:13Z A measurement of the depth of the wall of an artery, one of the large blood vessels carrying blood in a direction away from the heart to the tissues. artery wall thickness JSmith 2012-07-26T12:27:42Z A measurement of the depth of the wall of an artery which has been normalized or adjusted by a mathematical process or computation. An artery is one of the large blood vessels carrying blood in a direction away from the heart to the tissues. Not4Curation calculated artery wall thickness measurement JSmith 2012-07-26T12:32:00Z artery diameter JSmith 2012-07-26T12:39:26Z The length of a line which crosses a transverse view of a blood vessel, passing through its center and ending on either side at the inner surface of the blood vessel wall. blood vessel lumen diameter blood vessel inner diameter JSmith 2012-07-26T12:41:25Z The length of a line which crosses a transverse view of a blood vessel, passing through its center and ending on either side at the outer surface of the blood vessel wall. blood vessel outer diameter JSmith 2012-07-26T12:43:00Z The length of a line which crosses a transverse view of an artery, passing through its center and ending on either side at the inner surface of the blood vessel wall. artery lumen diameter artery inner diameter JSmith 2012-07-26T12:44:18Z The length of a line which crosses a transverse view of an artery, passing through its center and ending on either side at the outer surface of the blood vessel wall. artery outer diameter JSmith 2012-07-26T12:48:55Z Measurement of the length of a line which crosses a transverse view of an artery, passing through its center and ending on either side at either the inner surface or outer surface of the blood vessel wall, which has been normalized or adjusted by a mathematical process or computation. Not4Curation calculated artery diameter measurement JSmith 2012-07-26T12:57:08Z Any measurement of one of the large blood vessels carrying blood in a direction away from the heart to the tissues. artery measurement JSmith 2012-07-26T12:59:52Z Measurement of any localized pathological change in structure of an artery, one of the large blood vessels carrying blood in a direction away from the heart to the tissues, due to injury or disease; especially one that is circumscribed and well defined. artery lesion measurement JSmith 2012-07-26T02:04:57Z Measurement which has been normalized or adjusted by a mathematical process or computation of any localized pathological change in structure of an artery due to injury or disease; especially one that is circumscribed and well defined. Not4Curation calculated artery lesion measurement JSmith 2012-07-26T02:13:01Z Measurement which has been normalized or adjusted by a mathematical process or computation of any localized pathological change in structure of a blood vessel due to injury or disease; especially one that is circumscribed and well defined. Not4Curation calculated blood vessel lesion measurement JSmith 2012-07-26T02:14:51Z A calculated measurement in which the ratio of the wall thickness (WT) of a blood vessel is divided by the inner diameter (ID) of that vessel at that location, and the result presented as a ratio, fraction, quotient or percentage, for example, WT/ID x 100. This measurement is often used to assess stenosis, a pathological narrowing of a blood vessel. blood vessel wall thickness as percentage of blood vessel lumen diameter blood vessel stenosis measurement blood vessel wall thickness as percentage of blood vessel inner diameter blood vessel wall thickness to blood vessel inner diameter ratio JSmith 2012-07-26T02:16:51Z Ratio of the wall thickness (WT) of an artery to inner diameter (ID) of that artery at that location, usually expressed as a percentage, i.e. WT/ID x 100, but could also be expressed as a ratio, fraction or quotient. This measurement can be used to assess stenosis, a pathological narrowing of a blood vessel. arterial stenosis measurement artery wall thickness as percentage of artery inner diameter artery wall thickness as percentage of artery lumen diameter artery wall thickness to artery inner diameter ratio JSmith 2012-07-26T02:25:16Z A measurement of the length of a line which crosses a transverse view of an artery, passing through its center and ending on either side at the inner surface of the blood vessel wall, after that measurement has been normalized or adjusted by a mathematical process or computation. An artery is a blood vessel that carries blood away from the heart. Not4Curation calculated artery inner diameter measurement JSmith 2012-07-26T03:24:53Z Any measurement of components of the periodic tightening and loosening of the muscles of a ventricle of the heart. ventricle contraction measurement JSmith 2012-07-27T03:14:05Z The diameter across the left ventricle of the heart at the end of diastole, that is, when the heart muscle is maximally relaxed, and usually corresponds to its largest diameter. LVDD LVEDD left ventricular end-diastolic dimension heart left ventricular end-diastolic diameter JSmith 2012-07-27T03:32:16Z The diameter across the left ventricle of the heart at the end of systole, that is, when the heart muscle is maximally contracted, and usually corresponds to its smallest diameter. LVESD LVSD left ventricular end-systolic dimension heart left ventricle end-systolic diameter JSmith 2012-07-27T03:42:40Z A measurement of the physical form or structure of the left ventricle of the heart which has been normalized or adjusted by a mathematical process or computation. The heart left ventricle is the lower chamber of the left side of the heart, which pumps oxygenated blood out through the aorta to all the tissues of the body. calculated heart left ventricle morphological measurement JSmith 2012-07-27T03:51:33Z A calculated measurement corresponding to the ratio or percent reduction in left ventricular diameter between end-diastole and end-systole. Can be calculated as the left ventricle end-diastolic diameter (LVDd) minus the left ventricle end-systolic diameter (LVSd) divided by the left ventricle end-diastolic diameter (LVDd) with the quotient multiplied by 100, i.e. FS = [(LVDd-LVSd)/LVDd] x 100. heart left ventricle fractional shortening JSmith 2012-07-27T04:11:09Z The thickness or depth of the ventral/anterior wall of the left ventricle of the heart. The ventral/anterior wall is the portion of the muscle enclosing the ventricle which is farthest from the spine and closest to the chest wall of the organism. heart left ventricle ventral wall thickness heart left ventricle anterior wall thickness JSmith 2012-07-27T05:59:34Z The thickness or depth of the septal wall of the heart ventricles. The septal wall is the portion of the heart left ventricle ventral/anterior wall and right ventricle dorsal/posterior wall which is shared between the ventricles. heart ventricle septal wall thickness SWT antero-septal wall thickness heart interventricular septum thickness heart intraventricular wall thickness heart ventricle septum thickness heart ventricle septal wall thickness JSmith 2012-07-27T06:00:34Z A calculated measurement of left ventricular geometry and is calculated by dividing the end-diastolic diameter into 2x the posterior wall thickness, 2x the septal wall thickness or the sum of the posterior and septal wall thicknesses. It represents a measure of the wall thickness normalized to the size of the ventricle lumen. heart left ventricle relative wall thickness JSmith 2012-07-27T06:15:29Z A calculated measurement of left ventricular geometry and is calculated by dividing the end-diastolic diameter into 2x the posterior wall thickness at end-diastole, 2x the septal wall thickness at end-diastole or the sum of the posterior and septal wall thicknesses at end-diastole. It represents a measure of the wall thickness normalized to the size of the ventricle lumen. heart left ventricle end-diastolic relative wall thickness JSmith 2012-07-30T10:15:23Z The thickness or depth of the ventral/anterior wall of the heart. The ventral wall is the portion of the heart muscle which is farthest from the spine and closest to the chest wall of the organism. heart ventral wall thickness heart anterior wall thickness JSmith 2012-07-30T10:31:58Z Not4Curation calculated heart wall thickness measurement JSmith 2012-07-30T11:04:28Z heart relative wall thickness JSmith 2012-07-30T11:05:55Z heart ventricle relative wall thickness JSmith 2012-07-30T01:25:59Z The extent of shortening of the minor internal circumference (at the midpoint of the long axis) between end-diastole and end-systole, divided by the time required for shortening. mean circumferential fiber shortening rate mean VCF mean velocity of circumferential fiber shortening JSmith 2012-07-30T02:57:57Z The thickness or depth of the ventral/anterior wall of the right ventricle of the heart. The ventral wall is the portion of the muscle enclosing the ventricle which is farthest from the spine and closest to the chest wall of the organism. heart right ventricle ventral wall thickness heart right ventricle anterior wall thickness JSmith 2012-08-02T01:00:46Z Count of the number of glomeruli located in the superficial layer of the renal cortex, the cortex corticis. Glomeruli are the tufts of capillaries each situated within a Bowman's capsule at the end of a renal tubule in the vertebrate kidney that filter waste products from the blood and thus initiate urine formation. superficial glomeruli count superficial glomerulus count JSmith 2012-08-02T01:14:28Z Count of the number of glomeruli located in the superficial layer of the renal cortex, the cortex corticis, and directly in contact with the surface of the kidney, i.e. the renal capsule. Glomeruli are the tufts of capillaries each situated within a Bowman's capsule at the end of a renal tubule in the vertebrate kidney that filter waste products from the blood and thus initiate urine formation. surface glomeruli count count of superficial glomeruli directly contacting the kidney surface JSmith 2012-08-02T01:15:32Z Count of the number of glomeruli located in the superficial layer of the renal cortex, the cortex corticis but without any direct contact with the surface of the kidney, i.e. the renal capsule. Glomeruli are the tufts of capillaries each situated within a Bowman's capsule at the end of a renal tubule in the vertebrate kidney that filter waste products from the blood and thus initiate urine formation. count of superficial glomeruli not directly contacting the kidney surface JSmith 2012-08-03T06:05:33Z heart infarction volume JSmith 2012-08-03T06:17:05Z Measurement of any change or difference in the diastolic blood pressure between two points or two conditions. The diastolic pressure is the minimum arterial pressure within the cardiac cycle, usually at the point at which the heart is in a state of relaxation and expansion. This is the time when the ventricles fill with blood. Not4Curation change in diastolic blood pressure JSmith 2012-08-03T06:19:27Z The relative difference in the diastolic blood pressure between two points or two conditions, expressed as a percentage. The diastolic pressure is the minimum arterial pressure within the cardiac cycle, usually at the point at which the heart is in a state of relaxation and expansion. This is the time when the ventricles fill with blood. percent change in diastolic blood pressure JSmith 2012-08-13T01:16:23Z Calculated measurement of a difference in the pressure within the heart left ventricle at the point of maximal contraction, when the blood is forced from the left ventricle into the aorta, between two points in time or two conditions expressed as the result of the subtraction in and of itself without comparison by ratio with another quantity. The term "absolute change" refers to the subtraction of one value from another, as opposed to a dissimilarity of two values expressed as a ratio or as a percentage. In this context it is not intended to necessarily imply the difference expressed as an absolute value |n|, that is, the numeric value of the difference without regard to its sign. absolute change in left ventricular systolic blood pressure jsmith 2012-08-23T03:27:50Z Temperature measured at the surface of or within the head of an experimental subject. Because the temperature of the head/brain can influence neurological measurements, head temperature is or can be considered to be distinct from core body temperature. cranial temperature head temperature jsmith 2012-08-23T04:06:16Z The temperature of the internal tissues and organs of the body. core temperature core body temperature JSmith 2012-09-13T06:09:33Z A measurement which has been normalized or adjusted by a mathematical process or computation of the weight of the left ventricle of the heart, that is, its the heaviness or degree to which it is drawn toward the earth by gravity. The heart left ventricle is the lower chamber of the left side of the heart, which pumps oxygenated blood out through the aorta to all the tissues of the body. calculated heart left ventricle weight JSmith 2012-09-13T06:11:08Z calculated heart right ventricle weight JSmith 2012-09-13T06:14:55Z calculated heart right ventricle morphological measurement JSmith 2012-10-03T05:31:53Z The length of a line which crosses a transverse view of a cerebral artery, passing through its center and ending on either side at the inner surface of the blood vessel wall. The cerebral arteries are those which supply blood to the brain, more specifically, to the cerebrum. cerebral artery lumen diameter cerebral artery inner diameter JSmith 2012-10-03T05:39:47Z The length of a line which crosses a transverse view of an anterior cerebral artery, passing through its center and ending on either side at the inner surface of the blood vessel wall. The anterior cerebral artery (ACA) is one of a pair of arteries that supply oxygenated blood to the most medial portions of the frontal lobes and superior medial parietal lobes of the brain. ACA inner diameter anterior cerebral artery lumen diameter anterior cerebral artery inner diameter JSmith 2012-10-03T05:48:00Z The length of a line which crosses a transverse view of a middle cerebral artery, passing through its center and ending on either side at the inner surface of the blood vessel wall. The middle cerebral arteries are the largest of the cerebral arteries and supply blood to the lateral cerebral cortex, anterior temporal lobes and insular cortices of the brain. MCA inner diameter middle cerebral artery lumen diameter middle cerebral artery inner diameter JSmith 2012-10-03T05:59:18Z The length of a line which crosses a transverse view of a posterior cerebral artery, passing through its center and ending on either side at the inner surface of the blood vessel wall. The posterior cerebral artery (PCA) is one of a pair of blood vessels that supply blood to the posterior aspect, i.e. the occipital lobe, of the brain. PCA inner diameter posterior cerebral artery lumen diameter posterior cerebral artery inner diameter JSmith 2012-10-08T02:59:36Z Measurement of a lesion in kidney, he organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes. A lesion is a localized pathological change in structure of an organ or tissue due to injury or disease; especially one that is circumscribed and well defined. kidney lesion measurement JSmith 2012-10-08T03:01:39Z Measurement of a lesion in the kidney, he organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes, which is not neoplastic in origin. A lesion is a localized pathological change in structure of an organ or tissue due to injury or disease; especially one that is circumscribed and well defined. Examples of non-tumorous lesions would include wounds, sores, ulcers, infarctions, etc. kidney non-tumorous lesion measurement JSmith 2012-10-08T03:03:01Z Measurement of a lesion in the kidney, he organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes, which is or has the potential to become a tumor, that is, a neoplasm or new growth of tissue in which cell multiplication is more or less uncontrolled and progressive. Tumorous lesions include tumors, preneoplastic lesions, and hyperplastic lesions composed of histologically normal cells. kidney tumorous lesion measurement JSmith 2012-10-08T03:09:04Z Any measurement of lesions resulting from fibrosis, scarring or hyaline deposits within a kidney glomerulus, a tuft of capillaries situated within a Bowman's capsule at the end of a renal tubule in the vertebrate kidney, that filters waste products from the blood and thus initiates urine formation. kidney glomerulosclerosis measurement renal glomerulosclerosis measurement renal glomerulosclerotic lesion measurement kidney glomerulosclerotic lesion measurement JSmith 2012-10-08T03:43:25Z A measurement of lesions resulting from fibrosis, scarring or hyaline deposits within one or more kidney glomeruli which has been normalized, adjusted or derived by a mathematical process or computation. calculated kidney glomerulosclerosis measurement calculated renal glomerulosclerosis measurement calculated renal glomerulosclerotic lesion measurement calculated kidney glomerulosclerotic lesion measurement JSmith 2012-10-08T03:45:56Z A measurement of lesions resulting from fibrosis, scarring or hyaline deposits within kidney glomeruli which is derived from a combination of multiple measurements and/or objective or subjective severity scores according to a specified formula or set of criteria. glomerular damage composite score glomerulosclerosis composite score glomerulosclerosis damage index index of glomerular damage JSmith 2012-10-12T05:28:37Z Any measurement, morphological or physiological of a muscle or a group of muscles. Muscles are organs or tissues composed of bundles of fibers that have the power to contract and hence to produce movement. muscle measurement JSmith 2012-10-15T11:45:27Z Measurement of the physical form or structure of one or more glomeruli in the kidney. Glomeruli are the tufts of capillaries each situated within a Bowman's capsule at the end of a renal tubule in the vertebrate kidney that filter waste products from the blood and thus initiate urine formation. kidney glomerulus morphological measurement JSmith 2012-10-15T11:48:00Z The length of a straight line passing through the center of a kidney glomerulus and connecting opposite points on its circumference. kidney glomerular diameter kidney glomerulus diameter JSmith 2012-10-15T11:55:42Z A measurement of the volume of blood delivered to or exiting from the kidneys per unit time, which has been normalized, adjusted or derived by a mathematical process or computation. calculated renal blood flow rate JSmith 2012-10-15T11:59:32Z The difference in the volume of blood delivered to or exiting from the kidneys per unit time between two points in time or two conditions expressed as the result of the subtraction in and of itself without comparison by ratio with another quantity. The term "absolute change" refers to the subtraction of one value from another, as opposed to a dissimilarity of two values expressed as a ratio or as a percentage. In this context it is not intended to necessarily imply the difference expressed as an absolute value |n|, that is, the numeric value of the difference without regard to its sign. absolute change in renal blood flow rate JSmith 2012-10-22T12:14:30Z The number of kidney glomeruli with lesions resulting from fibrosis, scarring or hyaline deposits, or the number of such lesions in a specified sample. damaged glomeruli count number of sclerotic glomeruli sclerotic glomeruli count sclerotic glomerulus count kidney glomerulosclerotic lesion count JSmith 2012-10-22T01:31:20Z Any measurement involving the composition, that is, the absolute amount, relative amount or type of one or more proteins (complex high molecular weight organic compounds containing carbon, hydrogen, oxygen, nitrogen, and sulfur consisting of alpha-amino acids joined by peptide linkages) or peptides (low molecular weight compounds composed of at least two amino acids joined by peptide linkages) in kidney. kidney tissue protein/peptide composition measurement kidney protein/peptide composition measurement JSmith 2012-10-22T03:13:42Z Any measurement, morphological or physiological of the outer part of the kidney, composed mainly of glomeruli and convoluted tubules. kidney cortex measurement renal cortex measurement JSmith 2012-10-22T03:20:09Z Any measurement, morphological or physiological, of the renal medulla, the innermost part of the kidney which contains the structures of the nephrons responsible for maintaining the salt and water balance of the blood. kidney medulla measurement renal medulla measurement JSmith 2012-10-22T03:28:36Z Any measurement involving the amount, composition or type of protein, the complex organic compounds containing carbon, hydrogen, oxygen, nitrogen, and sulfur consisting of alpha-amino acids joined by peptide linkages, in kidney medulla, the innermost part of the kidney which contains the structures of the nephrons responsible for maintaining the salt and water balance of the blood. kidney medulla protein measurement renal medulla protein measurement JSmith 2012-10-22T03:31:18Z Any measurement involving the amount, composition or type of protein, the complex organic compounds containing carbon, hydrogen, oxygen, nitrogen, and sulfur consisting of alpha-amino acids joined by peptide linkages, in renal cortex, the outer part of the kidney, composed mainly of glomeruli and convoluted tubules. kidney cortex protein measurement renal cortex protein measurement JSmith 2012-10-22T03:34:08Z A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of the composition, that is, the absolute amount, relative amount or type, of protein (the complex organic compounds containing carbon, hydrogen, oxygen, nitrogen, and sulfur consisting of alpha-amino acids joined by peptide linkages) in kidney. calculated renal protein composition measurement calculated kidney protein composition measurement JSmith 2012-10-22T03:41:53Z A measurement which has been normalized, adjusted or derived by a mathematical process or computation involving the amount, composition or type of protein in the kidney cortex, the outer part of the kidney, composed mainly of glomeruli and convoluted tubules. calculated kidney cortex protein composition measurement calculated renal cortex protein composition measurement JSmith 2012-10-22T03:43:38Z A measurement which has been normalized, adjusted or derived by a mathematical process or computation involving the amount, composition or type of protein in the renal medulla, the innermost part of the kidney which contains the structures of the nephrons responsible for maintaining the salt and water balance of the blood. calculated kidney medulla protein composition measurement calculated renal medulla protein composition measurement JSmith 2012-10-22T04:00:13Z A calculated value in which the amount of TRPV4 protein in a specified sample of kidney is divided by the amount of beta-actin protein in the same or a corresponding sample of kidney and presented as a ratio, fraction or quotient, thus normalizing it to the beta-actin protein level. renal TRPV4 protein level to beta-actin protein level ratio kidney TRPV4 protein level to beta-actin protein level ratio JSmith 2012-10-22T04:33:48Z A calculated value in which the amount of TRPV4 protein in a specified sample of renal cortex is divided by the amount of beta-actin protein in the same or a corresponding sample of renal cortex and presented as a ratio, fraction or quotient, thus normalizing it to the beta-actin protein level. kidney cortex TRPV4 protein level to beta-actin protein level ratio renal cortex TRPV4 protein level to beta-actin protein level ratio JSmith 2012-10-22T04:35:29Z A calculated value in which the amount of TRPV4 protein in a specified sample of renal medulla is divided by the amount of beta-actin protein in the same or a corresponding sample of renal medulla and presented as a ratio, fraction or quotient, thus normalizing it to the beta-actin protein level. kidney medulla TRPV4 protein level to beta-actin protein level ratio renal medulla TRPV4 protein level to beta-actin protein level ratio JSmith 2012-10-23T10:05:50Z The length of a line which crosses a transverse view of a cerebral artery, passing through its center and ending on either side at the inner surface of the blood vessel wall, after that measurement has been normalized or adjusted by a mathematical process or computation. The cerebral arteries are those which supply blood to the brain, more specifically, to the cerebrum. calculated cerebral artery inner diameter measurement JSmith 2012-10-23T10:06:14Z The length of a line which crosses a transverse view of a middle cerebral artery, passing through its center and ending on either side at the inner surface of the blood vessel wall, after that measurement has been normalized or adjusted by a mathematical process or computation. The middle cerebral arteries are the largest of the cerebral arteries and supply blood to the lateral cerebral cortex, anterior temporal lobes and insular cortices of the brain. calculated middle cerebral artery inner diameter measurement JSmith 2012-10-23T10:09:32Z A calculated measurement of the relative difference in the middle cerebral artery inner diameter between a treated state and a control state or between two points in time, expressed as a percentage. percent change in middle cerebral artery inner diameter JSmith 2012-11-12T15:45:39Z A measurement of the extent of a two-dimensional plane through the left ventricle of the heart at the end of diastole, that is, when the heart muscle is maximally relaxed, and usually corresponds to its largest diameter. EDA LVAd LVDa heart left ventricle end-diastolic area JSmith 2012-11-12T15:47:47Z A measurement of the extent of a two-dimensional plane through the left ventricle of the heart at the end of systole, that is, when the heart muscle is maximally contracted, and usually corresponds to its smallest diameter. ESA LVAs LVSa heart left ventricle end-systolic area JSmith 2012-11-15T15:35:17Z A calculated value in which the weight of the heart, the chambered, muscular organ that maintains the circulation of the blood, is divided by the length of the tibia, the inner and larger bone of the lower leg or hindlimb, and presented as a ratio, fraction, quotient or percentage, thus normalizing it to the length of the leg and, by extension, to the length of the body. heart weight to tibia length ratio JSmith 2012-11-15T15:38:38Z A calculated value in which the total weight after removal from the body but without desiccation of both kidneys is divided by the length of the tibia, the inner and larger bone of the lower leg or hindlimb, and presented as a ratio, fraction, quotient or percentage, thus normalizing it to the length of the leg and, by extension, to the length of the body. both kidneys wet weight to tibia length ratio JSmith 2013-01-07T13:24:24Z A calculated measurement of the ratio between the change in mean arterial blood pressure and the concentration of sodium infused directly into the ventricle(s) of the brain; calculated as the slope of the curve of mean arterial blood pressure versus intracerebroventricular-infused sodium concentration. change in mean arterial blood pressure to change in intracerebroventricular sodium concentration ratio JSmith 2013-01-07T13:34:46Z A calculated measurement of the ratio between the change in heart rate and the concentration of sodium infused directly into the ventricle(s) of the brain; calculated as the slope of the curve of heart rate versus intracerebroventricular-infused sodium concentration. change in heart rate to change in intracerebroventricular sodium concentration ratio JSmith 2013-01-07T15:55:09Z A value calculated by dividing the proportionate change in renal blood flow (RBF) by the proportionate change in renal perfusion pressure (RPP), i.e. (RBF2 - RBF1)/RBF1 divided by (RPP2 - RPP1)/RPP1. autoregulatory index ratio of renal blood flow change to renal perfusion pressure change ratio of change in renal blood flow to change in renal perfusion pressure JSmith 2013-01-08T14:41:50Z Any measurement of a lesion in the kidney characterized by an abnormal proliferation of fibrous connective tissue. A lesion is a localized pathological change in structure of an organ or tissue due to injury or disease; especially one that is circumscribed and well defined. kidney fibrotic lesion measurement JSmith 2013-01-08T14:54:45Z Any measurement of the physical dimensions, proportions, magnitude, or extent of a lesion in the kidney characterized by an abnormal proliferation of fibrous connective tissue. A lesion is a localized pathological change in structure of an organ or tissue due to injury or disease; especially one that is circumscribed and well defined. kidney fibrotic lesion size measurement JSmith 2013-01-08T15:03:27Z A measurement of the extent of a two-dimensional surface of or plane through a single kidney fibrotic lesion, or a measurement of the total area occupied by fibrotic lesions in a cross-section of the kidney. kidney fibrotic lesion area measurement JSmith 2013-01-08T15:17:52Z A measurement of the extent of a two-dimensional surface of or plane through a single kidney fibrotic lesion, or a measurement of the total area occupied by fibrotic lesions in a cross-section of the kidney, when that value has been normalized, adjusted or derived by a mathematical process or computation. calculated kidney fibrotic lesion area measurement JSmith 2013-01-08T15:20:55Z A calculated value in which the extent of the two-dimensional surface occupied by fibrotic lesions is divided by the total extent of the two-dimensional surface of the kidney and presented as a ratio, fraction, quotient or percentage, thus normalizing it to the size of the kidney. kidney fibrotic lesion area to total kidney area ratio JSmith 2013-01-08T16:28:12Z A calculated value in which the number of glomeruli with lesions resulting from fibrosis, scarring or hyaline deposits is divided by the total number of glomeruli in a specified sample of kidney and presented as a ratio, fraction or quotient, thus normalizing it to the total number of glomeruli. sclerotic glomeruli to total glomeruli ratio kidney glomerulosclerotic lesion count to total glomeruli count ratio kidney sclerotic glomeruli count to total glomeruli count ratio JSmith 2013-01-09T15:09:49Z The combined weight of both ventricles of the heart, that is, their heaviness or the degree to which they are drawn toward the earth by gravity. The ventricles are the lower chambers of the heart that pump blood away from the heart either to the lungs to be oxygenated or, once oxygenated, to the rest of the body. total heart ventricle weight JSmith 2013-01-09T16:00:43Z A measurement of the combined weight of both heart ventricles that has been normalized, adjusted or derived by a mathematical process or computation. Not4Curation calculated total heart ventricle weight JSmith 2013-01-09T16:03:12Z A calculated value in which the combined weight of both the left and right ventricles, the lower chambers of the heart that pump blood away from the heart either to the lungs to be oxygenated or, once oxygenated, to the rest of the body, is presented as percentage of the total weight of the body thus normalizing it to body weight. total heart ventricle weight as a percentage of body weight JSmith 2013-01-15T10:37:51Z Any measurement of the cavity or channel within an artery, one of the large blood vessels carrying blood in a direction away from the heart to the tissues. artery lumen measurement JSmith 2013-01-15T10:50:23Z A measurement of the two-dimensional extent of the enclosed cavity or channel in a cross-section of an artery, one of the large blood vessels carrying blood in a direction away from the heart to the tissues. artery lumen area JSmith 2013-01-15T11:04:30Z Any measurement of the fibrous and muscular structure of one of the large blood vessels carrying blood in a direction away from the heart to the tissues. The wall of an artery is composed of three layers: the tunica intima, the inner coat; the tunica media, the middle coat; and the tunica adventitia, the outer coat. arterial wall measurement artery wall measurement JSmith 2013-01-15T11:17:48Z Any measurement of the tunica media, or middle coat, of the wall of an artery, one of the large blood vessels carrying blood in a direction away from the heart to the tissues. arterial tunica media measurement artery tunica media measurement JSmith 2013-01-15T11:21:04Z A direct measurement of two dimensional extent of the tunica media, the middle coat of the arterial wall, in a cross-section of an artery, one of the large blood vessels carrying blood in a direction away from the heart to the tissues. The total area of the tunica media gives an indication of the thickness of the arterial wall. arterial tunica media area media area (MA) of artery artery tunica media area JSmith 2013-01-15T11:34:35Z A calculated measurement of the average width of the tunica media, the middle coat of the arterial wall. Can be calculated using the media area and the length of the internal elastic lamina. arterial tunica media width media width (MW) of artery artery tunica media width JSmith 2013-01-15T12:10:01Z A measurement of the extent of a two-dimensional surface of or plane through a single hyperplastic lesion of the tunica intima, that is, the inner coat of the arterial wall, or a measurement of the total area occupied by hyperplastic lesions of the tunica intima in a cross-section of an artery, one of the large blood vessels carrying blood in a direction away from the heart to the tissues. A hyperplastic lesion is a localized pathological increase in the number of cells of an organ or tissue resulting from an increased rate of cellular division due to injury or disease; especially one that is circumscribed and well defined. artery intimal hyperplastic lesion area neointimal hyperplasia area of artery artery neointimal hyperplastic lesion area JSmith 2013-01-15T12:33:00Z Any measurement of one or more hyperplastic lesions of the arterial tunica intima which has been normalized, adjusted or derived by a mathematical process. calculated arterial intima hyperplasia area calculated artery neointimal hyperplastic lesion area JSmith 2013-01-15T12:33:16Z A calculated measurement in which the area of the arterial tunica intima occupied by one or more hyperplastic lesions is divided by the total cross-sectional area of the artery wall and presented as a ratio, fraction, quotient or percentage. ratio of neointimal hyperplasia area to total wall area of artery artery neointimal hyperplastic lesion area to total wall area ratio JSmith 2013-01-15T12:50:46Z The area of the arterial lumen remaining when the luminal space is restricted by a pathological process, e.g. hyperplasia. residual lumen area of diseased artery lesioned artery residual lumen area JSmith 2013-01-16T13:36:09Z The weight after desiccation of both kidneys, the paired organs which function to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes. both kidneys dry weight JSmith 2013-01-16T13:36:57Z The weight after desiccation of a single kidney, one of the paired organs which function to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes. individual kidney dry weight single kidney dry weight JSmith 2013-01-21T16:32:31Z Any measurement of the great artery arising from the left ventricle from which the systemic arterial system proceeds. aorta measurement JSmith 2013-01-21T16:37:23Z Any quantification of the physical form or structure of the great artery arising from the left ventricle from which the systemic arterial system proceeds. aorta morphological measurement JSmith 2013-01-25T12:50:21Z The speed at which the blood flows through the circulatory system or through a specific segment of a vein or artery, expressed as distance per unit of time. blood flow velocity JSmith 2013-01-25T12:56:43Z The speed at which the blood flows through an artery, expressed as distance per unit of time. arterial blood flow velocity JSmith 2013-01-25T13:10:05Z The speed at which the blood flows through the aorta, the great artery arising from the left ventricle from which the systemic arterial system proceeds, expressed as distance per unit of time. aortic blood flow velocity JSmith 2013-01-25T13:15:01Z Any measurement of the movement of blood through the aorta, the great artery arising from the left ventricle from which the systemic arterial system proceeds. aortic blood flow measurement JSmith 2013-01-25T13:18:41Z The volume of blood flowing through the aorta, the great artery arising from the left ventricle from which the systemic arterial system proceeds, per unit of time. aortic blood flow rate JSmith 2013-01-25T13:21:50Z The maximum speed at which the blood flows through the aorta during the cardiac cycle, expressed as distance per unit of time. aortic peak velocity (APV) maximum aortic velocity peak aortic blood flow velocity peak of aortic outflow velocity (PAV) peak aortic velocity JSmith 2013-01-25T13:29:29Z The length of time in the cardiac cycle between the closing of the aortic and pulmonic/pulmonary semilunar valves and opening of the atrioventricular (AV) valves marking the beginning of ventricular filling. Used as an indicator of diastolic dysfunction. IVRT heart isovolumetric relaxation time JSmith 2013-01-25T13:35:08Z Measurement of the physical form or structure of the left upper chamber of the heart that receives blood from the veins and forces it into the left ventricle. heart left atrium morphological measurement JSmith 2013-01-25T13:42:05Z Measurement of the physical form or structure of the right upper chamber of the heart that receives blood from the veins and forces it into the right ventricle. heart right atrium morphological measurement JSmith 2013-01-25T13:51:15Z The distance between two specified opposite points on the periphery of the left atrium of the heart at the end of systole, that is, when the left ventricle is maximally contracted, and usually corresponds to the left atrium's largest diameter. heart left atrium end-systolic diameter JSmith 2013-01-25T15:50:33Z The distance between two specified opposite points on the periphery of the left atrium of the heart at the end of diastole, that is, when the left ventricle is maximally dilated, and usually corresponds to the left atrium's smallest diameter. heart left atrium end-diastolic diameter JSmith 2013-01-25T15:51:30Z A measurement of the physical form or structure of the left atrium, the left upper chamber of the heart that receives blood from the veins and forces it into the left ventricle, which has been normalized, adjusted or derived by a mathematical process or computation. calculated heart left atrium morphological measurement JSmith 2013-01-25T16:00:18Z A calculated measurement corresponding to the ratio or percent reduction in left atrial diameter between end-systole and end-diastole. It is calculated as the left atrium end-systolic diameter (LADs) minus the left atrium end-diastolic diameter (LADd) divided by the left atrium end-systolic diameter (LADs). heart left atrium fractional shortening JSmith 2013-01-28T16:41:10Z Measurement of the number of white blood cells, including lymphocytes and monocytes, with a single round or oval nucleus in a specified volume of blood. mononuclear leukocyte count blood mononuclear cell count JSmith 2013-01-30T14:16:47Z A measurement of the movement of blood through one or more vessels or organs in the body which has been normalized, adjusted or derived by a mathematical process or computation. calculated blood flow measurement JSmith 2013-03-15T17:22:25Z Any measurement of the thick contractile middle layer of uniquely constructed and arranged muscle cells that forms the bulk of the heart wall. myocardium measurement JSmith 2013-03-15T17:29:25Z The volume of fluid flowing into, out of or through the blood vessels and microvasculature of the myocardium, the thick contractile middle layer of uniquely constructed and arranged muscle cells that forms the bulk of the heart wall, per unit time. myocardial flow rate JSmith 2013-03-15T17:38:35Z Measurement of the amount of radioactive or other tracer is lost from the myocardium, the thick contractile middle layer of uniquely constructed and arranged muscle cells that forms the bulk of the heart wall, per unit time. myocardial clearance rate JSmith 2013-06-18T10:33:25Z A value resulting from the quantification of a morphological or physiological parameter of vascular smooth muscle, the contractile soft tissue having fine myofibrils but lacking transverse striations composing the majority of the wall of blood vessels, the network of muscular tubes that carry blood through the body. vascular smooth muscle measurement Not4Curation blood vessel smooth muscle measurement JSmith 2013-06-18T10:41:10Z Any quantification of the physical form or structure of the layered tissue which encloses and constitutes the structural component of the great artery arising from the left ventricle from which the systemic arterial system proceeds. aortic wall morphological measurement aorta wall morphological measurement JSmith 2013-06-18T10:42:34Z Measurement of the total number of cells, membrane-enclosed protoplasmic masses constituting the smallest structural unit of an organism that is capable of independent functioning, in a specified sample of the aorta smooth muscle, the contractile soft tissue having fine myofibrils but lacking transverse striations composing the majority of the wall of the great artery arising from the left ventricle from which the systemic arterial system proceeds. aortic smooth muscle cell count aorta smooth muscle cell count JSmith 2013-06-18T11:29:28Z Measurement of the total number of cells, membrane-enclosed protoplasmic masses constituting the smallest structural unit of an organism that is capable of independent functioning, in a specified sample of vascular smooth muscle, the contractile soft tissue having fine myofibrils but lacking transverse striations composing the majority of the wall of blood vessels, the network of muscular tubes that carry blood through the body. vascular smooth muscle cell count blood vessel smooth muscle cell count JSmith 2013-06-18T12:57:40Z A measurement which has been normalized, adjusted or derived by a mathematical process or computation of the total number of cells, membrane-enclosed protoplasmic masses constituting the smallest structural unit of an organism that is capable of independent functioning, in a specified sample of vascular smooth muscle, the contractile soft tissue having fine myofibrils but lacking transverse striations composing the majority of the wall of blood vessels, the network of muscular tubes that carry blood through the body. calculated vascular smooth muscle cell count calculated blood vessel smooth muscle cell count JSmith 2013-06-18T12:59:11Z A measurement which has been normalized, adjusted or derived by a mathematical process or computation of the total number of cells, membrane-enclosed protoplasmic masses constituting the smallest structural unit of an organism that is capable of independent functioning, in a specified sample of the aorta smooth muscle, the contractile soft tissue having fine myofibrils but lacking transverse striations composing the majority of the wall of the great artery arising from the left ventricle from which the systemic arterial system proceeds. calculated aortic smooth muscle cell count calculated aorta smooth muscle cell count JSmith 2013-06-18T13:25:39Z A calculated value in which the total number of cells, membrane-enclosed protoplasmic masses constituting the smallest structural unit of an organism that is capable of independent functioning, in a specified sample of the aorta smooth muscle, the contractile soft tissue having fine myofibrils but lacking transverse striations composing the majority of the wall of the great artery arising from the left ventricle from which the systemic arterial system proceeds, is divided by the length of the smooth muscle section in which that number is determined. aortic smooth muscle cell count per unit vessel length aorta smooth muscle cell count per unit vessel length JSmith 2013-06-18T14:44:11Z The amount of deoxyribonucleic acid (DNA), the molecule composed of the sugar deoxyribose, phosphate groups and any combination of the bases adenine, guanine, cytosine, and/or thymine, extracted from or contained in the heart left ventricle, the lower chamber of the left side of the heart (from the perspective of the organism rather than the observer), which pumps oxygenated blood out through the aorta to all the tissues of the body. heart LV DNA content heart left ventricle DNA content heart left ventricle deoxyribonucleic acid content JSmith 2013-06-18T14:46:40Z A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of the amount of deoxyribonucleic acid (DNA), the molecule composed of the sugar deoxyribose, phosphate groups and any combination of the bases adenine, guanine, cytosine, and/or thymine, extracted from or contained in the heart left ventricle, the lower chamber of the left side of the heart (from the perspective of the organism rather than the observer), which pumps oxygenated blood out through the aorta to all the tissues of the body. calculated heart LV DNA content calculated heart left ventricle DNA content calculated heart left ventricle deoxyribonucleic acid content JSmith 2013-06-18T14:49:33Z A calculated measurement in which amount of deoxyribonucleic acid (DNA), the molecule composed of the sugar deoxyribose, phosphate groups and any combination of the bases adenine, guanine, cytosine, and/or thymine, extracted from or contained in the heart left ventricle, the lower chamber of the left side of the heart (from the perspective of the organism rather than the observer), which pumps oxygenated blood out through the aorta to all the tissues of the body, is divided by the total weight or heaviness of the body and presented as a ratio, fraction, quotient or percentage, thus normalizing it to body weight and, by extension, to the size of the organism. heart LV DNA content to body weight ratio heart left ventricle DNA content to BW ratio heart left ventricle DNA content to body weight ratio heart left ventricle deoxyribonucleic acid content to body weight ratio JSmith 2013-06-18T14:52:32Z The amount of deoxyribonucleic acid (DNA), the molecule composed of the sugar deoxyribose, phosphate groups and any combination of the bases adenine, guanine, cytosine, and/or thymine, extracted from or contained in the heart right ventricle, the lower chamber of the right side of the heart (from the perspective of the organism rather than the observer), which pumps venous blood through the pulmonary trunk and arteries to the capillaries of the lung. heart RV DNA content heart right ventricle DNA content heart right ventricle deoxyribonucleic acid content JSmith 2013-06-18T14:54:27Z A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of the amount of deoxyribonucleic acid (DNA), the molecule composed of the sugar deoxyribose, phosphate groups and any combination of the bases adenine, guanine, cytosine, and/or thymine, extracted from or contained in the heart right ventricle, the lower chamber of the right side of the heart (from the perspective of the organism rather than the observer), which pumps venous blood through the pulmonary trunk and arteries to the capillaries of the lung. calculated heart RV DNA content calculated heart right ventricle DNA content calculated heart right ventricle deoxyribonucleic acid content JSmith 2013-06-18T14:56:34Z A calculated measurement in which amount of deoxyribonucleic acid (DNA), the molecule composed of the sugar deoxyribose, phosphate groups and any combination of the bases adenine, guanine, cytosine, and/or thymine, extracted from or contained in the heart right ventricle, the lower chamber of the right side of the heart (from the perspective of the organism rather than the observer), which pumps venous blood through the pulmonary trunk and arteries to the capillaries of the lung, is divided by the total weight or heaviness of the body and presented as a ratio, fraction, quotient or percentage, thus normalizing it to body weight and, by extension, to the size of the organism. heart RV DNA content to body weight ratio heart right ventricle DNA content to BW ratio heart right ventricle DNA content to body weight ratio heart right ventricle deoxyribonucleic acid content to body weight ratio JSmith 2013-06-20T14:09:54Z Measurement of the highest achievable amount of energy produced by the active reduction in the diameter of a blood vessel, any one of the network of muscular tubes that carry blood through the body, resulting from a contraction of the muscular wall of the vessel which does not involve the action of a receptor, a molecule on the surface or within a cell that recognizes and binds with specific molecules, producing a specific effect. blood vessel receptor-independent maximum contractility receptor-independent blood vessel maximum contractile force JSmith 2013-06-20T14:10:59Z Measurement of the highest achievable amount of energy produced by the active reduction in the diameter of a blood vessel, any one of the network of muscular tubes that carry blood through the body, resulting from a contraction of the muscular wall of the vessel which is instigated by the activation of a receptor, a molecule on the surface or within a cell that recognizes and binds with specific molecules, producing a specific effect. blood vessel receptor-dependent maximum contractility receptor-dependent blood vessel maximum contractile force JSmith 2013-06-20T14:12:17Z A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of the highest achievable amount of energy produced by the active reduction in the diameter of a blood vessel, any one of the network of muscular tubes that carry blood through the body, resulting from contraction of the muscular wall of the vessel. calculated blood vessel maximum contractile force measurement JSmith 2013-06-20T14:14:00Z A calculated measurement in which the receptor-dependent maximum contractile force of a blood vessel is divided by the receptor-independent maximum contractile force of a blood vessel and presented as a ratio, fraction, quotient or percentage. The maximum contractile force of a blood vessel is the highest achievable amount of energy produced by the active reduction in the diameter of a blood vessel, any one of the network of muscular tubes that carry blood through the body, resulting from a contraction of the muscular wall of the vessel. Receptor-dependent refers to such a contraction which is instigated by the activation of a receptor, a molecule on the surface or within a cell that recognizes and binds with specific molecules, producing a specific effect. Receptor-independent denotes such a contraction that does not involve the action of a receptor. blood vessel receptor-dependent contractility to receptor-independent contractility ratio receptor-dependent blood vessel maximum contractile force exoressed as a percentage of receptor-independent blood vessel maximum contractile force receptor-dependent blood vessel maximum contractile force to receptor-independent blood vessel maximum contractile force ratio JSmith 2013-06-20T14:22:08Z A calculated value for the concentration of angiotensin II (AngII), the octapeptide, Asp-Arg-Val-Tyr-Ile-His-Pro-Phe, that is derived from angiotensinogen and acts as a powerful vasopressor and stimulator of aldosterone secretion, at which the energy produced by the active reduction in the diameter of a blood vessel in response to the application of AngII is halfway between the baseline value and the highest achievable value of such AngII-induced contractile energy. Ang2 half maximal effective concentration AngII half maximal effective concentration angiotensin 2 half maximal effective concentration angiotensin II half maximal effective concentration (EC50) concentration of angiotensin II at which the force of blood vessel contraction is half the maximum value (EC50) JSmith 2013-06-20T14:24:41Z A calculated value for logarithm of the concentration of angiotensin II (AngII), the octapeptide, Asp-Arg-Val-Tyr-Ile-His-Pro-Phe, that is derived from angiotensinogen and acts as a powerful vasopressor and stimulator of aldosterone secretion, at which the energy produced by the active reduction in the diameter of a blood vessel in response to the application of AngII is halfway between the baseline value and the highest achievable value of such AngII-induced contractile energy. The logarithm of the concentration is the exponent indicating the power to which 10 must be raised to obtain that concentration value. Ang2 Log half maximal effective concentration AngII Log half maximal effective concentration angiotensin 2 Log half maximal effective concentration angiotensin II Log half maximal effective concentration (EC50) logarithm of the concentration of angiotensin II at which the force of blood vessel contraction is half the maximum value (Log EC50) JSmith 2013-06-20T15:45:33Z Measurement of an organism's, organ's, tissue's or cell's capacity to respond, such as by a change in activity, state or condition, to angiotensin II (AngII), the octapeptide, Asp-Arg-Val-Tyr-Ile-His-Pro-Phe, that is derived from angiotensinogen and acts as a powerful vasopressor and stimulator of aldosterone secretion. angiotensin II response/sensitivity measurement JSmith 2013-07-31T13:40:52Z The difference in left ventricular diastolic blood pressure between two points in time or two conditions expressed as the result of the subtraction in and of itself without comparison by ratio with another quantity. absolute change in LVDBP The term "absolute change" refers to the subtraction of one value from another, as opposed to a dissimilarity of two values expressed as a ratio or as a percentage. In this context it is not intended to necessarily imply the difference expressed as an absolute value |n|, that is, the numeric value of the difference without regard to its sign. absolute change in left ventricular diastolic blood pressure JSmith 2013-07-31T15:17:53Z Any measurement of the blood pressure in the left ventricle of the heart which has been normalized or adjusted by a mathematical process or computation. Left ventricular blood pressure is the pressure, or force per area, exerted by circulating blood against the walls of the left ventricle, the lower chamber of the left side of the heart, which pumps oxygenated blood out through the aorta to all the tissues of the body. calculated left ventricular pressure calculated left ventricular blood pressure JSmith 2013-07-31T15:24:11Z A calculated measurement that is used as an index to characterize the contractile ability of the heart. It is believed that maximum dP/dt is a reasonable index of the initial velocity of myocardial contraction. LV +dP/dt Max peak +LVdP/dt rate of maximum positive change in left ventricular blood pressure maximum rate of positive change in left ventricular blood pressure JSmith 2013-07-31T15:27:12Z A calculated hemodynamic measurement related to the ability of the heart left ventricle to relax. The point at which the negative pressure fall velocity reaches its peak is taken to be the onset of isovolumic relaxation of the left ventricle. LV -dP/dt Max peak -LVdP/dt rate of maximum negative change in left ventricular blood pressure maximum rate of negative change in left ventricular blood pressure JSmith 2013-07-31T15:29:00Z A calculated hemodynamic value related to the ability of the heart left ventricle to relax. Tau is calculated as an exponential function of the change in intraventricular pressure during the diastolic isovolumic left ventricular pressure decrease. time constant of left ventricular relaxation time constant of left ventricular pressure decay JSmith 2013-10-16T12:18:32Z The thickness or depth (i.e. the measurement of the two-dimensional extent of the distance between the inner and outer surfaces) of the dorsal/posterior wall of the left ventricle of the heart at the end of systole, that is, when the heart muscle is maximally contracted. The dorsal wall is the portion of the muscle enclosing the ventricle which is closest to the spine and farthest from the chest wall of the organism. The left ventricle is the lower chamber of the left side of the heart, which pumps oxygenated blood out through the aorta to all the tissues of the body. end-systolic heart left ventricle posterior wall thickness end-systolic heart left ventricle PWT Note that "left" in this context refers to the perspective of the organism, not that of the observer. heart left ventricle end-systolic posterior wall thickness JSmith 2013-11-04T17:14:28Z Any quantification of the amounts or proportions of proteins, lipids, minerals, nutrients, gases, or other substances ina specified sample of kidney tissue, that is, tissue from one or both of the paired organs which function to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes. kidney molecular composition measurement JSmith 2013-11-04T17:16:16Z Quanitification of one or more lipids in a specified sample of kidney tissue, that is, tissue from one or both of the paired organs which function to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes. A lipid is any of a structurally diverse group of organic compounds that are insoluble in water but soluble innonpolar solvents that, among other biological functions, serve as a source of fuel and are an important constituent of cell structure. kidney lipid composition measurement JSmith 2013-11-04T17:22:56Z The amount of 20-hydroxyeicosatetraenoic acid, a vasoconstrictor that consists of arachidonic acid (a C20, polyunsaturated fatty acid having four (Z)-double bonds at positions 5, 8, 11 and 14) bearing a hydroxy substituent at position 20, in a specified sample of kidney tissue, that is, tissue from one or both of the paired organs which function to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes. kidney 20-hydroxyeicosatetraenoic acid level kidney 20-HETE level JSmith 2013-11-07T16:12:26Z The number of immune cells in a specified sample. An immune cell is any cell involved in the immune system, a complex set of interconnected and interdependent cellular and molecular components having the primary functions of distinguishing self from not self and of defense against foreign organisms or substances. A cell is a membrane-enclosed protoplasmic mass constituting the smallest structural unit of an organism that is capable of independent functioning. immune cell count JSmith 2013-11-08T16:00:08Z The difference in the pulse pressure of an individual between two points in time or two conditions expressed as the result of the subtraction in and of itself without comparison by ratio with another quantity. Pulse pressure is the difference between systolic and diastolic blood pressures, i.e. the difference between the maximal arterial pressure and minimal arterial pressure during the cardiac cycle. The term "absolute change" refers to the subtraction of one value from another, as opposed to a dissimilarity of two values expressed as a ratio or as a percentage. In this context it is not intended to necessarily imply the difference expressed as an absolute value |n|, that is, the numeric value of the difference without regard to its sign. absolute change in pulse pressure JSmith 2013-11-18T15:00:01Z A calculated measurement of the degree to which a change in the size of the remaining kidney after surgical removal of the other kidney can be attributed to compensatory growth, calculated as the ratio of the normalized weight of a single kidney at the time of surgical removal divided by the similarly normalized weight of the single remaining kidney at a specified period of time after removal. The normalized kidney weight is the weight of the kidney corrected for body weight using an empirically determined allometric scaling factor (i.e., an exponential factor which adjusts for the normal increase in kidney weight due to normal growth and development of the individual). Compensatory growth is the phenomenon in which the impaired function of one organ in a paired organ system or of part of an organ in a single organ system is followed by enlargement of the surviving organ or tissue so that functional capacity is maintained. Kidney is the paired organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes. CRG score compensatory renal growth score JSmith 2013-11-18T16:20:39Z A calculated measurement in which the difference in the volume of blood delivered to and/or exiting from the kidneys per unit time between two points in time or two conditions is divided by the weight (heaviness or degree to which a body is drawn toward the earth by gravity) of one or both kidneys, and presented as a ratio, fraction, quotient or percentage. The kidney is the paired organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes. ratio of change in renal blood flow rate to kidney weight JSmith 2013-11-18T17:22:16Z A measurement of the degree to which the blood vessels of the kidneys impede the flow of blood through them. Renal vascular resistance is calculated as the renal blood flow rate divided by the mean arterial pressure. kidney vascular resistance renal vascular resistance JSmith 2013-11-18T17:23:40Z A measurement that has been normalized, adjusted or derived by a mathematical process or computation, of the degree to which the blood vessels of the kidneys impede the flow of blood through them. Blood vessels are the network of muscular tubes that carry blood throughout the body. Blood is the fluid that circulates through the heart, arteries, capillaries and veins carrying nutrients and oxygen to the body tissues and metabolites away from them. Kidney is the paired organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes. calculated kidney vascular resistance calculated renal vascular resistance JSmith 2013-11-18T17:26:57Z The difference in renal vascular resistance between two points in time or two conditions expressed as the result of the subtraction in and of itself without comparison by ratio with another quantity. Renal vascular resistance is the degree to which the blood vessels of the kidneys impede the flow of blood through them. Blood vessels are the network of muscular tubes that carry blood throughout the body. Blood is the fluid that circulates through the heart, arteries, capillaries and veins carrying nutrients and oxygen to the body tissues and metabolites away from them. Kidney is the paired organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes. absolute change in kidney vascular resistance The term "absolute change" refers to the subtraction of one value from another, as opposed to a dissimilarity of two values expressed as a ratio or as a percentage. In this context it is not intended to necessarily imply the difference expressed as an absolute value |n|, that is, the numeric value of the difference without regard to its sign. absolute change in renal vascular resistance JSmith 2013-11-18T17:27:01Z A calculated measurement of the slope, the ratio of vertical change to horizontal change, of the line of a graph designating the change in renal vascular resistance in response to a drug or other condition which causes constriction or reduction of the interior diameter of blood vessels. Renal vascular resistance is the degree to which the blood vessels of the kidneys impede the flow of blood through them. Blood vessels are the network of muscular tubes that carry blood throughout the body. Blood is the fluid that circulates through the heart, arteries, capillaries and veins carrying nutrients and oxygen to the body tissues and metabolites away from them. Kidney is the paired organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes. slope of constriction-induced renal vascular resistance curve slope of contraction-induced kidney vascular resistance curve slope of contraction-induced renal vascular resistance curve JSmith 2013-11-19T13:00:18Z The enumeration, i.e. measurement of the total number, of defects or lesions of the internal elastic lamina which are not hyperplastic or neoplastic in origin in a specified sample of artery. A lesion is a localized pathological change in structure of an organ or tissue due to injury or disease; especially one that is circumscribed and well defined. The internal elastic lamina (IEL) is a fenestrated (perforated) layer of elastic tissue, i.e., one having the property of returning to the original shape after being distorted, that is the outermost part of the intima (innermost layer) of an artery. The IEL is the elastic layer that is situated between the tunica intima (inner layers) and tunica media (middle layers) of artery walls. An artery is any one of the branching system of muscular, elastic blood vessels that carry blood away from the heart. artery internal elastic lamina defect count artery internal elastic lamina non-tumorous lesion count JSmith 2013-11-19T14:28:34Z The amount of plasma that perfuses the kidneys per unit time. Plasma is the fibrinogen-containing fluid portion of the blood in which the particulate components are suspended. The kidneys are the paired organs that function to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes. renal plasma flow rate RPF renal plasma flow JSmith 2013-11-19T14:51:51Z A calculated measurement in which the effective renal plasma flow rate (eRPF) is divided by weight (i.e. the heaviness or the degree to which an object is drawn toward the earth by gravity) of both kidneys and presented as a ratio, fraction, quotient or percentage. The eRPF is the amount of plasma that perfuses the renal tubules per unit time, derived by measurement of the clearance rate of a non-metabolizable solute such as para-aminohippurate (PAH). Plasma is the fibrinogen-containing fluid portion of the blood in which the particulate components are suspended. The kidneys are the paired organs that function to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes. effective renal plasma flow rate to both kidney weight ratio eRPF to both kidney weight ratio ratio of the effective renal plasma flow to the weight of both kidneys JSmith 2013-11-19T14:52:06Z A calculated measurement of the amount of plasma that perfuses the renal tubules per unit time, derived by measurement of the clearance rate of a non-metabolizable solute such as para-aminohippurate (PAH). The effective RPF is approximately 10% less than the actual RPF. Plasma is the fibrinogen-containing fluid portion of the blood in which the particulate components are suspended. The kidneys are the paired organs that function to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes. effective renal plasma flow rate eRPF effective renal plasma flow JSmith 2013-11-19T14:52:10Z A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of the amount of plasma that perfuses the kidneys per unit time. Plasma is the fibrinogen-containing fluid portion of the blood in which the particulate components are suspended. The kidneys are the paired organs that function to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes. calculated renal plasma flow rate calculated RPF calculated renal plasma flow JSmith 2013-11-26T15:36:46Z Any measurement that has been normalized, adjusted or derived by a mathematical process or computation, of the weight of only one of the kidneys, the paired organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes. calculated single kidney weight JSmith 2013-11-26T15:39:42Z Any measurement that has been normalized, adjusted or derived by a mathematical process or computation, of the weight of both (the complete set of two) of the kidneys, the paired organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes. calculated both kidneys weight JSmith 2013-11-26T15:48:04Z A calculated measurement in which the weight after removal from the body but without desiccation of only the single right kidney is divided by the total weight of the body and presented as a ratio, fraction, quotient or percent, thus normalizing it to body weight and by extension to the size of the organism. The right kidney is the organ which lies on the right side of the body from the perspective of the subject. individual right kidney wet weight to body weight ratio right kidney wet weight to body weight ratio JSmith 2013-11-26T15:48:07Z A calculated measurement in which the weight after removal from the body but without desiccation of only the left kidney is divided by the total weight of the body and presented as a ratio, fraction, quotient or percent, thus normalizing it to body weight and, by extension, to the size of the organism. The left kidney is the organ which lies on the left side of the body from the perspective of the subject. individual left kidney wet weight to body weight ratio left kidney wet weight to body weight ratio JSmith 2013-11-26T16:04:13Z A calculated measurement in which the value for the volume of blood delivered to and/or exiting from the kidneys per unit time is divided by the weight (heaviness or degree to which an object is drawn toward the earth by gravity) of one or both kidneys, and presented as a ratio, fraction, quotient or percentage. renal blood flow rate to kidney weight ratio JSmith 2013-12-02T10:53:31Z A calculated measurement in which difference in the mean arterial blood pressure between two or more dosages of a drug or chemical which reduces the interior diameter of blood vessels is divided by difference in the logarithm of the applied dosages and presented as a ratio, fraction, quotient or percentage. The value is calculated as the slope of the curve of the mean arterial blood pressure versus log of the vasoconstrictor dose [VC] graph, given by the equation (log[VC]2 - log[VC]1)/(MAP