This file is based on checkout of our SVN repository revision $Revision: 204$ https://github.com/obi-bcgo/bcgo Chris Stoeckert Emily Greenfest-Allen The ontology is built based on OBI release 2015-04-13 Elisabetta Manduchi Jie Zheng preceded by 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. http://www.obofoundry.org/ro/#OBO_REL:preceded_by is preceded by preceded by preceded_by precedes precedes BFO OWL specification label BFO OWL specification label Really of interest to developers only 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. BFO CLIF specification label BFO CLIF specification label Person:Alan Ruttenberg Really of interest to developers only Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 editor preferred label editor preferred term editor preferred term GROUP:OBI:<http://purl.obolibrary.org/obo/obi> PERSON:Daniel Schober The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) editor preferred label editor preferred term 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 GROUP:OBI:<http://purl.obolibrary.org/obo/obi> PERSON:Daniel Schober example example of usage has curation status OBI_0000281 PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot has curation status definition textual definition definition definition definition 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. GROUP:OBI:<http://purl.obolibrary.org/obo/obi> The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. definition PERSON:Daniel Schober The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. definition editor note editor note 1 IAO:0000116 editor_note editor_note uberon 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. GROUP:OBI:<http://purl.obfoundry.org/obo/obi> PERSON:Daniel Schober editor note term editor 20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115. GROUP:OBI:<http://purl.obolibrary.org/obo/obi> 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 PERSON:Daniel Schober term editor alternative term An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) GROUP:OBI:<http://purl.obolibrary.org/obo/obi> PERSON:Daniel Schober alternative term definition source Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> PERSON:Daniel Schober 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 has obsolescence reason PERSON:Alan Ruttenberg PERSON:Melanie Courtot 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. has obsolescence reason curator notes curator note 1 IAO:0000232 curator_notes curator_notes uberon An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg curator note imported from imported from For external terms/classes, the ontology from which the term was imported GROUP:OBI:<http://purl.obolibrary.org/obo/obi> PERSON:Alan Ruttenberg PERSON:Melanie Courtot imported from expand expression to expand expression to expand assertion to first order logic expression elucidation 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 person:Alan Ruttenberg has associated axiom(nl) An axiom associated with a term expressed using natural language Person:Alan Ruttenberg Person:Alan Ruttenberg has associated axiom(nl) has associated axiom(fol) An axiom expressed in first order logic using CLIF syntax Person:Alan Ruttenberg Person:Alan Ruttenberg has associated axiom(fol) has axiom label term replaced by Add as annotation triples in the granting ontology Person:Alan Ruttenberg Person:Alan Ruttenberg Use on obsolete terms, relating the term to another term that can be used as a substitute term replaced by ISA alternative term Requested by Alejandra Gonzalez-Beltran https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891&atid=886178 ISA alternative term Person: Philippe Rocca-Serra Person: Alejandra Gonzalez-Beltran ISA tools project (http://isa-tools.org) An alternative term used by the ISA tools project (http://isa-tools.org). 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). NIAID GSCID-BRC alternative term PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group IEDB alternative term An alternative term used by the IEDB. IEDB IEDB alternative term PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters temporal interpretation https://code.google.com/p/obo-relations/wiki/ROAndTime temporal interpretation Abnormal/normal slim Attribute slim cell_quality Disposition slim Pathology slim Relational slim: types of quality that require an additional entity in order to exist Scalar slim Value slim abstract upper-level terms not directly useful for analysis Description Description An account of the content of the resource. 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. Source Source A reference to a resource from which the present resource is derived. 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. subset_property has_alternative_id has_broad_synonym database_cross_reference has_exact_synonym has_narrow_synonym has_obo_namespace has_related_synonym in_subset shorthand label has_genetic_background_of strain a has genetic backgroud as strain b is that strain a is derived from strain b and genetic make-up (all its alleles at all loci) of strain a is same to strain b except the mutated gene of interest and a very small amount of other genetic material, generally from one or two other strains. For example, the genetic background of the mutant strains NOD.129S7(B6)-Rag1tm1Mom/J (003729) and NOD.Cg-Rag1tm1Mom Prf1tm1Sdz/SzJ (004848) is NOD. Person: Jie Zheng produces_low_amount Person: Jie Zheng a produces b if some process that occurs_in a has_output b and amount of b is low relative to normal cases, where a and b are material entities. Examples: defective beta ccell line produces less amount of insulin produces_high_amount a produces b if some process that occurs_in a has_output b and amount of b is high relative to generally cases, where a and b are material entities. Person: Jie Zheng not_produce Person: Jie Zheng a produces_no b if some process that occurs_in a and has_no_output b, where a and b are material entities. has contact relates an entity to a person or an organization that can be contacted for information regarding the entity. has external resource relates an entity to the information about it in an external database. has external identifier relates an entity to an identifier assigned by an external resource which denotes the entity. has email address Person: Jie Zheng a instance-level relation between a person or an organization to an email address the person or organization has. executes shortcut relation of a planned process realizes or concretizes some plan specification has experimental factor relates an investigation to an experimental factor which is a study independent variable specified in a study design. An experimental factor can be a material entity (such as treated and untreated specimen), a quality (such as sex of an organism), a process (such as developmental stage of an organism), or an information about a process (such as duration of a treatment), etc. has experimental factor value relates experimental factor (could be anything that a study independent variable specification is about) to its values For example, biological sex can be a study independent variable, potential values can be male or female. value of experimental factor relates experimental factor values to its factor type (could be anything that a study independent variable specification is about) For example, male/female could be values for biological sex, 0, 0.01, 0.02 mg/L for glucose concentation, 1,5,20 minutes for treatment duration, etc. examines relates an invesitigation to any biologically-related entity that is examined as part of that process, such as a protein, a biological process, etc. associated PubMed ID Person: Jie Zheng a instance-level relation between an entity to a PubMed ID that denotes a publication associated with the entity. is about organism species relates an information artifact to the species of an organism that it is about. Person: Jie Zheng is denoted by is denoted by is an instance-level, relation obtaining between an entity to an information content entity that is created to specifically refer to something. It is the inverse relation of 'denotes'. Person: Jie Zheng is about genotype relates an information artifact to the genotype of an organism that it is about. Person: Jie Zheng is about cell type relates an information artifact to the type of a cell that it is about. Person: Jie Zheng is about cell line relates an information artifact to the cell line that it is about. Person: Jie Zheng is about tissue Person: Jie Zheng relates an information artifact to the tissue of an organism that it is about. has gene member relates the member (a data item) of a gene list (a data set) to the gene that it is about. is about strain relates an information artifact to the strain of an organism that it is about. is about phenotype relates an information artifact to the phenotype born by an organism that it is about. is about development stage relates an information artifact to the development stage of an organism that it is about. is about treatment relates an information artifact to the treatment that it is about. For specimens in an assay, the treatment referred to was performed prior to specimen collection. has duration relates a process to a time-measurement-datum that represents the duration of the process has concentration relates a molecular entity to its concentration measurement datum that is the measurement of its concentration quality binding context relates a gene that has protein binding to the biological context in which that binding was identified. differential expression context relates a gene that is differentially expressed to the biological context in which that differential expression was identified. context of differential expression relates a biological context (e.g., cell, developmental stage, etc.) to a gene whose protein binding was identified in this specific context. context of binding relates the context to a gene that protein binding is identified in this specific context part of Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. a core relation that holds between a part and its whole http://www.obofoundry.org/ro/#OBO_REL:part_of 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) part_of this day is part of this year (occurrent parthood) has part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. a core relation that holds between a whole and its part has part 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) realized in 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 [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]) is realized by realized in 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 realizes 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 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]) preceded by 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. http://www.obofoundry.org/ro/#OBO_REL:preceded_by is preceded by preceded by preceded_by precedes precedes occurs in Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant 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 occurs_in unfolds in unfolds_in contains process Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant [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 site of has disease Jie Zheng, Yongqun He, Yu Lin, Allen Xiang has measurement unit label has measurement unit label is about 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. Smith, Ceusters, Ruttenberg, 2000 years of philosophy This document is about information artifacts and their representations is about is_about is a (currently) primitive relation that relates an information artifact to an entity. person:Alan Ruttenberg denotes 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 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. Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan denotes 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 person:Alan Ruttenberg is quality measurement of 8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later Alan Ruttenberg From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important] This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. -- From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009] unit of measure is a quality, e.g. the length of a ruler. [We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label] [Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory] a represents b means either a denotes b or a describes describe: a describes b means a is about b and a allows an inference of at least one quality of b We have had a long discussion about denotes versus describes. From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully. a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality. From the second meeting on IAO: An attempt at defining assay using Barry's "reliability" wording assay: process and has_input some material entity and has_output some information content entity and which is such that instances of this process type reliably generate outputs that describes the input. This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. is quality measurement of m is a quality measurement of q at t when q is a quality there is a measurement process p that has specified output m, a measurement datum, that is about q is duration of Person:Alan Ruttenberg is duration of relates a process to a time-measurement-datum that represents the duration of the process is_supported_by_data Philly 2011 workshop 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 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. is_supported_by_data OBI OBI has_specified_input 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: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Coutot 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. PERSON: Alan Ruttenberg has_specified_input see is_input_of example_of_usage has_specified_output PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Courtot 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. PERSON: Alan Ruttenberg has_specified_output is_manufactured_by Alan Ruttenberg Liju Fan c is_manufactured_by o means that there was a process p in which c was built in which a person, or set of people or machines did the work(bore the "Manufacturer Role", and those people/and or machines were members or of directed by the organization to do this. has_make has_manufacturer http://www.affymetrix.com/products/arrays/specific/hgu133.affx is_manufactered_by http://www.affymetrix.com/ (if we decide to use these URIs for the actual entities) is_manufactured_by is_specified_output_of PERSON:Bjoern Peters A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. Alan Ruttenberg is_specified_output_of achieves_planned_objective A cell sorting process achieves the objective specification 'material separation objective' BP, AR, PPPB branch PPPB branch derived 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. achieves_planned_objective modified according to email thread from 1/23/09 in accordince with DT and PPPB branch has grain 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 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 supplies A relation between an organisation or person and a material entity who owned or has license to the material entity and there was a legal transfer of ownership or licensing of the material entity to the current owner. GROUP: Relations branch supplies has_supplier A relation between a material entity and an organisation or person who owned or has license to the material entity and there was a legal transfer of ownership or licensing of the material entity to the current owner. PERSON: Alan Rutternberg PERSON: Cristian Cocos PERSON: Frank Gibson PERSON: Melanie Courtot has_supplier objective_achieved_by This relation obtains between a a objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. objective_achieved_by OBI OBI is member of organization 2009/09/28 Alan Ruttenberg. Fucoidan-use-case 2009/10/01 Alan Ruttenberg. Barry prefers generic is-member-of. Question of what the range should be. For now organization. Is organization a population? Would the same relation be used to record members of a population JZ: Discussed on May 7, 2012 OBI dev call. Bjoern points out that we need to allow for organizations to be members of organizations. And agreed by the other OBI developers. So, human and organization were specified in 'Domains'. The textual definition was updated based on it. Person:Alan Ruttenberg Person:Alan Ruttenberg Person:Helen Parkinson Person:Helen Parkinson Relating a legal person or organization to an organization in the case where the legal person or organization has a role as member of the organization. is member of organization has value specification has value specification PERSON: James A. Overton OBI A relation between an information content entity and a value specification that specifies its value. inheres in A dependent inheres in its bearer at all times for which the dependent exists. 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 inheres in inheres_in this fragility inheres in this vase this red color inheres in this apple bearer of 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. 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 bearer of bearer_of is bearer of this apple is bearer of this red color this vase is bearer of this fragility participates in a relation between a continuant and a process, in which the continuant is somehow involved in the process participates in 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 has participant 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. a relation between a process and a continuant, in which the continuant is somehow involved in the process has participant http://www.obofoundry.org/ro/#OBO_REL:has_participant 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) is concretized as A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. 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). 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). 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. 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). function of 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. a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence function_of is function of this catalysis function is a function of this enzyme quality of A quality inheres in its bearer at all times for which the quality exists. a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence is quality of quality_of this red color is a quality of this apple role of 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. a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence is role of role_of this investigator role is a role of this person has function 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. a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence has_function this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) has quality 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. a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence has_quality this apple has quality this red color has role A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence has_role this person has role this investigator role (more colloquially: this person has this role of investigator) derives from This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations. 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 derives_from this cell derives from this parent cell (cell division) this nucleus derives from this parent nucleus (nuclear division) derives into 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'. 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 derives_into this parent cell derives into this cell (cell division) this parent nucleus derives into this nucleus (nuclear division) location of 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 a relation between two independent continuants, the location and the target, in which the target is entirely within the location is location of location_of my head is the location of my brain this cage is the location of this rat located in http://www.obofoundry.org/ro/#OBO_REL:located_in 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 a relation between two independent continuants, the target and the location, in which the target is entirely within the location located in located_in my brain is located in my head this rat is located in this cage 2D boundary of 2D_boundary_of A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity boundary of is 2D boundary of is boundary of the surface of my skin is a 2D boundary of my body has 2D boundary A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity has boundary has_2D_boundary my body has 2D boundary the surface of my skin immediately preceded by starts_at_end_of David Osumi-Sutherland X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately precedes David Osumi-Sutherland ends_at_start_of X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) meets has plasma membrane part <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y) Alexander Diehl Lindsay Cowell Chris Mungall Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. PMID:19243617 develops from Chris Mungall Melissa Haendel David Osumi-Sutherland This is the transitive form of the develops from relation Terry Meehan x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y develops into Chris Mungall David Osumi-Sutherland Terry Meehan has prototype Chris Mungall heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation') x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a "canonical" heart, which participates in blood circulation. Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from) 'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair')) capable of Chris Mungall PMID:20123131 osteoclast SubClassOf 'capable of' some 'bone resorption' mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) RO_0000053 some (RO_0000054 only ?Y) has function realized in PMID:21208450 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)". 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. actively participates in agent in x actively participates in y if and only if x participates in y and x realizes some active role has active participant has agent 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 'heart development' has active development some Shh protein temporal relation A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. move to BFO? Allen member of is member of is a mereological relation between a item and a collection. An organism that is a member of a population of organisms SIO member part of is member of has member has member is a mereological relation between a collection and an item. SIO has potential to develop into x has the potential to develop into y iff x develops into y or if x is capable of developing into y produces Melissa Haendel Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. produced by Melissa Haendel translates_to Example: codon translates_to amino_acid. Inverse of translation _of. Wed Aug 19 00:11:53 PDT 2009 kareneilbeck translation_of Example: Polypeptide translation_of CDS. Wed Aug 19 00:09:59 PDT 2009 X is translation of Y if X is translated by ribosome to create Y. kareneilbeck has_high_plasma_membrane_amount A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617). has_low_plasma_membrane_amount A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617). lacks_part http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 ?Y lacks_plasma_membrane_part http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 (http://purl.obolibrary.org/obo/GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y) different_in_magnitude_relative_to different_in_magnitude_relative_to q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. quality has_cross_section Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round. has_cross_section quality s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2. increased_in_magnitude_relative_to This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'. increased_in_magnitude_relative_to q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. quality has NCBI gene id differential expression pattern has measurement value has measurement value has specified value OBI A relation between a value specification and a number that quantifies it. PERSON: James A. Overton A range of 'real' might be better than 'float'. For now we follow 'has measurement value' until we can consider technical issues with SPARQL queries and reasoning. has specified value has last name Called Family Name in vCard first name called Given Name invCard mouse strain Mus musculus that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organism. Person: Jie Zheng rat strain Person: Jie Zheng Rattus norvegicus that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organism. insulin expressing cell a cell that expresses a gene for insulin. sequence feature quantification UPenn Group Person: Chris Stoeckert, Jie Zheng, Elisabetta Manduchi A data transformation that attaches quantified values to specific sequence features, e.g. transcript, exon, etc. high throughput sequence alignment EFO_0004917 high throughput sequence alignment protocol a data transformation that aligns sequencing reads to reference sequence. Person: Chris Stoeckert, Jie Zheng Tg(Ins1-EGFP/GH1)14Hara mouse strain A mouse strain containing a transgene in which EGFP (transgene) is driven by the Ins1 promoter (NCBI Gene ID: 16333). Hemizygous mice show expression of EGFP in beta lineage cells of the pancreas. MIP-GFP mouse strain Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler RES188 mouse strain STOCK Tg(Ins1-EGFP/GH1)14Hara/Mmmh mouse strain Tg(Ins1-EGFP/GH1)14Hara Vanderbilt University Medical Center C57BL/6 mouse strain A mouse strain that is a laboratory mouse generated from long inbreeding with nearly identical genotype. C57BL/6 mouse has a dark brown, nearly black coat, and an easily irritable temperament. It has a good reproductive performance and is the most widely used "genetic background" for genetically modified mice for use as models of human disease. black 6 C57 http://en.wikipedia.org/wiki/C57BL/6 Person:Jie Zheng C57 black 6 functional beta cell like cell A cell that has all features and genetic signatures as functional beta cell. It may not be part of pancreas. Sox17{(GFPCre)Mgn} mouse strain STOCK Sox17tm2(EGFP/cre)Mgn/Mmnc mouse strain RES1681 mouse strain Sox17tm1.3(Cre.GFP)Mgn mouse strain A mouse strain in which part or all of the targeted gene, SRY-box containing gene 17 (NCBI Gene ID: 20671) is replaced to create Sox17{GFPCre} using the Loxed Cassette Acceptor allele Sox17{tm1(LCA)}). Using an RMCE strategy, we inserted a GFP-Cre (Green fluorescent protein-Cre-recombinase) fusion protein into a Sox17 LCA allele thereby replacing Sox17 coding sequences. The Sox17{GFPCre} mice may be used to track Sox17-expressing cells and their early progeny, or to conditionally inactivate genes in Sox17-expressing cells. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Sox17{(GFPCre)Mgn} Vanderbilt University Medical Center Pdx1{(CFP)Mgn} mouse strain A mouse strain in which part or all of the targeted gene, pancreatic and duodenal homeobox 1 (NCBI Gene ID: 18609) is replaced to create Pdx1{tm1.2(CFP)} using the Loxed Cassette Acceptor allele Pdx1{tm1(LCA)}). This mouse contains a cyan fluorescent protein (CFP, Cerulean), tagged with 3 copies of an SV40 NLS knocked into the endogenous Pdx1 gene. This mouse strain enables pre-pancreatic endoderm to be easily identified in the developing mouse embryo and the isolation of Pdx1(+) cells by FACS. RES1301 mouse strain B6.129S6-Pdx1tm2Mgn/Mmnc mouse strain Pdx1CFP mouse strain Pdx1{(CFP)Mgn} Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Ptf1a{tm1Mgn} mouse strain A mouse strain in which part or all of the targeted gene, pancreas specific transcription factor, 1a (NCBI Gene ID: 19213) is replaced to create ptf1a{tm1.1(YFP)} using the Loxed Cassette Acceptor allele Ptf1a{tm1(LCA)}). <p>Ptf1a{YFP} mice may be used to visualize yellow fluorescent protein (YFP) expression from the ptf1a allele. Ptf1a is expressedin pancreatic buds beginning at E9.5 andplays a vital role in the growth and lineage specification of pancreatic multipotent progenitor cells (MPCs). Ptf1a is also expressed in the neuronal precursors of the cerebellum, spinal cord, and retina where it also performs fate determining roles.</p> Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Ptf1a{tm1Mgn} STOCK Ptf1atm1.1Mgn/Mmmh mouse strain ptf1aYFP mouse strain RES236 mouse strain Vanderbilt University Medical Center B6.129S-Neurog3{tm1(EGFP)Khk}/Mmcd mouse strain A mouse strain in which the targeted gene, Neurogenin 3 (NCBI Gene ID: 11925), has been modified (allele type: Gene Replacement) to targeted mutation 1, Klaus H Kaestner (MGI ID: Neurog3{tm1(EGFP)Khk}). A targeted mutation at the Neurogenin 3 locus where EGFP replaces entire coding region of Neurogenin3. The basic phenotype is EGFP expression in developing endocrine cells of pancreas and in glandular regions of the stomach. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler ngn3-EGFP mouse strain RES176 mouse strain B6.129S-Neurog3tm1(EGFP)Khk/Mmcd mouse strain B6.129S-Neurog3{tm1(EGFP)Khk}/Mmcd Vanderbilt University Medical Center Insm1tm2Mgn mouse strain RES661 mouse strain http://www.betacell.org/resource/view/resource_id/661/ Person: Jie Zheng, Chris Stoeckert http://www.betacell.org/resource/view/resource_id/661/ provide the definition of 'Insm1tm1.1Mgn mouse strain' which might be the early version of 'Insm1tm2Mgn mouse strain'. However, we are not clear the difference between two strains. We borrowed the definition of 'Insm1tm1.1Mgn mouse strain'. In the webpage, it has strain name 'Mouse Strain RES661' and common name 'lnsm1GFP.Cre mouse strain'. We added 'lnsm1GFP.Cre mouse strain' as alternative term which is true to 'Insm1tm2Mgn mouse strain' too . A mouse strain contains a GFP-Cre fusion protein which replaces the Insm1 coding sequence. These mice express green fluorescent protein (GFP) under control of the Insm1 gene locus. Insm1 is expressed in pancreatic primordium starting at E9.5. Insm1 is also expressed in neural precursor cells and tumors of may be used for lineage tracing of Insm1-positive cells in both wild-type and Insm1-null mice. Insm1GFP.Cre mouse strain obsolete_STOCK Tg(Tnpo1-EGFP)6729Hara/Mmmh mouse strain true http://purl.obolibrary.org/obo/BCGO_0000012 http://www.betacell.org/resource/view/resource_id/188/ A mouse strain which is hemizygous and shows expression of EGFP in beta lineage cells of the pancreas. RES188 mouse strain Person: Jie Zheng MIP-GFP mouse strain 129X1/SvJ mouse strain A mouse strain that is a laboratory mouse generated from inbreeding. It has white-bellied, pink-eyed, light chinchilla (off-white) or albino or white-bellied, pink-eyed, light chinchilla (light tan). It has a good reproductive performance and is widely used in the production of targeted mutations due to the availability of multiple embryonic stem cell lines derived from them. Person:Jie Zheng http://www.informatics.jax.org/mgihome/nomen/strain_129.shtml http://jaxmice.jax.org/strain/000691.html 129X1 129/SvJ C3H mouse strain A mouse strain that Inbred from F130 to F170 depending on substrain original generated from a cross of a Bagg albino female and a DBA male by Strong in 1920. It has Agouti coat color. Most substrains have a good reproductive performance. It is widely used in a wide variety of research areas including cancer, immunology and inflammation, sensorineural, and cardiovascular biology. Person:Jie Zheng http://www.informatics.jax.org/external/festing/mouse/docs/C3H.shtml http://www.criver.com/EN-US/PRODSERV/BYTYPE/RESMODOVER/RESMOD/Pages/C3HMouse.aspx black swiss mouse strain Person: Jie Zheng Sox17-expressing definitive endodermal cell Person: Chris Stoeckert, Jie Zheng Chris Stoeckert Sox17 expressing cell from the embryo body proper an endodermal cell that is part of the definitive endoderm and expresses a gene for SOX-17 Sox17-expressing Epcam+ pancreatic epithelial cell an epithelial cell that is part of the ventral pancreatic bud, expresses a gene for SOX-17 and has Epcam in the plasma membrane. Person: Chris Stoeckert, Jie Zheng Sox17 expressing cell in ventral pancreatic bud Chris Stoeckert Pdx1-expressing foregut endodermal cell Pdx1-expressing endoderm cell an endodermal cell that is part of the foregut endoderm and expresses the gene for pancreas/duodenum homeobox protein 1 Person: Chris Stoeckert, Jie Zheng Chris Stoeckert Ptf1a-expressing multipotent pancreatic cell Chris Stoeckert Person: Chris Stoeckert, Jie Zheng a non-terminally differentiated cell that is part of the pancreatic bud, participates in pancreas development and expresses the gene for pancreas transcription factor 1 subunit alpha. Ptf1a-expressing cell Ptf1a-lacking pancreatic progenitor cell Ptf1a-null cell Chris Stoeckert a non-terminally differentiated cell that is part of the pancreatic bud but lacks pancreas transcription factor 1 subunit alpha. Person: Chris Stoeckert, Jie Zheng neurogenin-3-expressing endocrine progenitor cell Chris Stoeckert Ngn3-expressing cell a non-terminally differentiated cell that participates in endocrine pancreas developement and expresses the gene for neurogenin-3. Person: Chris Stoeckert, Jie Zheng neurogenin-3-lacking pancreatic progenitor cell Chris Stoeckert a non-terminally differentiated cell that is part of the pancreas, participates in pancreas development and lacks neurogenin-3. Ngn3-null cell Person: Chris Stoeckert, Jie Zheng Insm1-expressing endocrine progenitor cell Chris Stoeckert a non-terminally differentiated cell that participates in endocrine pancreas development and expresses a gene for insulinoma-associated protein 1 Person: Chris Stoeckert, Jie Zheng Insm1 expressing pancreatic endocrine cell Insm1-lacking endocrine progenitor cell Chris Stoeckert Person: Chris Stoeckert, Jie Zheng a non-terminally differentiated cell that is part of the endocrine pancreas and lacks insulinoma-associated protein 1 Non-functional Insm1 expressing pancreatic endocrine cell insulin-expressing immature beta cell Chris Stoeckert a type B pancreatic cell that is immature and expresses a gene for insulin Person: Chris Stoeckert, Jie Zheng insulin-expressing nascent beta cells insulin-expressing mature beta cell a type B pancreatic cell that is mature and expresses a gene for insulin Chris Stoeckert Person: Chris Stoeckert, Jie Zheng insulin-expressing mature beta cells Insm1-expressing Pdx1 high-positive pancreatic endocrine progenitor cell A Insm1-expressing endocrine progenitor cell that expresses the gene for pancreas/duodenum homeobox protein 1 at a high level. Person: Jie Zheng, Chris Stoeckert Insm1-expressing Pdx1 low-positive pancreatic endocrine progenitor cell Person: Jie Zheng, Chris Stoeckert A Insm1-expressing endocrine progenitor cell that expresses the gene for pancreas/duodenum homeobox protein 1 at a low level. Insm1tm2(GFP.Cre)Mgn/Pdx1tm2(CFP)Mgn mouse strain A mouse strain that is the result of mating between a Insm1GFPCre/+ mouse and a Pdx1CFP/+ mouse both on a CD-1 background Person: Chris Stoeckert, Anna Osipovich differential expression software GBCO A software implementing a higher level analysis protocol of type differential expresssion. B6.Cg-Tg(Ins1-EGFP)1Hara/J mouse strain A mouse strain that is genetically modified expressing Enhanced Green Fluorescent