at [VC]2 - MAP at [VC]1). A logarithm is the power to which a base, such as 10, must be raised to produce a given number. change in MAP to change in log[vasoconstrictor] ratio change in mean arterial blood pressure to change in the logarithm of the vasoconstrictor dose ratio JSmith 2013-12-02T11:03:44Z Measurement of the length of a straight line passing through the center and connecting opposite points on the circumference of a circle delineating the outer limits of a glomerulosclerotic lesion. kidney glomerulosclerotic lesion diameter JSmith 2013-12-02T11:54:57Z A calculated measurement in which the diameter of kidney glomerular injury is divided by the value of the mean arterial blood pressure and presented as a ratio, fraction, quotient or percentage, for example to give an index of kidney damage relative to the level of hypertension. kidney glomerulosclerotic lesion diameter to mean arterial blood pressure ratio JSmith 2013-12-03T17:32:45Z Measurement of the physical form or structure of one or more blood vessels, the network of muscular tubes that carry blood through the body. blood vessel morphological measurement JSmith 2013-12-03T18:01:02Z Any quantitation of the molecules, atoms and/or ions which constitute the chemical make-up of the wall of the aorta, the layered tissue which encloses and constitutes the structural component of the great artery arising from the left ventricle from which the systemic arterial system proceeds. A molecule is an aggregation of atoms, specifically a chemical combination of two or more atoms forming a specific chemical substance. aortic wall molecular composition measurement aorta wall molecular composition measurement JSmith 2013-12-03T18:08:51Z The amount of elastin in a specified sample of aorta wall tissue. Elastin is an elastic, fibrous mucoprotein, similar to collagen, and the major connective tissue protein of elastic fibers, such as those in arterial walls. aortic wall elastin level aorta wall extracellular elastin level JSmith 2013-12-03T18:13:06Z The amount of collagen in a specified sample of aorta wall tissue. Collagen refers to any of a family of extracellular, closely related proteins occurring as a major component of connective tissue, giving it strength and flexibility. aortic wall collagen level aorta wall extracellular collagen level JSmith 2013-12-03T18:14:39Z A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of the molecules, atoms and/or ions which constitute the chemical make-up of the wall of the aorta. calculated aortic wall molecular composition measurement calculated aorta wall molecular composition measurement JSmith 2013-12-03T18:21:20Z A calculated measurement in which the weight after dessication of the extracellular elastin in a specified sample of aorta wall is divided by the total weight after dessication of that sample of aorta wall, and the result presented as a ratio, fraction, quotient or percentage. aortic wall elastin dry weight to total aortic wall dry weight ratio aorta wall extracellular elastin dry weight to aorta wall dry weight ratio JSmith 2013-12-03T18:29:26Z A calculated measurement in which the weight after dessication of the extracellular elastin in a specified sample of aorta wall is divided by the weight of extracellular collagen in that sample of aorta wall, and the result presented as a ratio, fraction, quotient or percentage. aortic wall elastin dry weight to aortic wall collagen weight ratio aorta wall extracellular elastin dry weight to aorta wall extracellular collagen weight ratio JSmith 2013-12-04T10:31:25Z The total amount of protein extracted from within the cells of the aortic wall in a specified sample of aorta. Protein is any of a group of complex organic compounds containing carbon, hydrogen, oxygen, nitrogen, and sulfur consisting of alpha-amino acids joined by peptide linkages. aorta cellular protein level aorta wall total intracellular protein level aorta wall intracellular protein level JSmith 2014-01-07T16:35:21Z The difference in mean arterial blood pressure between two points in time or two conditions expressed as a percentage (the proportion or rate per hundred parts). The term "absolute change" refers to the subtraction of one value from another, as opposed to a dissimilarity of two values expressed as a ratio or as a percentage. In this context it is not intended to necessarily imply the difference expressed as an absolute value |n|, that is, the numeric value of the difference without regard to its sign. percent change in mean arterial blood pressure JSmith 2014-01-07T16:51:06Z Average slope of the line defined by the change in heart rate (the number of contractions of the cardiac ventricles per unit of time) relative to the change in mean arterial blood pressure (the average force the blood exerts on an artery wall) over time and/or in response to a change in conditions. change in heart rate to change in mean arterial blood pressure ratio JSmith 2014-01-07T16:53:44Z Maximum, largest or steepest slope of the line defined by the change in heart rate (the number of contractions of the cardiac ventricles per unit of time) relative to the change in mean arterial blood pressure (the average blood pressure within an artery over a specified period of time) over time and/or in response to a change in conditions. maximum change in heart rate to change in mean arterial blood pressure ratio JSmith 2014-01-23T17:03:36Z The amount of sterol, any of a group of steroids with a long (8 to 10 carbons) aliphatic side-chain at position 17 and at least one alcoholic group, in a specified sample of blood. blood sterol level JSmith 2014-01-23T17:04:50Z The amount of sterol, any of a group of steroids with a long (8 to 10 carbons) aliphatic side-chain at position 17 and at least one alcoholic group, in a specified sample of serum, the clear liquid that separates from blood after it has clotted completely, i.e. blood plasma from which fibrinogen has been removed. serum sterol level JSmith 2014-01-24T15:13:32Z Any quantitation of the molecules, atoms and/or ions which constitute the chemical make-up of a specified tissue or set of tissues. tissue molecular composition measurement JSmith 2014-01-27T15:49:38Z Determination of the number of mononuclear cells, i.e. leukocytes such as lymphocytes and monocytes with a single round or oval nucleus (including but not limited to such cells found in blood, lymph or spleen) found in a specified sample. mononuclear cell number mononuclear cell count JSmith 2014-01-28T16:41:28Z A calculated measurement in which .the number of kidney glomeruli displaying an abnormal (i.e., pathogenic) crescentic morphology is divided by the number of kidney glomeruli displaying normal morphology, and the result presented as a ratio, fraction, quotient or percentage. kidney crescentic glomeruli count to kidney normal glomeruli count ratio JSmith 2014-01-31T16:39:20Z A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of heart rate, the number of contractions of the cardiac ventricles per unit of time. calculated heart rate measurement JSmith 2014-01-31T16:41:23Z The difference between two points in time or two conditions in heart rate expressed as the ratio of the low frequency R-R interval component of the power spectrum analysis to the high frequency R-R interval component of the power spectrum analysis, expressed as the result of the subtraction in and of itself without comparison by ratio with another quantity. absolute change in heart rate variability absolute change in ECG LF/HF ratio absolute change in EKG LF/HF ratio absolute change in electrocardiographic low frequency R-R interval to high frequency R-R interval ratio The term "absolute change" refers to the subtraction of one value from another, as opposed to a dissimilarity of two values expressed as a ratio or as a percentage. In this context it is not intended to necessarily imply the difference expressed as an absolute value |n|, that is, the numeric value of the difference without regard to its sign. absolute change in electrocardiographic low frequency R-R spectral component to high frequency R-R spectral component ratio JSmith 2014-02-03T17:42:14Z Any quantitation of the molecules, atoms and/or ions which constitute the chemical make-up of the tissue(s) of the heart left ventricle. A molecule is an aggregation of atoms, specifically a chemical combination of two or more atoms forming a specific chemical substance. heart left ventricle molecular composition measurement JSmith 2014-02-03T17:43:11Z The amount in a specified sample of tissue from the heart left ventricle, of natriuretic peptide A (NPPA), a powerful vasodilator and peptide hormone secreted mainly by heart muscle cells and involved in control of extracellular fluid volume and electrolyte homeostasis. heart left ventricle atrial natriuretic factor level heart left ventricle natriuretic peptide A protein level heart left ventricle NPPA level heart left ventricle natriuretic peptide A level JSmith 2014-02-03T17:55:31Z The amount of renin in a specified sample of kidney tissue. Renin, an aspartyl protease, catalyzes the cleavage of angiotensinogen to form angiotensin I, the first step in the activation pathway of angiotensinogen--a cascade that can result in aldosterone release,vasoconstriction, and increase in blood pressure. kidney renin protein level kidney REN level kidney renin level JSmith 2014-03-10T15:24:43Z Any quantification of the ability of a protein of the kidney to accomplish an effect, e.g. take part in a chemical reaction or carry out a specified molecular function. kidney protein activity measurement JSmith 2014-03-10T15:31:04Z Any quantification of the ability of a kidney enzyme, i.e. a protein located in the kidney that catalyzes chemical reactions of other substances without itself being destroyed or altered upon completion of the reactions, to carry out its specified molecular function. kidney enzyme activity measurement JSmith 2014-03-10T17:51:03Z A calculated measurement in which the level of catalase enzyme activity in a specified sample of kidney is divided by the weight of total protein in that sample. Catalase converts the reactive oxygen species hydrogen peroxide to water and oxygen. kidney catalase activity to total protein level ratio JSmith 2014-03-10T17:52:00Z A calculated measurement in which the level of glucose-6-phosphate dehydrogenase enzyme activity in a specified sample of kidney is divided by the weight of total protein in that sample. Glucose-6-phosphate dehydrogenase catalizes the conversion of D-glucose 6-phosphate + NADP+ to 6-phospho-D-glucono-1,5-lactone + NADPH. kidney G6PD activity to total protein level ratio kidney glucose-6-phosphate dehydrogenase activity to total protein level ratio JSmith 2014-03-10T17:53:05Z A calculated measurement in which the level of glutathione reductase (GSR) enzyme activity in a specified sample of kidney is divided by the weight of total protein in that sample. GSR reduces oxidized glutathione disulfide (GSSG) to the sulfhydryl form GSH. kidney GSR activity to total protein level ratio kidney glutathione reductase activity to total protein level ratio JSmith 2014-03-10T17:54:38Z A calculated measurement in which the level of glutathione peroxidase enzyme activity in a specified sample of kidney is divided by the weight of total protein in that sample. Glutathione peroxidases constitute a family of proteins that reduce lipid hydroperoxides to their corresponding alcohols and reduce free hydrogen peroxide to water. kidney glutathione peroxidase activity to total protein level ratio JSmith 2014-03-10T17:55:21Z A calculated measurement in which the level of glutathione-S-transferase enzyme activity in a specified sample of kidney is divided by the weight of total protein in that sample. Glutathione-S-transferase refers to any of a family of proteins with the ability to catalyze the conjugation of the reduced form of glutathione (GSH) to xenobiotic substrates for the purpose of detoxification. kidney glutathione-S-transferase activity to total protein level ratio JSmith 2014-03-10T17:55:56Z A calculated measurement in which the level of superoxide dismutase enzyme activity in a specified sample of kidney is divided by the weight of total protein in that sample. superoxide dismutases constitute a family of proteins that convert naturally-occuring but harmful superoxide radicals to molecular oxygen and hydrogen peroxide. kidney superoxide dismutase activity to total protein level ratio JSmith 2014-03-10T17:56:39Z A calculated measurement in which the level of paraoxonase 1 enzyme activity in a specified sample of kidney is divided by the weight of total protein in that sample. Paraoxonase 1 is an arylesterase that mainly hydrolyzes paroxon, an organophosphorus anticholinesterase compound, to produce p-nitrophenol. kidney paraoxonase-1 activity to total protein level ratio kidney paraoxonase1 activity to total protein level ratio JSmith 2014-03-10T17:57:32Z A calculated measurement in which the level of glutathione peroxidase enzyme activity in a specified sample of kidney is divided by the level of glutathione reductase enzyme activity in that same sample. kidney glutathione peroxidase activity to glutathione reductase activity ratio JSmith 2014-03-10T17:58:30Z A calculated measurement in which the level of superoxide dismutase enzyme activity in a specified sample of kidney is divided by the level of catalase enzyme activity in that same sample. kidney superoxide dismutase to catalase activity ratio JSmith 2014-03-10T17:59:04Z A calculated measurement in which the level of superoxide dismutase enzyme activity in a specified sample of kidney is divided by the level of glutathione peroxidase enzyme activity in that same sample. kidney superoxide dismutase to glutathione peroxidase ratio JSmith 2014-03-10T17:59:34Z A calculated measurement in which the level of superoxide dismutase enzyme activity in a specified sample of kidney is divided by the level of paraoxonase 1 enzyme activity in that same sample. kidney superoxide dismutase to paraoxonase-1 activity ratio kidney superoxide dismutase to paraoxonase1 activity ratio JSmith 2014-03-10T18:02:47Z The amount of glutathione in a specified sample of kidney tissue. Glutathione (GSH/GSSG) is an antioxidant tripeptide with a gamma peptide linkage between the amine group of cysteine (which is attached by normal peptide linkage to a glycine) and the carboxyl group of the glutamate side-chain. kidney GSH level kidney glutathione level JSmith 2014-03-10T18:03:40Z The amount of malondialdehyde in a specified sample of kidney tissue. Malondialdehyde is an organic compound with the formula CH2(CHO)2. It is a reactive species which occurs naturally, is generally found in the enol form (HOCH=CH-CHO), and is a marker for oxidative stress. kidney malondialdehyde level JSmith 2014-03-10T18:04:53Z A calculated measurement in which the level of protein carbonyl (PCO) derivatives in a specified sample of kidney is divided by the total amount of protein in the sample. Protein carbonyl (PCO) derivatives are produced by the oxidation of amino acids and can be used as a marker of oxidative stress. kidney protein carbonyl level to total protein level ratio JSmith 2014-03-10T18:06:09Z The amount of platinum, the chemical element with atomic number 78, in a specified sample of kidney tissue. kidney platinum level JSmith 2014-03-11T14:14:26Z The amount of enzymatic activity of creatine kinase (CK) enzyme in a specified sample of serum. CK catalyses the reversible transfer of phosphate between ATP and various phosphogens such as creatine phosphate. Serum CK level is used as an enzymatic marker for myocardial infarction, rhabdomyolysis and acute renal failure. serum creatine phosphokinase activity level serum CK activity level serum CPK activity level serum creatine kinase activity level JSmith 2014-03-11T16:52:38Z The amount of lipid peroxidation end products in a specified sample of kidney tissue. Lipid peroxidation is the oxidative degradation of lipids. kidney LPO level kidney lipid peroxidation level kidney lipid peroxide level JSmith 2014-03-12T15:00:11Z Measurement of the size of the three dimensional space occupied by a single kidney glomerulus. kidney glomerulus volume JSmith 2014-03-24T12:45:12Z Calculated measurement of a difference in the maximum arterial blood pressure, that is the pressure at the point of maximal contraction of the heart, between two points in time, one during the day and the other at night, expressed as a number (positive or negative), not as a ratio or percentage relative to another quantity. absolute circadian change in systolic blood pressure systolic diurnal amplitude The term "absolute change" refers to the subtraction of one value from another, as opposed to a dissimilarity of two values expressed as a ratio or as a percentage. In this context it is not intended to necessarily imply the difference expressed as an absolute value |n|, that is, the numeric value of the difference without regard to its sign. absolute diurnal change in systolic blood pressure JSmith 2014-03-24T13:34:25Z The amount of cholesterol, a eukaryotic sterol that in higher animals is the precursor of bile acids and steroid hormones and a key constituent of cell membranes, in a specified sample of blood. Cholesterol in the blood is generally associated with various lipoproteins. Not4Curation blood cholesterol level JSmith 2014-03-24T13:36:35Z The amount of cholesterol, a eukaryotic sterol that in higher animals is the precursor of bile acids and steroid hormones and a key constituent of cell membranes, in a specified sample of serum, the clear liquid that separates from blood after it has clotted completely, i.e. blood plasma from which fibrinogen has been removed. Cholesterol in the serum is associated with various lipoproteins. Not4Curation serum cholesterol level JSmith 2014-03-28T12:01:46Z A calculated measurement in which difference in the mean arterial blood pressure between two or more dosages of a drug or chemical which reduces or increases the interior diameter of blood vessels is divided by difference the applied dosages and presented as a ratio, fraction, quotient or percentage. The value is calculated as the slope of the curve of the mean arterial blood pressure versus the chemical dose graph. beta coefficient of mean arterial blood pressure change change in MAP to change in [vasoactive chemical] ratio slope of the change in mean arterial blood pressure change in mean arterial blood pressure to change in vasoactive chemical dose ratio JSmith 2014-03-28T16:44:54Z Ratio of the wall thickness (WT) of an artery to outer diameter (OD) of that artery at that location, usually expressed as a percentage, i.e. WT/OD x 100, but could also be expressed as a ratio, fraction or quotient. This measurement can be used to assess stenosis, a pathological narrowing of a blood vessel. arterial stenosis measurement artery wall thickness as percentage of artery outer diameter artery wall thickness as percentage of artery total diameter artery wall thickness to artery total diameter ratio JSmith 2014-04-24T12:47:44Z Any value resulting from the quantification of a morphological or physiological parameter of leukocytes, largely colorless blood corpuscles capable of ameboid movement, whose chief function is to protect the body against microorganisms and other disease-causing entities. leukocyte measurement white blood cell measurement JSmith 2014-05-13T18:19:12Z A calculated measurement in which the number of white blood cells of one or more specific types in a specified sample of blood is divided by the total number of white blood cells in the sample, and the result presented as a ratio, fraction, quotient or percentage. Not4Curation blood differential leukocyte count to total WBC count ratio blood differential leukocyte count as percentage of total white blood cells differential white blood cell percentage blood differential leukocyte count to total leukocyte count ratio JSmith 2014-05-27T13:59:17Z Any measurement which has been normalized, adjusted or derived by a mathematical process or computation, of a morphological or physiological parameter of non-neoplastic lesions in the kidney. Not4Curation calculated renal non-tumorous lesion measurement calculated kidney non-tumorous lesion measurement JSmith 2014-05-27T14:01:07Z A calculated measurement in which the area occupied by renal protein casts is divided by the total, combined area of the outer stripe of the kidney outer medulla and the kidney cortex, and the result presented as a ratio, fraction, quotient or percentage. Renal protein casts are gelled proteins precipitated in the renal tubules and molded to the tubular lumen. The medulla outer stripe is the section of the renal medula adjacent to the renal cortex and contains portions of the nephron, including the straight proximal tubules, and portions of the loops of henle and outer medullary collecting ducts. percent area of renal protein casting ratio of the area occupied by protein casts to the total area of the kidney outer medulla outer stripe and cortex JSmith 2014-05-28T15:22:49Z A calculated value in which the weight of the heart after removal from the body but without dessication is divided by the total weight of the body, and the result presented as a ratio, fraction, quotient or percentage, thus normalizing it to body weight and, by extension, to the size of the organism. heart wet weight as a percentage of body weight heart wet weight to body weight ratio JSmith 2014-06-09T17:16:49Z A calculated measurement in which the difference between the contractile force of a blood vessel in response to a vasoconstrictor and the baseline contractile force exerted by that vessel in the absence of any external stimuli, is divided by the baseline contractile force measurement and the result expressed as a percentage. A vasoconstrictor is any agent or condition that narrows blood vessels by constricting the smooth muscle in the vessel walls. vasoconstrictor-induced blood vessel contractile force expressed as percent of force at baseline JSmith 2014-06-09T17:21:51Z A calculated measurement in which the difference between the contractile force of a blood vessel in response to a specified dosage of phenylephrine and the baseline contractile force exerted by that vessel in the absence of any external stimuli, is divided by the baseline contractile force measurement and the result expressed as a percentage. Phenylephrine is an adrenergic drug that is a powerful vasoconstrictor. phenylephrine-induced blood vessel constriction expressed as percent of force at baseline phenylephrine-induced blood vessel contractile force expressed as percent of force at baseline JSmith 2014-06-09T17:30:04Z A calculated measurement in which the difference between the contractile force of a blood vessel in response to a specified dosage of potassium chloride and the baseline contractile force exerted by that vessel in the absence of any external stimuli, is divided by the baseline contractile force measurement and the result expressed as a percentage. Potassium chloride is the salt of the potassium cation (K+) and the chlorine/chloride anion (Cl-). It is used as an eletroylyte replenisher and has mild vasoconstrictive properties when applied directly to blood vessels. KCl-induced blood vessel constriction expressed as percent of force at baseline potassium chloride-induced blood vessel contractile force expressed as percent of force at baseline JSmith 2014-06-09T18:11:50Z Measurement of an organism's, organ's, tissue's or cell's capacity to respond, such as by a change in activity, state or condition, to potassium chloride, the salt of the potassium cation (K+) and the chlorine/chloride anion (Cl-). Potassium chloride is used as an eletroylyte replenisher and has mild vasoconstrictive properties when applied directly to blood vessels. KCl response/sensitivity measurement potassium chloride response/sensitivity measurement JSmith 2014-06-09T18:19:26Z A calculated value for the concentration of potassium chloride (KCl) at which the energy produced by the active reduction in the diameter of a blood vessel in response to the application of KCl is halfway between the baseline value and the highest achievable value of such KCl-induced contractile energy. Potassium chloride is the salt of the potassium cation (K+) and the chlorine/chloride anion (Cl-). It is used as an eletroylyte replenisher and has mild vasoconstrictive properties when applied directly to blood vessels. potassium chloride half maximal effective concentration (EC50) KCl half maximal effective concentration (EC50) concentration of potassium chloride at which the force of blood vessel contraction is half the maximum value (EC50) JSmith 2014-06-09T18:28:02Z A calculated value for logarithm of the concentration of potassium chloride (KCl) at which the energy produced by the active reduction in the diameter of a blood vessel in response to the application of KCl is halfway between the baseline value and the highest achievable value of such KCl-induced contractile energy. The logarithm of the concentration is the exponent indicating the power to which 10 must be raised to obtain that concentration value. potassium chloride Log half maximal effective concentration (Log EC50) KCl Log half maximal effective concentration (Log EC50) logarithm of the concentration of potassium chloride at which the force of blood vessel contraction is half the maximum value (Log EC50) JSmith 2014-06-09T18:33:14Z A calculated value for the concentration of a vasoconstrictor at which the energy produced by the active reduction in the diameter of a blood vessel in response to the application of the stimulus is halfway between the baseline value and the highest achievable value of such stimulus-induced contractile energy. A vasoconstrictor is any agent or condition that narrows blood vessels by constricting the smooth muscle in the vessel walls. vasoconstrictor half maximal effective concentration (EC50) concentration of vasoconstrictor at which the force of blood vessel contraction is half the maximum value (EC50) JSmith 2014-06-09T18:47:36Z A calculated value for logarithm of the concentration of a vasoconstrictor at which the energy produced by the active reduction in the diameter of a blood vessel in response to the application of the stimulus is halfway between the baseline value and the highest achievable value of such stimulus-induced contractile energy. The logarithm of the concentration is the exponent indicating the power to which 10 must be raised to obtain that concentration value. A vasoconstrictor is any agent or condition that narrows blood vessels by constricting the smooth muscle in the vessel walls. vasoconstrictor Log half maximal effective concentration (Log EC50) logarithm of the concentration of vasoconstrictor at which the force of blood vessel contraction is half the maximum value (Log EC50) JSmith 2014-06-24T10:28:27Z The thickness or depth of the ventral/anterior wall of the left ventricle of the heart at the end of diastole, that is, when the heart muscle is maximally relaxed. The ventral/anterior wall is the portion of the muscle enclosing the ventricle which is farthest from the spine and closest to the chest wall of the organism. heart left ventricle end-diastolic ventral wall thickness LVAWd heart left ventricle end-diastolic anterior wall thickness JSmith 2014-06-24T10:38:32Z A calculated measurement in which the weight of the left ventricle of the heart is divided by its area at end-diastole, that is, when the heart muscle is maximally relaxed, and the result presented as a ratio, fraction, quotient or percentage. heart left ventricle weight to heart left ventricle end-diastolic area ratio JSmith 2014-07-01T11:15:11Z Any measurement of the movement of blood into, through or out of the heart. heart blood flow measurement JSmith 2014-07-01T11:21:13Z Measurement of the speed at which blood flows into the ventricle during passive filling, that is, during the period when the blood flows from the atrium to the ventricle due to gravity rather than as a result of active contraction of the atrium. E wave velocity JSmith 2014-07-01T11:23:06Z An echocardiographic measurement of the amount of time between the maximum 'E point', that is, the maximum velocity of passive blood flow from the atrium to the ventricle, and the return to baseline at the end of early mitral flow. DT EDT E wave deceleration time JSmith 2014-07-01T11:26:09Z Measurement of the decrease in transmitral blood flow velocity per unit time or the rate at which the velocity of passive blood flow from the atrium to the ventricle decreases over time as the ventricle fills and the atrium empties, calculated as the slope of transmitral velocity vs time. EDR E wave deceleration rate JSMITH 2014-08-05T16:41:32Z Any measurement of the physical form or structure of a muscle fiber, any of the cells of skeletal or cardiac muscle tissue. Each cell is one fiber of the muscle. muscle fiber morphological measurement JSMITH 2014-08-05T16:42:27Z Any measurementof the physical form or structure of a skeletal muscle fiber, a cylindrical multinucleate cell of skeletal muscle tissue containing contracting myofibrils and across which run transverse striations. skeletal muscle fiber morphological measurement JSMITH 2014-08-05T16:43:25Z The average number of capillaries associated with and/or surrounding an individual skeletal muscle fiber, a cylindrical multinucleate cell of skeletal muscle tissue containing contracting myofibrils and across which run transverse striations. Capillaries are the minute vessels connecting arterioles and venules, the walls of which act as a semipermeable membrane for interchange of various substances between the blood and tissue fluid. number of capillaries per skeletal muscle cell number of capillaries per skeletal muscle fiber JSMITH 2014-08-05T16:46:26Z Any measurement, morphological or physiological of the minute vessels connecting arterioles and venules, the walls of which act as a semipermeable membrane for interchange of various substances between the blood and tissue fluid. capillary measurement JSMITH 2014-08-06T10:31:27Z The length of time in the cardiac cycle between the end of left ventricular relaxation and the start of left ventricular filling. This represents the time in the cardiac cycle between closure of the aortic valve and opening of the mitral valve. time constant of isovolumetric LV fall LV-IVRT left ventricular isovolumetric relaxation time JSMITH 2014-08-06T10:46:35Z The time interval from the completion of the mitral valve closure to the beginning of the aortic valve opening, that is, the period of contraction during which both the mitral and aortic valves are closed so that the volume of the ventricular space doesn't change. left ventricular isovolumetric contraction time JSMITH 2014-08-18T11:44:51Z The length of time in the cardiac cycle between the end of right ventricular relaxation and the start of right ventricular filling. RV-IVRT right ventricular isovolumetric relaxation time JSMITH 2014-08-18T11:59:50Z A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of the length of time in the cardiac cycle between the end of left ventricular relaxation and the start of left ventricular filling. calculated LV-IVRT calculated left ventricular isovolumetric relaxation time JSMITH 2014-08-18T12:04:19Z A calculated measurement in which the value of the left ventricular isovolumetric relaxation time is corrected by the square root of the R-R interval [IVRT/(RR)1/2] on a simultaneously-recorded ECG. heart rate-corrected left ventricular isovolumetric relaxation time JSMITH 2014-08-18T12:19:05Z Measurement of the length of time between the closing of the mitral valve (the dual-flap valve in the heart that controls blood flow between the left atrium and the left ventricle) at the end of ventricular filling (that is, after atrial contraction) and its opening at the beginning of the next round of ventricular filling. MV co mitral valve closure to opening time JSMITH 2014-08-18T13:27:39Z The time interval from the opening to the closing of the aortic valve (mechanical systole). LVET left ventricular ejection time JSMITH 2014-08-18T13:54:20Z A calculated measurement comprised of the sum of left ventricular isovolumetric contraction time and isovolumetric relaxation time divided by the left ventricular ejection time. MPI TEI-Doppler index myocardial performance index JSMITH 2014-08-18T14:05:03Z Any measurement of the degree to which the presentation of any cardiovascular disease state, causes pain or damage, or interferes with the normal functioning of an organism or of any part thereof. cardiovascular disease severity measurement JSMITH 2014-08-18T14:20:49Z Any measurement related to a deviation from or interruption of the normal structure or function of the cardiovascular system that is manifested by a characteristic set of symptoms and signs. cardiovascular disease measurement JSMITH 2014-08-18T14:23:23Z Any measurement of the degree to which the presentation of an arterial disease state, causes pain or damage, or interferes with the normal functioning of an organism or of any part thereof. Arterial disease is a deviation from or interruption of the normal structure or function of one or more arteries, the vessels in which blood flows away from the heart carrying oxygenated blood, that is manifested by a characteristic set of symptoms and signs. arterial disease severity measurement JSMITH 2014-08-18T15:16:50Z Measurement of the degree to which a tear or break in the continuity or configuration of the aorta (the great artery arising from the left ventricle and from which the systemic arterial system proceeds) causes pain or damage, or interferes with the normal functioning of an organism or of any part thereof. aortic rupture severity measurement JSMITH 2014-08-18T15:33:42Z The value or quantity determined by count of tears or breaks in the continuity or configuration of the fenestrated layer of elastic tissue that is the outermost part of the intima of an artery. number of ruptures of internal elastic lamina in arteries number of ruptures of internal elastic laminae in arteries number of RIEL in arteries number of ruptures of arterial IEL number of ruptures of arterial internal elastic lamina JSMITH 2014-08-18T15:35:18Z The value or quantity determined by count of tears or breaks in the continuity or configuration of the internal elastic lamina (IEL) of the abdominal aorta and iliac arteries, that is, the distal segment of the descending aorta and the large arteries that originate from it. number of AA- and IA-RIEL number of RIEL in abdominal aorta and iliac arteries number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries JSMITH 2014-08-18T15:47:20Z The value or quantity determined by count of tears or breaks in the continuity or configuration of the internal elastic lamina (IEL) of the renal arteries, that is, the ateries which arise from the side of the abdominal aorta and which supply the kidneys with blood. number of RIEL in renal arteries number of ruptures of the internal elastic lamina of the renal arteries JSMITH 2014-08-18T15:50:34Z A measurement of the severity of tears or breaks in the arterial internal elastic lamina (IEL) which is derived from a combination of multiple measurements and/or objective or subjective severity scores according to a specified formula or set of criteria. The IEL is the fenestrated layer of elastic tissue that is the outermost part of the intima of an artery. arterial RIEL score arterial internal elastic lamina rupture composite score JSMITH 2014-08-18T18:42:12Z A calculated measurement in which the weight after dessication of the extracellular elastin in a specified sample of the wall of the aorta is divided by the length (that is, the distance between the two ends) of that segment, and the result presented as a ratio, fraction, quotient or percentage. aorta wall extracellular elastin dry weight to aorta length ratio JSMITH 2014-08-18T18:54:19Z A measurement of the existance and severity of a patent ductus arteriosus (PDA) when such a measurement is derived from a combination of multiple measurements and/or an objective or subjective ranking or rating system according to a specified formula or set of criteria. PDA is the abnormal persistence of an open lumen in the ductus arteriosus, between the aorta and the pulmonary artery, after birth. PDA score score for PDA patent ductus arteriosus score JSmith 2014-08-26T13:32:08Z Any measurement involving the composition, that is, the absolute amount, relative amount or type of one or more proteins (complex high molecular weight organic compounds containing carbon, hydrogen, oxygen, nitrogen, and sulfur consisting of alpha-amino acids joined by peptide linkages) or peptides (low molecular weight compounds composed of at least two amino acids joined by peptide linkages) in a specified tissue or set of tissues. tissue protein/peptide composition measurement JSmith 2014-08-26T13:35:55Z Any measurement involving the composition, that is, the absolute amount, relative amount or type of one or more proteins or peptides in a specified sample of tissue from the wall of the aorta. aortic wall protein/peptide composition measurement aorta wall protein/peptide composition measurement JSmith 2014-09-11T17:13:44Z A calculated parameter derived from a a sequence of blood pressure measurements taken sequentially and ordered in time. A parameter is a mathematical and statistical variable in a model system that partially or completely characterises the mathematical model. blood pressure time series calculated parameter JSmith 2014-09-11T18:09:25Z A mathematical and statistical variable in a model system that partially or completely characterises the baroreceptor response in a blood pressure time series calculation. The baroreceptor response is the system whereby specific nerve terminals that stabilize moment to moment blood pressure variability in the carotid sinus and aortic arch sense deviations from the baseline pressure and initiate signals that dampens such deviations. blood pressure time series baroreceptor response calculation parameter JSmith 2014-09-11T18:10:33Z The first order coefficient parameter derived from a blood pressure time series moving average (also known as a rolling average, running average, moving mean, or rolling mean) calculation. blood pressure time series first order moving average coefficient JSmith 2014-09-11T18:24:22Z The fractal parameter derived from a blood pressure time series calculation based on a autoregressive fractionally integrated moving average time series model (ARFIMA, FARIMA, or fARIMA). blood pressure time series fractal parameter JSmith 2014-09-11T18:26:20Z The experimental set point parameter of the blood pressure time series baroreceptor response calculation. blood pressure time series experimental set point of the baroreceptor response JSmith 2014-09-11T18:28:14Z The average exponential scaling factor parameter of the blood pressure time series baroreceptor response calculation. blood pressure time series average exponential scaling factor of the baroreceptor response JSmith 2014-09-11T18:33:18Z A parameter based on a blood pressure time series calculation using a first order mechanistic model. blood pressure time series linear term first order parameter JSmith 2014-09-11T18:33:53Z A parameter based on a blood pressure time series calculation using a second order mechanistic model. blood pressure time series linear term second order parameter JSmith 2014-10-29T10:36:08Z The thickness or depth (i.e. the measurement of the two-dimensional extent of the distance between the inner and outer surfaces) of the dorsal/posterior wall of the left ventricle of the heart at the end of diastole, that is, when the heart muscle is maximally relaxed. The dorsal wall is the portion of the muscle enclosing the ventricle which is closest to the spine and farthest from the chest wall of the organism. end-diastolic heart left ventricle posterior wall thickness end-diastolic heart left ventricle PWT Note that "left" in this context refers to the perspective of the organism, not that of the observer. heart left ventricle end-diastolic posterior wall thickness jesmith 2015-12-03T15:18:18Z A value resulting from the quantification of a morphological or physiological parameter of a blood-derived lipoprotein, any of a class of complex molecules found in blood that consist of a protein membrane surrounding a core of lipids. blood lipoprotein measurement jesmith 2015-12-03T15:41:10Z Measurement of the amount of cholesterol, a eukaryotic sterol that in higher animals is the precursor of bile acids and steroid hormones and a key constituent of cell membranes, carried in lipoprotein molecules in a specified volume of blood. Lipoprotein particles are complex molecules that consist of a protein membrane surrounding a core of lipids. blood lipoprotein cholesterol level jesmith 2017-02-22T13:08:55Z The distance between the two ends, that is, of the extent of the longest dimension, of the aorta, the main trunk from which the arterial system proceeds. aorta length jesmith 2017-02-22T13:12:37Z A measurement which has been normalized, adjusted or derived by a mathematical process or computation of the physical form or structure of the aorta, the main trunk from which the arterial system proceeds. calculated aorta morphological measurement jesmith 2017-02-22T13:14:54Z A calculated measurement in which the weight of the aorta is divided by its length and the resulting quantity is divided by the total body weight of the organism. Am/AI/Bm aorta mass to aorta length to body mass ratio aorta weight to aorta length to body weight ratio jesmith 2017-02-22T13:28:13Z A calculated measurement of the relative difference in pulse pressure between a treated state and a control state or between two points in time, expressed as a percentage. percent change in pulse pressure jesmith 2017-07-19T12:56:36Z Any quantification of the ability of a protein of the heart to accomplish an effect, e.g. take part in a chemical reaction or carry out a specified molecular function. heart protein activity measurement jesmith 2017-07-19T13:02:57Z Any quantification of the ability of a heart enzyme, i.e. a protein located in the heart that catalyzes chemical reactions of other substances without itself being destroyed or altered upon completion of the reactions, to carry out its specified molecular function. heart enzyme activity level jesmith 2017-07-19T13:04:34Z Quantitation of the catalytic effect exerted by angiotensin I converting enzyme 2 (ACE2) in a specified sample of heart tissue. ACE2, an ACE homolog, is a zinc-dependent peptidase of the M2-metalloprotease family that is sensitive to chloride ion concentration, is a membrane-bound enzyme that acts as a monocarboxypeptidase, and is an essential regulator of heart function. heart ACE2 activity level heart angiotensin II converting enzyme activity level heart angiotensin I converting enzyme 2 activity level jesmith 2017-07-19T13:05:42Z Quantitation of the catalytic effect exerted by angiotensin I converting enzyme (ACE) in a specified sample of heart tissue. ACE is one of the enzymes of the renin-angiotensin system, and catalyzes the conversion of angiotensin I into a physiologically active vasoconstrictor peptide angiotensin II. heart ACE activity level heart angiotensin I converting enzyme activity level jesmith 2017-07-20T10:00:38Z Quantitation of the catalytic effect exerted by angiotensin converting enzyme2 (ACE2) in a specified sample of kidney. ACE2, an ACE homolog, is a zinc-dependent peptidase of the M2-metalloprotease family that is sensitive to chloride ion concentration, and is a membrane-bound enzyme that acts as a monocarboxypeptidase and is an essential regulator of heart function. kidney ACE2 activity level kidney angiotensin II converting enzyme activity level kidney angiotensin I converting enzyme 2 activity level jesmith 2017-07-20T10:01:18Z Quantitation of the catalytic effect exerted by angiotensin I converting enzyme (ACE) in a specified sample of kidney tissue. ACE is one of the enzymes of the renin-angiotensin system, and catalyzes the conversion of angiotensin I into a physiologically active vasoconstrictor peptide angiotensin II. kidney ACE activity level kidney angiotensin I converting enzyme activity level jesmith 2017-07-20T13:40:53Z Any measurement of the physical form or structure of a cardiac muscle fiber, a striated cardiac muscle cell (cardiomyocyte) that is responsible for heart contraction. cardiac muscle cell morphological measurement cardiac myocyte morphological measurement cardiomyocyte morphological measurement heart muscle cell morphological measurement cardiocyte morphological measurement cardiac muscle fiber morphological measurement jesmith 2017-07-20T13:43:26Z The length of a straight line passing through a cardiac muscle fiber, that is a cardiomyocyte, for instance through the center of its nucleus, and connecting opposite points on its periphery. cardiac myocyte diameter cardiomyocyte diameter heart muscle cell diameter cardiocyte diameter cardiomyocyte width cardiac muscle fiber diameter jrsmith 2018-05-03T09:34:26Z A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of the amount of plasma that perfuses the kidneys per unit time per amount of body weight. renal plasma flow to body weight ratio jrsmith 2018-05-03T17:41:50Z A calculated measurement in which glomerular filtration rate, an estimate of the volume of fluid filtered from the kidney glomerular capillaries into the Bowman's capsule per specified unit of time, is divided by the total weight of the body and the result is presented as a ratio, fraction, quotient or percentage. glomerular filtration rate to body weight ratio jrsmith 2018-05-11T12:56:54Z A calculated value in which the volume of glomeruli with lesions resulting from fibrosis, scarring or hyaline deposits is divided by the total volume of glomeruli in a specified sample of kidney and presented as a ratio, fraction or quotient, thus normalizing it to the total volume of glomeruli. kidney sclerotic glomerular volume to total kidney glomerular volume ratio jrsmith 2018-05-15T16:59:53Z A calculated value in which the weight of the heart left ventricle is divided by the length of the tibia (the medial and larger of the two bones of the lower leg of bipeds or hindlimb of quadrupeds which articulates with the femur, fibula, and talus), and the result is presented as a ratio, fraction, quotient or percentage,thus normalizing it to the length of the leg and, by extension, to the size of the body. LV weight/tibial length heart left ventricle weight to tibia length ratio jrsmith 2018-05-15T17:02:51Z Any measurement which has been normalized, adjusted or derived by a mathematical process or computation, of the movement of blood into, through or out of the heart. calculated heart blood flow measurement jrsmith 2018-05-15T17:05:23Z A calculated measurement in which the value of the E wave (that is, the velocity of the blood flow across the mitral valve during passive filling of the left ventricle in early diastole) is divided by the value of the A wave (that is, the velocity of the blood flow across the mitral valve during active filling of the left ventricle caused by atrial contraction in late diastole). mitral E/A wave ratio E/A wave ratio jrsmith 2018-05-15T17:08:42Z A calculated measurement in which the average width of the tunica media is divided by the inner diameter (that is, the diameter of the lumen) of the artery and the result is presented as a ratio, fraction, quotient or percentage. artery tunica media width to artery inner diameter ratio jrsmith 2018-05-15T17:12:15Z The thickness, width or depth of the septal wall of the heart ventricles (that is, the portion of the wall between the left and right ventricles that is shared between the two) at the end of diastole when the heart muscle is maximally relaxed. heart intraventricular septum end-diastolic thickness IVSd heart intraventricular end-diastolic wall thickness jrsmith 2018-05-15T17:13:43Z The thickness, width or depth of the septal wall of the heart ventricles (that is, the portion of the wall between the left and right ventricles that is shared between the two) at the end of systole when the heart muscle is maximally contracted. heart intraventricular septum end-systolic thickness IVSs heart intraventricular end-systolic wall thickness sjwang 2018-11-13T15:00:11Z A variability measurement in which the mean is calculated from the standard deviations or the standard deviation is calculated from the means of sequential one hour systolic blood pressure measurements. systolic blood pressure variability sjwang 2018-11-13T15:02:20Z A variability measurement in which the mean is calculated from the standard deviations or the standard deviation is calculated from the means of sequential one hour diastolic blood pressure measurements. diastolic blood pressure variability sjwang 2018-11-13T15:04:28Z A variability measurement in which the mean is calculated from the standard deviations or the standard deviation is calculated from the means of sequential one hour mean arterial blood pressure measurements. mean arterial blood pressure variability sjwang 2018-11-13T15:12:25Z A variability measurement in which the mean is calculated from the standard deviations or the standard deviation is calculated from the means of sequential one hour heart rate measurements. heart rate variability sjwang 2018-11-14T10:49:02Z A calculated value in which the number of glomeruli with microaneurysm (focal dilation of arteriocapillary junctions), is divided by the total number of glomeruli in the kidney and presented as a ratio, fraction or quotient, thus normalizing it to the total number of glomeruli. ratio of number of glomeruli with microaneurysms to number of total glomeruli sjwang 2018-11-14T11:16:40Z A calculated value in which the area of glomeruli with activated mesangial cells (determined by the expression of &#945;-smooth muscle actin), is divided by the total area of glomeruli counted in the kidney and presented as a ratio, fraction or quotient, thus normalizing it to the total number of glomeruli. ratio of glomerular area occupied by activated mesangial cells to total glomerular area sjwang 2018-11-14T11:19:47Z Any measurement that has been normalized, adjusted or derived by a mathematical process or computation, of the glomeruli of one or both kidneys, the paired organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes. calculated kidney glomerulus morphological measurement calculated kidney glomerulus measurement sjwang 2018-11-19T15:28:14Z Any measurement of the physical form or structure of one or more of the mesenteric arteries, which arise from the anterior surface of the abdominal aorta, just inferior to the origin of the celiac trunk, and supplies blood to the intestine from the lower part of the duodenum through two-thirds of the transverse colon, as well as the pancreas. mesenteric artery morphological measurement sjwang 2018-11-19T15:30:34Z Any quantitation of the molecules, atoms and/or ions which constitute the chemical make-up of the wall of one or more of the mesenteric arteries. mesenteric artery molecular composition measurement sjwang 2018-11-19T15:33:20Z A measurement which has been normalized, adjusted or derived by a mathematical process or computation of the physical form or structure of any of the mesenteric arteries. calculated mesenteric artery wall molecular composition measurement calculated mesenteric artery molecular composition measurement sjwang 2018-11-19T15:35:54Z A calculated measurement in which mesenteric artery phosphorylated eNOS protein level is divided by aorta wall total eNOS protein level and presented as a ratio, fraction, quotient or percentage. Phosphorylation of eNOS is a mechanism that catylzes a structural change of the enzyme to an activated form. mesenteric artery phosphylated eNOS protein level to total eNOS protein level ratio mesenteric artery wall phosphylated eNOS level to total eNOS level ratio mesenteric artery phosphylated eNOS level to total eNOS level ratio sjwang 2018-11-19T15:53:29Z A calculated measurement in which aorta wall phosphorylated eNOS protein level is divided by aorta wall total eNOS protein level and presented as a ratio, fraction, quotient or percentage. Phosphorylation of eNOS is a mechanism that catylzes a structural change of the enzyme to an activated form. aorta wall phosphylated eNOS protein level to total eNOS protein level ratio aorta wall phosphylated eNOS level to total eNOS level ratio sjwang 2018-11-26T13:03:49Z Monophasic action potentials (MAPs) are recorded using contact electrode catheters. The recordings provide local information about the actual cellular depolarization and repolarization process of myocardial tissue. They are different from body surface electrocardiographic (ECG) recordings or standard endocardial electrograms, which produce a summative or derivative view of the heart's electrical activity Monophasic action potential sjwang 2018-11-26T13:39:11Z Conduction velocity is calculated as the distance from pacing electrode to the monophasic action potential recording electrode across the epicardial surface, divided by the conduction time, the time from the pacing spike to monophasic action potential onset. Conduction velocity sjwang 2018-11-26T14:10:18Z The E/E' is a ratio of peak velocity of early diastolic trans-mitral flow (E) to the peak velocity of early diastolic mitral annular motion (E') E wave velocity to E' wave velocity ratio E/E' wave ratio sjwang 2018-11-26T14:27:05Z Any quantitation of the molecules, atoms and/or ions which constitute the chemical make-up of the tissue(s) of the heart. cardiac molecular composition measurement heart molecular composition measurement sjwang 2018-11-26T14:31:33Z Measurement of the amount of free fatty acids within the heart. cardiac free fatty acid level cardiac non-esterified fatty acid level heart NEFA level heart non-esterified fatty acid level heart free fatty acid level sjwang 2018-11-26T14:35:50Z Measurement of the amount of triglycerides within the heart. cardiac triglyceride level heart triglyceride level sjwang 2018-11-26T14:44:30Z A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of the end-systolic heart left ventricle posterior wall thickness. calculated heart left ventricle end-systolic posterior wall thickness sjwang 2018-11-26T14:50:07Z A calculated measurement in which the heart left ventricle end-systolic posterior wall thickness is divided by the weight of the body, and the result presented as a ratio, fraction, quotient or percentage. heart left ventricle end-systolic posterior wall index sjwang 2018-11-26T14:59:27Z A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of the heart left ventricle end-systolic internal diameter. calculated heart left ventricle end-systolic internal dimension calculated heart left ventricle end-systolic internal diameter sjwang 2018-11-26T15:03:09Z A calculated measurement in which the heart left ventricle end-systolic internal diameter is divided by the weight of the body, and the result presented as a ratio, fraction, quotient or percentage. heart left ventricle end-systolic internal dimension index heart left ventricle end-systolic internal diameter index sjwang 2018-11-26T15:08:05Z A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of the heart ventricle end-systolic septal wall thickness. calculated heart end-systolic intraventricular wall thickness calculated heart ventricle end-systolic septal wall thickness sjwang 2018-11-26T15:11:20Z A calculated measurement in which the heart ventricle end-systolic septal wall thickness is divided by the weight of the body, and the result presented as a ratio, fraction, quotient or percentage. heart ventricle end-systolic septal wall index sjwang 2018-11-26T15:13:54Z Peak velocity of late atrial diastolic trans-mitral flow (A). A wave velocity sjwang 2018-11-26T15:20:51Z E' wave velocity is the peak velocity of early mitral annular diastolic motion. e' wave velocity E' wave velocity sjwang 2018-11-26T15:23:27Z A' wave velocity (A') is the peak velocity of late (atrial) diastolic mitral annular motion. a' wave velocity A' wave velocity sjwang 2018-11-27T15:03:00Z A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of cardiac output. calculated cardiac output measurement sjwang 2018-11-27T15:09:41Z A calculated measurement in which the cardiac output is divided by the weight of the body, and the result presented as a ratio, fraction, quotient or percentage. cardiac index sjwang 2018-11-27T15:14:24Z A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of cardiac stroke volume. calculated stroke volume sjwang 2018-11-27T15:16:25Z A calculated measurement in which the cardiac stroke volume is divided by the weight of the body, and the result presented as a ratio, fraction, quotient or percentage. stroke index sjwang 2018-11-27T15:20:50Z A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of the left ventricular end-systolic blood pressure. calculated left ventricular end-systolic blood pressure sjwang 2018-11-27T15:23:57Z Effective arterial elastance (Ea), defined as the ratio of left ventricular (LV) end-systolic pressure and stroke volume, lumps the steady and pulsatile components of the arterial load in a concise way. arterial elastance sjwang 2018-11-27T15:29:19Z Defined as the work performed by the left or right ventricle to eject the stroke volume into the aorta or pulmonary artery, respectively. ventricle stroke work sjwang 2018-11-27T15:32:24Z Defined as the work performed by the left ventricle to eject the stroke volume into the aorta. left ventricle stroke work sjwang 2018-11-27T15:34:52Z Preload recruitable stroke work (PRSW) is determined by the linear regression of stroke work with the end-diastolic volume. The slope of the PRSW relationship is a highly linear index of myocardial contractility that is insensitive to preload and afterload. preload recruitable left ventricle stroke work sjwang 2018-11-27T15:38:49Z A calculated measurement in which the maximum rate of positive change in left ventricular blood pressure is divided by the left ventricular end-diastolic volume, and the result presented as a ratio, fraction, quotient or percentage. maximum rate of positive change in left ventricular blood pressure to left ventricular end-diastolic volume ratio sjwang 2018-11-27T15:46:13Z A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of the end-diastolic heart left ventricle posterior wall thickness. calculated heart left ventricle end-diastolic posterior wall thickness sjwang 2018-11-27T15:56:21Z A calculated measurement in which the heart left ventricle end-diastolic posterior wall thickness is divided by the weight of the body, and the result presented as a ratio, fraction, quotient or percentage. heart left ventricle end-diastolic posterior wall index sjwang 2018-11-27T15:58:19Z A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of the heart left ventricle end-diastolic anterior wall thickness. calculated heart left ventricle end-diastolic anterior wall thickness sjwang 2018-11-27T16:14:56Z A calculated measurement in which the heart left ventricle end-diastolic anterior wall thickness is divided by the weight of the body, and the result presented as a ratio, fraction, quotient or percentage. heart left ventricle end-diastolic anterior wall index sjwang 2018-11-27T16:18:07Z A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of the heart ventricle end-diastolic septal wall thickness. calculated heart ventricle end-diastolic septal wall thickness sjwang 2018-11-27T16:19:43Z A calculated measurement in which the heart ventricle end-diastolic septal wall thickness is divided by the weight of the body, and the result presented as a ratio, fraction, quotient or percentage. heart ventricle end-diastolic septal wall index sjwang 2018-11-30T15:55:22Z Renal medullary blood flow (MBF) is the volume of blood delivered to or exiting from the renal medulla per unit time. renal medullary blood flow rate sjwang 2018-12-03T16:21:42Z Left ventricle end-diastolic elastance (Eed) is the estimate of the slope of the line Ped=Eed(Ved-V0), which is based on linear regression of points determined by iterative calculation of the LV end-diastolic pressure–volume relationship. heart left ventricle end-diastolic elastance sjwang 2018-12-03T16:24:05Z Left ventricle end-systolic elastance (Ees) is the estimate of the slope of the line Pes=Ees(Ves-V0), which is based on linear regression of points determined by iterative calculation of the LV end-systolic pressure–volume relationship. heart left ventricle end-systolic elastance sjwang 2018-12-04T12:06:42Z A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of components of the periodic tightening and loosening of the muscles of a ventricle of the heart. calculated ventricle contraction measurement sjwang 2018-12-04T12:31:25Z Left ventricle diastolic volume-axis intercept (V0) is determined by the line Ped=Eed(Ved-V0), which is based on linear regression of points determined by interative calculation of the LV end-diastolic pressure–volume relationship. Heart left ventricle diastolic volume-axis intercept (V0) sjwang 2018-12-04T12:34:18Z Left ventricle systolic volume-axis intercept (V0) is determined by the line Pes=Ees(Ves-V0), which is based on linear regression of points determined by iterative calculation of the LV end-diastolic pressure–volume relationship. Heart left ventricle systolic volume-axis intercept (V0) sjwang 2018-12-04T12:46:20Z A measurement of the volume of blood in ventricle immediately before a contraction which has been normalized or adjusted by a mathematical process or computation. . Calculated endo-diastolic volume sjwang 2018-12-04T12:59:56Z A measurement of the volume of blood in a ventricle at the end of a contraction which has been normalized or adjusted by a mathematical process or computation. Calculated endo-systolic volume sjwang 2018-12-05T13:54:43Z The amount of adrenomedullin in a specified sample of kidney tissue. kidney adrenomedullin level sjwang 2018-12-05T13:57:39Z The amount of adrenomedullin in a specified sample of medullary kidney tissue. kidney medullary adrenomedullin level sjwang 2018-12-05T13:59:17Z The amount of adrenomedullin in a specified sample of cortical kidney tissue. kidney cortical adrenomedullin level sjwang 2018-12-07T10:37:27Z Any measurement which has been normalized, adjusted or derived by a mathematical process or computation, of the volume of fluid filtered from the kidney glomerular capillaries into the Bowman's capsule per specified unit of time based on serum creatinine level, wieght and age of organism and other factors. calculated glomerular filtration rate sjwang 2018-12-07T11:57:13Z Any quantification of a morphological or physiological parameter of one or more nucleic acids in the heart. Nucleic acids are high-molecular-weight polymeric compounds composed of nucleotides, each consisting of a purine or pyrimidine base, a ribose or deoxyribose sugar, and a phosphate group, and are involved in the determination and transmission of genetic characteristics. heart nucleic acid measurement sjwang 2018-12-07T12:02:20Z Any measurement of the absolute or relative amount(s) of one or more of the ribonucleic acids (RNAs) of which the heart is formed or composed. heart ribonucleic acid composition measurement sjwang 2018-12-07T12:04:28Z heart Igf1 mRNA level heart insulin-like growth factor 1 mRNA level sjwang 2018-12-07T12:09:49Z Any measurement of the absolute or relative amount(s) of one or more of the ribonucleic acids (RNAs) of which the heart left ventricle is formed or composed. heart left ventricle ribonucleic acid content sjwang 2018-12-07T12:23:27Z heart right ventricle insulin-like growth factor 1 mRNA level sjwang 2018-12-07T12:28:34Z The amount of ribonucleic acid (DNA), the molecule composed of the sugar ribose, phosphate groups and any combination of the bases adenine, guanine, cytosine, and/or uracil , extracted from or contained in the heart right ventricle, the lower chamber of the right side of the heart (from the perspective of the organism rather than the observer), which pumps venous blood through the pulmonary trunk and arteries to the capillaries of the lung. heart right ventricle ribonucleic acid content sjwang 2018-12-07T12:30:31Z heart right ventricle molecular composition measurement sjwang 2018-12-07T12:35:54Z heart left ventricle Igf1r mRNA level heart left ventricle insulin-like growth factor 1 mRNA level sjwang 2018-12-07T12:44:11Z heart Igf1r mRNA level heart insulin-like growth factor 1 receptor mRNA level sjwang 2018-12-07T12:46:44Z heart right ventricle insulin-like growth factor 1 receptor mRNA level sjwang 2018-12-07T12:49:23Z heart left ventricle insulin-like growth factor 1 receptor mRNA level sjwang 2018-12-07T14:45:56Z Filtration fraction is the ratio of the glomerular filtration rate (GFR) to the renal plasma flow (RPF). Filtration Fraction, FF = GFR/RPF. The filtration fraction, therefore, represents the proportion of the fluid reaching the kidneys which passes into the renal tubules. FF filtration fraction renal filtration fraction sjwang 2018-12-07T14:51:40Z glomerular filtration rate to kidney weight ratio sjwang 2018-12-07T14:54:49Z A calculated measurement to determine the volume of fluid filtered from the renal (kidney) glomerular capillaries of a single nephron into Bowman's capsule per unit time. SNGFR single nephron glomerular filtration rate sjwang 2018-12-07T14:57:04Z A calculated measurement to determine the ratio of the single nephron glomerular filtration rate (SNGFR) to the renal plasma flow (RPF). Single nephron filtration Fraction, SNFF = SNGFR/RPF. The single nephron filtration fraction, therefore, represents the proportion of the fluid reaching the kidneys which passes into the renal tubules from a single nephron. SNFF single nephron filtration fraction sjwang 2018-12-07T15:14:18Z calculated kidney morphological measurement sjwang 2018-12-07T15:16:47Z ""A semiquantitative evaluation of the renal interstitium using a grading system with a score of 0 to 4+, which assesses the tubules and the interstitium for the presence of (1) tubular atrophy, (2) tubular dilatation, (3) interstitial inflammatory cell infiltrates, and (4) interstitial fibrosis. A score of 0 indicates no lesion (normal kidney), 1+ indicates a single, small focal lesion with very minimal tubular alterations and interstitial inflammatory cell infiltration, and 2+ to 4+ indicated increasing severity of tubular lesions, interstitial inflammatory cell infiltration, and/or fibrosis. A score of 4+ indicates involvement of approximately 50% or more of the renal parenchyma or interstitium." [PMID:PMID\:9369281] kidney tubulointerstitial score renal tubulointerstitial score sjwang 2018-12-20T14:50:34Z A calculated value in which the weight of the left atrium, the upper chamber on the left side of the heart which empties into the lower left chamber, is divided by the total weight of the body and the result presented as a ratio, fraction, quotient or percentage, thus normalizing it to body weight. heart left atrium weight to body weight ratio sjwang 2018-12-20T14:57:33Z A measurement of the physical form or structure of the right atrium, the right upper chamber of the heart that receives blood from the vena cava and forces it into the right ventricle, which has been normalized, adjusted or derived by a mathematical process or computation. calculated heart right atrium morphological measurement sjwang 2018-12-20T14:59:58Z A calculated value in which the weight of the right atrium, the upper chamber on the right side of the heart which empties into the lower right left chamber, is divided by the total weight of the body and the result presented as a ratio, fraction, quotient or percentage, thus normalizing it to body weight. heart right atrium weight to body weight ratio sjwang 2018-12-20T15:02:38Z The weight of the septum of the heart, which is the portion of the heart left ventricle ventral/anterior wall and right ventricle dorsal/posterior wall which is shared between the ventricles, after removal from the body and separation from the rest of the heart. Heart septum weight sjwang 2018-12-20T15:09:32Z The average number of podocytes in the kidney glomeruli. number of podocytes per kidney glomerulus sjwang 2018-12-20T15:13:54Z A calculated measurement in which the average number of podocytes is divided by the average volume of kidney glomeruli. number of podocytes to glomerular volume ratio sjwang 2018-12-26T16:17:20Z The average number of nucleated cells in the kidney glomeruli. number of nucleated cells per kidney glomerulus sjwang 2018-12-26T16:20:07Z An injury score obtained by multiplying the degree of glomerular damage (0 to 4) with the percentage of the glomeruli with that type of injury (i.e., increase in mesangial matrix material or glomerulosclerosis). mesangial injury score sjwang 2018-12-27T11:44:39Z Volume of blood plasma delivered to a single glomerulus per unit time Qa glomerular capillary plasma flow rate sjwang 2018-12-27T11:55:22Z Force exerted on the luminal capillary wall from fluid flowing through the capillary. glomerular capillary hydraulic pressure sjwang 2018-12-27T12:03:45Z Any measurement of one of the small blood vessels carrying blood between arteries and capillaries. arteriole measurement sjwang 2018-12-27T12:07:55Z Resistance that must be overcome to push blood through arterioles to create flow. arteriolar resistance sjwang 2018-12-27T12:21:25Z Resistance to blood flow measured within the efferent arteriole proximal to a glomerular capillary network. Re efferent glomerular arteriolar resistance efferent arteriolar resistance sjwang 2018-12-27T12:27:17Z Resistance to blood flow measured within the afferent arteriole distal to a glomerular capillary network. Ra afferent glomerular arteriolar resistance afferent arteriolar resistance sjwang 2018-12-27T12:33:35Z Total resistance to blood flow measured within the afferent arteriole proximal and distal to a glomerular capillary network (Rt = Ra + Re). Rt; total glomerular arteriolar resistance total arteriolar resistance sjwang 2018-12-27T12:45:26Z Measurement of the total amount of all proteins found in a specific volume of afferent arteriolar plasma. Ca afferent arteriolar plasma protein concentration sjwang 2018-12-27T12:49:32Z Measurement of the total amount of all proteins found in a specific volume of efferent arteriolar plasma. Ce efferent arteriolar plasma protein concentration sjwang 2018-12-27T12:53:15Z A form of osmotic pressure exerted by proteins, notably albumin, in the afferent arteriole's plasma that tends to pull water into the circulatory system. It is the opposing force to hydrostatic pressure. It has a major effect on the pressure across the glomerular filter. afferent colloid osmotic pressure sjwang 2018-12-27T13:07:24Z A form of osmotic pressure exerted by proteins, notably albumin, in the efferent arteriole's plasma that tends to pull water into the circulatory system. It is the opposing force to hydrostatic pressure. It has a major effect on the pressure across the glomerular filter efferent colloid osmotic pressure sjwang 2018-12-27T13:11:50Z A measure of a membrane's permeability to water; specifically, the volume of fluid filtered in unit time through a unit area of membrane per unit pressure difference, and it is defined as the glomerular filtration rate (GFR) for both kidneys per millimeter of mercury (mmHg) of filtration pressure. Kf glomerular capillary ultrafiltration coefficient sjwang 2018-12-27T14:28:13Z A calculated measurement in which the area occupied by renal cysts is divided by the total the kidney, and the result presented as a ratio, fraction, quotient or percentage. ratio of the area occupied by cysts to the total area of the kidney sjwang 2018-12-27T15:20:35Z Force exerted on the luminal surface of the proximal tubule from fluid flowing through the tubule. mean proximal tubular hydraulic pressure sjwang 2018-12-27T15:22:41Z Force exerted on the luminal vessel wall from fluid flowing through the efferent arteriole. efferent glomerular arteriolar hydraulic pressure efferent arteriolar hydraulic pressure sjwang 2018-12-27T15:27:01Z The difference between the force exerted on the luminal glomerular capillary wall and the force exerted on the luminal proximal tubular membrane (Pgc - Pt = delta P). Pgc - Pt = delta P glomerular transcapillary hydraulic pressure gradient sjwang 2018-12-27T15:58:18Z calculated left ventricular end-diastolic blood pressure measurement sjwang 2018-12-27T16:00:35Z A calculated measurement in which the pressure in the heart left ventricle at the end of diastole, the period when the heart is in a state of relaxation and expansion and the ventricles fill with blood, divided by the diameter across the left ventricle of the heart at the end of diastole and the result presented as a ratio, fraction, quotient or percentage. LVEDP/LVDd heart left ventricular end-diastolic blood pressure to heart left ventricular end-diastolic diameter ratio sjwang 2019-01-02T13:36:28Z Rate-pressure product is defined as the product of the heart rate (the number of contractions of the cardiac ventricles per unit of time) and mean arterial blood pressure (the average force the blood exerts on an artery wall). RPP rate-pressure product sjwang 2019-01-22T15:47:09Z A calculated measurement of the average width of the tunica media (the middle coat of the arterial wall) divided by the artery total diameter (measured as the length of a line which crosses a transverse view of an artery, passing through its center and ending on either side at the outer surface of the blood vessel wall). artery tunica media to artery total diameter ratio sjwang 2019-01-22T15:50:45Z A calculated measurement of the average width of the artery lumen (measured as the length of a line which crosses a transverse view of an artery, passing through its center and ending on either side at the inner surface of the blood vessel wall) divided by the artery total diameter (measured as the length of a line which crosses a transverse view of an artery, passing through its center and ending on either side at the outer surface of the blood vessel wall). artery lumen to artery total diameter ratio the role of a material entity to prevent, diagnose, treat, or study disease and/or its effects William Hogan William Hogan clinical drug role a material entity (1) containing at least one scattered molecular aggregate as part that is the bearer of an active ingredient role and (2) that is itself the bearer of a clinical drug role William Hogan William Hogan drug product active ingredient role a role of a scattered molecular aggregate that is part of a drug product that is realized by (1) administration of the drug to an organism followed by (2) some change in the structure or functioning of some part of the organism William R. Hogan active ingredient role of a scattered molecular aggregate a role borne by a scattered molecular aggregate and realized by its grains participating in one or more processes William R. Hogan role of scattered molecular aggregate administration of a drug product to an organism a treatment that has as participants an extended organism and a drug product and that results in part of the drug product being located in the extended organism William R. Hogan drug administration https://en.wikipedia.org/wiki/Geographic_feature macroscopic spatial feature envoPolar May appear on a map. geographic feature An anthropogenic geographic feature is a geographic feature resulting from the influence of human beings on nature. An anthropogenic geographic feature is a geographic feature resulting from the influence of human beings on nature. FTT:78 TGN:50001 man-made feature manmade feature anthropogenic geographic feature FTT:1242 FTT:1252 FTT:15 FTT:16 FTT:18 FTT:19 FTT:21 FTT:22 FTT:23 FTT:24 FTT:25 FTT:26 FTT:27 FTT:28 FTT:29 FTT:37 SWEETRealm:AdministrativeRegion TGN:80001 TGN:81099 TGN:81123 https://en.wikipedia.org/wiki/Administrative_region administrative area administrative division administrative entity boundary region civil area district free trade zone governed place leased area (government) leased zone (government) neutral zone (political) prefecture protectorate sheikdom sultanate trade zone administrative region A political association with effective dominion over a geographic area. FTT:424 FTT:566 FTT:567 FTT:571 SWEETRealm:Country SWEETRealm:State TGN:80006 TGN:81010 TGN:81011 TGN:81102 https://en.wikipedia.org/wiki/Nation nation independent nation independent political entity independent sovereign nation ENVO country political entity state ENVO:00000009 national geopolitical entity 1 Place or area with clustered or scattered buildings and a permanent human population. place FTT:1097 FTT:33 Geonames:P.PPL Geonames:P.PPLS TGN:22201 TGN:83002 https://en.wikipedia.org/wiki/Populated_place inhabited place populated place populated places settlement ENVO inhabited region populated locality ENVO:00000062 populated place A feature that has been constructed by deliberate human effort. "constructed" should probably be made something like a quality and this class obsoleted or filled only by inference constructed feature construction A permanent walled and roofed construction. FTT:42 Geonames:S.BLDG LTER:76 TGN:51011 https://en.wikipedia.org/wiki/Building BUILDING building building A geographical region whose affairs and population are administered by an authority. FTT:1093 Geonames:A.PCL TGN:80002 political entity political entity Incorporated populated place. urban area EcoLexicon:city FTT:430 FTT:483 FTT:484 FTT:485 SWEETRealm:City TGN:83020 TGN:83040 TGN:83043 https://en.wikipedia.org/wiki/City ENVO ENVO:00000856 city An environmental feature that is, or can be, contained and is predominantly composed of one or a few types of stuff. An object which is large enough to be visible to humans, but small enough that humans can handle the object (i.e. transport it, examine it, etc) in its entirety with little to no technological assistance. mesoscopic physical object This is a legacy class from ENVO's early versions. It will be depopulated and filled in by inference using a PATO quality. Not to be confused with "mesoscopic" as defined in physics, which deals with objects typically between 10e-6 and 10-8 meters in diameter. mesoscopic physical object physical object of mesoscopic geological size A material entity which determines an environmental system. ENVO ENVO:00002297 A material entity determines an environmental system when its removal would cause the collapse of that system. For example, a seamount determines a seamount environment, acting as its 'hub'. This class is currently being aligned to the Basic Formal Ontology. Following this alignment, its definition and the definitions of its subclasses will be revised. environmental feature A material entity that has been processed by humans or their technology in any way, including intermediate products as well as final products. manufactured good manufactured product ENVO ENVO:00003075 anthropogenic abiotic mesoscopic feature A portion of environmental material is a fiat object part which forms the medium or part of the medium of an environmental system. A portion of environmental material is a fiat object which forms the medium or part of the medium of an environmental system. portion of environmental material Everything under this parent must be a mass noun. All subclasses are to be understood as being composed primarily of the named entity, rather than restricted to that entity. For example, "ENVO:water" is to be understood as "environmental material composed primarly of some CHEBI:water". This class is currently being aligned to the Basic Formal Ontology. Following this alignment, its definition and the definitions of its subclasses will be revised. environmental material ENVO ENVO:01000010 abiotic mesoscopic physical object A system which has the disposition to environ one or more material entities. 2013-09-23T16:04:08Z EcoLexicon:environment environment In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised. environmental system An anthropogenic environment is an environmental system which is the product of human activity. Unsatisfactory definition here. Must consider the threshold that makes an environmental system anthropogenic. anthropogenic environment A site which has its extent determined by the presence or influence of one or more components of an environmental system or the processes occurring therein. environmental area envoPolar Formerly, this class was an experimental class and a subclass of "environmental feature". It is now aligned to BFO. The class was not obsoleted as the core semantics maintained their stability through its transition. environmental zone A building part is a construction which is part of a building. Not recommended for annotation. This class is likely to be made into an inferred class as its subclasses are distributed among more meaningful superclasses (i.e. ceiling is_a surface layer). See for example, "building floor". The boundaries between building parts may be bona fide or fiat. building part Outer space is a hard vacuum containing a low density of particles, predominantly a plasma of hydrogen and helium as well as electromagnetic radiation, magnetic fields, neutrinos, dust and cosmic rays that exists between celestial bodies. space envoAstro outer space A settlement with a high density of buildings and inhabitants. See also: http://www.ecotope.org/anthromes/v1/guide/urban/12_dense_settlements/default.aspx The thresholds for what makes a settlment "dense" can be determined as needed. If there is a specific threshold that should be added to ENVO, please make a new class request. dense settlement A self-contained constructed feature used by one or more households as a home, such as a house, apartment, mobile home, houseboat or other 'substantial' structure. A dwelling typically includes nearby outbuildings, sheds etc. within the curtilage of the property, excluding any 'open fields beyond'. It has significance in relation to search and seizure, conveyancing of real property, burglary, trespass, and land use planning. See https://github.com/EnvironmentOntology/envo/issues/264 for discussion. This definition needs a lot of clean up and links to household and related classes must be made to form logical definitions for inference to work. Subclasses will be added by inference. human dwelling A village is a clustered human settlement or community, larger than a hamlet but smaller than a town, with a population ranging from a few hundred to a few thousand. Though often located in rural areas, the term urban village is also applied to certain urban neighbourhoods. Villages are normally permanent, with fixed dwellings; however, transient villages can occur. Further, the dwellings of a village are fairly close to one another, not scattered broadly over the landscape, as a dispersed settlement. This class may be split. "urban village" doesn't sit well and prevents relations to village biomes. village An object which is naturally occuring, bound together by gravitational or electromagnetic forces, and surrounded by space. celestial body envoAstro Astronomical bodies are usually cohesive, thus the use of the term 'object' sensu BFO 'object'. astronomical body 1 An object which is composed of one or more gravitationally bound structures that are associated with a position in space. celestial object envoAstro If there is only one astronomical body involved, this class is equivalent to ENVO:01000799. This may be problematic with reasoning, but it seems to be true to the rather fuzzy definitions found thus far. astronomical object A material part of an astronomical body. envoAstro envoPolar astronomical body part A biosphere is a part of an astronomical body which includes, as parts, all the living entities within the gravitational sphere of influence of that body, as well as the non-living and dead entities with which they interact. A biosphere is an environmental system which includes, as parts, all the living entities within the gravitational sphere of influence of an astronomical body, and the non-living and dead entities which they interact with. Whether this class should be grouped with classes such as "hydrosphere" and "cryosphere" requires some discussion. envoAstro envoPolar The gravitational sphere of influence referenced in this class' definition is the Hill sphere: a region in which an object dominates the attraction of satellites despite gravitational perturbations. biosphere An environmental system in which minimal to no anthropisation has occurred and non-human agents are the primary determinants of the system's dynamics and composition. non-anthropised environment non-anthropized environment In most contexts, 'natural' is defined by the lack of intervention or influence by humans and their activities. On Earth, most environments fall on a scale between completely natural and anthropised. natural environment A process during which a natural environmental system is altered by human action. anthropization An area may be classified as anthropized even though it looks natural, such as grasslands that have been deforested by humans. It can be difficult to determine how much a site has been anthropized in the case of urbanization because one must be able to estimate the state of the landscape before significant human action. anthropisation A part of an astronomical body which includes, as parts, all the entities which have been constructed or manufactured by humans or their technology and which are within the gravitational sphere of influence of that body. An environmental system which includes, as parts, all the entities which have been constructed or manufactured by humans or their technology within the gravitational sphere of influence of an astronomical body. envoAstro The gravitational sphere of influence referenced in this class' definition is the Hill sphere: a region in which an object dominates the attraction of satellites despite gravitational perturbations. technosphere A planned process during which raw or recycled materials are transformed into products for use or sale using labour and machines, tools, chemical and biological processing, or formulation. The term may refer to a range of human activity, from handicraft to high tech, but is most commonly applied to industrial production, in which raw materials are transformed into finished goods on a large scale. manufacturing process An process during which natural or manufactured materials and products are processed and arranged by humans or their technology into structures. The nature of "structures" must be further specified. construction process An environmental system which includes both living and non-living components. LTER:173 This class will be primarily filled by inference, any environmental system which necessarily includes living parts should be autoclassified here. ecosystem A quality which inheres in a astronomical body or astronomical body part by virtue of the variation in its material composition, participation in geological processes, and the variation in is land- and hydroforms. Materials which are usually assessed when appraising geodiversity include minerals, rocks, sediments, fossils, soils and water. Landforms factored into geodiversity metrics typically include folds, faults, and other expressions of morphology or relations between units of earth material. Natural processes that are included in measures of geodiversity are those which either maintain or change materials or geoforms, including tectonics, sediment transport, and pedogenesis. Geodiversity does not usually factor in anthropogenic entities. geodiversity A process during which an ecosystem, its parts, or the processes it participates in are modified by human intervention to accomplish an objective. ecosystem management Umweltmaßnahme environmental management active ecosystem management process A process during which an ecosystem - natural or anthropised - is changed by the actions of humans. http://orcid.org/0000-0002-4366-3088 anthropogenic ecosystem conversion process A planned process during which humans access and obtain resources, benefits, or services from a natural or anthropised ecosystem. http://orcid.org/0000-0002-4366-3088 planned environmental usage process A planned environmental usage process during which an environment supports the settlement and dwelling of a community of humans. http://orcid.org/0000-0002-4366-3088 residential This class does not include environments which are primarily used for commerce or industry. usage of an environment for residential activity A building which is primarily used for the long-term habitation of humans. http://orcid.org/0000-0002-4366-3088 2018-10-04T14:04:49Z domestic building A process in which includes the components of an environmental system as participants. This is a convenience class for organisation and should not be used for annotation. environmental system process A process during which humans apply technology to alter the magnitude, duration, rate, or impact of an environmental process. Relabel the obo foundry unique label to be generic process anthropogenic modulatory intervention process An environmental process which is driven by the action of humans. anthropogenic environmental process A process during which material is displaced from its original location and transported either to a new location or back to the original location. http://orcid.org/0000-0002-3410-4655 http://orcid.org/0000-0002-4366-3088 envoPolar Experimental class for structural purposes not recommended for annotation. material transport process A process during which a portion of some environmental material is converted into a different material or a collection of materials. A different material transformation process class (or similarly named class) pertaining to the conversion of a specific chemical into another belongs in CHEBI and or REX ontologies. http://orcid.org/0000-0002-3410-4655 http://orcid.org/0000-0002-4366-3088 envoPolar Experimental class for structural purposes not recommended for annotation. A material transformation process only refers to ENVO:environmental material classes (e.g. bulk and typically impure substances), rather than transformations converting a specific chemical into another. material transformation process immunoglobulin complex A protein complex that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains, held together by disulfide bonds and sometimes complexed with additional proteins. An immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. immunoglobulin complex B cell receptor complex An immunoglobulin complex that is present in the plasma membrane of B cells and that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins. B cell receptor complex protein-containing complex A ribosome is a protein complex. A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. protein complex protein-containing complex T cell receptor complex A protein complex that contains a disulfide-linked heterodimer of T cell receptor (TCR) chains, which are members of the immunoglobulin superfamily, and mediates antigen recognition, ultimately resulting in T cell activation. The TCR heterodimer is associated with the CD3 complex, which consists of the nonpolymorphic polypeptides gamma, delta, epsilon, zeta, and, in some cases, eta (an RNA splice variant of zeta) or Fc epsilon chains. T cell receptor complex immunoglobulin complex, circulating An immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph. In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component. antibody antibody immunoglobulin complex, circulating A phenotypic abnormality. Phenotypic abnormality Osteoporosis is a systemic skeletal disease characterized by low bone density and microarchitectural deterioration of bone tissue with a consequent increase in bone fragility. According to the WHO, osteoporosis is characterized by a value of BMD 2.5 standard deviations or more below the young adult mean. Osteoporosis Eczema is a form of dermatitis. The term eczema is broadly applied to a range of persistent skin conditions and can be related to a number of underlying conditions. Manifestations of eczema can include dryness and recurring skin rashes with redness, skin edema, itching and dryness, crusting, flaking, blistering, cracking, oozing, or bleeding. Eczema Any abnormality of the cardiovascular system. Abnormality of the cardiovascular system Abnormality of metabolism/homeostasis Elevated body temperature due to failed thermoregulation. Fever A condition in which the stomach contents leak backwards from the stomach into the esophagus through the lower esophageal sphincter. Gastroesophageal reflux A lack or loss of appetite for food (as a medical condition). Anorexia An abnormality of the respiratory system, which include the airways, lungs, and the respiratory muscles. Abnormality of the respiratory system Difficult or labored breathing. Dyspnea Cephalgia, or pain sensed in various parts of the head, not confined to the area of distribution of any nerve. Headache Excessive daytime sleepiness. Drowsiness Functional respiratory abnormality An atrial arrhythmia characterized by disorganized atrial activity without discrete P waves on the surface EKG, but instead by an undulating baseline or more sharply circumscribed atrial deflections of varying amplitude an frequency ranging from 350 to 600 per minute. Atrial fibrillation Stridor is a high pitched sound resulting from turbulent air flow in the upper airway. Stridor An abnormal accumulation of fluid beneath the skin of the legs. Edema of the lower limbs An abnormality of the gastrointestinal tract. Abnormality of the gastrointestinal tract Abnormal functionality of the cardiovascular system. Abnormality of cardiovascular system physiology An infection of the upper or lower respiratory tract. Respiratory tract infection Edema (swelling) of the bulbar conjunctiva. Chemosis A functional anomaly of the nervous system. Abnormality of nervous system physiology Abnormal structure of the gastrointestinal tract. Morphological abnormality of the gastrointestinal tract Abnormal functionality of the gastrointestinal tract. Functional abnormality of the gastrointestinal tract A sudden, audible expulsion of air from the lungs through a partially closed glottis, preceded by inhalation. Cough Abnormality of the digestive system A functional anomaly of the digestive system. Abnormality of digestive system physiology Abnormality of vascular function. Abnormal vascular physiology A high-pitched whistling sound associated with labored breathing. Wheezing An anomalous (adventitious) sound produced by the breathing process. Abnormal breath sound Abnormal breath sounds characterized by discontinuous clicking or rattling. Rales Abnormal breath sounds characterized by low-pitched, snoring or rattle-like sounds. Rhonchi Increased jugular venous pressure. Elevated jugular venous pressure 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 model number A model number is an information content entity specifically borne by catalogs, design specifications, advertising materials, inventory systems and similar that is about manufactured objects of the same class. The model number is an alternative term for the class. The manufactered objects may or may not also bear the model number. Model numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. manufactered items may have more than one model number, sometimes by rebranding, or because companies are sold and the products issued new model numbers Person: Alan Ruttenberg model number data item Data items include counts of things, analyte concentrations, and statistical summaries. 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. 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 symbol a serial number such as "12324X" a stop sign a written proper name such as "OBI" An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. 20091104, MC: this needs work and will most probably change 2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://code.google.com/p/information-artifact-ontology/issues/detail?id=154). 2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154). PERSON: James A. Overton PERSON: Jonathan Rees based on Oxford English Dictionary symbol numeral A symbol that denotes a number. PERSON: Jonathan Rees numeral 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. 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 information content entity integer numeral a numeral that denotes an integer PERSON: Jonathan Rees integer numeral 1 1 10 feet. 3 ml. a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label. 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them. PERSON: Alan Ruttenberg PERSON: Melanie Courtot scalar measurement datum 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 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 contour plot Contour plot of SSC-H, FSC-H, and FL1-H. generically_dependent_continuants person:Allyson Lister person:Chris Stoeckert OBI_0000246 group:Flow Cytometry community contour plot 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 density plot Density plot of SSC-H and FSC-H. A density plot is a report graph which is a graphical representation of data where the tint of a particular pixel corresponds to some kind of function corresponding the the amount of data points relativelly with their distance from the the pixel. person:Allyson Lister person:Chris Stoeckert OBI_0000179 group:Flow Cytometry community density plot 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 Data about an ontology part is a data item about a part of an ontology, for example a term data about an ontology part is a data item about a part of an ontology, for example a term Person:Alan Ruttenberg 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 measurement datum Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}. A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. 2/2/2009 is_specified_output of some assay? person:Chris Stoeckert OBI_0000305 group:OBI measurement datum version number A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name. Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version GROUP: IAO version number serial number A serial number is an information content entity which is a unique sequence of characters borne by part of manufactured product or its packaging that is assigned to each individual in some class of products, and so can serve as a way to identify an individual product within the class. Serial numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. Note: during the call there was some confusion between serial number and model number. We agreed that it would be very helpful for all those terms to have example of usages - please add if you have any :-) GROUP: IAO serial number lot number A lot number is an information content entity which is an identical sequence of character borne by part of manufactured product or its packaging for each instances of a product class in a discrete batch of an item. Lot numbers are usually assigned to each separate production run of an item. Manufacturing as a lot might be due to a variety of reasons, for example, a single process during which many individuals are made from the same portion of source material. Lot numbers can be encoded in a pattern of other information objects, such as bar codes, numerals, or patterns of dots. GROUP: IAO batch number lot number 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 Venn diagram A Venn diagram is a report graph showing all hypothetically possible logical relations between a finite collection of sets. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot WEB: http://en.wikipedia.org/wiki/Venn_diagram Venn diagram 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 A photograph is created by projecting an image onto a photosensitive surface such as a chemically treated plate or film, CCD receptor, etc. PERSON:Alan Ruttenberg PERSON:Joanne Luciano PERSON:Melanie Courtot WEB: http://en.wiktionary.org/wiki/photograph photograph textual entity Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc. AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc. MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities. PERSON: Lawrence Hunter text textual entity citation Verspoor, K., Cohen, KB., Hunter, L. Textual characteristics of traditional and Open Access scientific journals are similar, BMC Bioinformatics 2009, 10:183. a textual entity intended to identify a particular publication PERSON: Lawrence Hunter citation document title Textual characteristics of traditional and Open Access scientific journals are similar A textual entity that names a document PERSON: Lawrence Hunter document title table | T F --+----- T | T F F | F F A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions PERSON: Lawrence Hunter table 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 hypothesis textual entity that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660 A textual entity that expresses an assertion that is intended to be tested. 2009/09/28 Alan Ruttenberg. Fucoidan-use-case Person:Alan Ruttenberg hypothesis textual entity A scalar measurement datum that is the result of measuring a temporal interval 2009/09/28 Alan Ruttenberg. Fucoidan-use-case Person:Alan Ruttenberg time measurement datum A textual entity that is used as directive to deliver something to a person, or organization 2010-05-24 Alan Ruttenberg. Use label for the string representation. See issue https://github.com/information-artifact-ontology/IAO/issues/59 postal address email address Alan Ruttenberg 1/3/2012 - Provisional id, see issue at https://github.com/information-artifact-ontology/IAO/issues/130&thanks=130&ts=1325636583 Person:Alan Ruttenberg Person:Chris Stoeckart email address Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database. A planned process in which a document is created or added to by including the specified input in it. a planned process in which a document is created or added to by including the specified input in it. 6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape Bjoern Peters wikipedia http://en.wikipedia.org/wiki/Documenting documenting line graph A line graph is a type of graph created by connecting a series of data points together with a line. PERSON:Chris Stoeckert PERSON:Melanie Courtot line chart GROUP:OBI WEB: http://en.wikipedia.org/wiki/Line_chart line graph A new pubmed ID being created for a journal article, and the associated pubmed record containing information to the journal article. A license plate number registered at the DMV to be belonging to a specific vehicle and owner. Placing a barcode on a product and entering information in a database that this barcode is assigned. A planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity 2014-05-05: It is the CRID registry that assigns CRIDs, not the users of the registry. Person:Alan Ruttenberg Person:Bjoern Peters Person:Melanie Courtot assigning a CRID assigning a centrally registered identifier The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed. A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry. PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot CRID symbol Original proposal from Bjoern, discussions at IAO calls centrally registered identifier symbol Entries in a Column of which the header is "Pubmed ID" PMID:12345 The following URL: "http://www.ncbi.nlm.nih.gov/pubmed/19918065" The following sentence contains a CRID: "The article with Pubmed ID: 19918065". The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed. An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs. An information content entity that consists of a CRID symbol and additional information about which CRID registry it belongs. 2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records'). Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation. Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered. PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot CRID Centrally Registered IDentifier Original proposal from Bjoern, discussions at IAO calls http://purl.obolibrary.org/obo/iao.owl CRID centrally registered identifier PubMed is a CRID registry. It has a dataset of PubMed identifiers associated with journal articles. A CRID registry is a dataset of CRID records, each consisting of a CRID symbol and additional information which was recorded in the dataset through a assigning a centrally registered identifier process. PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot CRID registry Original proposal from Bjoern, discussions at IAO calls centrally registered identifier registry written name "Bill Clinton" "The Eiffel Tower" "United States of America" A textual entity that denotes a particular in reality. PERSON: Bill Hogan https://github.com/information-artifact-ontology/IAO/issues/114 The qualifier "written" is to set it apart from spoken names. Also, note the restrictions to particulars. We are not naming universals. We could however, be naming, attributive collections which are particulars, so "All people located in the boundaries of the city of Little Rock, AR on June 18, 2011 at 9:50a CDT" would be a name. written name author information textual entity From Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/): IT [the author] is the lead paediatrician for ADHD services in East Hertfordshire, UK, where she runs a weekly joint ADHD clinic with the Child and Adolescent psychiatrist and works within an ADHD specialist team. IT also sees children with other neurodisability issues who may have comorbid ADHD, where the presentation may be more complex and challenging to manage. IT has vast experience in managing children with complex ADHD. She has 18 years of experience in paediatrics and also has extensive experience in the use of psychopharmacologic agents in managing children with ADHD. A textual entity expression information about an author of a document. This information may include biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document. PERSON: Bill Baumgartner author information textual entity case report textual entity Excerpt from Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/): The patient is a 50-year-old man. His medical history was not contributory. At the age of 37 years, he complained of persistent fatigue and dyspnoea even for modest efforts and oedema of lower limbs. The patient was examined at the department of internal medicine of the local hospital, and hospitalised with a diagnosis of dilated cardiomyopathy probably consequence of a myocarditis process. Soon after he was transferred to the cardiologic department of the regional hospital, and pharmacologically treated for heart failure and pulmonary hypertension. A textual entity that expresses a detailed account of a portion of the medical history for a specific patient. PERSON: Bill Baumgartner case report textual entity Colonel Klink giving Sergeant Schultz an order, Jake promising Jill to take her to the junior prom A planned process that is carried out by a conscious being or an organization, and is self-generated, directed towards another conscious being or an aggregate of conscious beings, an organization or an aggregate of organizations, and that needs to be perceived. A process that is carried out by a conscious being or an aggregate of conscious beings and is spontaneous, directed towards other conscious beings and aggregates thereof and needs to be perceived. Mathias Brochhausen MB: Regarding the use of the term 'sponteneous' in the definition: The term is used in the following meaning of being self generated. It does not stand in contrast to being planned. social act the claim of a piece of land, the obligation to pay rent to the owner of a rental property Socio-legal generically dependent continuants are generically dependent continuants that come into existence through declarations and are concretized as roles. They differ from information content entities in that they are not about something, but exist as quasi-abstract social entities. Socio-legal generically dependent continuants are not concretized as qualities inhering in independent continuants, but only as realizable entities borne by an organism or an aggregate of organisms. Mathias Brochhausen socio-legal generically dependent continuant my consenting verbally to buy a used TV set for $ 500, Jane Doe's signing of the divorce papers, John Robie's taking of Mrs. Steven's jewels A social act that brings about, transfers or revokes a socio-legal generically dependent continuant or brings about or revokes a role. Declarations do not depend on words spoken or written, but sometimes are merely actions, for instance the signing of a document. Mathias Brochhausen declaration A document that is intended to be the specified input in a document act. It has a plan specification as a part that specifies the intended socio-legal entities that are created through the document (objective specification) and the way in which the document act is to be performed (by signing, by stamping, etc.) (action specification). Mathias Brochhausen document act input document a judge's role of signing a court order, a hospital committee's to sanction conformance to a specific guideline for hospital employees. A role inhering in a human being or an organization or an aggregate of any of the aforementioned that is realized by the bearer being the agent in a declaration. Mathias Brochhausen declaration performer role A document that explains all relevant information to assist a human being in understanding the expectations and requirements of participation in a process, and is an instrument in obtaining consent and, after having obtained consent, is a record that such a consent has occurred. The term definition is adapted from NCIt definition of 'consent form' (C16468) with modification. For instance, whereas the NCIt definition restricted informed consent forms to clinical trials, the present definition does not. Alla Karnovsky, Frank Manion, Yongqun He, Asiyah Yu Lin, Marcy Harris, Elizabeth Eisenhauer, Jonathan Vajda, Cooper Stansbury, J. Neil Otte informed consent document NCIt C16468 See curator note for 'incomplete informed consent form'. C0009797 C16468 informed consent form A social act that is a part of an informed consent process and has output of a signed informed consent form. The signing process leads to a legal obligation. Alla Karnovsky, Frank Manion, Yongqun He, Jihad Obeid, Chris Stoeckert, and Mathias Brochhausen This class is under group discussion as of 03/26/2019. Signing here does not mean that we have to sign with a pen. It may happen in terms of signing a piece of a paper or an electronic form. signing an informed consent form A document act input document that explains all relevant information to assist a human being in understanding the expectations and requirements of participation in a process, and whose purpose is to assist in obtaining consent. J. Neil Otte Note: instances of 'incomplete informed consent form' include both blank informed consent forms that are waiting to be used in a process of informed consent, as well as those that have been left blank by a patient, whether on purpose or in error. Those that have been left blank on purpose have been used in a process of informed consent, where the patient must have reached a decision. incomplete informed consent form A document act input document that has, as part, an incomplete informed consent form, along with some additional parts, such as a signature, stamp, or initials, which serve as a record to an act of consent that had the incomplete informed consent form as a specified input. J. Neil Otte complete informed consent form indicating consent An information content entity that is a handwritten depiction of a name. Jonathan Vajda, Cooper Stansbury, J. Neil Otte. signature Sudden and sustained deterioration of the kidney function characterized by decreased glomerular filtration rate, increased serum creatinine or oliguria. DOID:3021 ICD10:N17 MESH:D058186 NCIT:C26808 AKI ARF acute kidney injury acute renal failure kidney failure, acute MONDO:0002492 acute kidney failure Progressive kidney disorder caused by vascular damage to the glomerular capillaries, in patients with diabetes mellitus. It is usually manifested with nephritic syndrome and glomerulosclerosis. EFO:0000401 ICD9:250.4 ICD9:250.40 ICD9:583.81 MESH:D003928 NCIT:C84417 SCTID:127013003 diabetic Nephropathy diabetic kidney disease MONDO:0005016 diabetic nephropathy A disease involving the kidney. DOID:557 EFO:0003086 ICD10:N08 ICD10:N28.9 ICD9:583.81 MESH:D007674 NCIT:C3149 SCTID:90708001 UMLS:C0022658 disease of kidney disease or disorder of kidney disorder of kidney kidney disease kidney disease or disorder kidney disorder nephropathy renal disease renal disorder disorder of kidney MONDO:0005240 kidney disease Impairment of the renal function secondary to chronic kidney damage persisting for three or more months. COHD:46271022 DOID:784 EFO:0003884 ICD10:N18.9 ICD9:585 ICD9:585.6 MESH:D007676 NCIT:C80078 SCTID:709044004 UMLS:C0022661 CKD CKD - chronic kidney disease chronic kidney disease chronic kidney failure chronic renal disease kidney disease, chronic renal failure - chronic chronic renal failure syndrome chronic renal insufficiency MONDO:0005300 chronic kidney disease Viruses GC_ID:1 ncbi_taxonomy Vira Viridae viruses Viruses Teleostomi Euteleostomi bony vertebrates bony vertebrates Euteleostomi Dipnotetrapodomorpha Boreotheria Boreoeutheria 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:7520741 PMID:8123559 PMID:8186100 PMID:8590690 PMID:9103655 PMID:9336922 eubacteria ncbi_taxonomy Monera Procaryotae Prokaryota Prokaryotae bacteria not Bacteria Haeckel 1894 prokaryote prokaryotes Bacteria Homo/Pan/Gorilla group Homininae Archaea 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:11541975 PMID:11542064 PMID:11542149 PMID:11760965 PMID:12054223 PMID:2112744 PMID:25527841 PMID:270744 PMID:8123559 PMID:8590690 PMID:9103655 PMID:9336922 ncbi_taxonomy Archaebacteria Mendosicutes Metabacteria Monera Procaryotae Prokaryota Prokaryotae archaea prokaryote prokaryotes Archaea Eukaryota eucaryotes eukaryotes GC_ID:1 PMID:23020233 PMID:30257078 eucaryotes eukaryotes ncbi_taxonomy Eucarya Eucaryotae Eukarya Eukaryotae eukaryotes NCBITaxon:2759 Eukaryota Euarchontoglires Euarchontoglires Anthropoidea Simiiformes ape apes Hominoidea Tetrapoda tetrapods tetrapods Tetrapoda Amniota amniotes amniotes Amniota Theria Theria <Mammalia> Opisthokonta GC_ID:1 ncbi_taxonomy Fungi/Metazoa group opisthokonts NCBITaxon:33154 Opisthokonta metazoans multicellular animals Animalia animals Metazoa Bilateria Bilateria deuterostomes Deuterostomia A misfolded protein that has the ability to transmit its misfolded shape onto normal variants of the same protein. https://en.wikipedia.org/wiki/Prion GC_ID:1 ncbi_taxonomy prion Haplorrhini Mammalia mammals mammals mammals Mammalia Eumetazoa chordates chordates Chordata Vertebrata <vertebrates> Vertebrata vertebrates Vertebrata vertebrates vertebrates Vertebrata <Metazoa> Vertebrata <vertebrates> Gnathostomata jawed vertebrates Gnathostomata <vertebrate> Sarcopterygii Craniata Craniata <chordata> eutherian mammals placental mammals placentals Placentalia placentals Eutheria primate Primata primates Primates Catarrhini great apes Pongidae Hominidae humans Homo Homo sapiens Homo sapiens human human being man person GC_ID:1 human man ncbi_taxonomy humans Homo sapiens Homo sapiens An individual's total number of brothers and sisters. C102469 Qualitative Concept Number of Siblings C0557094 FDA Number of Siblings Number of Siblings The age of the subject at the time of the vaccination. C103173 Organism Attribute Age at Time of Vaccination C3641107 FDA Age at Time of Vaccination Age at the Time of Vaccination Age at Time of Vaccination A group of people characterized by the practice of a common religion. C103282 Population Group Religious Group C0597369 Religious Group Religious Group A member of the Jewish faith whose ancestors lived in North Africa, the Middle East, Portugal or Spain. C103283 Population Group Sephardic Jew C0574825 A person of Sephardic Jewish descent. SEPHARDIC JEW Sephardi Sephardic Jew Sephardic Jew Individuals who do not necessarily identify with any particular race or others who do not wish to self select into a racial category(ies). C104495 Population Group Other Race C0425379 OTHER RACE Other Race RACEOTH Other Race The age at which permanent cessation of menses occurs. C106497 Clinical Attribute Age at Menopause C1629609 CDISC The age at which permanent cessation of menses occurred. (NCI) Age at Menopause MENOAGE Menopause Age Age at Menopause A person having origins in the original peoples of Asia, but not China, India, Korea, the Philippine Islands or Vietnam. C107601 Population Group Other Asian C0438971 FDA Other Asian Other Asian A person having origins in the original peoples of the Pacific Islands, but not Guam, Hawaii, the Mariana Islands or Samoa. C107602 Population Group Other Pacific Islander C1553351 FDA Other Pacific Islander Other Pacific Islander A person of Mexican or Mexican American culture or origin, regardless of race. C107607 Population Group Mexican or Mexican American C3829110 FDA Mexican or Mexican American Mexican or Mexican American A person of Cuban culture or origin, regardless of race. C107608 Population Group Cuban C1553379 FDA A person of Cuban descent. CUBAN Cuban Cuban A person of Spanish culture or origin, but not Cuban, Mexican, Puerto Rican, South or Central American, regardless of race. C107609 Population Group Other Hispanic or Latino(a) C3828691 FDA Other Hispanic or Latino(a) Other Hispanic or Latino(a) The time elapsed between the day of conception and the day of delivery. C114088 Organism Attribute Conception Age C3827345 NICHD The time elapsed between the day of conception and the day of delivery. Conception Age Conception Age Conceptional Age Conceptual Age Post-Conceptional Age Post-Conceptual Age Conception Age Chronological age reduced by the number of weeks born before 40 weeks of gestation; most appropriately used to describe children up to 3 years of age who were born preterm. C114089 Organism Attribute Corrected Age C3831006 NICHD Chronological age reduced by the number of weeks born before 40 weeks of gestation; most appropriately used to describe children up to 3 years of age who were born preterm. Corrected Age Adjusted Age Corrected Age Corrected Gestational Age Corrected Age Best estimate of the first day of last menstrual period to birth plus time elapsed from day of birth. C114090 Organism Attribute Postmenstrual Age C3828508 NICHD Best estimate of the first day of last menstrual period to birth plus time elapsed from day of birth. Postmenstrual Age Postmenstrual Age Postmenstrual Age Birth weight less than 1500 grams. C114935 Finding Very Low Birth Weight C0282666 GAIA NICHD Birth weight less than 1500 grams. Very Low Birth Weight VLBW Very Low Birth Weight Very Low Birth Weight Birth weight less than 1000 grams. C114936 Finding Extremely Low Birth Weight C0456065 GAIA NICHD Birth weight less than 1000 grams. Extremely Low Birth Weight ELBW Extremely Low Birth Weight Extremely Low Birth Weight Birth weight less than 750 grams. C114937 Finding Ultra Low Birth Weight C3896584 ULBW Ultra Low Birth Weight Ultra Low Birth Weight A person's optimum weight as calculated by a standard methodology. C117976 Quantitative Concept Ideal Body Weight C0421272 CDISC A person's optimum weight as calculated by a standard methodology. IDEALWT Ideal Body Weight Ideal Body Weight The money received by retired workers who have paid in to the Social Security system during their working years. C120451 Group Attribute Social Security Retirement Benefit C0037435 Social Security Social Security Retirement Benefit Social Security Retirement Benefit A fixed sum paid regularly to a person by their former employer. C120452 Group Attribute Pension C0030854 Pension Pension The pressure within the left ventricle following the completion of diastolic filling, just prior to systole. C120919 Quantitative Concept Left Ventricular End Diastolic Pressure C0456190 CDISC The pressure within the left ventricle of the heart at the end of the period when the chambers of the heart refill with blood and just before the contraction begins. LVEDP Left Ventricular End Diastolic Pressure Left Ventricular End Diastolic Pressure The pressure in the left ventricle at any point prior to the ejection of its contents into the aorta (systole). C120920 Quantitative Concept Left Ventricular Systolic Pressure C0456189 CDISC The pressure within the left ventricle of the heart during the contraction of the left ventricle of the heart. LVSYSBP Left Ventricular Systolic Pressure Left Ventricular Systolic Pressure An approximate calculation of the gestational age of the fetus. C122188 Organism Attribute Estimated Gestational Age C0262472 CDISC An approximate calculation of the gestational age of the fetus. EGESTAGE Estimated Gestational Age Estimated Gestational Age The number of education years that a subject has competed. C122393 Qualitative Concept Number of Years of Education C4054327 CDISC The number of years of education that a person has completed. EDUYRNUM Number of Years of Education Number of Years of Education The age at which the first episode occurred. C124438 Organism Attribute Age at First Episode C4085940 CDISC The age at which the first episode occurred. AGEEPSD1 Age At First Episode Age at First Episode Age at First Episode The age at which the first hospitalization event occurred. C124439 Organism Attribute Age at First Hospitalization C4085941 CDISC The age at which the first hospitalization event occurred. AGEHOSP1 Age At First Hospitalization Age at First Hospitalization Age at First Hospitalization The age at which the first treatment event occurred. C124440 Organism Attribute Age at First Treatment C4085942 CDISC The age at which the first treatment for the condition occurred. AGETRT1 Age At First Treatment Age at First Treatment Age at First Treatment The maternal body weight adjusted for the weight of the gravid uterus. This is derived by subtracting the gravid uterus weight from the total maternal body weight. C124477 Conceptual Entity Gravid Uterus Adjusted Maternal Body Weight C4086368 CDISC The maternal body weight adjusted for the weight of the gravid uterus. This is derived by subtracting the gravid uterus weight from the total maternal body weight. BWADJGU Gravid Uterus Adjusted Body Weight Gravid Uterus Adjusted Maternal Body Weight Gravid Uterus Adjusted Maternal Body Weight An estimate or direct measurement of the heaviness of a fetus. C124479 Conceptual Entity Fetal Body Weight C0751992 CDISC The weight of a fetus. BWFETAL Fetal Body Weight Fetal Body Weight A measurement of the average weight of all live fetuses. C124627 Conceptual Entity Average Live Fetal Weight C4086012 CDISC A measurement of the average weight of all live fetuses. Average Live Fetal Weight FWAVGL Average Live Fetal Weight A measurement of the average weight of all live female fetuses. C124628 Conceptual Entity Average Female Live Fetal Weight C4086011 CDISC A measurement of the average weight of all live female fetuses. Average Female Live Fetal Weight FWAVGLF Average Female Live Fetal Weight A measurement of the average weight of all live male fetuses. C124629 Conceptual Entity Average Male Live Fetal Weight C4086996 CDISC A measurement of the average weight of all live male fetuses. Average Male Live Fetal Weight FWAVGLM Average Male Live Fetal Weight A measurement of the total weight of all live fetuses. C124630 Conceptual Entity Total Live Fetal Weight C4086909 CDISC A measurement of the total weight of all live fetuses. FWTOTL Total Live Fetal Weight Total Live Fetal Weight The age at which a minor assumes legal control over their person, actions, and decisions. C126362 Organism Attribute Age of Majority CL504920 Age of Majority Age of Majority Denotes a person whose ancestry is in any of the countries of the central part of the African continent: Burundi, the Central African Republic, Chad, the Democratic Republic of the Congo, and Rwanda. C126528 Population Group Central African C0238602 Central African Central African Denotes a person whose ancestry is in any of the countries of the northern part of the African continent: Algeria, Egypt, Libya, Morocco, Sudan, Tunisia, and Western Sahara. C126529 Population Group North African C0238604 North African North African Denotes a person whose ancestry is in the country of South Africa. C126530 Population Group South African C0238605 South African South African Denotes a person whose ancestry is in any of the countries of the Americas or the Caribbean where Spanish or Portuguese is spoken. C126531 Population Group Latin American C1553378 A person of Latin American descent. LATIN AMERICAN Latin American Latin American Denotes a person whose ancestry is in any of the countries of South America. C126532 Population Group South American C0425359 A person of South American descent. SOUTH AMERICAN South American South American Denotes a person whose ancestry is in any of the Asian countries south of China, east of India, west of New Guinea and north of Australia. C126533 Population Group Southeast Asian C0238697 Southeast Asian Southeast Asian Denotes a person whose ancestry is in any of the Asian countries between the Caspian Sea in the west, China in the east, Afghanistan in the south, and Russia in the north. C126534 Population Group Central Asian C0238696 Central Asian Central Asian Denotes a person whose ancestry is in the country or continent of Australia. C126535 Population Group Australian C0238711 Australian Australian Denotes a person whose ancestry is in the country of New Zealand. C126536 Population Group New Zealander CL505027 New Zealander New Zealander Denotes a person whose ancestry is in the country of Iceland. C126537 Population Group Icelander C0337808 Icelander Icelandic Icelander Denotes a person whose ancestry is in the countries of Scandinavia: Denmark, Norway and Sweden. Finland and Iceland are generally included as part of the Scandinavian region. C126538 Population Group Scandinavian C0240951 Scandinavian Scandinavian A collection of ethnic geographical categories including African American, North American, Latin American, Caribbean, and South American. C128457 Population Group American Ethnicity C0596070 American American Ethnicity Americas American Ethnicity A collection of ethnic geographical categories including Australian and New Zealander. C128458 Population Group Australian/New Zealand Ethnicity CL509688 Australian/New Zealand Australian/New Zealand Ethnicity Australian/New Zealand Ethnicity A collection of ethnic geographical categories including Middle Eastern and Hispanic. C128459 Population Group Intercontinental Ethnicity CL509475 Intercontinental Intercontinental Ethnicity Intercontinental Ethnicity Denotes a person of African ancestral origins whose family settled in America. C128937 Population Group African American CL415133 A person having origins in the original peoples of sub-Saharan Africa and the United States. AFRICAN AMERICAN African American Afro American African American C128938 Population Group Black C0005680 CDISC A person having origins in the original peoples of sub-Saharan Africa or the Caribbean. BLACK Black Black Populations Black Denotes a person of African ancestral origins whose family settled in Central America. C128991 Population Group Black Central American CL512097 A person having origins in the original peoples of sub-Saharan Africa and Central America. BLACK CENTRAL AMERICAN Black Central American Black Central American Denotes a person of African ancestral origins whose family settled in South America. C128992 Population Group Black South American CL512098 A person having origins in the original peoples of sub-Saharan Africa and South America. BLACK SOUTH AMERICAN Black South American Black South American A person having origins in any of the original peoples of Europe, the Middle East, or North Africa and Central America. C128993 Population Group White Central American CL512246 A person having origins in the original peoples of Europe, the Middle East, or North Africa, and Central America. WHITE CENTRAL AMERICAN White Central American White Central American A person having origins in any of the original peoples of Europe, the Middle East, or North Africa and South America. C128994 Population Group White South American CL512247 A person having origins in the original peoples of Europe, the Middle East, or North Africa, and South America. WHITE SOUTH AMERICAN White South American White South American The maximum pressure exerted into the systemic arterial circulation during the contraction of the right ventricle of the heart. C129953 Quantitative Concept Right Ventricular Systolic Pressure C0456181 RVSP Right Ventricular Systolic Pressure Right Ventricular Systolic Pressure Blood pressure in the pulmonary artery. C129958 Clinical Attribute Pulmonary Artery Pressure C0428642 PAP Pulmonary Artery Pressure Pulmonary Artery Pressure Blood pressure within the left atrium. It is commonly measured indirectly by a pulmonary capillary wedge pressure. C129959 Clinical Attribute Left Atrial Pressure C0456170 LAP Left Atrial Pressure PLA Left Atrial Pressure The estimated arithmetic average of atrial pressure. C130056 Quantitative Concept Estimated Mean Atrial Pressure CL514049 Estimated Mean Atrial Pressure Estimated Mean Atrial Pressure An approximate determination of the weight of a body. C132482 Conceptual Entity Estimated Body Weight CL521346 CDISC An approximate determination of the weight of the subject. EWEIGHT Estimated Body Weight Estimated Weight Estimated Body Weight The age at which death occurred. C135383 Organism Attribute Age at Death C1546180 CDISC The age at which death occurred. (NCI) AGEDTH Age at Death Age at Death The result of a body mass index measurement. C138901 Finding Body Mass Index Finding BMI Body Mass Index Body Mass Index Finding Body Mass Index Finding Indicates a body mass index measurement less than 19. C138932 Finding Body Mass Index Less Than 19 BMI < 19 Body Mass Index Less Than 19 Body Mass Index Less Than 19 Indicates a body mass index measurement greater than or equal to 19 but below 21. C138933 Finding Body Mass Index 19 to Less Than 21 BMI 19 to < 21 Body Mass Index 19 to Less Than 21 Body Mass Index 19 to Less Than 21 Indicates a body mass index measurement greater than or equal to 21 but below 23. C138934 Finding Body Mass Index 21 to Less Than 23 BMI 21 to < 23 Body Mass Index 21 to Less Than 23 Body Mass Index 21 to Less Than 23 Indicates a body mass index measurement greater than or equal to 23. C138935 Finding Body Mass Index Greater Than or Equal to 23 BMI > 23 Body Mass Index Greater Than or Equal to 23 Body Mass Index Greater Than or Equal to 23 An indication that an individual's age is or was greater than 85 years. C138936 Organism Attribute Age Greater than 85 Years Age > 85 Age Greater than 85 Years Age Greater than 85 Years An indication that an individual's age is or was between 80 and 85 years. C138937 Organism Attribute Age Between 80 and 85 Years Age 80-85 Age Between 80 and 85 Years Age Between 80 and 85 Years An indication that an individual's age is or less than 80 years. C138938 Organism Attribute Age Less than 80 Years Age < 80 Age Less than 80 Years Age Less than 80 Years A quantitative estimate of the pressure in a given cardiovascular structure during ventricular systole. C139031 Quantitative Concept Estimated Systolic Blood Pressure CDISC A quantitative estimate of the pressure in a given cardiovascular structure during ventricular systole. Estimated Systolic Blood Pressure SYSPRS_E Systolic Pressure, Estimated Estimated Systolic Blood Pressure The age at which the full-time use of an entity occurred. C139175 Organism Attribute Age at Full-Time Use CDISC The age at which the full-time use of a pre-specified object first occurred. AGEFTUSE Age at Full-Time Use Age at Full-Time Use Denotes a person having origins in any of the original peoples of the Far East, Southeast Asia, or the Indian subcontinent, and who was either born in the United States or who was naturalized as a citizen of the United States. C16310 Population Group Asian American C0003988 A person having origins in the original peoples of Asia and the United States. Asian_American ASIAN AMERICAN Asian American Asian Americans Asian American A person having origins in any of the Black racial groups of Africa. Terms such as "Haitian" or "Negro" can be used in addition to "Black or African American". (OMB) C16352 Population Group Black or African American C0085756 CDISC FDA A person having origins in any of the black racial groups of Africa. Terms such as "Haitian" or "Negro" can be used in addition to "Black or African American." (FDA) African_American BLACK OR AFRICAN AMERICAN Black or African American Black or African American A general indicator of the body fat an individual is carrying based upon the ratio of weight to height. C16358 Clinical Attribute Body Mass Index C1305855 CDISC NCPDP A general indicator of the body fat an individual is carrying based upon the ratio of weight to height. (NCI) A measure that relates body weight to height. BMI is sometimes used to measure total body fat and whether a person is a healthy weight. Excess body fat is linked to an increased risk of some diseases including heart disease and some cancers. Body_Mass_Index BMI Body Mass Index Quetelet Index body mass index Body Mass Index A social group characterized by a distinctive social and cultural tradition that is maintained from generation to generation. Members share a common history and origin and a sense of identification with the group. They have similar and distinctive features in their lifestyle habits and shared experiences. They often have a common genetic heritage which may be reflected in their experience of health and disease. C16564 Population Group Ethnic Group C0015031 CDISC CDISC-GLOSS NICHD Denotes social groups with a shared history, sense of identity, geography, and cultural roots. Ethnic_Group Ethnic Group ETHNIC Ethnic Group Ethnic Origin Ethnic Origins Ethnicity ethnicity Ethnic Group A group of individuals united by a common factor (e.g., geographic location, ethnicity, disease, age, gender) C17005 Population Group Population Group C1257890 CDISC-GLOSS Any finite or infinite collection of subjects from which a sample is drawn for a study to obtain estimates for values that would be obtained if the entire population were sampled. [AMA style Manual] Population_Group Group Population Population Group Subpopulation population Population Group A subjective and comparative term describing a lack of sufficient wealth (usually understood as capital, money, material goods, or resources especially natural resources) to live what is understood in a society as a "normal" life: for instance, to be capable of raising a healthy family, and especially educating children and participating in society. A person living in this condition of poverty is said to be poor. The meaning of "sufficient" varies widely across the different political and economic areas of the world. C17009 Group Attribute Poverty C0032854 Poverty Low Income Poor Poverty Poverty An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation within a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution. C17049 Population Group Race C0034510 FDA NICHD Race Race RACE Race Racial Group Race A person of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin, regardless of race. The term, "Spanish origin," can be used in addition to "Hispanic or Latino." (OMB) C17459 Population Group Hispanic or Latino C0086409 CDISC FDA A person of Mexican, Puerto Rican, Cuban, Central or South American or other Spanish culture or origin, regardless of race. (NCI) Hispanic HISPANIC OR LATINO Hispanic Hispanic Populations Hispanic or Latino Hispanics or Latinos Latino Population Spanish Origin Hispanic or Latino Characteristics of a person such as education and occupation, used to describe the person's position in stratification systems, access to services, etc. C17468 Qualitative Concept Socioeconomic Factors C0086996 Socioeconomic_Factors Socioeconomic Factors Socioeconomic Status Socioeconomic Factors Ashkenazi Jews, also called Ashkenazim, are Jews who are descendants of Jews from Germany, Poland, Austria and Eastern Europe. C17950 Population Group Ashkenazi Jew C0337704 A person of Ashkenazi Jewish descent. One of two major ancestral groups of Jewish individuals, comprised of those whose ancestors lived in Eastern Europe (Germany, Poland, Russia). The other group is designated Sephardic Jews and includes those whose ancestors lived in North Africa, the Middle East, and Spain. Most Jews living in the United States are Ashkenazi Jews. Ashkenazi_Jew ASHKENAZI JEW Ashkenazi Jew Ashkenazim Ashkenazi Jew Denotes a person having origins in any indigenous people of Alaska and their descendants and who maintains tribal affiliation, or community or cultural attachment. The concept refers to population subgroups such as Eskimos, Aleuts, Inupiat, Yupik, Alutiiq, Egegik,and Pribilovian, Alaskan Athabascan, Tlingit, and Haida. The concept refers also to individuals who classify themselves as such. C18237 Population Group Alaska Native C0682125 The native people of Alaska. Alaska_Native ALASKA NATIVE Alaska Indian Alaska Indians Alaska Native Alaska Natives Alaska Native A demographic parameter indicating the average amount of earnings made by a family in a particular population or/and during a particular period of time. C19308 Quantitative Concept Average Household Income C1510993 Average_Household_Income Average Household Income Average Household Income a demographics parameter useful for identifying socio-economic groups. C19309 Quantitative Concept Number of Children in Household C1518468 Number_of_Children_in_Household Number of Children in Household Number of Children in Household The distinguishing qualities or prominent aspects of an individual person. C19332 Organism Attribute Personal Attribute C0681884 Personal_Attribute Personal Personal Attribute Subject Characteristics Personal Attribute Age of first menstruation. A risk factor for breast cancer C19666 Clinical Attribute Age at Menarche C1314691 CDISC The age at which the first menstruation event occurred. (NCI) Age_at_Menarche Age at Menarche MENARAGE Menarche Age Age at Menarche The age at which a woman gave birth to her first live child. C19667 Clinical Attribute Age at First Live Birth C1510831 Age_at_First_Live_Birth Age at First Full-Term Pregnancy Age at First Live Birth Age at First Live Birth An indication of a person's current tobacco and nicotine consumption as well as some indication of smoking history. C19796 Organism Attribute Smoking Status C1519386 Smoking_Status Current Tobacco and Nicotine Consumption Status Smoking Status Smoking Status How long something has existed; elapsed time since birth. C25150 Organism Attribute Age C0001779 CDISC FDA NICHD How long something has existed; elapsed time since birth. (NCI) The time elapsed since birth. Age Chronological Age AGE Age Aged Chronological Age Postnatal Age age Age The maximum pressure exerted into the systemic arterial circulation during the contraction of the left