Protein (EGFP) under the control of the mouse insulin 1 promoter. Fluorescence is detected in tissues where insulin I is normally expressed; fluorescent protein expression in pancreatic beta-cells is evident from embryonic day (E)13.5 through adulthood. The fluorescence expression pattern is similar to the patterns seen in two other strains STOCK Tg(Ins1-Cerulean)24Hara/J and STOCK Tg(Ins1-DsRed*T4)32Hara/J. This mutant mouse strain exhits normal glucose tolerance and pancreatic insulin levels and may be useful in studies of diabetes and pancreatic beta islet cell biology. Person: Jie Zheng http://jaxmice.jax.org/strain/006864.html ArrayExpress ID A CRID symbol assigned by ArrayExpress to uniquely identify a study in ArrayExpress GEO ID A CRID symbol assigned by Gene Expression Omnibus (GEO) to uniquely identify a study in GEO. cellular marker expression Person: Chris Stoeckert, Jie Zheng Penn Group Beta Cell Biology Consoritum A gene expression that produces cellular surface proteins that can be used to identify and isolate specific cells. pancreatic material Beta Cell Biology Consoritum Person: Chris Stoeckert, Jie Zheng Penn Group A material entity that could be whole pancreas, part of pancreas (including a single cell type (e.g., beta cell), or precursor to pancreas. characterization of cell differentiation objective A cellular feature identification objective that aims to examine or characterize cell development or differentiation. Person: Chris Stoeckert, Jie Zheng Beta Cell Biology Consoritum Penn group characterization of differentiation of insulin-producing cells objective A characterization of cell differentiation objective that aims to examine the influence of specific protocols with regard to generating insulin-producing cells from putative progenitors or other mechanisms (e.g., transdifferentiation). Beta Cell Biology Consoritum Penn group Person: Chris Stoeckert, Jie Zheng characterization of islet/beta-cell stimulation/injury objective Penn group Beta Cell Biology Consoritum Person: Chris Stoeckert, Jie Zheng A characterization of cell stimulation or injury objective that aims to address the effects of compounds, hormones, or cell manipulations on the ability of islets and/or beta-cells to secrete insulin or respond to glucose levels. characterization of pancreas development and growth objective Penn group A biological feature identification objective that aims to examine changes in gene expression and/or epigenome during pancreas development or regeneration. Person: Chris Stoeckert, Jie Zheng Beta Cell Biology Consoritum characterization of cell stimulation or injury objective A cellular feature identification objective that aims to address the effects of compounds, hormones, or cell manipulations on the ability of tissues or specific cell types to perform their normal functions or respond to insult. Beta Cell Biology Consoritum Penn group Person: Chris Stoeckert, Jie Zheng targets and roles of transcriptional regulators objective A molecular feature identification objective that aims to identify genes and processes regulated by transcription factors, co-activators, and other types of transcriptional regulators. Person: Chris Stoeckert, Jie Zheng Penn group Beta Cell Biology Consoritum tissue expression survey objective Penn group Person: Chris Stoeckert, Jie Zheng A biological feature identification objective that aims to address the question of what genes are expressed in a given tissue or cell type or the expression of genes across multiple cells and tissues. Beta Cell Biology Consoritum epigenetic modification process Beta Cell Biology Consoritum A biological process of generating epigenetic modifications, such as DNA methylation and histone modifications. Penn Group Person: Chris Stoeckert, Jie Zheng islet expansion in vitro Penn Group Beta Cell Biology Consoritum A planned process that aims to expand islets in culture and redifferentiate them to insulin producing cells. Person: Chris Stoeckert, Jie Zheng islets in diabetes Person: Chris Stoeckert, Jie Zheng islet of Langerhans that is part of a person who has diabetes. Will add following axiom after import 'has disease' from CLO 'is part of' some ('Homo sapiens' and 'has disease' some 'diabetes mellitus') Penn Group Beta Cell Biology Consoritum long non-coding RNA http://en.wikipedia.org/wiki/Long_non-coding_RNA Beta Cell Biology Consoritum Person: Chris Stoeckert, Jie Zheng lncRNA A ncRNA which is transcribed, non-protein coding, and longer than 200 nucleotides. stress and apoptosis in islets or beta cells Beta Cell Biology Consoritum Penn Group Person: Chris Stoeckert, Jie Zheng transcription factor binding site identification by SACO assay TF Binding SACO Person: Chris Stoeckert, Jie Zheng An assay that uses chromatin immunoprecipitation combined with serial analysis of chromatin occupancy (SACO) to identify binding sites for transcription factors. Beta Cell Biology Consoritum Penn group transcriptional profiling by MARIS assay MARIS Person: Chris Stoeckert, Jie Zheng An assay that aims to measure abundance of transcripts using high-quality RNA isolated from cells following intracellular antibody staining and fluorescence-activated cell sorting (FACS). Beta Cell Biology Consoritum http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0089459 age datum A data item of age. It could be measurement datum like 10 weeks, 2 years, or categorical datum like young, adult. concentration datum A data item of how much of a given substance there is mixed with another substance.Annotations. It could be measurement datum like 10 mM, or categorical datum like low, high concentration. Black and tan, brachyury mouse strain Person: Jie Zheng, Chris Stoeckert BTBR PMID: 25034792, Nephron Exp Nephrol. 2014;126(4):191-5. doi: 10.1159/000363300. "Recent advances in animal models of diabetic nephropathy." A mouse strain that is deficient for the leptin receptor (ob/ob) which is naturally insulin resistant and develops many of the pathological features of human Diabetic nephropathy. large pancreatic ductal cell http://www.sciencedirect.com/science/article/pii/S1357272504002717 large duct cell Person: Chris Stoeckert A pancreatic ductal cell of the large pancreatic duct. small pancreatic ductal cell' http://www.sciencedirect.com/science/article/pii/S1357272504002717 small duct cell Person: Chris Stoeckert A pancreatic ductal cell of a small interlobular pancreatic duct. Tet-On/Ngn3 embryonic stem cell ES (Tet-On/Ngn3) Person: Jie Zheng, Chris Stoeckert Penn Group An embryonic stem cell line that contains a ‘tet-on’ operon system and expresses Ngn3 in the presence of Tetracycline. GKP2 cell An immortal animal cell line cell which was derived from an insulinoma and expresses insulin and pdx1. GKP2 Person: Jie Zheng, Chris Stoeckert BCBC (http://www.betacell.org/resource/view/resource_id/1038) GKP4 cell An immortal animal cell line cell which was derived from a periductal tumor that did not express insulin or pdx1 but expressed genes of the endocrine lineage, such as Isl1 and Nkx2.2. GKP4 BCBC (http://www.betacell.org/resource/view/resource_id/1038) Person: Jie Zheng, Chris Stoeckert Sox17 expressiong H9 cell A H9 cell that expresses Sox17. BCBC (http://www.betacell.org/resource/view/resource_id/4216) Person: Jie Zheng, Chris Stoeckert INS-1 (832/1 and 832/2) PMID:17185391 Person: Jie Zheng, Chris Stoeckert An INS-1 cell which is poorly responsive to glucose. It is a mixture of INS-1 (832/1) and INS-1 (832/2). INS-1 (832/1) cell Person: Jie Zheng, Chris Stoeckert PMID:17185391 An INS-1 cell which is poorly responsive to glucose. INS-1 (832/13 and 833/15) Person: Jie Zheng, Chris Stoeckert An INS-1 cell which is highly responsive to glucose. It is a mixture of INS-1 (832/13) and INS-1 (832/15). PMID:17185391 INS-1 (832/13) cell Person: Jie Zheng, Chris Stoeckert An INS-1 cell which is highly responsive to glucose. PMID:17185391 INS-1 (832/2) cell PMID:17185391 An INS-1 cellwhich is poorly responsive to glucose. Person: Jie Zheng, Chris Stoeckert INS-1 (833/117) cell An INS-1 cell which is cytokine resistant. Person: Jie Zheng, Chris Stoeckert BCBC INS-1 (833/15) cell An INS-1 cell which is cytokine resistant and highly glucose-responsive. BCBC Person: Jie Zheng, Chris Stoeckert INS-1 (834/40) cell An INS-1 cell which is cytokine sensitive. BCBC Person: Jie Zheng, Chris Stoeckert INS-1E An INS-1 cell which has high insulin secretion in responses to glucose. PMID: 10037448 Person: Jie Zheng, Chris Stoeckert mPAC L20 cell An immortal animal cell line cell which is a pancreatic duct cell and contains an Ngn3-expressing adenovirus. Person: Jie Zheng, Chris Stoeckert mPAC L20 PMID: 15340143 PANC-1 cell Person: Jie Zheng, Chris Stoeckert PANC-1 An immortal animal cell line cell which was established from a pancreatic carcinoma of ductal origin from a 56-year-old Caucasian male. The cell possesses the type B phenotype for G6PD. http://www.sigmaaldrich.com/catalog/product/sigma/87092802 R7T1 cell Person: Jie Zheng, Chris Stoeckert PMID: 19164755 R7T1 An immortal animal cell line cell that is a rat beta-cell line. B6.CBA-{Tg(Gcg-cre)1Herr}/Mmnc mouse strain A mouse strain containing a transgene in which Cre (transgene) is driven by the Gcg promoter (NCBI Gene ID: 14526). <p>A transgenic alteration consisting of a SacI fragment containing the glucagon promoter, inserted at SacI of pBS-beta globin-Cre, resulting in Cre expression in pancreatic lineage cells.</p> B6.CBA-{Tg(Gcg-cre)1Herr}/Mmnc Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center B6.CBA-{Tg(Ipf1-EGFP)1Herr}/Mmnc mouse strain A mouse strain containing a transgene in which EGFP (transgene) is driven by the Ipf1 promoter (NCBI Gene ID: 18609). This strain allows Expression of EGFP in pancreatic precursor populations. B6.CBA-{Tg(Ipf1-EGFP)1Herr}/Mmnc Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center B6;D2-Tg(Ins-cre)23Herr mouse strain A mouse strain containing a transgene in which Cre (transgene) is driven by the Ins1 promoter (NCBI Gene ID: 24505). This strain relies on the recombination of floxed DNA in insulin-producing beta cells. B6;D2-Tg(Ins-cre)23Herr Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center B6;D2-Tg(NEUROG3-cre)1Herr mouse strain A mouse strain containing a transgene in which Cre (transgene) is driven by the Neurog3 promoter (NCBI Gene ID: 11925). <p>All islet endocrine cells inherit a recombination event, if a segment of DNA is loxP-flanked. Transgene encoding Cre recombinase under the control of a human Neurogenin3 promoter.</p> B6;D2-Tg(NEUROG3-cre)1Herr Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center BX129-Neurod1{tmAK71(lacZ)Jle/Mmcd} mouse strain A mouse strain containing a transgene in which LacZ-Neo (transgene) is driven by the Neurod1 promoter (NCBI Gene ID: 18012). Homozygous phenotype: Postnatal lethal due to neonatal diabetes Pancreas--5% insulin production, no islet formation Gut--no CCK or secretin production Inner ear defects resulting in deafness--no cochlear ganglia and poor vestibular ganglia formation Cerebellar defect resulting in ataxia-- >90% depletion of cerebellar granule cells Hippocampal defects--no dentate gyrus. BX129-Neurod1{tmAK71(lacZ)Jle/Mmcd} Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center STOCK Ipf1{tm1Cvw} mouse strain A mouse strain in which the targeted gene, insulin promoter factor 1, homeodomain transcription factor (NCBI Gene ID: 18609), has been modified (allele type: Global Null) to targeted mutation 1, Christopher V E Wright (MGI ID: Ipf1{tm1Cvw}). Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler STOCK Ipf1{tm1Cvw} Vanderbilt University Medical Center STOCK Ipf1{tm2Cvw}/Mmnc mouse strain A mouse strain in which the targeted gene, insulin promoter factor 1, homeodomain transcription factor (NCBI Gene ID: 18609), has been modified (allele type: Gene Replacement) to insulin promoter factor 1, homeodomain transcription factor / targeted mutation 2, Christopher V E Wright (MGI ID: Ipf1{tm2Cvw}). The homozygous phenotype of these animals show growth retardation and dehydration with lack of gastric emptying; ie. a-pancreatic. Heterozygous phenotype includes expression of beta-galactosidase in developing stomach, bile duct and cystic ducts and early pancreatic buds. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler STOCK Ipf1{tm2Cvw}/Mmnc Vanderbilt University Medical Center STOCK Ptf1a{tm1(cre)Cvw} mouse strain A mouse strain in which the targeted gene, pancreas specific transcription factor, 1a (NCBI Gene ID: 19213), has been modified (allele type: Gene Replacement) to targeted mutation 1.1, Christopher VE Wright (MGI ID: Ptf1a{tm1.1(cre)Cvw}). <p>Homozygous phenotype is altered pancreatic development with loss of exocrine acini.</p> Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler STOCK Ptf1a{tm1(cre)Cvw} Vanderbilt University Medical Center STOCK Tg(Foxa3-cre)1Khk mouse strain A mouse strain containing a transgene in which Cre (transgene) is driven by the Foxa3 promoter (NCBI Gene ID: 15377). Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler STOCK Tg(Foxa3-cre)1Khk Vanderbilt University Medical Center STOCK Tg(Ipf1-cre/Esr1)1Dam/Mmcd mouse strain A mouse strain containing a transgene in which Cre (transgene) is driven by the Ipf1 promoter (NCBI Gene ID: 18609). Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler STOCK Tg(Ipf1-cre/Esr1)1Dam/Mmcd Vanderbilt University Medical Center STOCK-Tg(Ipf1-cre)89.1Dam/Mmcd mouse strain A mouse strain containing a transgene in which Cre (transgene) is driven by the Ipf1 promoter (NCBI Gene ID: 18609). Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler STOCK-Tg(Ipf1-cre)89.1Dam/Mmcd Vanderbilt University Medical Center STOCK Tg(Neurog3-cre)1Dam/Mmcd mouse strain A mouse strain containing a transgene in which Cre (transgene) is driven by the Neurog3 promoter (NCBI Gene ID: 11925). Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler STOCK Tg(Neurog3-cre)1Dam/Mmcd Vanderbilt University Medical Center Gck{tm3Mgn} mouse strain A mouse strain in which the targeted gene, Glucokinase (NCBI Gene ID: 103988), has been modified (allele type: Global Mutation) to targeted mutation 3 (MGI ID: Gck{tm3Mgn}). This line of mice provides a model for Persistant Hyperinsulinemic Hypoglycemia of Infancy, or PHHI-GK, a rare genetic disease of humans. A gk{A456V} mutation, originally identified in a human pedigree with PHHI-GK, was introduced into these mice by gene knock-in. These mice may be useful for studies of sustained hypoglycemia. The mutation has been bred into a C57BL/6J strain thereby facilitating direct comparisons to both wild type C57BL/6J animals and to animals with a gk{K414E} mutation. Gck{tm3Mgn} Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Gck{tm2Mgn} mouse strain A mouse strain in which the targeted gene, Glucokinase (NCBI Gene ID: 103988), has been modified (allele type: Global Mutation) to targeted mutation 2 (MGI ID: Gck{tm2Mgn}). This line of mice contains a gk{K414E} point mutation that was introduced by gene knock-in. This point mutation wasidentified in aMODY-GK pedigree. These mice will be useful for studies of sustained hyperglycemia since they contain only a single mutation and are congenic with the C57BL/6J strain. Gck{tm2Mgn} Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Gck{tm1.1Mgn} mouse strain A mouse strain in which the targeted gene, Glucokinase (NCBI Gene ID: 103988), has been modified (allele type: Conditional Null) to targeted mutation 1.1 (MGI ID: Gck{tm1.1Mgn}). Gk{lox} mice may be used to generate cell specific knock-outs of glucokinase, depending which cre-expressing transgenic mouse is used. In humans, glucokinase gene mutations cause maturity onset diabetes of the young (MODY-GK), a disease that is characterized by early onset and persistent hyperglycemia. Thus, these mice are useful in determining how diminished experssion of glucokinase in specific cells causes hyperglycemia. Gck{tm1.1Mgn} Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center pck{tm1.1Mgn} mouse strain A mouse strain in which the targeted gene, phosphoenolpyruvate carboxykinase 1 (NCBI Gene ID: 18534), has been modified (allele type: Conditional Null) to targeted mutation 1.1, Mark A Magnuson (MGI ID: Pck1{tm1.1Mgn} ). These mice may be used to study tissue-specific functions of phosphoenolpyruvate carboxykinase (Pck1). This enzyme is essential for gluconeogenesis and also is important for regulating anapleurosis/catapleurosis of TCA cycle intermediates. By generating mice that are homozygous for the pck{lox} allele and that contain a tissue-specific Cre transgene, Pck1 can be deleted from various sites. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center pck{tm1.1Mgn} Rik{tm1.3Mgn} mouse strain A mouse strain in which the targeted gene, Rictor (NCBI Gene ID: 78757), has been modified (allele type: Global Null) to targeted mutation 1.3 (MGI ID: 4921505C17Rik{tm2Mgn}). Rictor is an essential part of mTOR complex 2 (mTORC2). mTORC2 phosphorylates Ser473 of Akt/PKB. Eliminating this gene disrupts the function of mTORC2, thereby preventing growth factor mediated activation of Akt/PKB. Thus, these mice have utility for studying both the sites of expression and function of rictor. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Rik{tm1.3Mgn} Vanderbilt University Medical Center Rik{tm1.1Mgn} mouse strain A mouse strain in which the targeted gene, Rictor (NCBI Gene ID: 78757), has been modified (allele type: Conditional Null) to targeted mutation 1.1 (MGI ID: 4921505C17Rik{tm1.1Mgn}). These mice carrya conditional allele for Rictor, a component mTOR complex 2 (mTORC2). Disruption of the Rictor gene attenuates phosphorylation ofSer473 of Akt/PKB, which is important for a normal response to growth factor stimulation acting through the PI3-kinase signaling pathway. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Rik{tm1.1Mgn} Vanderbilt University Medical Center Pparg{tm1.1Mgn} mouse strain A mouse strain in which the targeted gene, Peroxisome proliferator-activated receptor gamma (NCBI Gene ID: 19016), has been modified (allele type: Conditional Null) to targeted mutation 1.1Mgn (MGI ID: Pparg{tm1.1Mgn}). These mice carry a conditional allele for PPARgamma that can be used in combination with various cre-expressing transgenes. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Pparg{tm1.1Mgn} Vanderbilt University Medical Center B6.129X1-Abcc8{tm1.1Mgn} mouse strain A mouse strain in which the targeted gene, ATP-binding cassette, sub-family C (CFTR/MRP), member 8 (NCBI Gene ID: 20927), has been modified (allele type: Global Null) to targeted mutation 1.1Mgn (MGI ID: Sur1{neotm1.1Mgn}). These mice contain a global knock-out of the sulfonylurea receptor (Sur1), which is part of the ATP-dependent potassium channel. In humans, mutations in Sur1 cause persistent hyperinsulinemic hypoglycemia of infancy (PHHI). B6.129X1-Abcc8{tm1.1Mgn} Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Tg(Pdx1-Neurog3-ER)1Agb mouse strain A mouse strain containing a transgene in which Neurog3-ER (transgene) is driven by the Pdx1 promoter (NCBI Gene ID: 18609). The transgene is driven by the Pdx1 promoter whcih targets it in pancreas progenitor during development. These mice express a fusion protein between the pro-endocrine transcription factor Ngn3 and the tamoxifen responsive estrogen receptor. An IRES site allows GFP to be co-expressed with Ngn3-ER. The protein is active only upon tamoxifen injection. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Tg(Pdx1-Neurog3-ER)1Agb Vanderbilt University Medical Center Glucagon:rtta mouse strain A mouse strain containing a transgene in which rtTA (transgene) is driven by the Gcg promoter (NCBI Gene ID: 14562). These mice expresses the rtTA (tetracycline transactivator) in islet alpha cells upon treatment with doxicycline. Glucagon:rtta Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center C57/CBAJ-Hprt{tm3(Ins2-HBEGF)Ugfm} mouse strain A mouse strain in which the targeted gene, hypoxanthine guanine phosphoribosyl transferase 1 (NCBI Gene ID: 15452), has been modified (allele type: Gene Replacement) to (MGI ID: ). C57/CBAJ-Hprt{tm3(Ins2-HBEGF)Ugfm} carries a transgene encoding the human diphtheria toxin receptor under the control of rat insulin II promoter, was inserted by homologous recombination at the Hprt locus of the X chromosome. It provides a model for depletion of 50% of beta cells using Diphtheria toxin. C57/CBAJ-Hprt{tm3(Ins2-HBEGF)Ugfm} Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center B6-Nkx6-1{tm1Msan} mouse strain A mouse strain in which the targeted gene, Nkx6.1 (NCBI Gene ID: 18096), has been modified (allele type: Global Null) to targeted mutation (MGI ID: Nkx6.1{tm1(DsRed2)}). An IRES-DsRed2 cassette was introduced into exon 1 of the Nkx6.1 genomic sequence. The insertion generates a null allele. DsRed2 expression is not detected in these mice. B6-Nkx6-1{tm1Msan} Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Tg(RIP-Cre/ESR1){Ydor} mouse strain A mouse strain containing a transgene in which CreER (transgene) is driven by the Ins promoter (NCBI Gene ID: 16333). A transgenic mouse expression tamoxifen-inducible Cre recombinase under rat insulin promoter. Upon the injection of tamoxifen, loxP-flanked DNA sequences in beta cells will be deleted. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Tg(RIP-Cre/ESR1){Ydor} Vanderbilt University Medical Center Ptf1a{tm1(tTAoff)Macd} mouse strain A mouse strain in which part or all of the targeted gene, pancreas specific transcription factor, 1a (NCBI Gene ID: 19213) is replaced to create Ptf1a{tTA} using the Loxed Cassette Acceptor allele Ptf1a{tm1(LCA)}). Mice heterozygous for the tTA replacement of the Ptf1a gene are viable, fertile, of normal size, and do not display any behavioral abnormalities. The replacement places the expression of tTAoff (Gossen &amp; Bujard, PNAS 89:5547, 1992) under the control of the regulatory sequences of the endogenous Ptf1a gene. This mouse was initially designed to be mated to a mouse (see BCBC #M461) bearing a bicistronic Ptf1a-lacZ transgene driven by the tetracycline-regulatory element (TRE: 7 copies of tetO with the CMV minimal promoter). For offspring homozygous for the tTA allele of Ptf1a and hemi- or homozygous for the transgene, the production of PTF1a is due solely to tTA-activation of the transgene, which is repressed by administration of tetracycline/doxycycline. This strategy allows embryonic developmental arrest at desired stages or cessation of gene function in adult mice for the pancreas (similar to that for Pdx1 described in Holland et al., PNAS 99:12236, 2002) and also for the cerebellum, retina, dorsal spinal cord and possibly hypothalamus. This transgenic mouse may be useful in studies of pancreatic endocrine/exocrine development and function, diabetes, and certain defects of the CNS. This tissue-specific expresser of tTA can also be bred with strains bearing other TRE-transgenes for organ-specific conditional expression analyses. Nearly all of the Ptf1a transcription unit has been replaced by a tTAoff coding sequence with accessory translational and RNA-processing signals, as follows, from 5' to 3': the Ptf1a gene transcriptional start and 49-bp of its 5'UTR; the Xenopus laevis beta-globin 5'UTR with Kozak initiator codon; the tTA coding sequence; and a 990-bp rabbit beta-globin gene fragment encoding the last 14-bp of its second exon, the 573-bp second intron, and the 364-bp last exon including a 98-bp 3'UTR with the polyA addition signal and addition site, and 39-bp of 3' beta-globin gene flanking sequence. The Ptf1a locus was modified by recombination-mediated cassette exchange using the cassette exchange allele in Ptf1a-LCA ES cells (Burlison et al., submitted). Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Ptf1a{tm1(tTAoff)Macd} Vanderbilt University Medical Center NOD.Cg-Prkdc{scid} Il2rg{tm1Wjl} Tg(Ins2-HBEGF){6832Ugfm}/Sz mouse strain A mouse strain containing a transgene in which DTR (transgene) is driven by the RIP promoter (NCBI Gene ID: ). NOD-Prkdc{scid} IL2rg{null}Tg(Ins2-HBEGF){6832Ugfm} mice are deficient in mature lymphocytes and NK cells, survive beyond 16 months of age, and even after sublethal irradiation resist lymphoma development. They can be induced to become hypoglycemic when Diphtheria toxin is used. 100% of beta cells will be depleted upon administration of diphtheria toxin. NOD.Cg-Prkdc{scid} Il2rg{tm1Wjl} Tg(Ins2-HBEGF){6832Ugfm}/Sz Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center NOD.Cg-Prkdc{scid} Il2rg{tm1Wjl}Hprt{tm3(Ins2-HBEGF)Ugfm}/Sz mouse strain A mouse strain containing a transgene in which DTR (transgene) is driven by the RIP promoter (NCBI Gene ID: ). NOD-scid IL2rg{null}Hprt{tm3(Ins2-HBEGF)Ugfm} mice are deficient in mature lymphocytes and NK cells, survive beyond 16 months of age, and even after sublethal irradiation resist lymphoma development. They can be induced to become hypoglycemic when Diphtheria toxin is used. 50% of beta cells will be depleted after diphtheria toxin administration. NOD.Cg-Prkdc{scid} Il2rg{tm1Wjl}Hprt{tm3(Ins2-HBEGF)Ugfm}/Sz Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center NOD.Cg-Rag1{tm1Mom} Ins2{Akita} Prf1{tm1Sdz}/Sz mouse strain A mouse strain in which the targeted gene, recombination activating gene 1 (NCBI Gene ID: 19373), has been modified (allele type: Global Null) to (MGI ID: ). The NOD-Rag1{null} Prf1{null} Ins2{Akita} mouse is the first immunodeficient, spontaneously hyperglycemic mouse strain described that is based on the Ins2{Akita} mutation. This strain is suitable as hosts for human islet and human beta stem and progenitor cell transplantation in the absence of the need for pharmacological induction of diabetes. This strain of mice also has low levels of innate immunity and can be engrafted with a human immune system for the study of human islet allograft rejection. NOD.Cg-Rag1{tm1Mom} Ins2{Akita} Prf1{tm1Sdz}/Sz Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center NOD.Cg-Rag1{tm1Mom} Il2rg{tm1Wjl}/Sz mouse strain A mouse strain in which the targeted gene, interleukin 2 receptor, gamma chain (NCBI Gene ID: 16186), has been modified (allele type: Global Null) to (MGI ID: Il2rg{tm1Wjl}). Backcrossing of the Rag1 null allele onto the NOD/Lt strain background (NOD-Rag1{null} mice) provided a radio-resistant and longer-lived model for human-cell engraftment. Mutations in X-chromosome-linked Il2rg gene cause X-linked severe combined immunodeficiency (XSCID). Immunodeficient NOD-Rag1{null} IL2rg {null}mice tolerated much higher levels of irradiation conditioning than did NOD-Prkdc{scid} IL2rg {null} mice. NOD.Cg-Rag1{tm1Mom} Il2rg{tm1Wjl}/Sz Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center NOD.Cg-Prkdc{scid} Il2rg{tm1Wjl} Tg(Ins1-EGFP/GH1){14Hara}/Sz mouse strain A mouse strain in which the targeted gene, interleukin 2 receptor, gamma chain (NCBI Gene ID: 16186), has been modified (allele type: Global Null) to targeted mutation 1 (MGI ID: Il2rg{tm1Wjl}). NOD.Cg-Prkdc{scid}Il2rg{tm1Wjl}Tg(Ins1-EGFP/GH1){14Hara}/Sz is a immunodeficient mouse carries a GFP transgene under the control of mouse insulin promoter 1, which leads to expression of eGFP in the beta cells. NOD.Cg-Prkdc{scid} Il2rg{tm1Wjl} Tg(Ins1-EGFP/GH1){14Hara}/Sz Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Neurog3{tm1Ggr} mouse strain A mouse strain in which the targeted gene, Neurogenin 3 (NCBI Gene ID: 11925), has been modified (allele type: Other) to targeted mutation 1 (MGI ID: Ngn3{EYFP/+}). A targeting construct was designed to insert an IRES-EYFP and a floxed puro downstream of the coding sequence. Crossing with mice expressing Cre in the germ line excised the puromycin resistance gene. Coding region for Ngn3 is kept intact consequentely homozygous mice express Ngn3 protein , do not develop diabetes and behave like wild-types. in these mice, Ngn3-positive progenitors express EYFP and can be purified by FACS. Neurog3{tm1Ggr} Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Tg(tetO-Ptf1a,lacZ)Macd mouse strain A mouse strain containing a transgene in which bicistronic Ptf1a-lacZ (transgene) is driven by the TRE promoter (NCBI Gene ID: ). Mice hemi- or homozygous for the transgene are viable, fertile, normal size, and do not display any behavioral abnormalities. Expression of the bicistronic transgene is directed by a heptameric tetO repeat linked to the CMV minimal promoter (collectively the tetracycline-response element). The mice do not express lacZ until a tetracycline-gransactivator (tTA) protein is produced; thereafter Ptf1a and lacZ genes are highly expressed. This mouse was designed to be mated to an apancreatic targeted mutant with tTAoff in place of the Ptf1a coding sequence (see BCBC strain M321). The combined genetic alterations provide normal pancreatic development and function until doxycycline-administration render the mice conditionally null of Ptf1a. This approach allows embryonic developmental arrest at desired stages or cessation of gene function in adult mice for the pancreas, cerebellum, retina, dorsal spinal cord and possibly hypothalamus. This transgenic mouse may be useful in studies of pancreatic endocrine/exocrine development and function, diabetes, and and certain defects of the CNS. This transgenic can also be bred with other tTA strains for conditional mutation analysis. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Tg(tetO-Ptf1a,lacZ)Macd Vanderbilt University Medical Center Ptf1a{tm2(W298A)Macd} mouse strain A mouse strain in which part or all of the targeted gene, pancreas specific transcription factor, 1a (NCBI Gene ID: 19213) is replaced to create Ptf1a{tm2(W298A)} using the Loxed Cassette Acceptor allele Ptf1a{tm1(LCA)}). This mouse strain has a 2-bp site-directed mutation in the endogenous Ptf1a locus that changes codon 298 from tryptophan to alanine. The mutation disrupts the ability of the PTF1a protein to bind RBPJ. Mice heterozygous for the mutation are viable, fertile, of normal size, and do not display any behavioral abnormalities. Mice homozygous for the mutation phenocopy the homozygous Ptf1a-null. Newborn homozygotes are apancreatic, devoid of the dI4 and dILA GABAergic dorsal interneurons, have an incomplete cerebellum, and die shortly after birth. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Ptf1a{tm2(W298A)Macd} Vanderbilt University Medical Center Rbpjl{tm1(lacZ)Macd} mouse strain A mouse strain in which the targeted gene, Recombination signal binding protein for immunoglobulin kappa J region-like (NCBI Gene ID: 19668), has been modified (allele type: Global Mutation) to Rbpjl{tm1Macd} (MGI ID: Rbpjl{tm1(lacZ)}). This mouse strain has the Rbpjl gene region spanning exons 7, 8, and 9 replaced with lacZ in-frame. A pgk-neo resistance cassette has been removed by Cre-loxP deletion from the founder. Mice heterozygous and homozygous for the lacZ replacement are viable, fertile, of normal size, and do not display any behavioral abnormalities. In mature mice, the pancreas is one-third smaller than normal, due to less acinar tissue. Expression of the lacZ, measured by bet-galactosidase histostaining is very low. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Rbpjl{tm1(lacZ)Macd} Vanderbilt University Medical Center STOCK Pdx1{tm1Macd}/J mouse strain A mouse strain in which the targeted gene, Pancreatic and duodenal homeobox 1 (NCBI Gene ID: 18609), has been modified (allele type: Gene Replacement) to targeted mutation 1 (MGI ID: Pdx1{tmd1Macd}). Mice homozygous for the targeted mutation fail to develop a pancreas. Heterozygous mice have normal pancreatic development, but have partially impaired glucose tolerance in adulthood. The substitution of the targeted Ipf1/Pdx1 gene with tTAoff inactivates the endogenous allele and places tTAoff expression under the control of the endogenous transcriptional regulatory sequences of the Pdx1 locus. Identical to the endogenous allele, mutant locus expression is detectable in the pancreas and adjacent duodenum but not in other visceral organs or salivary glands. This mutant may be useful to direct tetracycline-regulated expression of responder transgenes in studies of pancreatic endocrine/exocrine development and function and diabetes. This mutant can also be bred with other tetO/TRE strains for pancreas-specific applications. This mutant was originally designed to be mated with mice engineered with a heptameric tetracycline operator (tetO)-controlled bicistronic transgene coding for a normal PDX1 protein and with a beta-galactosidase or EGFP reporter (see BCBC mouse M561). The combined modifications allow normal pancreatic development and function until doxycycline-administration renders the mouse conditionally null of the Pdx1 gene. This configuration for conditional expression of Pdx1is most effective when the transgene locus is homozygous. This allows embryonic developmental arrest at desired stages or cessation of function in adult mice by tetracycline administration. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler STOCK Pdx1{tm1Macd}/J Vanderbilt University Medical Center STOCK Tg(tetO-Pdx1,lacZ)958.1Macd mouse strain A mouse strain containing a transgene in which bicistronic Pdx1-lacZ (transgene) is driven by the TRE promoter (NCBI Gene ID: ). Mice hemizygous and homozygous for the transgenic insert are viable, fertile, of normal size, and do not display any behavioral abnormalities. Expression of the bicistronic transgene is directed by a heptameric tetO repeat fused to a minimal promoter (collectively the tetracycline-response element, or TRE). Transgenic mice do not express lacZ until a tetracycline-transactivator (tTA) protein is introduced; thereafter Pdx1 and lacZ from the transgene are expressed. All cells expressing transgenic Pdx1 coexpress the reporter. Further, mRNA levels of the transgene and endogenous Pdx1 fluctuate in concert during development. This mouse was originally designed to be mated to an apancreatic targeted mutant with the coding sequence of the Pdx1 locus replaced with that for tTAoff (see BCBC #M541). The combined mutations allow normal pancreatic development and function until doxycycline treatments render the mouse conditionally null of the endogenous gene. For this configuration, rescue of pancreatic development is most effective when the transgene locus is homozygous. This allows embryonic developmental arrest at desired stages or cessation of function in adult mice by administration of tetracycline/doxycycline. This transgenic strain may be useful in studies of pancreatic development and endocrine/exocrine function and diabetes. This strain can also be bred with other tTA strains for regulating Pdx1 expression in other contexts. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler STOCK Tg(tetO-Pdx1,lacZ)958.1Macd Vanderbilt University Medical Center Neurog3{tm2(EGFP)Ggr} mouse strain A mouse strain in which the targeted gene, Neurogenin 3 (NCBI Gene ID: 11925), has been modified (allele type: Other) to targeted mutation 2 (MGI ID: Neurog3{tm2(EGFP)Ggr). A targeting construct was designed to insert an IRES-EGFP and a floxed puro downstream of the coding sequence. Crossing with mice expressing Cre in the germ line excised the puromycin resistance gene. Homozygous mice express Ngn3 protein, do not develop diabetes and behave like wild-types. Ngn3-positive cells are labeled with EGFP and can be purified by FACS. Neurog3{tm2(EGFP)Ggr} Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Tg(Neurog3-IRES-NLS-LacZ)1Ggr mouse strain A mouse strain containing a transgene in which LacZ (transgene) is driven by the Neurog3 promoter (NCBI Gene ID: 11925). Transgenic mice where Ngn3-positive cell are labeled with beta-galactosidase. Due to the stability of beta-galactosidase protein, the early descendants of Ngn3-positve cells are also labeled. To generate the Ngn3 promoter::LacZ construct, a 6.86 kb XbaI-XhoI fragment (6696 bp of 5' genomic and untranslated region sequences and 176 bp of ngn3 coding region) of mouse ngn3 genomic DNA was cloned upstream of the IRES-NLS-LacZ-pA sequence in pBS-INL vector resulting in plasmid pngn3(6.8)-INL. The 10.6 kb Ngn3-IRES-NLS-LacZ insert was released by NotI digestion and microinjected into murine oocyte pronuclei, and transgenic line was generated and maintained by crossing into a CD1 outbred background. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Tg(Neurog3-IRES-NLS-LacZ)1Ggr Vanderbilt University Medical Center Tg(Ins1-mRFP)2Ggr mouse strain A mouse strain containing a transgene in which mRFP (transgene) is driven by the Ins1 promoter (NCBI Gene ID: 1633). These transgenic mice express the monomeric red fluorescent protein under the control of Ins1 gene (BAC) regulatory elements. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Tg(Ins1-mRFP)2Ggr Vanderbilt University Medical Center Arx{tm1Pgr} mouse strain A mouse strain in which the targeted gene, Arx (NCBI Gene ID: 11878), has been modified (allele type: Gene Replacement) to targeted mutation 1 (MGI ID: Arx{tm1Pgr}). These mice were created by insertion of the LacZ gene (with nuclear localization signal) into the Arx locus by homologous recombination in embryonic stem cells. The Arx gene is localized on the X chromosome. Knockout mice die after birth with due to hypoglycemia. Therefore male mice die at day 2 past birth. The colony has to be propagated with female mice. Arx-deficient mice do not produce alpha cells in the islets of Langerhans. Arx{tm1Pgr} Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Mafa{tm1.1Rwst} mouse strain A mouse strain in which the targeted gene, v-maf musculoaponeurotic fibrosarcoma oncogene family, protein A (avian) (NCBI Gene ID: 378435), has been modified (allele type: Conditional Null) to targeted mutation 1.1 (MGI ID: Mafa{tm1.1(lox)}). Mafa is a basic leucine-zipper containing member of the large Maf transcription factor family.It is part of the RIPE3b1 activator complex and functions as a key activator of insulin and pdx-1 gene transcription. Mafa{lox} mice may be used to generate both global and cell-specific Mafa null mice, depending on which cre-expressing transgenic mouse is used. Removal of Mafa gene might have a profound effect on beta cell function; thus we can closely monitor the expression of islet hormones, transcription functions and the glucose sensing machinery immunohistochemically. The experiment will provide us with the information about the role of Mafa plays in vivo in islet beta cells and the developing pancreas, thus helping us to understand how transcription activator contribute to the pathogenesis and the treatment of diabetes. Mafa{tm1.1Rwst} Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Myt1{tm1.1Ggu} mouse strain A mouse strain in which the targeted gene, Myt1 (myelin transcriptioin factor 1) (NCBI Gene ID: 1100535 ), has been modified (allele type: Conditional Null) to targeted mutation 1.1 (MGI ID: Myt1{tm1.1Ggu}). Two loxP sites flank exon 6 of Myt1b. The allele behaves as wild type allele without Cre-mediated deletion. Cre-mediated deletion creates null Myt1 allele. The homozygous null is neonatal lethal. Myt1 null pancreas has abnormal islet cell differentiation, ie. single cells produce multiple hormones. Pancreatic-specific Myt1 deletion results in glucose intolerance in males. Myt1{tm1.1Ggu} Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center OC-1{tm1.1Mga} mouse strain A mouse strain in which the targeted gene, Onecut1 (NCBI Gene ID: 15379), has been modified (allele type: Conditional Null) to targeted mutation 1.1 (MGI ID: OC-1{tm1.1Mga}). This line of mice allows for conditional inactivation of the OC-1 (HNF6) gene using Cre recombinase. Thus, HNF6 function can be assessed in the different tissues in which it is expressed. OC-1{tm1.1Mga} Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Nkx2-2{tm3Suss} mouse strain A mouse strain in which part or all of the targeted gene, NK2 transcription factor related, locus 2 (NCBI Gene ID: 18088) is replaced to create Nkx2.2(TNmut) using the Loxed Cassette Acceptor allele Nkx2.2{tm1(LCA)}). These mice contain mutations in the central core of the Nkx2.2 TN domain (putative groucho-interaction domain). Nkx2-2{tm3Suss} Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Nkx2-2{tm2Suss} mouse strain A mouse strain in which part or all of the targeted gene, NK2 transcription factor related, locus 2 (NCBI Gene ID: 18088) is replaced to create Nkx2.2:rtTA using the Loxed Cassette Acceptor allele Nkx2.2{tm1(LCA)}). The reverse tetracycline transactivator (rtTA) is knocked into the Nkx2.2 coding region, effectively knocking out one Nkx2.2 allele. Nkx2-2{tm2Suss} Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center C57/CBAJ-TgN(Glucagon- hHB EGF)Ugfm mouse strain A mouse strain containing a transgene in which Diphtheria Toxin Receptor (transgene) is driven by the Gcg promoter (NCBI Gene ID: 14526). Transgenic strain (generated by pronuclear microinjection) of a transgene containing the rat glucagon promoter (1.6kb fragment) upstream of a rabbit beta-globin intron and the coding sequence of the human diphtheria toxin receptor (heparin-binding epidermal growth factor, membrane form). Downstream, there is a rabbit beta-globin stop codon and the polyadenylation signal. C57/CBAJ-TgN(Glucagon- hHB EGF)Ugfm Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center C57/CBAJ-TgN(Glucagon- rtTA)Ugfm mouse strain A mouse strain containing a transgene in which rtTA (transgene) is driven by the Gcg promoter (NCBI Gene ID: 14526). Transgenic strain (generated by pronuclear microinjection) of a transgene containing the rat glucagon promoter (1.6kb fragment) upstream of the coding region of the reverse transactivator doxycycline-dependent. The rtTA is flanked by a rabbit beta-globin intron and downstream there is a stop and polyA signal from the same rabbit beta-globin gene. C57/CBAJ-TgN(Glucagon- rtTA)Ugfm Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center C57/CBAJ-Tg(Ins2- HBEGF){6832Ugfm} mouse strain A mouse strain containing a transgene in which DTR (transgene) is driven by the Ins promoter (NCBI Gene ID: 16333). Transgenic mice generated by pronuclear microinjection of a transgene encoding the human diphtheria toxin receptor (heparin binding epidermal growth factor, also termed DTR) under the control of the rat insulin II gene promoter (0.6kb-long fragment). The DTR coding sequence is flanked by the rabbit beta-globin intron and stop/polyA sequences. C57/CBAJ-Tg(Ins2- HBEGF){6832Ugfm} Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center FVB/NJ-Tg(MIP-Luc-VU)3Pwrs/J mouse strain A mouse strain containing a transgene in which Luc (transgene) is driven by the MIP promoter (NCBI Gene ID: 16333). We generated a transgenic mouse expressing the luciferase optical reporter under control of the mouse insulin I promoter (MIP-Luc-VU) and characterized this model in mice with increased or decreased beta-cell mass and after islet transplantation. MIP-Luc-VU mice emitted strong and consistent bioluminescence emanating exclusively from beta-cells of the pancreatic islet. MIP-Luc-VU islets had normal islet architecture and secreted insulin normally in vivo and in vitro. By tracking changes in &beta; cell mass using bioluminescence imaging (BLI) and post-mortem metrics, streptozotocin-induced, diabetic MIP-Luc-VU mice had a progressive decline in bioluminescence that correlated with a decrease in pancreatic insulin content and beta-cell mass. MIP-Luc-VU animals fed a high fat diet displayed a progressive increase in bioluminescence that reflected an immunohistochemically verified increase in beta-cell mass. MIP-Luc-VU islets transplanted beneath the renal capsule or into the liver emitted bioluminescence proportional to the number of islets transplanted and graft insulin content and could be imaged for more than a year. Since bioluminescence in the MIP-Luc-VU mouse model is proportional to beta-cell mass in the setting of increased and decreased beta-cell mass and after transplantation, this approach should be useful for non-invasively assessing beta-cell mass in pre-clinical mouse models of glucose homeostasis, beta-cell growth and regeneration, and diabetes. FVB/NJ-Tg(MIP-Luc-VU)3Pwrs/J Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Gt(ROSA)26Sor{tm1(Myt1*)Hri} mouse strain A mouse strain in which the targeted gene, ROSA26 (NCBI Gene ID: 14910), has been modified (allele type: Conditional Activating) to ROSA26-loxp-STOP-loxp-Myt1 (MGI ID: Not yet available). Targeted insertion of a LoxP-STOP-LoxP-Myt1 casette into the ROSA26 locus. The presence of Cre recombinase will lead to activation of the 7 zinc finger isoform of Myt1. Gt(ROSA)26Sor{tm1(Myt1*)Hri} Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Ngn3{tm1(tTA)Hri} mouse strain A mouse strain in which the targeted gene, Neurogenin 3 (NCBI Gene ID: 11925), has been modified (allele type: Gene Replacement) to Ngn3 tTA knockin (MGI ID: Ngn3tTA). The mouse contains a Ngn3 knock-in allele. IRES-tTA-rabbit beta globin polyA signal replaced the entire Ngn3 cDNA coding sequence. This is therefore also a Ngn3 null allele. Ngn3 is a bHLH transcription factor that is required for the differentiation of endocrine islet and some neuronal cells. Ngn3{tm1(tTA)Hri} Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Nkx2-2{tm1Suss} mouse strain A mouse strain in which part or all of the targeted gene, NK2 transcription factor related, locus 2 (NCBI Gene ID: 18088) is replaced to create Nkx2.2:LacZ using the Loxed Cassette Acceptor allele Nkx2.2{tm1(LCA)}). The lacZ gene has been knocked in to the Nkx2.2 genomic locus using RMCE, effectively replacing the two coding exons. Nkx2-2{tm1Suss} Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Nkx2-2{tm4Suss} mouse strain A mouse strain in which part or all of the targeted gene, NK2 transcription factor related, locus 2 (NCBI Gene ID: 18088) is replaced to create Nkx2.2-NK2 mutation using the Loxed Cassette Acceptor allele Nkx2.2{tm1(LCA)}). The strain carries a mutant Nkx2.2 allele in which conserved residues of the NK2 domain are mutated to alanines. Nkx2-2{tm4Suss} Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Pdx1{tm6Cvw} mouse strain A mouse strain in which part or all of the targeted gene, pancreatic and duodenal homeobox 1 (NCBI Gene ID: 18609) is replaced to create Pdx1{AIId} using the Loxed Cassette Acceptor allele Pdx1{tm1(LCA)}). This is a targeted deletion of Area II 5' cis-regulatory region of Pdx1. Pdx1{tm6Cvw} Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Pdx1{tm4Cvw} mouse strain A mouse strain in which the targeted gene, Pancreatic and Duodenal homeobox 1 (NCBI Gene ID: 18609), has been modified (allele type: Conditional Null) to targeted mutation 4 (MGI ID: Pdx1{tm4(E2)}). This is a conditional null allele of Pdx1. LoxP sites for Cre recombinase were inserted to flank exon 2 of the gene. Pdx1{tm4Cvw} Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Ptf1a{tm2(cre/ESR1)Cvw} mouse strain A mouse strain in which part or all of the targeted gene, pancreas specific transcription factor, 1a (NCBI Gene ID: 19213) is replaced to create Ptf1a{tm2(cre/ESR1)} using the Loxed Cassette Acceptor allele Ptf1a{tm1(LCA)}). CreER knock-in into Ptf1a locus replacing part of the exon1 at the translation initiator ATG position using RMCE method. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Ptf1a{tm2(cre/ESR1)Cvw} Vanderbilt University Medical Center Pdx1{tm5Cvw} mouse strain A mouse strain in which the targeted gene, Pancreatic and Duodenal homeobox 1 (NCBI Gene ID: 18609), has been modified (allele type: Other) to targeted mutation 5 (MGI ID: Pdx1{tm5(AI-II-III)}). LoxP sites for cre recombinase were inserted to flank Area I-II-III, a conserved 5' cis-regulatory region of Pdx1. This allele was shown to be a conditional hypomorph by Fujitani et al. (2006) (PMID 16418487). Pdx1{tm3Cvw} (Pdx1{deltaI-II-III}) is generated by Cre-mediated recombination in the germline of this allele. Pdx1{tm5Cvw} Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Dll1{tm1Hri} mouse strain A mouse strain in which the targeted gene, Delta-like 1 (NCBI Gene ID: 13388), has been modified (allele type: Conditional Null) to targeted mutation 1 (MGI ID: Dll1{tm1Hri}). This is a targeted mutation of the Notch ligand Dll1, introducing two loxP sites flanking the exons encoding the DSL domain. Dll1{tm1Hri} Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Pdx1{tm3Cvw} mouse strain A mouse strain in which the targeted gene, Pancreatic and Duodenal homeobox 1 (NCBI Gene ID: 18609), has been modified (allele type: Global Mutation) to targeted mutation 3 (MGI ID: Pdx1{tm3(deltaI-II-III)). Area I-II-III, a conserved 5' cis-regulatory region of Pdx1, was removed by Cre mediated recombination in the germline of Pdx1{tm5Cvw} (Pdx1{Flox123}) by crossing to deleter Cre mice. This allele was shown to be a hypomorph. Pdx1{tm3Cvw} Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Ptf1a{tm3Cvw} mouse strain A mouse strain in which the targeted gene, Pancreas Specific Transcription Factor, 1a (NCBI Gene ID: 19213), has been modified (allele type: Cassette Acceptor) to Targeted Mutation 3 (MGI ID: Ptf1a{tm3Cvw}). This mouse strain is a conditional null allele of Ptf1a. LoxP sites flanking exon 1 and 2 (entire coding region of Ptf1a). Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Ptf1a{tm3Cvw} Vanderbilt University Medical Center Ptf1a{LCA} mouse ESC line A mouse ESC line in which the targeted gene, pancreas specific transcription factor, 1a (NCBI Gene ID: 19213), has been modified (allele type: Cassette Acceptor) to targeted mutation 1 (MGI ID: Ptf1a{tm1(LCA)}). This ES cell line contains a loxed cassette acceptor (LCA) allele in which a 4.1 kb region of this gene (including the proximal promoter and both exons 1 and 2) was replaced with a loxP site, an inverted loxP site, and both positive and negative selectable markers. This enables the use of Recombinase-Mediated Cassette Exchange (RMCE) to easily insert various reporter genes or to make other modifications of the Ptf1a gene locus. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Ptf1a{YFP} mouse ESC line A mouse ESC line in which part or all of the targeted gene, pancreas specific transcription factor, 1a (NCBI Gene ID: 19213) is replaced to create Ptf1a{LCA} using the Loxed Cassette Acceptor allele Ptf1a{tm1.1(YFP)}). This ES cell line contains YFP inserted into a Ptf1a{LCA} allele by recombinase mediated cassette exchange. These cells may be useful for identifying pancreatic progenitor cells in cultures that have been stimulated to differentiate towards endodermal and pancreatic fates. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Gck{LCA} mouse ESC line A mouse ESC line in which the targeted gene, glucokinase (NCBI Gene ID: 19213), has been modified (allele type: Cassette Acceptor) to targeted mutation 4 (MGI ID: gk{tm4(LCA)}). This ES cell line contains a loxed cassette acceptor (LCA) allele that may be utilized for the exchange of DNAs of interest into the glucokinase locus by recombinase mediated cassette exchange (RMCE). This LCA uses a loxP/inverted loxP strategy for RMCE and allows sequences between - 6 kb and + 5 kb (relevative to the hepatic-specific promoter) to be manipulated. This enables a variety of different types of experiments to be performed using a range of cassette designs. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Insm1{LCA} mouse ESC line A mouse ESC line in which the targeted gene, insulinoma-associated 1 (NCBI Gene ID: 53626), has been modified (allele type: Cassette Acceptor) to targeted mutation 1 (MGI ID: Insm1{tm1(LCA)}). This ES cell line contains a loxed cassette acceptor(LCA)allele that may be utilized for the exchange of DNAs of interest into the Insm1 gene locus by recombinase mediated cassette exchange (RMCE). This LCA uses a lox 66/71 and lox 2272 strategy for RMCE and allows a ~5.2 kb region of this single exon gene to be manipulated. This enables a variety of different types of experiments to be performed using a range of cassette designs. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Nkx2.2{LCA} mouse ESC line A mouse ESC line in which the targeted gene, NK2 transcription factor related, locus 2 (NCBI Gene ID: 18088), has been modified (allele type: Cassette Acceptor) to targeted mutation 1 (MGI ID: Nkx2.2{tm1(LCA)}). This ES cell line contains a loxed cassette acceptor (LCA) allele that may be utilized for the exchange of DNAs of interest into the Nkx2.2 locus by recombinase mediated cassette exchange (RMCE). This LCA uses a Lox71/66 and Lox2272 strategy for RMCE and allows for manipulation of a 5.1 kb region of the gene (contains promoter, exon 1, and exon 2). This leads to a variety of experiments that can be performed using a wide range of cassette designs. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center MIP-GFP mouse ESC line A mouse ESC line containing a transgene in which Gfp (transgene) is driven by the Ins1 promoter (NCBI Gene ID: 16333). New ESC line derived from MIP-GFP mice (Hara et al. 2003,Am J Physiol Endocrinol Metab. 284: E177-83). Genetic background is C57Bl6/J. When injected into E3.5 mouse blastocysts this line contributes to chimeras and Insulin+/GFP+ double positive cells are found in E14.5 embryonic pancreas. No GFP+ cells are seen outside the pancreas. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Ngn3-GFP mouse ESC line A mouse ESC line containing a transgene in which Gfp (transgene) is driven by the Neurog3 promoter (NCBI Gene ID: 11925). Mouse ESC line derived from Ngn3-GFP transgenic mice (Gradwohl et al. unpublished). Genetic background is CD1. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{LCA} mouse ESC line A mouse ESC line in which the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910), has been modified (allele type: Cassette Acceptor) to targeted mutation 1 (MGI ID: Rosa26{tm1(LCA)}). This ES cell line contains a loxed cassette acceptor (LCA) allele in which a 5.17 kb region of the gene has been replaced by a Lox66 site, a puromycin-(delta)-thymidine kinase fusion gene driven by the mouse phosphoglycerol kinase promoter, a kanamycin resistance gene driven by the bacterial EM7 promoter, and a Lox2272 site. These features enable use of Recombinase-Mediated Cassette Exchange for the rapid insertion of various DNAs into the Rosa26 gene locus. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Sox17{LCA} mouse ESC line A mouse ESC line in which the targeted gene, SRY-box containing gene 17 (NCBI Gene ID: 20671), has been modified (allele type: Cassette Acceptor) to targeted mutation 1 (MGI ID: Sox17{tm1(LCA)}). This mouse ES cell line contains a loxed cassette acceptor (LCA) allele that may be utilized for the exchange of DNAs of interest into the Sox17 gene locus by recombinase mediated cassette exchange (RMCE). A 3.79 kb region of the gene (exons 3-5) was replaced by tandemly oriented lox66 and lox2272 sites as well as both positive and negative selectable markers. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal rat IAPP raised in rabbit A polyclonal antibody raised in rabbit that targets the rat "IAPP" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal rat C-peptide 2 raised in rabbit A polyclonal antibody raised in rabbit that targets the rat "C-peptide 2" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal rat C-peptide 1 raised in rabbit A polyclonal antibody raised in rabbit that targets the rat "C-peptide 1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse C-peptide 1 raised in rabbit A polyclonal antibody raised in rabbit that targets the mouse "C-peptide 1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Insulin raised in mouse A monoclonal antibody raised in mouse that targets the human "Insulin" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal rat PDX1 raised in rabbit A polyclonal antibody raised in rabbit that targets the rat "PDX1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal rat PDX1 raised in rabbit A polyclonal antibody raised in rabbit that targets the rat "PDX1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal rat Nkx6.1 raised in rabbit A polyclonal antibody raised in rabbit that targets the rat "Nkx6.1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human Nkx2.2 raised in goat A polyclonal antibody raised in goat that targets the human "Nkx2.2" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human ghrelin raised in goat A polyclonal antibody raised in goat that targets the human "ghrelin" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse Pax6 raised in rabbit A polyclonal antibody raised in rabbit that targets the mouse "Pax6" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human b-catenin raised in goat A polyclonal antibody raised in goat that targets the human "b-catenin" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal mouse smooth muscle actin raised in mouse A monoclonal antibody raised in mouse that targets the mouse "smooth muscle actin" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human amylase raised in rabbit A polyclonal antibody raised in rabbit that targets the human "amylase" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human c-myc raised in rabbit A polyclonal antibody raised in rabbit that targets the human "c-myc" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal rat Glut-2 raised in rabbit A polyclonal antibody raised in rabbit that targets the rat "Glut-2" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal bovine Carboxypeptidase A raised in rabbit A polyclonal antibody raised in rabbit that targets the bovine "Carboxypeptidase A" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human Chromogranin A raised in rabbit A polyclonal antibody raised in rabbit that targets the human "Chromogranin A" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Chromogranin A raised in mouse A monoclonal antibody raised in mouse that targets the human "Chromogranin A" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Cytokeratin 7 raised in mouse A monoclonal antibody raised in mouse that targets the human "Cytokeratin 7" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human PECAM-1 raised in mouse A monoclonal antibody raised in mouse that targets the human "PECAM-1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal aequorea victoria Green Fluorescent Protein raised in rabbit A polyclonal antibody raised in rabbit that targets the aequorea victoria "Green Fluorescent Protein" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal chicken Nkx2.2 raised in mouse A monoclonal antibody raised in mouse that targets the chicken "Nkx2.2" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal rat ghrelin raised in rabbit A polyclonal antibody raised in rabbit that targets the rat "ghrelin" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal chicken Islet-1 raised in mouse A monoclonal antibody raised in mouse that targets the chicken "Islet-1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human GATA-4 raised in rabbit A polyclonal antibody raised in rabbit that targets the human "GATA-4" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse PDX1 raised in rabbit A polyclonal antibody raised in rabbit that targets the mouse "PDX1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse PDX1 raised in chicken A polyclonal antibody raised in chicken that targets the mouse "PDX1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Glucagon raised in mouse A monoclonal antibody raised in mouse that targets the human "Glucagon" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Somatostatin raised in mouse A monoclonal antibody raised in mouse that targets the human "Somatostatin" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal rat Pancreatic Ducts raised in mouse A monoclonal antibody raised in mouse that targets the rat "Pancreatic Ducts" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal rat Pancreatic Ducts raised in mouse A monoclonal antibody raised in mouse that targets the rat "Pancreatic Ducts" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal rat Islet Delta Cells raised in rat A monoclonal antibody raised in rat that targets the rat "Islet Delta Cells" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal rat Pancreatic Ducts raised in rat A monoclonal antibody raised in rat that targets the rat "Pancreatic Ducts" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Pro-Insulin raised in mouse A monoclonal antibody raised in mouse that targets the human "Pro-Insulin" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse Ngn3 raised in rabbit A polyclonal antibody raised in rabbit that targets the mouse "Ngn3" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse Ngn3 raised in rabbit A polyclonal antibody raised in rabbit that targets the mouse "Ngn3" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal mouse Ngn3 raised in mouse A monoclonal antibody raised in mouse that targets the mouse "Ngn3" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal mouse Ngn3 raised in mouse A monoclonal antibody raised in mouse that targets the mouse "Ngn3" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal rat Nkx6.1 raised in mouse A monoclonal antibody raised in mouse that targets the rat "Nkx6.1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal rat Nkx6.1 raised in mouse A monoclonal antibody raised in mouse that targets the rat "Nkx6.1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal rat Nkx6.1 raised in mouse A monoclonal antibody raised in mouse that targets the rat "Nkx6.1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal rat Nkx6.1 raised in mouse A monoclonal antibody raised in mouse that targets the rat "Nkx6.1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human HNF6 raised in rabbit A polyclonal antibody raised in rabbit that targets the human "HNF6" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse PDX1 raised in goat A polyclonal antibody raised in goat that targets the mouse "PDX1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse PDX1 raised in guinea pig A polyclonal antibody raised in guinea pig that targets the mouse "PDX1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human ghrelin raised in rabbit A polyclonal antibody raised in rabbit that targets the human "ghrelin" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human ghrelin raised in rabbit A polyclonal antibody raised in rabbit that targets the human "ghrelin" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal rat PDX1 raised in mouse A monoclonal antibody raised in mouse that targets the rat "PDX1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal rat PDX1 raised in mouse A monoclonal antibody raised in mouse that targets the rat "PDX1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal rat PDX1 raised in mouse A monoclonal antibody raised in mouse that targets the rat "PDX1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human Sox2 raised in rabbit A polyclonal antibody raised in rabbit that targets the human "Sox2" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse FoxA2 raised in goat A polyclonal antibody raised in goat that targets the mouse "FoxA2" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human E-cadherin raised in mouse A monoclonal antibody raised in mouse that targets the human "E-cadherin" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human Sox17 raised in rabbit A polyclonal antibody raised in rabbit that targets the human "Sox17" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human Sox17 raised in rabbit A polyclonal antibody raised in rabbit that targets the human "Sox17" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Pancreatic endocrine cells raised in mouse A monoclonal antibody raised in mouse that targets the human "Pancreatic endocrine cells" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Pancreatic endocrine cells raised in mouse A monoclonal antibody raised in mouse that targets the human "Pancreatic endocrine cells" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Pancreatic endocrine cells raised in mouse A monoclonal antibody raised in mouse that targets the human "Pancreatic endocrine cells" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Pancreatic endocrine cells raised in mouse A monoclonal antibody raised in mouse that targets the human "Pancreatic endocrine cells" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Pancreatic endocrine cells raised in mouse A monoclonal antibody raised in mouse that targets the human "Pancreatic endocrine cells" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human Sox17 raised in goat A polyclonal antibody raised in goat that targets the human "Sox17" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse Shh raised in goat A polyclonal antibody raised in goat that targets the mouse "Shh" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal e. coli beta Galactosidase raised in chicken A polyclonal antibody raised in chicken that targets the e. coli "beta Galactosidase" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal aequorea victoria Green Fluorescent Protein raised in mouse A monoclonal antibody raised in mouse that targets the aequorea victoria "Green Fluorescent Protein" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse Ptf1a raised in rabbit A polyclonal antibody raised in rabbit that targets the mouse "Ptf1a" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse IA1 (Insm-1) raised in rabbit A polyclonal antibody raised in rabbit that targets the mouse "IA1 (Insm-1)" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Pancreatic duct cells raised in mouse A monoclonal antibody raised in mouse that targets the human "Pancreatic duct cells" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Pancreatic duct cells raised in mouse A monoclonal antibody raised in mouse that targets the human "Pancreatic duct cells" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Pancreatic exocrine cells raised in mouse A monoclonal antibody raised in mouse that targets the human "Pancreatic exocrine cells" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Pancreatic exocrine cells raised in mouse A monoclonal antibody raised in mouse that targets the human "Pancreatic exocrine cells" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Pancreatic endocrine cells raised in mouse A monoclonal antibody raised in mouse that targets the human "Pancreatic endocrine cells" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Alpha cells raised in mouse A monoclonal antibody raised in mouse that targets the human "Alpha cells" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Alpha cells raised in mouse A monoclonal antibody raised in mouse that targets the human "Alpha cells" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal mouse Mo ES-Derived Definitive Endoderm raised in rat A monoclonal antibody raised in rat that targets the mouse "Mo ES-Derived Definitive Endoderm" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal mouse Mo ES-Derived Definitive Endoderm raised in rat A monoclonal antibody raised in rat that targets the mouse "Mo ES-Derived Definitive Endoderm" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human T (Brachyury) raised in goat A polyclonal antibody raised in goat that targets the human "T (Brachyury)" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse Laminin raised in rabbit A polyclonal antibody raised in rabbit that targets the mouse "Laminin" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal chicken Pax6 raised in mouse A monoclonal antibody raised in mouse that targets the chicken "Pax6" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Sox17{GFPCre} mouse ESC line A mouse ESC line in which part or all of the targeted gene, SRY-box containing gene 17 (NCBI Gene ID: 20671) is replaced to create Sox17{Cre-GFP} using the Loxed Cassette Acceptor allele Sox17{tm1(LCA)}). Using an RMCE strategy, we inserted a Cre-GFP (Green fluorescent protein) fusion protein into a Sox17[LCA] allele thereby replacing Sox17 coding sequences. The Sox17-CreGFP ESCs may be used to track Sox17-expressing cells and their progeny, or to conditionally inactivate genes in Sox17-expressing cells. Mark the expression of Sox17 with both Cre and GFP. Cre will enable lineage tracing using reporter alleles that are activated by cre recombination. GFP will enable direct visualization of Sox17 gene expression. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Insm1{tm1.1Mgn} mouse strain A mouse strain in which part or all of the targeted gene, insulinoma-associated 1 (NCBI Gene ID: 53626) is replaced to create Insm1{tm1.1(GFP-Cre)} using the Loxed Cassette Acceptor allele Insm1{tm1(LCA)}). <p>Insm1{GFPCre} mice contain a GFP-Cre fusion protein which replaces the Insm1 coding sequence. These mice express green fluorescent protein (GFP) under control of theInsm1gene locus. Insm1 is expressed in pancreatic primordium starting at E9.5. Insm1 is also expressed in neural precursor cells and tumors of may be used for lineage tracing of Insm1-positive cells in both wild-type and Insm1-null mice.</p> Insm1{tm1.1Mgn} Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Ghrl{LCA} mouse ESC line A mouse ESC line in which the targeted gene, Ghrelin (NCBI Gene ID: 58991), has been modified (allele type: Cassette Acceptor) to targeted mutation (MGI ID: Ghrl{LCA}). ES cells were modified by homologous recombination to replace a 6.912 kb region of the Ghrelin (GHRL) gene from 2.7 kb upstream of exon 1 to 0.5 kb downstream of exon 5 with tandemly oriented lox71 and lox2272 sites as well as both positive and negative selectable markers. The gene was replaced by tandemly oriented lox71 and lox2272 sitesas well as both positive and negative selectable markers. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Ghrl{Cre-eGFP} mouse ESC line A mouse ESC line in which part or all of the targeted gene, Ghrelin (NCBI Gene ID: 58991) is replaced to create Ghrl{Cre-eGFP} using the Loxed Cassette Acceptor allele Ghrl{LCA}). Recombinase mediated cassette exchange (RMCE) was used to insert the Cre-eGFP fusion protein into the ghrelin locus using ES cells containing the Ghrl{LCA} allele. The Cre-eGFP protein uses the endogenous AUG start codon and polyadenylation sequence. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal mouse BetaTC6 raised in mouse A monoclonal antibody raised in mouse that targets the mouse "BetaTC6" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Gt(ROSA)26Sor{tm1(GCK*)Ydor} mouse strain A mouse strain containing a transgene in which GCK (transgene) is driven by the ROSA26 promoter (NCBI Gene ID: 14910). Glucokinase containing the Y214C activating mutation, causing severe persistent hyperinsulinemic hypoglycemia (Diabetes 53:2164-2168, 2004) was targeted to the ROSA26 locus, preceded by a lox-stop-lox sequence and followed by IRES-EGFP. Gt(ROSA)26Sor{tm1(GCK*)Ydor} Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal rat CART raised in rabbit A polyclonal antibody raised in rabbit that targets the rat "CART" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal mouse Mo ES-Derived Early Endoderm raised in rat A monoclonal antibody raised in rat that targets the mouse "Mo ES-Derived Early Endoderm" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal mouse Mo ES-Derived Early Endoderm raised in rat A monoclonal antibody raised in rat that targets the mouse "Mo ES-Derived Early Endoderm" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal mouse Mo ES-Derived Early Endoderm raised in rat A monoclonal antibody raised in rat that targets the mouse "Mo ES-Derived Early Endoderm" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal mouse Mo ES-Derived Early Endoderm raised in rat A monoclonal antibody raised in rat that targets the mouse "Mo ES-Derived Early Endoderm" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal mouse Mo ES-Derived Early Endoderm raised in rat A monoclonal antibody raised in rat that targets the mouse "Mo ES-Derived Early Endoderm" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal mouse Mo ES-Derived Early Endoderm raised in rat A monoclonal antibody raised in rat that targets the mouse "Mo ES-Derived Early Endoderm" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal mouse Mo ES-Derived Early Endoderm raised in rat A monoclonal antibody raised in rat that targets the mouse "Mo ES-Derived Early Endoderm" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Hu ES-Derived Early Endoderm raised in mouse A monoclonal antibody raised in mouse that targets the human "Hu ES-Derived Early Endoderm" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Hu ES-Derived Early Endoderm raised in mouse A monoclonal antibody raised in mouse that targets the human "Hu ES-Derived Early Endoderm" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Hu ES-Derived Early Endoderm raised in mouse A monoclonal antibody raised in mouse that targets the human "Hu ES-Derived Early Endoderm" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal mouse Pancreatic duct cells raised in rat A monoclonal antibody raised in rat that targets the mouse "Pancreatic duct cells" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal mouse Pancreatic duct and acinar cells raised in rat A monoclonal antibody raised in rat that targets the mouse "Pancreatic duct and acinar cells" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal mouse Endothelial cells raised in rat A monoclonal antibody raised in rat that targets the mouse "Endothelial cells" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal mouse BetaTC6 raised in mouse A monoclonal antibody raised in mouse that targets the mouse "BetaTC6" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal mouse BetaTC6 raised in mouse A monoclonal antibody raised in mouse that targets the mouse "BetaTC6" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Disp2 raised in mouse A monoclonal antibody raised in mouse that targets the human "Disp2" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Disp2 raised in mouse A monoclonal antibody raised in mouse that targets the human "Disp2" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse Lrp11 raised in rabbit A polyclonal antibody raised in rabbit that targets the mouse "Lrp11" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse Sez6l2 raised in rabbit A polyclonal antibody raised in rabbit that targets the mouse "Sez6l2" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse Sez6l2 raised in rabbit A polyclonal antibody raised in rabbit that targets the mouse "Sez6l2" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human DDR1 raised in goat A polyclonal antibody raised in goat that targets the human "DDR1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human DDR1 raised in mouse A monoclonal antibody raised in mouse that targets the human "DDR1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse Gpr39-1a raised in rabbit A polyclonal antibody raised in rabbit that targets the mouse "Gpr39-1a" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal rat CART raised in rabbit A polyclonal antibody raised in rabbit that targets the rat "CART" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal rat CART raised in mouse A monoclonal antibody raised in mouse that targets the rat "CART" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{R26-60-DR5-TA-Cerulean} mouse ESC line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{R26-60-DR5-TA-Cerulean} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). In these cells Rosa26 gene sequences from -60 to +81 were replaced by a retinoic acid response element (DR5) fused to a TATA-Cerulean (CFP) reporter. These ESCs may be useful for assess retinoic acid responsiveness. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{R26-228-DR5-TA-Cerulean} mouse ESC line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Roas26{R26-228-DR5-TA-Cerulean} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). In these cells Rosa26 gene sequences from -228 to +81 were replaced by a retinoic acid response element (DR5) fused to a TATA-Cerulean (CFP) reporter. These ESCs may be useful for assess retinoic acid responsiveness. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Ptf1a{tm3Macd} mouse strain A mouse strain in which part or all of the targeted gene, pancreas specific transcription factor, 1a (NCBI Gene ID: 19213) is replaced to create Ptf1a{tm3Macd} using the Loxed Cassette Acceptor allele Ptf1a{tm1(LCA)}). Modified allele of Ptf1a with a biotinylation Tag sequence attached to the amino terminus of Ptf1a. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Ptf1a{tm3Macd} Vanderbilt University Medical Center Sox17{tm1.2Mgn} mouse strain A mouse strain in which part or all of the targeted gene, SRY-box containing gene 17 (NCBI Gene ID: 20671) is replaced to create Sox17{CreERT2} using the Loxed Cassette Acceptor allele Sox17{tm1(LCA)}). Sox17{CreERT2} mice may be used either to track Sox17-expressing cells or their progeny or to conditionally inactivate genes in Sox17-expressing cells at specific time points by tamoxifen injection. This line is complementary to Sox17-CreGFP and may avoid possible interferences of expression in the extra-embryonic visceral endoderm. We plan to analyze the effects of a direct activation/deletion of the Wnt pathway in the endoderm by crossing the Sox17-CreERT2 with the gain- and loss-of-function of beta-catenin. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Sox17{tm1.2Mgn} Vanderbilt University Medical Center Polyclonal mouse Carboxypeptidase A1 (CPA1) raised in goat A polyclonal antibody raised in goat that targets the mouse "Carboxypeptidase A1 (CPA1)" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human Muc1 raised in rabbit A polyclonal antibody raised in rabbit that targets the human "Muc1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human Cleaved Notch1 raised in rabbit A polyclonal antibody raised in rabbit that targets the human "Cleaved Notch1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human Jagged1 raised in goat A polyclonal antibody raised in goat that targets the human "Jagged1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Pdx1{CFP} mouse ESC line A mouse ESC line in which part or all of the targeted gene, pancreatic and duodenal homeobox 1 (NCBI Gene ID: 18609) is replaced to create Pdx1{CFP} using the Loxed Cassette Acceptor allele Pdx1{tm1(LCA)}). This ES cell line contains cyan fluorescent protein (CFP, Cerulean variant) inserted into a Pdx1{LCA} allele by recombinase mediated cassette exchange. These cells may be useful for identifying pancreatic progenitor cells in cultures that have been stimulated to differentiate towards endodermal and pancreatic fates. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Gt(ROSA)26Sor{tm1(Ccnd1T286A)Stang} mouse strain A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{(Ccnd1T286A)} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This strain expresses both mutant cyclin D1{T286A} and a cherry reporter under the regulation of a tetracycline-responsive bi-directional minimal CMV promoter (TRE-Tight; tetO). The cyclin D1-T286A mutant cannot be phosphorylated by GSK-3beta and is resistant to polyubiquitination. Therefore, cyclin D1-T286A remains nuclear throughout the cell cycle and has an extended half-life relative to wild-type cyclin D1. This strain represents an effective tool for generating inducible tissue-specific cyclin D1{T286A} mutants with a cherry reporter. Gt(ROSA)26Sor{tm1(Ccnd1T286A)Stang} Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{tm1.1(R26-60-DR5-TA-Cerulean)Mgn} mouse strain A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{tm1.1(R26-DR5-TA-Cerulean)} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). These mice were generated using RMCE to insert an exchange vector containing a modified Rosa26 promoter linked to a Cerulean fluorescent protein (CFP) reporter gene into mESCs containing a Loxed Cassette Acceptor (LCA) allele within the Rosa26 gene locus. The Rosa26 promoter in this mouse was altered by replacing DNA sequences from -60 to +81 with a multimerized retinoic acid response element (DR5) fused to a TATA box. This mouse will facilitate studies of retinoic acid signaling in an intact animal. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Rosa26{tm1.1(R26-60-DR5-TA-Cerulean)Mgn} Vanderbilt University Medical Center NOD.Cg-Rag1{tm1Mom}Ins2{Akita}Il2rg{tm1Wjl}/Sz mouse strain A mouse strain in which the targeted gene, recombination activating gene 1 (NCBI Gene ID: 19373), has been modified (allele type: Global Null) to (MGI ID: Rag1{tm1Mom}). Backcrossing of the Rag1 null allele onto the NOD/Lt strain background (NOD-Rag1{null} mice) provided a radio-resistant and longer-lived model for human-cell engraftment. Mutations in X-chromosome-linked Il2rg gene cause X-linked severe combined immunodeficiency (XSCID). Immunodeficient NOD-Rag1{null} IL2rg nullmice tolerated much higher levels of irradiation conditioning than did NOD-Prkdcscid IL2rg{null} mice. This immunodeficient mouse also develops spontaneous hyperglycemia based on the Ins2{Akita} mutation. NOD.Cg-Rag1{tm1Mom}Ins2{Akita}Il2rg{tm1Wjl}/Sz Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center NOD.Cg-Prkdc{scid}Il2rg{tm1Wjl}/Sz mouse strain A mouse strain in which the targeted gene, interleukin 2 receptor, gamma chain (NCBI Gene ID: 16186), has been modified (allele type: Global Null) to targeted mutation 1 (MGI ID: Il2rg{tm1Wjl}). NOD-scid IL2rg{null} mice are deficient in mature lymphocytes and NK cells, survive beyond 16-month of age, and even after sublethal irradiation resist lymphoma development. Moreover, cytokine-mobilized human peripheral blood stem cells engraft at high levels in NOD-scid IL2rg{null} mice and develop into human CD3+CD4+ and CD3+CD8+ T cells, Ig+B cells, myeloid cells, NK cells and plasmacytoid dentritic cells. NOD.Cg-Prkdc{scid}Il2rg{tm1Wjl}/Sz Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{tm1.2(R26-228-DR5-TA-Cerulean)Mgn} mouse strain A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{tm1.2((R26-228-DR5-Cerulean) using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). These mice were generated using RMCE to insert an exchange vector containing a modified Rosa26 promoter linked to a Cerulean fluorescent protein (CFP) reporter gene into mESCs containing a Loxed Cassette Acceptor (LCA) allele within the Rosa26 gene locus. The Rosa26 promoter in this mouse was altered by replacing DNA sequences from -228 to +81 with a multimerized retinoic acid response element (DR5) fused to a TATA box. This mouse will facilitate studies of retinoic acid signaling in an intact animal. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Rosa26{tm1.2(R26-228-DR5-TA-Cerulean)Mgn} Vanderbilt University Medical Center Nkx2-2{tm5(null)Suss} mouse strain A mouse strain in which the targeted gene, Nkx2.2 (NCBI Gene ID: 18088), has been modified (allele type: Global Null) to Null (MGI ID: Nkx2.2{tm5(null)}). These mice contain a deletion of the Nkx2.2 coding region to create a null allele. Nkx2-2{tm5(null)Suss} Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Nkx6-1{tm2(flox)Msan} mouse strain A mouse strain in which the targeted gene, Nk6 Homeobox 1 (NCBI Gene ID: 18096), has been modified (allele type: Conditional Null) to targeted mutation 1.1 (MGI ID: Nkx6.1{tm1.1Msan}). A conditional allele for nkx6.1 is necessary to study the function of Nkx6.1 in adult mice. A homozygous nkx6.1 null allele results in neonatal lethality due to a paralytic state, which is a direct result of Nkx6.1 function in the development of motor neurons. Conditional loss of Nkx6.1 is achieved through Cre mediated recombination of a floxed exon II of nkx6.1. Our use for a conditional nkx6.1 allele is to study its function in beta cells of the adult pancreas. Nkx6-1{tm2(flox)Msan} Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center NOD.Cg-Rag1{tm1Mom}Prf1{tm1Sdz}/SzJ mouse strain A mouse strain in which the targeted gene, Perforin 1 (Pore forming protein) (NCBI Gene ID: 18646), has been modified (allele type: Global Null) to (MGI ID: ). Mice that are homozygous for both targeted mutations are viable, fertile, normal in size and do not display any gross physical or behavioral abnormalities when housed under specific pathogen free conditions. These double homozygote mutant mice have no mature T or B lymphocytes, no detectable NK cell cytotoxic activity, and lack serum immunoglobulin. The number of nucleated spleen cells is significantly reduced in double mutant mice, when compared to the single homozygote, NOD.129S7(B6)-Rag1tm1Mom/J (Stock No. 003729). Although an increased number of DX5+CD122+ NK cells are found in the spleens of double mutants, these NK cells have impaired cytotoxic activity. The disruption of Prf1 ablates NK cell cytotoxic activity resulting in increased engraftment levels over that observed with Stock No. 003729. All mutant mice develop thymic lymphomas. This double mutant mouse strain may be useful in studies involving engraftment of human hematolymphoid cells. NOD.Cg-Rag1{tm1Mom}Prf1{tm1Sdz}/SzJ Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Foxo1{tm1(DBD)Dac} mouse strain A mouse strain in which part or all of the targeted gene, forkhead box O1 (NCBI Gene ID: 56458) is replaced to create Foxo1{DBD} using the Loxed Cassette Acceptor allele Foxo1{tm1(LCA)}). <p>This line contains a DNA binding-deficient mutant of Foxo1. The mutation may be useful for assessing the contribution of DNA co-activation in the function of Foxo1.</p> Foxo1{tm1(DBD)Dac} Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{tm1(Ccnd1)} mouse ESC line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{Ccnd1} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). ES cells express mutant cyclin D1-T286A and a cherry reporter under the regulation of a tetracycline-responsive bi-directional minimal CMV promoter (TRE-Tight; tetO) targeted to the ROSA26 locus. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{R26-60-IBRE4-TA-Cerulean} mouse ESC line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{R26-60-IBRE4-TA-Cerulean} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). In these cells Rosa26 gene sequences from -60 to +81 were replaced by a BMP response element (IBRE4) fused to a TATA-Cerulean (CFP) reporter. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{R26-228-IBRE4-TA-Cerulean} mouse ESC line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{R26-228-IBRE4-TA-Cerulean} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). In these cells Rosa26 gene sequences from -228 to +81 were replaced by a BMP response element (IBRE4) fused to a TATA-Cerulean (CFP) reporter. These ESCs may be useful for assess BMP responsiveness. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Foxo1{tm1(GFP)Dac} mouse strain A mouse strain in which part or all of the targeted gene, forkhead box O1 (NCBI Gene ID: 56458) is replaced to create Foxo1{GFP} using the Loxed Cassette Acceptor allele Foxo1{tm1(LCA)}). A GFP cDNA has been knocked into the Foxo1 locus at the 3' end of the endogenous Foxo1 cDNA to generate a Foxo1-gfp fusion protein that can be used to study Foxo1 translocation in vivo. Foxo1{tm1(GFP)Dac} Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse DNER raised in goat A polyclonal antibody raised in goat that targets the mouse "DNER" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal rat Shh raised in mouse A monoclonal antibody raised in mouse that targets the rat "Shh" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal chicken Chick HNF3Beta raised in mouse A monoclonal antibody raised in mouse that targets the chicken "Chick HNF3Beta" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Pdx1{LCA} mouse ESC line A mouse ESC line in which the targeted gene, pancreatic and duodenal homeobox 1 (NCBI Gene ID: 18609), has been modified (allele type: Cassette Acceptor) to targeted mutation 1 (MGI ID: Pdx1{tm1(LCA)}). This mouse ES cell line contains a loxed cassette acceptor (LCA) allele that may be utilized for the exchange of DNAs of interest into the Pdx1 gene locus by recombinase mediated cassette exchange (RMCE). An 8.62 kb region of the gene was replaced by tandemly oriented Lox66 and Lox2272 sites flanking both positive (puromycin) and negative (HSV-TK)selectable markers. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse Pax4 raised in guinea pig A polyclonal antibody raised in guinea pig that targets the mouse "Pax4" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{EN-Cherry-Neo} mouse ESC line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{EN-Cherry-Neo} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This ES cell line expresses mCherry, a red fluorescent protein, under control of the endogenous Rosa26gene. A cassette containing mCherry and other sequences to assure efficient expression were inserted into the Rosa26[LCA] allele by recombinase mediated cassette exchange. These cells will be used to identify an optimal combination of regulatory elements for fluorescent protein expression from a single gene copy and as a reference cell line for fluorescent cell sorting. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Neurog3{tm1.1(nCre)Ggu} mouse strain A mouse strain in which the targeted gene, Neurogenin 3 (NCBI Gene ID: 11925), has been modified (allele type: Gene Replacement) to Ngn3{nCre} (MGI ID: Neurog3{nCre}). A nCre-iRES (n-terminal half of Cre followed by internal ribosomal entry site) was inserted after Ngn3ATG. This allele is confirmed to express both nCre and Ngn3 (no visible phenotype in homozygous animals). Neurog3{tm1.1(nCre)Ggu} Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{Non-EN-CFP-Neo} mouse ESC line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{LCA} using the Loxed Cassette Acceptor allele Rosa26{tm1.8(Non-EN-CFP)}). This ES cell line contains CFP (Cerulean) inserted into a Rosa26{LCA} allele by recombinase mediated cassette exchange. These cells were used to identifythe optimal arrangement of regulatory elements for fluorescent protein expression from a single genomic copy. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse Ngn3 raised in goat A polyclonal antibody raised in goat that targets the mouse "Ngn3" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{EN-CFP-Neo} mouse ESC line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{EN.CFP} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This ES cell line contains CFP (Cerulean) inserted into a Rosa26 LCA allele by recombinase mediated cassette exchange. These cells were used to identify the optimal arrangement of regulatory elements for fluorescent protein expression from a single genomic copy. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{EN.CFP.SV40.Neo} mouse ESC line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{CFP.SV40} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This ES cell line contains CFP (Cerulean) inserted into a Rosa26 LCA allele by recombinase mediated cassette exchange. These cells were used to identify the optimal arrangement of regulatory elements for fluorescent protein expression from a single genomic copy. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{EN-GFP-Neo} mouse ESC line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{EN.GFP} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This ES cell line contains eGFP inserted into the Rosa26 gene locus. These cells were used to identify an optimal combination of regulatory elements for fluorescent protein expression from a single genomic copy and can serve as a reference cell line for fluorescent cell sorting. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{EN-CFP-bGpA-Neo} mouse ESC line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{CFP} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This ES cell line contains CFP (Cerulean) inserted into a Rosa26{LCA} allele by recombinase mediated cassette exchange. These cells were used to identify an optimal combination of regulatory elements for fluorescent protein expression from single a genomic copy. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{(Ngn3.CFP)Mgn} mouse strain A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{Ngn3-CFP} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse contains a bidirectional TetO-regulated fusion gene that has been inserted into a disabled Rosa26 locus. In one direction the tetO/CMV promoter drives expression of CFP (Cerulean). In the other direction it drives Ngn3. Mice containing this allelecan be used to drive the expression of Ngn3 under control of both doxycycline and either an rtTA or tTA transgene. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Rosa26{(Ngn3.CFP)Mgn} Vanderbilt University Medical Center Rosa26{tm1.4(MafA-Cherry)Mgn} mouse strain A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{MafA-Cherry} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse contains a bidirectional Tet0-regulated fusion gene that has been inserted into adisabled Rosa26 loxed cassette acceptor allele by RMCE. In one direction the tetO/CMV promoter drives expression of a red fluorescent protein (Cherry) while in the other direction it drives MafA expression. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Rosa26{tm1.4(MafA-Cherry)Mgn} Vanderbilt University Medical Center Rosa26{R26-60-3XCNotch-TA-Cerulean} mouse ESC line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{(R26-60-CNotch-TA-Cerulean)} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). The Rosa26 gene sequences from -228 to +81 were replaced with a repeat of alternating 32-bp C-elements and 31-bp Rbpj-binding sites (i.e.,C-R-C-R-C-R). The 31 base-pair region is derived from the CBF1/Rbpj binding region of the C-promoter of EBV (cataaattTTTTCCCACGgcgtgtttacacc; uppercase letters are the consensus Rbpj binding sequence within the 31-bp element) (Hsieh, MCB 16:952, 1996). The 32-bp C-element is from the Ela1 enhancer (Kruse et al., MCB 15:4385, 1995). Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{R26-60-AR8-TA-mCherry} mouse ESC line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{R26-60-AR8-TA-mCherry} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). In these cells Rosa26 gene sequences from -60 to +81 were replaced by an Activin response element (AR8) fused to a TATA-mCherry reporter Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{R26-228-AR8-TA-mCherry} mouse ESC line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{tm2.2(R26-228-AR8-TA-mCherry)} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). In these cells Rosa26 gene sequences from -228 to +81 were replaced by an Activin response element (AR8) fused to a TATA-mCherry reporter. These ESCs may be usefulto assess Activin, Nodal, and TGFbeta responsiveness. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{R26-60-6XNotch-TA-Cerulean} mouse ESC line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26(R26-60-6XNotch-TA-Cerulean) using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). The binding site for Rbpj, the transcriptional mediator of Notch signaling was inserted into the Rosa 26 locus replacing nucleotides -60 to -228.The complete insert contains the Rbpj cis element in a series of six repeats. Each repeat includes a 31 base-pair region derived from the CBF1/Rbpj binding region of the C-promoter of EBV (cataaattTTTTCCCACGgcgtgtttacacc). Uppercase letters are the consensus Rbpj binding sequence within the 31-bp element) (Hsieh et al., MCB 16:952, 1996). Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{-228.3XCNotch.TA.Cerulean} mouse ESC line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26(R26-228-3XCNotch-TA-Cerulean) using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). The Rosa26 gene sequences from -60 to -228 were replaced with a repeat of alternating 32-bp C-elements and 31-bp Rbpj-binding sites (i.e.,C-R-C-R-C-R). The 31 base-pair region is derived from the CBF1/Rbpj binding region of the C-promoter of EBV (cataaattTTTTCCCACGgcgtgtttacacc; uppercase letters are the consensus Rbpj binding sequence within the 31-bp element) (Hsieh, MCB 16:952, 1996). The 32-bp C-element is from the Ela1 enhancer (Kruse et al., MCB 15:4385, 1995). Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{-228.6XNotch.TA.Cerulean} mouse ESC line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26(Rbpj(R26-228-6XNotch-TA-Cerulean)) using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). The binding site for Rbpj, the transcriptional mediator of Notch signaling was inserted into the Rosa 26 locus replacing nucleotides -60 to -228.The complete insert contains the Rbpj cis element in a series of six repeats. Each repeat includes a 31 base-pair region derived from the CBF1/Rbpj binding region of the C-promoter of EBV (cataaattTTTTCCCACGgcgtgtttacacc). Uppercase letters are the consensus Rbpj binding sequence within the 31-bp element) (Hsieh et al., MCB 16:952, 1996). Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse Irx2 raised in rabbit A polyclonal antibody raised in rabbit that targets the mouse "Irx2" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse Arx raised in rabbit A polyclonal antibody raised in rabbit that targets the mouse "Arx" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center ROSA26{(Nkx2.2.CFP)Suss} mouse strain A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{Nkx2.2/CFP} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). In this strain both CFP and myc-tagged Nkx2.2 were inserted into a ROSA26 LCA allele under control of a bidirectional tetO/CMV promoter element. The mouse line will allow us to explore the contribution of Nkx2.2 to progenitor cell population competency by allowing for the manipulation of Nkx2.2 gene expression within the developing pancreas. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler ROSA26{(Nkx2.2.CFP)Suss} Vanderbilt University Medical Center Polyclonal mouse mArx raised in guinea pig A polyclonal antibody raised in guinea pig that targets the mouse "mArx" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human C-peptide raised in rat A monoclonal antibody raised in rat that targets the human "C-peptide" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{(-60.IBRE4.TACerulean)Hri} mouse strain A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{tm2.1(R26-60-IBRE4-TA-Cerulean)} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse contains aBMP reporter element withina modified ROSA26 promoter followed by a CFP reporter. This mouse is identical to the -228 variant except for the amount of ROSA26 DNA. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Rosa26{(-60.IBRE4.TACerulean)Hri} Vanderbilt University Medical Center Ptf1a{rtTA} mouse ESC line A mouse ESC line in which part or all of the targeted gene, pancreas specific transcription factor, 1a (NCBI Gene ID: 19213) is replaced to create Ptf1a{rtTA} using the Loxed Cassette Acceptor allele Ptf1a{tm1(LCA)}). These mESCs contain the reverse tetracycline transactivator (rtTA) under control of the Ptf1a regulatory sequences. rtTA is a transcriptional activator, which can inducibly (in the presence of the tetracycline analog doxycycline) activate the genes under Tet-O activator/promoter element. The rtTA sequences were introduced in to Ptf1a[LCA] by Recombinase-Mediated Cassette Exchange using standard methods.These cells were made in order togenerate a mouse line that express rtTA under control of the Ptf1a gene locus. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{Nepn.Cherry} mouse ESC line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Nepn-Cherry using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This ES cell line was generated by RMCE usingthe Rosa26.LCA allele. To create a Nepn reporter allele, a 9kb promoter region of the Nepn gene is inserted upstream of the red fluorescent protein mCherry-pA sequence. Since Nepn is expressed during endoderm development, this cell line can be used for visualisation and sorting of endodermal cell populations. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{EN.YFP.bGsplicepA.Neo} mouse ESC line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{YFP} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). These mESCs contain yellow fluorescent protein (YFP, Citrine) under control of the ROSA26 gene locus. They were made as part of a study to quantify variables that affect fluorescent protein expression levels in mESCs. TheYFP sequences are flanked by a translational enhancer and beta-globin splice/polyA sequences. The cassette containing the YFP was inserted intoa ROSA26 LCA allel using Recombinase-Mediated Cassette Exchange. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{Apple.bGsplicepA.Neo} mouse ESC line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{EN.Apple.bGspliceA.neo} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). To better quantify protein expression levels via confocal microscopy, flow sorting and western blot analysis this cell line contains a 4kb R26 promoter element, Apple (a red fluorescent protein) with an upstream enhancer element, a splicing beta-globin polyA tail and the neomycin gene as a selection agent. Through Recombinase-Mediated Cassette Exchange this construct was inserted into the Rosa26 locus. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{Ngn3.Mafa} mouse ESC line A mouse ESC line in which part or all of the targeted gene, Gt(ROSA)26Sor gene trap ROSA 26, Philippe Soriano [ Mus musculus ] (NCBI Gene ID: 14910) is replaced to create Rosa26 LCA using the Loxed Cassette Acceptor allele ). Recombinase mediated cassette exchange was performed to introduce a bidirectional tetO-regulated cassette containing coding sequences for transcription factors MafA and Ngn3 into Rosa26 LCA mESCs. ThismESC line can be used to generate mice that will simultaneously overexpress MafA and Ngn3 using tet-inducible activation with rtTA. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{tm2Mgn} mouse strain A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{EN-Cherry-Neo} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse line expresses mCherry, a red fluorescent protein, under control of the endogenous ROSA26 gene locus. This mouse was generated as part of a study to identify the optimal combination of regulatory elements for fluorescent protein expression from a single gene copy. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Rosa26{tm2Mgn} Vanderbilt University Medical Center Ptf1a{tm2(rtTA)Mgn} mouse strain A mouse strain in which part or all of the targeted gene, pancreas specific transcription factor, 1a (NCBI Gene ID: 19213) is replaced to create Ptf1a{tm1.2(rtTA)Mgn} using the Loxed Cassette Acceptor allele Ptf1a{tm1(LCA)}). This mouse line expresses the reverse tetracycline transactivator (rtTA) under control of the Ptf1a regulatory sequences. This mouseisuseful for activating expression of various TetO-regulated genes in sites where Ptf1a is normally expressed. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Ptf1a{tm2(rtTA)Mgn} Vanderbilt University Medical Center Rosa26{(Nepn.Cherry)Mgn} mouse strain A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26[Nepn.Cherry] using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). Nephrocan (Nepn) has been shown to be expressed specifically during early endoderm development. A Nepn promoter driven reporter (Cherry) has been inserted in the Rosa26LCA locus by recombinase mediated cassette exchange. This mouse line will be useful in visualizing whether Nepn can be used as a specific DE marker for beta-cell development. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Rosa26{(Nepn.Cherry)Mgn} Vanderbilt University Medical Center Rosa26{mIre1.WT.Cherry} mouse ESC line A mouse ESC line in which part or all of the targeted gene, Gt(ROSA)26Sor gene trap ROSA 26, Philippe Soriano [ Mus musculus ] (NCBI Gene ID: 14910) is replaced to create Rosa26 LCA using the Loxed Cassette Acceptor allele Rosa26{tm1.1(mlre1.WT.Cherry)FerozPapa}). This mESC line contains a bidirectional Tet0-regulated fusion gene that has been inserted into a disabled Rosa26 loxed cassette acceptor allele by RMCE. In one direction the tetO/CMV promoter drives expression of a red fluorescent protein (Cherry) while in the other direction it drives the wild type form of mlre1. mlre1 is an endoplasmic reticulum (ER) membrane kinase response to unfolded protein response (UPR). Activated mlre1 endonucleases leads to the splicing of XBP-1 (a transcription factor which is upregulated in times of ER stress) which transcriptionally increases the expression of ER chaperones and alleviates UPR. This cell line should be useful for studying the role of mlre1 in the response to ER stress. By generating mice with this allele Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{mIre1.IG.Cherry} mouse ESC line A mouse ESC line in which part or all of the targeted gene, Gt(ROSA)26Sor gene trap ROSA 26, Philippe Soriano [ Mus musculus ] (NCBI Gene ID: 14910) is replaced to create Rosa26 LCA using the Loxed Cassette Acceptor allele Rosa26{tm1.1(mlre1.IG.Cherry)FerozPapa}). This mESC line contains a bidirectional Tet0-regulated fusion gene that has been inserted into a disabled Rosa26 loxed cassette acceptor allele by RMCE. In one direction the tetO/CMV promoter drives expression of a red fluorescent protein (Cherry) while in the other direction it drives a mutant version of mlre1. mlre1 is an endoplasmic reticulum (ER) membrane kinase response to unfolded protein response (UPR). Activated mlre1 endonucleases leads to the splicing of XBP-1 (a transcription factor which is upregulated in times of ER stress) which transcriptionally increases the expression of ER chaperones and alleviates UPR. This cell line should be useful for studying the role of mlre1 in the response to ER stress. By generating mice with this allele t Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{(mlre1.WT.Cherry)Fpa} mouse strain A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{mlre1.WT-Cherry} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse line contains a bidirectional Tet0-regulated fusion gene that has been inserted into a disabled Rosa26 loxed cassette acceptor allele by RMCE. In one direction the tetO/CMV promoter drives expression of a red fluorescent protein (Cherry) while in the other direction it drives a wild type mlre1. mlre1 is an endoplasmic reticulum (ER) membrane kinase response to unfolded protein response (UPR). Activated mlre1 endonucleases leads to the splicing of XBP-1 (a transcription factor which is upregulated in times of ER stress) which transcriptionally increases the expression of ER chaperones and alleviates UPR. These mice may be useful for studying the role of mlre1 in the response to ER stress in the setting of diet induced obesity and insulin resistance. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Rosa26{(mlre1.WT.Cherry)Fpa} Vanderbilt University Medical Center Rosa26{(mlre1.IG.Cherry)Fpa} mouse strain A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{mlre1.IG-Cherry} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse line contains a bidirectional Tet0-regulated fusion gene that has been inserted into a disabled Rosa26 loxed cassette acceptor allele by RMCE. In one direction the tetO/CMV promoter drives expression of a red fluorescent protein (Cherry) while in the other direction it drives a mutant mlre1. mlre1 is an endoplasmic reticulum (ER) membrane kinase response to unfolded protein response (UPR). Activated mlre1 endonucleases leads to the splicing of XBP-1 (a transcription factor which is upregulated in times of ER stress) which transcriptionally increases the expression of ER chaperones and alleviates UPR. These mice may be usefulfor studying the role of mlre1 in the response to ER stress in the setting of diet induced obesity and insulin resistance. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Rosa26{(mlre1.IG.Cherry)Fpa} Vanderbilt University Medical Center Rosa26{(R26-228-IBRE4-TA-Cerulean)Hri} mouse strain A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{R26-228-IBRE4-TA-Cerulean} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). These mice were generated by performing recombinase mediated cassette exchange on the Rosa26 LCA. The sequence from -228 to +81 of the Rosa26 gene was replaced with a BMP responsive element (IBRE4) fused to a TATA-Cerulean (CFP) reporter. These mice may be useful in visualizing BMP responsiveness. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Rosa26{(R26-228-IBRE4-TA-Cerulean)Hri} Vanderbilt University Medical Center Rosa26{Sox9.Cherry} mouse ESC line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Sox9/mCherry using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This ES line contains bidirectional TetO-regulated genes inserted into the Rosa26.LCA allele by RMCE. In one direction the TetO/CMV promoter drives the expression of transcription factor Sox9. In the other direction it drives the expression of red fluorescent protein mCherry. This ES cell line can be used to simultaneously over-express Sox9 and mCherry upon administration of doxycyline when the effector protein rtTA is expressed. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{(TetO.Sox9)Msan} mouse strain A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Sox9 using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse line contains bidirectional TetO-regulated genes inserted into the Rosa26{LCA} allele by RMCE. In one direction, the TetO/CMV promoter drives the expression of the transcription factor Sox9. In the other direction, it drives the expression of the red fluorescent protein mCherry. In this mouse line, when the effector protein rtTA is expressed, Sox9 and mCherry will be over-expressed simultaneously upon administration of doxycyline. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Rosa26{(TetO.Sox9)Msan} Vanderbilt University Medical Center Rosa26{TetO.NRSF} mouse ESC line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create NRSF using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This cell line contains bidirectional TetO-regulated genes inserted into the Rosa26{LCA} allele by RMCE. In one direction, the TetO/CMV promoter drives expression of the transcription factor NRSF/REST. In the other direction, it drives the expression of the red fluorescent protein mCherry. In this cell line, when the effector protein rtTA is expressed, NRSF and mCherry are simultaneously over-expressed upon administration of doxycyline. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Ptf1a{tdTOM} mouse ESC line A mouse ESC line in which part or all of the targeted gene, pancreas specific transcription factor, 1a (NCBI Gene ID: 19213) is replaced to create Ptf1a{td.TOM} using the Loxed Cassette Acceptor allele Ptf1a{tm1(LCA)}). Recombinase mediated cassette exchange was performed using the Ptf1aLCA. This cell line expresses both tdTOM (a red fluorescent protein) and an N-terminal epitope tagged Strep/Flag (NSF) fusion of ptf1a in the adult pancreas. These cells will be useful in a variety of applications such as FACS sorting of ptf1a expressing cells, chromatin immunoprecipitation and proteomic analyses. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human TSPAN7 raised in rabbit A polyclonal antibody raised in rabbit that targets the human "TSPAN7" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human FXYD2 raised in mouse A monoclonal antibody raised in mouse that targets the human "FXYD2" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse Sez6l2 raised in rabbit A polyclonal antibody raised in rabbit that targets the mouse "Sez6l2" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human Lrp11 raised in rabbit A polyclonal antibody raised in rabbit that targets the human "Lrp11" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse Onecut1 raised in guinea pig A polyclonal antibody raised in guinea pig that targets the mouse "Onecut1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{tm3Mgn} mouse strain A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create CFP using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse line was made by RMCE in the Rosa26[LCA] allele and has a cyan fluorescent protein (CFP, Cerulean) expressed under the control of the ROSA26 promoter. The CFP sequence is preceded by a translational enhancer and followed by intron-containing rabbit beta-globin polyA sequences. This mouse has ubiquitously expressed CFP protein and can be used for transplantation and other experiments where tracing of source cells is required. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Rosa26{tm3Mgn} Vanderbilt University Medical Center Rosa26{tm4Mgn} mouse strain A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create YFP using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse line was made by RMCE in the Rosa26[LCA] allele and has yellow fluorescent protein (YFP, Citrine) expressed under control of the ROSA26 promoter. The YFP sequence is preceded by a translational enhancer and followed by intron-containing rabbit beta-globin polyA sequences. This mouse has ubiquitously expressed YFP protein and can be used for transplantation and other experiments where tracing of source cells is required. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Rosa26{tm4Mgn} Vanderbilt University Medical Center Rosa26{Setd5.GFP} mouse ESC line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Setd5/GFP using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This ES cell line was generated by RMCE in the Rosa26{LCA} allele. A coding sequence for green fluorescent protein (GFP) was inserted into the first exon of the Setd5 gene. This exon is located upstream of the Rosa26 transcribed sequence and is transcribed in an opposite orientation. The GFP-polyA cassette, transcribed from the Setd5 promoter, knocks out Setd5 transcription and provides a reporter for Setd5 gene expression. The purpose of this cell line is to study the molecular function of the Setd5 gene. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Pdx1{(H2B.Apple)Mgn} mouse strain A mouse strain in which part or all of the targeted gene, pancreatic and duodenal homeobox 1 (NCBI Gene ID: 18609) is replaced to create Pdx1{H2B.Apple} using the Loxed Cassette Acceptor allele Pdx1{tm1(LCA)}). This mouse contains a coding sequence for the mApple-H2B fusion protein in order to tag cells expressing Pdx1 with a red fluorescent protein. The generation of a Pdx-1 red fluorescent marker will enable the isolation of pancreatic lineage progenitors by FACS. The presence of the H2B sequences may also be useful in allowing the plane of cell division to be analyzed. Pdx1{(H2B.Apple)Mgn} Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Ngn3{HA.LCA} mouse ESC line A mouse ESC line in which the targeted gene, Neurogenin 3 (NCBI Gene ID: 11925), has been modified (allele type: Cassette Acceptor) to (MGI ID: ). This ES cell line was made by gene targeting and designed to express an HA-tagged version of the transcription factor Ngn3. The Lox71 and Lox2272 sites were inserted flanking the Ngn3 coding sequence. Within the flanked region an HA-tag was placed at the N-terminus of the Ngn3 protein. This allele can be used to study chromatin and protein-protein interactions of Ngn3. Additionally, the Lox71 and Lox2272 sites allow for manipulations of the flanked region by RMCE. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Foxm1{LCA} mouse ESC line A mouse ESC line in which the targeted gene, Forkhead box M1 (NCBI Gene ID: 14235), has been modified (allele type: Gene Replacement) to (MGI ID: ). This ES cell line was made by gene targeting and is designed to serve as a cassette acceptor allele at the Foxm1 locus. The portion of genomic DNA containing exons 2-4 of Foxm1 was flanked with Lox71 and Lox2272 sites and replaced with a selection marker. This line allows for modification of the flanked sequences through RMCE. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{Pdx1.YFP} mouse ESC line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Pdx1/YFP using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This ES cell line contains bidirectional TetO-regulated genes inserted into the Rosa26{LCA} allele by RMCE. In one direction, the tetO/CMV promoter will drive expression of Pdx1. In the other direction, it will drive the expression of yellow fluorescent protein (YFP). In this cell line, when the effector protein rtTA is expressed, Pdx1 and YFP will be over-expressed simultaneously upon administration of doxycyline. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{(Pdx1.YFP)Mgn} mouse strain A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Pdx1/YFP using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse line contains bidirectional TetO-regulated genes inserted into the Rosa26[LCA] allele by RMCE. In one direction, the TetO/CMV promoter will drive expression of Pdx1. In the other direction, it will drive the expression of yellow fluorescent protein (YFP). In this mouse line, when the effector protein rtTA is expressed, Pdx1 and YFP will be over-expressed simultaneously upon administration of doxycyline. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Rosa26{(Pdx1.YFP)Mgn} Vanderbilt University Medical Center Insm1{Pdx1.YFP} mouse ESC line A mouse ESC line in which part or all of the targeted gene, insulinoma-associated 1 (NCBI Gene ID: 53626) is replaced to create Pdx1/YFP using the Loxed Cassette Acceptor allele Insm1{tm1(LCA)}). This ES cell line contains bidirectional TetO-regulated genes inserted into the Insm1{LCA} allele by RMCE. In one direction, the TetO/CMV promoter drives the expression of the transcription factor Pdx1. In the other direction, it drives the expression of yellow fluorescent protein (YFP). In this cell line, when the effector protein rtTA is expressed, Pdx1 and YFP will be over-expressed simultaneously upon administration of doxycyline. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{3TF.Cherry} mouse ESC line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create mCherry/MafA/Pdx1/Ngn3 using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This ES cell line contains bidirectional TetO-regulated genes inserted into the Rosa26{LCA} allele by RMCE. In one direction, the TetO/CMV promoter drives the expression of a polycistronic mRNA with transcription factors MafA, Pdx1, and Ngn3 linked by 2A peptide cleavage sequences. In the other direction, it drives the expression of the red fluorescent protein mCherry. In this cell line, when the effector protein rtTA is expressed, all three transcription factors and mCherry will be over-expressed simultaneously upon administration of doxycyline. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{(3TF.Cherry)Mgn} mouse strain A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create mCherry/MafA/Pdx1/Ngn3 using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse line contains bidirectional TetO-regulated genes inserted into the Rosa26[LCA] by RMCE. In one direction, the TetO/CMV promoter drives expression of a polycistronic mRNA with transcription factors MafA, Pdx1, and Ngn3 linked by 2A peptide cleavage sequences. In the other direction, it drives the expression of red fluorescent protein mCherry. In this mouse line, when the effector protein rtTA is expressed, all three transcription factors and mCherry will be over-expressed simultaneously upon administration of doxycyline. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Rosa26{(3TF.Cherry)Mgn} Vanderbilt University Medical Center Pdx1{AIVd} mouse ESC line A mouse ESC line in which part or all of the targeted gene, pancreatic and duodenal homeobox 1 (NCBI Gene ID: 18609) is replaced to create Pdx1{aIVd} using the Loxed Cassette Acceptor allele Pdx1{tm1(LCA)}). In this ES cell line, Area IV of the Pdx1 enhancer (-2168/-1913 relative to the primary transcription start site) was deleted using RMCE in the Pdx1{LCA} allele. This cell line allows for assessment of the role of these DNA sequences in the regulation and function of Pdx1. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Pdx1{(AIVd)Rwst} mouse strain A mouse strain in which part or all of the targeted gene, pancreatic and duodenal homeobox 1 (NCBI Gene ID: 18609) is replaced to create Pdx1{area IV deletion} using the Loxed Cassette Acceptor allele Pdx1{tm1(LCA)}). In this mouse line, Area IV of the Pdx1 enhancer (-2168/-1913 relative to the primary transcription start site) was deleted using RMCE in the Pdx1[LCA] allele. This mouse line allows for assessment of the role of these DNA sequences in the regulation and function of Pdx1. Pdx1{(AIVd)Rwst} Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Nkx2.2{cCre-Knock-in} mouse ESC line A mouse ESC line in which part or all of the targeted gene, NK2 transcription factor related, locus 2 (NCBI Gene ID: 18088) is replaced to create Nkx2.2{Cre} using the Loxed Cassette Acceptor allele Nkx2.2{tm1(LCA)}). In this ES cell line, the sequence for one of the two bi-partite Cre molecules (cCre) and the IRES sequence were knocked into a site directly upstream of the Nkx2.2 start codon using RMCE in the Nkx2.2{LCA} allele. The presence of the IRES sequence allows for the transcription of cCre and Nkx2.2 from the native Nkx2.2 locus at the same time. This results in the labeling of pancreatic epithelium cells that co-express high levels of Ngn3 and Nkx2.2 during mouse embryonic development. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Nkx2.2{(Cre-Knock-in)} mouse strain A mouse strain in which part or all of the targeted gene, NK2 transcription factor related, locus 2 (NCBI Gene ID: 18088) is replaced to create Nkx2.2{Cre-knock-in)} using the Loxed Cassette Acceptor allele Nkx2.2{tm1(LCA)}). In this mouse line, one of the two bi-partite Cre molecules, cCre, together with the IRES sequence was knocked into the site directly upstream of the Nkx2.2 start codon using RMCE in the Nkx2.2[LCA] allele. The presence of the IRES sequence allows for transcription of cCre and Nkx2.2 from the native Nkx2.2 locus at the same time. This mouse line allows the labeling of pancreatic epithelium cells that co-express high levels of Ngn3 and Nkx2.2 during mouse embryonic development. Nkx2.2{(Cre-Knock-in)} Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Nkx2.2{3XHA.Nkx2.2} mouse ESC line A mouse ESC line in which part or all of the targeted gene, NK2 transcription factor related, locus 2 (NCBI Gene ID: 18088) is replaced to create Nkx2.2{3XHA-Nkx2.2} using the Loxed Cassette Acceptor allele Nkx2.2{tm1(LCA)}). In this cell line RMCE in the Nkx2.2.LCA allele was used to introduce a triple HA tag in frame at the N-terminus of the transcription factor Nkx2.2. This allows for efficient immunoprecipitation of HA-tagged Nkx2.2 protein from mouse tissues to perform ChIP and protein-protein interaction studies. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Nkx2.2{(3XHA.Nkx2.2)Suss} mouse strain A mouse strain in which part or all of the targeted gene, NK2 transcription factor related, locus 2 (NCBI Gene ID: 18088) is replaced to create Nkx2.2{3XHA-Nkx2.2} using the Loxed Cassette Acceptor allele Nkx2.2{tm1(LCA)}). In this mouse line, RMCE in the Nkx2.2{LCA} allele was used to introduce a triple HA tag in frame at the N-terminus of the transcription factor Nkx2.2. This allows for efficient immunoprecipitation of HA-tagged Nkx2.2 protein from mouse tissues to perform ChIP and protein-protein interaction studies. Nkx2.2{(3XHA.Nkx2.2)Suss} Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Nkx2.2{Cre.EGFP} mouse ESC line A mouse ESC line in which part or all of the targeted gene, NK2 transcription factor related, locus 2 (NCBI Gene ID: 18088) is replaced to create Nkx2.2{Cre-EGFP} using the Loxed Cassette Acceptor allele Nkx2.2{tm1(LCA)}). In this ES cell line, a coding portion of the transcription factor Nkx2.2 was replaced with a Cre-EGFP cassette, in frame to the Nkx2.2 ATG. This allows for sites of Nkx2.2 gene expression to be identified in mice using direct immunofluorescence, FACS purification of Nkx2.2 expressing cells, and lineage tracing using Nkx2.2 driven Cre expression. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Pdx1{(Cre-ER)} mouse strain A mouse strain in which part or all of the targeted gene, pancreatic and duodenal homeobox 1 (NCBI Gene ID: 18609) is replaced to create Pdx1/cre-ER using the Loxed Cassette Acceptor allele Pdx1{tm1(LCA)}). In this mouse line, the first exon of the transcription factor Pdx1 was replaced with the coding sequence for a Cre-ER fusion protein using RMCE in the Pdx1[LCA] allele. Pdx1-promoter driven Cre-ER expressing mice enable tamoxifen-inducible Cre-LoxP manipulation of pancreatic lineage cells. Pdx1{(Cre-ER)} Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Nkx2.2{Cherry} mouse ESC line A mouse ESC line in which part or all of the targeted gene, NK2 transcription factor related, locus 2 (NCBI Gene ID: 18088) is replaced to create Cherry using the Loxed Cassette Acceptor allele Nkx2.2{tm1(LCA)}). In this ES cell, 1.956 kb of the native Nkx2.2 gene, containing a portion of exon 1 (all but the first 214 bp) and all of exon 2, was replaced by the mCherry cassette in frame to the Nkx2.2 ATG. This allows for sites of Nkx2.2 gene expression in the mouse to be identified using direct immunofluorescence and FACS purification of Nkx2.2 expressing cells. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal enterobacteria phage p1 Cre raised in guinea pig A polyclonal antibody raised in guinea pig that targets the enterobacteria phage p1 "Cre" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Pax4{HA.LCA} mouse ESC line A mouse ESC line in which the targeted gene, paired box 4 (NCBI Gene ID: 18506), has been modified (allele type: Cassette Acceptor) to targeted mutation 1 (MGI ID: Pax4{tm1(LCA)Ggu}). This ES cell line is made by gene targeting and is designed to express an HA-tagged version of the transcription factor Pax4. Lox71 and Lox2272 sites are inserted, flanking the last coding exon of the Pax4 gene. In the flanked region, an HA-tag was placed at the C-terminus of the PAX4 protein. This allele can be used to study chromatin and protein-protein interactions of PAX4. Additionally, the Lox71 and Lox2272 sites allow for future manipulations of the flanked region by RMCE. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human CDCP1 raised in goat A polyclonal antibody raised in goat that targets the human "CDCP1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human CD-200 raised in goat A polyclonal antibody raised in goat that targets the human "CD-200" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human Coagulation factor 3(rhF3) raised in goat A polyclonal antibody raised in goat that targets the human "Coagulation factor 3(rhF3)" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human Ngn3 raised in sheep A polyclonal antibody raised in sheep that targets the human "Ngn3" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal mouse Pax4 raised in mouse A monoclonal antibody raised in mouse that targets the mouse "Pax4" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal mouse Pax4 raised in mouse A monoclonal antibody raised in mouse that targets the mouse "Pax4" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal mouse Pax4 raised in mouse A monoclonal antibody raised in mouse that targets the mouse "Pax4" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human CD142 raised in mouse A monoclonal antibody raised in mouse that targets the human "CD142" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal rat Beta cell, IC2 raised in rat A monoclonal antibody raised in rat that targets the rat "Beta cell, IC2" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human CD-200 raised in goat A polyclonal antibody raised in goat that targets the human "CD-200" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center NOD.Cg-Prkdc{scid} Il2rg{tm1Wjl}/SzJ mouse strain A mouse strain in which the targeted gene, protein kinase, DNA activated, catalytic polypeptide (NCBI Gene ID: 19090), has been modified (allele type: Other) to severe combined immunodeficiency (MGI ID: Prkdc{scid}). The NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ mice, commonly known as NOD scid gamma (NSG), do not express the Prkdc gene nor the X-linked Il2rg gene. NSG mice are viable, fertile, normal in size and do not display any gross physical or behavioral abnormalities. Histological examination of lymphoid tissues reveals absence of lymphoid cells and some cystic structures in the thymus, an absence of follicles in the spleen and markedly diminished celluarity of lymph nodes. NSG mice are deficient in mature lymphocytes, serum Ig is not detectable and natural killer (NK) cell cytotoxic activity is extremely low. These mice are resistant to lymphoma development even after sublethal irradiation treatment. These mutant mice have been shown to readily support engraftment of human CD34+ hematopoietic stem cells and represent a superior, long-lived model suitable for studies employing xenotransplantation strategies. Please note that the NSG carries the true null interleukin-2 receptor gamma chain mutation and should not be confused with other strains that express a truncated interleukin-2 receptor gamma chain as described in: "Modulation of hematopoiesis in mice with a truncated mutant of the interleukin-2 receptor gamma chain". NOD.Cg-Prkdc{scid} Il2rg{tm1Wjl}/SzJ Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center NOD.Cg-Rag1{tm1Mom}Ins2{Akita}Il2rg{tm1Wjl}/SzJ mouse strain A mouse strain in which the targeted gene, insulin II (NCBI Gene ID: 16334), has been modified (allele type: Other) to Akita (MGI ID: Ins2{Akita}). NRG-Akita mice, which are homozygous for the Rag1tm1Mom and the Il2rgtm1Wjl alleles (males are hemizygous for the X-linked Il2rgtm1Wjl allele) and heterozygous for the Ins2Akita allele, develop spontaneous hyperglycermia. No mature T, B or NK cells are detected in flow cytometric analysis of splenocytes from NRG-Akita mutant mice. Granulocyte and macrophage populations are similar to those seen in NRG mice. NRG-Akita mice develop hyperglycemia between 3 and 5 weeks of age. Histological examination at 3 weeks of age reveals normal pancreas morphology, and routine insulin and glucagon staining. By approximately 32 weeks of age, NRG-Akita mice display disorganized, condensed pancreatic islet architecture, with loss of insulin-positive cells. Euglycemia is restored by subrenal transplantation of mouse or human islets or intrapancreatic transplantation of dissociated mouse islet cells. NRG-Akita mice engrafted with human hematopoietic stem cells (HSC) develop humanized immune systems. Approximately 60% of the human HSC engrafted NRG-Akita mice reject human islet allografts. NOD.Cg-Rag1{tm1Mom}Ins2{Akita}Il2rg{tm1Wjl}/SzJ Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Pdx1{Cre.ER} mouse ESC line A mouse ESC line in which part or all of the targeted gene, pancreatic and duodenal homeobox 1 (NCBI Gene ID: 18609) is replaced to create Pdx1/cre-ER using the Loxed Cassette Acceptor allele Pdx1{tm1(LCA)}). In this cell line, the first exon of the transcription factor Pdx1 was replaced with the coding sequence for a Cre-ER fusion protein using RMCE in the Pdx1{LCA} allele. Pdx1-promoter driven Cre-ER expressing mice enable tamoxifen-inducible Cre-LoxP manipulation of pancreatic lineage cells. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Ngn3{(HA.LCA)} mouse strain A mouse strain in which the targeted gene, Neurogenin 3 (NCBI Gene ID: 11925), has been modified (allele type: Cassette Acceptor) to (MGI ID: ). This mouse line was made by gene targeting and designed to express an HA-tagged version of the transcription factor Ngn3. The Lox71 and Lox2272 sites were inserted flanking the Ngn3 coding sequence. Within the flanked region an HA-tag was placed at the N-terminus of the Ngn3 protein. This allele can be used to study chromatin and protein-protein interactions of Ngn3. Additionally, the Lox71 and Lox2272 sites allow for manipulations of the flanked region by RMCE. Ngn3{(HA.LCA)} Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Pax4{(HA.LCA)Ggu} mouse strain A mouse strain in which the targeted gene, paired box 4 (NCBI Gene ID: 18506), has been modified (allele type: Cassette Acceptor) to targeted mutation 1 (MGI ID: Pax4{tm1(LCA)Ggu}). This mouse line was made by gene targeting and designed to express an HA-tagged version of the transcription factor Pax4. The Lox71 and Lox2272 sites were inserted flanking the last coding exon of the Pax4 gene. Within the flanked region an HA-tag was placed at the C-terminus of the PAX4 protein. This allele can be used to study chromatin and protein-protein interactions of PAX4. Additionally, the Lox71 and Lox2272 sites allow for manipulations of the flanked region by RMCE in the future. Pax4{(HA.LCA)Ggu} Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{(Setd5.GFP)Mgn} mouse strain A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Setd5/GFP using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse line was generated by RMCE in the Rosa26[LCA] allele. A coding sequence for green fluorescent protein (GFP) was inserted into the first exon of the Setd5 gene. This exon is located upstream of the Rosa26 transcribed sequence and is transcribed in an opposite orientation. The GFP-polyA cassette, transcribed from the Setd5 promoter, knocks out Setd5 transcription and provides a reporter for Setd5 gene expression. The purpose of this mouse line is to study the molecular function of the Setd5 gene. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Rosa26{(Setd5.GFP)Mgn} Vanderbilt University Medical Center Rosa26{228.TOP.CFP} mouse ESC line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create 7xTcf/Lef binding site using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This ES cell line was generated by RMCE in the Rosa26{LCA} allele. The Rosa26 gene sequence (from -228 to +81) was replaced by a Wnt response element (7xTcf/Lef binding site) fused to a TATA-Cerulean (CFP) reporter. This ES cell line may be useful for assessing canonical Wnt responsiveness. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Ptf1a{(tdTomato)} mouse strain A mouse strain in which part or all of the targeted gene, pancreas specific transcription factor, 1a (NCBI Gene ID: 19213) is replaced to create Ptf1a{td.TOM} using the Loxed Cassette Acceptor allele Ptf1a{tm1(LCA)}). This mouse cell line was generated by RMCE in the Ptf1a[LCA] allele. Pancreata of this mouse line express both td.Tomato (a red fluorescent protein) and an N-terminal epitope tagged Strep/Flag (NSF) fusion of the transcription factor Ptf1a. This line may be used in a variety of applications such as FACS sorting of Ptf1a expressing cells, chromatin immunoprecipitation, and proteomic analyses. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Ptf1a{(tdTomato)} Vanderbilt University Medical Center Nkx2.2{(Cre.EGFP)Suss} mouse strain A mouse strain in which part or all of the targeted gene, NK2 transcription factor related, locus 2 (NCBI Gene ID: 18088) is replaced to create Nkx2.2{Cre-EGFP} using the Loxed Cassette Acceptor allele Nkx2.2{tm1(LCA)}). In this mouse, a coding portion of the transcription factor Nkx2.2 was replaced with a Cre-EGFP cassette, in frame to the Nkx2.2 ATG. This allows for sites of Nkx2.2 gene expression to be identified in mice using direct immunofluorescence, FACS purification of Nkx2.2 expressing cells, and lineage tracing using Nkx2.2 driven Cre expression. Nkx2.2{(Cre.EGFP)Suss} Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{(TetO.NRSF)Msan} mouse strain A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create NRSF using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse line contains bidirectional TetO-regulated genes inserted into the Rosa26[LCA] allele by RMCE. In one direction, the TetO/CMV promoter drives the expression of the transcription factor NRSF/REST. In the other direction, it drives the expression of red fluorescent protein mCherry. In this mouse line, when the effector protein rtTA is expressed, NRSF and mCherry will be simultaneously over-expressed upon administration of doxycyline. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Rosa26{(TetO.NRSF)Msan} Vanderbilt University Medical Center Gt(ROSA)26Sor{tm2.1(mix1b-mCherry)Mgn} mouse strain A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{(R26-228-AR8-TA-mCherry)} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse line was generated by RMCE in the Rosa26[LCA] allele. In this mouse line, the Rosa26 gene sequence (-228 to +81) was replaced by the Foxh1/Smad2-dependent, Mix2-derived Activin response element (AR8) fused to a TATA-mCherry reporter. These mice may be useful to assess Activin, Nodal, and TGFbeta responsiveness. Gt(ROSA)26Sor{tm2.1(mix1b-mCherry)Mgn} Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Nepn{Cherry} mouse ESC line A mouse ESC line in which the targeted gene, Nephrocan (NCBI Gene ID: 66650), has been modified (allele type: Global Null) to (MGI ID: Neph(mCherry)). This ES cell line was made by gene targeting and was designed to express red fluorescent protein (mCherry) from the Nepn promoter thereby disrupting the expression of Nepn. The FP coding sequence was inserted dowstream of the Nepn start codon, in front of the Nepn first exon. This cell line is used to study the function and expression of Nepn. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Ins2{Apple.LCA} mouse ESC line A mouse ESC line in which the targeted gene, Insulin 2 (NCBI Gene ID: 20671), has been modified (allele type: Cassette Acceptor) to (MGI ID: Ins2{(apple.LCA)}). This ES cell line was made by gene targeting and designed to express a H2B-Apple fusion protein (nuclear red fluorescent protein) from the Ins2 promoter. The FP coding sequence is downsteam of the Ins2 start codon (replacing exon 2 of Ins2) and is flanked by Lox66/Lox2272 sites to allow for future manipulations of the flanked region by RMCE. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Pdx1{rTTA} mouse ESC line A mouse ESC line in which part or all of the targeted gene, pancreatic and duodenal homeobox 1 (NCBI Gene ID: 18609) is replaced to create Pdx1{rTTA} using the Loxed Cassette Acceptor allele Pdx1{tm1(LCA)}). In this cell line, thefirst exon of Pdx1 was replaced with the coding sequence for rTTA protein, using RMCE in the Pdx1{LCA} allele. Generation of Pdx1-promoter driven rTTA expressing mice will enable tetracycline-inducible manipulation of pancreatic lineage cells. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Pdx1{Cre} mouse ESC line A mouse ESC line in which part or all of the targeted gene, pancreatic and duodenal homeobox 1 (NCBI Gene ID: 18609) is replaced to create Pdx1/cre using the Loxed Cassette Acceptor allele Pdx1{tm1(LCA)}). In this cell line, thefirst exon of Pdx1 was replaced with the coding sequence for Cre-recombinase using RMCE in the Pdx1{LCA} allele. Generation of Pdx1-promoter driven Cre-expressing cells will enable Cre-LoxP manipulation of pancreatic lineage cells. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{228.3TF.GFP.Cre} mouse ESC line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create 3TF.GFP-Cre using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This cell line contains TetO-regulated genes inserted into the Rosa26{LCA} allele by RMCE. The TetO/miniCMV promoter was placed (at -228) upstream of the putative ROSA26 transcription start site and drives the expression of a polycistronic mRNA with transcription factors MafA, Pdx1, and Ngn3 together with a GFP-Cre fusion protein. The sequences are linked by 2A peptide cleavage sequences. In this cell line, when the effector protein rtTA is expressed, all three transcription factors and GFP-Cre will be over-expressed simultaneously upon administration of doxycyline. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{mIre1.N906A.Cherry} mouse ESC line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{mIre1.N906A.Cherry} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This ES line contains bidirectional TetO-regulated genes inserted into the Rosa26{LCA} allele by RMCE. In one direction the TetO/CMV promoter drives the expression of point mutant(N906A) of IRE1, an ER transmenbrane kinase response to unfolded protein response (UPR). In the other direction it drives the expression of red fluorescent protein mCherry. This ES cell line can be used to simultaneously over-express Ire1(N906A) and mCherry upon administration of doxycyline when the effector protein rtTA is expressed. This line can be used to study the roles of IRE1 in the response to ER stress, diet induced obesity and insulin resistance. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human HIP-14 ZDHHC17 raised in rabbit A polyclonal antibody raised in rabbit that targets the human "HIP-14 ZDHHC17" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Ghrl{tm1(Cre-eGFP)Suss} mouse strain A mouse strain in which part or all of the targeted gene, Ghrelin (NCBI Gene ID: 58991) is replaced to create Ghrl Cre-eGFP CEV using the Loxed Cassette Acceptor allele Ghrl{LCA}). Ghrl{Cre-eGGP} mice contain a Cre-eGFP fusion protein which replaces the Ghrelin coding sequence. These mice expressc Cre-eGFP phusion protein under control of the Ghrelin gene locus. The Ghrl{Cre-eGGP} mice may be used to track ghrelin-expressing cells progeny,or to conditionally inactivate genes in ghrelin-expressing cells. Ghrl{tm1(Cre-eGFP)Suss} Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Cd31 (PECAM1) raised in mouse A monoclonal antibody raised in mouse that targets the human "Cd31 (PECAM1)" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal cow GFAP raised in rabbit A polyclonal antibody raised in rabbit that targets the cow "GFAP" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human Glucagon (GCG) raised in rabbit A polyclonal antibody raised in rabbit that targets the human "Glucagon (GCG)" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human Glucagon (GCG) raised in guinea pig A polyclonal antibody raised in guinea pig that targets the human "Glucagon (GCG)" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal pig Insulin raised in guinea pig A polyclonal antibody raised in guinea pig that targets the pig "Insulin" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human Ki67 raised in rabbit A polyclonal antibody raised in rabbit that targets the human "Ki67" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human MafA raised in rabbit A polyclonal antibody raised in rabbit that targets the human "MafA" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human MafB raised in rabbit A polyclonal antibody raised in rabbit that targets the human "MafB" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human Pancreatic Polypeptide (PPY) raised in rabbit A polyclonal antibody raised in rabbit that targets the human "Pancreatic Polypeptide (PPY)" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human Somatostatin (Sst) raised in sheep A polyclonal antibody raised in sheep that targets the human "Somatostatin (Sst)" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal rat Tuj1 (TUBB3) raised in rabbit A monoclonal antibody raised in rabbit that targets the rat "Tuj1 (TUBB3)" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal rat VEGFA raised in goat A polyclonal antibody raised in goat that targets the rat "VEGFA" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse Foxa2 (HNF3b) raised in goat A polyclonal antibody raised in goat that targets the mouse "Foxa2 (HNF3b)" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Muc1 raised in hamster (armenian) A monoclonal antibody raised in hamster (armenian) that targets the human "Muc1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human HNF-1β raised in goat A polyclonal antibody raised in goat that targets the human "HNF-1β" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human Sox9 raised in rabbit A polyclonal antibody raised in rabbit that targets the human "Sox9" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human CDCP1 raised in goat A polyclonal antibody raised in goat that targets the human "CDCP1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human α-Amylase (AMY2A) raised in rabbit A polyclonal antibody raised in rabbit that targets the human "α-Amylase (AMY2A)" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal cow Insulin raised in guinea pig A polyclonal antibody raised in guinea pig that targets the cow "Insulin" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human Insulin raised in guinea pig A polyclonal antibody raised in guinea pig that targets the human "Insulin" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human Insulin raised in goat A polyclonal antibody raised in goat that targets the human "Insulin" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human Glucagon raised in rabbit A polyclonal antibody raised in rabbit that targets the human "Glucagon" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human Somatostatin (Sst) raised in goat A polyclonal antibody raised in goat that targets the human "Somatostatin (Sst)" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal rat Synaptophysin (SYP) raised in rabbit A polyclonal antibody raised in rabbit that targets the rat "Synaptophysin (SYP)" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Ngn3{T2A.nCre} mouse ESC line A mouse ESC line in which part or all of the targeted gene, Neurogenin 3 (NCBI Gene ID: 11925) is replaced to create Ngn3{T2A.nCre} using the Loxed Cassette Acceptor allele ). In this mouse ES cell line, one of the two bi-partite Cre molecules, nCre, was knocked in upstream of Ngn3 coding sequence by RMCE in Ngn3.HA.LCA ES cell line. nCre sequence is expressed from policistronic mRNA linked by 2a peptide to Ngn3 coding sequence allowing for simultanious expression of both proteins from Ngn3 promoter. This mouse line, in combination with Nkx2.2-cCre mouse line, allows to label pancreatic epithelium cells that co-express high levels of Ngn3 and Nkx2.2 during mouse embryonic development. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Nkx2.2{T2A.cCre} mouse ESC line A mouse ESC line in which part or all of the targeted gene, NK2 transcription factor related, locus 2 (NCBI Gene ID: 18088) is replaced to create Nkx2.2{T2A.cCre} using the Loxed Cassette Acceptor allele Nkx2.2{tm1(LCA)}). In this line, one of the two bi-partite Cre molecules, cCre, is inserted downstream of Nkx2.2 coding sequence fused with 2a peptide using RMCE in the Nkx2.2{LCA}allele. The presence of the T2A sequence allows for transcription of Nkx2.2 and cCre from the native Nkx2.2 locus at the same time. Mouse lines obtained from these ES cells allow the labeling of pancreatic epithelium cells that co-express high levels of Ngn3 and Nkx2.2 during mouse embryonic development. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Neurog3{Cre-ER.BAC} mouse ESC line A mouse ESC line containing a transgene in which Cre (transgene) is driven by the Neurog3 promoter (NCBI Gene ID: 11925). This line has a single copy of Neurog3.Cre-ER.LCA BAC transgene inserted in a genome. The transgene is designed to express Cre-ER under control of Neurog 3 promoter and will allow inducible tracking or gene inactivation in the Ngn3-LOW and Ngn3-HIGH populations of pre-endocrine cells. Additionally, the lox66 and lox2272 sites will allow the BAC transgene to serve as a loxed cassette acceptor (LCA) in ES cells for future recombinase-mediated cassette exchange (RMCE). Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Pdx1{CreMgn} mouse strain A mouse strain in which part or all of the targeted gene, pancreatic and duodenal homeobox 1 (NCBI Gene ID: 18609) is replaced to create Pdx1{Cre} using the Loxed Cassette Acceptor allele Pdx1{tm1(LCA)}). In this mouse strain, the first exon of Pdx1 is replaced with coding sequence for Cre recombinase using RMCE in the Pdx1{LCA} allele. Generation of Pdx-promoter driven Cre expressing mice will enable Cre-LoxP manipulation of pancreatic lineage cells. Pdx1{CreMgn} Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{228.TOP.CFPHri} mouse strain A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{228.TOP.CFP} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). In this mouse strain the Rosa26 gene sequence from -228 to +81 was replaced by a Wnt response element (7xTcf/Lef binding site) fused to a TATA-Cerulean (CFP) reporter. These mice may be useful in assessing Canonical Wnt responsiveness. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Rosa26{228.TOP.CFPHri} Vanderbilt University Medical Center Neurog3{RG.BAC} mouse ESC line A mouse ESC line containing a transgene in which RG (transgene) is driven by the Neurog3 promoter (NCBI Gene ID: 11925). This line has a single copy of Neurog3.RG.LCA BAC transgene inserted in the genome. The transgene is designed to express an H2B-mCherry fusion protein in the nucleus and a membrane anchored EGFP (via GPI), both under the control of the Neurog3 promoter. This will allow for live-cell imaging of mitotic nuclear/chromosome dynamics and membrane protrusive behavior in endocrine progenitors. Additionally, Lox71 and Lox2272 sites flanking the transgene will allow for manipulations by RMCE in the future. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{228.3TF.GFP-CreMgn} mouse strain A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create ROSA26{228.3TF.GFP-Cre} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse strain contains TetO-regulated genes inserted into the Rosa 26{LCA} allele by RMCE. TetO/miniCMV promoter is placed at -228 position upstream of putative ROSA26 transcription start site and drives the expression of a polycistronic mRNA with transcription factors MafA, Pdx1, and Ngn3 together with GFP-Cre fusion protein linked by 2A peptide cleavage sequences. These mice will be able to simultaneously over-express all three transcription factors and GFP-Cre upon administration of doxycyline when the effector protein rtTA is expressed. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Rosa26{228.3TF.GFP-CreMgn} Vanderbilt University Medical Center Ngn3{T2A.nCreGgu} mouse strain A mouse strain in which part or all of the targeted gene, Neurogenin 3 (NCBI Gene ID: 11925) is replaced to create Ngn3{T2A.nCre} using the Loxed Cassette Acceptor allele ). In this mouse line, one of the two bi-partite Cre molecules, nCre, was knocked in upstream of Ngn3 coding sequence by RMCE in Ngn3{HA.LCA} ES cell line. nCre sequence is expressed from policistronic mRNA linked by 2a peptide to Ngn3 coding sequence allowing for simultanious expression of both proteins from the Ngn3 promoter. This mouse line, in combination with Nkx2.2{cCre} mouse line, allows for the labeling of pancreatic epithelium cells that co-express high levels of Ngn3 and Nkx2.2 during mouse embryonic development. Ngn3{T2A.nCreGgu} Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Pdx1{H2B.Neptune} mouse ESC line A mouse ESC line in which part or all of the targeted gene, pancreatic and duodenal homeobox 1 (NCBI Gene ID: 18609) is replaced to create Pdx1{H2B.Neptune} using the Loxed Cassette Acceptor allele Pdx1{tm1(LCA)}). In this line, the first exon of Pdx1 is replaced with coding sequence for mNeptune (a far red fluorescent protein) using RMCE in the Pdx1 LCA allele. Generation of a Pdx-promoter driven mNeptune fluorescent allele will enable the isolation of pancreatic lineage cells by FACS and broaden the possibilities for combinatorial sorting with other fluorescent alleles. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Sst.rTTA.LCA mouse ESC line A mouse ESC line in which the targeted gene, Somatostatin (NCBI Gene ID: 20604), has been modified (allele type: Cassette Acceptor) to Sst.rTTA loxed cassette acceptor (MGI ID: Sst.rTTA{LCA}). This allelle is designed to express a tet-inducible reverse-transactivator under control of the somatostatin promoter. Lox66 and Lox2272 sites are inserted flanking 500bp of Sst promoter region, Sst exons I and II and Sst poly A site. The rTTA-beta-globin poly A cassete replaces Sst coding exons (I and II). The allele can be used to drive tet-inducible expression in somatostatin expressing cells (Delta-cells). Additionally, the Lox66 and Lox2272 sites allow for manipulations of the flanked region by RMCE in the future. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Foxa2{LCA} mouse ESC line A mouse ESC line in which the targeted gene, forkhead box A2 (NCBI Gene ID: 15376), has been modified (allele type: Cassette Acceptor) to Forkhead box A2 loxed cassette acceptor (MGI ID: Foxa2{LCA}). This ES cell line contains a loxed cassette acceptor (LCA) allele that may be utilized for the exchange of DNAs of interest into the Foxa2 locus by recombinase mediated cassette exchange (RMCE). This LCA uses a Lox66/71 and Lox2272 strategy for RMCE and allows for manipulation of a 4.7 kb region of the gene (contains a promoter and all exons: exon 1, 2 and 3). This leads to a variety of experiments that can be performed using a wide range of cassette designs. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse Ngn3 raised in chicken A polyclonal antibody raised in chicken that targets the mouse "Ngn3" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse Ngn3 raised in chicken A polyclonal antibody raised in chicken that targets the mouse "Ngn3" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse Nkx6.1 raised in chicken A polyclonal antibody raised in chicken that targets the mouse "Nkx6.1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse Nkx6.1 raised in chicken A polyclonal antibody raised in chicken that targets the mouse "Nkx6.1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse PDX1 raised in chicken A polyclonal antibody raised in chicken that targets the mouse "PDX1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse PDX1 raised in chicken A polyclonal antibody raised in chicken that targets the mouse "PDX1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse Prox1 raised in chicken A polyclonal antibody raised in chicken that targets the mouse "Prox1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse Prox1 raised in chicken A polyclonal antibody raised in chicken that targets the mouse "Prox1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Nkx2.2{T2A.cCreGgu} mouse strain A mouse strain in which part or all of the targeted gene, NK2 transcription factor related, locus 2 (NCBI Gene ID: 18088) is replaced to create Nkx2.2{T2A.cCre} using the Loxed Cassette Acceptor allele Nkx2.2{tm1(LCA)}). In this line, one of the two bi-partite Cre molecules, cCre, is placed downstream of Nkx2.2 coding sequence fused with 2a peptide using RMCE in the Nkx2.2[LCA] allele. The presence of the T2A sequence allows for transcription of Nkx2.2 and cCre from the native Nkx2.2 locus at the same time. This mouse line allows the labeling of pancreatic epithelium cells that co-express high levels of Ngn3 and Nkx2.2 during mouse embryonic development. Nkx2.2{T2A.cCreGgu} Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{mIre1.N906A.CherryMgn} mouse strain A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26.mIre1.N906A.Cherry using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse contains bidirectional TetO-regulated genes inserted into the Rosa26.LCA allele by RMCE. In one direction the TetO/CMV promoter drives the expression of point mutant (N906A) of IRE1, an ER transmembrane kinase response to unfolded protein response (UPR). In the other direction it drives the expression of red fluorescent protein mCherry. This mouse can be used to simultaneously over-express Ire1 (N906A) and mCherry upon administration of doxycyline when the effector protein rtTA is expressed. This line can be used to study the roles of IRE1 in the response to ER stress, diet induced obesity and insulin resistance. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Rosa26{mIre1.N906A.CherryMgn} Vanderbilt University Medical Center Sst{rTTA.LCA.Mgn} mouse strain A mouse strain in which the targeted gene, Somatostatin (NCBI Gene ID: 20604), has been modified (allele type: Gene Replacement) to (MGI ID: Sst{rTTA.LCA}). TheSst.rTTA.LCA mice are designed to express a tet-inducible reverse-transactivator under control of somatostatin promoter. Lox66 and Lox2272 sites are inserted flanking 500bp of Sst promoter region, Sst exons I and II and Sst poly A site. The rTTA-beta-globin poly A cassete is put in place of Sst coding exons (I and II). The mice can be used to drive tet-inducible expression in somatostatin expressing cells (Delta-cells). Additionally, the Lox66 and Lox2272 sites allow for manipulations of the flanked region by RMCE in the future. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Sst{rTTA.LCA.Mgn} Vanderbilt University Medical Center Monoclonal human ghrelin raised in mouse A monoclonal antibody raised in mouse that targets the human "ghrelin" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Gallbladder mucosal epithelium raised in mouse A monoclonal antibody raised in mouse that targets the human "Gallbladder mucosal epithelium" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Gallbladder mucosal epithelium raised in mouse A monoclonal antibody raised in mouse that targets the human "Gallbladder mucosal epithelium" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Gallbladder mucosal epithelium raised in mouse A monoclonal antibody raised in mouse that targets the human "Gallbladder mucosal epithelium" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Gallbladder mucosal epithelium raised in mouse A monoclonal antibody raised in mouse that targets the human "Gallbladder mucosal epithelium" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Alpha cells raised in mouse A monoclonal antibody raised in mouse that targets the human "Alpha cells" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Pancreatic duct cells raised in mouse A monoclonal antibody raised in mouse that targets the human "Pancreatic duct cells" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center NOD.Cg-Prkdc{scid} Il2rg{tm1Wjl} Tg(HLA-A/H2-D/B2M)1Dvs/SzJ mouse strain A mouse strain that is immunodeficient and express human HLA class 1 heavy and light chains. This strain may be useful as a human hematopoietic engraftment host that supports the maturation of human T cells with transplantation http://jaxmice.jax.org/strain/014570.html. NOD.Cg-Prkdc{scid} Il2rg{tm1Wjl} Tg(HLA-A/H2-D/B2M)1Dvs/SzJ Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center NOD.Cg-Prkdc{scid} Il2rg{tm1Wjl} H2-Ab1{tm1Gru} Tg(HLA-DRB1)31Dmz/SzJ mouse strain A mouse strain that lacks expression of the murine Prkdc gene, the X-linked Il2rg gene, and MHC class II, but express the human leukocyte antigen DR4 gene. These mice may be useful for targeting human CD4{+} T cells in transplantation studies in the absence of xeno-GVHD.More details are available at http://jaxmice.jax.org/strain/017637.html. NOD.Cg-Prkdc{scid} Il2rg{tm1Wjl} H2-Ab1{tm1Gru} Tg(HLA-DRB1)31Dmz/SzJ Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center entity 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 entity An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) Entity 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 Julius Caesar Verdi’s Requiem the Second World War your body mass index An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) per discussion with Barry Smith 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 continuant (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] 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]) Continuant continuant (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] 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 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] 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]) 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 (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [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]) 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]) (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] occurrent Occurrent (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] occurrent (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] An entity that has temporal parts and that happens, unfolds or develops through time. 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]) 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. Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) 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. b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) per discussion with Barry Smith 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. (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] 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]) independent continuant (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] (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. 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]) a chair a heart a molecule an orchestra. an organism 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]) ic IndependentContinuant a leg a spatial region an atom the bottom right portion of a human torso the interior of your mouth (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] 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]) 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]) (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] 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]) (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] obsolete dependent continuant true A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities. spatial region (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) s-region SpatialRegion A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) BFO 2 Reference: Spatial regions do not participate in processes. Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) per discussion with Barry Smith Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] temporal region (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] t-region (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] 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]) TemporalRegion Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) 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 All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) 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]) Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [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 doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional per discussion with Barry Smith (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] two-dimensional spatial region 2d-s-region (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] TwoDimensionalSpatialRegion A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) an infinitely thin plane in space. the surface of a sphere-shaped part of space A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] spatiotemporal region (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] SpatiotemporalRegion st-region (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) Every spatiotemporal region occupies_spatiotemporal_region itself. Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) the spatiotemporal region occupied by a human life the spatiotemporal region occupied by a process of cellular meiosis. the spatiotemporal region occupied by the development of a cancer tumor (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) process An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. 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) a process of cell-division, \ a beating of the heart process Process (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] a process of meiosis a process of sleeping 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]) the course of a disease the flight of a bird the life of an organism your process of aging. (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] 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]) disposition disposition (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] Disposition (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. 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]) an atom of element X has the disposition to decay to an atom of element Y 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]) 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 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]) 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]) (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] realizable entity (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] RealizableEntity realizable 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. All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) 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]) 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 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] zero-dimensional spatial region ZeroDimensionalSpatialRegion (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] 0d-s-region A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] quality (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 (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] 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]) quality 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]) 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 (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [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]) 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]) (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] specifically dependent continuant (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] sdc (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] 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. 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 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. SpecificallyDependentContinuant 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]) 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 (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] 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]) (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] per discussion with Barry Smith 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. 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]) role role (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] 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. 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. Role 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]) 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 (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] 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]) fiat object (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions FiatObjectPart b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) fiat-object or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29 the FMA:regional parts of an intact human body. the Western hemisphere of the Earth the division of the brain into regions the division of the planet into hemispheres the dorsal and ventral surfaces of the body the upper and lower lobes of the left lung (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) one-dimensional spatial region (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] OneDimensionalSpatialRegion 1d-s-region A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) an edge of a cube-shaped portion of space. (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) object aggregate object-aggregate 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. (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] ObjectAggregate 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). 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) 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]) 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 An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] three-dimensional spatial region (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] 3d-s-region ThreeDimensionalSpatialRegion A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) a cube-shaped region of space a sphere-shaped region of space, A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] site Site (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] 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 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]) site Manhattan Canyon) 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) (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] 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]) object 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: ‘objects’ are sometimes referred to as ‘grains’ [74 Object object 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: an object is a maximal causally unified material entity atom 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]) cell cells and organisms engineered artifacts grain of sand molecule organelle organism planet solid portions of matter star 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]) generically dependent continuant gdc GenericallyDependentContinuant (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] 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. 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. 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]) 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. b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] function function (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] 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]) 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. 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 (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] 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]) process boundary ProcessBoundary p-boundary (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) the boundary between the 2nd and 3rd year of your life. (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] one-dimensional temporal region (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] 1d-t-region A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) 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). OneDimensionalTemporalRegion the temporal region during which a process occurs. (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) material entity material (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] MaterialEntity (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] 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]) 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. Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) 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 every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) the undetached arm of a human being 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]) (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] Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) continuant fiat boundary (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions. Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. ContinuantFiatBoundary Every continuant fiat boundary is located at some spatial region at every time at which it exists cf-boundary BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29 b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. immaterial 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 one-dimensional continuant fiat boundary OneDimensionalContinuantFiatBoundary (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] 1d-cf-boundary The Equator a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) all geopolitical boundaries all lines of latitude and longitude the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin. the median sulcus of your tongue (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) process profile (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] ProcessProfile 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. process-profile (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] 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 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]) 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] 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]) relational quality (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] 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. RelationalQuality a marriage bond, an instance of love, an obligation between one person and another. b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) r-quality (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) two-dimensional continuant fiat boundary 2d-cf-boundary TwoDimensionalContinuantFiatBoundary (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] zero-dimensional continuant fiat boundary (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] 0d-cf-boundary ZeroDimensionalContinuantFiatBoundary a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) the geographic North Pole the point of origin of some spatial coordinate system. the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] requested by Melanie Courtot zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. zero-dimensional temporal region 0d-t-region (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) ZeroDimensionalTemporalRegion a temporal region that is occupied by a process boundary right now temporal instant. the moment at which a child is born the moment at which a finger is detached in an industrial accident the moment of death. A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] history 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 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]) insulinoma cell A cell of a usually benign tumor of the insulin-secreting cells of the pancreas. lymphoblastoid cell line Human cell line from tissue infected with Epstein-Barr virus, resembling a lymphoblast. embryonic stem cell line pancreatic ductal adenocarcinoma cell CCE cell CCE is a mouse embryonic stem cell line derived from 129/Sv mouse strain and has been provided for research use only. gross anatomical part Anatomical structure that is part of a multicellular organism and is at the gross anatomical level, e.g. above the level of a cell. Included are portions of organism substances such as blood, multi-cell-part structures such as axon tracts, acellular anatomical structures such as hair, and organism subdivisions such as head. Excluded is the whole organism and more granular parts of the organism, such as atoms, molecules, macromolecular complexes and cells. gross anatomical part biotin An organic heterobicyclic compound that consists of 2-oxohexahydro-1H-thieno[3,4-d]imidazole having a valeric acid substituent attached to the tetrahydrothiophene ring. The parent of the class of biotins. biotin polynucleotide A nucleobase-containing molecular entity with a polymeric structure comprised of a linear sequence of 13 or more nucleotide residues. polynucleotide 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 deoxyribonucleic acid High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms. deoxyribonucleic acid hydrogensulfite A sulfur oxoanion that has formula HO3S. hydrogensulfite polysaccharide A biomacromolecule consisting of large numbers of monosaccharide residues linked glycosidically. This term is commonly used only for those containing more than ten monosaccharide residues. polysaccharide 2'-deoxyribonucleoside 2'-deoxyribonucleoside pyrimidine 2'-deoxyribonucleoside pyrimidine 2'-deoxyribonucleoside N-glycosyl compound A glycosyl compound arising formally from the elimination of water from a glycosidic hydroxy group and an H atom bound to a nitrogen atom, thus creating a C-N bond. N-glycosyl compound benzopyrrole benzopyrrole molecular entity Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. molecular entity deoxyribonucleoside deoxyribonucleoside chemical entity A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances. chemical entity organic heterocyclic compound A cyclic compound having as ring members atoms of carbon and at least of one other element. organic heterocyclic compound hydroxides Hydroxides are chemical compounds containing a hydroxy group or salts containing hydroxide (OH(-)). hydroxides indoles Any compound containing an indole skeleton. indoles ion A molecular entity having a net electric charge. ion agarose agarose molecule Any polyatomic entity that is an electrically neutral entity consisting of more than one atom. molecule organic heteromonocyclic compound organic heteromonocyclic compound oxide An oxide is a chemical compound of oxygen with other chemical elements. oxide oxygen molecular entity oxygen molecular entity pyrimidine nucleoside pyrimidine nucleoside sulfur molecular entity sulfur molecular entity oxolanes Any oxacycle having an oxolane (tetrahydrofuran) skeleton. oxolanes organic heterobicyclic compound organic heterobicyclic compound phosphorus atom A pnictogen that has formula P. phosphorus atom atom A chemical entity constituting the smallest component of an element having the chemical properties of the element. atom primary amide 