ventricle of the heart. C25298 Quantitative Concept Systolic Blood Pressure C0871470 CDISC NCPDP The maximum blood pressure in the systemic arterial circulation during the cardiac cycle. Systolic_Pressure SYSBP Systolic Blood Pressure Systolic Pressure Systolic Blood Pressure The minimum pressure exerted into the systemic arterial circulation during cardiac ventricular relaxation and filling. C25299 Clinical Attribute Diastolic Blood Pressure C0428883 CDISC NCPDP The minimum blood pressure in the systemic arterial circulation during the cardiac cycle. Diastolic_Pressure DIABP Diastolic Blood Pressure Diastolic Pressure Diastolic Blood Pressure The vertical measurement or distance from the base to the top of an object; the vertical dimension of extension. C25347 Quantitative Concept Height C0489786 CDISC FDA NCPDP The vertical measurement or distance from the base to the top of an object; the vertical dimension of extension. (NCI) Vertical measurement value. Height HEIGHT Height Height A system, commonly called the INR, established by the World Health Organization (WHO) and the International Committee on Thrombosis and Hemostasis for reporting the results of blood coagulation (clotting) tests. All results are standardized using the international sensitivity index (ISI) for the particular thromboplastin reagent and instrument combination utilized to perform the test; the ratio of a patient's clotting time to the lab's mean reference value is normalized against the ISI. (from medterms.com and medicine.ucsf.edu) C25352 Quantitative Concept International Normalized Ratio CL448971 International_Normalized_Ratio INR International Normalized Ratio International Normalized Ratio A birth weight that is less than 2500 grams. C34724 Finding Low Birth Weight C0024032 GAIA NICHD Birth weight less than 2500 grams. Low_Birth_Weight Low Birth Weight Low Birth Weight Low Birth Weight The length of a person's life, stated in months since birth. C37907 Organism Attribute Age-Months C1510828 NCPDP Age-Months Age, in Months Age-Months Age-Months The length of a person's life, stated in years since birth. C37908 Organism Attribute Age-Years C1510829 NCPDP Age-Years Age, in Years Age-Years Age-Years A gain or recurrent benefit during a period of time, usually measured in money that derives from capital or labor. C41150 Group Attribute Income C0021162 Income Income is one of the major demographic parameters used in population-based biomedical research. Income Income A person having origins in any of the original peoples of Hawaii, Guam, Samoa, or other Pacific Islands. (OMB) C41219 Population Group Native Hawaiian or Other Pacific Islander C1513907 CDISC FDA Denotes a person having origins in any of the original peoples of Hawaii, Guam, Samoa, or other Pacific Islands. The term covers particularly people who identify themselves as part-Hawaiian, Native Hawaiian, Guamanian or Chamorro, Carolinian, Samoan, Chuu. (FDA) Native_Hawaiian_or_Other_Pacific_Islander NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER Native Hawaiian or Other Pacific Islander Native Hawaiian or Other Pacific Islander A person not of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin, regardless of race. C41222 Population Group Not Hispanic or Latino C1518424 CDISC FDA A person not of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin, regardless of race. An arbitrary ethnic classification. (NCI) Not_Hispanic_or_Latino NOT HISPANIC OR LATINO Non-Hispanic Non-Hispanic or Latino Not Hispanic or Latino Not Hispanic/Spanish origin Not Hispanic or Latino Denotes a person of African ancestral origins whose family settled in the Caribbean region. C41226 Population Group African Caribbean C0422771 A person having origins in the original peoples of sub-Saharan Africa and the Caribbean. African_Caribbean AFRICAN CARIBBEAN African Caribbean African Caribbean A person having origins in any of the original peoples of North and South America (including Central America) and who maintains tribal affiliation or community attachment. (OMB) C41259 Population Group American Indian or Alaska Native C0282204 CDISC FDA A person having origins in any of the original peoples of North and South America (including Central America), and who maintains tribal affiliation or community attachment. (FDA) American_Indian_or_Alaska_Native AMERICAN INDIAN OR ALASKA NATIVE American Indian or Alaska Native First Nations Native American Native Americans American Indian or Alaska Native A person having origins in any of the original peoples of the Far East, Southeast Asia, or the Indian subcontinent, including for example, Cambodia, China, India, Japan, Korea, Malaysia, Pakistan, the Philippine Islands, Thailand, and Vietnam. (OMB) C41260 Population Group Asian C0078988 CDISC FDA A person having origins in any of the original peoples of the Far East, Southeast Asia, or the Indian subcontinent including, for example, Cambodia, China, India, Japan, Korea, Malaysia, Pakistan, the Philippine Islands, Thailand, and Vietnam. (FDA) Asian ASIAN Asian Asians Asian A person having origins in any of the original peoples of Europe, the Middle East, or North Africa. (OMB) C41261 Population Group White C0043157 CDISC FDA Denotes a person with European, Middle Eastern, or North African ancestral origin who identifies, or is identified, as White. (FDA) White Caucasian Caucasians Caucasoid Occidental WHITE White Whites White A person having origins in the original peoples of the Indian sub-continent. C41262 Population Group Asian Indian C1524069 CDISC FDA A person having origins in any of the original peoples of the Indian subcontinent. Asian_Indian The concept is close to the term South Asian but several major South Asian populations such as Pakistani and Bangladeshi may not identify with it. ASIAN INDIAN Asian Indian Asian Indians Indian Asian Indian Denotes a person whose ancestry is in the countries of the Indian sub-continent, including India, Pakistan, Bangladesh, and Sri Lanka. C41263 Population Group South Asian C1519427 South_Asian South Asian South Asians South Asian Denotes a person with African ancestral origins who self identifies, or is identified, as African. The concept does not refer to those of other ancestry, for example, European and South Asian. In practice, the term mainly refers to people originated from forty-eight sub-Saharan Africa nations; and excludes individuals from North Africa countries, e.g. such as Algeria, Morocco, Egypt, Tunisia with Arab and Berber ethnicity. C42331 Population Group African C0027567 A person having origins in any of the original peoples of sub-Saharan Africa. African AFRICAN African African C42568 Classification Unit by Category C1710551 Header_Concept Unit_by_Category Unit by Category Unit by Category Aleutian - a person having origins from the Aleut indigenous group of Alaska and their descendants and who maintains tribal affiliation, or community or cultural attachment. C43389 Population Group Aleutian C1553304 Aleutian Aleutian Aleutian The native people inhabiting the Arctic of northern Canada, Greenland, Alaska, or eastern Siberia. The two main groups referred to as Eskimo are the Yupik and Inuit. A third group, the Aleut, is related. In Canada and Greenland, the term Eskimo has fallen out of favor, as it is considered pejorative by the natives and has been replaced by the term Inuit. C43390 Population Group Eskimo C0014845 Eskimo Eskimo Inuit Eskimo A person having origins in any of the original peoples of China. C43391 Population Group Chinese C0152035 FDA A person having origins in any of the original peoples of China. Chinese CHINESE Chinese Chinese A person having origins in any of the original peoples of Japan.. C43392 Population Group Japanese C1556094 FDA A person having origins in any of the original peoples of Japan. Japanese JAPANESE Japanese Japanese A person having origins in any of the original peoples of the Philippine Islands. C43393 Population Group Filipino C1556093 FDA A person having origins in any of the original peoples of the Philippines. Filipino FILIPINO Filipino Filipino A person having origins in any of the original peoples of Hawaii. C43394 Population Group Native Hawaiian C0337920 FDA Hawaiian Hawaiian Native Hawaiian Native Hawaiian A person having origins in any of the original peoples of Korea. C43395 Population Group Korean C1556095 A person having origins in any of the original peoples of North and South Korea. Korean KOREAN Korean Korean A person having origins in any of the original peoples of Viet Nam. C43396 Population Group Vietnamese C1561452 FDA A person having origins in any of the original peoples of Viet Nam. Vietnamese VIETNAMESE Vietnamese Vietnamese Denotes the inhabitants of Laos, a person from there, or their descendants elsewhere. C43397 Population Group Laotian C1553325 A person having origins in any of the original peoples of Laos. Laotian LAOTIAN Laotian Laotian Denotes a person having origins in any of the original Hmong people originating in China around the Yellow River or Hoang Ho. C43398 Population Group Hmong C1553324 The native people originating in China around the Yellow River or Hoang Ho. Hmong Early in the 19th century, the Hmong migrated to French Indochina, which comprised Vietnam, Cambodia and Laos. In 1947, Hmong officially became citizens of Loas. Later a number of Hmong emigrated to Thailand and the United States. HMONG Hmong Hmong Denotes the inhabitants of Cambodia (formerly Kampuchea), a person from there, or their descendants elsewhere. C43399 Population Group Cambodian C1553323 A person having origins in any of the original peoples of Cambodia (formerly Kampuchea). Kampuchean CAMBODIAN Cambodian Kampuchean Cambodian Denotes the inhabitants of Thailand, a person from there, or their descendants elsewhere. C43400 Population Group Thai C0337910 A person having origins in any of the original peoples of Thailand. Thai THAI Thai Thai Denotes a person from any of the islands in the western pacific encompassing the area from the Philippines in the west, Indonesia to the south west, Papua New Guinea and Melanesia to the south, and Polynesia to the south-east and east. C43402 Population Group Micronesian C1556099 A person having origins in any of the original peoples of Micronesia. Micronesian MICRONESIAN Micronesian Micronesian Denotes any of the indigenous Chamorro people of Guam and the Mariana Islands or persons of that ancestry. C43403 Population Group Chamorran C1553343 Chamorran Chamorran Chamorro Chamorran Denotes the inhabitants of Guam, a person from there, or their descendants elsewhere. C43404 Population Group Guamanian C0920541 Guamanian Guamanian Guamanian Denotes a person from any of the over 1,000 islands in the central and southern Pacific Ocean bounded by a triangle with its three corners at Hawaii, New Zealand, and Easter Island or a person of that ancestry. C43405 Population Group Polynesian C0240790 A person having origins in any of the original peoples of Polynesia. Polynesian POLYNESIAN Polynesian Polynesian Denotes the inhabitants of Tahiti, a person from there, or their descendants elsewhere. C43406 Population Group Tahitian C0241329 Tahitian Tahitian Tahitian A person having origins in any of the original peoples of Samoa. C43407 Population Group Samoan C1556103 FDA Samoan Samoan Samoan Denotes the inhabitants of Tonga, a person from there, or their descendants elsewhere. C43408 Population Group Tongan C0337933 Tongan Tongan Tongan Denotes a person from any of the islands in the region extending from the west Pacific to the Arafura Sea, north and north-east of Australia. or of that ancestry. C43409 Population Group Melanesian C0337924 A person having origins in any of the original peoples of Melanesia. Melanesian MELANESIAN Melanesian Melanesian Denotes the inhabitants of Fiji, a person from there, or their descendants elsewhere. C43410 Population Group Fiji Islander C1556097 Fiji_Islander Fiji Islander Fijian Fiji Islander Denotes the inhabitants of Papua New Guinea, a person from there, or their descendants elsewhere. C43411 Population Group Papua New Guinean C1553350 New_Guinean New Guinean Papua New Guinean Papua New Guinean Primarily refers to a person having origins in the original peoples of the Indian sub-continent, a subset of which formed Pakistan. The term also refers to a person from Pakistan, whether or not ancestors were from India. C43427 Population Group Pakistani C0240620 A person having origins in any of the original peoples of Pakistan. Pakistani PAKISTANI Pakistani Pakistani C43650 Population Group Alaska Indian CL333681 Alaska_Indian Alaska Indian Alaska Indian Denotes the inhabitants of Bangladesh, a person from there, or their descendants elsewhere. C43671 Population Group Bangladeshi C1556107 A person having origins in any of the original peoples of Bangladesh. Bangladeshi BANGLADESHI Bangladeshi Bangladeshi Denotes the inhabitants of Sri Lanka, a person from there, or their descendants elsewhere. C43672 Population Group Sri Lankan C1553327 A person having origins in any of the original peoples of Sri Lanka. Sri_Lankan SRI LANKAN Sri Lankan Sri Lankan Denotes the inhabitants of Bhutan, a person from there, or their descendants elsewhere. C43673 Population Group Bhutanese C0337894 CDISC A person having origins in any of the original peoples of Bhutan. Bhutanese BHUTANESE Bhutanese Bhutanese Denotes the inhabitants of Myanmar (formerly Burma), a person from there, or their descendants elsewhere. C43674 Population Group Burmese C1553322 A person having origins in any of the original peoples of Myanmar (formerly Burma). Burmese BURMESE Burmese Burmese Denotes the inhabitants of Taiwan, a person from there, or their descendants elsewhere. C43675 Population Group Taiwanese C1556096 A person having origins in any of the original peoples of Taiwan. Taiwanese TAIWANESE Taiwanese Taiwanese Denotes the inhabitants of Indonesia, a person from there, or their descendants elsewhere. C43715 Population Group Indonesian C0337900 A person having origins in any of the original peoples of Indonesia. Indonesian INDONESIAN Indonesian Indonesian Denotes the inhabitants of Malaysia, a person from there, or their descendants elsewhere. C43716 Population Group Malaysian C0240293 A person having origins in any of the original peoples of Malaysia. Malaysian MALAYSIAN Malaysian Malaysian Denotes the inhabitants of the japanese island of Okinawa, a person from there, or their descendants elsewhere. C43717 Population Group Okinawan C1553326 A person having origins in any of the original peoples of Okinawa. Okinawan OKINAWAN Okinawan Okinawan Denotes the inhabitants of Iwo Jima, a person from there, or their descendants elsewhere. C43718 Population Group Iwo Jiman C1553328 A person having origins in any of the original peoples of Iwo Jima. Iwo_Jiman IWO JIMAN Iwo Jiman Iwo Jiman Denotes the inhabitants of the Maldives, a person from there, or their descendants elsewhere. C43719 Population Group Maldivian C1553329 A person having origins in any of the original peoples of the Maldives. Maldivian MALDIVIAN Maldivian Maldivian Denotes the inhabitants of Nepal, a person from there, or their descendants elsewhere. C43720 Population Group Nepalese C1553330 A person having origins in any of the original peoples of Nepal. Nepalese NEPALESE Nepalese Nepalese Denotes the inhabitants of Singapore, a person from there, or their descendants elsewhere. C43721 Population Group Singaporean C1553331 A person having origins in any of the original peoples of Singapore. Singaporean SINGAPOREAN Singaporean Singaporean Denotes the inhabitants of Madagascar, a person from there, or their descendants elsewhere. C43722 Population Group Malagasy C1553332 A person having origins in any of the original peoples of Madagascar. Madagascar_Race MALAGASY Madagascar Malagasy Malagasy Denotes the inhabitants of Barbados, a person from there, or their descendants elsewhere. C43823 Population Group Barbadian C1553337 A person having origins in any of the original peoples of Barbados. Barbadian BARBADIAN Barbadian Barbadian Denotes the inhabitants of Dominica, a person from there, or their descendants elsewhere. C43824 Population Group Dominica Islander C1553338 A person having origins in any of the original peoples of Dominica. Dominican DOMINICA ISLANDER Dominica Islander Dominican Dominica Islander Denotes the inhabitants of Haiti, a person from there, or their descendants elsewhere. C43825 Population Group Haitian C0239806 A person having origins in any of the original peoples of Haiti. Haitian HAITIAN Haitian Haitian Denotes the inhabitants of Jamaica, a person from there, or their descendants elsewhere. C43826 Population Group Jamaican C0240072 A person having origins in any of the original peoples of Jamaica. Jamaican JAMAICAN Jamaican Jamaican Denotes the inhabitants of Tobago, a person from there, or their descendants elsewhere. C43827 Population Group Tobagoan C1553339 A person having origins in any of the original peoples of Tobago. Tobagoan TOBAGOAN Tobagoan Tobagoan Denotes the inhabitants of Trinidad, a person from there, or their descendants elsewhere. C43828 Population Group Trinidadian C1553340 A person having origins in any of the original peoples of Trinidad. Trinidadian TRINIDADIAN Trinidadian Trinidadian Denotes the inhabitants of the West Indies, a person from there, or their descendants elsewhere. C43829 Population Group West Indian C0425373 A person having origins in any of the original peoples of the West Indies. West_Indian WEST INDIAN West Indian West Indian Denotes the inhabitants of Botswana, a person from there, or their descendants elsewhere. C43830 Population Group Botswanan C1553333 A person having origins in any of the original peoples of Botswana. Botswanan BOTSWANAN Botswanan Motswana Botswanan Denotes the inhabitants of Ethiopia, a person from there, or their descendants elsewhere. C43831 Population Group Ethiopian C0239304 A person having origins in any of the original peoples of Ethiopia. Ethiopian ETHIOPIAN Ethiopian Ethiopian Denotes the inhabitants of Liberia, a person from there, or their descendants elsewhere. C43832 Population Group Liberian C1556088 A person having origins in any of the original peoples of Liberia. Liberian LIBERIAN Liberian Liberian Denotes the inhabitants of Namibia, a person from there, or their descendants elsewhere. C43833 Population Group Namibian C1553334 A person having origins in any of the original peoples of Namibia. Namibian NAMIBIAN Namibian Namibian Denotes the inhabitants of Nigeria, a person from there, or their descendants elsewhere. C43834 Population Group Nigerian C1556089 A person having origins in any of the original peoples of Nigeria. Nigerian NIGERIAN Nigerian Nigerian Denotes the inhabitants of the Democratic Republic of the Congo (formerly Zaire), a person from there, or their descendants elsewhere. C43835 Population Group Zairean C1553335 A person having origins in any of the original peoples of Zaire. Zairean ZAIREAN Zairean Zairean Denotes the inhabitants of Tokelau, a person from there, or their descendants elsewhere. C43836 Population Group Tokelauan C0438967 Tokelauan Tokelauan Tokelauan A person having origins in any of the original peoples of Guam or the Mariana Islands. C43837 Population Group Guamanian or Chamorro C1553342 FDA Guamanian_or_Chamorro Guamanian or Chamorro Guamanian or Chamorro Denotes the inhabitants of the Northern Mariana Islands, a person from there, or their descendants elsewhere. C43838 Population Group Mariana Islander C1553344 Mariana_Islander Mariana Islander Mariana Islander Denotes the inhabitants of the Marshall Islands, a person from there, or their descendants elsewhere. C43839 Population Group Marshallese C1556098 Marshallese Marshallese Marshallese Denotes the inhabitants of Palau, a person from there, or their descendants elsewhere. C43840 Population Group Palauan C0337928 Palauan Palauan Palauan Denotes the inhabitants of the Caroline Islands, a person from there, or their descendants elsewhere. C43841 Population Group Carolinian C1553345 Carolinian Carolinian Carolinian Denotes the inhabitants of the island of Kosrae, a person from there, or their descendants elsewhere. C43842 Population Group Kosraean C1553346 Kosraean Kosraean Kosraean Denotes the inhabitants of the island of Pohnpei, a person from there, or their descendants elsewhere. C43843 Population Group Pohnpeian C1553347 Pohnpeian Pohnpeian Pohnpeian Denotes the inhabitants of the Saipan Islands, a person from there, or their descendants elsewhere. C43844 Population Group Saipanese C1556102 Saipanese Saipanese Saipanese Denotes the inhabitants of Kiribati, a person from there, or their descendants elsewhere. C43845 Population Group Kiribati C1553348 Kiribati_Race Kiribati Kiribati Denotes the inhabitants of the island of Chuuk, a person from there, or their descendants elsewhere. C43846 Population Group Chuukese C1553349 Chuukese Chuukese Chuukese Denotes the inhabitants of the island of Yap, a person from there, or their descendants elsewhere. C43847 Population Group Yapese C1556105 Yapese Yapese Yapese Denotes the inhabitants of the Solomon Islands, a person from there, or their descendants elsewhere. C43849 Population Group Solomon Islander C0337932 Solomon_Islander Solomon Islander Solomon Islander Denotes the inhabitants of the islands of Vanuatu, a person from there, or their descendants elsewhere. C43850 Population Group New Hebrides C1571857 New_Hebrides New Hebrides New Hebrides Denotes the inhabitants of any of the countries of Europe, a person from there, or their descendants elsewhere. C43851 Population Group European C1535514 A person having origins in any of the original peoples of Europe. European EUROPEAN European European Denotes the inhabitants of Armenia, a person from there, or their descendants elsewhere. C43852 Population Group Armenian C0337794 Armenian Armenian Armenian Denotes the inhabitants of England, a person from there, or their descendants elsewhere. C43853 Population Group English C1556083 English English English Denotes the inhabitants of France, a person from there, or their descendants elsewhere. C43854 Population Group French C1556084 French French French Denotes the inhabitants of Germany, a person from there, or their descendants elsewhere. C43855 Population Group German C1556085 German German German Denotes the inhabitants of Ireland, a person from there, or their descendants elsewhere. C43856 Population Group Irish C0087186 Irish Irish Irish Denotes the inhabitants of Italy, a person from there, or their descendants elsewhere. C43857 Population Group Italian C0337810 Italian Italian Italian Denotes the inhabitants of Poland, a person from there, or their descendants elsewhere. C43858 Population Group Polish C0220896 Polish Polish Polish Denotes the inhabitants of Scotland, a person from there, or their descendants elsewhere. C43859 Population Group Scottish C0240966 Scottish Scottish Scottish Denotes the inhabitants of Russia, a person from there, or their descendants elsewhere. C43860 Population Group Russian C0337816 A person having origins in any of the original peoples of Russia. Russian RUSSIAN Russian Russian Denotes the inhabitants of Sweden, a person from there, or their descendants elsewhere. C43861 Population Group Swedish C1710263 Swedish Swedish Swedish Denotes the inhabitants of Norway, a person from there, or their descendants elsewhere. C43862 Population Group Norwegian C0337812 Norwegian Norwegian Norwegian Denotes the inhabitants of Ukraine, a person from there, or their descendants elsewhere. C43863 Population Group Ukranian C1710525 Ukranian Ukranian Ukranian Denotes the inhabitants of Mongolia, a person from there, or their descendants elsewhere. C43864 Population Group Mongolian C1709065 A person having origins in any of the original peoples of Mongolia. Mongolian MONGOLIAN Mongolian Mongolian Denotes the inhabitants of Finland, a person from there, or their descendants elsewhere. C43865 Population Group Finnish C1711254 Finnish Finnish Finnish Denotes a person from any of the countries of southwest Asia and northeastern Africa; this region includes those countries east of Egypt and south of Turkey and extending to Iran in the east. C43866 Population Group Middle Eastern or North African C1553353 Middle_Eastern_or_North_African Middle Eastern or North African Middle Eastern or North African A collective term used to identify indigenous peoples of northern Iraq and neighboring areas of Syria and Turkey, who also identify themselves as Aramaeans and Chaldeans. They are the survivors of the formerly extensive Aramaic- or Syriac- speaking Christian community of northern Iraq, southeastern Turkey, and northwestern Iran. C43867 Population Group Assyrian C1553354 Assyrian Assyrian Assyrian Denotes the inhabitants of Egypt, a person from there, or their descendants elsewhere. C43868 Population Group Egyptian C0337801 Egyptian Egyptian Egyptian Denotes the inhabitants of Iran, a person from there, or their descendants elsewhere. C43869 Population Group Iranian C1553355 Iranian Iranian Iranian Denotes the inhabitants of Iraq, a person from there, or their descendants elsewhere. C43870 Population Group Iraqi C1556087 Iraqi Iraqi Iraqi Denotes the inhabitants of Lebanon, a person from there, or their descendants elsewhere. C43871 Population Group Lebanese C1553356 Lebanese Lebanese Lebanese Denotes those persons of mainly Arabic speakers who regard themselves as a distinct branch of the Arabic-speaking peoples, with family origin in Palestine being the defining characteristic. C43872 Population Group Palestinian C0282539 Palestinian Palestinian Palestinian Denotes the inhabitants of Syria, a person from there, or their descendants elsewhere. C43873 Population Group Syrian C0337819 Syrian Syrian Syrian Denotes the inhabitants of Afghanistan, a person from there, or their descendants elsewhere. C43874 Population Group Afghanistani C1553357 Afghanistani Afghanistani Afghanistani Denotes the inhabitants of Israel, a person from there, or their descendants elsewhere. C43875 Population Group Israeli C0240069 Israeli Israeli Israeli Denotes a person with ethnic origins in the Semitic people originally from the Arabian peninsula and surrounding territories in the Middle East and northern Africa. C43876 Population Group Arab C0282540 A person having origins in any of the original peoples of the Arabian peninsula and surrounding territories in the Middle East and northern Africa. Arab ARAB Arab Arab Denotes a person having origins in one of the indigenous peoples of North America, who lived on the continent prior to the European colonization. The term includes individuals belonging to a large number of tribes, states, and ethnic groups, many of them still enduring as communities. C43877 Population Group American Indian C0002460 The native people of North America. American_Indian AMERICAN INDIAN American Indian American Indian C43878 Population Group Abenaki C1555038 Abenaki Abenaki Abenaki C43879 Population Group Algonquian C1555039 Algonquian Algonquian Algonquian C43880 Population Group Apache C0337855 Apache Apache Apache C43881 Population Group Chiricahua C1555040 Chiricahua Chiricahua Chiricahua C43882 Population Group Fort Sill Apache C1555041 Fort_Sill_Apache Fort Sill Apache Fort Sill Apache C43883 Population Group Jicarilla Apache C1555042 Jicarilla_Apache Jicarilla Apache Jicarilla Apache C43884 Population Group Lipan Apache C1555043 Lipan_Apache Lipan Apache Lipan Apache C43885 Population Group Mescalero Apache C1555044 Mescalero_Apache Mescalero Apache Mescalero Apache C43886 Population Group Oklahoma Apache C1555045 Oklahoma_Apache Oklahoma Apache Oklahoma Apache C43887 Population Group Payson Apache C1555046 Payson_Apache Payson Apache Payson Apache C43888 Population Group San Carlos Apache C1555047 San_Carlos_Apache San Carlos Apache San Carlos Apache C43889 Population Group White Mountain Apache C1555048 White_Mountain_Apache White Mountain Apache White Mountain Apache C43890 Population Group Arapaho C0682104 Arapaho Arapaho Arapaho C43891 Population Group Northern Arapaho C1555049 Northern_Arapaho Northern Arapaho Northern Arapaho C43892 Population Group Southern Arapaho C1555050 Southern_Arapaho Southern Arapaho Southern Arapaho C43893 Population Group Wind River Arapaho C1555051 Wind_River_Arapaho Wind River Arapaho Wind River Arapaho C43894 Population Group Arikara C1555052 Arikara Arikara Arikara C43895 Population Group Assiniboine C1555053 Assiniboine Assiniboine Assiniboine C43896 Population Group Assiniboine Sioux C1555054 Assiniboine_Sioux Assiniboine Sioux Assiniboine Sioux C43897 Population Group Fort Peck Assiniboine Sioux C1555055 Fort_Peck_Assiniboine_Sioux Fort Peck Assiniboine Sioux Fort Peck Assiniboine Sioux C43898 Population Group Bannock C1555056 Bannock Bannock Bannock C43899 Population Group Blackfeet C0337860 Blackfeet Blackfeet Blackfeet C43900 Population Group Brotherton C1555057 Brotherton Brotherton Brotherton C43901 Population Group Burt Lake Band C1555058 Burt_Lake_Band Burt Lake Band Burt Lake Band C43902 Population Group Caddo C1555059 Caddo Caddo Caddo C43903 Population Group Oklahoma Cado C1555060 Oklahoma_Cado Oklahoma Cado Oklahoma Cado C43904 Population Group Cahuilla C1555061 Cahuilla Cahuilla Cahuilla C43905 Population Group Agua Caliente Cahuilla C1555062 Agua_Caliente_Cahuilla Agua Caliente Cahuilla Agua Caliente Cahuilla C43909 Population Group Augustine C1555063 Augustine Augustine Augustine C43910 Population Group Cabazon C1555064 Cabazon Cabazon Cabazon C43911 Population Group Los Coyotes C1555065 Los_Coyotes Los Coyotes Los Coyotes C43912 Population Group Morongo C1555066 Morongo Morongo Morongo C43913 Population Group Santa Rosa Cahuilla C1555067 Santa_Rosa_Cahuilla Santa Rosa Cahuilla Santa Rosa Cahuilla C43914 Population Group Torres-Martinez C1555068 Torres_Martinez Torres-Martinez Torres-Martinez C43915 Population Group California Tribes C1555069 California_Tribes California Tribes California Tribes C43916 Population Group Canadian and Latin American Indian C1555083 Canadian_and_Latin_American_Indian Canadian and Latin American Indian Canadian and Latin American Indian C43917 Population Group Catawba C0682102 Catawba Catawba Catawba C43918 Population Group Cayuse C1555088 Cayuse Cayuse Cayuse C43919 Population Group Chehalis C1555089 Chehalis Chehalis Chehalis C43920 Population Group Chemakuan C1555090 Chemakuan Chemakuan Chemakuan C43921 Population Group Hoh C1555091 Hoh Hoh Hoh C43922 Population Group Quileute C1555092 Quileute Quileute Quileute C43923 Population Group Chemehuevi C1555093 Chemehuevi Chemehuevi Chemehuevi C43924 Population Group Cherokee C0682103 Cherokee Cherokee Cherokee C43925 Population Group Cherokee Shawnee C1555104 Cherokee_Shawnee Cherokee Shawnee Cherokee Shawnee C43926 Population Group Cheyenne C0682106 Cheyenne Cheyenne Cheyenne C43927 Population Group Northern Cheyenne C1555105 Northern_Cheyenne Northern Cheyenne Northern Cheyenne C43928 Population Group Southern Cheyenne C1555106 Southern_Cheyenne Southern Cheyenne Southern Cheyenne C43929 Population Group Cheyenne-Arapaho C1555107 Cheyenne_Arapaho Cheyenne-Arapaho Cheyenne-Arapaho C43930 Population Group Chickahominy C1555108 Chickahominy Chickahominy Chickahominy C43931 Population Group Eastern Chickahominy C1555109 Eastern_Chickahominy Eastern Chickahominy Eastern Chickahominy C43932 Population Group Western Chickahominy C1555110 Western_Chickahominy Western Chickahominy Western Chickahominy C43933 Population Group Chickasaw C0682101 Chickasaw Chickasaw Chickasaw C43934 Population Group Chinook C1555111 Chinook Chinook Chinook C43935 Population Group Chippewa C0337862 Chippewa Chippewa Chippewa C43936 Population Group Chippewa Cree C1555144 Chippewa_Cree Chippewa Cree Chippewa Cree C43937 Population Group Rocky Boy's Chippewa Cree C1555145 Rocky_Boy_s_Chippewa_Cree Rocky Boy's Chippewa Cree Rocky Boy's Chippewa Cree C43938 Population Group Chitimacha C1555146 Chitimacha Chitimacha Chitimacha C43939 Population Group Choctaw C0682100 Choctaw Choctaw Choctaw C43940 Population Group Clifton Choctaw C1555147 Clifton_Choctaw Clifton Choctaw Clifton Choctaw C43941 Population Group Jena Choctaw C1555148 Jena_Choctaw Jena Choctaw Jena Choctaw C43942 Population Group Mississippi Choctaw C1555149 Mississippi_Choctaw Mississippi Choctaw Mississippi Choctaw C43943 Population Group Mowa Band of Choctaw C1555150 Mowa_Band_of_Choctaw Mowa Band of Choctaw Mowa Band of Choctaw C43944 Population Group Oklahoma Choctaw C1555151 Oklahoma_Choctaw Oklahoma Choctaw Oklahoma Choctaw C43945 Population Group Chumash C0682116 Chumash Chumash Chumash C43946 Population Group Santa Ynez C1555152 Santa_Ynez Santa Ynez Santa Ynez C43947 Population Group Clear Lake C1555153 Clear_Lake Clear Lake Clear Lake C43948 Population Group Coeur D'Alene C1555154 Coeur_D_Alene Coeur D'Alene Coeur D'Alene C43949 Population Group Coharie C1555155 Coharie Coharie Coharie C43950 Population Group Colorado River C1555156 Colorado_River Colorado River Colorado River C43951 Population Group Colville C1555157 Colville Colville Colville C43952 Population Group Comanche C0682105 Comanche Comanche Comanche C43953 Population Group Oklahoma Comanche C1555158 Oklahoma_Comanche Oklahoma Comanche Oklahoma Comanche C43954 Population Group Coos Lower Umpqua Siuslaw C1555159 Coos_Lower_Umpqua_Siuslaw Coos Lower Umpqua Siuslaw Coos Lower Umpqua Siuslaw C43955 Population Group Coos C1555160 Coos Coos Coos C43956 Population Group Coquilles C1555161 Coquilles Coquilles Coquilles C43957 Population Group Costanoan C1555162 Costanoan Costanoan Costanoan C43958 Population Group Coushatta C0337865 Coushatta Coushatta Coushatta C43959 Population Group Alabama Coushatta C1555163 Alabama_Coushatta Alabama Coushatta Alabama Coushatta C43961 Population Group Cowlitz C1555164 Cowlitz Cowlitz Cowlitz C43962 Population Group Cree C0702268 Cree Cree Cree C43963 Population Group Creek C1555165 Creek Creek Creek C43964 Population Group Croatan C1555178 Croatan Croatan Croatan C43965 Population Group Crow C1555179 Crow Crow Crow C43967 Population Group Cupeno C1555180 Cupeno Cupeno Cupeno C43968 Population Group Agua Caliente C1555181 Agua_Caliente Agua Caliente Agua Caliente C43969 Population Group Delaware C1555182 Delaware_Indian Delaware Delaware C43970 Population Group Diegueno C0337867 Diegueno Diegueno Diegueño Diegueno C43971 Population Group Eastern Tribes C1555198 Eastern_Tribes Eastern Tribes Eastern Tribes C43972 Population Group Esselen C1555214 Esselen Esselen Esselen C43973 Population Group Fort Belknap C1555215 Fort_Belknap Fort Belknap Fort Belknap C43974 Population Group Fort Berthold C1555216 Fort_Berthold Fort Berthold Fort Berthold C43975 Population Group Fort McDowell C1555217 Fort_McDowell Fort McDowell Fort Mcdowell Fort McDowell C43976 Population Group Fort Hall C1555218 Fort_Hall Fort Hall Fort Hall C43977 Population Group Gabrieleno C1555219 Gabrieleno Gabrieleno Gabrieleno C43978 Population Group Grand Ronde C1555220 Grand_Ronde Grand Ronde Grand Ronde C43979 Population Group Gros Ventres C1555221 Gros_Ventres Gros Ventres Gros Ventres C43980 Population Group Atsina C1555222 Atsina Atsina Atsina C43981 Population Group Haliwa C1555223 Haliwa Haliwa Haliwa C43982 Population Group Hidatsa C1555224 Hidatsa Hidatsa Hidatsa C43983 Population Group Hoopa C1555225 Hoopa Hoopa Hoopa C43984 Population Group Trinity C1555226 Trinity Trinity Trinity C43985 Population Group Whilkut C1555227 Whilkut Whilkut Whilkut C43986 Population Group Hoopa Extension C1555228 Hoopa_Extension Hoopa Extension Hoopa Extension C43987 Population Group Houma C1555229 Houma Houma Houma C43988 Population Group Inaja-Cosmit C1555230 Inaja_Cosmit Inaja-Cosmit Inaja-Cosmit C43989 Population Group Iowa C1555231 Iowa_Indian Iowa Iowa C43990 Population Group Iowa of Kansas-Nebraska C1555232 Iowa_of_Kansas_Nebraska Iowa of Kansas-Nebraska Iowa of Kansas-Nebraska C43991 Population Group Iowa of Oklahoma C1555233 Iowa_of_Oklahoma Iowa of Oklahoma Iowa of Oklahoma C43992 Population Group Iroquois C0682098 Iroquois Iroquois Iroquois C43993 Population Group Juaneno C1555243 Juaneno Juaneno Juaneno C43994 Population Group Kalispel C1555244 Kalispel Kalispel Kalispel C43995 Population Group Karuk C1555245 Karuk Karuk Karuk C43996 Population Group Kaw C1555246 Kaw Kaw Kaw C43997 Population Group Kickapoo C1555247 Kickapoo Kickapoo Kickapoo C43998 Population Group Oklahoma Kickapoo C1555248 Oklahoma_Kickapoo Oklahoma Kickapoo Oklahoma Kickapoo C43999 Population Group Texas Kickapoo C1555249 Texas_Kickapoo Texas Kickapoo Texas Kickapoo C44000 Population Group Kiowa C1555250 Kiowa Kiowa Kiowa C44001 Population Group Oklahoma Kiowa C1555251 Oklahoma_Kiowa Oklahoma Kiowa Oklahoma Kiowa C44002 Population Group Klallam C1555252 Klallam Klallam Klallam C44003 Population Group Jamestown C1555253 Jamestown Jamestown Jamestown C44004 Population Group Lower Elwha C1555254 Lower_Elwha Lower Elwha Lower Elwha C44005 Population Group Port Gamble Klallam C1555255 Port_Gamble_Klallam Port Gamble Klallam Port Gamble Klallam C44006 Population Group Klamath C1555256 Klamath Klamath Klamath C44007 Population Group Konkow C1555257 Konkow Konkow Konkow C44008 Population Group Kootenai C1555258 Kootenai Kootenai Kootenai C44009 Population Group Lassik C1555259 Lassik Lassik Lassik C44010 Population Group Long Island C1555260 Long_Island Long Island Long Island C44011 Population Group Matinecock C1555261 Matinecock Matinecock Matinecock C44012 Population Group Montauk C1555262 Montauk Montauk Montauk C44013 Population Group Poospatuck C1555263 Poospatuck Poospatuck Poospatuck C44014 Population Group Setauket C1555264 Setauket Setauket Setauket C44015 Population Group Luiseno C0682114 Luiseno Luiseno Luiseno C44016 Population Group La Jolla C1555265 La_Jolla La Jolla La Jolla C44017 Population Group Pala C1555266 Pala Pala Pala C44018 Population Group Pauma C1555267 Pauma Pauma Pauma C44019 Population Group Pechanga C1555268 Pechanga Pechanga Pechanga C44020 Population Group Soboba C1555269 Soboba SoboInOwlba Soboba C44021 Population Group Twenty-Nine Palms C1555270 Twenty_Nine_Palms Twenty-Nine Palms Twenty-Nine Palms C44022 Population Group Temecula C1555271 Temecula Temecula Temecula C44023 Population Group Lumbee C1555272 Lumbee Lumbee Lumbee C44024 Population Group Lummi C1555273 Lummi Lummi Lummi C44025 Population Group Maidu C1555274 Maidu Maidu Maidu C44026 Population Group Mountain Maidu C1555275 Mountain_Maidu Mountain Maidu Mountain Maidu C44027 Population Group Nishinam C1551415 Nishinam Nishinam Nishinam C44028 Population Group Makah C1551416 Makah Makah Makah C44029 Population Group Maliseet C1551417 Maliseet Maliseet Maliseet C44030 Population Group Mandan C1551418 Mandan Mandan Mandan C44031 Population Group Mattaponi C1551419 Mattaponi Mattaponi Mattaponi C44032 Population Group Menominee C1551420 Menominee Menominee Menominee C44033 Population Group Miami C1551421 Miami Miami Miami C44034 Population Group Illinois Miami C1551422 Illinois_Miami Illinois Miami Illinois Miami C44035 Population Group Indiana Miami C1551423 Indiana_Miami Indiana Miami Indiana Miami C44036 Population Group Oklahoma Miami C1551424 Oklahoma_Miami Oklahoma Miami Oklahoma Miami C44037 Population Group Miccosukee C1551425 Miccosukee Miccosukee Miccosukee C44038 Population Group Micmac C1551426 Micmac Micmac Micmac C44039 Population Group Aroostook C1551427 Aroostook Aroostook Aroostook C44040 Population Group Mission Indians C1551428 Mission_Indians Mission Indians Mission Indians C44041 Population Group Miwok C1551429 Miwok Miwok Miwok C44042 Population Group Modoc C1551430 Modoc Modoc Modoc C44043 Population Group Mohegan C1551431 Mohegan Mohegan Mohegan C44044 Population Group Mono C1551432 Mono Mono Mono C44045 Population Group Nanticoke C1551433 Nanticoke Nanticoke Nanticoke C44046 Population Group Narragansett C1551434 Narragansett Narragansett Narragansett C44048 Population Group Dine C0337879 Dine Dine Navaho Navajo Dine C44049 Population Group Alamo Dine C1551435 Alamo_Dine Alamo Dine Alamo Navaho Alamo Navajo Alamo Dine C44050 Population Group Canoncito Dine C1551436 Canoncito_Dine Canoncito Dine Canoncito Navaho Canoncito Navajo Canoncito Dine C44051 Population Group Ramah Dine C1551437 Ramah_Dine Ramah Dine Ramah Navaho Ramah Navajo Ramah Dine C44052 Population Group Nez Perce C0337880 Nez_Perce Nez Perce Nez Percé Nez Perce C44053 Population Group Nomalaki C1551438 Nomalaki Nomalaki Nomalaki C44054 Population Group Northwest Tribes C1551439 Northwest_Tribes Northwest Tribes Northwest Tribes C44055 Population Group Alsea C1551440 Alsea Alsea Alsea C44056 Population Group Celilo C1551441 Celilo Celilo Celilo C44057 Population Group Columbia C1551442 Columbia_Indian Columbia Columbia C44058 Population Group Kalapuya C1551443 Kalapuya Kalapuya Kalapuya C44059 Population Group Molala C1551444 Molala Molala Molala C44060 Population Group Talakamish C1551445 Talakamish Talakamish Talakamish C44061 Population Group Tenino C1551446 Tenino Tenino Tenino C44062 Population Group Tillamook C1551447 Tillamook Tillamook Tillamook C44063 Population Group Wenatchee C1551448 Wenatchee Wenatchee Wenatchee C44064 Population Group Yahooskin C1551449 Yahooskin Yahooskin Yahooskin C44065 Population Group Omaha C1551450 Omaha Omaha Omaha C44066 Population Group Oregon Athabaskan C1551451 Oregon_Athabaskan Oregon Athabaskan Oregon Athabaskan C44067 Population Group Osage C1551452 Osage Osage Osage C44068 Population Group Otoe-Missouria C1551453 Otoe_Missouria Otoe-Missouria Otoe-Missouria C44069 Population Group Ottawa C1551454 Ottawa Ottawa Ottawa C44070 Population Group Burt Lake Ottawa C1551455 Burt_Lake_Ottawa Burt Lake Ottawa Burt Lake Ottawa C44071 Population Group Michigan Ottawa C1551456 Michigan_Ottawa Michigan Ottawa Michigan Ottawa C44072 Population Group Oklahoma Ottawa C1551457 Oklahoma_Ottawa Oklahoma Ottawa Oklahoma Ottawa C44073 Population Group Paiute C0682113 Paiute Paiute Paiute C44074 Population Group Pamunkey C1551479 Pamunkey Pamunkey Pamunkey C44075 Population Group Passamaquoddy C1551480 Passamaquoddy Passamaquoddy Passamaquoddy C44076 Population Group Indian Township C1551481 Indian_Township Indian Township Indian Township C44077 Population Group Pleasant Point Passamaquoddy C1551482 Pleasant_Point_Passamaquoddy Pleasant Point Passamaquoddy Pleasant Point Passamaquoddy C44078 Population Group Pawnee C0682108 Pawnee Pawnee Pawnee C44079 Population Group Oklahoma Pawnee C1551483 Oklahoma_Pawnee Oklahoma Pawnee Oklahoma Pawnee C44080 Population Group Penobscot C0682097 Penobscot Penobscot Penobscot C44081 Population Group Peoria C1551484 Peoria Peoria Peoria C44082 Population Group Oklahoma Peoria C1551485 Oklahoma_Peoria Oklahoma Peoria Oklahoma Peoria C44083 Population Group Pequot C1551486 Pequot Pequot Pequot C44084 Population Group Marshantucket Pequot C1551487 Marshantucket_Pequot Marshantucket Pequot Marshantucket Pequot C44085 Population Group Pima C1551488 Pima Pima Pima C44086 Population Group Gila River Pima-Maricopa C1551489 Gila_River_Pima_Maricopa Gila River Pima-Maricopa Gila River Pima-Maricopa C44087 Population Group Salt River Pima-Maricopa C1551490 Salt_River_Pima_Maricopa Salt River Pima-Maricopa Salt River Pima-Maricopa C44088 Population Group Piscataway C1551491 Piscataway Piscataway Piscataway C44089 Population Group Pit River C1551492 Pit_River Pit River Pit River C44090 Population Group Pomo C1551493 Pomo Pomo Pomo C44091 Population Group Ponca C1551502 Ponca Ponca Ponca C44092 Population Group Nebraska Ponca C1551503 Nebraska_Ponca Nebraska Ponca Nebraska Ponca C44093 Population Group Oklahoma Ponca C1551504 Oklahoma_Ponca Oklahoma Ponca Oklahoma Ponca C44094 Population Group Potawatomi C1551505 Potawatomi Potawatomi Potawatomi C44095 Population Group Powhatan C1551513 Powhatan Powhatan Powhatan C44096 Population Group Pueblo C1556090 Pueblo Pueblo Pueblo C44102 Population Group Puget Sound Salish C1551539 Puget_Sound_Salish Puget Sound Salish Puget Sound Salish C44103 Population Group Quapaw C1551561 Quapaw Quapaw Quapaw C44104 Population Group Quinault C1551562 Quinault Quinault Quinault C44105 Population Group Rappahannock C1551563 Rappahannock Rappahannock Rappahannock C44106 Population Group Reno-Sparks C1551564 Reno_Sparks Reno-Sparks Reno-Sparks C44107 Population Group Round Valley C1551565 Round_Valley Round Valley Round Valley C44108 Population Group Sac and Fox C1551566 Sac_and_Fox Sac and Fox Sac and Fox C44109 Population Group Iowa Sac and Fox C1551567 Iowa_Sac_and_Fox Iowa Sac and Fox Iowa Sac and Fox C44110 Population Group Missouri Sac and Fox C1551568 Missouri_Sac_and_Fox Missouri Sac and Fox Missouri Sac and Fox C44111 Population Group Oklahoma Sac and Fox C1551569 Oklahoma_Sac_and_Fox Oklahoma Sac and Fox Oklahoma Sac and Fox C44112 Population Group Salinan C1551570 Salinan Salinan Salinan C44113 Population Group Salish C1551571 Salish Salish Salish C44114 Population Group Salish and Kootenai C1551572 Salish_and_Kootenai Salish and Kootenai Salish and Kootenai C44115 Population Group Schaghticoke C1551573 Schaghticoke Schaghticoke Schaghticoke C44116 Population Group Scott Valley C1551574 Scott_Valley Scott Valley Scott Valley C44117 Population Group Seminole C1556091 Seminole Seminole Seminole C44118 Population Group Big Cypress C1551575 Big_Cypress Big Cypress Big Cypress C44119 Population Group Brighton C1551576 Brighton Brighton Brighton C44120 Population Group Florida Seminole C1551577 Florida_Seminole Florida Seminole Florida Seminole C44121 Population Group Hollywood Seminole C1551578 Hollywood_Seminole Hollywood Seminole Hollywood Seminole C44122 Population Group Oklahoma Seminole C1551579 Oklahoma_Seminole Oklahoma Seminole Oklahoma Seminole C44123 Population Group Serrano C1551580 Serrano Serrano Serrano C44124 Population Group San Manual C1551581 San_Manual San Manual San Manual C44125 Population Group Shasta C1551582 Shasta Shasta Shasta C44126 Population Group Shawnee C1551583 Shawnee Shawnee Shawnee C44127 Population Group Absentee Shawnee C1551584 Absentee_Shawnee Absentee Shawnee Absentee Shawnee C44128 Population Group Eastern Shawnee C1551585 Eastern_Shawnee Eastern Shawnee Eastern Shawnee C44129 Population Group Shinnecock C1551586 Shinnecock Shinnecock Shinnecock C44130 Population Group Shoalwater Bay C1551587 Shoalwater_Bay Shoalwater Bay Shoalwater Bay C44131 Population Group Shoshone C0337886 Shoshone Shoshone Shoshone C44132 Population Group Shoshone Paiute C1551602 Shoshone_Paiute Shoshone Paiute Shoshone Paiute C44133 Population Group Duck Valley C1551603 Duck_Valley Duck Valley Duck Valley C44134 Population Group Fallon C1551604 Fallon Fallon Fallon C44135 Population Group Fort McDermitt C1551605 Fort_McDermitt Fort McDermitt Fort McDermitt C44136 Population Group Siletz C1551606 Siletz Siletz Siletz C44137 Population Group Sioux C0682107 Sioux Sioux Sioux C44138 Population Group Blackfoot Sioux C1551607 Blackfoot_Sioux Blackfoot Sioux Blackfoot Sioux C44139 Population Group Brule Sioux C1551608 Brule_Sioux Brule Sioux Brule Sioux C44140 Population Group Cheyenne River Sioux C1551609 Cheyenne_River_Sioux Cheyenne River Sioux Cheyenne River Sioux C44141 Population Group Lakota C1551631 Lakota Lakota Lakota Sioux Teton Sioux Lakota C44142 Population Group Dakota C1551611 Dakota Dakota Dakota Sioux Dakota C44143 Population Group Nakota CL448673 Nakota Nakota Nakota Sioux Nakota C44144 Population Group Crow Creek Sioux C1551610 Crow_Creek_Sioux Crow Creek Sioux Crow Creek Sioux C44145 Population Group Flandreau Santee C1551612 Flandreau_Santee Flandreau Santee Flandreau Santee C44146 Population Group Lake Traverse Sioux C1551614 Lake_Traverse_Sioux Lake Traverse Sioux Lake Traverse Sioux C44147 Population Group Fort Peck Sioux C1551613 Fort_Peck_Sioux Fort Peck Fort Peck Sioux Fort Peck Sioux C44148 Population Group Lower Brule Sioux C1551615 Lower_Brule_Sioux Lower Brule Sioux Lower Brule Sioux C44149 Population Group Lower Sioux C1551616 Lower_Sioux Lower Sioux Lower Sioux C44150 Population Group Mdewakanton Sioux C1551617 Mdewakanton_Sioux Mdewakanton Sioux Mdewakanton Sioux C44151 Population Group Miniconjou C1551618 Miniconjou Miniconjou Miniconjou C44152 Population Group Oglala Sioux C1551619 Oglala_Sioux Oglala Sioux Oglala Sioux C44153 Population Group Pine Ridge Sioux C1551620 Pine_Ridge_Sioux Pine Ridge Sioux Pine Ridge Sioux C44154 Population Group Pipestone Sioux C1551621 Pipestone_Sioux Pipestone Sioux Pipestone Sioux C44155 Population Group Prairie Island Sioux C1551622 Prairie_Island_Sioux Prairie Island Sioux Prairie Island Sioux C44156 Population Group Prior Lake Sioux C1551623 Prior_Lake_Sioux Prior Lake Sioux Prior Lake Sioux C44157 Population Group Rosebud Sioux C1551624 Rosebud_Sioux Rosebud Sioux Rosebud Sioux C44158 Population Group Sans Arc Sioux C1551625 Sans_Arc_Sioux Sans Arc Sioux Sans Arc Sioux C44159 Population Group Santee Sioux C1551626 Santee_Sioux Santee Sioux Santee Sioux C44160 Population Group Sisseton-Wahpeton C1551627 Sisseton_Wahpeton Sisseton-Wahpeton Sisseton-Wahpeton C44161 Population Group Sisseton Sioux C1551628 Sisseton_Sioux Sisseton Sioux Sisseton Sioux C44162 Population Group Wahpeton Sioux C1551635 Wahpeton_Sioux Wahpeton Sioux Wahpeton Sioux C44163 Population Group Spirit Lake Sioux C1551629 Spirit_Lake_Sioux Spirit Lake Sioux Spirit Lake Sioux C44164 Population Group Standing Rock Sioux C1551630 Standing_Rock_Sioux Standing Rock Sioux Standing Rock Sioux C44165 Population Group Two Kettle Sioux C1551632 Two_Kettle_Sioux Two Kettle Sioux Two Kettle Sioux C44187 Population Group Upper Sioux C1551633 Upper_Sioux Upper Sioux Upper Sioux C44188 Population Group Wahpekute Sioux C1551634 Wahpekute_Sioux Wahpekute Sioux Wahpekute Sioux C44189 Population Group Wazhaza Sioux C1551636 Wazhaza_Sioux Wazhaza Sioux Wazhaza Sioux C44190 Population Group Yankton Sioux C1551637 Yankton_Sioux Yankton Sioux Yankton Sioux C44191 Population Group Yanktonai Sioux C1551638 Yanktonai_Sioux Yanktonai Sioux Yanktonai Sioux C44192 Population Group Siuslaw C1551639 Siuslaw Siuslaw Siuslaw C44193 Population Group Spokane C1551640 Spokane Spokane Spokane C44194 Population Group Stewart C1551641 Stewart Stewart Stewart C44195 Population Group Stockbridge C1551642 Stockbridge Stockbridge Stockbridge C44196 Population Group Susanville C1551643 Susanville Susanville Susanville C44197 Population Group Tohono O'Odham C1551644 Tohono_O_Odham Tohono O'Odham Tohono O'Odham C44198 Population Group Ak-Chin C1551645 Ak_Chin Ak-Chin Ak-Chin C44199 Population Group Gila Bend C1551646 Gila_Bend Gila Bend Gila Bend C44200 Population Group San Xavier C1551647 San_Xavier San Xavier San Xavier C44201 Population Group Sells C1551648 Sells Sells Sells C44202 Population Group Tolowa C1551649 Tolowa Tolowa Tolowa C44203 Population Group Tonkawa C1551650 Tonkawa Tonkawa Tonkawa C44204 Population Group Tygh C1551651 Tygh Tygh Tygh C44205 Population Group Umatilla C1551652 Umatilla Umatilla Umatilla C44206 Population Group Umpqua C1551653 Umpqua Umpqua Umpqua C44207 Population Group Cow Creek Umpqua C1551654 Cow_Creek_Umpqua Cow Creek Umpqua Cow Creek Umpqua C44208 Population Group Ute C1556092 Ute Ute Ute C44209 Population Group Allen Canyon C1551655 Allen_Canyon Allen Canyon Allen Canyon C44210 Population Group Uintah Ute C1551656 Uintah_Ute Uintah Ute Uintah Ute C44211 Population Group Ute Mountain Ute C1551657 Ute_Mountain_Ute Ute Mountain Ute Ute Mountain Ute C44212 Population Group Wailaki C1551658 Wailaki Wailaki Wailaki C44213 Population Group Walla-Walla C1551659 Walla_Walla Walla-Walla Walla-Walla C44214 Population Group Wampanoag C1551660 Wampanoag Wampanoag Wampanoag C44215 Population Group Gay Head Wampanoag C1551661 Gay_Head_Wampanoag Gay Head Wampanoag Gay Head Wampanoag C44216 Population Group Mashpee Wampanoag C1551662 Mashpee_Wampanoag Mashpee Wampanoag Mashpee Wampanoag C44217 Population Group Warm Springs C1551663 Warm_Springs Warm Springs Warm Springs C44218 Population Group Wascopum C1551664 Wascopum Wascopum Wascopum C44219 Population Group Washoe C1551665 Washoe Washoe Washoe C44220 Population Group Alpine C1551666 Alpine Alpine Alpine C44221 Population Group Carson C1551667 Carson Carson Carson C44222 Population Group Dresslerville C1551668 Dresslerville Dresslerville Dresslerville C44223 Population Group Wichita C1551669 Wichita Wichita Wichita C44224 Population Group Wind River C1551670 Wind_River Wind River Wind River C44225 Population Group Winnebago C1551671 Winnebago Winnebago Winnebago C44226 Population Group Ho-Chunk C1551672 Ho_Chunk Ho-Chunk Ho-Chunk C44227 Population Group Nebraska Winnebago C1551673 Nebraska_Winnebago Nebraska Winnebago Nebraska Winnebago C44228 Population Group Winnemucca C1551674 Winnemucca Winnemucca Winnemucca C44229 Population Group Wintun C1551675 Wintun Wintun Wintun C44230 Population Group Wiyot C1551676 Wiyot Wiyot Wiyot C44231 Population Group Table Bluff C1551677 Table_Bluff Table Bluff Table Bluff C44232 Population Group Yakama C1551678 Yakama Yakama Yakama C44233 Population Group Yakama Cowlitz C1551679 Yakama_Cowlitz Yakama Cowlitz Yakama Cowlitz C44234 Population Group Yaqui C1551680 Yaqui Yaqui Yaqui C44236 Population Group Barrio Libre C1551681 Barrio_Libre Barrio Libre Barrio Libre C44237 Population Group Pascua Yaqui C1551682 Pascua_Yaqui Pascua Yaqui Pascua Yaqui C44238 Population Group Yavapai Apache C1551683 Yavapai_Apache Yavapai Apache Yavapai Apache C44239 Population Group Yokuts C1551684 Yokuts Yokuts Yokuts C44240 Population Group Chukchansi C1551685 Chukchansi Chukchansi Chukchansi C44241 Population Group Tachi C1551686 Tachi Tachi Tachi C44242 Population Group Tule River C1551687 Tule_River Tule River Tule River C44244 Population Group Yuchi C1551688 Yuchi Yuchi Yuchi C44245 Population Group Yuman C1551689 Yuman Yuman Yuman C44246 Population Group Cocopah C1551690 Cocopah Cocopah Cocopah C44247 Population Group Havasupai C1551691 Havasupai Havasupai Havasupai C44248 Population Group Hualapai C1551692 Hualapai Hualapai Hualapai C44249 Population Group Maricopa C1551693 Maricopa Maricopa Maricopa C44250 Population Group Mohave C1551694 Mohave Mohave Mohave C44251 Population Group Quechan C1551695 Quechan Quechan Quechan C44252 Population Group Yurok C1551697 Yurok Yurok Yurok C44253 Population Group Coast Yurok C1551698 Coast_Yurok Coast Yurok Coast Yurok C44254 Population Group Alaskan Athabascan C1551699 Alaskan_Athabascan Alaskan Athabascan Alaskan Athabascan C44257 Population Group Southeast Alaska C1551770 Southeast_Alaska Southeast Alaska Southeast Alaska C44259 Population Group Tlingit-Haida C1551771 Tlingit_Haida Tlingit-Haida Tlinit-Haida Tlingit-Haida C44261 Population Group Tsimshian C1551792 Tsimshian Tsimshian Tsimshian C44263 Population Group Metlakatla C1551793 Metlakatla Metlakatla Metlakatla C44265 Population Group Greenland Eskimo C1551794 The native people of Greenland. Greenland_Eskimo GREENLAND INUIT Greenland Eskimo Greenland Eskimo C44268 Population Group Inupiat Eskimo C1551795 The native people inhabiting the territory spanning the Norton Sound on the Bering Sea to the Canadian border. Inupiat_Eskimo INUPIAT INUIT Inupiat Eskimo Inupiat Eskimo C44269 Population Group Siberian Eskimo C1551841 The native Yupik people inhabiting the coast of the Chukchi Peninsula in the far northeast of the Russian Federation and on St. Lawrence Island in Alaska. Siberian_Eskimo SIBERIAN ESKIMO Siberian Eskimo Siberian Eskimo C44270 Population Group Yupik Eskimo C1551845 The native people inhabiting western, southwestern, and southcentral Alaska and the Russian Far East. Yupik_Eskimo YUPIK ESKIMO Yupik Eskimo Yupik Eskimo C44286 Population Group Alutiiq Aleut C1553271 Alutiiq_Aleut Alutiiq Aleut Alutiiq Aleut C44287 Population Group Tatitlek C1553272 Tatitlek Tatitlek Tatitlek C44288 Population Group Ugashik C1553273 Ugashik Ugashik Ugashik C44289 Population Group Bristol Bay Aleut C1553507 Bristol_Bay_Aleut Bristol Bay Aleut Bristol Bay Aleut C44290 Population Group Chugach Aleut C1553284 Chugach_Aleut Chugach Aleut Chugach Aleut C44486 Population Group Eyak C1553289 Eyak Eyak Eyak C44487 Population Group Koniag Aleut C1553290 Koniag_Aleut Koniag Aleut Koniag Aleut C44488 Population Group Sugpiaq C1553299 Sugpiaq Sugpiaq Sugpiaq C44489 Population Group Suqpigaq C1553300 Suqpigaq Suqpigaq Suqpigaq C44490 Population Group Unangan Aleut C1553301 Unangan_Aleut Unangan Aleut Unangan Aleut C44491 Population Group Chenega C1553285 Chenega Chenega Chenega C44492 Population Group Chugach Corporation C1553286 Chugach_Corporation Chugach Corporation Chugach Corporation C44493 Population Group English Bay C1553287 English_Bay English Bay English Bay C44494 Population Group Port Graham C1553288 Port_Graham Port Graham Port Graham C44495 Population Group Akhiok C1553291 Akhiok Akhiok Akhiok C44496 Population Group Agdaagux C1553292 Agdaagux Agdaagux Agdaagux C44497 Population Group Karluk C1553293 Karluk Karluk Karluk C44498 Population Group Kodiak C1553294 Kodiak Kodiak Kodiak C44499 Population Group Larsen Bay C1553295 Larsen_Bay Larsen Bay Larsen Bay C44500 Population Group Old Harbor C1553296 Old_Harbor Old Harbor Old Harbor C44501 Population Group Ouzinkie C1553297 Ouzinkie Ouzinkie Ouzinkie C44502 Population Group Port Lions C1553298 Port_Lions Port Lions Port Lions C44503 Population Group Gambell C1551842 Gambell Gambell Gambell C44504 Population Group Savoonga C1551843 Savoonga Savoonga Savoonga C44505 Population Group Siberian Yupik C1551844 Siberian_Yupik Siberian Yupik Siberian Yupik C44506 Population Group Cahto C1555070 Cahto Cahto Cahto C44507 Population Group Chimariko C1555071 Chimariko Chimariko Chimariko C44508 Population Group Coast Miwok C1555072 Coast_Miwok Coast Miwok Coast Miwok C44509 Population Group Digger C1555073 Digger Digger Digger C44510 Population Group Kawaiisu C1555074 Kawaiisu Kawaiisu Kawaiisu C44511 Population Group Kern River C1555075 Kern_River Kern River Kern River C44512 Population Group Mattole C1555076 Mattole Mattole Mattole C44513 Population Group Red Wood C1555077 Red_Wood Red Wood Red Wood C44514 Population Group Santa Rosa C1555078 Santa_Rosa Santa Rosa Santa Rosa C44515 Population Group Takelma C1555079 Takelma Takelma Takelma C44516 Population Group Wappo C1555080 Wappo Wappo Wappo C44517 Population Group Yana C1555081 Yana Yana Yana C44518 Population Group Yuki C1555082 Yuki Yuki Yuki C44525 Population Group Campo C1555189 Campo Campo Campo C44526 Population Group Capitan Grande C1555190 Capitan_Grande Capitan Grande Capitan Grande C44527 Population Group Cuyapaipe C1555191 Cuyapaipe Cuyapaipe Cuyapaipe C44528 Population Group La Posta C1555192 La_Posta La Posta La Posta C44529 Population Group Manzanita C1555193 Manzanita Manzanita Manzanita C44530 Population Group Mesa Grande C1555194 Mesa_Grande Mesa Grande Mesa Grande C44531 Population Group San Pasqual C1555195 San_Pasqual San Pasqual San Pasqual C44532 Population Group Santa Ysabel C1555196 Santa_Ysabel Santa Ysabel Santa Ysabel C44533 Population Group Sycuan C1555197 Sycuan Sycuan Sycuan C44534 Population Group Bishop C1551458 Bishop Bishop Bishop C44535 Population Group Bridgeport C1551459 Bridgeport Bridgeport Bridgeport C44536 Population Group Burns Paiute C1551460 Burns_Paiute Burns Paiute Burns Paiute C44537 Population Group Cedarville C1551461 Cedarville Cedarville Cedarville C44538 Population Group Fort Bidwell C1551462 Fort_Bidwell Fort Bidwell Fort Bidwell C44539 Population Group Fort Independence C1551463 Fort_Independence Fort Independence Fort Independence C44540 Population Group Kaibab C1551464 Kaibab Kaibab Kaibab C44541 Population Group Las Vegas C1551465 Las_Vegas Las Vegas Las Vegas C44542 Population Group Lone Pine C1551466 Lone_Pine Lone Pine Lone Pine C44543 Population Group Lovelock C1551467 Lovelock Lovelock Lovelock C44544 Population Group Malheur Paiute C1551468 Malheur_Paiute Malheur Paiute Malheur Paiute C44545 Population Group Moapa C1551469 Moapa Moapa Moapa C44546 Population Group Northern Paiute C1551470 Northern_Paiute Northern Paiute Northern Paiute C44547 Population Group Owens Valley C1551471 Owens_Valley Owens Valley Owens Valley C44548 Population Group Pyramid Lake C1551472 Pyramid_Lake Pyramid Lake Pyramid Lake C44549 Population Group San Juan Southern Paiute C1551473 San_Juan_Southern_Paiute San Juan Southern Paiute San Juan Southern Paiute C44550 Population Group Southern Paiute C1551474 Southern_Paiute Southern Paiute Southern Paiute C44551 Population Group Summit Lake C1551475 Summit_Lake Summit Lake Summit Lake C44552 Population Group Utu Utu Gwaitu Paiute C1551476 Utu_Utu_Gwaitu_Paiute Utu Utu Gwaitu Paiute Utu Utu Gwaitu Paiute C44553 Population Group Walker River C1551477 Walker_River Walker River Walker River C44554 Population Group Yerington Paiute C1551478 Yerington_Paiute Yerington Paiute Yerington Paiute C44555 Population Group Battle Mountain C1551588 Battle_Mountain Battle Mountain Battle Mountain C44556 Population Group Duckwater C1551589 Duckwater Duckwater Duckwater C44557 Population Group Elko C1551590 Elko Elko Elko C44558 Population Group Ely C1551591 Ely Ely Ely C44559 Population Group Goshute C1551592 Goshute Goshute Goshute C44560 Population Group Panamint C1551593 Panamint Panamint Panamint C44561 Population Group Ruby Valley C1551594 Ruby_Valley Ruby Valley Ruby Valley C44562 Population Group Skull Valley C1551595 Skull_Valley Skull Valley Skull Valley C44563 Population Group South Fork Shoshone C1551596 South_Fork_Shoshone South Fork Shoshone South Fork Shoshone C44564 Population Group Te Moak Western Shoshone C1551597 Te_Moak_Western_Shoshone Te Moak Western Shoshone Te-Moak Western Shoshone Te Moak Western Shoshone C44565 Population Group Timbi Sha Shoshone C1551598 Timbi_Sha_Shoshone Timbi Sha Shoshone Timbi-Sha Shoshone Timbi Sha Shoshone C44566 Population Group Washakie C1551599 Washakie Washakie Washakie C44567 Population Group Wind River Shoshone C1551600 Wind_River_Shoshone Wind River Shoshone Wind River Shoshone C44568 Population Group Yomba C1551601 Yomba Yomba Yomba C44569 Population Group Akiachak C1551846 Akiachak Akiachak Akiachak C44570 Population Group Akiak C1551847 Akiak Akiak Akiak C44571 Population Group Alakanuk C1551848 Alakanuk Alakanuk Alakanuk C44572 Population Group Aleknagik C1551849 Aleknagik Aleknagik Aleknagik C44573 Population Group Andreafsky C1551850 Andreafsky Andreafsky Andreafsky C44574 Population Group Aniak C1551851 Aniak Aniak Aniak C44575 Population Group Atmautluak C1551852 Atmautluak Atmautluak Atmautluak C44576 Population Group Bethel C1551853 Bethel Bethel Bethel C44577 Population Group Bill Moore's Slough C1551854 Bill_Moore_s_Slough Bill Moore's Slough Bill Moore's Slough C44578 Population Group Bristol Bay Yupik C1551855 Bristol_Bay_Yupik Bristol Bay Yupik Bristol Bay Yupik C44579 Population Group Calista Yupik C1551856 Calista_Yupik Calista Yupik Calista Yupik C44580 Population Group Chefornak C1551857 Chefornak Chefornak Chefornak C44581 Population Group Chevak C1551858 Chevak Chevak Chevak C44582 Population Group Chuathbaluk C1551859 Chuathbaluk Chuathbaluk Chuathbaluk C44583 Population Group Clark's Point C1551860 Clark_s_Point Clark's Point Clark's Point C44584 Population Group Crooked Creek C1551861 Crooked_Creek Crooked Creek Crooked Creek C44585 Population Group Dillingham C1551862 Dillingham Dillingham Dillingham C44586 Population Group Eek C1551863 Eek Eek Eek C44587 Population Group Ekuk C1551864 Ekuk Ekuk Ekuk C44588 Population Group Ekwok C1551865 Ekwok Ekwok Ekwok C44589 Population Group Emmonak C1551866 Emmonak Emmonak Emmonak C44590 Population Group Goodnews Bay C1551867 Goodnews_Bay Goodnews Bay Goodnews Bay C44591 Population Group Hooper Bay C1551868 Hooper_Bay Hooper Bay Hooper Bay C44592 Population Group Iqurmuit Russian Mission C1551869 Iqurmuit_Russian_Mission Iqurmuit (Russian Mission) Iqurmuit Russian Mission Iqurmuit Russian Mission C44593 Population Group Kalskag C1551870 Kalskag Kalskag Kalskag C44594 Population Group Kasigluk C1551871 Kasigluk Kasigluk Kasigluk C44595 Population Group Kipnuk C1551872 Kipnuk Kipnuk Kipnuk C44596 Population Group Koliganek C1551873 Koliganek Koliganek Koliganek C44597 Population Group Kongiganak C1551874 Kongiganak Kongiganak Kongiganak C44598 Population Group Kotlik C1551875 Kotlik Kotlik Kotlik C44599 Population Group Kwethluk C1551876 Kwethluk Kwethluk Kwethluk C44600 Population Group Kwigillingok C1551877 Kwigillingok Kwigillingok Kwigillingok C44601 Population Group Levelock C1551878 Levelock Levelock Levelock C44602 Population Group Lower Kalskag C1551879 Lower_Kalskag Lower Kalskag Lower Kalskag C44603 Population Group Manokotak C1551880 Manokotak Manokotak Manokotak C44604 Population Group Marshall C1551881 Marshall Marshall Marshall C44605 Population Group Mekoryuk C1551882 Mekoryuk Mekoryuk Mekoryuk C44606 Population Group Mountain Village C1551883 Mountain_Village Mountain Village Mountain Village C44607 Population Group Naknek C1551884 Naknek Naknek Naknek C44608 Population Group Napaumute C1551885 Napaumute Napaumute Napaumute C44609 Population Group Napakiak C1551886 Napakiak Napakiak Napakiak C44610 Population Group Napaskiak C1551887 Napaskiak Napaskiak Napaskiak C44611 Population Group Newhalen C1553245 Newhalen Newhalen Newhalen C44612 Population Group New Stuyahok C1553246 New_Stuyahok New Stuyahok New Stuyahok C44613 Population Group Newtok C1553247 Newtok Newtok Newtok C44614 Population Group Nightmute C1553248 Nightmute Nightmute Nightmute C44615 Population Group Nunapitchukv C1553249 Nunapitchukv Nunapitchukv Nunapitchukv C44616 Population Group Oscarville C1553250 Oscarville Oscarville Oscarville C44617 Population Group Pilot Station C1553251 Pilot_Station Pilot Station Pilot Station C44618 Population Group Pitkas Point C1553252 Pitkas_Point Pitkas Point Pitkas Point C44619 Population Group Portage Creek C1553254 Portage_Creek Portage Creek Portage Creek C44620 Population Group Quinhagak C1553255 Quinhagak Quinhagak Quinhagak C44621 Population Group Red Devil C1553256 Red_Devil Red Devil Red Devil C44623 Population Group Scammon Bay C1553258 Scammon_Bay Scammon Bay Scammon Bay C44624 Population Group Sheldon's Point C1553259 Sheldon_s_Point Sheldon's Point Sheldon's Point C44625 Population Group Sleetmute C1553260 Sleetmute Sleetmute Sleetmute C44626 Population Group Stebbins C1553261 Stebbins Stebbins Stebbins C44627 Population Group Togiak C1553262 Togiak Togiak Togiak C44628 Population Group Toksook C1553263 Toksook Toksook Toksook C44629 Population Group Tulukskak C1553264 Tulukskak Tulukskak Tulukskak C44630 Population Group Tuntutuliak C1553265 Tuntutuliak Tuntutuliak Tuntutuliak C44631 Population Group Tununak C1553266 Tununak Tununak Tununak C44632 Population Group Twin Hills C1553267 Twin_Hills Twin Hills Twin Hills C44633 Population Group Georgetown C1553268 Georgetown Georgetown Georgetown C44635 Population Group Umkumiate C1553270 Umkumiate Umkumiate Umkumiate C44636 Population Group Akutan C1553302 Akutan Akutan Akutan C44637 Population Group Aleut Corporation C1553303 Aleut_Corporation Aleut Corporation Aleut Corporation C44638 Population Group Aleutian Islander C1553305 Aleutian_Islander Aleutian Islander Aleutian Islander C44639 Population Group Atka C1553306 Atka Atka Atka C44640 Population Group Belkofski C1553307 Belkofski Belkofski Belkofski C44641 Population Group Chignik Lagoon C1553308 Chignik_Lagoon Chignik Lagoon Chignik Lagoon C44642 Population Group King Cove C1553309 King_Cove King Cove King Cove C44643 Population Group False Pass C1553310 False_Pass False Pass False Pass C44644 Population Group Nelson Lagoon C1553311 Nelson_Lagoon Nelson Lagoon Nelson Lagoon C44645 Population Group Nikolski C1553312 Nikolski Nikolski Nikolski C44646 Population Group Pauloff Harbor C1553313 Pauloff_Harbor Pauloff Harbor Pauloff Harbor C44647 Population Group Qagan Toyagungin C1553314 Qagan_Toyagungin Qagan Toyagungin Qagan Toyagungin C44648 Population Group Qawalangin C1553315 Qawalangin Qawalangin Qawalangin C44651 Population Group Sand Point C1553318 Sand_Point Sand Point Sand Point C44652 Population Group South Naknek C1553319 South_Naknek South Naknek South Naknek C44653 Population Group Unalaska C1553320 Unalaska Unalaska Unalaska C44654 Population Group Unga C1553321 Unga Unga Unga C44655 Population Group Chignik C1553274 Chignik Chignik Chignik C44656 Population Group Chignik Lake C1553275 Chignik_Lake Chignik Lake Chignik Lake C44657 Population Group Egegik C1553276 Egegik Egegik Egegik C44658 Population Group Igiugig C1553277 Igiugig Igiugig Igiugig C44659 Population Group Ivanof Bay C1553278 Ivanof_Bay Ivanof Bay Ivanof Bay C44660 Population Group King Salmon C1553279 King_Salmon King Salmon King Salmon C44661 Population Group Kokhanok C1553280 Kokhanok Kokhanok Kokhanok C44662 Population Group Perryville C1553281 Perryville Perryville Perryville C44663 Population Group Pilot Point C1553282 Pilot_Point Pilot Point Pilot Point C44664 Population Group Port Heiden C1553283 Port_Heiden Port Heiden Port Heiden C44665 Population Group Ambler C1551796 Ambler Ambler Ambler C44666 Population Group Anaktuvuk C1551797 Anaktuvuk Anaktuvuk Anaktuvuk C44667 Population Group Anaktuvuk Pass C1551798 Anaktuvuk_Pass Anaktuvuk Pass Anaktuvuk Pass C44668 Population Group Arctic Slope Inupiat C1551799 Arctic_Slope_Inupiat Arctic Slope Inupiat Arctic Slope Inupiat C44669 Population Group Arctic Slope Corporation C1551800 Arctic_Slope_Corporation Arctic Slope Corporation Arctic Slope Corporation C44670 Population Group Atqasuk C1551801 Atqasuk Atqasuk Atqasuk C44671 Population Group Barrow C1551802 Barrow Barrow Barrow C44672 Population Group Bering Straits Inupiat C1551803 Bering_Straits_Inupiat Bering Straits Inupiat Bering Straits Inupiat C44673 Population Group Brevig Mission C1551804 Brevig_Mission Brevig Mission Brevig Mission C44674 Population Group Buckland C1551805 Buckland Buckland Buckland C44675 Population Group Chinik C1551806 Chinik Chinik Chinik C44676 Population Group Council C1551807 Council Council Council C44677 Population Group Deering C1551808 Deering Deering Deering C44678 Population Group Elim C1551809 Elim Elim Elim C44679 Population Group Golovin C1551810 Golovin Golovin Golovin C44680 Population Group Inalik Diamede C1551811 Inalik_Diamede Inalik Diamede Inalik Diomede Inalik Diamede C44681 Population Group Inupiaq C1551812 Inupiaq Inupiaq Inupiaq C44682 Population Group Kaktovik C1551813 Kaktovik Kaktovik Kaktovik C44683 Population Group Kawerak C1551814 Kawerak Kawerak Kawerak C44684 Population Group Kiana C1551815 Kiana Kiana Kiana C44685 Population Group Kivalina C1551816 Kivalina Kivalina Kivalina C44686 Population Group Kobuk C1551817 Kobuk Kobuk Kobuk C44687 Population Group Kotzebue C1551818 Kotzebue Kotzebue Kotzebue C44688 Population Group Koyuk C1551819 Koyuk Koyuk Koyuk C44689 Population Group Kwiguk C1551820 Kwiguk Kwiguk Kwiguk C44690 Population Group Mauneluk Inupiat C1551821 Mauneluk_Inupiat Mauneluk Inupiat Mauneluk Inupiat C44691 Population Group Nana Inupiat C1551822 Nana_Inupiat Nana Inupiat Nana Iñupiat Nana Inupiat C44692 Population Group Noatak C1551823 Noatak Noatak Noatak C44693 Population Group Nome C1551824 Nome Nome Nome C44694 Population Group Noorvik C1551825 Noorvik Noorvik Noorvik C44695 Population Group Nuiqsut C1551826 Nuiqsut Nuiqsut Nuiqsut C44696 Population Group Point Hope C1551827 Point_Hope Point Hope Point Hope C44697 Population Group Point Lay C1551828 Point_Lay Point Lay Point Lay C44698 Population Group Selawik C1551829 Selawik Selawik Selawik C44699 Population Group Shaktoolik C1551830 Shaktoolik Shaktoolik Shaktoolik C44700 Population Group Shishmaref C1551831 Shishmaref Shishmaref Shishmaref C44701 Population Group Shungnak C1551832 Shungnak Shungnak Shungnak C44702 Population Group Solomon C1551833 Solomon Solomon Solomon C44703 Population Group Teller C1551834 Teller Teller Teller C44704 Population Group Unalakleet C1551835 Unalakleet Unalakleet Unalakleet C44705 Population Group Wainwright C1551836 Wainwright Wainwright Wainwright C44706 Population Group Wales C1551837 Wales Wales Wales C44707 Population Group White Mountain C1551838 White_Mountain White Mountain White Mountain C44708 Population Group White Mountain Inupiat C1551839 White_Mountain_Inupiat White Mountain Inupiat White Mountain Inupiat C44709 Population Group Mary's Igloo C1551840 Mary_s_Igloo Mary's Igloo Mary's Igloo C44710 Population Group Angoon C1551772 Angoon Angoon Angoon C44711 Population Group Central Council of Tlingit and Haida Tribes C1551773 Central_Council_of_Tlingit_and_Haida_Tribes Central Council of Tlingit and Haida Tribes Central Council of Tlingit and Haida Tribes C44712 Population Group Chilkat C1551774 Chilkat Chilkat Chilkat C44713 Population Group Chilkoot C1551775 Chilkoot Chilkoot Chilkoot C44714 Population Group Craig C1551776 Craig Craig Craig C44715 Population Group Douglas C1551777 Douglas Douglas Douglas C44716 Population Group Haida C0682117 Haida Haida Haida C44717 Population Group Hoonah C1551778 Hoonah Hoonah Hoonah C44718 Population Group Hydaburg C1551779 Hydaburg Hydaburg Hydaburg C44719 Population Group Kake C1551780 Kake Kake Kake C44720 Population Group Kasaan C1551781 Kasaan Kasaan Kasaan C44721 Population Group Kenaitze C1551782 Kenaitze Kenaitze Kenaitze C44722 Population Group Ketchikan C1551783 Ketchikan Ketchikan Ketchikan C44723 Population Group Klawock C1551784 Klawock Klawock Klawock C44724 Population Group Pelican C1551785 Pelican Pelican Pelican C44725 Population Group Petersburg C1551786 Petersburg Petersburg Petersburg C44726 Population Group Saxman C1551787 Saxman Saxman Saxman C44727 Population Group Sitka C1551788 Sitka Sitka Sitka C44728 Population Group Tenakee Springs C1551789 Tenakee_Springs Tenakee Springs Tenakee Springs C44729 Population Group Tlingit C0682118 Tlingit Tlingit Tlingit C44730 Population Group Wrangell C1551790 Wrangell Wrangell Wrangell C44731 Population Group Yakutat C1551791 Yakutat Yakutat Yakutat C44732 Population Group Ahtna C1551700 Ahtna Ahtna Ahtna C44733 Population Group Alatna CL334372 Alatna Alatna Alatna C44734 Population Group Alexander C1551702 Alexander Alexander Alexander C44735 Population Group Allakaket C1551703 Allakaket Allakaket Allakaket C44736 Population Group Alanvik C1551704 Alanvik Alanvik Alanvik C44737 Population Group Anvik C1551705 Anvik Anvik Anvik C44738 Population Group Arctic CL337306 Arctic Arctic Arctic C44739 Population Group Beaver C1551707 Beaver Beaver Beaver C44740 Population Group Birch Creek C1551708 Birch_Creek Birch Creek Birch Creek C44741 Population Group Cantwell C1551709 Cantwell Cantwell Cantwell C44742 Population Group Chalkyitsik C1551710 Chalkyitsik Chalkyitsik Chalkyitsik C44743 Population Group Chickaloon C1551711 Chickaloon Chickaloon Chickaloon C44744 Population Group Chistochina C1551712 Chistochina Chistochina Chistochina C44745 Population Group Chitina C1551713 Chitina Chitina Chitina C44746 Population Group Circle Tribe C1551714 Circle_Tribe Circle Circle Tribe Circle Tribe C44747 Population Group Cook Inlet C1551715 Cook_Inlet Cook Inlet Cook Inlet C44748 Population Group Copper Center C1551716 Copper_Center Copper Center Copper Center C44749 Population Group Copper River C1551717 Copper_River Copper River Copper River C44750 Population Group Dot Lake C1551718 Dot_Lake Dot Lake Dot Lake C44751 Population Group Doyon C1551719 Doyon Doyon Doyon C44752 Population Group Eagle C1551720 Eagle Eagle Eagle C44753 Population Group Eklutna C1551721 Eklutna Eklutna Eklutna C44754 Population Group Evansville C1551722 Evansville Evansville Evansville C44755 Population Group Fort Yukon C1551723 Fort_Yukon Fort Yukon Fort Yukon C44756 Population Group Gakona C1551724 Gakona Gakona Gakona C44757 Population Group Galena C1551725 Galena Galena Galena C44758 Population Group Grayling C1551726 Grayling Grayling Grayling C44759 Population Group Gulkana C1551727 Gulkana Gulkana Gulkana C44760 Population Group Healy Lake C1551728 Healy_Lake Healy Lake Healy Lake C44761 Population Group Holy Cross C1551729 Holy_Cross Holy Cross Holy Cross C44762 Population Group Hughes C1551730 Hughes Hughes Hughes C44763 Population Group Huslia C1551731 Huslia Huslia Huslia C44764 Population Group Iliamna C1551732 Iliamna Iliamna Iliamna C44765 Population Group Kaltag C1551733 Kaltag Kaltag Kaltag C44766 Population Group Kluti Kaah C1551734 Kluti_Kaah Kluti Kaah Kluti Kaah C44767 Population Group Knik C1551735 Knik Knik Knik C44768 Population Group Koyukuk C1551736 Koyukuk Koyukuk Koyukuk C44769 Population Group Lake Minchumina C1551737 Lake_Minchumina Lake Minchumina Lake Minchumina C44770 Population Group Lime C1551738 Lime Lime Lime C44771 Population Group Mcgrath C1551739 Mcgrath Mcgrath Mcgrath C44772 Population Group Manley Hot Springs C1551740 Manley_Hot_Springs Manley Hot Springs Manley Hot Springs C44773 Population Group Mentasta Lake C1551741 Mentasta_Lake Mentasta Lake Mentasta Lake C44774 Population Group Minto CL334407 Minto Minto Minto C44775 Population Group Nenana C1551743 Nenana Nenana Nenana C44776 Population Group Nikolai C1551744 Nikolai Nikolai Nikolai C44777 Population Group Ninilchik C1551745 Ninilchik Ninilchik Ninilchik C44778 Population Group Nondalton C1551746 Nondalton Nondalton Nondalton C44779 Population Group Northway C1551747 Northway Northway Northway C44780 Population Group Nulato C1551748 Nulato Nulato Nulato C44781 Population Group Pedro Bay C1551749 Pedro_Bay Pedro Bay Pedro Bay C44782 Population Group Rampart C1551750 Rampart Rampart Rampart C44783 Population Group Ruby C1551751 Ruby Ruby Ruby C44784 Population Group Salamatof CL334417 Salamatof Salamatof Salamatof C44785 Population Group Seldovia C1551753 Seldovia Seldovia Seldovia C44786 Population Group Slana C1551754 Slana Slana Slana C44787 Population Group Shageluk C1551755 Shageluk Shageluk Shageluk C44788 Population Group Stevens CL334421 Stevens Stevens Stevens C44789 Population Group Stony River C1551757 Stony_River Stony River Stony River C44790 Population Group Takotna C1551758 Takotna Takotna Takotna C44791 Population Group Tanacross C1551759 Tanacross Tanacross Tanacross C44792 Population Group Tanaina C1551760 Tanaina Tanaina Tanaina C44793 Population Group Tanana C1551761 Tanana Tanana Tanana C44794 Population Group Tanana Chiefs C1551762 Tanana_Chiefs Tanana Chiefs Tanana Chiefs C44795 Population Group Tazlina CL334428 Tazlina Tazlina Tazlina C44796 Population Group Telida C1551764 Telida Telida Telida C44797 Population Group Tetlin C1551765 Tetlin Tetlin Tetlin C44798 Population Group Tok C1551766 Tok Tok Tok C44799 Population Group Tyonek C1551767 Tyonek Tyonek Tyonek C44800 Population Group Venetie C1551768 Venetie Venetie Venetie C44801 Population Group Wiseman C1551769 Wiseman Wiseman Wiseman C44802 Population Group Duwamish C1551540 Duwamish Duwamish Duwamish C44803 Population Group Kikiallus C1551541 Kikiallus Kikiallus Kikiallus C44804 Population Group Lower Skagit C1551542 Lower_Skagit Lower Skagit Lower Skagit C44805 Population Group Muckleshoot C1551543 Muckleshoot Muckleshoot Muckleshoot C44806 Population Group Nisqually C1551544 Nisqually Nisqually Nisqually C44807 Population Group Nooksack C1551545 Nooksack Nooksack Nooksack C44808 Population Group Port Madison C1551546 Port_Madison Port Madison Port Madison C44809 Population Group Puyallup C1551547 Puyallup Puyallup Puyallup C44810 Population Group Samish C1551548 Samish Samish Samish C44811 Population Group Sauk-Suiattle C1551549 Sauk-Suiattle Sauk-Suiattle Sauk-Suiattle C44812 Population Group Skokomish C1551550 Skokomish Skokomish Skokomish C44813 Population Group Skykomish C1551551 Skykomish Skykomish Skykomish C44814 Population Group Snohomish C1551552 Snohomish Snohomish Snohomish C44815 Population Group Snoqualmie C1551553 Snoqualmie Snoqualmie Snoqualmie C44816 Population Group Squaxin Island C1551554 Squaxin_Island Squaxin Island Squaxin Island C44817 Population Group Steilacoom C1551555 Steilacoom Steilacoom Steilacoom C44818 Population Group Stillaguamish C1551556 Stillaguamish Stillaguamish Stillaguamish C44819 Population Group Suquamish C1551557 Suquamish Suquamish Suquamish C44820 Population Group Swinomish C1551558 Swinomish Swinomish Swinomish C44821 Population Group Tulalip C1551559 Tulalip Tulalip Tulalip C44822 Population Group Upper Skagit C1551560 Upper_Skagit Upper Skagit Upper Skagit C44823 Population Group Acoma C1551514 Acoma Acoma Acoma C44824 Population Group Arizona Tewa C1551515 Arizona_Tewa Arizona Tewa Arizona Tewa C44825 Population Group Cochiti C1551516 Cochiti Cochiti Cochiti C44826 Population Group Hopi C0682111 Hopi Hopi Hopi C44827 Population Group Isleta C1551517 Isleta Isleta Isleta C44828 Population Group Jemez C1551518 Jemez Jemez Jemez C44829 Population Group Keres C1551519 Keres Keres Keres C44830 Population Group Laguna C1551520 Laguna Laguna Laguna C44831 Population Group Nambe C1551521 Nambe Nambe Nambe C44832 Population Group Picuris C1551522 Picuris Picuris Picuris C44833 Population Group Piro C1551523 Piro Piro Piro C44834 Population Group Pojoaque C1551524 Pojoaque Pojoaque Pojoaque C44835 Population Group San Felipe C1551525 San_Felipe San Felipe San Felipe C44836 Population Group San Ildefonso C1551526 San_Ildefonso San Ildefonso San Ildefonso C44837 Population Group San Juan Pueblo C1551527 San_Juan_Pueblo San Juan Pueblo San Juan Pueblo C44838 Population Group San Juan De C1551528 San_Juan_De San Juan De San Juan De C44839 Population Group San Juan C1551529 San_Juan San Juan San Juan C44840 Population Group Sandia C1551530 Sandia Sandia Sandia C44841 Population Group Santa Ana C1551531 Santa_Ana Santa Ana Santa Ana C44842 Population Group Santa Clara C1551532 Santa_Clara Santa Clara Santa Clara C44843 Population Group Santo Domingo C1551533 Santo_Domingo Santo Domingo Santo Domingo C44844 Population Group Taos C1551534 Taos Taos Taos C44845 Population Group Tesuque C1551535 Tesuque Tesuque Tesuque C44846 Population Group Tewa C1551536 Tewa Tewa Tewa C44847 Population Group Tigua C1551537 Tigua Tigua Tigua C44848 Population Group Zia C1551538 Zia Zia Zia C44849 Population Group Zuni C0682110 Zuni Zuni Zuñi Zuni C44850 Population Group Citzen Band Potawatomi C1551506 Citzen_Band_Potawatomi Citizen Band Potawatomi Citzen Band Potawatomi Citzen Band Potawatomi C44851 Population Group Forest County C1551507 Forest_County Forest County Forest County C44852 Population Group Hannahville C1551508 Hannahville Hannahville Hannahville C44853 Population Group Huron Potawatomi C1551509 Huron_Potawatomi Huron Potawatomi Huron Potawatomi C44854 Population Group Pokagon Potawatomi C1551510 Pokagon_Potawatomi Pokagon Potawatomi Pokagon Potawatomi C44855 Population Group Prairie Band C1551511 Prairie_Band Prairie Band Prairie Band C44856 Population Group Wisconsin Potawatomi C1551512 Wisconsin_Potawatomi Wisconsin Potawatomi Wisconsin Potawatomi C44857 Population Group Central Pomo C1551494 Central_Pomo Central Pomo Central Pomo C44858 Population Group Dry Creek C1551495 Dry_Creek Dry Creek Dry Creek C44859 Population Group Eastern Pomo C1551496 Eastern_Pomo Eastern Pomo Eastern Pomo C44860 Population Group Kashia C1551497 Kashia Kashia Kashia C44861 Population Group Northern Pomo C1551498 Northern_Pomo Northern Pomo Northern Pomo C44862 Population Group Scotts Valley C1551499 Scotts_Valley Scotts Valley Scotts Valley C44863 Population Group Stonyford C1551500 Stonyford Stonyford Stonyford C44864 Population Group Sulphur Bank C1551501 Sulphur_Bank Sulphur Bank Sulphur Bank C44865 Population Group Cayuga C1555234 Cayuga Cayuga Cayuga C44866 Population Group Mohawk C0682099 Mohawk Mohawk Mohawk C44867 Population Group Oneida C1555235 Oneida Oneida Oneida C44868 Population Group Onondaga C1555236 Onondaga Onondaga Onondaga C44869 Population Group Seneca C1555237 Seneca Seneca Seneca C44870 Population Group Seneca Nation C1555238 Seneca_Nation Seneca Nation Seneca Nation C44871 Population Group Seneca-Cayuga C1555239 Seneca-Cayuga Seneca-Cayuga Seneca-Cayuga C44872 Population Group Tonawanda Seneca C1555240 Tonawanda_Seneca Tonawanda Seneca Tonawanda Seneca C44873 Population Group Tuscarora C1555241 Tuscarora Tuscarora Tuscarora C44874 Population Group Wyandotte C1555242 Wyandotte Wyandotte Wyandotte C44875 Population Group Attacapa C1555199 Attacapa Attacapa Attacapa C44876 Population Group Biloxi C1555200 Biloxi Biloxi Biloxi C44877 Population Group Moor C1555202 Moor Moor Moor C44878 Population Group Nansemond C1555203 Nansemond Nansemond Nansemond C44879 Population Group Natchez C1555204 Natchez Natchez Natchez C44880 Population Group Nausu Waiwash C1555205 Nausu_Waiwash Nausu Waiwash Nausu Waiwash C44881 Population Group Nipmuc C1555206 Nipmuc Nipmuc Nipmuc C44882 Population Group Paugussett C1555207 Paugussett Paugussett Paugussett C44883 Population Group Pocomoke Acohonock C1555208 Pocomoke_Acohonock Pocomoke Acohonock Pocomoke Acohonock C44884 Population Group Southeastern Indians C1555209 Southeastern_Indians Southeastern Indians Southeastern Indians C44885 Population Group Susquehanock C1555210 Susquehanock Susquehanock Susquehanock C44886 Population Group Tunica Biloxi C1555211 Tunica_Biloxi Tunica Biloxi Tunica Biloxi C44887 Population Group Waccamaw Siousan C1555212 Waccamaw_Siousan Waccamaw Siousan Waccamaw Siousan C44888 Population Group Wicomico C1555213 Wicomico Wicomico Wicomico C44889 Population Group Eastern Delaware C1555183 Eastern_Delaware Eastern Delaware Eastern Delaware C44890 Population Group Lenni Lenape C1555184 Lenni_Lenape Lenni Lenape Lenni Lenape C44891 Population Group Munsee C1555185 Munsee Munsee Munsee C44892 Population Group Oklahoma Delaware C1555186 Oklahoma_Delaware Oklahoma Delaware Oklahoma Delaware C44893 Population Group Rampough Mountain C1555187 Rampough_Mountain Rampough Mountain Rampough Mountain C44894 Population Group Sand Hill C1555188 Sand_Hill Sand Hill Sand Hill C44895 Population Group Alabama Creek C1555166 Alabama_Creek Alabama Creek Alabama Creek C44896 Population Group Alabama Quassarte C1555167 Alabama_Quassarte Alabama Quassarte Alabama Quassarte C44897 Population Group Eastern Creek C1555168 Eastern_Creek Eastern Creek Eastern Creek C44898 Population Group Eastern Muscogee C1555169 Eastern_Muscogee Eastern Muscogee Eastern Muscogee C44899 Population Group Kialegee C1555170 Kialegee Kialegee Kialegee C44900 Population Group Lower Muscogee C1555171 Lower_Muscogee Lower Muscogee Lower Muscogee C44901 Population Group Machis Lower Creek Indian C1555172 Machis_Lower_Creek_Indian Machis Lower Creek Indian Machis Lower Creek Indian C44902 Population Group Poarch Band C1555173 Poarch_Band Poarch Band Poarch Band C44903 Population Group Principal Creek Indian Nation C1555174 Principal_Creek_Indian_Nation Principal Creek Indian Nation Principal Creek Indian Nation C44904 Population Group Star Clan of Muscogee Creeks C1555175 Star_Clan_of_Muscogee_Creeks Star Clan of Muscogee Creeks Star Clan of Muscogee Creeks C44905 Population Group Thlopthlocco C1555176 Thlopthlocco Thlopthlocco Thlopthlocco C44906 Population Group Tuckabachee C1555177 Tuckabachee Tuckabachee Tuckabachee C44907 Population Group Bad River C1555119 Bad_River Bad River Bad River C44908 Population Group Bay Mills Chippewa C1555120 Bay_Mills_Chippewa Bay Mills Chippewa Bay Mills Chippewa C44909 Population Group Bois Forte C1555121 Bois_Forte Bois Forte Bois Forte C44910 Population Group Burt Lake Chippewa C1555122 Burt_Lake_Chippewa Burt Lake Chippewa Burt Lake Chippewa C44911 Population Group Fond du Lac C1555123 Fond_du_Lac Fond du Lac Fond du Lac C44912 Population Group Grand Portage C1555124 Grand_Portage Grand Portage Grand Portage C44913 Population Group Grand Traverse Band of Ottawa Chippewa C1555125 Grand_Traverse_Band_of_Ottawa_Chippewa Grand Traverse Band of Ottawa Chippewa Grand Traverse Band of Ottawa Chippewa C44914 Population Group Keweenaw C1555126 Keweenaw Keweenaw Keweenaw C44915 Population Group Lac Courte Oreilles C1555127 Lac_Courte_Oreilles Lac Courte Oreilles Lac Courte Oreilles C44916 Population Group Lac du Flambeau C1555128 Lac_du_Flambeau Lac du Flambeau Lac du Flambeau C44917 Population Group Lac Vieux Desert Chippewa C1555129 Lac_Vieux_Desert_Chippewa Lac Vieux Desert Chippewa Lac Vieux Desert Chippewa C44918 Population Group Lake Superior C1555130 Lake_Superior Lake Superior Lake Superior C44919 Population Group Leech Lake C1555131 Leech_Lake Leech Lake Leech Lake C44920 Population Group Little Shell Chippewa C1555132 Little_Shell_Chippewa Little Shell Chippewa Little Shell Chippewa C44921 Population Group Mille Lacs C1555133 Mille_Lacs Mille Lacs Mille Lacs C44922 Population Group Minnesota Chippewa C1555134 Minnesota_Chippewa Minnesota Chippewa Minnesota Chippewa C44923 Population Group Ontonagon C1555135 Ontonagon Ontonagon Ontonagon C44924 Population Group Red Cliff Chippewa C1555136 Red_Cliff_Chippewa Red Cliff Chippewa Red Cliff Chippewa C44925 Population Group Red Lake Chippewa C1555137 Red_Lake_Chippewa Red Lake Chippewa Red Lake Chippewa C44926 Population Group Saginaw Chippewa C1555138 Saginaw_Chippewa Saginaw Chippewa Saginaw Chippewa C44929 Population Group Sokoagon Chippewa C1555141 Sokoagon_Chippewa Sokoagon Chippewa Sokoagon Chippewa C44930 Population Group Turtle Mountain C1555142 Turtle_Mountain Turtle Mountain Turtle Mountain C44931 Population Group White Earth C1555143 White_Earth White Earth White Earth C44932 Population Group Clatsop C1555112 Clatsop Clatsop Clatsop C44934 Population Group Kathlamet C1555114 Kathlamet Kathlamet Kathlamet C44935 Population Group Upper Chinook C1555115 Upper_Chinook Upper Chinook Upper Chinook C44936 Population Group Wakiakum Chinook C1555116 Wakiakum_Chinook Wakiakum Chinook Wakiakum Chinook C44937 Population Group Willapa Chinook C1555117 Willapa_Chinook Willapa Chinook Willapa Chinook C44938 Population Group Wishram C1555118 Wishram Wishram Wishram C44939 Population Group Cherokee Alabama C1555094 Cherokee_Alabama Cherokee Alabama Cherokee Alabama C44940 Population Group Cherokees of Northeast Alabama C1555095 Cherokees_of_Northeast_Alabama Cherokees of Northeast Alabama Cherokees of Northeast Alabama C44941 Population Group Cherokees of Southeast Alabama C1555096 Cherokees_of_Southeast_Alabama Cherokees of Southeast Alabama Cherokees of Southeast Alabama C44942 Population Group Eastern Cherokee C1555097 Eastern_Cherokee Eastern Cherokee Eastern Cherokee C44943 Population Group Echota Cherokee C1555098 Echota_Cherokee Echota Cherokee Echota Cherokee C44944 Population Group Etowah Cherokee C1555099 Etowah_Cherokee Etowah Cherokee Etowah Cherokee C44946 Population Group Tuscola C1555101 Tuscola Tuscola Tuscola C44947 Population Group United Keetowah Band of Cherokee C1555102 United_Keetowah_Band_of_Cherokee United Keetowah Band of Cherokee United Keetowah Band of Cherokee C44948 Population Group Western Cherokee C1555103 Western_Cherokee Western Cherokee Western Cherokee C44949 Population Group Canadian Indian C1555084 Canadian_Indian Canadian Indian Canadian Indian C44950 Population Group Central American Indian C0021207 The native people of Central America. Central_American_Indian CENTRAL AMERICAN INDIAN Central American Indian Central American Indian C44951 Population Group French American Indian C1555085 French_American_Indian French American Indian French American Indian C44952 Population Group Mexican American Indian C1555086 Mexican_American_Indian Mexican American Indian Mexican American Indian C44953 Population Group South American Indian C1610165 The native people of South America. South_American_Indian SOUTH AMERICAN INDIAN South American Indian South American Indian C44954 Population Group Spanish American Indian C1555087 Spanish_American_Indian Spanish American Indian Spanish American Indian C45170 Population Group Aleut C0085766 Aleut Aleut Aleut C45218 Population Group Columbia River Chinook C1555113 Columbia_River_Chinook Columbia River Chinook Columbia River Chinook C45220 Population Group Northern Cherokee C1555100 Northern_Cherokee Northern Cherokee Northern Cherokee C45221 Population Group Platinum Eskimo C1553253 Platinum_Eskimo Platinum Platinum Eskimo Platinum Eskimo C45222 Population Group Deleware Indian C1707669 Deleware_Indian Deleware Deleware Indian Deleware Indian C45223 Population Group Sault Ste. Marie Chippewa C1555140 Sault_Ste_Marie_Chippewa Sault Ste. Marie Chippewa Sault Ste. Marie Chippewa C45224 Population Group St. Croix Chippewa C1555139 St_Croix_Chippewa St. Croix Chippewa St. Croix Chippewa C45225 Population Group St. George C1553316 St_George St. George St. George C45226 Population Group St. Paul C1553317 St_Paul St. Paul St. Paul C45227 Population Group St. Mary's C1553269 St_Marys St. Mary's St. Mary's C45228 Population Group St. Michael C1553257 St_Michael St. Michael St. Michael C45229 Population Group Yavapai C1551696 Yavapai Yavapai Yavapai The mean pressure of the blood within the arterial circulation. The arterial pressure may be directly measured by insertion of an intra-arterial catheter connected to a transducer. The mean arterial pressure (MAP) can be calculated by subsequent analysis of the waveform. MAP can be approximated without an invasive procedure using the following formula: diastolic pressure plus 1/3 of the pulse pressure, where pulse pressure is systolic pressure - diastolic pressure. C49679 Quantitative Concept Mean Arterial Pressure C0428886 CDISC NCPDP The mean pressure of the blood within the arterial circulation. The arterial pressure may be directly measured by insertion of an intra-arterial catheter connected to a transducer. The mean arterial pressure (MAP) can be calculated by subsequent analysis of the waveform. MAP can be approximated without an invasive procedure using the following formula: diastolic pressure plus 1/3 of the pulse pressure, where pulse pressure is systolic pressure - diastolic pressure. (NCI) Mean_Arterial_Pressure MAP Mean Arterial Pressure Mean Arterial Pressure The pressure of the circulating blood against the walls of the blood vessels. C54706 Clinical Attribute Blood Pressure C0005823 NICHD The force of circulating blood on the walls of the arteries. Blood pressure is taken using two measurements: systolic (measured when the heart beats, when blood pressure is at its highest) and diastolic (measured between heart beats, when blood pressure is at its lowest). Blood pressure is written with the systolic blood pressure first, followed by the diastolic blood pressure (for example 120/80). Blood_Pressure Blood Pressure BP Blood Pressure blood pressure Blood Pressure A person who was not smoking at the time of the interview and has smoked less than 100 cigarettes in their life. C65108 Organism Attribute Never Smoker Never Smoker C0425293 CTRP Never_Smoker Never Smoked Never Smoker Non-Smoker Never Smoker Having ancestors of several or various races. C67109 Population Group Multiracial C1881928 Multiracial Multiracial Multiracial A person living in the United States of Mexican, Puerto Rican, Cuban, Central or South American, or other Spanish culture or origin. The concept does not include Brazilian Americans or Portuguese Americans. C67111 Population Group Multiple Hispanic C1881927 Multiple_Hispanic Multiple Hispanic Multiple Hispanic A person of Puerto Rican culture or origin, regardless of race. C67112 Population Group Puerto Rican C0034043 FDA A person of Puerto Rican descent. Puerto_Rican PUERTO RICAN Puerto Rican Puertorican Puerto Rican Denotes a person from or of Mexico. C67113 Population Group Mexican C0240339 A person of Mexican descent. Mexican MEXICAN Mexican Mexican Denotes an american citizen of Mexican descent. C67114 Population Group Mexican American C0025884 A person of Mexican and American descent. Mexican_American MEXICAN AMERICAN Mexican American Mexican American Denotes a person from or of Cuba or an American citizen of Cuban descent. C67115 Population Group Cuban or Cuban American C0010436 A person of Cuban and American descent. Cuban_or_Cuban_American CUBAN AMERICAN Cuban or Cuban American Cuban or Cuban American Denotes the inhabitants of the Dominican Republic, a person from there, or their descendants elsewhere. C67117 Population Group Dominican CL388698 A person having origins in any of the original peoples of the Dominican Republic. Dominican_Republican DOMINICAN Dominican Dominican Denotes a person from the area between north and south America including persons from Belize, Costa Rica, El Salvador, Guatemala, Honduras, Nicaragua, Panama, and the Panama Canal zone. C67118 Population Group Central American C0238914 A person of Central American descent. Cental_American CENTRAL AMERICAN Central American Central American Denotes a person from Spain or of Spanish descent. C67120 Population Group Spanish C3161473 A person from Spain or of Spanish descent. Spanish SPANISH Spanish Spanish Indicates a person who has smoked at least 100 cigarettes in his or her lifetime and who currently smokes every day. C67145 Organism Attribute Current Every Day Smoker C3266136 Current_Every_Day_Smoker Current Every Day Smoker Daily Smoker Every Day Smoker Current Every Day Smoker Indicates a person who has smoked at least 100 cigarettes in his or her lifetime, who smokes now, but does not smoke every day. C67146 Organism Attribute Current Some Day Smoker C1880200 Current_Some_Day_Smoker Chipper Current Some Day Smoker Non-Daily Smoker Occasional Smoker Some Day Smoker Current Some Day Smoker An adult who has smoked 100 cigarettes in his or her lifetime and who currently smokes cigarettes. Includes daily smokers and non-daily smokers (also known as occasional smokers). C67147 Organism Attribute Current Smoker Current Smoker C3241966 CTRP Current_Smoker Current Smoker Smoker Current Smoker A person who was not smoking at the time of the interview but has smoked at least 100 cigarettes in their life. C67148 Organism Attribute Former Smoker Former Smoker C0337671 CTRP Former_Smoker Former Smoker Prior Smoker Former Smoker Indicates a person who is known to have smoked but whose current smoking status is unknown. C67150 Organism Attribute Smoker, Current Status Unknown C1883049 Smoker_Current_Status_Unknown Smoker, Current Status Unknown Smoker, Current Status Unknown Indicates that a person's smoking status is unknown. C67151 Organism Attribute Unknown If Ever Smoked C1883465 Unknown_If_Ever_Smoked Unknown If Ever Smoked Unknown If Ever Smoked Denotes the inhabitants of the Bahamas, a person from there, or their descendants elsewhere. C67271 Population Group Bahamian C1553336 A person having origins in any of the original peoples of the Bahamas. Bahamian BAHAMIAN Bahamian Bahamian A person who inhales or has inhaled combustible products of organic material during their lifetime. C68751 Organism Attribute Smoker C0337664 Smoker Smoker Smoker The age of a person at the start of a specific event. C69217 Organism Attribute Age Started C2348002 The age of a patient on the first occurrence of an event, such as the first use of a medication. Age_Started Age Started Age Started The age of a person who is the subject in a study. C69260 Organism Attribute Subject Age C2348575 Age of patient who is the subject of observations. Subject_Age Subject Age Subject Age A demographic parameter indicating the amount of earnings made by a family. C70811 Quantitative Concept Household Income C0557163 Household_Income Household Income Household Income The first weight of a newborn obtained after birth. C76325 Quantitative Concept Birth Weight C0005612 NICHD A measured weight of a newborn obtained immediately or shortly after birth. Birth_Weight_New Birth Weight Birth Weight Birth Weight (NCIT) Denotes a person having origins in one of the indigenous people of South or Central America such as Mayans or Incas. C77809 Population Group South or Central American Indian C2699496 South_or_Central_American_Indian South or Central American Indian South or Central American Indian Denotes a person having origins in one of the indigenous people of the Caribbean. C77810 Population Group Caribbean Indian C2698999 The native people of the Caribbean. Caribbean_Indian CARIBBEAN INDIAN Caribbean Indian Caribbean Indian Denotes a person having origins in any of the countries abutting the Mediterranean Sea, principally those of Europe. C77811 Population Group Mediterranean C0240321 A person having origins in any of the original peoples of the countries surrounding the Mediterranean sea. Mediterranean MEDITERRANEAN Mediterranean Mediterranean Denotes a person of European, Middle Eastern, or North African ancestral origins whose family settled in a North American country such as the United States of America or Canada. C77812 Population Group North American C0425358 North_American North American North American Denotes a person having origins in a northern country of Africa such as Egypt, Sudan, Libya, Algeria, Morocco, or Tunisia. C77813 Population Group North Coast of Africa C2698500 A person having origins in any of the original peoples of North Africa. North_Coast_of_Africa_Origin NORTH AFRICAN North Coast of Africa North Coast of Africa Origin North Coast of Africa Denotes a person having origins in any of the countries of northern Europe such as Belgium, Denmark, Austria, Switzerland, Norway, Sweden, or Great Britain. C77814 Population Group Northern European C0239310 A person having origins in any of the original peoples of Northern Europe. Northern_European NORTHERN EUROPEAN Northern European Northern European Denotes a person having origins in any of the black racial groups of Africa whose family settled in a South or Central American country such as Argentina, Brazil, or Mexico. C77815 Population Group Black South or Central American C2698522 Black_South_or_Central_American Black South or Central American Black South or Central American Denotes a person with European, Middle Eastern, or North African ancestral origin whose family settled in the Caribbean region. C77816 Population Group White Caribbean C2700273 A person having origins in the original peoples of Europe, the Middle East, or North Africa, and the Caribbean. White_Caribbean WHITE CARIBBEAN White Caribbean White Caribbean Denotes a person having origins in any of the countries of Western Europe such as Spain, Portugal, or France. C77817 Population Group Western European C0239312 A person having origins in any of the original peoples of Western Europe. Western_European WESTERN EUROPEAN Western European Western European Denotes a person of European ancestral origins whose family settled in a South or Central American country such as Argentina, Brazil, or Mexico. C77818 Population Group White South or Central American C2700274 White_South_or_Central_American White South or Central American White South or Central American Denotes a person having origins in any of the countries of Eastern Europe such as Czechoslovakia, Poland, Croatia, Hungary, Slovenia, Former Soviet Union, or Finland. It also includes persons who call themselves Gypsies from this region. C77819 Population Group Eastern European C0239309 A person having origins in any of the original peoples of Eastern Europe. Eastern_European EASTERN EUROPEAN Eastern European Eastern European Denotes a person having origins in the region of southwest Asia, between the India subcontinent and Europe, including Kuwait, Turkey, Lebanon, Israel, Iraq, Iran, Jordan, Saudi Arabia, lands east of Pakistan or the other countries of the Arabian Peninsula. Also includes people of Jewish ethnicity including Sephardic and Ashkenazic. C77820 Population Group Middle Eastern C2698217 A person having origins in any of the original peoples of the Middle East. Middle_Eastern MIDDLE EASTERN Middle Eastern Middle Eastern The weight of a subject. C81328 Conceptual Entity Body Weight C0005910 CDISC NCPDP NICHD The weight of a subject. (NCI) Weight_of_Body Body Weight BW Body Weight Body Weight A person's total income before taxes, exclusions, and deductions. C85406 Group Attribute Gross Income C2827632 Gross Income Gross Income A general term for a group of culturally similar indigenous peoples inhabiting the Arctic regions of Canada, Greenland, Russia and the United States. In Alaska, the term Eskimo is commonly used, because it includes both Yupik and Inupiat, while Inuit is not accepted as a collective term. In Canada and Greenland, the term Eskimo has fallen out of favor, as it is considered pejorative by the natives and has been replaced by the term Inuit. C86558 Population Group Inuit C0086484 Inuit Inuit The systolic and diastolic blood pressure of the newborn upon examination; the normal range of the systolic blood pressure is 60 - 90, while the normal range of the diastolic blood pressure is 20-60. C87105 Clinical Attribute Newborn Blood Pressure C2828171 NICHD Newborn Blood Pressure Newborn Blood Pressure Newborn Blood Pressure The weight of a subject at a specified end point. C90464 Quantitative Concept Terminal Body Weight C2983672 CDISC The weight of a subject at a specified end point. (NCI) TERMBW Terminal Body Weight Terminal Body Weight The height of a person while standing. C94488 Conceptual Entity Stature C0424639 The height of a person while standing. Stature stature Stature standing height a pathological bodily process that occurs after a medical intervention. An adverse event is likely caused by the medical intervention; however, such a causal association is not required to be an adverse event. Melanie Courtot and YH: More work is needed on how to restrict the scope of a term to be an 'adverse event', notably regarding temporal association. When is an appropirate time interval between a medical intervention and an adverse event observed? One week, one month, one year, or a lifetime? For some well-studied medical interventions (e.g., administration of many vaccines or drugs), we probably have a general idea. For many new interventions, we don't know much. In OAE, this issue is associated with defining the 'adverse event incubation time'. YH: An adverse event is a process that has specified output of some adverse medical outcome (e.g., symptom, sign or accident) after a medical intervention (or process) (e.g., administration of drug or vaccine). The medical intervention can be an administration of a drug, a vaccine (i.e., vaccination), or a special nutritional product (for example, dietary supplement, infant formula, medical food), surgery, or usage of a medical device. YH: An adverse event is possibly induced by the medical intervention. It can be caused by the medical intervention, or may not be caused by the medical intervention. One ultimate goal (or the goal in clinics) of study adverse events is to assess if the adverse event outcome is due to the medical intervention. YH: In development of OAE, we initially use vaccine adverse event as our use case. A vaccine adverse event is associated with a vaccination (i.e. a medical intervention), regardless of whether it is considered vaccine-related, and includes any side effect, injury, toxicity, or sensitivity reaction or significant failure of immunization (i.e., a pharmacologic action). Ref: Baylor NW and Midthum K. Regulation and testing of vaccines. In: Vaccines (Editors: Plotkin S, Orenstein W, and Offit P). 2008. p1623. YH: The current term 'adverse event' is different from the term definition shown in our paper: He Y, Xiang Z, Sarntivijai S, Toldo L, Ceusters W. OAE: a realism-based biomedical ontology for the representation of adverse events. Adverse Event Representation Workshop, International Conference on Biomedical Ontologies (ICBO), University at Buffalo, NY, July 26-30, 2011. Full lenghth conference proceeding paper. We made the name changing in order to make OAE cover the broader sense of the 'adverse event' which does not assume definite causal effect between an adverse event and a medical intervention. In current definition, the adverse event emphasizes the time association and assumes a likelihood of such a causal association. This term 'adverse event' is stil under the OGMS:pathological bodily process. The 'adverse event' defined in the above paper has now been changed to a new term: 'causal adverse event'. See more information in the new publication: Yongqun He Y, Sirarat Sarntivijai, Yu Lin, Zuoshuang Xiang, Abra Guo, Shelley Zhang, Desikan Jagannathan, Luca Toldo, Cui Tao and Barry Smith. OAE: The Ontology of Adverse Events. Journal of Biomedical Semantics. 2014, 5:29 doi:10.1186/2041-1480-5-29. PMID: 25093068.PMCID: PMC4120740. YH: The main scope of OAE includes: (1) represent terms and relations in the area of adverse events, (2) assess possible associations between an adverse event and a medical intervention, particularly, identify any causal effect of a medical intervention to an adverse event; and (2) understand the mechanism (including molecular mechanisms) of causal adverse events. YH: There has been discussion regarding whether the term 'side effect' is an alternative term for 'adverse event'. In AERO, the term 'AERO:adverse event' represents a subset of those adverse events for which causality has been established. In OAE, an adverse event for which causality has been established is called 'causal adverse event'. Yongqun He AE adverse reaction WEB: http://en.wikipedia.org/wiki/Adverse_event WEB: http://www.fda.gov/Safety/MedWatch/HowToReport/ucm053087.htm WEB: http://www.ncbi.nlm.nih.gov/pubmed/25093068 The OAE official website is: http://www.oae-ontology.org/. adverse event medical intervention is a planned process that has the goal of diagnosing, preventing or relieving illness or injury. The act of intervening, interfering or interceding with the intent of modifying the outcome. In medicine, an intervention is usually undertaken to help treat or cure a condition. For example, "Acupuncture as a therapeutic intervention is widely practiced in the United States," Reference: http://www.medterms.com/script/main/art.asp?articlekey=34214 . Some interventions can be used for diagnosis. YH WEB: http://wiki.answers.com/Q/What_is_medical_intervention medical intervention a medical intervention where a patient is administered with a drug YH drug administration an adverse event that has an outcome of abnormal sign in a musculoskeletal or connective tissue. YH, RR, JX musculoskeletal and connective tissue disorder AE WEB: http://www.cdc.gov/niosh/programs/msd/ 10028395 A musculoskeletal disorder is an injury or disorder of the muscles, nerves, tendons, joints, cartilage, or supporting structures of the upper or lower limbs, neck, or lower back that are caused, precipitated, or exacerbated by sudden exertion or prolonged exposure to physical factors such as repetition, force, vibration, or awkward posture musculoskeletal or connective tissue AE CTCAE: E13872 an adverse event that shows a complication that occurs after a medical procedure and is directly related to the precedure itself. SS, YH post-procedural AE procedural disorder AE procedure AE procedural complication AE a procedure complication AE that occurs after a surgery. YH surgery adverse event surgical procedure AE The key difference between a surgery and a procedure is the need for an incision. Making an incision, or cutting into the skin to gain access to the body’s deeper tissues or organs, is a defining characteristic of surgery. Technically speaking, a surgery is a specific type of procedure. A procedure is a broad general term that refers to any series of pre-defined steps that should be followed to achieve a desired result. Therefore, a “surgical procedure” is synonymous with a “surgery.” See more: http://www.wisegeekhealth.com/what-is-the-difference-between-a-surgery-and-a-procedure.htm. surgery AE Surgery is a medical procedure that uses operative manual and instrumental techniques on a patient to investigate and/or treat a pathological condition such as disease or injury, to help improve bodily function or appearance. The key difference between a surgery and a general procedure is the need for an incision. Making an incision, or cutting into the skin to gain access to the body’s deeper tissues or organs, is a defining characteristic of surgery. YH, SS surgical procedure WEB: http://en.wikipedia.org/wiki/Surgery WEB: http://www.wisegeekhealth.com/what-is-the-difference-between-a-surgery-and-a-procedure.htm 10042609 surgery a musculoskeletal and connective tissue AE that displays an outcome of fistula, a permanent abnormal passageway between two organs in the body or between an organ and the exterior of the body. WEB: http://medical-dictionary.thefreedictionary.com/fistula 10067143 YH, SS fistula AE HPO: HP_0010294 SIDER: C0016169 a serious AE that is due to an allergic brochospasm, which causes a serious problem with breathing and requires treatment in an emergency room. YH, JX URL: http://www.fda.gov/Safety/MedWatch/HowToReport/ucm053087.htm URL: https://en.wikipedia.org/wiki/Bronchospasm allergic brochospasm AE that requires treatment in emergency a sensory capability AE that has an outcome of pain in a patient YH, MW 10033371 pain AE CTCAE: E11167 HPO: HP_0010833 NCIt: C3303 SIDER: C0030193 a sudden death AE that occurs to an infant. According to the Vaccine Adverse Event Reporting System (VAERS), 'sudden infant death' is an adverse event that was mentioned in 808 VAERS reports (0.6%) during1991-2001 (Reference: PMID: 12825543). YH sudden infant death AE an AE that occurs in cardiovascular system. YH cardiovascular disorder AE 10007649 cardiovascular AE HPO: HP_0001626 SIDER: C0007222 an adverse event that has an outcome of an abnormal behavior and neurological phenotype. YH, JX behavior AE behavioral AE behavioral disorder AE disruptive behavioral disorder AE WEB: http://www.psychguides.com/guides/behavioral-disorder-symptoms-causes-and-effects/ any anomaly in the actions, reactions, or performance of an organism in response to external or internal stimuli compared to controls behavioral and neurological AE MP: MP_0004924 a behavior and neurological AE that has an outcome of inability or altered ability to respond to a sensory stimulus sensory capability AE MP: MP_0002067 a urinary system AE that results in the presence of blood in the urine YH, SJ, MW UMLS CUI: C0018965 (hematuria AND haematuria); UMLS CUI: C0947999 (blood urine presence) blood urine blood urine presence haematuria AE WEB: http://kidney.niddk.nih.gov/kudiseases/pubs/hematuria/ 10018867 10018870 10019450 hematuria Hematuria AE can be caused by menstruation, vigorous exercise, sexual activity, viral illness, trauma, or infection, such as a urinary tract infection (UTI), along with more serious disorders such as cancer, disease, and clotting. hematuria AE CTCAE: E13000 MP: MP_0005161 NCIt: C3090 an adverse event that has an outcome of urinary system AE is a functional anomaly of any of the organs involved in the production or excretion of urine YH urinary system AE MP: MP_0005502 serious adverse event is an adverse event that requires in-patient hospitalization, or prolongation of existing hospitalization, or that causes congenital malformation, or that results in persistent or significant disability or incapacity, or that is life threatening or results in death. YH, MC serious adverse event severe adverse event WEB: http://en.wikipedia.org/wiki/Serious_adverse_event WEB: http://www.fda.gov/Safety/MedWatch/HowToReport/ucm053087.htm WEB: http://www.google.ca/url?sa=t&source=web&ct=res&cd=1&ved=0CA4QFjAA&url=http%3A%2F%2Fwww.irrd.ca%2Fethics%2Fimages%2FAdverse-event-definition.doc&ei=eqFMS-yFNZSoswOt6siKAQ&usg=AFQjCNGnQcwI8OXH7dqxwo4RgZEEn8X6lg&sig2=UNngkCdO5ZTFvbIB1pKuaA serious adverse event a serious adverse event that has an outcome of death. YH WEB: http://www.fda.gov/Safety/MedWatch/HowToReport/ucm053087.htm 10011906 10011914 death death AE CTCAE: E11080 HPO: HP_0001645 NCIt: C28554 SIDER: C1306577 a serious AE that is suspected to put the patient at substantial risk of dying at the time of the adverse event, or that the use or continued use of the device or other medical product might have resulted in the death of the patient. DJ, SS, YH, JX apparent life threatening event AE WEB: http://www.fda.gov/Safety/MedWatch/HowToReport/ucm053087.htm 10065044 life-threating AE a serious adverse event that leads to hospitalization. Such an adverse event resulted in an admission to the hospital or prolongation of hospitalization. YH, JX adverse event leading to hospitalization WEB: http://www.fda.gov/Safety/MedWatch/HowToReport/ucm053087.htm hospitalization AE a serious adverse event that leads to disability or permanent damage. Such an adverse event results in a substantial disruption of a person's ability to conduct normal life functions, i.e., the adverse event resulted in a significant, persistent or permanent change, impairment, damage or disruption in the patient's body function/structure, physical activities and/or quality of life. YH, JX adverse event leading to disability WEB: http://www.fda.gov/Safety/MedWatch/HowToReport/ucm053087.htm disability or permanent damage AE a serious adverse event that resulted in congenital anomaly and bith defect, leading to suspicions that an exposure to a medical product prior to conception or during pregnancy resulted in an adverse outcome in the child. YH, JX adverse event leading to congenital anomaly WEB: http://www.fda.gov/Safety/MedWatch/HowToReport/ucm053087.htm WEB: http://www.thefreedictionary.com/birth+defect 10010356 congenital anomaly or birth defect AE a serious adverse event which is an adverse event that requires intervention to prevent permanent impairment or damage leads to suspicions that the use of a medical product may result in a condition which requires a medical or surgical intervention to preclude permanent impairment or damage to a patient. YH, JX WEB: http://www.fda.gov/Safety/MedWatch/HowToReport/ucm053087.htm adverse event that requires intervention to prevent permanent impairment or damage an cardiovascular adverse event that is a collection of blood outside the blood vessels, generally the result of hemorrhage, or more specifically, internal bleeding. It is commonly called a bruise. YH: MedDRA ID: 10018852 is for "haematoma"; MedDRA ID: 10019428 is for "hematoma". SS, YH bruise AE bruising AE ecchymoses AE haematoma AE WEB: http://en.wikipedia.org/wiki/Hematoma 10006504 10018852 10019428 hematoma AE CTCAE: E13775 (hematoma); CTCAE: E11666 (brruising) HPO: HP_0001892 NCIt: C37921 (Bruising); NCIt: C50579 (Hematoma) SIDER: C0018944 an adverse event that has an outcome of disease in the biological tissue that supports, binds together and protects organs DJ, SS, YH WEB: http://medical-dictionary.thefreedictionary.com/connective+tissue+disease 10061087 connective tissue disorder AE HPO: HP_0003549 SIDER: C0009782 a connective tissue disorder AE that occurs in the non-skeletal tissue, usually subcutaneous and muscle tissue SZ, SS, YH WEB: http://www.reference.md/files/D018/mD018461.html 10062255 soft tissue infection soft tissue infection AE CTCAE: E11579 HPO: HP_0002719 NCIt: C79745 SIDER: C0149778 a death AE that has an outcome of unexpected death, 1 to 24 hours after the onset of symptoms SZ, SS, YH WEB: http://medical-dictionary.thefreedictionary.com/sudden+death 10042434 10042435 sudden death AE CTCAE: E11171 HPO: HP_0001645 NCIt: C50911 SIDER: C0011071 a process quality that represents the level of severity of an adverse event. YH, SS AE severity severity of adverse event a severity of AE that shows sign and symptom within normal limits. YH, SS AE severity Grade 0 Web: http://ncicb.nci.nih.gov/xml/owl/EVS/ctcae.owl#Grade_0_Adverse_Event Note the AE severity Grade 0 equals to CTCAE G0 AE severity. AE severity G0 CTCAE4: E10004 (Grade 0 Adverse Event) a severity of AE that shows asymptomatic, or involves mild or minor symptoms, or is of marginal clinical relevance, or consists of clinical or diagnostic observations alone, or where intervention is not indicated, or where only non-prescription intervention is indicated. YH, SS AE severity Grade 1 Web: http://ncicb.nci.nih.gov/xml/owl/EVS/ctcae.owl#Grade_1_Adverse_Event Note the AE severity Grade 1 equals to CTCAE G1 AE severity. AE severity G1 CTCAE4: E10005 (Grade 1 Adverse Event) a severity of AE for which only minimal, local, or noninvasive intervention (e.g. packing, cautery) is indicated, or that limits instrumental activities of daily living (ADLs, e.g., shopping, laundry, transportation, or ability to conduct finances). YH, SS AE severity Grade 2 Web: http://ncicb.nci.nih.gov/xml/owl/EVS/ctcae.owl#Grade_2_Adverse_Event Note the AE severity Grade 2 equals to CTCAE G2 AE severity. AE severity G2 CTCAE4: E10006 (Grade 2 Adverse Event) a severity of AE that shows an outcome which is medically significant but not life-threatening; or for which inpatient care or prolongation of hospitalization are indicated; or that is an important medical event that does not result in hospitalization, but may jeopardize the patient or may require intervention either to prevent hospitalization, to prevent the AE from becoming life-threatening or causing death; or that is disabling; or that results in persistent or significant disability, incapacity, or limitation of self care activities of daily living (ADLs, getting in and out of bed, dressing, eating, getting around inside, bathing, or using the toilet). YH, SS AE severity Grade 3 Web: http://ncicb.nci.nih.gov/xml/owl/EVS/ctcae.owl#Grade_3_Adverse_Event Note the AE severity Grade 3 equals to CTCAE G3 AE severity. AE severity G3 CTCAE4: E10007 (Grade 3 Adverse Event) a severity of AE that has life-threatening consequences, for which urgent intervention is indicated, that puts the patient is at risk of death at the time of the event if immediate intervention is not undertaken, or that causes blindness or deafness (need to decide if unilateral or bilateral). YH, SS AE severity Grade 4 Web: http://ncicb.nci.nih.gov/xml/owl/EVS/ctcae.owl#Grade_4_Adverse_Event Note the AE severity Grade 4 equals to CTCAE G4 AE severity. AE severity G4 CTCAE4: E10008 (Grade 4 Adverse Event) a severity of AE that results in death. YH, SS AE severity Grade 5 Web: http://ncicb.nci.nih.gov/xml/owl/EVS/ctcae.owl#Grade_5_Adverse_Event Note the AE severity Grade 5 equals to CTCAE G5 AE severity. AE severity G5 CTCAE4: E10009 (Grade 5 Adverse Event) a hospitalization AE that leads to an intial hospitalization. YH, JX WEB: http://www.fda.gov/Safety/MedWatch/HowToReport/ucm053087.htm initial hospitalization AE a hospitalization AE that leads to a prolonged hospitalization. YH, JX WEB: http://www.fda.gov/Safety/MedWatch/HowToReport/ucm053087.htm prolonged hospitalization AE an adverse event that shows a result of injury or procedural complication. JX, YH injury and procedural complication AE injury or procedural complication AE a pain AE that has marked discomfort sensation on the lateral side of the body in the region below the ribs and above the hip. MW, YH 10016750 flank pain flank pain AE CTCAE: E12414 NCIt: C34615 a death AE that has death in utero; failure of the product of conception to show evidence of respiration, heartbeat, or definite movement of a voluntary muscle after expulsion from the uterus, without possibility of resuscitation. MW, YH 10016479 fetal death AE CTCAE: E12855 NCIt: C50620 a medical intervention that refers to any series of pre-defined steps that should be followed to achieve a desired result. YH, SS WEB: http://www.wisegeekhealth.com/what-is-the-difference-between-a-surgery-and-a-procedure.htm medical procedure YH, JX a behavioral quality where the behavior in an organism is abnormal. WEB: https://en.wikipedia.org/wiki/Abnormality_(behavior) behavior abnormal quality a death AE that has cessation of life occurring during the first 28 days of life. MW, YH 10011912 death neonatal AE CTCAE: E11078 NCIt: C80082 An adverse event of hematoma in the subcapsular space of the kidney. This event occurs after a medical intervention, and may be caused by a tumor, trauma, vasculitis, renal infarction, or other disease process. YH, EO https://medical-dictionary.thefreedictionary.com/subcapsular+hematoma subcapsular hematoma subcapsular hematoma AE An adverse event of hematoma occurring around the kidney. YH, EO perinephric hematoma perinephric hematoma AE YH, EO arteriovenous fistulae arteriovenous fistula arteriovenous fistula AE An adverse event of surgery that leads to the puncturing of an adjacent organ. For example, a needle to the kidney may puncture the adjacent organs. Jennifer Schaub, Oliver He puncturing of adjacent organs https://www.ncbi.nlm.nih.gov/books/NBK493205/ puncturing of adjacent organ AE A date of specimen collection for the first collection of blood from a donor. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB first blood draw date A date of specimen collection for the first collection of a tissue from a donor. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB first tissue removed date A date of specimen collection on which the surgery was performed during which the specimen was collected. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB date of surgical removal of specimen A data item that indicates the time when the collection of a specimen occurred. Alice Nzinga Mathias Brochhausen date of specimen preparation It is denoted by Date in ISO-standard (8601) time format. date of specimen collection planned process planned process Injecting mice with a vaccine in order to test its efficacy A process that realizes a plan which is the concretization of a plan specification. 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) http://purl.obolibrary.org/obo/obi.owl planned process planned process clinical research coordinator role a worker role comprised of handling the administrative duties of a trial or study. Person:Jennifer Fostel clinical research coordinator clinical research coordinator role 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 investigation Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). Bjoern Peters OBI branch derived Could add specific objective specification Following OBI call November 2012,26th: it was decided there was no need for adding "achieves objective of drawing conclusion" as existing relations were providing equivalent ability. this note closes the issue and validates the class definition to be part of the OBI core editor = PRS study investigation evaluant role When a specimen of blood is assayed for glucose concentration, the blood has the evaluant role. When measuring the mass of a mouse, the evaluant is the mouse. When measuring the time of DNA replication, the evaluant is the DNA. When measuring the intensity of light on a surface, the evaluant is the light source. a role that inheres in a material entity that is realized in an assay in which data is generated about the bearer of the evaluant role Role call - 17nov-08: JF and MC think an evaluant role is always specified input of a process. Even in the case where we have an assay taking blood as evaluant and outputting blood, the blood is not the specified output at the end of the assay (the concentration of glucose in the blood is) examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected") GROUP: Role Branch OBI Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. evaluant role assay Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house. A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies. 12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation. PlanAndPlannedProcess Branch measuring scientific observation OBI branch derived study assay any method assay sample preparation for assay A sample_preparation_for_assay is a protocol_application including material_enrollments and biomaterial_transformations. definition_source: OBI. PlanAndPlannedProcess Branch study OBI branch derived sample preparation for assay diagnosis textual entity diagnosis is an assessment of a disease or injury, its likely prognosis and treatment. Jennifer Fostel diagnosis textual entity 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 reagent role Buffer, dye, a catalyst, a solvating agent. A role inhering in a biological or chemical entity that is intended to be applied in a scientific technique to participate (or have molecular components that participate) in a chemical reaction that facilitates the generation of data about some entity distinct from the bearer, or the generation of some specified material output distinct from the bearer. PERSON:Matthew Brush reagent PERSON:Matthew Brush Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. May 28 2013. Updated definition taken from ReO based on discussions initiated in Philly 2011 workshop. Former defnition described a narrower view of reagents in chemistry that restricts bearers of the role to be chemical entities ("a role played by a molecular entity used to produce a chemical reaction to detect, measure, or produce other substances"). Updated definition allows for broader view of reagents in the domain of biomedical research to include larger materials that have parts that participate chemically in a molecular reaction or interaction. (copied from ReO) Reagents are distinguished from instruments or devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, instruments do not participate in a chemical reaction/interaction during the technique. Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance will realize only one of these roles in the execution of a given assay or technique. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated. In regard to the statement that reagents are 'distinct' from the specified outputs of a technique, note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some modified cell specimen which shares identity with the input unmodified cell specimen, and not with the biotin label. Thus, we see that an important criteria of 'reagent-ness' is that it is a facilitator, and not the primary focus of an investigation or material processing technique (ie not the specified subject/evaluant about which knowledge is sought, or the specified output material of the technique). reagent role 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 study subject role Human subjects in a clinical trial, rats in a toxicogenomics study, tissue cutlures subjected to drug tests, fish observed in an ecotoxicology study. Parasite example: people are infected with a parasite which is then extracted; the particpant under investigation could be the parasite, the people, or a population of which the people are members, depending on the nature of the study. Lake example: a lake could realize this role in an investigation that assays pollution levels in samples of water taken from the lake. A role that is realized through the execution of a study design in which the bearer of the role participates and in which data about that bearer is collected. A participant can realize both "specimen role" and "participant under investigation role" at the same time. However "participant under investigation role" is distinct from "specimen role", since a specimen could somehow be involved in an investigation without being the thing that is under investigation. GROUP: Role Branch OBI Following OBI call November 2012,26th: 1. it was decided there was no need for moving the children class and making them siblings of study subject role. 2. it also settles the disambiguation about 'study subject'. This is about the individual participating in the investigation/study, Not the 'topic' (as in 'toxicity study') of the investigation/study This note closes the issue and validates the class definition to be part of the OBI core editor = PRS participant under investigation role responsible party role he THERAPIST has the ability to print a separate statement for the patient and each responsible party. http://www.beaverlog.com/therapist/ez_support/billing/responsible_party_statements.htm a study personnel role played by a party who is accountable for the execution of a study component and can make decisions about the conduct of the study Person: Jennifer Fostel responsible party OBI responsible party role 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 worker role Public sector workers in states that run their own OSHA programs are covered by those states. http://www.osha.gov/as/opa/worker/index.html a personnel role played by a party who executes a component of the study plan; this can occur before, during, after or outside the study timeline "executes the study plan" includes the suppliers and manufacturers of reagents and other materials used in the study Person:Jennifer Fostel worker OBI worker role population PMID12564891. Environ Sci Technol. 2003 Jan 15;37(2):223-8. Effects of historic PCB exposures on the reproductive success of the Hudson River striped bass population. a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area 1/28/2013, BP, on the call it was raised that we may want to switch to an external ontology for all populatin terms: http://code.google.com/p/popcomm-ontology/ PERSON: Philippe Rocca-Serra adapted from Oxford English Dictionnary rem1: collection somehow always involve a selection process population investigation agent role The person perform microarray experiments and submit microarray results (including raw data, processed data) with experiment description to ArrayExpress. A role borne by an entity and that is realized in a process that is part of an investigation in which an objective is achieved. These processes include, among others: planning, overseeing, funding, reviewing. Implementing a study means carrying out or performing the study and providing reagents or other materials used in the study and other tasks without which the study would not happen. Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable representing investigations run by robot scientists such as ADAM (King et al, Science, 2009) GROUP: Role Branch investigator OBI Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. study person role Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable investigations run by robot scientists such as ADAM (King et al, Science, 2009) investigation agent role sponsor role a responsible party role involved with any of the following activities: initiating, managing and funding a study Person: Jennifer Fostel sponsor CDISC definition: sponsor. 1. An individual, company, institution, or organization that takes responsibility for the initiation, management, and/or financing of a clinical trial. 2. A corporation or agency whose employees conduct the investigation is considered a sponsor; employees are considered investigators sponsor 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. An organization is a continuant entity which can play 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 protocol PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR. A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process. PlanAndPlannedProcess Branch OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29) study protocol protocol analyte role Glucose in blood (measured in an assay to determine the concentration of glucose). A measurand role borne by a molecular entity or an atom and realized in an analyte assay which achieves the objective to measure the magnitude/concentration/amount of the analyte in the entity bearing evaluant role. interestingly, an analyte is still an analyte even if it is not detected. for this reason it does not bear a specified input role pH (technically the inverse log of [H+]) may be considered a quality; this remains to be tested. qualities such as weight, color are not assayed but measured, so they do not fall into this category. GROUP: Role Branch OBI Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. analyte role interpreting data Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. Concluding that 'defects in gene XYZ cause cancer due to improper DNA repair' based on data from experiments in that study that gene XYZ is involved in DNA repair, and the conclusion of a previous study that cancer patients have an increased number of mutations in this gene. A planned process in which data gathered in an investigation is evaluated in the context of existing knowledge with the objective to generate more general conclusions or to conclude that the data does not allow one to draw general conclusion PERSON: Bjoern Peters PERSON: Jennifer Fostel Bjoern Peters drawing a conclusion based on data planning The process of a scientist thinking about and deciding what reagents to use as part of a protocol for an experiment. Note that the scientist could be human or a "robot scientist" executing software. a process of creating or modifying a plan specification 7/18/2011 BP: planning used to itself be a planned process. Barry Smith pointed out that this would lead to an infinite regression, as there would have to be a plan to conduct a planning process, which in itself would be the result of planning etc. Therefore, the restrictions on 'planning' were loosened to allow for informal processes that result in an 'ad hoc plan '. This required changing from 'has_specified_output some plan specifiction' to 'has_participant some plan specification'. Bjoern Peters Bjoern Peters Plans and Planned Processes Branch planning hypothesis driven investigation is an investigation with the goal to test one or more hypothesis PlanAndPlannedProcess Branch OBI branch derived hypothesis driven investigation hypothesis generating investigation is an investigation in which data is generated and analyzed with the purpose of generating new hypothesis PlanAndPlannedProcess Branch OBI branch derived hypothesis generating investigation transfer function A transfer function is a function to displace a material from one location to another. Bill Bug Daniel Schober Frank Gibson Melanie Courtot transfer function extract Up-regulation of inflammatory signalings by areca nut extract and role of cyclooxygenase-2 -1195G>a polymorphism reveal risk of oral cancer. Cancer Res. 2008 Oct 15;68(20):8489-98. PMID: 18922923 an extract is a material entity which results from an extraction process PERSON: Philippe Rocca-Serra extracted material GROUP: OBI Biomatrial Branch extract needle Ovarian carcinoma presenting with axillary lymph node metastasis: A case diagnosed by fine-needle aspiration and brief review of the literature. Diagn Cytopathol. 