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. primary amide organosulfur compound An organosulfur compound is a compound containing at least one carbon-sulfur bond. organosulfur compound polyatomic anion An anion consisting of more than one atom. polyatomic anion heteroorganic entity A heteroorganic entity is an organic molecular entity in which carbon atoms or organic groups are bonded directly to one or more heteroatoms. heteroorganic entity chalcogen molecular entity Any p-block molecular entity containing a chalcogen. chalcogen molecular entity main group element atom An atom belonging to one of the main groups (found in the s- and p- blocks) of the periodic table. main group element atom sulfur oxoacid derivative sulfur oxoacid derivative sulfur oxoanion sulfur oxoanion organosulfonic acid An organic derivative of sulfonic acid in which the sulfo group is linked directly to carbon. organosulfonic acid carboxylic acid 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. carboxylic acid main group molecular entity 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. main group molecular entity cyclic compound Any molecule that consists of a series of atoms joined together to form a ring. cyclic compound organic aromatic compound organic aromatic compound heteromonocyclic compound heteromonocyclic compound heteropolycyclic compound heteropolycyclic compound heterobicyclic compound A bicyclic compound in which at least one of the rings contains at least one skeletal heteroatom. heterobicyclic compound p-block molecular entity A p-block molecular entity is a molecular entity containing one or more atoms of a p-block element. p-block molecular entity biomacromolecule A macromolecule formed by a living organism. biomacromolecule 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 ribonucleic acid High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins. ribonucleic acid organic cyclic compound Any organic molecule that consists of atoms connected in the form of a ring. organic cyclic compound heteroarene A heterocyclic compound formally derived from an arene by replacement of one or more methine (-C=) and/or vinylene (-CH=CH-) groups by trivalent or divalent heteroatoms, respectively, in such a way as to maintain the continuous pi-electron system characteristic of aromatic systems and a number of out-of-plane pi-electrons corresponding to the Hueckel rule (4n+2). heteroarene nucleoside An N-glycosyl compound that has both a nucleobase, normally adenine, guanine, xanthine, thymine, cytosine or uracil, and either a ribose or deoxyribose as functional parents. nucleoside organonitrogen compound Any heteroorganic entity containing at least one carbon-nitrogen bond. organonitrogen compound oxoanion An oxoanion is an anion derived from an oxoacid by loss of hydron(s) bound to oxygen. oxoanion carbon oxoacid carbon oxoacid polyatomic entity Any molecular entity consisting of more than one atom. polyatomic entity polyatomic ion An ion consisting of more than one atom. polyatomic ion carbonyl compound 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 compound organochalcogen compound An organochalcogen compound is a compound containing at least one carbon-chalcogen bond. organochalcogen compound organooxygen compound An organochalcogen compound containing at least one carbon-oxygen bond. organooxygen compound heteroatomic molecular entity A molecular entity consisting of two or more chemical elements. heteroatomic molecular entity carboxamide 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. carboxamide cyanine dye Cyanine dyes are synthetic dyes with the general formula R2N[CH=CH]nCH=N(+)R2 <-> R2N(+)=CH[CH=CH]nNR2 (n is a small number) in which the nitrogen and part of the conjugated chain usually form part of a heterocyclic system, such as imidazole, pyridine, pyrrole, quinoline and thiazole. cyanine dye phosphorus-32 atom The radioactive isotope of phosphorus with relative atomic mass 31.973907 and half-life of 14.26 days. phosphorus-32 atom phosphorus-33 atom The radioactive isotope of phosphorus with relative atomic mass 32.971725, half-life of 25.34 days and nuclear spin (1)/2. phosphorus-33 atom Cy3 dye Cy3 dye Cy5 dye Cy5 dye organonitrogen heterocyclic compound Any organonitrogen compound containing a cyclic component with nitrogen and at least one other element as ring member atoms. organonitrogen heterocyclic compound oxacycle Any organic heterocyclic compound containing at least one ring oxygen atom. oxacycle organosulfur heterocyclic compound organosulfur heterocyclic compound organic heteropentacyclic compound organic heteropentacyclic compound organic heteropolycyclic compound organic heteropolycyclic compound azabicycloalkane azabicycloalkane thiabicycloalkane thiabicycloalkane diazines Any organic heterocyclic compound containing a benzene ring in which two of the C-H fragments have been replaced by isolobal nitrogens (the diazine parent structure). diazines double-stranded DNA double-stranded DNA 5-bromo-2'-deoxyuridine 5-bromo-2'-deoxyuridine A pyrimidine 2'-deoxyribonucleoside compound having 5-bromouracil as the nucleobase. organic molecular entity Any molecular entity that contains carbon. organic molecular entity nitrogen molecular entity nitrogen molecular entity biotins Compounds containing a biotin (5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid) skeleton. biotins Alexa Fluor 532 Alexa Fluor 532 An organosulfonic acid that has formula C34H33N3O11S2. Alexa Fluor 546 Alexa Fluor 546 An organic heteropentacyclic compound that has formula C44H46Cl3N4NaO14S3. heterocyclic compound A cyclic compound having as ring members atoms of at least two different elements. heterocyclic compound nucleobase-containing molecular entity Any compound that has a nucleobase as a part. nucleobase-containing molecular entity pyrimidine deoxyribonucleoside A deoxyribonucleoside containing a pyrimidine base. pyrimidine deoxyribonucleoside organic molecule Any molecule that consists of at least one carbon atom as part of the electrically neutral entity. organic molecule carbohydrates and carbohydrate derivatives Any organooxygen compound that is a polyhydroxy-aldehyde or -ketone, or a compound derived from one. Carbohydrates contain only carbon, hydrogen and oxygen and usually have an empirical formula Cm(H2O)n; carbohydrate derivatives may contain other elements by substitution or condensation. carbohydrates and carbohydrate derivatives cell line cell A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture immortal cell line cell A cell line cell that is expected to be capable of an unlimited number of divisions, and is thus able to support indefinite propagation in vitro as part of an immortal cell line. cell line A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture). immortal stem cell line cell a cell line that is derived from stem cell immortal neuron cell line cell a immortal electrically responsive cell line cell that is derived from neuron immortal animal cell line cell a immortal eukaryotic cell line that is derived from animal cell immortal hematopoietic cell line cell a immortal animal cell line that is derived from hematopoietic cell immortal neural cell line cell a immortal animal cell line that is derived from neural cell immortal somatic cell line cell a cell line that is derived from somatic cell immortal mouse embryo-derived cell line cell An immortal embryo-derived cell line cell that derives from mouse. 3T3-L1 cell Ainv15 cell BETA-TC-3 cell CGR8 cell Daudi cell H9 cell JURKAT cell K 562 cell Raji cell SW480 cell immortal cell line A cell line that is expected to be capable of indefinite propagation in an vitro culture. cell A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. CALOHA:TS-2035 FMA:68646 GO:0005623 KUPO:0000002 The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). VHOG:0001533 WBbt:0004017 XAO:0003012 cell primary cultured cell A cultured cell that is freshly isolated from a organismal source, or derives in culture from such a cell prior to the culture being passaged. BTO:0002290 Covers cells actively being cultured or stored in a quiescent state for future use. cell primary cell culture cell primary cell line cell unpassaged cultured cell native cell A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment). CARO:0000013 To accommodate unicellular organisms better, 'cell in vivo' has been re-labeled 'native cell' to better represent its intended meaning - that is, that it is a cell in the context of a multicellular organism or in a natural environment. 'Native' is intended to contrast with 'in vitro', which refers to cells or other biological entities that have been intentionally placed in a controlled, non-natural setting for the purpose of study or manipulation. (MAH 1.12.12). cell cell in vivo cultured cell A cell in vitro that is or has been maintained or propagated as part of a cell culture. Note that this class was re-labeled to 'cultured cell' instead of 'cell line cell', as it intent was clarified to cover any cultured cells of multicellular and unicellular organisms. This includes cells actively being cultured, or cells that have been cultured but are stored in a quiescent state for future use. In having been cultured, cells must establish homeostasis and often replicate in a foreign environment. Accomodation of this stress initiates a selection of cells fit for such challenges, wherein necessary adaptive biochemical and.or genetic changes can occur. These changes can set them apart from the in vivo cells from which they derive, and such changes will typically accumulate and change over increasing time in culture. cell female germ cell Female germ cell is a germ cell that supports female gamete production. MA:0000388 VHOG:0001530 cell ncithesaurus:Egg oocyte A female germ cell that has entered meiosis. BTO:0000964 CALOHA:TS-0711 FBbt:00004886 FMA:18644 WBbt:0006797 cell oogonium stem cell A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells. CALOHA:TS-2086 FMA:63368 cell hematopoietic stem cell A stem cell from which all cells of the lymphoid and myeloid lineages develop, including blood cells and cells of the immune system. Hematopoietic stem cells lack cell markers of effector cells (lin-negative). Lin-negative is defined by lacking one or more of the following cell surface markers: CD2, CD3 epsilon, CD4, CD5 ,CD8 alpha chain, CD11b, CD14, CD19, CD20, CD56, ly6G, ter119. BTO:0000725 CALOHA:TS-0448 FMA:70337 FMA:86475 HSC Markers differ between species, and two sets of markers have been described for mice. HSCs are reportedly CD34-positive, CD45-positive, CD48-negative, CD150-positive, CD133-positive, and CD244-negative. VHOG:0001485 blood forming stem cell cell colony forming unit hematopoietic hemopoietic stem cell erythroid progenitor cell A progenitor cell committed to the erythroid lineage. BFU-E BTO:0004911 CFU-E blast forming unit erythroid burst forming unit erythroid cell colony forming unit erythroid erythroid stem cell germ line cell A cell that is within the developmental lineage of gametes and is able to pass along its genetic material to offspring. Originally this term had some plant germ line cell children. cell monoblast A myeloid progenitor cell committed to the monocyte lineage. This cell is CD11b-positive, has basophilic cytoplasm, euchromatin, and the presence of a nucleolus. CALOHA:TS-1195 CFU-M FMA:83553 Morphology: mononuclear cell, diameter 12-20 _M, non-granular, N/C ratio 3/1 - 4/1; markers: CD11b (shared with many other myeloid cells); location: Adult: bone marrow; fetal: liver, Yolk Sac; role or process: hematopoiesis, monocyte development; lineage: hematopoietic, myeloid. cell colony forming unit macrophage colony forming unit monocyte monocyte stem cell multi fate stem cell A stem cell that can give rise to multiple lineages of cells. FMA:84789 cell multi-fate stem cell multifate stem cell multipotent cell multipotent stem cell common myeloid progenitor A progenitor cell committed to myeloid lineage, including the megakaryocyte and erythroid lineages. BTO:0004730 CFU-GEMM CFU-S CMP cell colony forming unit granulocyte, erythrocyte, macrophage, and megakaryocyte common myeloid precursor multipotential myeloid stem cell myeloid stem cell pluripotent stem cell (bone marrow) This cell type is intended to be compatible with any vertebrate common myeloid progenitor. For mammalian CMP known to be CD34-positive, please use the term 'common myeloid progenitor, CD34-positive' (CL_0001059). megakaryocyte-erythroid progenitor cell A progenitor cell committed to the megakaryocyte and erythroid lineages. CFU-EM CFU-MegE MEP MEPs are reportedly CD19-negative, CD34-negative, CD45RA-negative, CD110-positive, CD117-positive, and SCA1-negative and reportedly express the transcription factors GATA-1 and NF-E2. Meg/E progenitor cell colony forming unit erythroid megakaryocyte megakaryocyte/erythrocyte progenitor megakaryocyte/erythroid progenitor cell common lymphoid progenitor A oligopotent progenitor cell committed to the lymphoid lineage. CL:0000044 CLP CLP are CD7-positive, CD10-positive, CD19-negative, CD34-positive, CD45RA-positive, CD79a-negative, CD127-positive, AA4.1-positive, RAG-negative, Sca-1-low, sIgM-negative, sIgD-negative, TdT-negative, Vpre-B-negative, and pre-BCR-negative. Expression of transcription factors include E2A-positive, EBF-positive, Ikaros-negative, PU.1-negative, and Pax5-negative. ELP cell committed lymphopoietic stem cell common lymphocyte precursor common lymphocyte progenitor common lymphoid precursor early lymphocyte progenitor lymphoid stem cell lymphopoietic stem cell non-terminally differentiated cell A precursor cell with a limited number of potential fates. BTO:0000125 FMA:84782 blast cell cell define using PATO mulit-potent or oligopotent? myoblast A cell that is commited to differentiating into a muscle cell. Embryonic myoblasts develop from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes. Myoblasts also occur as transient populations of cells in muscles undergoing repair. BTO:0000222 CALOHA:TS-0650 FBbt:00005083 FMA:70335 VHOG:0001529 cell fibroblast A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped. BTO:0000452 CALOHA:TS-0362 FMA:63877 These cells may be vimentin-positive, fibronectin-positive, fsp1-positive, MMP-1-positive, collagen I-positive, collagen III-positive, and alpha-SMA-negative. VHOG:0001482 cell epithelial cell A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina. BTO:0000414 CALOHA:TS-2026 CARO:0000077 FBbt:00000124 FMA:66768 WBbt:0003672 cell epitheliocyte duct epithelial cell cell branched duct epithelial cell cell blood vessel endothelial cell An endothelial cell that lines the vasculature. cell cuboidal endothelial cell of vascular tree squamous epithelial cell CALOHA:TS-1249 cell blood cell A cell found predominately in the blood. FMA:62844 cell epithelial cell of pancreas An epithelial cell of the pancreas. BTO:0000028 cell pancreatic epithelial cell pancreas epithelial cell T cell A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex. BTO:0000782 CALOHA:TS-1001 CL:0000804 CL:0000812 FMA:62870 T lymphocyte T-cell T-lymphocyte VHOG:0001479 cell immature T cell mature T cell granulocyte A leukocyte with abundant granules in the cytoplasm. BTO:0000539 BTO:0001026 CALOHA:TS-0422 FMA:62854 cell granular leucocyte granular leukocyte polymorphonuclear leukocyte endothelial cell An endothelial cell comprises the outermost layer or lining of anatomical structures and can be squamous or cuboidal. In mammals, endothelial cell has vimentin filaments and is derived from the mesoderm. BTO:0001176 CALOHA:TS-0278 FMA:66772 From FMA: 9.07.2001: Endothelial cell has always been classified as a kind of epithelial cell, specifically a squamous cell but that is not true. First, endothelial cell can either be squamous or cuboidal (e.g. high-endothelial cell) and secondly, it has different embryological derivation (mesodermal) than a true epithelial cell (ectodermal and endodermal). The basis for present classification is the fact that it comprises the outermost layer or lining of anatomical structures (location-based) but a better structural basis for the differentia is the cytoskeleton of the cell. Endothelial cell has vimentin filaments while an epithelial cell has keratin filaments. [Onard]. cell endotheliocyte neurectodermal cell Ectoderm destined to be nervous tissue. cell neurectoderm cell mesenchymal stem cell A connective tissue cell that normally gives rise to other cells that are organized as three-dimensional masses. This cell type is CD73-positive, CD90-positive, CD105-positive, CD45-negative, CD34-negative, and MHCII-negative. They may further differentiate into osteoblasts, adipocytes, myocytes, neurons, or chondroblasts in vitro. Originally described as residing in the bone marrow, this cell type is now known to reside in many, if not all, adult organs. BMSC BTO:0002625 BTO:0003298 CFU-F CL:0002452 FMA:70546 MSC Many but not all mesenchymal cells derive from the mesoderm. MSCs are reportedly CD3-negative, CD4-negative, CD5-negative, CD8-negative, CD11a-negative, CD11b-negative, CD14-negative, CD19-negative, CD29-positive, CD31-negative, CD34-negative, CD38-negative, CD40-negative, CD44-positive, CD45-negative, CD49-positive, CD54-positive, CD66b-negative, CD79a-negative, CD80-negative, CD102-positive, CD106-positive, CD117-positive, CD121a-positive, CD121b-positive, CD123-positive, CD124-positive, CD133-negative, CD146-positive, CD166-positive, CD271-positive, B220-negative, Gr1-negative, MHCI-positive, MHCII-negative, SSEA4-negative, sca1-positive, Ter119-negative, and glycophorin A-negative. Cultured MSCs are capable of producing stem cell factor, IL7, IL8, IL11, TGF-beta, cofilin, galectin-1, laminin-receptor 1, cyclophilin A, and MMP-2. bone marrow stromal cells cell colony-forming unit-fibroblast marrow stromal cells mesenchymal precursor cell mesenchymal progenitor cells mesenchymal stem cell mesenchymal stromal cell mesenchymal stromal cells stem cells, mesenchymal fat cell A fat-storing cell found mostly in the abdominal cavity and subcutaneous tissue of mammals. Fat is usually stored in the form of triglycerides. BTO:0000443 CALOHA:TS-0012 CL:0000450 FMA:63880 adipocyte adipose cell cell pigment cell A pigment cell is a cell that contains pigment granules. VHOG:0001678 cell chromatocyte chromatophore melanocyte A pigment cell derived from the neural crest. Contains melanin-filled pigment granules, which gives a brown to black appearance. BTO:0000847 CALOHA:TS-0613 CL:0000572 FMA:70545 VHOG:0001679 cell melanophore glandular epithelial cell A specialized epithelial cell that is capable of synthesizing and secreting certain biomolecules. CALOHA:TS-2085 FMA:86494 cell secretory cell A cell that specializes in controlled release of one or more substances. BTO:0003659 FMA:86916 cell exocrine cell A cell of an exocrine gland; i.e. a gland that discharges its secretion via a duct. FMA:16014 cell protein secreting cell cell endocrine cell A cell of an endocrine gland, ductless glands that secrete substances which are released directly into the circulation and which influence metabolism and other body functions. FMA:83809 cell endocrinocyte enteroendocrine cell An endocrine cell that is located in the epithelium of the gastrointestinal tract or in the pancreas. BTO:0003865 FMA:62930 cell peptide hormone secreting cell cell insulin secreting cell BTO:0000783 cell type B pancreatic cell A cell that secretes insulin and is located towards the center of the islets of Langerhans. B-cell of pancreatic islet BTO:0000783 EV:0200009 FMA:70586 MA:0002419 Pancreatic beta cells are also reportedly CD284-positive. Upon activation, they upregulate their CD14 expression. beta cell beta cell islet beta cell of pancreatic islet cell insulin-secreting cell ncithesaurus:Beta_Cell pancreatic B cell pancreatic B-cell pancreatic beta cell pancreatic islet core type B enteroendocrine cell glucagon secreting cell A cell that secretes glucagon. FMA:84045 cell glucagon-secreting cell pancreatic A cell A type of enteocrine cell found in the periphery of the islets of Langerhans that secretes glucagon. BTO:0000990 FMA:70585 alpha cell of iselt of Langerhans cell pancreatic alpha cell somatostatin secreting cell cell pancreatic D cell A D cell located in the pancreas. Peripherally placed within the islets like type A cells; contains somatostatin. BTO:0000803 D-cell of pancreatic islet FMA:70587 cell delta cell of islet delta cell of pancreatic islet pancreatic D-cell pancreatic delta cell somatostatin-secreting pancreatic cell metabolising cell A cell whose primary function is intermediary metabolism. cell hepatocyte BTO:0000575 CALOHA:TS-0454 FMA:14515 Hepatocytes are reportedly MHC Class I-positive and MHC Class II-positive. The main structural component of the liver. They are specialized epithelial cells that are organized into interconnected plates called lobules. Majority of cell population of liver, polygonal in shape, arranged in plates or trabeculae between sinusoids; may have single nucleus or binucleated. cell contractile cell A cell whose primary function is to shorten. cell muscle cell A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns. BTO:0000888 BTO:0000902 CALOHA:TS-2032 FBbt:00005074 FMA:67328 WBbt:0003675 cell muscle fiber myocyte electrically active cell A cell whose function is determined by the generation or the reception of an electric signal. cell lining cell A cell within an epithelial cell sheet whose main function is to act as an internal or external covering for a tissue or an organism. boundary cell cell barrier cell A cell whose primary function is to prevent the transport of stuff across compartments. cell motile cell A cell that moves by its own activities. cell ectodermal cell A cell of the outer of the three germ layers of the embryo. FMA:72549 cell ectoderm cell mesodermal cell A cell of the middle germ layer of the embryo. FMA:72554 cell mesoblast mesoderm cell endodermal cell A cell of the inner of the three germ layers of the embryo. FMA:72555 cell endoderm cell anucleate cell A cell that lacks a nucleus. FMA:68647 cell non-nucleated cell single nucleate cell A cell with a single nucleus. cell erythrocyte A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen. BTO:0000424 CALOHA:TS-0290 FMA:81100 RBC cell red blood cell platelet A non-nucleated disk-shaped cell formed by extrusion from megakaryocytes, found in the blood of all mammals, and mainly involved in blood coagulation. BTO:0000132 CALOHA:TS-0803 FMA:62851 Platelets are reportedly CCR1-positive, CCR2-negative, CCR3-positive, CCR4-positive, CCR5-negative, CCR6-negative, CCR7-negative, CCR8-negative, CCR9-negative, CCR10-negative, CD16-positive, CD23-positive, CD32-positive, CD40-positive, CD41-positive CD42-positive, CD61-positive, CD62P-positive, CD64-positive, CD89-positive, CD102-positive, CD147-positive (activated platelets), CD154-positive (activated platelets), CD162-positive, CD209, CD282-positive, CD284-positive, CD289-positive, CD181-negative, CD182-negative, CD183-negative, CD184-positive, CLEC2-positive, GPVI-positive, JAMC-positive, PAR1-positive, PAR2-negative, PAR3-positive, PAR4-positive, TSP1-positive, and TXA2R-positive. Platelets can reportedly produce CCL2, CCL3, CCL5, CCL7, CCL17, CD40L, CXCL1, CXCL4, CXCL4L1, CXCL5, CXCL7, CXCL8, CXCL12, EGF, factor V, factor VII, factor XI, factor XIII, bFGF, histamine, IGF-1, IL-1beta, PAI-1, PDGF, plasminogen, protein S, serotonin, TGF-beta, TFPI, VEGF, and vWF. anucleate thrombocyte blood platelet cell enucleate thrombocyte B cell A lymphocyte of B lineage with the phenotype CD19-positive, CD20-positive, and capable of B cell mediated immunity. B lymphocyte B-cell B-lymphocyte BTO:0000776 CALOHA:TS-0068 FMA:62869 VHOG:0001480 cell eukaryotic cell cell stuff accumulating cell A cell that is specialised to accumulate a particular substance(s). cell oxygen accumulating cell cell migratory neural crest cell A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body. FMA:86667 cell electrically responsive cell A cell whose function is determined by its response to an electric signal. cell polyploid cell A cell whose nucleus, or nuclei, each contain more than two haploid genomes. cell endopolyploid cell cell white fat cell CALOHA:TS-1119 FMA:83434 Fat cells with light coloration and few mitochondria. They contain a scant ring of cytoplasm surrounding a single large lipid droplet or vacuole. cell white adipocyte white adipose cell white fat cell dendritic cell A cell of hematopoietic origin, typically resident in particular tissues, specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation. These cells are lineage negative (CD3-negative, CD19-negative, CD34-negative, and CD56-negative). BTO:0002042 CALOHA:TS-0194 FMA:83036 cell interdigitating cell veiled cell biogenic amine secreting cell cell serotonin secreting cell 5-HT secreting cell 5-Hydroxytryptamine secreting cell A cell type that secretes 5-Hydroxytryptamine (serotonin). cell type D enteroendocrine cell A cell found throughout the gastrointestinal tract and in the pancreas. They secrete somatostatin in both an endocrine and paracrine manner. Somatostatin inhibits gastrin, cholecystokinin, insulin, glucagon, pancreatic enzymes, and gastric hydrochloric acid. A variety of substances which inhibit gastric acid secretion (vasoactive intestinal peptide, calcitonin gene-related peptide, cholecystokinin, beta-adrenergic agonists, and gastric inhibitory peptide) are thought to act by releasing somatostatin. D cell FMA:62935 cell cardiac muscle myoblast A precursor cell destined to differentiate into cardiac muscle cell. CL:0000714 FMA:84797 cell melanoblast A cell that originates from the neural crest and differentiates into a pigment cell. BTO:0003217 Derived from UBERON:0002342 neural crest. FMA:83377 cell lymphocyte A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin. BTO:0000775 CALOHA:TS-0583 Editors note: consider adding taxon constraint to vertebrata (PMID:18025161) FMA:62863 VHOG:0001535 cell proerythroblast An immature, nucleated erythrocyte occupying the stage of erythropoeisis that follows formation of erythroid progenitor cells. This cell is CD71-positive, has both a nucleus and a nucleolus, and lacks hematopoeitic lineage markers. FMA:83518 cell pronormoblast rubriblast animal cell cell basophilic erythroblast A nucleated immature erythrocyte, having cytoplasm generally similar to that of the earlier proerythroblast but sometimes even more basophilic, and usually regular in outline. The nucleus is still relatively large, but the chromatin strands are thicker and more deeply staining, giving a coarser appearance; the nucleoli have disappeared. This cell is CD71-positive and lacks hematopoeitic lineage markers. FMA:83505 basophilic normoblast cell early erythroblast early normoblast prorubricyte polychromatophilic erythroblast A nucleated, immature erythrocyte in which the nucleus occupies a relatively smaller part of the cell than in its precursor, the basophilic erythroblast. The cytoplasm is beginning to acquire hemoglobin and thus is no longer a purely basophilic, but takes on acidophilic aspects, which becomes progressively more marked as the cell matures. The chromatin of the nucleus is arranged in coarse, deeply staining clumps. This cell is CD71-positive and lacks hematopoeitic lineage markers. FMA:83506 cell intermediate erythroblast intermediate normoblast polychromatic erythroblast polychromatic normoblast polychromatophilic normoblast rubricyte orthochromatic erythroblast FMA:84646 The final stage of the nucleated, immature erythrocyte, before nuclear loss. Typically the cytoplasm is described as acidophilic, but it still shows a faint polychromatic tint. The nucleus is small and initially may still have coarse, clumped chromatin, as in its precursor, the polychromatophilic erythroblast, but ultimately it becomes pyknotic, and appears as a deeply staining, blue-black, homogeneous structureless mass. The nucleus is often eccentric and sometimes lobulated. acidophilic erythroblast cell eosinophilic erythroblast late erythoblast orthochromatic normoblast pyknotic eto enrythroblast megakaryocyte progenitor cell BTO:0001164 CALOHA:TS-0610 CFU-Meg FMA:84235 Lineage negative is described here as CD2-negative, CD3-negative, CD4-negative, CD5-negative, CD8a-negative, CD14-negative, CD19-negative, CD20-negative, CD56-negative, Ly6g-negative, and Ter119-negative. Meg-CFC MkP The earliest cytologically identifiable precursor in the thrombocytic series. This cell is capable of endomitosis and lacks expression of hematopoieitic lineage markers (lin-negative). cell colony-forming unit-megakaryocyte megacaryoblast megacaryocyte progenitor cell megakaryoblast megakaryocytic progenitor cell promegacaryocyte promegakaryocyte megakaryocyte A giant cell 50 to 100 micron in diameter, with a greatly lobulated nucleus, found in the bone marrow; mature blood platelets are released from its cytoplasm. BTO:0000843 CALOHA:TS-0611 FMA:83555 Megakaryocytes are reportedly CD181-positive and CD182-positive. cell megacaryocyte megalocaryocyte megalokaryocyte granulocyte monocyte progenitor cell A hematopoietic progenitor cell that is committed to the granulocyte and monocyte lineages. These cells are CD123-positive, and do not express Gata1 or Gata2 but do express C/EBPa, and Pu.1. CFU-C , Colony forming unit in culture CFU-GM GMP Originally described in the dendritic cell ontology (DC_CL:0000042)(PMID:19243617). GMPs are reportedly CD16-positive, CD32-positive, CD34-positive, CD38-positive, CD45RA-positive, CD110-negative, CD117-positive, CD123-positive, and SCA1-negative. cell colony forming unit granulocyte macrophage granulocyte-macrophage progenitor granulocyte/monocyte precursor granulocyte/monocyte progenitor reticulocyte An immature erythrocyte that changes the protein composition of its plasma membrane by exosome formation and extrusion. The types of protein removed differ between species though removal of the transferrin receptor is apparent in mammals and birds. BTO:0001173 CALOHA:TS-0864 cell promonocyte A precursor in the monocytic series, being a cell intermediate in development between the monoblast and monocyte. This cell is CD11b-positive and has fine azurophil granules. BTO:0004657 FMA:83551 Morphology: Mononuclear cell, diameter 14-18 _M, fine azurophilic granules; markers: CD11b (shared with many other myeloid cells); location: Adult: bone marrow; Fetal: Liver, Yolk Sac; role or process: hematopoiesis, monocyte development; lineage: hematopoietic, myeloid. cell angioblastic mesenchymal cell A mesenchymal stem cell capable of developing into blood vessel endothelium. These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive. angioblast cell chondroplast monocyte BTO:0000876 CALOHA:TS-0638 FMA:62864 Morphology: Mononuclear cell, diameter, 14 to 20 _M, N/C ratio 2:1-1:1. Nucleus may appear in variety of shapes: round, kidney, lobulated, or convoluted. Fine azurophilic granules present; markers: CD11b (shared with other myeloid cells), human: CD14, mouse: F4/80-mid,GR1-low; location: Blood, but can be recruited into tissues; role or process: immune & tissue remodelling; lineage: hematopoietic, myeloid. Myeloid mononuclear recirculating leukocyte that can act as a precursor of tissue macrophages, osteoclasts and some populations of tissue dendritic cells. 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. This class has been re-labeled to imply reference only to in vitro experimentally modified cells, similarly, the definition has been slightly updated to reflect this. 