2008 Oct 16. PMID: 18925569 A needle is a sharp, hollow device used to penetrate tissue or soft material. When attached to a syringe. it allows delivery of a specific volume of liquid or gaseous mixture. Philippe Rocca-Serra OBI Instrument needle analyte measurement objective The objective to measure the concentration of glucose in a blood sample an assay objective to determine the presence or concentration of an analyte in the evaluant PERSON: Bjoern Peters PPPB branch analyte measurement objective assay objective the objective to determine the weight of a mouse. an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role) PPPB branch PPPB branch assay objective analyte assay example of usage: In lab test for blood glucose, the test is the assay, the blood bears evaluant_role and glucose bears the analyte role. The evaluant is considered an input to the assay and the information entity that records the measurement of glucose concentration the output An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant. Alan Ruttenberg Bjoern Peters Helen Parkinson Philippe Rocca-Serra Alan Ruttenberg Bjoern Peters Helen Parkinson OBI Planned process branch Philippe Rocca-Serra analyte assay measure function A glucometer measures blood glucose concentration, the glucometer has a measure function. Measure function is a function that is borne by a processed material and realized in a process in which information about some entity is expressed relative to some reference. PERSON: Daniel Schober PERSON: Helen Parkinson PERSON: Melanie Courtot PERSON:Frank Gibson measure function 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 study design execution injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design. a planned process that carries out a study design removed axiom has_part some (assay or 'data transformation') per discussion on protocol application mailing list to improve reasoner performance. The axiom is still desired. branch derived 6/11/9: edited at workshop. Used to be: study design execution is a process with the objective to generate data according to a concretized study design. The execution of a study design is part of an investigation, and minimally consists of an assay or data transformation. study design execution clinical chemistry assay Influence of hydroxyethyl starch (6% HES 130/0.4) administration on hematology and clinical chemistry parameters. An analyte assay which uses analytical methods to produce measurements and data on the concentration of chemical parameters (analytes) present in a bodily fluid collected from an organism. Philippe Rocca-Serra chemical pathology detection of analyte in blood sample url:https://en.wikipedia.org/wiki/Clinical_chemistry clinical chemistry assay scattered molecular aggregate the sodium and chloride ions in a glass of salt water A scattered molecular aggregate is a material entity that consists of all the molecules of a specific type that are located in some bounded region and which is part of a more massive material entity that has parts that are other such aggregates a material entity that consists of all the molecules of a specific type that are located in some bounded region and which is part of a more massive material entity that has parts that are other such aggregates PERSON: Alan Ruttenberg Collective Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. With inspiration from the paper Granularity, scale and collectivity: When size does and does not matter, Alan Recto, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349 scattered molecular aggregate 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 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 enzyme-linked immunosorbent assay 1) Detection of IL-2 (analyte) in a cell supernatant (evaluant), using plate bound anti IL-2 antibodies, and a reporter enzyme-linked reporter antibody. 2) Measurement of IgG antibody (analyte) titer in a serum sample (evaluant) using plate bound antigen and a reporter anti-IgG antibody. An analyte assay where binding of an enzyme linked antibody to a material entity that is immobilized on solid support is detected utilizing a chemiluminescent reaction. Depending on the setup, the enzyme-linked antibody could be binding directly to the analyte, or it serves as a secondary antibody detecting binding of the primary antibody to the analyte. IEDB ELISA IEDB enzyme-linked immunosorbent assay sample from organism a material obtained from an organism in order to be a representative of the whole 5/29: This is a helper class for now we need to work on this: Is taking a urine sample a material separation process? If not, we will need to specify what 'taking a sample from organism' entails. We can argue that the objective to obtain a urine sample from a patient is enough to call it a material separation process, but it could dilute what material separation was supposed to be about. sample from organism 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 material sample role a role borne by a portion of blood taken to represent all the blood in an organism; the role borne by a population of humans with HIV enrolled in a study taken to represent patients with HIV in general. A material sample role is a specimen role borne by a material entity that is the output of a material sampling process. 7/13/09: Note that this is a relational role: between the sample taken and the 'sampled' material of which the sample is thought to be representative off. material sample role material sample blood drawn from patient to measure his systemic glucose level. A population of humans with HIV enrolled in a study taken to represent patients with HIV in general. A material entity that has the material sample role OBI: workshop sample population sample material sample 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 informed consent process A planned process in which a person or their legal representative is informed about key facts about potential risks and benefits of a process and makes a documented decision as to whether the person in question will participate. 09/28/2009 Alan Ruttenberg: This is made a subclass of the higher level processual entity in BFO because I don't want to take a stand on whether it is a process aggregate. Analogous to the situation with Material entity. Person:Alan Ruttenberg http://clinicaltrials.gov/ct2/info/glossary#informed 2009/09/28 Alan Ruttenberg. Fucoidan-use-case informed consent process measurement device A ruler, a microarray scanner, a Geiger counter. A device in which a measure function inheres. GROUP:OBI Philly workshop OBI measurement device 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 categorical measurement datum A measurement datum that is reported on a categorical scale Bjoern Peters nominal mesurement datum Bjoern Peters categorical measurement datum service consumer role A biologist who uses a sequencing services fulfills the role of a service consumer a role which inheres in a person who uses a service Person:Helen Parkinson OBI service consumer role 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 device A voltmeter is a measurement device which is intended to perform some measure function. An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure. A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. 2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: (1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. (2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. (3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay. PERSON: Helen Parkinson instrument OBI development call 2012-12-17. device sequence data example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search. A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement. Person:Chris Stoeckert GROUP: OBI sequence data dose An organism has been injected 1ml of vaccine A measurement datum that measures the quantity of something that may be administered to an organism or that an organism may be exposed to. Quantities of nutrients, drugs, vaccines and toxins are referred to as doses. dose nucleic acid extract An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen. PERSON: Jie Zheng UPenn Group nucleic acid extract nucleic acid sequencer An device that is used to determine the order of nucleotides in nucleic acid sequences. PERSON: Erik Segerdell PERSON: Erik Segerdell nucleic acid sequencer protein sequencer An device that is used to determine the order of amino acids in protein sequences. PERSON: Erik Segerdell PERSON: Erik Segerdell protein sequencer service providing a training course for UCSD employees how to run a DNA sequencer; sequencing a DNA sample provided by a service consumer restricted to non-human samples; giving access to tissue samples in a biobank within OHSU; JAX shipping mice from their colony A planned process in which a service provider performs a task (i.e. a planned process) for a service consumer. Carlo; Matt OBI workshop San Diego 2011 service 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 material maintenance service model organism colony maintanance A material processing service in which a service provider makes physical modifications to a specified input material, such that at least one of the specified outputs of this process is a modified version of a specified input material. PERSON: Carlo Torniai PERSON: Matthew Brush PERSON: Matthew Brush Here we need to go back to the defintoin of storage process. It has object specification which is material maintenance. Not necessareley a material maintenance is needed in a storage process. material maintenance service material service A service performing DNA sequencing, a service preforming cell analysis. A service performing cell line immortalization A service which has a material entity as specified input and/or specified output. PERSON: Carlo Torniai PERSON: Matthew Brush PERSON: Carlo Torniai material service material analysis service Services performing DNA sequencing or Cell Analysis A service in which a service consumer provides some input material and a service provider performs some analysis of this material to generate data that is returned to the service consumer. PERSON: Carlo Torniai PERSON: Matthew Brush PERSON: Matthew Brush material analysis service material storage service A service that offers liquid nitrogen stroage. A storage service in which a service consumer provides some material as input which a service provider stores and returns as output. PERSON: Carlo Torniai PERSON: Matthew Brush PERSON: Matthew Brush material storage service specimen identifier A CRID symbol denotes a specimen and used to distinguish one specimen from another in an investigation. Person: Chris Stoeckert, Jie Zheng specimen ID NIAID GSCID-BRC metadata working group Specimen ID NIAID GSCID-BRC specimen identifier selection criterion rats should be aged between 6 and 8 weeks and weight between 180-250grams A directive information entity which defines and states a principle of standard by which selection process may take place. Person: Philippe Rocca-Serra selection rule OBI discussion summarized under the following tracker item : http://sourceforge.net/p/obi/obi-terms/678/ selection criterion specimen repository organization An organization that provides a service to store and distribute specimens PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Specimen Repository NIAID GSCID-BRC specimen repository organization sequencing facility organization An organization that provides sequence determination service PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sequencing Facility NIAID GSCID-BRC sequencing facility organization comment on investigation A textual entity that is about any of the aspects of an investigation worth noting PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Comments NIAID GSCID-BRC comment on investigation specimen identifier assigned by specimen repository A specimen identifier which is assigned by a specimen repository PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Specimen Repository Sample ID NIAID GSCID-BRC specimen identifier assigned by specimen repository specimen identifier assigned by sequencing facility A specimen identifier which is assigned by a sequencing facility PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sample ID - Sequencing Facility NIAID GSCID-BRC specimen identifier assigned by sequencing facility sequencing service A service provides sequencing service which is the realization of some sequencing such as RNA and DNA sequencing in which the service provider role is realized. Person: Jie Zheng Adpated from 'DNA sequencing service' NIAID GSCID-BRC sequencing service conclusion based on data The conclusion that a gene is upregulated in a tissue sample based on the band intensity in a western blot. The conclusion that a patient has a infection based on measurement of an elevated body temperature and reported headache. The conclusion that there were problems in an investigation because data from PCR and microarray are conflicting. The following are NOT conclusions based on data: data themselves; results from pure mathematics, e.g. "13 is prime". An information content entity that is inferred from data. In the Philly 2013 workshop, we recognized the limitations of "conclusion textual entity", and we introduced this as more general. The need for the 'textual entity' term going forward is up for future debate. Group:2013 Philly Workshop group Group:2013 Philly Workshop group conclusion based on data 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 selection PMID: 24023800. In this study, a set of eleven genes (VATP16, 60 S, UQCC, SMD3, EF1α, UBQ, SAND, GAPDH, ACT, PsaB, PTB2) was evaluated to identify reference genes during the first hours of interaction (6, 12, 18 and 24 hpi) between two V. vinifera genotypes and P. viticola. Two analyses were used for the selection of reference genes: direct comparison of susceptible, Trincadeira, and resistant, Regent, V. vinifera cultivars at 0 h, 6, 12, 18 and 24 hours post inoculation with P. viticola (genotype effect); and comparison of each genotype with mock inoculated samples during inoculation time-course (biotic stress effect). Three statistical methods were used, GeNorm, NormFinder, and BestKeeper, allowing to identify UBQ, EF1α and GAPDH as the most stable genes for the genotype effect. A planned process which results in the creation of group of entity from a larger group by the application of predefined criteria. this term refers to a planned process and therefore is distinct from the notion of 'natural selection', a process covering the operation of natural causes by which those individuals of a species that are best adapted to the environment tend to be preserved and to transmit their characters, while those less adapted die out, so that in the course of generations the degree of adaptation to the environment tends progressively to increase. (as defined by Oxford English Dictionary) Person: Philippe Rocca-Serra selection process OBI selection 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 molecular analysis facility organization An analysis facility that includes analysis of molecular metabolites, as well as the various DNAs and RNAs. An organization that provides molecular analysis service. Chris Stoeckert, Helena Ellis MAF NCI BBRB, OBIB NCI BBRB molecular analysis facility organization age of majority inclusion criterion An inclusion criterion that uses the age of majority for a state or institution, where one is generally considered to be an adult, which if met, makes an individual suitable for a given task or participation in a given process. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB age of majority inclusion criterion chemotherapy treatment exclusion criterion An exclusion criterion that defines whether chemotherapy was received or is being received for a previous or current cancer, which when met, makes an individual unsuitable for a given task or participation in a given process Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB chemotherapy treatment exclusion criterion radiation treatment exclusion criteria An exclusion criterion that defines whether radiation was received or is being received for a previous or current cancer, which when met, makes an individual unsuitable for a given task or participation in a given process Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB radiation treatment exclusion criteria chemotherapy treatment within the recent past exclusion criterion An exclusion criterion defined by the pathologist is defined as whether the individual received chemotherapy within the last two years. An exclusion criterion that defines whether chemotherapy was received within a certain timeframe, which when met, makes an individual unsuitable for a given task or participation in a given process. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB chemotherapy treatment within the recent past exclusion criterion radiation treatment within the recent past exclusion criterion An exclusion criterion defined by the pathologist is defined as whether the individual received radiation therapy within the last two years. An exclusion criterion that defines whether radiation was received within a certain timeframe, which when met, makes an individual unsuitable for a given task or participation in a given process. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB radiation treatment within the recent past exclusion criterion BMI range inclusion criterion An important inclusion criterion is for for the individual to have a BMI between 18.5 and 35.0 An inclusion criterion that defines and states a Body Mass Index range, which if met, makes an individual suitable for a given task or participation in a given process. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB BMI range inclusion criterion blood transfusion exclusion criterion An exclusion criterion that is defined by whether the specimen donor received a whole blood transfusion within 48 hours prior to death. An exclusion criterion that is defined by whether the specimen donor received a whole blood transfusion within a specified time frame prior to death, which if met, makes a specimen donor unsuitable for a given task or participation in a given process. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB blood transfusion exclusion criterion history of metastatic cancer exclusion criterion An exclusion criterion defined as whether an individual has ever been diagnosed with metastatic cancer (cancer that spread beyond the initial site such as to other organs like brain bone or liver), which if met, makes the individual unsuitable for a given task or participation in a given process. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB history of metastatic cancer exclusion criterion intravenous drug use exclusion criterion Donor eligibility based on history of intravenous drug abuse in the last 5 years. An exclusion criterion defined as when an individual has a history of intravenous drug abuse for a specific timeframe, which if met, makes the individual unsuitable for a given task or participation in a given process. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB intravenous drug use exclusion criterion history of sex with someone with a history of blood borne infection exclusion criterion Donor eligibility based on whether the donor has a history of sex with someone who has been diagnosed or at risk for HIV/AIDS and/or HCV and/or HBV in the last 5 years. An exclusion criterion defined as whether an individual has a history of sex with someone who has been diagnosed or at risk for a blood borne infections disease in a specified time frame, which if met, makes the individual unsuitable for a given task or participation in a given process. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB history of sex with someone with a history of blood borne infection exclusion criterion history of sex with someone with a history of intravenous drugs exclusion criterion Donor eligibility based on whether the donor has a history of sex with someone who has used intravenous drugs in the last 5 years. An exclusion criterion defined as whether an individual has a history of sex with someone who has used intravenous drugs in a specified time frame, which if met, makes the individual unsuitable for a given task or participation in a given process. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB history of sex with someone with a history of intravenous drugs exclusion criterion HIV exclusion criterion An exclusion criterion defined as whether an individual has a history of repeatedly reactive screening assays for HIV-1 or HIV-2 antibody regardless of the results of supplemental assays, which if met, makes the individual unsuitable for a given task or participation in a given process. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB HIV exclusion criterion exposure to blood borne infectious disease exclusion criterion Donor eligibility based on whether the donor has been exposed to HIV/AIDS. An exclusion criterion defined as whether an individual has been exposed to a blood borne infections disease through needle sticks and/or contact with non-intact skin and/or contact with open wounds and/or contact with mucous membranes, which if met, makes the individual unsuitable for a given task or participation in a given process. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB exposure to blood borne infectious disease exclusion criterion measurand role A role borne by a material entity and realized in an assay which achieves the objective to measure the magnitude/concentration/amount of the measurand in the entity bearing evaluant role. Person: Alan Ruttenberg, Jie Zheng https://en.wiktionary.org/wiki/measurand https://github.com/obi-ontology/obi/issues/778 measurand role health status inclusion criterion ‘diagnosed with Type 2 diabetes mellitus’, ‘E11.4’, ’not finding of hypertension' An inclusion criterion that defines and states one or more clinically significant bodily components, dispositions, and/or bodily processes of an entity that are inferred from relevant clinical findings or self-reported, which, if met, makes the entity suitable for a given task or participation in a given process. Mathias Brochhausen MIABIS2.0 health status inclusion criterion clinically relevant lifestyle inclusion criterion 'smoking behavior’ An inclusion criterion that defines and states one or more clinically relevant planned processes that a human being actively participates in , which, if met, makes the human being suitable for a given task or participation in a given process. Mathias Brochhausen MIABIS2.0 clinically relevant lifestyle inclusion criterion clinically relevant exposure inclusion criterion 'exposure to cigarette smoke’, ‘exposure to lead through drinking water' An inclusion criterion that defines and states one or more clinically relevant histories of exposure of an entity, which, if met, makes the entity suitable for a given task or participation in a given process. Mathias Brochhausen MIABIS2.0 clinically relevant exposure inclusion criterion gravidity inclusion criterion 'pregnant’, ‘not pregnant' An inclusion criterion that defines and states one or more gravidity statuses of an organism, which, if met, makes the entity suitable for a given task or participation in a given process. Mathias Brochhausen MIABIS2.0 gravidity inclusion criterion defined population inclusion criterion inclusion based on age, sex, and living region (rural area or specified city). An inclusion criterion that is based on fitting within the defined characteristics of a population based study design. Chris Stoeckert, Mathias Brochhausen MIABIS 2.0 920 MIABIS 2.0 defined population inclusion criterion age group inclusion criterion "18-33 years old" An inclusion criterion that defines and states an age bracket which, if met, makes an entity suitable for a given task or participation in a given process. Mathias Brochhausen #839 age group inclusion criterion minimum age value specification A value specifcation that specifies the youngest age when specifying an age range. Mathias Brochhausen minimum age value specification maximum age value specification A value specifcation that specifies the oldest age when specifying an age range. Mathias Brochhausen maximum age value specification use of medication inclusion criterion "received at least 2 days of vancomycin" An inclusion criterion that defines and states a a set of medications, which, if used by an entity, makes that entity suitable for a given task or participation in a given process. Mathias Brochhausen #840 use of medication inclusion criterion hospital patient inclusion criterion "included hospital patients" An inclusion criterion defines that a human being has to be a hospital patient to be suitable for a given task or participation in a given process. Mathias Brochhausen hospital patient inclusion criterion family status inclusion criterion "included married and unmarried patients", "included divorced individuals" An inclusion criterion that defines and states one or more family statuses, which, if met, makes a human being suitable for a given task or participation in a given process. Mathias Brochhausen family status inclusion criterion sex inclusion criterion "included males and females", "included male patients" An inclusion criterion that defines and states one or more sexes which, if met, makes an entity suitable for a given task or participation in a given process. Mathias Brochhausen sex inclusion criterion country of residence inclusion criteria "include US residents" An inclusion criterion that defines and states one or more countries of residence which, if met, makes a human being suitable for a given task or participation in a given process. Mathias Brochhausen country of residence inclusion criteria ethnicity inclusion criterion "include only Hispanic individuals" An inclusion criteria that defines and states one or more ethnicities which, if met, makes an entity suitable for a given task or participation in a given process. Mathias Brochhausen ethnicity inclusion criterion 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 http://purl.obolibrary.org/obo/obi.owl 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 extraction nucleic acid extraction using phenol chloroform A material separation in which a desired component of an input material is separated from the remainder Current the output of material processing defined as the molecular entity, main component in the output material entity, rather than the material entity that have grain molecular entity. 'nucleic acid extract' is the output of 'nucleic acid extraction' and has grain 'nucleic acid'. However, the output of 'nucleic acid extraction' is 'nucleic acid' rather than 'nucleic acid extract'. We are aware of this issue and will work it out in the future. Person:Bjoern Peters Philippe Rocca-Serra extraction storage PMID: 18550121.Total Prostate Specific Antigen Stability Confirmed After Long-Term Storage of Serum at -80C. J Urol. 2008 Jun 10. A maintenance process by which material entities that are not actively metabolizing are placed in well identified location and possibly under controlled environment in ad-hoc devices/structures in order to preserve and protect them from decay/alteration and maintain availability Philippe Rocca-Serra OBI-Branch storage DNA sequencer ABI 377 DNA Sequencer, ABI 310 DNA Sequencer A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences. Trish Whetzel MO DNA sequencer study design a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design. A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available. PERSON: Chris Stoeckert experimental design rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol. study design eligibility criterion PMID: 17579629 -Eligibility criteria included: untreated ED-SCLC; age >/=70 and performance status 0-2, or age <70 and PS 3. an eligibility criterion (rule) is_a selection criterion which defines and states the requirements (positive or negative) for an entity to be considered as suitable for a given task or participation in a process. Person: Philippe Rocca-Serra eligibility rule Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group eligibility criterion inclusion criterion PMID: 23979341-The major inclusion criterion was patients in whom severe cerebral embolism was diagnosed at age 75 or younger (more than 9 in the NIHSS score on day 7 after the onset of stroke) . an inclusion criterion (rule) is_a *eligibility criterion* which defines and states a condition which, if met, makes an entity suitable for a given task or participation in a given process. For instance, in a study protocol, inclusion criteria indicate the conditions that prospective subjects MUST meet to be eligible for participation in a study. Person: Philippe Rocca-Serra inclusion condition inclusion rule Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group inclusion criterion exclusion rule PMID: 17600285-Exclusion criteria included the use of any topical ophthalmic or topical oral medication and/or history of ocular or oral surgery within the past six months. an exclusion criterion (rule) is_a *eligibility criterion* which defines and states a condition which, if met, makes an entity unsuitable for a given task or participation in a given process. For instance, in a study protocol, exclusion criteria indicate the conditions that prospective subjects SHOULD NOT meet to be eligible for participation in a study Person: Philippe Rocca-Serra Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group exclusion criterion human subject enrollment enlisting familiy members of HIV patients into a study A planned process with the objective to obtain a population of human subjects to participate in an investigation by determining eligibility of subjects and obtaining informed consent. As with group assignment, should the specified output here be an organism which bears a role Bjoern Peters IEDB criteria come from plan / clinical trial branch human subject enrollment collecting specimen from organism taking a sputum sample from a cancer patient, taking the spleen from a killed mouse, collecting a urine sample from a patient a process with the objective to obtain a material entity that was part of an organism for potential future use in an investigation PERSON:Bjoern Peters IEDB collecting specimen from organism 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 sequencing assay The use of the Sanger method of DNA sequencing to determine the order of the nucleotides in a DNA template An assay the uses chemical or biochemical means to infer the sequence of a biomaterial PlanAndPlannedProcess Branch OBI branch derived sequencing assay nucleic acid extraction Phenol / chlorophorm extraction disolvation of protein content folllowed by ethanol precipitation of the nucleic acid fraction over night in the fridge followed by centrifugation to obtain a nucleic acid pellet. a material separation to recover the nucleic acid fraction of an input material PlanAndPlannedProcess Branch OBI branch derived requested by Helen Parkinson for MO. Could be defined class nucleic acid extraction adaptive immune receptor is a receptor produced by cells of the adaptive immune system with the purpose of binding epitopes. IEDB IEDB adaptive immune receptor bodily fluid specimen A specimen that is derived from some bodily fluid Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066 Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066 bodily fluid specimen A representation that is either the output of a clinical history taking or a physical examination or an image finding, or some combination thereof. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2010-07-19T10:18:02Z clinical finding A series of statements representing health-relevant qualities of a patient and of a patient's family. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2010-07-19T10:18:59Z clinical history A representation of an image that supports an inference to an assertion about some quality of a patient. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T10:21:10Z image finding A representation of a quality of a specimen that is the output of a laboratory test and that can support an inference to an assertion about some quality of the patient. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T10:21:58Z laboratory finding 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 Albert Goldfain creation date: 2009-06-23T11:53:49Z bodily process A bodily process that is clinically abnormal. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:54:29Z pathological bodily process The representation of a conclusion of a diagnostic process. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T12:42:23Z diagnosis TODO: Define. Albert Goldfain http://code.google.com/p/ogms/issues/detail?id=26 creation date: 2009-11-24T04:51:11Z physical examination finding A planned process whose completion is hypothesized by a health care provider to eliminate, prevent, or alleviate a disorder, the signs and symptoms of a disorder, or a pathological process A processual entity whose completion is hypothesized (by a healthcare provider) to alleviate the signs and symptoms associated with a disorder Albert Goldfain http://code.google.com/p/ogms/issues/detail?id=35 creation date: 2010-03-31T04:51:11Z http://purl.obolibrary.org/obo/ogms.owl treatment A planned process with the objective to improve the health status of a patient that directly involves the treatment, diagnosis, or prevention of disease or injury of a patient Albert Goldfain Sagar Jain http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 creation date: 2011-02-21T09:57:44Z editor date: 2017-04-18 health care process A temporally-connected health care process that has as participants an organization or person realizing the health care provider role and a person realizing the patient role. The health care provider role and patient are realized during the health care encounter Albert Goldfain http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 creation date: 2011-02-21T09:57:44Z health care encounter A part of an organism that has undergone a change in structural integrity and has a higher chance of dysfunction or causing dysfunction in another structure. At the scale of organism (as opposed to the cellular scale or the population scale), an injury is typically the result of a catastrophic event. Consider the implications of making 'injury' a subtype of 'disorder'. Albert Goldfain http://groups.google.com/group/ogms-discuss/browse_thread/thread/ca0ad373f27774c5 creation date: 2011-09-20T09:57:44Z http://purl.obolibrary.org/obo/ogms.owl injury A health care process that involves the interpretation of a clinical picture from a given patient (input) and the assertion to the effect that the patient has a disease, disorder, or syndrome of a certain type, or none of these (output). Albert Goldfain http://groups.google.com/group/ogms-discuss/browse_thread/thread/2a7008f311fac766/e7de486c94dfd82e creation date: 2011-09-20T09:57:44Z diagnostic process A data item that is about a patient and is the specified output of a health care process assay or diagnostic process creation date: 2018-11-27 clinical data item Social Security Number(SSN) is a Centrally Registered IDentifier that is a nine-digit number issued to U.S. citizens, permanent residents, and temporary (working) residents under section 205(c) of the Social Security Act, codified as 42 U.S.C. § 405(c). The number is issued to an individual by the Social Security Administration, an independent agency of the United States government. Its primary purpose is to track individuals for Social Security purposes. SSN http://en.wikipedia.org/wiki/Social_Security_number Cheng Chen(cxchen1@ualr.edu) social security number A social role inhering in a human being. Mathias Brochhausen William R. Hogan human social role party to a legal entity party to a legal proceeding party to a legal agreement party to a marriage contract party to a power of attorney A human social role borne by a human being being realized in behaviour which is considered socially appropriate for individuals of a specific sex in the context of a specific culture. Mathias Brochhausen http://en.wikipedia.org/wiki/Gender_role gender role A gender role borne by a human being that is realized in behaviour which is considered socially appropriate for individuals of the male sex in the context of the culture in question. Mathias Brochhausen male gender male gender role A gender role borne by a human being that is realized in behaviour which is considered socially appropriate for individuals of the female sex in the context of the culture in question. Mathias Brochhausen female gender female gender role A role in human social processes that is realized by health care processes such as seeking or providing treatment for disease and injury, diagnosing disease and injury, or undergoing diagnosis. William R. Hogan health care role Mathias Brochhausen human health care role A role borne by an organism and that is realized by presenting to a health care provider in a clinical encounter. Amanda Hicks Mathias Brochhausen patient CAFE domain expert working group. In order to avoid the presumption of the formal structures and institutions of Western civilization, bearing a patient role does not entail that the organism presents at an official place of business, with an organization formally and legally registered with various gov't entities, with a person endowed by the gov't with certain certifications. patient role A human health care role inhering in an organization or human being that is realized by a process of providing health care services to an organism. Mathias Brochhausen William R. Hogan health care provider role A health care role borne by a human being and realized by promoting, maintaining or restoring human health through the study, diagnosis, and treatment of disease, injury and other physical and mental impairments. Mathias Brochhausen physician http://en.wikipedia.org/wiki/Physician physician role A health care role borne by a human being and realized by the care of individuals, families, and communities so they may attain, maintain, or recover optimal health and quality of life. Mathias Brochhausen nurse based on: http://en.wikipedia.org/wiki/Nursing nurse role Definition needed, but the idea is that we want to differentiate between provider and payer organizations. Some organizaitons have both roles (e.g., UPMC has a Hospital Division, a Physician Divison, and an Insurance Division). health care provider organization role person health care provider role 2 A health care provider organization role that inheres in an organization consisting of two or more physicians. Amanda Hicks physician practice A health care provider organization role that inheres in an organization that is comprised of other organizations. Amanda Hicks integrated delivery network An object aggregate of organisms. Any arbitrary collection of organisms. They need not be of the same taxonomic class. collection of organisms An object aggregate all of whose components are human beings. collection of humans A role inhering in an entity realized by social interactions in human society. Mathias Brochhausen Previous definition: A role played by an entity in human social processes. role in human social processes A role in human social processes that inheres in an organization. William R. Hogan Defined class that we will ultimately move to an application ontology. We are leaving here for now until we determine which application ontology: it is likely going to be an ontology that does not currently (2012-06-05) exist. Ditto for its current descendants. organization social role A role in human social processes that inheres in an organism. William R. Hogan Mathias Brochhausen Defined class that we will ultimately move to an application ontology. We are leaving here for now until we determine which application ontology: it is likely going to be an ontology that does not currently (2012-06-05) exist. Ditto for its current descendants. Includes animals as well as humans. For example, pet, assistance animal, animal grown for food, work animal, domesticated animal, K-9, etc. Human roles include gender role, party to legal entities, health care provider roles like doctor, nurse, etc. Previous definition: A role in human social processes played by an organism. organism social role An organization social role that is realized by a health care process. Previous definition: An organization social role played by an organization in health care processes. organization health care role A patient role that inheres in a human being. human patient role 2 An object aggregate that is not itself an organization and whose members are only organizations that have some feature in common William R. Hogan Amanda Hicks It is often convenient to group organizations together that otherwise might not even interact with one another. aggregate of organizations A role borne by a human individual or by a collection of humans regarded as possessing rights and duties enforeable at law. Mathias Brochhausen Malcolm N. Shaw: International Law. Cambridge University Press, Cambridge, 2008. We are aware of the fact that Wikipedia's definition differs from ours by saying that "Legal personality (...) is the characteristic of a non-living entity regarded by law to have the status of personhood" (http://en.wikipedia.org/wiki/Legal_personality) However, Shaw explicates: "In any legal system, certain entities, whether they be individuals or companies, will be regarded as possessing rights and duties enforceable at law. Thus an individual may prosecute or be prosecuted for assault and a company can sue for breach of contract. They are able to do this because the law recognises them as 'legal persons' possessing the capacity to have and to maintain certain rights, and being subject to perform specific duties. (...) In municipal law individuals, limited companies and public corporations are recognized as each possessing a distinct legal personality, the terms of which are circumscribed by the relevant legislation" (Shaw MN: International Law. Sixth Edition. Cambridge University Press, Cambridge, 2008). We hold that Shaw's position is ontological more prolific since it not only allows to explain how groups of individuals become recognized as unities at law, but also how different individuals can hold different legal personality roles (always against the context of one legal system). The latter will proof useful when dealing with the representing comatous patients or minorsat law in ontologies. legal person role A role that inheres in an organism and is realized by habitually smoking tobacco products. smoker role material entity role A healthcare provider role that inheres in an organization and is realized by providing inpatient and outpatient care. Mathias Brochhausen hospital role An organization social role that inheres in an organization and is realized by providing formal education to students. Mathias Brochhausen school role An organization that is the bearer of a school role. Mathias Brochhausen school organization A human social role that is realized by the process of formal education that the bearer undergoes. Mathias Brochhausen student role Mathias Brochhausen nursery school role Mathias Brochhausen primary school role Mathias Brochhausen secondary school role A trauma patient role that inheres in a homo sapiens who is under the age of 15 years. Amanda Hicks pediatric trauma patient The following definition for 'pediatric trauma patient' was approved by the CAFE team of domain experts (experts in trauma care) May 29, 2015. "A trauma patient who is under the age of 15 years." pediatric trauma patient role A patient role that inheres an organism suffering one or more injuries. Amanda Hicks injured patient The following definition for 'injured patient' was approved by the CAFE team of domain experts (experts in trauma care) May 29, 2015. A patient suffering one or more injuries. injured patient role A patient role that inheres in an organism suffering a thermal, electrical, chemical or radiation burn. Amanda Hicks The following definition for 'burn patient' was approved by the CAFE team of domain experts (experts in trauma care) May 29, 2015. A patient suffering a thermal, electrical, chemical or radiation burn. burn patient burn patient role A physician role that is created by training and certification in rehabilitation/physical medicine and that is realized by the provision of or supervising of the provision of rehabilitation or physical therapy to a patient. Amanda Hicks physiatrist The following definition for 'physiatrist' was approved by the CAFE team of domain experts (experts in trauma care) May 29, 2015. A physician with training and certification in rehabilitation/physical medicine. Definition updated May 5, 2016. Original definitions was, a health care role borne by a human being and realized by training and certification in rehabilitation medicine. physiatrist role A patient role that inheres in an organism with some non-superficial traumatic injury. The role is realized by admision to a hospital, transfer from one hospital to another for the purpose of trauma care, or has death as a result of the traumatic injury. Amanda Hicks trauma patient The following definition for 'trauma patient' was approved by the CAFE team of domain experts (experts in trauma care) May 29, 2015. A patient sustaining an injury who has been admitted to the hospital, transferred from one hospital to another for the purpose of trauma care, or has died as a result of the traumatic injury. trauma patient role A function that inheres in a material entity and, if realized, is realized by protecting persons and their possessions from weather and by some person or group of persons habitually sleeping in at least one site that is contained by that material entity. Amanda Hicks residence function A human or collection of humans that occupies a housing unit by storing their possessions there and habitually sleeping there thereby participating in the realization of its residence function. Amanda Hicks household Amanda hicks employee employee role A US cenus reference person role is a human social role that inheres in a Homo sapiens who is a member of a household and is realized by other persons in the household being recorded in the US census in relation to that person. Amanda Hicks http://www.census.gov/cps/about/cpsdef.html last accessed June 30, 2015 US Census reference person role A role that concretizes a socio-lega generically dependent continuant Amanda Hicks socio-legal human social role A socio-legal human social role that concretizes a socio-legally generically dependent continuat that was created by a declaration performed by an organization. Amanda Hicks human role within an organization employer role payer role party to an insurance policy Amanda Hicks A US Census unemployed role is a human social role that inheres in a human who is legally eligible to work, is conferred by the U.S. Census Bureau, and is realized by the bearer not working and either making active efforts to find employment in the four weeks prior to the reference week or waiting to be recalled from temporary layoff. US Census unemployed role A human health care provider role that inheres in a human being that is created by state licensing and that is realized by taking patient histories, performing physical exams, diagnosing illnesses, developing treatment plans, ordering lab tests, prescribing medications, counselling and educating patients, suturing wounds, and assisting in surgery under the supervision of a physician or a surgeon. US physician assistant role A physician role that inheres a human being and, if it is realized, is realized either by administering medication for the temporary general or local suppression of sensory or motor nerve function during some health care encounter or by making decisions independently of a supervising physician regarding the adminstration of such medication. anesthesiologist role surgeon role A surgeon role realized by its bearer using performing neurosurgery. neurosurgereon role A role that inheres in an organism and is realized by habitually smoking 10 or more tobacco cigerettes a day or the equivalent in other tobacco products. heavy smoker role A role that inheres in an organism and is realized by habitually smoking 1>10 tobacco cigerettes a day or the equivalent in other tobacco products. light smoker role employment data income data government assistance health care plan data health care plan data government assistance income data WIC data socio-economic data A planned process that achieves the planned objective of precision medicine objective. Specifically, it is a medical process that includes the customization of healthcare, with medical decisions, treatments, practices, or products being tailored to the individual patient. Oliver He, Jie Zheng https://en.wikipedia.org/wiki/Precision_medicine precision medicine process An investigation that is targeted for precision medicine https://en.wikipedia.org/wiki/Precision_medicine precision medicine investigation the number of people living together supported jointly by an household income https://www.healthcare.gov/income-and-household-information/household-size/ We may use IRS's definition: https://www.healthcare.gov/income-and-household-information/household-size/ household size more than 5.5 pounds (2500 grams) birth weight less than 5.5 pounds (2500 grams) birth weight unknown birth weight birth weight declined to answer individual plan insurance (paid by the member) group plan insurance through employee union USA government health plan insurance no insurance status body temperature measured orally body temprature by ear (tempanic, aural) body temprature by forhead arterial line body temperature What is other? body temprature by other measurement An education level that indicates a grade of higher than 7th but lower than 12 as the highest level of educational achievement. higher than 7th but less than 12th Grade education level direct serum bilirubin level precision medicine objective An education level that indicates the 7th grade complete or less as the highest level of educational achievement. less than 8th Grade education level An education level that indicates that the highest level of education achievement for a person is a high school completion, GED, or equivalent high school completion, GED or equivalent An information content entity that is the answer to a specific question Fred Dowd, Oliver He answer to question An answer to question where the answer is Yes. Oliver He, Fred Dowd yes answer to question An answer to question where the answer is No. Fred Dowd, Oliver He no answer to question An answer to question that indicates the response to the specified question is unknown. Fred Dowd, Oliver He, Edison Ong do not know answer to question unknown answer to question A do not know answer to question that is answered due to data unavailable Fred Dowd, Oliver He do not know due to data unavailable answer to question An answer to question where one declines to answer the specified question. Fred Dowd, Oliver He decline to answer declined to provide refuse to answer refused to answer declined to answer to question An answer to question that is not enumerated in the list and then may be entered with free text in a separate text box Oliver He, Fred Dowd other answer to question An answer to question that is not listed in the whole list of response options Oliver He, Fred Dowd none answer to question A textual entity that is a question presented in text Fred Dowd, Oliver He textual question medical history form A form with questions that is used to assess a person's eligibility to participate in a specific study (e.g., kidney precision medicine project). Fred Down, Oliver He eligibility assessment form A form with questions that includes statistical data related to particular groups within a population where a person belongs to Fred Dowd, Oliver He demographics form https://www.investopedia.com/terms/d/demographics.asp demographic information form physical measurement form A textual question that includes a list of enumerated answers Fred Dowd, Oliver He question with enumerated responses A question that has two primary and definitive answers: Yes and No, and there may be other given options like Don't know or Decline to answer. Fred Dowd, Oliver He question with yes and no responses A question with enumerated responses where one can only choose one answer. Fred Dowd, Oliver He question with enumerated responses where only one answer chosen A question with enumerated responses where one can choose multiple answers. Fred Dowd, Oliver He question with enumerated responses where multiple answers may be chosen A case report form (or CRF) is a paper or electronic questionnaire specifically used in clinical trial research Oliver He, Edison Ong, Fred Dowd, Hong Yu CRF https://en.wikipedia.org/wiki/Case_report_form https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4170533/ case report form Fred Down, Oliver He laboratory result form Fred Down, Oliver He new patient form Fred Down, Oliver He biopsy procedure form kidney biopsy procedure form Fred Down, Oliver He consent form Fred Down, Oliver He paper form Medical records release form is usually required to be a paper form that should be signed by the patient who agrees to have his/her medical records released. Fred Dowd, Oliver He paper form with signature required A public health process that involves clean drinking water and adequate treatment and disposal of human and animal excreta and sewage. https://en.wikipedia.org/wiki/Sanitation sanitation A form that includes the information of contact for a person Edison Ong, Oliver He contact information form biosample collection form clinic reception form medications form participant study status form hospitalization form personal history form AKI hospitalization form CKD hospitalization form Fred Dowd, Oliver He This should be a paper form participant reported outcome measures form health literacy questionnaire form biopsy safety checklist form post biopsy form A clinical report form that covers the information about the tracking of biopsied tissue tissue tracking form pathology images upload form Dx core - .jpg images QC form diagnostic core .jpg images QC form Dx core - disease categories form diagnostic core - disease categories form central path quality metrics assessment Dx core form central path quality metrics assessment interrogation core form post-biopsy patient experience survey form adverse event entry form month of year The first month of the year in the Gregorian calendar https://en.wikipedia.org/wiki/Gregorian_calendar January The second month of the year in the Gregorian calendar. https://en.wikipedia.org/wiki/Gregorian_calendar February The third month of the year in the Gregorian calendar. https://en.wikipedia.org/wiki/Gregorian_calendar March The4th month of the year in the Gregorian calendar https://en.wikipedia.org/wiki/Gregorian_calendar April The 5th month of the year in the Gregorian calendar https://en.wikipedia.org/wiki/Gregorian_calendar May The 6th month of the year in the Gregorian calendar https://en.wikipedia.org/wiki/Gregorian_calendar June The 7th month of the year in the Gregorian calendar https://en.wikipedia.org/wiki/Gregorian_calendar July The 8th month of the year in the Gregorian calendar https://en.wikipedia.org/wiki/Gregorian_calendar August The 9th month of the year in the Gregorian calendar https://en.wikipedia.org/wiki/Gregorian_calendar September The 10th month of the year in the Gregorian calendar https://en.wikipedia.org/wiki/Gregorian_calendar October The 11th month of the year in the Gregorian calendar https://en.wikipedia.org/wiki/Gregorian_calendar November The 12th month of the year in the Gregorian calendar https://en.wikipedia.org/wiki/Gregorian_calendar December A day of a calendar week that includes covers 24 hours each day. https://en.wikipedia.org/wiki/Week day of week The first day of the week. https://en.wikipedia.org/wiki/Week Monday The second day of the week. https://en.wikipedia.org/wiki/Week Tuesday The third day of the week. https://en.wikipedia.org/wiki/Week Wednesday The fourth day of the week. https://en.wikipedia.org/wiki/Week Thursday The fifth day of the week. https://en.wikipedia.org/wiki/Week Friday The 6th day of the week. https://en.wikipedia.org/wiki/Week Saturday The 7th day of the week. https://en.wikipedia.org/wiki/Week Sunday A day when an organism (e.g., a human) is born. Oliver He, Long Tran birth date https://www.ohdsi.org/web/wiki/doku.php?id=documentation:cdm:person day of birth the anniversary of the birth of a person Oliver He https://en.wikipedia.org/wiki/Birthday There is a difference between birthday and birthdate: The former, such as February 29, occurs each year, while the latter is the exact date a person was born (e.g., January 15, 2001). birthday information associated with an individual Oliver He https://www.oic.qld.gov.au/guidelines/for-government/access-and-amendment/introduction-to-the-acts/what-is-personal-information personal information A name of a person, which can have different types human name https://en.wikipedia.org/wiki/Personal_name person name Christian name forename given name https://en.wikipedia.org/wiki/Personal_name person first name family name surname https://en.wikipedia.org/wiki/Personal_name person last name https://en.wikipedia.org/wiki/Personal_name person middle name 患者本人在公安户籍管理部门正式登记注册的姓氏和名称 Suyuan Peng, Hong Yu, Yongqun He https://en.wikipedia.org/wiki/Personal_name 《电子病历基本数据集 第10部分：住院病案首页》WS 445.10-2014 person full name A person name that identifies a person for legal, administrative and other official purposes Oliver He legal name https://en.wikipedia.org/wiki/Legal_name person legal name A person name that is given at birth birth name A person name that is used for a person to access a computer system. person login username A woman's surname before marriage Edison Ong, Oliver He https://en.wikipedia.org/wiki/Maiden_and_married_names maiden name A person name that is fictitious and generated for a person to perform a particular social role. pseudonym Personal information that indicates a person's status in marriage https://en.wikipedia.org/wiki/Marital_status marital status civil status married https://en.wikipedia.org/wiki/Marital_status married marital status single marrital status divorced marrital status A marital status that indicates no marriage status due to the death of his/her spouse and no remarriage. Oliver He https://en.wikipedia.org/wiki/Widow widowed marrital status legally separated marital status not married marital status An education level that indicates that the highest level of education achievement for a person. Oliver He, Edison Ong highest degree of education completed highest degree of education received highest degree of school completed education level A telephone number is a sequence of digits assigned to a fixed-line telephone subscriber station connected to a telephone line or to a wireless electronic telephony device, such as a radio telephone or a mobile telephone, or to other devices for data transmission via the public switched telephone network (PSTN) or other public and private networks. Oliver He phone number https://en.wikipedia.org/wiki/Telephone_number telephone number A telephone number used for a phone at home Oliver He home phone number home telephone number A telephone number used for a phone at work Oliver He work phone number work telephone number A telephone number that is used in a cellular device Oliver He cell phone number cellular phone number cellular telephone number The status of actively looking for employment, but not being currently employed. joblessness unemployment https://en.wikipedia.org/wiki/Unemployment NCIT_C75563 C0041674 unemployment status home postal address work postal address A series of letters or digits or both, sometimes including spaces or punctuation, included in a postal address for the purpose of sorting mail. Oliver He post code postcode https://en.wikipedia.org/wiki/Postal_code postal code A ZIP Code is a postal code used by the United States Postal Service (USPS). The term ZIP is an acronym for Zone Improvement Plan. Oliver He, Fred Dowd https://en.wikipedia.org/wiki/ZIP_Code ZIP code The personal information that indicates an individual's or his/her family's economic and social position in relation to others, based on income, education, and occupation. Oliver He https://en.wikipedia.org/wiki/Socioeconomic_status socioeconomic status An socioeconomic status that indicates the status of being employed in an occupation to perform an activity or service for wage or salary. It is the status of a worker in a company or institute on the basis of the contract of work or duration of work done. Oliver He https://definitions.uslegal.com/e/employment-status/ https://en.wikipedia.org/wiki/Employment NCIT_C25172 C0014003 employment status A state of employment in which a person works for a minimum number of hours defined as full-time by their employer. https://en.wikipedia.org/wiki/Full-time NCIT_C52658 C0682295 full time employment status a status of employment that carries fewer hours per week than a full-time job. part-time contract part-time employment https://en.wikipedia.org/wiki/Part-time_contract NCIT_C75562 C0682294 part time employment status an employment status where the work is arranged and paid on a hourly basis. NCIT_C116002 C0681101 hourly employment status The state of working for oneself rather than an employer. https://en.wikipedia.org/wiki/Self-employment NCIT_C116000 C0425092 self-employment status An employment situation where the working arrangement is limited to a certain period of time based on the needs of the employing organization. odd job temporary work https://en.wikipedia.org/wiki/Temporary_work temporary employment status An education level that indicates that the highest level of education achievement for a person is a Master's degree. M.S. degree education level MS degree completed Master's degree education level An education level that indicates that the highest level of education achievement for a person is an academic Doctorate degree Ph.D. degree education level PhD degree completed academic Doctorate degree education level An education level that indicates that a person does not have formal school education. no formal school education level An education level that indicates that the highest level of education achievement for a person is a high school completion. high school education level An education level that indicates that the highest level of education achievement for a person is a Bachelor's degree B.S. degree completed B.S. degree education level Bacholar's degree completed Bachelor's degree education level An education level that indicates that a person has obtained a degree allowing them to practice a profession, such as law, medicine, music, or ministry. NCIT_C70558 C2347690 professional doctorate degree education level M.D. completion education level Pharmacy complete education level An education level that indicates that the highest level of education achievement for a person is kindergarten completion. kindergarten completion education level An education level that indicates that the highest level of education achievement for a person is preschool. preschool completion education level An education level that indicates that the highest level of education achievement for a person is the pass of a General Education Development (GED) tests. The GED tests are a group of four subject tests which, when passed, provide certification that the test taker has United States or Canadian high school-level academic skills. general equivalency diploma completion https://en.wikipedia.org/wiki/General_Educational_Development GED education level An education level that indicates that the highest level of education achievement for a person is the 1st Grade elementary school completion. 1st Grade education level An education level that indicates that the highest level of education achievement for a person is the second Grade elementary school completion. 2nd Grade education level An education level that indicates that the highest level of education achievement for a person is the third Grade elementary school completion. 3rd Grade education level An education level that indicates that the highest level of education achievement for a person is the 4th Grade elementary school completion. 4th Grade education level An education level that indicates that the highest level of education achievement for a person is the 5th Grade elementary school completion. 5th Grade education level An education level that indicates that the highest level of education achievement for a person is the 6th Grade elementary school completion. 6th Grade education level An education level that indicates that the highest level of education achievement for a person is the 7th Grade elementary school completion. 7th Grade education level An education level that indicates that the highest level of education achievement for a person is the 8th Grade elementary school completion. 8th Grade education level An education level that indicates that the highest level of education achievement for a person is the 9th Grade elementary school completion. 9th Grade education level An education level that indicates that the highest level of education achievement for a person is the 10th Grade elementary school completion. 10th Grade education level An education level that indicates that the highest level of education achievement for a person is the 11th Grade elementary school completion. 11th Grade education level An education level that indicates that the highest level of education achievement for a person is the 12th Grade elementary school completion. 12th Grade education level An education level that indicates that the highest level of education achievement for a person is a degree from a 2 year college program. NCIT_C19752 C1879750 associate academic degree education level An education level that indicates that the highest level of education achievement for a person is a degree from an occupational, technical, or vocational program NCIT_C67141 C1883542 vocational program completion education level The code in the specific coding system for the payment method of the expenses incurred in a single hospitalization of the patient 患者单次住院诊疗所发生费用的支付方式的特定编码体系中的代码 Suyuan Peng, Hong Yu, Yongqun He 《电子病历基本数据集 第10部分：住院病案首页》WS 445.10-2014 NCIT_C16745 C0021672 医疗付费方式 health insurance plan A joint federal and state program that helps with medical costs for some people with limited income and resources. https://en.wikipedia.org/wiki/Medicaid Medicaid Medicare is a national health insurance program in the United States, begun in 1966 under the Social Security Administration and now administered by the Centers for Medicare and Medicaid Services (CMS). https://en.wikipedia.org/wiki/Medicare_(United_States) Medicare private health insurance plan worker compensation insurance plan body weight A body weight that is obtained immediately after birth Oliver He, Edison Ong NCIT_C76325 birth weight emergency contact phone number care provider 1st care provider primary care provider a centrally registered identifier symobol that refers to a specific study Oliver He, Edison Ong study ID centrally registered study identifier symbol 2nd care provider secondary care provider 3rd care provider tertiary care provider An email address that is used secondary after the de fault first email address. 2nd email address A textual question about age Fred Dowd, Oliver he age question A textual question that asks whether a person's age is less than 18 years old Fred Dowd, Oliver He Whether age less than 18 years old An eligibility assessment form that is designed and used by the Kidney Precision Medicine Project (KPMP; http://kpmp.org) organization. Oliver He, Edison Ong, Fred Dowd KPMP eligibility assessment form BMI question Whether BMI greater than 40 kg/m2 Whether BMI greater than 40 kg per m2 BMI greater than 40 kg per m2 question about blood transfusion Edison Ong, Oliver He Whether unwilling to receive blood transfusion pregnancy question A pregnancy question that asks whether a person is pregnant at the moment of being questioned Fred Dowd, Oliver He Whether pregnancy occurs now Whether pregnant transplant question A transplant question that asks whether a person has received some transplant (includes solid transplant and bone marrow). Example transplants are kidney transplant and heart transplant. Fred Dowd, Oliver He Whether transplant recipient A transplant question that asks whether a person has received a kidney transplant. Fred Dowd, Oliver He Whether kidney transplant recipient KPMP clinical report form A biopsy procedure form that is designed and used by the Kidney Precision Medicine Project (KPMP) organization. Oliver He, Fred Dowd, Edison Ong KPMP biopsy procedure form A biosample collection form that is designed and used by the Kidney Precision Medicine Project (KPMP) organization. KPMP biosample collection form An adverse event entry form that is designed and used by the Kidney Precision Medicine Project (KPMP) organization. KPMP adverse event entry form A biopsy safety checklist form that is designed and used by the Kidney Precision Medicine Project (KPMP) organization. Oliver He, Fred Dowd, Edison Ong KPMP biopsy safety checklist form A clinic reception form that is designed and used by the Kidney Precision Medicine Project (KPMP) organization. Oliver He, Edison Ong, Fred Dowd KPMP clinic reception form A contact information form that is designed and used by the Kidney Precision Medicine Project (KPMP) organization. KPMP contact information form KPMP demographic information form KPMP health literacy questionnaire form A textual question that is about eligibility of a person to participate in a project. Edison Ong, Oliver He eligibility question KPMP AKI hospitalization form KPMP CKD hospitalization form KPMP laboratory result form KPMP medical history form Fred Dowd, Oliver He This form is the end of a successful screening process KPMP consent form KPMP medications form KPMP new patient form KPMP participant reported outcome measures form KPMP participant study status form KPMP pathology images upload form KPMP patient experience survey form KPMP personal history form KPMP physical measurement form KPMP post biopsy form KPMP tissue tracking form KPMP Dx core - .jpg images QC form KPMP Dx core - disease categories form KPMP central path quality metrics assessment Dx core form KPMP central path quality metrics assessment interrogation core form The last four digits of a social security number, which is often asked in a survey form. Oliver He last 4 digits of SSN http://en.wikipedia.org/wiki/Social_Security_number last four digits of social security number A question in a survey form may ask whether a provided email address belongs to self The self is an individual person as the object of his or her own reflective consciousness. Oliver He human self https://en.wikipedia.org/wiki/Self self A textual question about age Fred Dowd, Oliver he email question An email question that asks the exact email address What email address An email question that asks whether the email address provided belongs to the person being surveyed. Whether self owns email address An email question that asks whether the email address provided belongs to the person being surveyed. Who owns email address A textual question that asks the birthday of the person being surveyed What is your birthday The textual name of the contact person or organization contact name The textual name of the contact person or organization that will be contacted during emergency emergency contact name Who owns the 2nd email address Who owns the 3rd email address physician information physician specialty information Health care or healthcare is the maintenance or improvement of health via the prevention, diagnosis, and treatment of disease, illness, injury, and other physical and mental impairments in human beings. Oliver He healthcare https://en.wikipedia.org/wiki/Health_care health care A health care rendered for the benefit of a patient. C0017313 C15239 patient care Primary care refers to the work of health professionals who act as a first point of consultation for all patients within the health care system Oliver He https://en.wikipedia.org/wiki/Health_care#Primary_care C94340 C0033137 primary care Secondary care includes acute care: necessary treatment for a short period of time for a brief but serious illness, injury, or other health condition. This care is often found in a hospital emergency department. Secondary care also includes skilled attendance during childbirth, intensive care, and medical imaging services. Oliver He https://en.wikipedia.org/wiki/Health_care#Secondary_care secondary care Tertiary care is specialized consultative health care, usually for inpatients and on referral from a primary or secondary health professional, in a facility that has personnel and facilities for advanced medical investigation and treatment, such as a tertiary referral hospital. Oliver He https://en.wikipedia.org/wiki/Health_care#Tertiary_care tertiary care The term quaternary care is sometimes used as an extension of tertiary care in reference to advanced levels of medicine which are highly specialized and not widely accessed. Oliver He https://en.wikipedia.org/wiki/Health_care#Quaternary_care quaternary care A patient care that is provided in hospital. Oliver He https://en.wikipedia.org/wiki/Health_care#Secondary_care It is sometimes the synonym of secondary care. However, many secondary care providers, such as psychiatrists, clinical psychologists, occupational therapists, most dental specialties or physiotherapists do not necessarily work in hospitals. Some primary care services are delivered within hospitals. Depending on the organization and policies of the national health system, patients may be required to see a primary care provider for a referral before they can access secondary care. hospital care nephrology care endocrinology care physician question What is the physician's specialty? What physician's specialty hospital question What is name of clinic or hospital what name of hospital postal address question address question What street name What is the city name? What city What state What Zip code What street number and name What apartment number What apartment Which country? What country Do you have physician who provides your usual medical care? Whether have physician for usual medical care nephrologist care provider nephrology care provider patient condition question Whether diabetic kidney disease (DKD) Whether hypertensive CKD (H-CKD) Whether diabetic nephropathy resisters percutaneous biopsy Whether AKI percutaneous biopsy Whether AKI open biopsy Whether biopsy CRF filled up by patient What postal code CRF filled up by research coordinator CRF filled up by biopsy operator biopsy-related CRF post biopsy hospitlization form A clinical report form that is related to the processing and analysis of tissue of diseased patient. pathology CRF screening and patient tracking CRF enrollment CRF A eligibility question that asks whether a patient is eligible to consent to participate in a project. Oliver He, Edison Ong Whether patient eligible to consent HIPAA release Whether patient signed HIPPA release form When HIPAA release form signed Whether scanned HIPAA release form uploaded A chronic kidney disease that is accompanied with elevated blood pressure or hypertension Oliver He H-CKD https://www.nejm.org/doi/full/10.1056/NEJMoa0910975 Oliver note: This term is not shown in MONDO or DOID. May request an addition. hypertensive chronic kidney disease a process that obtains a tissue from a living body in order to discover the presence, cause, or extent of a disease, or perform further biomeidcal investigation Oliver He, Hong Yu https://en.oxforddictionaries.com/definition/biopsy https://en.wikipedia.org/wiki/Biopsy biopsy A systematized collection of patient and population electronically-stored health information in a digital format Oliver He, Edison Ong EHR EMR electronic medical record https://en.wikipedia.org/wiki/Electronic_health_record NCIT_C142529 NCIT definition: A digital version of a patient's medical history. [def-source: NCI] electronic health record A biopsy that takes a small piece of tissue out of a living body through the skin, using only a tiny incision Oliver He, Hong Yu http://www.wales.nhs.uk/sitesplus/documents/866/PIU433%284%29%28ABUHB%29%28Active%29%28JAN%2017%29.pdf percutaneous biopsy AKi percutaneous biopsy A biopsy process in which a surgical incision (cut) is made through the skin to expose and remove tissues Oliver He, Hong Yu https://en.wikipedia.org/wiki/Open_biopsy open biopsy AKI open biopsy diabetic nephropathy resisters percutaneous biopsy The state of being free from illness or injury Oliver He, Edison Ong health state https://en.oxforddictionaries.com/definition/health https://en.wikipedia.org/wiki/Health https://www.healthknowledge.org.uk/public-health-textbook/research-methods/1c-health-care-evaluation-health-care-assessment/measures-health-status health status The medical state or condition of a patient Oliver He, Edison Ong medical state https://en.wikipedia.org/wiki/Medical_state medical condition Whether diseased Whether kidney diseased the date or time on which a visit occurs Oliver He clinical visit date visit time NCIT_C83031 C1320303 visit temporal region a machine-readable centrally registered identifier that is represented in a visual format on a surface bar code https://en.wikipedia.org/wiki/Barcode barcode a barcode that represents a specific specimen specimen barcode A planned process that tracks the tissue specimen including tissue vial number, storage location, time of vial arrival to storage, storage temperature, etc. Oliver He, Edison Ong tissue tracking A centrally registered identifier that is assigned for a specific clinical trial registered in the ClinicalTrials.gov. The format for the ClinicalTrials.gov registry number is “NCT” followed by an 8-digit number, e.g.: NCT00000419. Qingliang Leon Li, Asiyah Yu Lin, Oliver He NCT identifier NCT number National Clinical Trial identifier https://clinicaltrials.gov/ct2/about-site/link-to https://www.nlm.nih.gov/bsd/policy/clin_trials.html USA National Clinical Trial identifier A textual entity that is the title of a clinical trial https://prsinfo.clinicaltrials.gov/definitions.html title of clinical trial A title of clinical trial that is recorded as official https://prsinfo.clinicaltrials.gov/definitions.html official title of clinical trial A title of clinical trial that is meant for lay people understanding https://prsinfo.clinicaltrials.gov/definitions.html lay title of clinical trial A person who performs an investigation task and takes the role of an investigator role. Leon Li, Oliver He, Asiyah Lin https://prsinfo.clinicaltrials.gov/definitions.html investigator An investigator who is involved in a clinical trial and is responsible for ensuring that an investigation is conducted according to the signed investigator statement, the investigational plan, and applicable regulations; for protecting the rights, safety, and welfare of subjects under the investigator's care; and for the control of drugs under investigation. Oliver He https://en.wikipedia.org/wiki/Clinical_investigator clinical investigator The date on which a study starts study start date The (estimated) date on which the clinical study is open for recruitment of participants, or the actual date on which the first participant is enrolled. https://prsinfo.clinicaltrials.gov/definitions.html clinical trial start date The date on which a study completes Oliver He study completion date The date the final participant was examined or received an intervention for purposes of final collection of data for the primary and secondary outcome measures and adverse events (for example, last participant’s last visit), whether the clinical study concluded according to the pre-specified protocol or was terminated. https://prsinfo.clinicaltrials.gov/definitions.html clinical trial study completion date The date that the final participant was examined or received an intervention for the purposes of final collection of data for the primary outcome, whether the clinical study concluded according to the pre-specified protocol or was terminated. In the case of clinical studies with more than one primary outcome measure with different completion dates, this term refers to the date on which data collection is completed for all of the primary outcomes. https://prsinfo.clinicaltrials.gov/definitions.html clinical trial primary completion date The main objective of the intervention(s) being evaluated by the clinical trial. primary purpose of clinical trial https://prsinfo.clinicaltrials.gov/definitions.html clinical trial primary purpose specification a date when a registration occurs date of registration A primary outcome measure used to describe patterns of diseases or traits or associations with exposures, risk factors or treatment. primary outcome https://prsinfo.clinicaltrials.gov/definitions.html primary health outcome measurement datum The current stage of a clinical study and whether it is or will be open for enrollment Oliver He https://clinicaltrials.gov/ct2/help/glossary/recruitment-status recruitment status A case report form that is presented in an electronic format Fred Dowd, Oliver He eCRF https://en.wikipedia.org/wiki/Case_report_form#eCRF electronic case report form A human being who is a candidate to participant in a clinical study Fred Dowd, Oliver He clinical study participant candidate answering textual question a date of the present date Oliver He, Edison Ong today's date CRF filled up by participant candidate Fred Dowd, Edison Ong, Oliver He pregnancy test positive Fred Dowd, Edison Ong, Oliver He hemoglobin test finding Fred Dowd, Edison Ong, Oliver He In KPMP, the hemoglobin < 9 g/dl is considered as hemoblobin test positive. hemoglobin test positive with result < 9 g/dl a date when a test is performed at the first time Oliver He, Edison Ong date of first test a date when a test is performed Oliver He, Edison Ong date of test a date when a test is performed at the second time Oliver He, Edison Ong date of second test A person name that includes both the first and last name Edison Ong, Oliver He first and last name human first and last name person first and last name A date when a document is signed Oliver He, Edison Ong sign date Oliver He, Edison Ong status The current stage of a clinical study and whether it is or will be open for enrollment Oliver He https://clinicaltrials.gov/ct2/help/glossary/recruitment-status study status Oliver He, Edison Ong patient status a selection criterion (rule) which defines and states the exclusion condition for an entity to be considered as suitable for a given task or participation in a process. Oliver He, Edison Ong https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6044655/ Replace by a corresponding OBI term exclusion criterion - obsolete An exclusion criterion that relates to the process of bleeding Oliver He, Edison Ong bleeding exclusion criteria A case report form of PROMIS: Patient-Reported Outcomes Measurement Information System. PROMIS is a set of person-centered measures that evaluates and monitors physical, mental, and social health in adults and children. It can be used with the general population and with individuals living with chronic conditions. Fred Dowd, Edison Ong, Oliver He Patient-Reported Outcome Measures form http://www.healthmeasures.net/explore-measurement-systems/promis PROMIS form kit identifier A centrally registered identifier that is for a kit used in biopsy Fred Dowd, Edison Ong, Oliver He biopsy kit identifier A PROMIS form that is designed and used by the KPMP project (http://kpmp.org). Oliver He KPMP PROMIS form A biopsy attempt Fred Dowd, Edison Ong, Oliver He biopsy pass A biopsy that uses needle Fred Dowd, Edison Ong, Oliver He needle biopsy A textual question about health condition Oliver He, Edison Ong health status question A health status question that asks about the condition of a person's heath, which can be a selection from different options such as Excellent, Very good, Good, Fair, or Poor. Oliver He, Edison Ong what health status excellent health status very good health status good health status fair health status poor health status quality of life excellent quality of life very good quality of life good quality of life fair quality of life poor quality of life consent status A consent status that indicates a participant unwilling to receive a procedure of blood transfusion Edison Ong, Oliver He unwilling to receive a blood transfusion A consent status that indicates a participate willing to receive a procedure of blood transfusion Edison Ong, Oliver He willing to receive a blood transfusion year A textual quesition thta is about medical history of a person medical history question What birth weight Qingliang Leon Li, Asiyah Yu Lin, Oliver He https://pubchem.ncbi.nlm.nih.gov/source/NIPH%20Clinical%20Trials%20Search%20of%20Japan https://rctportal.niph.go.jp/en/ Japan clinical trial identifier A Japan clinical trial identifier provided by the University Hospital Medical Information Network Center (UMIN-CTR) Qingliang Leon Li, Asiyah Yu Lin, Oliver He https://rctportal.niph.go.jp/en/ UMIN-CTR clinical trial identifier Qingliang Leon Li, Asiyah Yu Lin, Oliver He https://rctportal.niph.go.jp/en/ JAPIC clinical trial identifier Qingliang Leon Li, Asiyah Yu Lin, Oliver He https://rctportal.niph.go.jp/en/ JMACCT clinical trial identifier EudraCT Number: 2007-002422-29 Qingliang Leon Li, Asiyah Yu Lin, Oliver He EudraCT identifier https://en.wikipedia.org/wiki/EudraCT https://www.clinicaltrialsregister.eu/ctr-search/search https://www.clinicaltrialsregister.eu/ctr-search/search?query=eudract European clinical trial registry identifier A clinical trial that covers both Phase 1 and 2 Leon Li, Asiyah Lin, Oliver He https://en.wikipedia.org/wiki/Clinical_trial Phase I/II clinical trial Leon Li, Asiyah Lin, Oliver He combinational intervention The quality of a clinical trial that studies a drug or biological product. The phase is based on the study's objective, the number of participants, and other characteristics. According to USA FDA, there are five phases: Early Phase 1 (formerly listed as Phase 0), Phase 1, Phase 2, Phase 3, and Phase 4. Leon Li, Asiyah Lin, Oliver He clinical trial stage https://www.clinicaltrials.gov/ct2/help/glossary/phase clinical trial phase A clinical trial phase that represents the first-in-man trial, which tests within a small group of people (typically 20-80) to evaluate safety, determine safe dosage ranges, and begin to identify side effects. A drug's side effects could be subtle or long term, or may only happen with a few people, so phase 1 trials are not expected to identify all side effects. Leon Li, Asiyah Lin, Oliver He Phase 1 Phase I http://purl.obolibrary.org/obo/NCIT_C15600 https://en.wikipedia.org/wiki/Clinical_trial C0920321 C15600 clinical trial phase 1 A clinical trial phase that is designed to study a biomedical or behavioral intervention in a larger group of people (several hundred), to evaluate the drug's effectiveness for a particular indication in patients with the disease or condition under study, and to determine the common short-term side effects and risks associated with the intervention. [def-source: NCI] Leon Li, Asiyah Lin, Oliver He Phase II http://purl.obolibrary.org/obo/NCIT_C15601 https://en.wikipedia.org/wiki/Clinical_trial C0282460 C15601 clinical trial phase 2 A clinical trial phase that is designed to investigate the efficacy of the biomedical or behavioral intervention in large groups of human subjects (from several hundred to several thousand), to confirm efficacy, to monitor adverse reactions to the new medication or treatment regimen with respect to long-term use and by comparing the intervention to other standard or experimental interventions as well as to a placebo. [def-source: NCI] Leon Li, Asiyah Lin, Oliver He Phase III http://purl.obolibrary.org/obo/NCIT_C15602 https://en.wikipedia.org/wiki/Clinical_trial C0282461 C15602 clinical trial phase 3 A clinical trial phase that is designed for a randomized, controlled trial to evaluate the long-term safety and efficacy of a drug for a given indication. Often they are designed to study side effects that may have become apparent after the phase III study was completed. [def-source: NCI] Leon Li, Asiyah Lin, Oliver He Phase IV https://en.wikipedia.org/wiki/Clinical_trial C0282462 C15603 clinical trial phase 4 A clinical trial phase that is designed to use an investigational agent that is available only in very limited quantities and which has never previously given to humans or for which there is extremely limited human experience. Phase 0 clinical trials are intended to enable researchers to understand the path of the drug in the body and its efficacy. Adverse event reporting in Phase 0 trials is expedited. [def-source: NCI] Leon Li, Asiyah Lin, Oliver He Early Phase 1 Pre-Clinical Phase clinical trial phase 0 http://purl.obolibrary.org/obo/NCIT_C54721 https://en.wikipedia.org/wiki/Clinical_trial C1882358 C54721 clinical trial early phase 1 A clinical trial that covers both Phase 2 and 3 Leon Li, Asiyah Lin, Oliver He https://en.wikipedia.org/wiki/Clinical_trial Phase II/III clinical trial Leon Li, Asiyah Lin, Oliver He radiation procedure radiation Leon Li, Asiyah Lin, Oliver He genetic intervention A medical intervention that involves a behavioral process to control, prevent, or treat a behavior problem. Leon Li, Asiyah Lin, Oliver He https://www.understood.org/en/learning-attention-issues/treatments-approaches/educational-strategies/behavior-intervention-plans-what-you-need-to-know behavioral intervention ImmPort study accession: SDY269 Edison Ong, Oliver He study accession study accession identifier Edison Ong, Oliver He title of investigation title of study A livinging individual who is or becomes a participant in research, either as a recipient of a test article or as a control. A subject may be either a healthy human or a patient. Based on the NIH definition, a living individual about whom an investigator (whether professional or student) conducting the following research: (1) Obtains information or biospecimens through intervention or interaction with the individual, and uses, studies, or analyzes the information or biospecimens; or (2) Obtains, uses, studies, analyzes, or generates identifiable private information or identifiable biospecimens. Oliver He, Anthony Huffman https://grants.nih.gov/policy/humansubjects/research.htm https://irb.research.chop.edu/who-human-subject https://nexus.od.nih.gov/all/2018/08/07/human-subjects-and-clinical-trial-glossary-updates/ human subject In clinicaltrials.gov, contact information character limits: First Name: 62 characters Last Name: 62 characters Degree: 30 characters Phone: 30 characters Phone Ext: 14 characters Email: 254 characters Citation: https://prsinfo.clinicaltrials.gov/definitions.html#StudyOfficials A person who serves as a contact role and has disclosed specified information to be reached. Usually the contact information, such as email and phone number, is provided., Leon, Asiyah, Oliver: Since each contact needs to provide some contact information, we may need to define the contact information. Leon Li, Asiyah Lin, Oliver He https://prsinfo.clinicaltrials.gov/definitions.html#StudyOfficials contact person A contact person for each facility participating in a study. Leon Li, Asiyah Lin, Oliver He https://prsinfo.clinicaltrials.gov/definitions.html facility contact biosample identifier GSM identiifier ImmPort biosample identifier Person to contact if Facility Contact is not available (that is, a second contact person). Leon Li, Asiyah Lin, Oliver He https://prsinfo.clinicaltrials.gov/definitions.html#StudyOfficials facility contact backup Leon Li, Asiyah Lin, Oliver He https://prsinfo.clinicaltrials.gov/definitions.html#StudyOfficials contact of scientific queries An investigation agent role that is taken by a human individual Leon Li, Asiyah Lin, Oliver He human investigator role investigator role a role taken by a person who serves as a contact for some process. Leon Li, Asiyah Lin, Oliver He contact person role Topical ocular hypotensive eye drops Leon Li, Asiyah Lin, Oliver He https://prsinfo.clinicaltrials.gov/definitions.html#StudyOfficials contact for public queries A person who is responsible for the overall scientific leadership of the protocol, including study principal investigator Leon Li, Asiyah Lin, Oliver He https://prsinfo.clinicaltrials.gov/definitions.html#StudyOfficials overall study official A person to whom questions concerning enrollment at any location of the study can be addressed. Leon Li, Asiyah Lin, Oliver He central contact person https://prsinfo.clinicaltrials.gov/definitions.html central contact person of study A person to contact if Central Contact is not available. Leon Li, Asiyah Lin, Oliver He central contact person https://prsinfo.clinicaltrials.gov/definitions.html central contact backup of study information content entity about a contact person Leon Li, Asiyah Lin, Oliver He contact person information A sponsor role taken by an individual, organization, group or other legal entity which takes responsibility for initiating, managing and/or financing a study. The Primary Sponsor is responsible for ensuring that the trial is properly registered. The Primary Sponsor may or may not be the main funder. Leon Li, Asiyah Lin, Oliver He https://www.who.int/ictrp/network/trds/en/ primary sponsor role A sponsor role taken by an additional individual, organization or another legal person, if any, that has agreed with the primary sponsor to take on responsibilities of sponsorship. Leon Li, Asiyah Lin, Oliver He collaborator role https://www.who.int/ictrp/network/trds/en/ A secondary sponsor may have agreed to: - take on all the responsibilities of sponsorship jointly with the primary sponsor; or - form a group with the Primary Sponsor in which the responsibilities of sponsorship are allocated among the members of the group; or - act as the Primary Sponsor’s legal representative in relation to some or all of the trial sites. by WHO (https://www.who.int/ictrp/network/trds/en/) In clinicaltrials.gov, the secondary sponsor role can be taken by a project collaborator (Reference: https://prsinfo.clinicaltrials.gov/trainTrainer/WHO-ICMJE-ClinTrialsgov-Cross-Ref.pdf). However, a secondary sponsor may serve as a collaborator role, but a collaborator may not serve as a secondary sponsor role. secondary sponsor role An investigator role taken by an individual who is designated as responsible party by the sponsor Leon Li, Asiyah Lin, Oliver He https://prsinfo.clinicaltrials.gov/definitions.html principal investigator role An investigator role taken by an individual who both initiates and conducts the study Leon Li, Asiyah Lin, Oliver He https://prsinfo.clinicaltrials.gov/definitions.html sponsor investigator role An investigation agent role taken by an agent (an individual, organization, group or another legal entity) who provides support to an investigation. The support may include funding, design, implementation, data analysis or reporting. The responsible party is responsible for confirming all collaborators before listing them. Leon Li, Asiyah Li, Oliver He collaborator role https://prsinfo.clinicaltrials.gov/definitions.html#Collaborators https://www.who.int/ictrp/network/trds/en/ A secondary sponsor may serve as a collaborator role. However, a collaborator may not serve as a secondary sponsor role. investigation collaborator role a selection criterion (rule) which defines and states the inclusion condition for an entity to be considered as suitable for a given task or participation in a process. Oliver He, Edison Ong, Leon Li, Asiyah Lin https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6044655/ Replace by a corresponding OBI term inclusion criterion - obsolete A centrally registered unique identifier assigned by the primary registry to a study including a clinical trial. Qingliang Leon Li, Asiyah Yu Lin, Oliver He https://www.who.int/ictrp/network/trds/en/ primary registry identifier An individual, organization, group or other legal entity that involves with any of the following activities: initiating, managing and funding a study Leon Li, Asiyah Lin, Oliver He https://www.who.int/ictrp/network/trds/en/ NCIT_C48355 sponsor investigation agent The individual, organization, group or other legal entity which takes responsibility for initiating, managing and/or financing a study. In clinical trial, the Primary Sponsor is responsible for ensuring that the trial is properly registered. The Primary Sponsor may or may not be the main funder. Leon Li, Asiyah Lin, Oliver He https://www.who.int/ictrp/network/trds/en/ primary sponsor An additional individual, organization or another legal person, if any, that has agreed with the primary sponsor to take on responsibilities of sponsorship. Leon Li, Asiyah Lin, Oliver He https://www.who.int/ictrp/network/trds/en/ A secondary sponsor may have agreed to: - take on all the responsibilities of sponsorship jointly with the primary sponsor; or - form a group with the Primary Sponsor in which the responsibilities of sponsorship are allocated among the members of the group; or - act as the Primary Sponsor’s legal representative in relation to some or all of the trial sites. Reference: https://www.who.int/ictrp/network/trds/en/ secondary sponsor A centrally registered unique identifier besides the primary registry identifier allocated by the Primary Registry, if any. Qingliang Leon Li, Asiyah Yu Lin, Oliver He https://www.who.int/ictrp/network/trds/en/ secondary registry identifier An agent (an individual, organization, group or another legal entity) who provides support to an investigation. The support may include funding, design, implementation, data analysis or reporting. The responsible party is responsible for confirming all collaborators before listing them. Leon Li, Asiyah Li, Oliver He investigation collaborator https://prsinfo.clinicaltrials.gov/definitions.html#Collaborators https://www.who.int/ictrp/network/trds/en/ collaborator An investigator who is designated as responsible party by the sponsor Leon Li, Asiyah Lin, Oliver He https://prsinfo.clinicaltrials.gov/definitions.html principal investigator An investigator role taken by an individual who both initiates and conducts the study Leon Li, Asiyah Lin, Oliver He https://prsinfo.clinicaltrials.gov/definitions.html sponsor investigator A role taken by a string (which may have mixed integer and text) that serves as a unique record. Leon Li, Asiyah Lin, Oliver He identifier role obsolete class An identifier role that inheres in a unique record which provides an identifier secondary to the primary registry identifier. Qingliang Leon Li, Asiyah Yu Lin, Oliver He https://www.who.int/ictrp/network/trds/en/ secondary registry identifier role An identifier role that is assigned by a primary registry and provides a unique record. Qingliang Leon Li, Asiyah Yu Lin, Oliver He https://www.who.int/ictrp/network/trds/en/ primary registry identifier role a human who is a recipient of a health care service performed by healthcare professionals. human patient https://en.wikipedia.org/wiki/Patient Hong Yu, Oliver He patient A systematic, scientific investigation that can be either interventional or observational and involves human beings as research subjects. Human subject research can be either medical (clinical) research or non-medical (e.g., social science) research. Oliver He human investigation human study https://en.wikipedia.org/wiki/Human_subject_research human subject study A collection of humans who share a defining characteristic, typically those who are collectively experiencing a common event (e.g., a clincal trial study) in a selected period. Anthony Huffman, Oliver He https://en.wikipedia.org/wiki/Cohort_study human cohort A material entity that is composed of organic structure and is capable of self-replication (with or without host support). Various types of self-replicating organic structures can be found at: https://en.wikipedia.org/wiki/Template:Self-replicating_organic_structures. Oliver He organic self-replicating system https://en.wikipedia.org/wiki/Self-replication https://en.wikipedia.org/wiki/Template:Self-replicating_organic_structures https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5496545/ self-replicating organic structure A self-replicating organic structure that is composed of one cell or multiple cells and embodies the properties of life. Oliver He cellular self-replicating organic structure organism https://en.wikipedia.org/wiki/Organism cellular organism A self-replicating organic structure that does not have the unit of cell but it may use the cells to replicate. Oliver He non-cellular self-replicating organic structure non-organism self-replicating organic structure https://en.wikipedia.org/wiki/Self-replication acellular self-replicating organic structure An non-organism infectious agent that is composed solely of a short strand of circular, single-stranded RNA and has no protein coating. Oliver He https://en.wikipedia.org/wiki/Mobile_genetic_elements https://en.wikipedia.org/wiki/Viroid viroid A process of a dynamic system that produces an identiical or similar copy of itself. Oliver He https://en.wikipedia.org/wiki/Self-replication self-replication organic chemical entity A measurement datum that is about the age of human subject Oliver He, Jie Zheng, Anthony Huffman https://nexus.od.nih.gov/all/2018/08/07/human-subjects-and-clinical-trial-glossary-updates/ human subject age data For the purposes of the NIH Policy and Guidelines on the Inclusion of Individuals Across the Lifespan as Participants in Research Involving Human Subjects, a child is defined as an individual under the age of 18 years. Oliver He, Jie Zheng, Anthony Huffman child human subject https://nexus.od.nih.gov/all/2018/08/07/human-subjects-and-clinical-trial-glossary-updates/ child age data of human subject (by NIH) The regular aged adult group is defined here as an individual over 18 years of age. Oliver He, Jie Zheng, Anthony Huffman adult human subject https://nexus.od.nih.gov/all/2018/08/07/human-subjects-and-clinical-trial-glossary-updates/ adult age data of human subject For the purposes of the NIH Policy and Guidelines on the Inclusion of Individuals Across the Lifespan as Participants in Research Involving Human Subjects, an older adult is defined as an individual 65 years of age or older. Oliver He, Jie Zheng, Anthony Huffman older adult human subject https://nexus.od.nih.gov/all/2018/08/07/human-subjects-and-clinical-trial-glossary-updates/ older adult data of human subject (by NIH) The representation of a positive conclusion of a diagnostic process, which indicates that the patient is diagnozed as positive for a hypothetic disease. Oliver He 阳性诊断 positive diagnosis The representation of a negative conclusion of a diagnostic process, which indicates that the patient is diagnozed as negative for a hypothetic disease. Oliver He 阴性诊断 negative diagnosis The representation of a presumptive positive conclusion of a diagnostic process, which indicates that the patient is diagnozed as presumptive positive for a hypothetic disease. Oliver He 假定阳性诊断 疑是诊断 presumptive positive diagnosis A human subject classified as adult, which is defined by NIH as an individual under the age of 18 years. For the purposes of the NIH Policy and Guidelines on the Inclusion of Individuals Across the Lifespan as Participants in Research Involving Human Subjects, a child is defined as an individual under the age of 18 years. Oliver He https://nexus.od.nih.gov/all/2018/08/07/human-subjects-and-clinical-trial-glossary-updates/ child human subject A human subject classified as adult, which is defined by NIH as an individual 65 years of age or older. For the purposes of the NIH Policy and Guidelines on the Inclusion of Individuals Across the Lifespan as Participants in Research Involving Human Subjects, an older adult is defined as an individual 65 years of age or older. Oliver He https://nexus.od.nih.gov/all/2018/08/07/human-subjects-and-clinical-trial-glossary-updates/ older adult human subject A human subject classified as adult, which is defined by NIH as an individual over 18 years of age. Oliver He https://nexus.od.nih.gov/all/2018/08/07/human-subjects-and-clinical-trial-glossary-updates/ adult human subject Yingtong Liu, Anthony Huffman, Oliver He biomarker role Anthony Huffman, Oliver He immune signature role Anthony Huffman, Oliver He cytokine signature role Anthony Huffman, Oliver He inflammatory cytokine signature role A material entity that has a measurable quality or process profile(s), which can be used as an indicator of an underlying biological state or identity. The NIH Biomarkers and Surrogate Endpoint Working Group defined a biomarker as “A characteristic that is objectively measured and evaluated as an indicator of normal biological processes, pathogenic processes, or pharmacological responses to a therapeutic intervention” (https://pubmed.ncbi.nlm.nih.gov/11240971/). However, the definition of 'characteriistc' is unclear, so we do not use the exact definintion in the ontology. Yingtong Liu, Anthony Huffman, Oliver He https://en.wikipedia.org/wiki/Biomarker https://en.wikipedia.org/wiki/Biomarker_(cell) https://en.wikipedia.org/wiki/Biomarker_(medicine) biomarker Anthony Huffman, Oliver He A biomarker that is indicative of an immune response https://pubmed.ncbi.nlm.nih.gov/22072636/ https://pubmed.ncbi.nlm.nih.gov/32286245/ immune biomarker Anthony Huffman, Oliver He cytokine biomarker Anthony Huffman, Oliver He inflammatory cytokine biomarker Yingtong Liu, Anthony Huffman, Oliver He disease biomarker role A biomarker that is indicative of a disease Yingtong Liu, Anthony Huffman, Oliver He https://en.wikipedia.org/wiki/Biomarker_(medicine) disease biomarker A biomarker that is an indicator of a cell lineage or cell type Yingtong Liu, Anthony Huffman, Oliver He cell marker cell type marker https://en.wikipedia.org/wiki/Biomarker_(medicine) cell lineage biomarker Oliver He, Yingtong Liu https://en.wikipedia.org/wiki/Biomarker_(cell)#Molecular_Biomarkers molecular biomarker Cellular biomarkers are marked cells that can be isolated, sorted, quantified and characterized by their morphology and physiology, and used in both clinical and laboratory settings for different biomarker applications. An example of a cellular biomarker sorting technique is Fluorescent-activated cell sorting. Oliver He, Yingtong Liu https://en.wikipedia.org/wiki/Biomarker https://en.wikipedia.org/wiki/Biomarker_(cell)#Cellular_Biomarkers cellular biomarker Oliver He, Yingtong Liu https://en.wikipedia.org/wiki/Biomarker https://en.wikipedia.org/wiki/Biomarker_(cell)#Imaging_Biomarkers imaging biomarker A biomarker that can predict clincal outcome. Oliver He, Yingtong Liu https://en.wikipedia.org/wiki/Biomarker predictive biomarker A biomarker that provides information about the patient's overall outcome, regardless of therapy. Oliver He, Yingtong Liu https://en.wikipedia.org/wiki/Biomarker prognostic biomarker A biomarker that can serve a role in narrowing down diagnosis, which can lead to diagnosis that is significantly more specific to individual patients. Oliver He, Yingtong Liu https://en.wikipedia.org/wiki/Biomarker diagnostic biomarker A molecular biomarker at the DNA gene level Oliver He, Yingtong Liu genomic biomarker https://en.wikipedia.org/wiki/Biomarker_(cell)#Molecular_Biomarkers DNA biomarker A molecular biomarker at the RNA level Oliver He, Yingtong Liu transcriptomic biomarker https://en.wikipedia.org/wiki/Biomarker_(cell)#Molecular_Biomarkers RNA biomarker A molecular biomarker at the protein level Oliver He, Yingtong Liu proteomic biomarker https://en.wikipedia.org/wiki/Biomarker_(cell)#Molecular_Biomarkers protein biomarker A biomarker that is indicative of a disease and achieved through imaging. https://en.wikipedia.org/wiki/Biomarker_(medicine)#Imaging_disease_biomarkers_by_magnetic_resonance_imaging_(MRI) imaging disease biomarker A disposition that a material entity (e.g., gene or protein) is susceptible to be up or down-regulated in an organism or virus. Oliver He, Anthony Huffman susceptibility to biological regulation Oliver He imaging disease biomarkers by magnetic resonance imaging https://en.wikipedia.org/wiki/Biomarker_(medicine)#Imaging_disease_biomarkers_by_magnetic_resonance_imaging_(MRI) imaging disease biomarkers by MRI Oliver He A biomarker that is indicative of the presence of cancer in the body https://en.wikipedia.org/wiki/Cancer_biomarker cancer marker A disposition that a material entity (e.g., gene or protein) is susceptible to be up-regulated in an organism or virus. Oliver He, Anthony Huffman susceptibility to biological up-regulation A disposition that a material entity (e.g., gene or protein) is susceptible to be down-regulated in an organism or virus. Oliver He, Anthony Huffman susceptibility to biological down-regulation A Unified Social Credit Identifier is issued to registered companies and other types of organization by the Chinese government. Suyuan Peng, Hong Yu, Oliver He https://en.wikipedia.org/wiki/Unified_Social_Credit_Identifier 组织机构代码 Unified Social Credit Identifier Suyuan Peng, Hong Yu, Oliver He health care organization https://www.sciencedirect.com/topics/nursing-and-health-professions/health-care-organization 医疗机构 healthcare organization A centrality registered identifier for a medical record. Suyuan Peng, Hong Yu, Oliver He medical record ID https://en.wikipedia.org/wiki/Medical_record 病案号 medical record number A centrally registered identifier that is uniquely assigned to a person. Oliver He, Long Tran https://www.ohdsi.org/web/wiki/doku.php?id=documentation:cdm:person person ID 指患者在本医疗机构住院诊治的次数 Suyuan Peng, Hong Yu, Oliver He 《卫生部关于修订住院病案首页的通知》卫医政发〔2011〕84号 住院次数 number of hospital admissions A time measurement datum that is about a human being who bears a patient role and specifies the date of the patient's admission to a hospital 指患者实际入病房的接诊时间 Suyuan Peng, Hong Yu, Oliver He http://purl.obolibrary.org/obo/EUPATH_0000319 《住院病案首页数据填写质量规范（暂行）》国卫办医发〔2016〕24号 入院时间 date of hospital admission A year when an organism (e.g., a human) is born. Oliver He, Long Tran https://www.ohdsi.org/web/wiki/doku.php?id=documentation:cdm:person year of birth A month when an organism (e.g., a human) is born. Oliver He, Long Tran https://www.ohdsi.org/web/wiki/doku.php?id=documentation:cdm:person month of birth The date and time of birth of a person. Oliver He, Long Tran https://www.ohdsi.org/web/wiki/doku.php?id=documentation:cdm:person https://www.ohdsi.org/web/wiki/doku.php?id=documentation:cdm:single-page This term is generated to be equivalent to the "birth_datetime" in OMOP. Also note: in OMOP v6.0, DATETIME fields were made mandatory and date fields were made optional. Reference: https://ohdsi.github.io/CommonDataModel/cdm60.html#PERSON birth datetime A time measurement datum that is about a human being who bears a patient role and specifies the date of the patient's discharge from a hospital 出院时间是指患者治疗结束或终止治疗离开病房的时间，其中死亡患者是指其死亡时间；记录时间应当精确到分钟 Suyuan Peng, Hong Yu, Oliver He http://purl.obolibrary.org/obo/EUPATH_0000320 《住院病案首页数据填写质量规范（暂行）》国卫办医发〔2016〕24号 入院时间 date of hospital discharge The number of health card for residents of the People's Republic of China 在已统一发放“中华人民共和国居民健康卡”的地区填写健康卡号码，尚未发放“健康卡”的地区填写“-” Suyuan Peng, Hong Yu, Yongqun He 《卫生部关于修订住院病案首页的通知》卫医政发〔2011〕84号 健康卡号 residents health card number time that is related to the birth Oliver He, Long Tran time of birth birth-related time A care site is a uniquely identified institutional (physical or organizational) unit where healthcare delivery is practiced, for example, office, ward, hospital, clinic, etc. Long Tran, Oliver He http://ohdsi.github.io/CommonDataModel/cdm54.html#CARE_SITE http://ohdsi.github.io/CommonDataModel/cdm54.html#PERSON https://en.wikipedia.org/wiki/Health_care According to OMOP, care site does not consider the provider (human) information such a specialty. Instead, care site is considered at the institutional level. care site A centrally registered identifier that refers to where the care provider typically provides the primary care. Oliver He, Long Tran care site id http://ohdsi.github.io/CommonDataModel/cdm54.html#CARE_SITE http://ohdsi.github.io/CommonDataModel/cdm54.html#PERSON care site identifier A medical occurrence where a person engages with the healthcare system for a duration of time. Oliver He, Long Tran visit occurrence http://ohdsi.github.io/CommonDataModel/cdm54.html#VISIT_OCCURRENCE medical visit A centrally registered identifier that refers to a specific visit occurrence. This identifier identifies a unique interaction between a person and the health care system. Oliver He, Long Tran visit occurrence id http://ohdsi.github.io/CommonDataModel/cdm54.html#VISIT_OCCURRENCE visit occurrence identifier A vist ocurrence in which the patient's condition requires admission to a hospital. Oliver He, Long Tran inpatient visit occurrence http://ohdsi.github.io/CommonDataModel/cdm54.html#VISIT_OCCURRENCE https://en.wikipedia.org/wiki/Inpatient_care inpatient visit A vist ocurrence in which a patient attends an outpatient clinic with no plan to stay beyond the duration of the visit. Oliver He, Long Tran outpatient visit occurrence http://ohdsi.github.io/CommonDataModel/cdm54.html#VISIT_OCCURRENCE https://en.wikipedia.org/wiki/Patient#Outpatients_and_inpatients outpatient visit A vist ocurrence in which a patient attends an outpatient clinic with no plan to stay beyond the duration of the visit. Oliver He, Long Tran ER visit http://ohdsi.github.io/CommonDataModel/cdm54.html#VISIT_OCCURRENCE https://en.wikipedia.org/wiki/Patient#Outpatients_and_inpatients emergency room visit The date on which a visit starts. In the case of an inpatient visit this should be the date the patient was admitted to the hospital or institution. In all other cases this should be the date of the patient-provider interaction. Oliver He, Long Tran clinical visit start date http://ohdsi.github.io/CommonDataModel/cdm54.html#VISIT_OCCURRENCE visit start date The date on which a visit ends. For inpatient visits the end date is typically the discharge date. If a Person is still an inpatient in the hospital at the time of the data extract and does not have a visit_end_date, then set the visit_end_date to the date of the data pull. Oliver He, Long Tran clinical visit end date http://ohdsi.github.io/CommonDataModel/cdm54.html#VISIT_OCCURRENCE visit end date A temporal region that covers the time period from the visit start time to the visit end time. Oliver He, Long Tran visit duration The date and time on which a visit starts. In the case of an inpatient visit this should be the date the patient was admitted to the hospital or institution. In all other cases this should be the date of the patient-provider interaction. Oliver He, Long Tran clinical visit start datetime http://ohdsi.github.io/CommonDataModel/cdm54.html#VISIT_OCCURRENCE visit start datetime The date and time on which a visit ends. For inpatient visits the end date is typically the discharge date. If a Person is still an inpatient in the hospital at the time of the data extract and does not have a visit_end_date, then set the visit_end_date to the date of the data pull. Oliver He, Long Tran clinical visit end datetime http://ohdsi.github.io/CommonDataModel/cdm54.html#VISIT_OCCURRENCE visit end datetime A visit occurrence that occurs for the person prior to the given visit. There could be a few days or a few years in between. Oliver He, Long Tran preceding visit preceding visit occurrence http://ohdsi.github.io/CommonDataModel/cdm54.html#VISIT_OCCURRENCE preceding medical visit A vist ocurrence that includes a visit to the emergency room followed by a subsequent inpatient visit. Oliver He, Long Tran http://ohdsi.github.io/CommonDataModel/cdm54.html#VISIT_OCCURRENCE https://en.wikipedia.org/wiki/Patient#Outpatients_and_inpatients emergency room and inpatient visit A visit to a dedicated institution for reasons of poor health, at a Care Site, long-term or permanently, with no physician but possibly other Providers permanently available to deliver service around the clock Oliver He, Long Tran http://ohdsi.github.io/CommonDataModel/cdm54.html#VISIT_OCCURRENCE https://en.wikipedia.org/wiki/Patient#Outpatients_and_inpatients non-hospital institution visit A visit where a provider visits a person, without a care site, within one day, delivering service Oliver He, Long Tran home visit http://ohdsi.github.io/CommonDataModel/cdm54.html#VISIT_OCCURRENCE https://en.wikipedia.org/wiki/Patient#Outpatients_and_inpatients home medical visit A visit in which a patient engages with a Provider through communication media. A patient can use digital information and communication technologies, such as computers and mobile devices, to access health care services remotely and manage their health care. Oliver He, Long Tran http://ohdsi.github.io/CommonDataModel/cdm54.html#VISIT_OCCURRENCE https://en.wikipedia.org/wiki/Patient#Outpatients_and_inpatients telehealth visit A visit to the pharmacy for dispensing of drug, at a care site, within one day Oliver He, Long Tran http://ohdsi.github.io/CommonDataModel/cdm54.html#VISIT_OCCURRENCE https://en.wikipedia.org/wiki/Patient#Outpatients_and_inpatients pharmacy visit A visit to a dedicated institution, at a care site, within one day, for the purpose of a measurement. The visit is carried out in a medical laboratory or clinical laboratory where tests are carried out on clinical specimens to obtain information about the health of a patient to aid in diagnosis, treatment, and prevention of disease Oliver He, Long Tran laboratory clinical visit laboratory visit http://ohdsi.github.io/CommonDataModel/cdm54.html#VISIT_OCCURRENCE https://en.wikipedia.org/wiki/Patient#Outpatients_and_inpatients laboratory medical visit A medical visit occurrence that involves an interaction with the healthcare system, without a care site, within a day, with no providers involved, for the administrative purpose of patient case management. Oliver He, Long Tran http://ohdsi.github.io/CommonDataModel/cdm54.html#VISIT_OCCURRENCE https://en.wikipedia.org/wiki/Patient#Outpatients_and_inpatients case management visit A site that is used as a permanent or semi-permanent residence for one or many humans. Long Tran, Oliver He https://en.wikipedia.org/wiki/Home home A centrally registered identifier that refers to the National Provider Number issued to health care providers in the US by the Centers for Medicare and Medicaid Services (CMS). NPI is assigned for use in all administrative and financial transactions specified by HIPAA. Oliver He, Long Tran National Providier Number http://ohdsi.github.io/CommonDataModel/cdm54.html#PERSON http://purl.obolibrary.org/obo/NCIT_C54633 National Provider Identifier A centrally registered identifier that is issued by the Drug Enforcement Administration (DEA), a US federal agency, that allows a provider to write prescriptions for controlled substances. Oliver He, Long Tran http://ohdsi.github.io/CommonDataModel/cdm54.html#PERSON https://en.wikipedia.org/wiki/Drug_Enforcement_Administration DEA identifier A medicl occurrence that is ordered by, or carried out by, a healthcare provider on a patient with a diagnostic or therapeutic purpose. Oliver He, Long Tran procedure occurrence https://ohdsi.github.io/CommonDataModel/cdm54.html#PROCEDURE_OCCURRENCE medical procedure occurrence A centrally registered identifier that refers to a procedure occurrence, which is an activity or process that is ordered by, or carried out by, a healthcare provider on a patient with a diagnostic or therapeutic purpose. Oliver He, Long Tran procedure occurrence ID https://ohdsi.github.io/CommonDataModel/cdm54.html#PROCEDURE_OCCURRENCE procedure occurrence identifier A temporal region that is associated with a procedure Long Tran, Oliver He procedure time http://ohdsi.github.io/CommonDataModel/cdm54.html#PROCEDURE_OCCURRENCE procedure temporal region The date when a procedure starts Long Tran, Oliver He procedure date http://ohdsi.github.io/CommonDataModel/cdm54.html#PROCEDURE_OCCURRENCE procedure start date The date and time when a procedure starts Long Tran, Oliver He procedure date http://ohdsi.github.io/CommonDataModel/cdm54.html#PROCEDURE_OCCURRENCE procedure start datetime The date when a procedure ends Long Tran, Oliver He procedure date http://ohdsi.github.io/CommonDataModel/cdm54.html#PROCEDURE_OCCURRENCE procedure end date The date and time when a procedure ends Long Tran, Oliver He procedure date http://ohdsi.github.io/CommonDataModel/cdm54.html#PROCEDURE_OCCURRENCE procedure end datetime The information content entity that represents the origin of record such as the clinical form as the origin record of death. Oliver He, Long Tran type concept https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT provenance of record As part of the OMOP CDM, PROCEDURE TYPE CONCEPT best represents the provenance of the record, for example whether it came from an EHR record or billing claim. If a procedure is recorded as an EHR encounter, the PROCEDURE_TYPE_CONCEPT would be ‘EHR encounter record’. A provenance of record that determines the provenance of the Procedure record, as in whether the procedure was from an EHR system, insurance claim, registry, or other sources. Long Tran, Oliver He Procedure Type Concept https://ohdsi.github.io/CommonDataModel/cdm54.html#PROCEDURE_OCCURRENCE provenance of procedure record The status of being diagnosed as death Oliver He, Long Tran death diagnosis https://athena.ohdsi.org/search-terms/terms/32895 https://athena.ohdsi.org/search-terms/terms?domain=Condition+Status death diagnosis status OMOP4976965 A provenance of record that designates the source (provenance) of the cost data. Long Tran, Oliver He Cost Type Concept https://ohdsi.github.io/CommonDataModel/cdm54.html#COST provenance of cost record As part of the OMOP CDM, use the type concept that be reflects the source of the death record. It is possible that an administrative claims database would source death information from a government file so do not assume the Death Type is the same as the Visit Type, etc. A provenance of record that determines the provenance of the death record, i.e., where it came from. Long Tran, Oliver He Death Type Concept https://ohdsi.github.io/CommonDataModel/cdm54.html#DEATH provenance of death record A provenance of record that determines the provenance of the record, as in whether the record is from administrative claims or EHR. Long Tran, Oliver He Device Exposure Type Concept Device Type Concept https://ohdsi.github.io/CommonDataModel/cdm54.html#DEVICE_EXPOSURE provenance of device record As part of the OMOP CDM, choose the drug_type_concept_id that best represents the provenance of the record, for example whether it came from a record of a prescription written or physician administered drug. A provenance of record that determines the provenance of a drug prescription, which delineates prescriptions written, prescriptions dispensed, medication history, patient-reported exposure, etc. Long Tran, Oliver He Drug Type Concept https://ohdsi.github.io/CommonDataModel/cdm54.html#DRUG_EXPOSURE provenance of drug record A provenance of record that determines the provenance of the Episode record, as in whether the procedure was from an EHR system, insurance claim, registry, or other sources. Long Tran, Oliver He Procedure Type Concept https://ohdsi.github.io/CommonDataModel/cdm54.html#EPISODE provenance of episode record A provenance of record that determines the provenance of the Measurement record, as in whether the procedure was from an EHR system, insurance claim, registry, or other sources. Long Tran, Oliver He Measurement Type Concept https://ohdsi.github.io/CommonDataModel/cdm54.html#MEASUREMENT provenance of measurement record As part of the OMOP CDM, the provenance of the notes most likely will be EHR. A provenance of record that determines the provenance of the note. Long Tran, Oliver He Note Type Concept https://ohdsi.github.io/CommonDataModel/cdm54.html#NOTE provenance of note record A provenance of record that determines the provenance of the Observation record, as in whether the measurement was from an EHR system, insurance claim, registry, or other sources. Long Tran, Oliver He Observation Period Type Concept Observation Type Concept https://ohdsi.github.io/CommonDataModel/cdm54.html#OBSERVATION provenance of observation record A provenance of record that determines the source of the specimen record, as in an EHR system. Long Tran, Oliver He Specimen Type Concept https://ohdsi.github.io/CommonDataModel/cdm54.html#SPECIMEN provenance of specimen record As part of the OMOP CDM, populate this field based on the provenance of the visit record, as in whether it came from an EHR record or billing claim. A provenance of record that determines the provenance of the visit record, or where the record comes from. Long Tran, Oliver He Visit Type Concept https://ohdsi.github.io/CommonDataModel/cdm54.html#PROCEDURE_OCCURRENCE provenance of visit record A provenance of record that determines the provenance of the Condition record, as in whether the condition was from an EHR system, insurance claim, registry, or other sources. Long Tran, Oliver He Condition Occurrence Type Concept https://ohdsi.github.io/CommonDataModel/cdm54.html#CONDITION_OCCURRENCE provenance of condition occurrence record The primary diagnosis refers to the patient condition that demands the most provider resources during the patient’s stay. Oliver He, Long Tran primary diagnosis https://athena.ohdsi.org/search-terms/terms/32902 https://athena.ohdsi.org/search-terms/terms?domain=Condition+Status https://www.definitivehc.com/resources/glossary/primary-diagnosis There is often confusion surrounding primary and principal diagnoses and, consequently, the terms are commonly used interchangeably. While these can be (and frequently are) the same diagnosis in practice, their definitions are distinct. While a principal diagnosis is the underlying cause of patient symptoms, the primary diagnosis is used for healthcare billing purposes. Reference: https://www.definitivehc.com/resources/glossary/primary-diagnosis primary diagnosis status OMOP4976972 A medicl occurrence where a person presents a disease or medical condition stated as a diagnosis, a sign, or a symptom, which is either observed by a Provider or reported by the patient. Oliver He, Long Tran condition occurrence medical condition occurrence https://ohdsi.github.io/CommonDataModel/cdm54.html#CONDITION_OCCURRENCE medical condition occurrence the date or time on which a condition occurs Oliver He, Long Tran clinical condition date condition time https://ohdsi.github.io/CommonDataModel/cdm54.html#CONDITION_OCCURRENCE condition temporal region The date on which a condition ends. Oliver He, Long Tran clinical condition end date https://ohdsi.github.io/CommonDataModel/cdm54.html#CONDITION_OCCURRENCE condition end date The date and time on which a clinical condition ends. Oliver He, Long Tran clinical condition end datetime https://ohdsi.github.io/CommonDataModel/cdm54.html#CONDITION_OCCURRENCE condition end datetime The date on which a condition starts. Oliver He, Long Tran clinical condition start date https://ohdsi.github.io/CommonDataModel/cdm54.html#CONDITION_OCCURRENCE condition start date The date and time on which a condition starts. Oliver He, Long Tran clinical condition start datetime https://ohdsi.github.io/CommonDataModel/cdm54.html#CONDITION_OCCURRENCE In OMOP CDM, most often data sources do not have the idea of a start date for a condition. Rather, if a source only has one date associated with a condition record it is acceptable to use that date for both the CONDITION_START_DATE and the CONDITION_END_DATE. Reference: https://ohdsi.github.io/CommonDataModel/cdm54.html#CONDITION_OCCURRENCE condition start datetime The state or status at the point during the visit the diagnosis was given (admitting diagnosis, final diagnosis), whether the diagnosis was determined due to laboratory findings, if the diagnosis was exclusionary, or if it was a preliminary diagnosis, among others. Oliver He, Long Tran diagnosis status https://athena.ohdsi.org/search-terms/terms?domain=Condition+Status https://build.fhir.org/ig/HL7/UTG/CodeSystem-condition-clinical.html https://ohdsi.github.io/CommonDataModel/cdm54.html#CONDITION_OCCURRENCE In OPMI, we treated medical condition status as a status, which is a realizable entitry. One major section of the branch is various diagnosis condition status. There are basically two types of diagnosis: one type diagnosis is treated as a condition status, the other is diagnosis (OGMS_0000073) as a type of clinical data item. One good example to illustrate the difference is the difference between primary and principal diagnoses. While these can be (and frequently are) the same diagnosis in practice, their definitions are distinct. While a principal diagnosis is the underlying cause of patient symptoms, the primary diagnosis is used for healthcare billing purposes and is a type of medical condition status. Reference: https://www.definitivehc.com/resources/glossary/primary-diagnosis medical condition status An action specification that indicates why a Condition is no longer valid with respect to the purpose specified within the source data. Oliver He, Long Tran https://ohdsi.github.io/CommonDataModel/cdm54.html#CONDITION_OCCURRENCE In OMOP CDM, a Stop Reason does not necessarily imply that the condition is no longer occurring. medical condition stop reason specification The status of have the primary admission diagnosis Oliver He, Long Tran primary admission diagnosis https://athena.ohdsi.org/search-terms/terms/32901 https://athena.ohdsi.org/search-terms/terms?domain=Condition+Status primary admission diagnosis status OMOP4976971 Oliver He, Long Tran https://athena.ohdsi.org/search-terms/terms?domain=Condition+Status confirmed diagnosis status OMOP4976963 Principal diagnosis describes the underlying cause behind a patient’s initial hospital admission and is assigned only after a physician has completed necessary tests and examinations. Oliver He, Long Tran https://www.definitivehc.com/resources/glossary/principal-diagnosis principal diagnosis A discharge diagnosis is a final diagnosis given a patient before release from the hospital after all testing, surgery, and workup are complete. Oliver He, Long Tran https://athena.ohdsi.org/search-terms/terms?domain=Condition+Status https://medical-dictionary.thefreedictionary.com/discharge+diagnosis discharge diagnosis status OMOP4976966 A postoperative diagnosis is a diagnosis or diagnoses discovered or confirmed during the surgery. Often it is the same as the preoperative diagnosis. Oliver He, Long Tran primary admission diagnosis https://athena.ohdsi.org/search-terms/terms?domain=Condition+Status https://ushik.ahrq.gov/ViewItemDetails?system=mdr&itemKey=85779000#:~:text=Definition%3A,same%20as%20the%20Preoperative%20Diagnosis. postoperative diagnosis status OMOP4976968 Oliver He, Long Tran https://athena.ohdsi.org/search-terms/terms?domain=Condition+Status preliminary diagnosis status OMOP4976969 A preoperative diagnosis is a surgical diagnosis or diagnoses that are assigned to the patient before the surgical procedure, and is the reason for the surgery. A preoperative diagnosis is, in the opinion of the surgeon, the diagnosis that will be confirmed during surgery. Oliver He, Long Tran https://athena.ohdsi.org/search-terms/terms?domain=Condition+Status https://ushik.ahrq.gov/ViewItemDetails?system=mdr&itemKey=85778000#:~:text=Definition%3A,will%20be%20confirmed%20during%20surgery. preoperative diagnosis status OMOP4976970 An admitting diagnosis is defined as the initial working diagnosis documented by the patient's admitting or attending physician who determined that inpatient care was necessary. Oliver He, Long Tran admission diagnosis https://athena.ohdsi.org/search-terms/terms?domain=Condition+Status https://manual.jointcommission.org/releases/TJC2016B/DataElem0540.html#:~:text=Definition%3A&text=The%20admitting%20diagnosis%20is%20defined,that%20inpatient%20care%20was%20necessary. admission diagnosis status OMOP4976960 A cause of death is an official determination of conditions resulting in a human's death, which may be recorded on a death certificate. A cause of death is determined by a medical examiner. Oliver He, Long Tran cause of death https://athena.ohdsi.org/search-terms/terms?domain=Condition+Status https://en.wikipedia.org/wiki/Cause_of_death https://www.cdc.gov/nchs/data/misc/hb_cod.pdf cause of death status OMOP4976961 Oliver He, Long Tran https://athena.ohdsi.org/search-terms/terms?domain=Condition+Status primary referral diagnosis status OMOP4976974 A referral is a written request from one health professional to another health professional or health service, asking them to diagnose or treat you for a particular condition. Oliver He, Long Tran https://athena.ohdsi.org/search-terms/terms?domain=Condition+Status https://www.healthdirect.gov.au/what-is-a-referral#:~:text=A%20referral%20is%20a%20written,you%20for%20a%20particular%20condition. referral diagnosis status OMOP4976975 A secondary diagnosis is a condition that coexists at the time of admission, that develops subsequently, or that affects the treatment received and/or length of stay. Oliver He, Long Tran https://athena.ohdsi.org/search-terms/terms?domain=Condition+Status https://medcom.uiowa.edu/theloop/announcements/understanding-principal-and-secondary-conditions-2 secondary diagnosis status OMOP4976978 Oliver He, Long Tran https://athena.ohdsi.org/search-terms/terms?domain=Condition+Status secondary discharge diagnosis status OMOP4976979 Oliver He, Long Tran https://athena.ohdsi.org/search-terms/terms?domain=Condition+Status secondary referral diagnosis status OMOP4976980 The status of have the primary admission diagnosis Oliver He, Long Tran https://athena.ohdsi.org/search-terms/terms/32901 https://athena.ohdsi.org/search-terms/terms?domain=Condition+Status preliminary admission diagnosis status OMOP4976971 The status of have the primary admission diagnosis Oliver He, Long Tran https://athena.ohdsi.org/search-terms/terms/32901 https://athena.ohdsi.org/search-terms/terms?domain=Condition+Status preliminary discharge diagnosis status OMOP4976971 Oliver He, Long Tran https://athena.ohdsi.org/search-terms/terms?domain=Condition+Status condition to be diagnosed by procedure status OMOP4976962 A contributory cause of death is a significant condition that unfavourably influences the course of the morbid process and thus contributes to the fatal outcome, but which is not related to the disease or condition directly causing death. Oliver He, Long Tran https://athena.ohdsi.org/search-terms/terms?domain=Condition+Status https://stats.oecd.org/glossary/detail.asp?ID=444 contributory cause of death status OMOP4976964 An immediate cause of death is a final disease, injury, or complication directly causing the death Oliver He, Long Tran https://athena.ohdsi.org/search-terms/terms?domain=Condition+Status https://www.cdc.gov/nchs/data/misc/hb_cod.pdf immediate cause of death status OMOP4976967 A process of a person’s exposure to a foreign physical object or instrument which is used for diagnostic or therapeutic purposes through a mechanism beyond chemical action. Devices include implantable objects (e.g. pacemakers, stents, artificial joints), medical equipment and supplies (e.g. bandages, crutches, syringes), other instruments used in medical procedures (e.g. sutures, defibrillators) and material used in clinical care (e.g. adhesives, body material, dental material, surgical material). Oliver He, Long Tran device exposure https://ohdsi.github.io/CommonDataModel/cdm54.html#DEVICE_EXPOSURE medical device exposure http://purl.obolibrary.org/obo/NCIT_C102617 Oliver He, Long Tran https://athena.ohdsi.org/search-terms/terms?domain=Condition+Status primary discharge diagnosis status OMOP4976973 the date or time on which a device exposure occurs Oliver He, Long Tran http://ohdsi.github.io/CommonDataModel/cdm54.html#DEVICE_EXPOSURE device exposure temporal region The date on which a device exposure ends. Oliver He, Long Tran http://ohdsi.github.io/CommonDataModel/cdm54.html#DEVICE_EXPOSURE "Put the end date or discontinuation date as it appears from the source data or leave blank if unavailable." http://ohdsi.github.io/CommonDataModel/cdm54.html#DEVICE_EXPOSURE device exposure end date The date and time on which a device exposure ends. Oliver He, Long Tran http://ohdsi.github.io/CommonDataModel/cdm54.html#DEVICE_EXPOSURE "If a source does not specify datetime the convention is to set the time to midnight (00:00:0000)." http://ohdsi.github.io/CommonDataModel/cdm54.html#DEVICE_EXPOSURE device exposure end datetime Oliver He, Long Tran https://athena.ohdsi.org/search-terms/terms?domain=Condition+Status secondary admission diagnosis status OMOP4976977 A medical condition status in which the subject is not presently experiencing the condition or situation and there is a negligible perceived risk of the condition or situation returning. Oliver He, Long Tran https://athena.ohdsi.org/search-terms/terms/32906 https://athena.ohdsi.org/search-terms/terms?domain=Condition+Status https://build.fhir.org/ig/HL7/UTG/CodeSystem-condition-clinical.html resolved condition status OMOP4976976 The underlying cause of death refers to the disease or injury that initiated the train of morbid events leading directly to death or the circumstances of the accident or violence that produced the injury. Oliver He, Long Tran https://athena.ohdsi.org/search-terms/terms?domain=Condition+Status https://stats.oecd.org/glossary/detail.asp?ID=2790 https://www.cdc.gov/nchs/data/misc/hb_cod.pdf underlying cause of death status OMOP4976981 The date on which a device exposure starts. Oliver He, Long Tran http://ohdsi.github.io/CommonDataModel/cdm54.html#DEVICE_EXPOSURE "Valid entries include a start date of a procedure to implant a device, the date of a prescription for a device, or the date of device administration." http://ohdsi.github.io/CommonDataModel/cdm54.html#DEVICE_EXPOSURE device exposure start date The date and time on which a device exposure starts. Oliver He, Long Tran http://ohdsi.github.io/CommonDataModel/cdm54.html#DEVICE_EXPOSURE "This is not required, though it is in v6. If a source does not specify datetime the convention is to set the time to midnight (00:00:0000)." http://ohdsi.github.io/CommonDataModel/cdm54.html#DEVICE_EXPOSURE device exposure start datetime the date or time on which a drug exposure occurs in a patient Oliver He, Long Tran http://ohdsi.github.io/CommonDataModel/cdm54.html#DRUG_EXPOSURE drug exposure temporal region The date on which a drug exposure starts. Oliver He, Long Tran http://ohdsi.github.io/CommonDataModel/cdm54.html#DRUG_EXPOSURE "Valid entries include a start date of a prescription, the date a prescription was filled, or the date on which a Drug administration was recorded. It is a valid ETL choice to use the date the drug was ordered as the DRUG_EXPOSURE_START_DATE." http://ohdsi.github.io/CommonDataModel/cdm54.html#DRUG_EXPOSURE drug exposure start date The date and time on which a drug exposure starts. Oliver He, Long Tran http://ohdsi.github.io/CommonDataModel/cdm54.html#DRUG_EXPOSURE "This is not required, though it is in v6. If a source does not specify datetime the convention is to set the time to midnight (00:00:0000)." http://ohdsi.github.io/CommonDataModel/cdm54.html#DRUG_EXPOSURE drug exposure start datetime The date on which a drug exposure ends for a patient. Oliver He, Long Tran http://ohdsi.github.io/CommonDataModel/cdm54.html#DRUG_EXPOSURE drug exposure end date The date and time on which a drug exposure ends for a patient. Oliver He, Long Tran http://ohdsi.github.io/CommonDataModel/cdm54.html#DRUG_EXPOSURE "This is not required, though it is in v6. If a source does not specify datetime the convention is to set the time to midnight (00:00:0000)". http://ohdsi.github.io/CommonDataModel/cdm54.html#DRUG_EXPOSURE drug exposure end datetime The reason a person stopped a medication as it is represented in the source. Reasons include regimen completed, changed, removed, etc. Oliver He, Long Tran http://ohdsi.github.io/CommonDataModel/cdm54.html#DRUG_EXPOSURE This information is often not populated in source data and it is a valid etl choice to leave it blank if the information does not exist. This field will be retired in v6.0 of the OMOP CDM, . http://ohdsi.github.io/CommonDataModel/cdm54.html#DRUG_EXPOSURE drug exposure stop reason specification An action specification that represents the intended refills at time of the prescription. Oliver He, Long Tran drug refills specification from prescription http://ohdsi.github.io/CommonDataModel/cdm54.html#DRUG_EXPOSURE This is only filled in when the record is coming from a prescription. http://ohdsi.github.io/CommonDataModel/cdm54.html#DRUG_EXPOSURE drug refills specification The end date of a drug exposure as it appears in the source data Oliver He, Long Tran http://ohdsi.github.io/CommonDataModel/cdm54.html#DRUG_EXPOSURE drug exposure verbatim end date An exposure or contact of a person to a drug. The drug exposure includes drug dispensing or administration for a person. http://ohdsi.github.io/CommonDataModel/cdm54.html#DRUG_EXPOSURE This term is used in OMOP CDM. This term appears similar to 'drug administration'. However, drug exposure also covers involuntary, but drug administration usually means voluntary. More discussion is needed. http://purl.obolibrary.org/obo/NCIT_C41362 drug exposure In drug exposure, the quantity refers to number of pieces, e.g. tablets. In the example: 20 Ingredient dose= quantity x amount_value [amount_unit_concept_id] Acetaminophen dose = 20 x 500mg = 10,000mg Daily dose = Acetaminophen dose/drug duration The quantity of drug exposure refers to the number of drug pieces, e.g. tablets, that are exposed to a person. Long Tran, Oliver He http://ohdsi.github.io/CommonDataModel/cdm54.html#DRUG_EXPOSURE https://ohdsi.github.io/CommonDataModel/drug_dose.html quantity of drug exposure This days of the supply of a drug that is given on the prescription. Long Tran, Oliver He days supply of drug http://ohdsi.github.io/CommonDataModel/cdm54.html#DRUG_EXPOSURE days of drug supply A period time when an observation is conducted. Oliver He, Long Tran participant observation duration time https://ohdsi.github.io/CommonDataModel/cdm60.html#OBSERVATION_PERIOD In OMOP, the observation table contains records that defines spans of time during which two conditions are expected to hold: (i) Clinical Events that happened to the Person are recorded in the Event tables, and (ii) absense of records indicate such Events did not occur during this span of time. observation period EUPATH_0000138 A temporal region that is associated with an observation Long Tran, Oliver He https://ohdsi.github.io/CommonDataModel/cdm60.html#OBSERVATION_PERIOD observation temporal region A date when an observation starts. Long Tran, Oliver He https://ohdsi.github.io/CommonDataModel/cdm60.html#OBSERVATION_PERIOD observation period start date A date when an observation ends. Long Tran, Oliver He https://ohdsi.github.io/CommonDataModel/cdm60.html#OBSERVATION_PERIOD observation period end date A time when a measurement is conducted. Long Tran, Oliver He https://ohdsi.github.io/CommonDataModel/cdm54.html#MEASUREMENT measurement time A date when a measurement is conducted. Long Tran, Oliver He https://ohdsi.github.io/CommonDataModel/cdm54.html#MEASUREMENT measurement date A datetime when a measurement is conducted. Long Tran, Oliver He https://ohdsi.github.io/CommonDataModel/cdm54.html#MEASUREMENT measurement datetime A unique key given to a Measurement record for a Person. Such record can be used in the ETL for how duplicate Measurements during the same Visit were handled. Oliver He, Long Tran measurement ID http://ohdsi.github.io/CommonDataModel/cdm54.html#MEASUREMENT clnical measurement identifier Payer plan is a plan specification that captures the details of the period of time that a person is continuously enrolled under a specific health Plan benefit structure from a given payer. Each person receiving healthcare is typically covered by a health benefit plan, which pays for (fully or partially), or directly provides, the care. These benefit plans are provided by payers, such as health insurances or state or government agencies. Long Tran, Oliver He http://ohdsi.github.io/CommonDataModel/cdm54.html#PAYER_PLAN_PERIOD payer plan A temporal region that is associated with the payment process defined in a payer plan Long Tran, Oliver He http://ohdsi.github.io/CommonDataModel/cdm54.html#PAYER_PLAN_PERIOD payer plan temporal region A period time of the payment that is covered by a payer plan for a person. Long Tran, Oliver He http://ohdsi.github.io/CommonDataModel/cdm54.html#PAYER_PLAN_PERIOD payer plan period A date when a payer plan period starts. Long Tran, Oliver He http://ohdsi.github.io/CommonDataModel/cdm54.html#PAYER_PLAN_PERIOD payer plan period start date A date when a payer plan period ends. Long Tran, Oliver He http://ohdsi.github.io/CommonDataModel/cdm54.html#PAYER_PLAN_PERIOD payer plan period end date A process that a patient experiences over a period of time. Oliver He, Long Tran https://ohdsi.github.io/CommonDataModel/cdm54.html medical occurrence An electronic health record that records the information of medical condition. Long Tran, Oliver He Condition Occurrence Type Concept https://ohdsi.github.io/CommonDataModel/cdm54.html#CONDITION_OCCURRENCE condition occurrence record An electronic health record that records the information of medical cost. Long Tran, Oliver He Cost Type Concept https://ohdsi.github.io/CommonDataModel/cdm54.html#COST electronic health cost record As part of the OMOP CDM, use the type concept that be reflects the source of the death record. It is possible that an administrative claims database would source death information from a government file so do not assume the Death Type is the same as the Visit Type, etc. An electronic health record that records the information of the death record of a person. Long Tran, Oliver He Death Type Concept https://ohdsi.github.io/CommonDataModel/cdm54.html#DEATH electronic death record An electronic health record that records the information of medical device usage. Long Tran, Oliver He Device Exposure Type Concept Device Type Concept https://ohdsi.github.io/CommonDataModel/cdm54.html#DEVICE_EXPOSURE electronic device record As part of the OMOP CDM, choose the drug_type_concept_id that best represents the provenance of the record, for example whether it came from a record of a prescription written or physician administered drug. An electronic health record that records the information of drug usage including drug prescriptions written, prescriptions dispensed, medication history, patient-reported exposure, etc. Long Tran, Oliver He Drug Type Concept https://ohdsi.github.io/CommonDataModel/cdm54.html#DRUG_EXPOSURE electronic drug record A data item that captures clinical facts about a patient obtained in the context of examination, questioning or a procedure. Long Tran, Oliver He medical observation observation http://ohdsi.github.io/CommonDataModel/cdm54.html#OBSERVATION This term is dervied from OMOP:Observation term. Observations differ from Measurements in that they do not require a standardized test or some other activity to generate clinical fact. Typical observations are medical history, family history, the stated need for certain treatment, social circumstances, lifestyle choices, healthcare utilization patterns, etc. medical observation data An electronic health record that records the information of medical Episode record. Long Tran, Oliver He Procedure Type Concept https://ohdsi.github.io/CommonDataModel/cdm54.html#EPISODE electronic episode record An electronic health record that records the information of medical measurement record. Long Tran, Oliver He Measurement Type Concept https://ohdsi.github.io/CommonDataModel/cdm54.html#MEASUREMENT electronic measurement record As part of the OMOP CDM, the provenance of the notes most likely will be EHR. An electronic health record that records the information of medical notes. Long Tran, Oliver He Note Type Concept https://ohdsi.github.io/CommonDataModel/cdm54.html#NOTE electronic health note record An electronic health record that records the information of medical observational record. Long Tran, Oliver He Observation Period Type Concept Observation Type Concept https://ohdsi.github.io/CommonDataModel/cdm54.html#OBSERVATION electronic health observation record As part of the OMOP CDM, PROCEDURE TYPE CONCEPT best represents the provenance of the record, for example whether it came from an EHR record or billing claim. If a procedure is recorded as an EHR encounter, the PROCEDURE_TYPE_CONCEPT would be ‘EHR encounter record’. An electronic health record that records the information of Procedure record. Long Tran, Oliver He Procedure Type Concept https://ohdsi.github.io/CommonDataModel/cdm54.html#PROCEDURE_OCCURRENCE electronic health procedure record An electronic health record that records the information of the specimen record. Long Tran, Oliver He Specimen Type Concept https://ohdsi.github.io/CommonDataModel/cdm54.html#SPECIMEN electronic specimen record As part of the OMOP CDM, populate this field based on the provenance of the visit record, as in whether it came from an EHR record or billing claim. An electronic health record that records the information of medical visit. Long Tran, Oliver He Visit Type Concept https://ohdsi.github.io/CommonDataModel/cdm54.html#PROCEDURE_OCCURRENCE electronic medical visit record Oliver He, Long Tran https://athena.ohdsi.org/search-terms/terms?domain=Condition+Status preliminary diagnosis OMOP4976969 Oliver He, Long Tran https://athena.ohdsi.org/search-terms/terms/32901 https://athena.ohdsi.org/search-terms/terms?domain=Condition+Status preliminary admission diagnosis OMOP4976971 Oliver He, Long Tran https://athena.ohdsi.org/search-terms/terms/32901 https://athena.ohdsi.org/search-terms/terms?domain=Condition+Status preliminary discharge diagnosis OMOP4976971 The primary diagnosis is a diagnosis of the patient condition that demands the most provider resources during the patient’s stay. Oliver He, Long Tran primary diagnosis https://athena.ohdsi.org/search-terms/terms/32902 https://athena.ohdsi.org/search-terms/terms?domain=Condition+Status https://www.definitivehc.com/resources/glossary/primary-diagnosis There is often confusion surrounding primary and principal diagnoses and, consequently, the terms are commonly used interchangeably. While these can be (and frequently are) the same diagnosis in practice, their definitions are distinct. While a principal diagnosis is the underlying cause of patient symptoms, the primary diagnosis is used for healthcare billing purposes. Reference: https://www.definitivehc.com/resources/glossary/primary-diagnosis primary diagnosis OMOP4976972 Oliver He, Long Tran primary admission diagnosis https://athena.ohdsi.org/search-terms/terms/32901 https://athena.ohdsi.org/search-terms/terms?domain=Condition+Status primary admission diagnosis OMOP4976971 Oliver He, Long Tran https://athena.ohdsi.org/search-terms/terms?domain=Condition+Status primary discharge diagnosis OMOP4976973 Oliver He, Long Tran https://athena.ohdsi.org/search-terms/terms?domain=Condition+Status primary referral diagnosis OMOP4976974 A secondary diagnosis is a diagnosis made at the time of admission, that develops subsequently, or that affects the treatment received and/or length of stay. Oliver He, Long Tran https://athena.ohdsi.org/search-terms/terms?domain=Condition+Status https://medcom.uiowa.edu/theloop/announcements/understanding-principal-and-secondary-conditions-2 secondary diagnosis OMOP4976978 Oliver He, Long Tran https://athena.ohdsi.org/search-terms/terms?domain=Condition+Status secondary admission diagnosis OMOP4976977 Oliver He, Long Tran https://athena.ohdsi.org/search-terms/terms?domain=Condition+Status secondary discharge diagnosis OMOP4976979 Oliver He, Long Tran https://athena.ohdsi.org/search-terms/terms?domain=Condition+Status secondary referral diagnosis OMOP4976980 An admitting diagnosis is defined as the initial working diagnosis documented by the patient's admitting or attending physician who determined that inpatient care was necessary. Oliver He, Long Tran admission diagnosis https://athena.ohdsi.org/search-terms/terms?domain=Condition+Status https://manual.jointcommission.org/releases/TJC2016B/DataElem0540.html#:~:text=Definition%3A&text=The%20admitting%20diagnosis%20is%20defined,that%20inpatient%20care%20was%20necessary. admission diagnosis OMOP4976960 Oliver He, Long Tran https://athena.ohdsi.org/search-terms/terms?domain=Condition+Status confirmed diagnosis OMOP4976963 The diagnosis of the death of a person Oliver He, Long Tran death diagnosis https://athena.ohdsi.org/search-terms/terms/32895 https://athena.ohdsi.org/search-terms/terms?domain=Condition+Status death diagnosis OMOP4976965 A discharge diagnosis is a final diagnosis given a patient before release from the hospital after all testing, surgery, and workup are complete. Oliver He, Long Tran https://athena.ohdsi.org/search-terms/terms?domain=Condition+Status https://medical-dictionary.thefreedictionary.com/discharge+diagnosis discharge diagnosis OMOP4976966 A postoperative diagnosis is a diagnosis or diagnoses discovered or confirmed during the surgery. Often it is the same as the preoperative diagnosis. Oliver He, Long Tran primary admission diagnosis https://athena.ohdsi.org/search-terms/terms?domain=Condition+Status https://ushik.ahrq.gov/ViewItemDetails?system=mdr&itemKey=85779000#:~:text=Definition%3A,same%20as%20the%20Preoperative%20Diagnosis. postoperative diagnosis OMOP4976968 A medical occurrence in which a patience is exposed to a medical related material entity such as drug or medical device. Medical exposure refers primarily to exposure incurred by patients for the purpose of medical diagnosis or treatment. Oliver He, Long Tran https://www.sciencedirect.com/topics/engineering/medical-exposure medical exposure A preoperative diagnosis is a surgical diagnosis or diagnoses that are assigned to the patient before the surgical procedure, and is the reason for the surgery. A preoperative diagnosis is, in the opinion of the surgeon, the diagnosis that will be confirmed during surgery. Oliver He, Long Tran https://athena.ohdsi.org/search-terms/terms?domain=Condition+Status https://ushik.ahrq.gov/ViewItemDetails?system=mdr&itemKey=85778000#:~:text=Definition%3A,will%20be%20confirmed%20during%20surgery. preoperative diagnosis OMOP4976970 A referral is a written request from one health professional to another health professional or health service, asking them to diagnose or treat you for a particular condition. Oliver He, Long Tran https://athena.ohdsi.org/search-terms/terms?domain=Condition+Status https://www.healthdirect.gov.au/what-is-a-referral#:~:text=A%20referral%20is%20a%20written,you%20for%20a%20particular%20condition. referral diagnosis OMOP4976975 An acellular self-replicating organic structure that is composed of nucleic acid Oliver He https://en.wikipedia.org/wiki/Template:Self-replicating_organic_structures self-replicating nucleic acid A self-replicating nucleic acid that can move around within a genome, or that can be transferred from one species or replicon to another. Oliver He https://en.wikipedia.org/wiki/Mobile_genetic_elements https://en.wikipedia.org/wiki/Template:Self-replicating_organic_structures mobile genetic element A mobile genetic element that is composed of a generally circular extrachromosomal DNA molecule and is able to replicate and be transmitted independent of chromosomal DNA. Oliver He https://en.wikipedia.org/wiki/Mobile_genetic_elements https://en.wikipedia.org/wiki/Template:Self-replicating_organic_structures plasmid A mobile genetic element that is composed of a DNA sequence and can move and replicate in different parts of a cell's genome. Oliver He https://en.wikipedia.org/wiki/Mobile_genetic_elements https://en.wikipedia.org/wiki/Template:Self-replicating_organic_structures transposon 17 A age quality that is measured by the value of less than 18 years old Fred Dowd, Oliver He age less than 18 years old age less than 18 years GFR 30-59 mL/min/1.73m2 eGFR >=60 mL/min/1.73m2 with urine albumin excretion >= 30 mg/g creatinine eGFR >= 60 mL/min/1.73m2 with urine protein excretion >= 150 mg/g creatinine A role of a person (e.g., a study participant, participant's family member, or participant's physician) who provides the medical history information. Edison Ong, Oliver He medical history information provider role A role of a person who is a family member of a participant in an investigation study. Edison Ong, Oliver He study participant's family member role a role of a physician who takes care of a study participant Edison Ong, Oliver He study participant's physician role An age when a disease is first diagnosed age at diagnosis of disease age at diagnosis of kidney disease Whether chronic kidney disease Whether acute kidney injury time of biopsy year of kidney biopsy time of kidney biopsy month of kidney biopsy age at the start of kidney stone An age when a disease started in a patient age at the start of disease Whether diabetes age at diagosis of diabetes What disease What type of diabetes treatment question medicatoin treatment question surgical treatment question Whether taking medication for diabetes An age when a medication is first used age at the start of medication age at the start of taking medication for diabetes What medication What medication taken for diabetes Whether insulin taken for diabetes Whether diabetes during pregnancy a clinical trial is a medical interventional study where participants are assigned prospectively to an intervention or interventions according to a protocol to evaluate the safety and efficacy of the intervention(s) on biomedical or other health related outcomes. The Interventions include but are not restricted to drugs, cells and other biological products, surgical procedures, radiologic procedures, devices, behavioral treatments, process-of-care changes, preventive care, etc. Oliver He, Asiyah Yu Lin, Qingliang Li interventional trial https://clinicaltrials.gov/ct2/search/map https://en.wikipedia.org/wiki/Clinical_trial https://prsinfo.clinicaltrials.gov/definitions.html https://www.who.int/ictrp/en/ clinical trial A clinical trial that is at Early Phase 1 or Phase 0 A clinical trial that is at an Early Phase i or Phase 0, which is designed to use an investigational agent that is available only in very limited quantities and which has never previously given to humans or for which there is extremely limited human experience. Phase 0 clinical trials are intended to enable researchers to understand the path of the drug in the body and its efficacy. Adverse event reporting in Phase 0 trials is expedited. [def-source: NCI] Leon Li, Asiyah Lin, Oliver He Phase 0 clinical trial Phase 0 trial Pre-Clinical Trial http://purl.obolibrary.org/obo/NCIT_C54721 https://en.wikipedia.org/wiki/Clinical_trial Early Phase 1 clinical trial A clinical trial that is at Phase 1, which is often the first-in-man trial, and it tests within a small group of people (typically 20-80) to evaluate safety, determine safe dosage ranges, and begin to identify side effects. A drug's side effects could be subtle or long term, or may only happen with a few people, so phase 1 trials are not expected to identify all side effects. Leon Li, Asiyah Lin, Oliver He Phase 1 trial Phase I clinical trial clinical trial for safety screening http://purl.obolibrary.org/obo/NCIT_C15600 https://en.wikipedia.org/wiki/Clinical_trial C0920321 C15600 Phase 1 clinical trial A clinical trial that is at Phase 2, which is designed to study a biomedical or behavioral intervention in a larger group of people (several hundred), to evaluate the drug's effectiveness for a particular indication in patients with the disease or condition under study, and to determine the common short-term side effects and risks associated with the intervention. [def-source: NCI] Leon Li, Asiyah Lin, Oliver He Phase 2 trial Phase II clinical trial Phase II trial http://purl.obolibrary.org/obo/NCIT_C15601 https://en.wikipedia.org/wiki/Clinical_trial C0282460 C15601 Phase 2 clinical trial A clinical trial that is at Phase 3 A clinical trial that is at Phase 3, which is designed to investigate the efficacy of the biomedical or behavioral intervention in large groups of human subjects (from several hundred to several thousand), to confirm efficacy, to monitor adverse reactions to the new medication or treatment regimen with respect to long-term use and by comparing the intervention to other standard or experimental interventions as well as to a placebo. [def-source: NCI] Leon Li, Asiyah Lin, Oliver He Phase III trial https://en.wikipedia.org/wiki/Clinical_trial C0282461 C15602 Phase 3 clinical trial A clinical trial that is at Phase 4 Leon Li, Asiyah Lin, Oliver He https://en.wikipedia.org/wiki/Clinical_trial C0282462 C15603 Phase 4 clinical trial A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities quality (PATO) trait quality A time quality inhering in a bearer by virtue of how long the bearer has existed. quality PATO:0000011 age An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved. 患者生理性别在特定编码体系中的代码 Suyuan Peng, Hong Yu, Yongqun He 《电子病历基本数据集 第10部分：住院病案首页》WS 445.10-2014 quality PATO:0000047 biological sex A 1-D extent quality inhering in a bearer by virtue of the bearer's vertical dimension of extension. quality PATO:0000119 height A physical quality inhering in a bearer that has mass near a gravitational body. quality PATO:0000128 weight A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity. location placement relational spatial quality position 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. PATO:0001722 behavioural quality quality PATO:0000186 behavioral quality A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes. quality PATO:0000383 female A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes. quality PATO:0000384 male A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. PATO:0002079 Wikipedia:Physical_property relational physical quality quality PATO:0001018 physical quality A quality which inheres in an process. PATO:0001239 PATO:0001240 quality of a process quality of occurrent quality of process relational quality of occurrent quality PATO:0001236 See comments of relational quality of a physical entity. process quality A quality which inheres in a continuant. PATO:0001237 PATO:0001238 snap:Quality monadic quality of a continuant multiply inhering quality of a physical entity multiply inhering quality of a physical entity quality of a continuant quality of a single physical entity quality of an object quality of continuant monadic quality of an object monadic quality of continuant quality PATO:0001241 Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles. physical object quality An organismal quality inhering in a bearer by virtue of the bearer's physical expression of sexual characteristics. quality PATO:0001894 phenotypic sex A quality that inheres in an entire organism or part of an organism. quality PATO:0001995 organismal quality A positional quality inhering in a bearer by virtue the bearer's being changed in position. displaced A material entity that consists of two or more organisms, viruses, or viroids. A material entity that consists of two or more organisms, viruses, or viroids. collection of organisms collection of organisms A community of at least two different species, living in a particular area. Must have at least two populations of different species as members. envoPolar ecological community A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other. community A collection of organisms that consists of two or more organisms from at least two species. multi-species collection of organisms A material entity that is one or more organisms, viruses or viroids. organismal entity An anatomical entity that is or was part of a plant. entidad anat&#243mica vegetal (Spanish, exact) 植物 解剖学（形態）的実体 (Japanese, exact) plant anatomical entity protein antithrombin III is a protein An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof. 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 region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. primary structure of sequence macromolecule sequence region 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 A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures. AEO:0000192 CARO:0000010 FMA:50705 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. anatomical boundary 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 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 EV:0100155 FBbt:00007000 HAO:0000144 MAT:0000023 MESH:D005121 MIAA:0000023 OpenCyc:Mx4rvViC-JwpEbGdrcN5Y29ycA UMLS:C0598782 VSAO:0000075 XAO:0000218 uberon appendages extremitaet extremity limbs/digits/tail UBERON:0000026 appendage 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 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 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 TAO:0005425 UMLS:C0036760 ZFA:0005425 tunica serosa wall of serous sac uberon serosa UBERON:0000042 serous membrane A tubular structure that contains, conveys body fluid, such as blood or lymph. uberon UBERON:0000055 vessel 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 TAO:0005171 UMLS:C0687028 XAO:0004000 ZFA:0005171 galen:Duct anatomical duct exocrine duct exocrine gland duct uberon ducts UBERON:0000058 duct 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 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:67135 GAID:781 HAO:0000003 MA:0003000 MESH:D000825 TAO:0000037 TGMA:0001823 VHOG:0001759 WBbt:0000100 XAO:0003000 ZFA:0000037 biological structure connected biological structure uberon UBERON:0000061 anatomical structure 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 OpenCyc:Mx4rv5XMb5wpEbGdrcN5Y29ycA OpenCyc:Mx4rwP3iWpwpEbGdrcN5Y29ycA UMLS:C0178784 WBbt:0003760 uberon anatomical unit body organ element UBERON:0000062 organ 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 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 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 A stage that is part of the embryo stage. embryonic stage part uberon UBERON:0000067 embryo stage part 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 End of the life of an organism. ncit:Death is an outcome XAO:0000437 XtroDO:0000085 uberon death UBERON:0000071 death stage Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism. UBERON:0010322 FMA:85544 UMLS:C1519343 galen:ComplexSkeletalStructure skeletal system subdivision uberon skeletal system part UBERON:0000075 subdivision of skeletal system 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 UMLS:C1515087 surface (external) ectoderm surface ectoderm uberon UBERON:0000076 external ectoderm 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 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 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 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 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 EMAPA:16033 FBdv:00005288 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 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 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 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 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 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 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 uberon UBERON:0000153 anterior region of body uberon UBERON:0000154 posterior region of body 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 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 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 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 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 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 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 FMA:62889 uberon UBERON:0000409 serous 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 UBERON:0006540 secretion AEO:0001005 BTO:0002977 BTO:0002979 EMAPA:36535 FMA:9675 MA:0002504 MESH:D012634 UMLS:C1516992 galen:Secretion exocrine gland fluid/secretion secreted substance uberon exocrine gland fluid exocrine gland fluid or secretion exocrine gland secretion external secretion UBERON:0000456 bodily secretion 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 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 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 TAO:0001668 TGMA:0001825 UMLS:C0524461 VHOG:0001728 XAO:0003190 ZFA:0001643 lumen space uberon anatomical spaces UBERON:0000464 anatomical space 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 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 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 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 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 AAO:0010026 AEO:0000191 BILA:0000012 BSA:0000038 BTO:0000042 CARO:0000012 EFO:0002906 EHDAA2:0003103 EHDAA2:0003191 EHDAA:1 EHDAA:9178 EMAPA:25765 EV:0100016 FBbt:00000001 FMA:256135 HAO:0000012 TADS:0000001 TAO:0001094 TGMA:0001832 VHOG:0000671 WBbt:0007833 XAO:0003004 ZFA:0001094 galen:Organism ncithesaurus:Whole_Organism multi-cellular organism organism whole organism animal uberon Koerper body whole body UBERON:0000468 multicellular organism 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 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 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 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 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 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 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 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 TAO:0001486 UMLS:C0014609 VHOG:0000387 XAO:0003045 ZFA:0001486 epithelial tissue portion of epithelium uberon UBERON:0000483 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] 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 TAO:0001494 UMLS:C0682575 XAO:0004006 ZFA:0001494 stratified epithelium uberon laminated epithelium UBERON:0000486 multilaminar epithelium 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 TAO:0001498 UMLS:C0836133 XAO:0004010 ZFA:0001498 epithelium simplex squamosum uberon simple squamous epithelia UBERON:0000487 simple squamous epithelium 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 TAO:0001495 UMLS:C0682574 XAO:0004007 ZFA:0001495 simple epithelium uberon unilaminar epithelia UBERON:0000490 unilaminar epithelium 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 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 OGEM:000001 OpenCyc:Mx4rwP1ceZwpEbGdrcN5Y29ycA UMLS:C0013935 VHOG:0001766 XAO:0000113 ZFA:0000103 embryonic organism uberon developing organism developmental tissue UBERON:0000922 embryo 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 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 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 TAO:0000016 UMLS:C0013574 VHOG:0000153 XAO:0000001 ZFA:0000016 embryonic ectoderm uberon UBERON:0000924 ectoderm 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 TAO:0000017 UMLS:C0014144 VHOG:0000154 XAO:0000090 ZFA:0000017 uberon entoderm UBERON:0000925 endoderm 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:168 EHDAA:183 EMAPA:16083 EV:0100006 FBbt:00000126 FMA:69072 GAID:522 MAT:0000174 MESH:A16.254.425.660 MIAA:0000174 TAO:0000041 UMLS:C0025485 VHOG:0000152 XAO:0000050 ZFA:0000041 uberon embryonic mesoderm entire mesoderm mesodermal mantle UBERON:0000926 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 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 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 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)" http://dx.doi.org/10.1101/gad.1485706 heart 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 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 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 TAO:0000105 UMLS:C0014520 VHOG:0000077 XAO:0000028 ZFA:0000105 vertebrate epidermis uberon UBERON:0001003 skin 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 UMLS:C0678727 XAO:0003043 uberon bud future organ placode primordia rudiment UBERON:0001048 primordium 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:16530 EMAPA:16757 FMA:293882 MAT:0000069 MIAA:0000069 TAO:0001135 UMLS:C0231024 VHOG:0000307 XAO:0003204 ZFA:0001135 uberon neural primordium presumptive central nervous system tubus neuralis UBERON:0001049 neural tube 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 TAO:0100000 TGMA:0001822 UMLS:C1515976 XAO:0000000 ZFA:0100000 uberon UBERON:0001062 anatomical entity Transudate contained in the synovial cavity of joints, and in the cavity of tendon sheaths and bursae. Portion of organism substance that is a clear fluid that occupies the space in synovial joints.[TAO] BTO:0001339 CALOHA:TS-0996 ENVO:02000039 FMA:12277 GAID:265 MA:0002544 MESH:D013582 TAO:0005154 UMLS:C0039097 ZFA:0005154 galen:SynovialFluid joint fluid uberon UBERON:0001090 synovial fluid 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 UMLS:C0086610 uberon UBERON:0001136 mesothelium 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 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 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 OpenCyc:Mx4rvViDlpwpEbGdrcN5Y29ycA OpenCyc:Mx4rvVkCG5wpEbGdrcN5Y29ycA TAO:0001514 UMLS:C0262950 VHOG:0001190 VSAO:0000057 XAO:0000169 ZFA:0001514 galen:Bone bone element bone organ uberon bone bones UBERON:0001474 bone element An articular capsule (or joint capsule) is an envelope surrounding a synovial joint. [WP,unvetted]. check ncita FMA:34836 GAID:263 MA:0001519 MESH:D017746 UMLS:C0206207 galen:JointCapsule capsula articularis fibrous capsule of joint joint capsule joint fibrous capsule uberon capsulae articulares UBERON:0001484 articular capsule 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 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 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 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 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 OpenCyc:Mx4rEg4ZYrIbEduAAAAOpmP6tw UMLS:C0032105 blood plasm portion of blood plasma uberon UBERON:0001969 blood plasma 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 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 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 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 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 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 TAO:0001119 UMLS:C0011646 VHOG:0000108 XAO:0000217 ZFA:0001119 vertebrate dermis uberon corium cutis UBERON:0002067 dermis 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 FMA:70544 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 The post-cranial 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 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 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 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 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 OpenCyc:Mx4rvVkJjpwpEbGdrcN5Y29ycA TAO:0001115 UMLS:C0460005 XAO:0000054 XAO:0003025 ZFA:0001115 galen:Trunk thoracolumbar region torso trunk region uberon Rumpf UBERON:0002100 trunk 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 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 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 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 OpenCyc:Mx4rQRpVNgAKEdyHxgDggVfs8g UMLS:C0026860 VHOG:0001275 VSAO:0000031 XAO:0000168 musculo-skeletal system uberon UBERON:0002204 musculoskeletal system 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 OpenCyc:Mx4rv2bBV5wpEbGdrcN5Y29ycA TAO:0005153 ZFA:0005153 galen:SynovialJoint articulatio synoviale diarthroses diarthrosis diarthrosis joint uberon diarthrodial joints UBERON:0002217 synovial joint 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 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 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 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 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 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 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 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 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 UMLS:C1516995 WikipediaCategory:Exocrine_system exocrine glandular system uberon UBERON:0002330 exocrine system 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 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 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 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 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 UMLS:C0015282 ducted gland glandula exocrina uberon UBERON:0002365 exocrine gland 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 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 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 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 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 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 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 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 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 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 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 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 OpenCyc:Mx4rwP3vyJwpEbGdrcN5Y29ycA UMLS:C1285092 WikipediaCategory:Glands galen:Gland glandular organ uberon Druese glandula UBERON:0002530 gland 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) 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 FMA:67552 MA:0002447 galen:Cavity uberon UBERON:0002553 anatomical cavity 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 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 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 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 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 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 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 RETIRED_EHDAA2:0001252 TAO:0000132 UMLS:C0920623 VHOG:0000068 XAO:0000249 ZFA:0000132 uberon lamina neuralis presumptive central nervous system UBERON:0003075 neural plate 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 TAO:0000255 UMLS:C1284009 VHOG:0000114 XAO:0000259 ZFA:0000255 paraxial mesenchyme somitic mesoderm uberon mesoderma paraxiale UBERON:0003077 paraxial mesoderm 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 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 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 TAO:0000028 UMLS:C1514450 XAO:0000336 ZFA:0000028 uberon cardiac field fused heart primordium UBERON:0003084 heart primordium 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 TAO:0001080 UMLS:C0183176 VHOG:0000680 XAO:0000397 ZFA:0001080 sclerotomes uberon sclerotomus UBERON:0003089 sclerotome 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] 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 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 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 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 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 OpenCyc:Mx4rVmfYCsQ_QdeM_bFAeS8NRQ UMLS:C0027757 nerve tissue nervous tissue portion of neural tissue uberon UBERON:0003714 neural tissue An anatomical cavity that has the potential to develop into a coelemic cavity lumen. uberon body cavity precursor UBERON:0003886 future coelemic cavity lumen 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 UMLS:C1512940 VHOG:0000316 somatic coelom uberon UBERON:0003887 intraembryonic coelom 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 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 UMLS:C0180383 XAO:0000220 cutis plate dermatomal mesenchyme uberon epimere mesoderm mesenchyma dermatomiale UBERON:0004016 dermatome 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 An anatomical structure that develops (entirely or partially) from the mesoderm. Grouping term for query purposes uberon UBERON:0004120 mesoderm-derived structure An anatomical structure that develops (entirely or partially) from the ectoderm. Grouping term for query purposes uberon UBERON:0004121 ectoderm-derived structure 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 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 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 TAO:0000360 XAO:0000337 ZFA:0000360 embryonic heart tube endocardial heart tube endocardial tube uberon UBERON:0004141 heart tube 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 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 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 TAO:0001513 UMLS:C1511786 VHOG:0000676 ZFA:0001513 uberon dermamyotome dermomyotomes UBERON:0004290 dermomyotome 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 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 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 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 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 UMLS:C1516779 embryo plus adnexa uberon UBERON:0004716 conceptus 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 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 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] 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 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 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 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 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 Anatomical cluster that connects two or more adjacent skeletal elements or hardened body parts. FBbt:00005811 joint uberon UBERON:0004905 articulation 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 part of a wall of an organ that forms a layer. FMA:82485 uberon UBERON:0004923 organ component layer 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 UMLS:C0814992 XAO:0000248 uberon UBERON:0005061 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 EMAPA:16142 EMAPA:16146 EMAPA:16151 EMAPA:16155 EMAPA:16159 EMAPA:16162 EMAPA:16288 EMAPA:16292 EMAPA:16295 EMAPA:16299 EMAPA:16303 EMAPA:16307 EMAPA:16528 FMA:295618 UMLS:C0814993 XAO:0004087 medullary fold uberon UBERON:0005062 neural fold 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 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 An epithelial sheet bent on a linear axis. uberon UBERON:0005157 epithelial fold 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. MA:0000516 trunk organ uberon UBERON:0005177 trunk region element An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli. MA:0000557 thoracic cavity organ uberon UBERON:0005178 thoracic cavity element An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions. MA:0000563 uberon upper body organ UBERON:0005181 thoracic segment organ 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 A portion of tissue that is part of an embryo. CALOHA:TS-2100 portion of embryonic tissue uberon developing tissue UBERON:0005291 embryonic tissue 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 Multi-tissue structure that arises from the heart rudiment and will become the heart tube. EHDAA2:0001512 EHDAA:424 EHDAA:436 EMAPA:16208 EMAPA:16215 FMA:321916 TAO:0000149 ZFA:0000149 primitive heart tube early primitive heart tube uberon UBERON:0005498 primitive heart tube A acellular anatomical structure that is the bounding layer of a anatomical structure. FMA:63871 uberon UBERON:0005764 acellular membrane 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 UMLS:C0004799 basement membrane of connective tissue membrana basalis uberon basement membrane UBERON:0005769 basement membrane of epithelium A delimited region of dense mesenchyme within looser mesenchyme. AEO:0000148 EHDAA2_RETIRED:0003148 EHDAA:8979 mesenchyme condensation uberon UBERON:0005856 developing mesenchymal condensation 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 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 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 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 UMLS:C1518429 VHOG:0001212 uberon UBERON:0006267 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 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 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. fluid FMA:280556 GAID:266 MESH:D001826 galen:BodyFluid body fluid uberon UBERON:0006314 bodily fluid 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 Presumptive structure of the blastula that will develop into endoderm. AAO:0000471 EFO:0003437 TAO:0000416 ZFA:0000416 uberon UBERON:0006595 presumptive 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 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 mesoderm. AAO:0000476 EFO:0003467 TAO:0001377 ZFA:0001377 uberon UBERON:0006603 presumptive mesoderm 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 UMLS:C0221909 uberon UBERON:0006914 squamous epithelium 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 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 AAO:0010270 BILA:0000010 CARO:0001002 EHDAA2:0003192 FMA:24137 ID:0000000 UMLS:C1515977 ZFA:0005594 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 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 uberon cardiogenic mesoderm cardiogenic region heart primordia UBERON:0007005 cardiac mesoderm Organism at the cleavage stage. BILA:0000058 uberon UBERON:0007010 cleaving embryo 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 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 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 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 Of or pertaining to the period of time immediately following birth, or to the newborn. consider splitting infant/newborn BTO:0001762 EV:0300037 HsapDv:0000082 MmusDv:0000096 NIF_Organism:birnlex_695 OGES:000025 neonatal stage fledgling stage hatchling hatchling stage infant stage nestling stage pouch stage puggle puggle stage uberon newborn stage UBERON:0007221 neonate stage 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 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 paraxial mesoderm. EFO:0003443 TAO:0000591 XAO:0004134 ZFA:0000591 future paraxial mesoderm uberon UBERON:0007285 presumptive paraxial mesoderm 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 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 uberon UBERON:0007377 stratum compactum 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 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 A closed epithelium with a lumen. EHDAA2:0003119 AEO:0000119 EHDAA2:0003119 uberon UBERON:0007503 epithelial vesicle Mesenchyme with little extracellular matrix. EHDAA2:0003146 AEO:0000146 EHDAA2:0003146 uberon UBERON:0007524 dense mesenchyme tissue 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 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 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 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 Any fluid produced by a serous gland. the FMA def is Transudate contained in a serous sac FMA:20932 serous gland fluid uberon UBERON:0007794 serous 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 UMLS:C0489903 uberon Gefaesssystem@ge UBERON:0007798 vascular system 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 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 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 FMA:25054 region of trunk trunk subdivision uberon UBERON:0009569 subdivision of trunk EHDAA2:0002094 trunk and cervical paraxial mesenchyme uberon trunk paraxial mesenchyme UBERON:0009618 trunk paraxial mesoderm 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 EFO:0003704 TAO:0005041 ZFA:0005041 ALPM uberon UBERON:0009881 anterior lateral plate mesoderm An anatomical structure that has more than one cell as a part. CARO:0010000 FBbt:00100313 multicellular structure uberon UBERON:0010000 multicellular anatomical structure Mesenchyme that has the potential to develop into a dermis. check development EHDAA2:0000598 uberon UBERON:0010083 future dermis 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 uberon UBERON:0010316 germ layer / neural crest Epithelium composed of cells that develops from the ectoderm[FMA,modified]. FMA:69064 ectoderm-derived epithelium uberon UBERON:0010371 ecto-epithelium 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 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 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 Subdivision of the skeletal system which consists of the post-cranial axial skeleton plus associated joints. axial skeletal system FMA:302077 uberon UBERON:0011138 post-cranial axial skeletal system http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton A subdivision of an anatomical system. FBbt:00007330 FMA:67509 uberon UBERON:0011216 organ system subdivision 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 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 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 cardiovascular system that is part of a conceptus. EHDAA2:0000216 FMA:305965 conceptus cardiovascular system uberon embryonic circulatory system fetal circulatory system UBERON:0011695 embryonic cardiovascular 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 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 UMLS:C0738366 irregular dense connective tissue typus irregularis (textus connectivus collagenosus compactus) uberon UBERON:0011822 dense irregular 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 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 UMLS:C1511770 uberon UBERON:0011823 dense connective tissue 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 textus connectivus collagenosus laxus textus connectivus laxus uberon UBERON:0011825 loose connective tissue An acinus that is part of a exocrine gland. exocrine gland acinus uberon UBERON:0011858 acinus of exocrine gland the FMA class specifically refers to ureter FMA:63212 MESH:D024022 NIF_Subcellular:sao7547390221 uberon UBERON:0011860 collection of collagen fibrils 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 Epithelium that derives from the mesoderm. [Automatically generated definition]. FMA:86452 mesoderm-derived epithelium mesoepithelium uberon UBERON:0012275 meso-epithelium 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 space that surrounds an organism. external to organism outside of body uberon UBERON:0013514 space surrounding organism uberon UBERON:0013522 subdivision of tube 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 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 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 A organ component layer that is part of a integumental system. layer of skin skin layer uberon UBERON:0013754 integumentary system layer 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 A portion of tissue that will develop into vasculature. EFO:0003708 TAO:0005076 ZFA:0005076 uberon UBERON:0014903 primordial vasculature 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 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 MA:0002449 heart/pericardium uberon UBERON:0015410 heart plus pericardium 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 nervous system UBERON:3000477 AAO:0000477 presumptive nervous system uberon UBERON:0016880 future nervous system 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 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 A mesenchyme-derived anatomical entity undergoing a transtion to become another structure. AEO:0001016 uberon UBERON:0017650 developing mesenchymal structure A mammalian developmental stage that covers the period from birth until weaning. suckling stage uberon UBERON:0018685 nursing stage Nursing stage that follows the neonate stage in mammals and ends at weaning. uberon UBERON:0034920 infant stage An multicellular anatomical structure that has subparts of multiple organs as a part. CARO:0020001 uberon anatomical cluster UBERON:0034921 multi organ part structure A cluster of cells, largely surrounded by a morphological boundary. CARO:0020002 FMA:62807 uberon UBERON:0034922 cell cluster 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 FMA:55268 organ sector organ zonal region organ zone uberon organ region with floating fiat boundary UBERON:0034944 zone of organ uberon duct epithelium ductal epithelium UBERON:0034969 epithelial layer of duct The primordial mouth region of the developing head. FMA:293105 primitive mouth primordial mouth uberon UBERON:0035804 future mouth 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 external integument structure time unit A unit which is a standard measure of the dimension in which events occur in sequence. time unit 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. vaccine a medical intervention that involves in adding vaccine into a host (e.g., human, mouse) in vivo with the intent to invoke an adaptive immune response. vaccination GAZ GAZ:00000464 Europe Part of the landmass of Eurasia, with the western portion of the latter occupied by Europe, lying east of the Suez Canal, east of the Ural Mountains, and south of the Caucasus Mountains and the Caspian and Black Seas. It is bounded on the east by the Pacific Ocean, on the south by the Indian Ocean, and on the north by the Arctic Ocean. GAZ GAZ:00000465 Asia GAZ GAZ:00002471 East Asia A sovereign island country located off the northwestern coast of mainland Europe comprising of the four constituent countries; England, Scotland, Wales and Northern Ireland. It comprises the island of Great Britain, the northeast part of the island of Ireland and many small islands. Apart from Northern Ireland the UK is surrounded by the Atlantic Ocean, the North Sea, the English Channel and the Irish Sea. The largest island, Great Britain, is linked to France by the Channel Tunnel. ISO3166-1:826 ISO3166-1:GB ISO3166-1:GBR ISO3166-2:GB Britain G.B GB U.K. {abbrevation} UK United Kingdom of Great Britain and Northern Ireland GAZ GAZ:00002637 United Kingdom An island country in East Asia. Located in the Pacific Ocean, it lies to the east of China, Korea and Russia, stretching from the Sea of Okhotsk in the north to the East China Sea in the south. Nippon-koku GAZ GAZ:00002747 Japan A large country in Northeast Asia. China borders 14 nations (counted clockwise from south): Vietnam, Laos, Burma, India, Bhutan, Nepal, Pakistan, Afghanistan, Tajikistan, Kyrgyzstan, Kazakhstan, Russia, Mongolia and North Korea. Additionally the border between PRC and ROC is located in territorial waters. The People's Republic of China has administrative control over twenty-two provinces and considers Taiwan to be its twenty-third province. There are also five autonomous regions, each with a designated minority group; four municipalities; and two Special Administrative Regions that enjoy considerable autonomy. The People's Republic of China administers 33 province-level regions, 333 prefecture-level regions, 2,862 county-level regions, 41,636 township-level regions, and several village-level regions. People's Republic of China Zhonghua Renmin Gongheguo GAZ GAZ:00002845 China GAZ GAZ:00002846 Northeast Asia A group of islands off the northwest coast of continental Europe that include the islands of Great Britain and Ireland, and over six thousand smaller islands. There are two sovereign states located on the islands: the United Kingdom and the Republic of Ireland. The British Isles also include two dependencies of the United Kingdom: the Isle of Man and, by tradition, the Channel Islands, although the latter are not physically a part of the island group. michaelashburner 2010-05-16T10:11:46Z GAZ GAZ:00281547 British Isles example to be eventually removed example to be eventually removed metadata complete 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 organizational term Term created to ease viewing/sort terms for development purpose, and will not be included in a release term created to ease viewing/sort terms for development purpose, and will not be included in a release PERSON:Alan Ruttenberg organizational term ready for release 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 metadata incomplete Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. metadata incomplete uncurated Nothing done yet beyond assigning a unique class ID and proposing a preferred term. uncurated pending final vetting 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 to be replaced with external ontology term Terms with this status should eventually replaced with a term from another ontology. Alan Ruttenberg group:OBI to be replaced with external ontology term requires discussion 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 KPMP organization participant candidate 1 participant candidate 2 participant candidate 3 filled CRF by candidate 1 filled CRF by candidate 2 filled CRF by candidate 3 European Union Drug Regulating Authorities Clinical Trials https://en.wikipedia.org/wiki/EudraCT EudraCT ClinicalTrials.gov is a resource provided by the U.S. National Library of Medicine. https://clinicaltrials.gov/ Clinicaltrials.gov SDY269 study SDY269 human subject SUB112829 ## 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 en Adam Goldstein Alan Ruttenberg Albert Goldfain Barry Smith Bjoern Peters Carlo Torniai Chris Mungall Chris Stoeckert Christian A. Boelling Darren Natale David Osumi-Sutherland Gwen Frishkoff Holger Stenzhorn James A. Overton James Malone Jennifer Fostel Jie Zheng Jonathan Rees Larisa Soldatova Lawrence Hunter Mathias Brochhausen Matt Brush Melanie Courtot Michel Dumontier Paolo Ciccarese Pat Hayes Philippe Rocca-Serra Randy Dipert Ron Rudnicki Satya Sahoo Sivaram Arabandi Werner Ceusters William Duncan William Hogan Yongqun (Oliver) He http://creativecommons.org/licenses/by/4.0/ An information artifact is, loosely, a dependent continuant or its bearer that is created as the result of one or more intentional processes. Examples: uniprot, the english language, the contents of this document or a printout of it, the temperature measurements from a weather balloon. For more information, see the project home page at https://github.com/information-artifact-ontology/IAO IDs allocated to related efforts: PNO: IAO_0020000-IAO_0020999, D_ACTS: IAO_0021000-IAO_0021999 IDs allocated to subdomains of IAO. pno.owl: IAO_0020000-IAO_0020999, d-acts.owl: IAO_0021000-IAO_0021999 The Information Artifact Ontology (IAO) is licensed under the Creative Commons Attribution License (CC-BY) version 4.0. You are free to share (copy and redistribute the material in any medium or format) and adapt (remix, transform, and build upon the material) for any purpose, even commercially. for any purpose, even commercially. The licensor cannot revoke these freedoms as long as you follow the license terms. You must give appropriate credit (by using the original ontology IRI for the whole ontology and original term IRIs for individual terms), provide a link to the license, and indicate if any changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. For more information see http://www.obofoundry.org/docs/Citation.html This version of the ontology is the merge of all its imports and has added axioms inferred by an OWL reasoner en Ontology for Biomedical Investigations Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester Alan Ruttenberg Allyson Lister Barry Smith Bill Bug Bjoern Peters Carlo Torniai Chris Mungall Chris Stoeckert Chris Taylor Christian Bolling Cristian Cocos Daniel Rubin Daniel Schober Dawn Field Dirk Derom Elisabetta Manduchi Eric Deutsch Frank Gibson Gilberto Fragoso Helen C. Causton Helen Parkinson Holger Stenzhorn James A. Overton James Malone Jay Greenbaum Jeffrey Grethe Jennifer Fostel Jessica Turner Jie Zheng Joe White John Westbrook Kevin Clancy Larisa Soldatova Lawrence Hunter Liju Fan Luisa Montecchi Matthew Brush Matthew Pocock Melanie Courtot Melissa Haendel Mervi Heiskanen Monnie McGee Norman Morrison Philippe Rocca-Serra Phillip Lord Pierre Grenon Richard Bruskiewich Richard Scheuermann Robert Stevens Ryan R. Brinkman Stefan Wiemann Susanna-Assunta Sansone Tanya Gray Tina Hernandez-Boussard Trish Whetzel Yongqun He 2009-07-31 The Ontology for Biomedical Investigations (OBI) is build in a collaborative, international effort and will serve as a resource for annotating biomedical investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. This ontology arose from the Functional Genomics Investigation Ontology (FuGO) and will contain both terms that are common to all biomedical investigations, including functional genomics investigations and those that are more domain specific. OWL-DL An ontology for the annotation of biomedical and functional genomics experiments. http://creativecommons.org/licenses/by/4.0/ Ontology for Biomedical Investigations Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them. 2022-01-03 GAZ:00000013 One of the large, unbroken masses of land into which the Earth's surface is divided. FTT:540 TGN:21402 continent GAZ GeoNames:CONT continental region GAZ:00190836 CONTIN continent {alternative name} Continent {alternative name} TGN:29000 GAZ:00000467 GAZ:00000448 A reference to a place on the Earth, by its name or by its geographical location. GAZ geographic location geographic region {alternative name} geographic location GAZ:00000460 Eurasia GAZ The convention used in gaz.obo is that the Europe-Asia boundary follows the watershed of the Ural Mountains from near Kara, Russia on the Kara Sea to the source of the Ural River, then follows that river to the Caspian Sea. The border then follows the watershed of the Caucasus Mountains from the Caspian Sea to the Black Sea. USA GAZ:00002459 GAZ ISO3166-1:US ISO3166-1:840 A federal constitutional republic comprising fifty states and a federal district. The country is situated mostly in central North America, where its forty-eight contiguous states and Washington, DC, the capital district, lie between the Pacific and Atlantic Oceans, bordered by Canada to the north and Mexico to the south. The State of Alaska is in the northwest of the continent, with Canada to its east and Russia to the west across the Bering Strait, and the State of Hawaii is in the mid-Pacific. The United States also possesses several territories, or insular areas, that are scattered around the Caribbean and Pacific. The states are divided into smaller administrative regions, called counties in most states, exceptions being Alaska (parts of the state are organized into subdivisions called boroughs; the rest of the state's territory that is not included in any borough is divided into "census areas"), and Louisiana (which is divided into county-equivalents that are called parishes). There are also independent cities which are within particular states but not part of any particular county or consolidated city-counties. Another type of organization is where the city and county are unified and function as an independent city. There are thirty-nine independent cities in Virginia and other independent cities or city-counties are San Francisco, California, Baltimore, Maryland, St. Louis, Missouri, Denver, Colorado and Carson City, Nevada. Counties can include a number of cities, towns, villages, or hamlets, or sometimes just a part of a city. Counties have varying degrees of political and legal significance, but they are always administrative divisions of the state. Counties in many states are further subdivided into townships, which, by definition, are administrative divisions of a county. In some states, such as Michigan, a township can file a charter with the state government, making itself into a "charter township", which is a type of mixed municipal and township status (giving the township some of the rights of a city without all of the responsibilities), much in the way a metropolitan municipality is a mixed municipality and county. United States of America U.S.A ISO3166-2:US ISO3166-1:USA An ontology of drugs. Josh Hanna William Hogan DrOn contains content developed by the National Library of Medicine in RxNorm. In creating DrOn, we have used RxNorm content only with SAB = RXNORM. https://creativecommons.org/licenses/by/3.0/ Eric Joseph Mathias Brochhausen When citing DrOn, use the permanent URL of the ontology: http://purl.obolibrary.org/obo/dron.owl. When referencing a specific component of the DrOn, such as a class, object property, annotation property, or individual, use the Uniform Resource Identifier (URI) of that component. http://orcid.org/0000-0002-8343-612X Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/entity_attribute.owl>) VersionIRI(<null>))) [Axioms: 114 Logical Axioms: 19] Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/process_attribute.owl>) VersionIRI(<null>))) [Axioms: 21 Logical Axioms: 2] Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/chemical_concentration.owl>) VersionIRI(<null>))) [Axioms: 186 Logical Axioms: 30] Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/entity_quality_location.owl>) VersionIRI(<null>))) [Axioms: 40 Logical Axioms: 6] http://orcid.org/0000-0002-4366-3088 http://orcid.org/0000-0002-6601-2165 http://orcid.org/0000-0003-1604-1512 Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/entity_attribute_location.owl>) VersionIRI(<null>))) [Axioms: 132 Logical Axioms: 23] ENVO is an ontology which represents knowledge about environments,environmental processes, ecosystems, habitats, and related entities. It interoperates with other ontologies in the OBO Foundry and Library. New terms or revisions can be requested at https://github.com/EnvironmentOntology/envo/issues/ Please see www.environmentontology.org for more information and citations. https://orcid.org/0000-0002-6962-2807 Desikan Jagannathan An ontology for the annotation of the adverse event domain. Vision Release; 1.2.19 Elizabeth Blair "Asiyah" Yu Lin Abra Guo Sydni Joubran OWL-DL Product version Darrell R. Abernethy Sirarat Sarntivijai Ling Wan Shelley Zhang Rebecca Racz Liwei Wang Meiu Wong The Ontology of Adverse Eventsy (OAE) is a biomedical ontology in the domain of adverse events. OAE aims to standardize adverse event annotation, integrate various adverse event data, and support computer-assisted reasoning. OAE is a community-based ontology. Its development follows the OBO Foundry principles. Vaccine adverse events have been used as an initial testing use case. OAE also studies adverse events associated with the administration of drug and nutritional products, the operation of surgeries, and the usage of medical devices, etc. Kevin Mo OAE: Ontology of Adverse Events Yongqun "Oliver" He (YH) Luca Toldo Noemi Garg Keith Burkhart Edison Ong Mathias Brochhausen Izabela Birsanescu Zuoshuang "Allen" Xiang Barry Smith Bingjian Yang Qingping Liu 2019-2-21 Jiangan Xie Sydni Joubran Kelly Yang David Ameriguian Alice Nzinga MIABIS_v2_accepted and UPenn Biobank ontology Roxana Merino-Martinez William R. Hogan Sanela Kjellqvist Loreana Norlin The Ontology for Biobanking (OBIB) is an ontology for the annotation and modeling of the activities, contents, and administration of a biobank. Biobanks are facilities that store specimens, such as bodily fluids and tissues, typically along with specimen annotation and clinical data. OBIB is based on a subset of the Ontology for Biomedical Investigation (OBI), has the Basic Formal Ontology (BFO) as its upper ontology, and is developed following OBO Foundry principles. The first version of OBIB resulted from the merging of two existing biobank-related ontologies, OMIABIS and biobank ontology. Jan-Eric Litton Chris Stoeckert development version Ontology for BIoBanking (OBIB) Jie Zheng Mathias Brochhausen Mikael Eriksson Maria Anderberg Martin N. Fransson 2021-11-12 Daniel Merico Ontology for General Medical Science Werner Ceusters Brian Aevermann Jie Zheng Bill Hogan Albert Goldfain Alan Ruttenberg The Ontology for General Medical Science (OGMS) is an ontology of entities involved in a clinical encounter. OGMS includes very general terms that are used across medical disciplines, including: 'disease', 'disorder', 'disease course', 'diagnosis', 'patient', and 'healthcare provider'. OGMS uses the Basic Formal Ontology (BFO) as an upper-level ontology. The scope of OGMS is restricted to humans, but many terms can be applied to a variety of organisms. OGMS provides a formal theory of disease that can be further elaborated by specific disease ontologies. This theory is implemented using OWL-DL and OBO Relation Ontology relations and is available in OWL and OBO formats. OGMS is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX) and the Signs, Symptoms, and Findings Workshop(Milan, Italy). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology. 2021-08-19 Sivaram Arabandi http://creativecommons.org/licenses/by/4.0/ Lindsay Cowell 2009-08-07 Richard Scheuermann Cornelius Rosse Anand Kumar The Ontology for General Medical Science (OGMS) is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology. The latest version of OGMS is available at http://purl.obolibrary.org/obo/ogms.owl The OGMS developer site is https://github.com/OGMS/ogms If you are interested in participating in the development of OGMS, please send email to baeverma Barry Smith William Hogan This ontology grew out of efforts to represent the reality underlying the demographic information required by the US federal government's "meaningful use" criteria for electronic medical records and a presentation by Dr. William Hogan at the Electronic Health Record of the Future conference in Buffalo, NY http://ontology.buffalo.edu/EHR/Demographics_Hogan_Buffalo_2010_09_22.ppt 2017-06-08 Amanda Hicks Mathias Brochhausen Swetha Garimalla Daniel Welch The Ontology of Medically Related Social Entities Shariq Tariq