'experimentally modified cell' refers only to cells in vitro, and not modified in vivo/in environment cells. There is currently no class representing unmodified in vitro cells (other than the parent 'cell in vitro'), or a class representing modified native cells. More granular subclassing of experimentally modified cell can be found in ReO. MHB 1.12.12 cell germ cell BTO:0000535 The reproductive cell in multicellular organisms. VHOG:0001534 WBbt:0006796 cell acinar cell A secretory cell that is grouped together with other cells of the same type to form grape shaped clusters known as acini (singular acinus). FMA:83625 acinic cell acinous cell cell natural killer cell A lymphocyte that can spontaneously kill a variety of target cells without prior antigenic activation via germline encoded activation receptors and also regulate immune responses via cytokine release and direct contact with other cells. BTO:0000914 BTO:0004716 CALOHA:TS-0664 FMA:63147 FMA:83601 NK cell VHOG:0001697 cell large granular lymphocyte null cell muscle precursor cell cell PP cell A cell that stores and secretes pancreatic polypeptide hormone. FMA:62938 FMA:83409 cell type F enteroendocrine cell somatic stem cell A stem cell that can give rise to cell types of the body other than those of the germ-line. CALOHA:TS-2086 FMA:63368 cell striated muscle cell BTO:0002916 CALOHA:TS-2157 FMA:86936 Muscle cell which has as its direct parts myofilaments organized into sarcomeres. cell leukocyte An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue. BTO:0000751 CALOHA:TS-0549 FMA:62852 cell immune cell leucocyte white blood cell cardiac muscle cell BTO:0001539 CALOHA:TS-0115 Cardiac muscle cells are striated muscle cells that are responsible for heart contraction. In mammals, the contractile fiber resembles those of skeletal muscle but are only one third as large in diameter, are richer in sarcoplasm, and contain centrally located instead of peripheral nuclei. FMA:14067 FMA:83808 This class encompasses the muscle cells responsible for heart* contraction in both vertebrates and arthropods. The ultrastucture of a wide range of arthropod heart cells has been examined including spiders, horseshoe crabs, crustaceans (see Sherman, 1973 and refs therein) and insects (see Lehmacher et al (2012) and refs therein). According to these refs, the cells participating in heart contraction in all cases are transversely striated. Insects hearts additionally contain ostial cells, also transversely striated muscle cells, but which do not participate in heart contraction. cardiac muscle fiber cardiac myocyte cardiocyte cardiomyocyte cell heart muscle cell myeloid cell A cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage. BTO:0001441 CALOHA:TS-0647 cell erythroid lineage cell A immature or mature cell in the lineage leading to and including erythrocytes. CALOHA:TS-0290 CL:0002156 FMA:62845 FMA:83516 Note that in FMA erythropoietic cells are types of nucleated erythrocytes and thus don't include erythrocytes. cell erythropoietic cell erythroblast A nucleated precursor of an erythrocyte that lacks hematopoietic lineage markers. BTO:0001571 CALOHA:TS-0289 FMA:83504 cell normoblast myeloid leukocyte A cell of the monocyte, granulocyte, or mast cell lineage. cell basophil Any of the immature or mature forms of a granular leukocyte that in its mature form has an irregularly shaped, pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm that contains coarse, bluish-black granules of variable size. Basophils contain vasoactive amines such as histamine and serotonin, which are released on appropriate stimulation. A basophil is CD123-positive, CD193-positive, CD203c-positive, and FceRIa-positive. BTO:0000129 CALOHA:TS-0073 FMA:62862 Matures in the bone marrow and account for <1% of leukocytes in the peripheral blood, spleen, and bone marrow. Basophils are described as being CD11a-positive, CD11b-positive, CD13-positive, CD15-positive, CD18-positive, CD21-positive, CD25-positive, CD29-positive, CD35-positive, CD40-positive, CD40L-positive, CD44-positive, CD45R-negative, CD46-positive, CD49a-positive, CD49b-positive, CD49d-positive, CD55-positive, CD59-positive, CD62L-positive, CD63-positive, CD69-positive, CD90-negative, CD116-positive, CD117-negative, CD124-positive, CD125-positive, CD131-positive, CD161-positive, CD184-positive, CD191-positive, CD192-positive, CD197-positive, CD200R3-positive, CD218-positive, CD282-positive, CD284-positive, CD289-positive, CD290-positive, CD294-positive, natural killer cell receptor 2B4-positive, smad1-positive, CD3-negative, CD4-negative, CD7-negative, CD8-negative, CD14-negative, CD15-negative, CD16-negative, CD19-negative, CD20-negative, CD34-negative, CD36-negative, CD45R-negative, CD56-negative, CD57-negative, CD235a-negative, and GR1-negative. Transcription factors- GATA1-positive, PU.1-positive. basophilic leucocyte basophilic leukocyte cell polymorphonuclear leucocyte polymorphonuclear leukocyte eosinophil Any of the immature or mature forms of a granular leukocyte with a nucleus that usually has two lobes connected by one or more slender threads of chromatin, and cytoplasm containing coarse, round granules that are uniform in size and which can be stained by the dye eosin. Eosinophils are CD9-positive, CD191-positive, and CD193-positive. BTO:0000399 CALOHA:TS-0279 Eosinophils are also CD14-negative, CD32-positive, CD44-positive, CD48-positive, CD69-positive, CD192-negative, MBP1-positive, MBP2-positive, TLR2-negative, TLR4-negative, and lineage-negative (B220, CD2, CD14, CD19, CD56, CD71, CD117, CD123, CD235a (glycophorin A), and TER119). The cytokines IL-3, IL-5, and GM-CSF are involved in their development and differentiation. Usually considered CD16-negative, CD16 is observed on eosinophilic metamyelocyte. FMA:62861 cell eosinocyte eosinophilic granulocyte eosinophilic leucocyte eosinophilic leukocyte polymorphonuclear leucocyte polymorphonuclear leukocyte neutrophil Any of the immature or mature forms of a granular leukocyte that in its mature form has a nucleus with three to five lobes connected by slender threads of chromatin, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes. BTO:0000130 CALOHA:TS-0688 FMA:62860 PMN cell neutrocyte neutrophil leucocyte neutrophil leukocyte neutrophilic leucocyte neutrophilic leukocyte poly polymorphonuclear leucocyte polymorphonuclear leukocyte polymorphonuclear neutrophil polynuclear neutrophilic leucocyte polynuclear neutrophilic leukocyte pro-NK cell A lymphoid progenitor cell that is committed to the natural killer cell lineage, expressing CD122 (IL-15) receptor, but lacking many of the phenotypic characteristics of later stages of natural killer cell development such as expression of NK activating and inhibitory molecules. In human this cell has the phenotype CD34-positive, CD45RA-positive, CD10-positive, CD117-negative, and CD161 negative. Most markers only described for human pro NK cells. NKP cell natural killer cell progenitor null cell preNK cell pro-natural killer cell pro-B cell A progenitor cell of the B cell lineage, with some lineage specific activity such as early stages of recombination of B cell receptor genes, but not yet fully committed to the B cell lineage until the expression of PAX5 occurs. BTO:0003104 Human pro-B cells are reportedly CD10-positive, CD22-positive, CD34-positive, CD38-positive, CD45-low, CD48-positive, CD79a-positive, CD127-positive, CD184-positive, RAG-positive, TdT-positive, Vpre-B-positive, pre-BCR-negative, IgD-negative, and IgM-negative. Transcription factors expressed: Pax5-positive, EBF-positive, E2A-negative, Ikaros-negative, and PU.1-negative. cell pre-B cell (Philadelphia nomenclature) pre-pro B cell pro-B lymphocyte pro-B-cell pro-B-lymphocyte progenitor B cell progenitor B lymphocyte progenitor B-cell progenitor B-lymphocyte pro-T cell A lymphoid progenitor cell of the T cell lineage, with some lineage specific marker expression, but not yet fully committed to the T cell lineage. DN1 cell DN1 thymocyte TN1 cell cell pro-T lymphocyte progenitor T cell myeloblast BTO:0000187 FMA:83524 The most primitive precursor in the granulocytic series, having fine, evenly distributed chromatin, several nucleoli, a high nuclear-to-cytoplasmic ration (5:1-7:1), and a nongranular basophilic cytoplasm. They reside in the bone marrow. cell promyelocyte A precursor in the granulocytic series, being a cell intermediate in development between a myeloblast and myelocyte, that has distinct nucleoli, a nuclear-to-cytoplasmic ratio of 5:1 to 3:1, and containing a few primary cytoplasmic granules. Markers for this cell are fucosyltransferase FUT4-positive, CD33-positive, integrin alpha-M-negative, low affinity immunoglobulin gamma Fc region receptor III-negative, and CD24-negative. CALOHA:TS-0825 FMA:83530 cell hematopoietic multipotent progenitor cell A hematopoietic multipotent progenitor cell is multipotent, but not capable of long-term self-renewal. These cells are characterized as lacking lineage cell surface markers and being CD34-positive in both mice and humans. BTO:0000725 CALOHA:TS-0448 MPP Markers differ between mouse and human. cell hemopoietic progenitor cell lymphoid lineage restricted progenitor cell A progenitor cell restricted to the lymphoid lineage. BTO:0004731 CALOHA:TS-2025 FMA:70338 Note that this is a class of cell types, not an identified single cell type. cell lymphoid progenitor cell myeloid lineage restricted progenitor cell A progenitor cell restricted to the myeloid lineage. BTO:0004730 CALOHA:TS-2099 FMA:70339 Note that this is a class of cell types, not an identified single cell type. cell myeloid progenitor cell mononuclear cell A leukocyte with a single non-segmented nucleus in the mature form. BTO:0000878 CALOHA:TS-0768 FMA:86713 cell peripheral blood mononuclear cell lymphocyte of B lineage A lymphocyte of B lineage is a lymphocyte that expresses CD19 on the cell surface. An additional defining characteristic is the commitment to express an immunoglobulin complex. Types of B lineage lymphocytes include B cells and antibody secreting cells (plasmablasts and plasma cells). Lymphocytes of B cell lineage can be distinguished from those of T cell lineage by their lack of CD3e (as part of the T cell receptor complex). cell hematopoietic cell A cell of a hematopoietic lineage. BTO:0000574 CALOHA:TS-2017 FMA:70366 FMA:83598 cell haematopoietic cell haemopoietic cell hemopoietic cell CD34-positive, CD38-positive common myeloid progenitor OR CD34-positive, CD38-positive common lymphoid progenitor CD71-positive common myeloid precursor OR CD7-negative lymphoid precursor OR CD7-positive lymphoid Originally described in the dendritic cell ontology (DC_CL:1100000)(PMID:19243617). cell CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor Originally described in the dendritic cell ontology (DC_CL:1110000)(PMID:19243617). cell CD34-positive, CD38-positive common lymphoid progenitor A common lymphoid progenitor that is CD10-positive, CD45RA-positive, CD34-positive and CD38-positive. CD10-positive common lymphocyte precursor CD10-positive common lymphocyte progenitor CD10-positive common lymphoid precursor These markers are associated with human common lymphoid progenitors. Originally described in the dendritic cell ontology (DC_CL:0000032)(PMID:19243617). cell CD34-positive, CD38-negative hematopoietic stem cell CALOHA:TS-0448 CD133-positive hematopoietic stem cell CD133-positive hematopoietic stem cell is a hematopoietic stem cell that is CD34-positive, CD90-positive, and CD133-positive. Cell markers are associated with human hematopoietic stem cells. Originally described in the dendritic cell ontology (DC_CL:0000035)(PMID:19243617). FMA:86475 cell CD34-positive, CD38-positive common myeloid progenitor A common myeloid progenitor that is CD34-positive, CD38-positive, IL3ra-low, CD10-negative, CD7-negative, CD45RA-negative, and IL-5Ralpha-negative. CD71-positive common myeloid precursor Markers are associated with human cell type. Originally described in the dendritic cell ontology (DC_CL:0000038)(PMID:19243617). cell CD7-negative lymphoid progenitor cell CD7-negative lymphoid precursor CD7-negative lymphoid progenitor cell is a lymphoid progenitor cell that is CD34-positive, CD7-negative and CD45RA-negative. These markers are associated with human cells. Originally described in the dendritic cell ontology (DC_CL:0000039)(PMID:19243617). cell cell in vitro 'In vitro', translating literally to 'in glass', typically refers to a controlled, often sterile, laboratory setting where cells or other specimens are placed by some agent for the purpose of studying or manipulating them as part of some research investigation. 'In vitro' is intended to contrast with 'native',which refers to cells or other biological entities that are found in a natural setting. It describes unicellular organisms removed from a natural environement and multicellular organism cells removed from an organism, or cells derived in culture from such displaced cells. 2012-01-12T09:58:38Z A cell that is maintained or propagated in a controlled artificial environment for use in an investigation. cell haendel bone cell 2011-11-16T04:28:16Z A connective tissue cell found in bone. adiehl cell common myeloid progenitor, CD34-positive multipotential myeloid stem cell CMP common myeloid precursor, CD34-positive CFU-GEMM CFU-S CMP are reportedly CD16-positive, CD32-positive, CD38-positive, CD45RA-negative, CD110-negative, CD117-positive, CD123-positive, and SCA1-negative. myeloid stem cell colony forming unit granulocyte, erythrocyte, macrophage, and megakaryocyte pluripotent stem cell (bone marrow) A progenitor cell committed to myeloid lineage, including the megakaryocyte and erythroid lineages. These cells are CD34-positive, and express Gata1, Gata2, C/EBPa, and Pu.1. cell hematopoietic oligopotent progenitor cell, lineage-negative 2010-01-06T03:43:27Z A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. Cell lacks hematopoeitic lineage markers. cell tmeehan macrophage dendritic cell progenitor 2010-01-19T02:51:58Z A progenitor cell that can give rise to plasmacytoid and myeloid dendritic cells, and to monocytes and macrophages. MDP cell tmeehan hematopoietic lineage restricted progenitor cell 2010-01-06T03:43:20Z A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells. cell tmeehan hematopoietic oligopotent progenitor cell 2010-01-06T03:43:27Z A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. Cell lacks hematopoeitic lineage markers. cell tmeehan This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060). CD34-positive, CD38-negative multipotent progenitor cell 2010-01-12T11:14:15Z A hematopoietic multipotent progenitor cell that is CD34-positive, CD38-negative, CD45RA-negative, and CD90-negative. Cell markers are associated with human hematopoietic multipotent progenitor cells. cell tmeehan pancreatic acinar cell 2010-06-24T03:16:29Z A secretory cell found in pancreatic acini that secretes digestive enzymes and mucins. This cell is a typical zymogenic cell, have a basal nucleus and basophilic cytoplasm consisting of regular arrays of granular endoplasmic reticulum with mitochondria and dense secretory granules. BTO:0000028 CALOHA:TS-0737 FMA:63032 acinar cell of pancreas cell tmeehan type A enterocrine cell 2010-09-10T10:48:54Z An enterocrine cell that produces glucagon. FMA:62939 cell tmeehan endo-epithelial cell 2010-06-29T03:38:14Z An epithelial cell derived from endoderm. FMA:69075 cell tmeehan meso-epithelial cell 2010-06-29T03:49:14Z Epithelial cell derived from mesoderm or mesenchyme. FMA:69076 cell epithelial mesenchymal cell tmeehan pancreatic ductal cell 2010-06-30T08:49:43Z Epithelial cell found in the ducts of the pancreas. This cell type contributes to the high luminal pH. FMA:63099 cell tmeehan nongranular leukocyte 2010-07-22T11:30:33Z A leukocyte that lacks granules. FMA:62855 agranular leukocyte cell tmeehan bone marrow cell 2010-07-22T04:48:15Z A cell found in the bone marrow. This can include fibroblasts, macrophages, adipocytes, osteoblasts, osteoclasts, endothelial cells and hematopoietic cells. BTO:0004850 FMA:83621 MH consider whether bone marrow cells are bone cells in the structural sense vs. being part of bone organ sense. cell tmeehan endothelial cell of vascular tree 2010-08-24T02:06:40Z An endothelial cell of the vascular tree, which includes blood vessels and lymphatic vessels. BTO:0001854 CALOHA:TS-1106 FMA:67755 These cells are reportedly CD31-positive, CD34-positive, CD144-positive, TAL1-positive. cell cubodial endothelial cell of vascular tree tmeehan vascular endothelial cell granulocytopoietic cell 2010-08-30T12:54:27Z A cell involved in the formation of a granulocyte. FMA:83519 cell tmeehan myelocyte 2010-08-30T01:08:19Z A cell type that is the first of the maturation stages of the granulocytic leukocytes normally found in the bone marrow. Granules are seen in the cytoplasm. The nuclear material of the myelocyte is denser than that of the myeloblast but lacks a definable membrane. The cell is flat and contains increasing numbers of granules as maturation progresses. BTO:0000734 FMA:83525 cell tmeehan monopoietic cell 2010-08-30T01:27:48Z A cell involved in the formation of a monocyte (monopoiesis). FMA:83552 cell tmeehan epithelial cell of tracheobronchial tree 2010-09-02T02:09:14Z An epithelial cell of the tracheobronchial tree. CL:1000407 FMA:66816 cell tmeehan nucleate cell 2010-09-07T03:32:33Z A cell containing at least one nucleus. FMA:67513 cell tmeehan pancreatic PP cell 2010-09-10T03:30:31Z A PP cell located in the islets of the pancreas. BTO:0000805 FMA:70588 PP cell of pancreatic islet PP-cell of pancreatic islet The term PP cell of pancreatic acinus was obsoleted due to a lack of evidence, making PP cell of pancreatic islets synonymous with pancreatic PP cell. cell pancreatic polypeptide-secreting cell tmeehan epithelial cell of thymus 2010-09-13T02:34:22Z An epithelial cell of the thymus. Epithelial reticular cells are pleomorphic, stellate, non-phagocytic cells which seem to be supportive in function and are held together by desmosomes. They replace the fibroblastoid reticular cells found in other lymphoid organs. Other epithelial cells in the medulla have the ultrastructure of secretory cells. Although different epithelial cells throughout the thymus appear alike by light microscopy their ultrastructure and function varies. CALOHA:TS-1040 CL:1000459 FMA:72208 cell epithelial cell of thymus gland epithelial reticular cell epithelial reticular cell of thymus thymic epithelial cell tmeehan connective tissue cell 2010-09-15T03:01:54Z A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone. CALOHA:TS-2096 CL:1000406 FMA:63875 cell tmeehan embryonic cell 2010-09-15T03:39:21Z A cell of the embryo. CALOHA:TS-0263 FMA:82840 FMA:82841 WBbt:0007028 cell tmeehan embryonic stem cell 2010-09-15T03:44:35Z A stem cell of embryonic origin. BTO:0001086 CALOHA:TS-0263 ESC FMA:82841 This is an in vitro cell type and may be removed in future releases. These cells are reportedly SSEA-4-positive, CD73-negative, and CD324-positive. cell tmeehan bronchial epithelial cell 2010-09-20T02:00:00Z An epithelial cell of the bronchus. BTO:0002922 cell tmeehan preadipocyte 2010-09-20T02:31:53Z An undifferentiated fibroblast that can be stimulated to form a fat cell. BTO:0001107 cell tmeehan progenitor cell of endocrine pancreas 2010-09-21T04:41:06Z A multi-fate stem cell that is able to differentiate into the pancreas alpha, beta and delta endocrine cells. This cell type expresses neurogenin-3 and Isl-1. cell pancreatic endocrine progenitor pancreatic islet progenitor cell tmeehan medullary thymic epithelial cell 2010-09-23T03:17:14Z An epithelial cell of the medullary thymus. This cell type expresses a diverse range of tissue-specific antigens. This promiscuous gene expression is a cell-autonomous property of medullary epithelial cells and is maintained during the entire period of thymic T cell output. BTO:0004563 cell mTEC tmeehan respiratory epithelial cell 2010-09-23T04:38:49Z An endo-epithelial cell of the respiratory tract. BTO:0004533 airway epithelial cell cell tmeehan somatic cell 2010-09-24T09:44:42Z A cell of an organism that does not pass on its genetic material to the organism's offspring (i.e. a non-germ line cell). BTO:0001268 FMA:72300 WBbt:0008378 cell tmeehan cardiocyte 2010-12-07T09:37:22Z A cell located in the heart, including both muscle and non muscle cells. BTO:0001539 CALOHA:TS-0115 FMA:83808 FMA:84791 From Onard of the FMA: Cardiac muscle cell or cardiac myocyte is a striated muscle cell. Cardiocyte on the other hand is any cell in the heart which includes cells other than muscle cells (e.g. endothelial cell of endocardium). Unless there is a consensus among anatomists that cardiocytes refer only to muscle cells, we will treat them as a general class of cells in the heart. cell heart cell tmeehan aortic endothelial cell 2011-02-28T03:54:42Z An arterial endothelial cell that is part of the aorta endothelium. BTO:0003245 CALOHA:TS-0047 cell tmeehan embryonic blood vessel endothelial progenitor cell 2011-02-28T04:20:39Z An endothelial progenitor cell that participates in angiogenesis during development. See CL:0002619. cell tmeehan epithelial cell of lower respiratory tract 2011-06-21T12:29:31Z cell tmeehan ghrelin secreting cell A cell that secretes ghrelin, the peptide hormone that stimulates hunger. cell pancreatic epsilon cell Ghrelin secreting cells found in the found in the exocrine pancreas. In mammals the endocrine pancreas is called the Islets of Langerhans. cell pancreatic E cell hepatoblast Multi fate stem cell that gives rise to to both hepatocytes and cholangiocytes as descendants. premigratory neural crest cell 2012-06-27T08:27:35Z Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells. cell haendel hematopoietic precursor cell Any hematopoietic cell that is a precursor of some other hematopoietic cell type. pancreatic endocrine cell An endocrine cell that is part of the pancreas. cell cardiac myoblast precursor cell A cell that, by division or terminal differentiation, can give rise to other cell types. Work is needed on GO 'cell differentiation' before it is clear whether the equivalent class definition 'native cell' that capable_of some 'cell differentiation' works. Also, may want to consider merging this with non-terminally differentiated cell. endothelial cell of artery A blood vessel endothelial cell that is part of an arterial endothelium. BTO:0004758 CL:0002542 FMA:67761 KUPO:0001095 arterial endothelial cell cell epithelial cell of gall bladder An epithelial cell that is part of the gallbladder. FMA:67780 cell cholangiocyte An epithelial cell that is part of the bile duct. Cholangiocytes contribute to bile secretion via net release of bicarbonate and water. They are cuboidal epithelium in the small interlobular bile ducts, but become columnar and mucus secreting in larger bile ducts approaching the porta hepatis and the extrahepatic ducts. FMA:86481 cell epithelial cell of bile duct epithelial cell of exocrine pancreas An epithelial cell of the exocrine pancreas. FMA:70986 cell exocrine pancreas cell pancreas exocrine glandular cell BTO:0000028 CALOHA:TS-1242 Glandular cell of exocrine pancreas epithelium. Example: pancreatic acinar cell, glandular cells in pancreatic canaliculi, glandular cells in pancreatic ducts. exocrine pancreas glandular cell pancreas exocrine glandular cells bone marrow hematopoietic cell CALOHA:TS-2109 Hematopoietic cells resident in the bone marrow. Include: hematopoietic stem cells (lymphoid stem cells and myeloid stem cells) and the precursor cells for thrombocytes, erythrocytes, basophils, neutrophils, eosinophils, monocytes and lymphocytes. bone marrow hematopoietic cells bone marrow poietic cells neutrophillic cytoplasm 2010-05-25T01:36:34Z Cytoplasm that exhibits molecular interaction for acidic dyes under specific pH conditions. cell tmeehan acidophilic cytoplasm 2009-12-22T04:23:25Z Cytoplasm that exhibits molecular interaction for acidic dyes under specific pH conditions. cell eosinophilic tmeehan basophilic cytoplasm 2009-12-22T04:24:54Z Cytoplasm that exhibits molecular interaction for basic dyes under specific pH conditions. cell tmeehan polychromatophilic cytoplasm 2009-12-28T04:25:23Z Cytoplasm that exhibits affinity for both basic and acid stains under specific pH conditions. cell tmeehan increased nucleus size 2009-12-23T10:53:24Z A nucleus size quality which is relatively high compared to the amount of cytoplasm present in the same cell. cell tmeehan soil Any material within 2 m from the Earth's surface that is in contact with the atmosphere, with the exclusion of living organisms, areas with continuous ice not covered by other material, and water bodies deeper than 2 m. environmental material A portion of environmental material is a fiat object which forms the medium or part of the medium of an environmental system. surgery A material processing technique that uses operative manual and instrumental techniques on a patient to investigate and/or treat a pathological condition such as disease or injury or to help improve bodily function or appearance. massively parallel signature sequencing A DNA sequencing by ligation technique that involves a bead-based method that uses a complex approach of adapter ligation followed by adapter decoding, reading the sequence in increments of four nucleotides; this method made it susceptible to sequence-specific bias or loss of specific sequences. biopsy Specimen creation of a sample of tissue from a living body for diagnostic purposes. stem cell derived cell line A cell line that is derived from a stem cell. database A database is an organized collection of data, today typically in digital form. Fetus Fetal structure, which is a developmental form of a vertebrate animal at any given time point from 8 weeks of gestation to birth (or hatching). Examples: There is only one fetus. geographical location A reference to a place on the Earth, by its name or by its geographical location. chromatin The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome. euchromatin A dispersed and relatively uncompacted form of chromatin. heterochromatin A compact and highly condensed form of chromatin. osteoblast differentiation The process whereby a relatively unspecialized cell acquires the specialized features of an osteoblast, a mesodermal or neural crest cell that gives rise to bone. ameboidal-type cell migration Cell migration that is accomplished by extension and retraction of a pseudopodium. cytokine production The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. serotonin secretion The regulated release of serotonin by a cell. Serotonin (5-hydroxytryptamine, or 5-HT) is a monoamine synthesised in serotonergic neurons in the central nervous system, enterochromaffin cells in the gastrointestinal tract and some immune system cells. somatic diversification of immune receptors The somatic process allowing for the production of immune receptors whose specificity is not encoded in the germline genomic sequences. natural killer cell mediated immunity The promotion of an immune response by natural killer cells through direct recognition of target cells or through the release of cytokines. hematopoietic progenitor cell differentiation The process in which precursor cell type acquires the specialized features of a hematopoietic progenitor cell, a class of cell types including myeloid progenitor cells and lymphoid progenitor cells. immune system process Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats. lymphocyte mediated immunity Any process involved in the carrying out of an immune response by a lymphocyte. T cell mediated immunity Any process involved in the carrying out of an immune response by a T cell. adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains An immune response based on directed amplification of specific receptors for antigen produced through a somatic diversification process that includes somatic recombination of germline gene segments encoding immunoglobulin superfamily domains, and allowing for enhanced responses upon subsequent exposures to the same antigen (immunological memory). Recombined receptors for antigen encoded by immunoglobulin superfamily domains include T cell receptors and immunoglobulins (antibodies). An example of this is the adaptive immune response found in Mus musculus. leukocyte differentiation The process in which a relatively unspecialized hemopoietic precursor cell acquires the specialized features of a leukocyte. A leukocyte is an achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue. somatic diversification of immune receptors via germline recombination within a single locus The process in which immune receptor genes are diversified through recombination of the germline genetic elements within a single genetic locus. myeloid leukocyte differentiation The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of any cell of the myeloid leukocyte lineage. regulation of immune system process Any process that modulates the frequency, rate, or extent of an immune system process. regulation of leukocyte activation Any process that modulates the frequency, rate, or extent of leukocyte activation. peptide secretion The controlled release of a peptide from a cell or a tissue. developmental process involved in reproduction A developmental process in which a progressive change in the state of some part of an organism specifically contributes to its ability to form offspring. circulatory system process A organ system process carried out by any of the organs or tissues of the circulatory system. The circulatory system is an organ system that moves extracellular fluids to and from tissue within a multicellular organism. molecular_function Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions. catalytic activity Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. RNA-directed DNA polymerase activity Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time. cellular_component The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together. nucleus A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. nucleolus A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome. cytoplasm All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. vacuole A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol. ribosome An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins. nucleobase-containing compound metabolic process Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids. DNA metabolic process Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides. DNA replication The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA. DNA modification The covalent alteration of one or more nucleotide sites in DNA, resulting in a change in its properties. DNA methylation The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine. DNA packaging Any process in which DNA and associated proteins are formed into a compact, orderly structure. chromatin remodeling Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation. cellular protein modification process The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification). cellular aromatic compound metabolic process The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells. transport The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore. ion transport The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. cation transport The directed movement of cations, atoms or small molecules with a net positive charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. serotonin transport The directed movement of serotonin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Serotonin (5-hydroxytryptamine) is a monoamine neurotransmitter occurring in the peripheral and central nervous systems. apoptotic process A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died. response to stress Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation). immune response Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. organelle organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. cell cycle The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division. endomitotic cell cycle A mitotic cell cycle in which chromosomes are replicated and sister chromatids separate, but spindle formation, nuclear membrane breakdown and nuclear division do not occur, resulting in an increased number of chromosomes in the cell. female meiotic division A cell cycle process by which the cell nucleus divides as part of a meiotic cell cycle in the female germline. leukocyte cell-cell adhesion The attachment of a leukocyte to another cell via adhesion molecules. gamete generation The generation and maintenance of gametes in a multicellular organism. A gamete is a haploid reproductive cell. germ cell development The process whose specific outcome is the progression of an immature germ cell over time, from its formation to the mature structure (gamete). A germ cell is any reproductive cell in a multicellular organism. female pregnancy The set of physiological processes that allow an embryo or foetus to develop within the body of a female animal. It covers the time from fertilization of a female ovum by a male spermatozoon until birth. blood coagulation The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers. blood circulation The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products. biological_process Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end. metabolic process The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. cell death Any biological process that results in permanent cessation of all vital functions of a cell. A cell should be considered dead when any one of the following molecular or morphological criteria is met: (1) the cell has lost the integrity of its plasma membrane; (2) the cell, including its nucleus, has undergone complete fragmentation into discrete bodies (frequently referred to as "apoptotic bodies"); and/or (3) its corpse (or its fragments) have been engulfed by an adjacent cell in vivo. biosynthetic process The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. macromolecule biosynthetic process The chemical reactions and pathways resulting in the formation of a macromolecule, any 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. protein secretion The controlled release of proteins from a cell. detection of carbohydrate stimulus The series of events in which a carbohydrate stimulus is received by a cell and converted into a molecular signal. detection of hexose stimulus The series of events in which a stimulus from a hexose is received and converted into a molecular signal. response to carbohydrate Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a carbohydrate stimulus. response to hexose Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hexose stimulus. hormone transport The directed movement of hormones into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. cellular process Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. gene expression The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form. regulation of hormone levels Any process that modulates the levels of hormone within an organism or a tissue. A hormone is any substance formed in very small amounts in one specialized organ or group of cells and carried (sometimes in the bloodstream) to another organ or group of cells in the same organism, upon which it has a specific regulatory action. protein transport The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. bicarbonate transmembrane transporter activity Catalysis of the transfer of bicarbonate from one side of a membrane to the other. Bicarbonate is the hydrogencarbonate ion, HCO3-. oxygen transport The directed movement of oxygen (O2) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. ammonium transport The directed movement of ammonium into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Ammonium is the cation NH4+ which is formed from N2 by root-nodule bacteria in leguminous plants and is an excretory product in ammonotelic animals. peptide transport The directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. monoamine transport The directed movement of monoamines, organic compounds that contain one amino group that is connected to an aromatic ring by an ethylene group (-CH2-CH2-), into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. organic hydroxy compound transport The directed movement of an organic hydroxy compound (organic alcohol) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. An organic hydroxy compound is an organic compound having at least one hydroxy group attached to a carbon atom. cytoplasmic membrane-bounded vesicle A membrane-bounded vesicle found in the cytoplasm of the cell. cellular component organization A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component. single organismal cell-cell adhesion The attachment of one cell to another cell via adhesion molecules, where both cells are part of the same organism. somatic recombination of immunoglobulin gene segments The process in which immunoglobulin genes are formed through recombination of the germline genetic elements, as known as immunoglobulin gene segments, within a single locus. cell migration The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms. chromatin modification The alteration of DNA, protein, or sometimes RNA, in chromatin, which may result in changing the chromatin structure. histone modification The covalent alteration of one or more amino acid residues within a histone protein. stem cell division The self-renewing division of a stem cell. A stem cell is an undifferentiated cell, in the embryo or adult, that can undergo unlimited division and give rise to one or several different cell types. regulation of nucleobase-containing compound metabolic process Any cellular process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids. regulation of metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. protein metabolic process The chemical reactions and pathways involving a specific protein, rather than of proteins in general. Includes protein modification. B cell mediated immunity Any process involved with the carrying out of an immune response by a B cell, through, for instance, the production of antibodies or cytokines, or antigen presentation to T cells. 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. 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. antigen processing and presentation The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex. regulation of cell-cell adhesion Any process that modulates the frequency, rate or extent of attachment of a cell to another cell. reproductive process A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents. biological adhesion The attachment of a cell or organism to a substrate or other organism. signal release The process in which a signal is secreted or discharged into the extracellular medium from a cellular source. sarcomere The repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs. peptide hormone secretion The regulated release of a peptide hormone from a cell. insulin secretion The regulated release of proinsulin from secretory granules (B granules) in the B cells of the pancreas; accompanied by cleavage of proinsulin to form mature insulin. lymphocyte differentiation The process in which a relatively unspecialized precursor cell acquires specialized features of a lymphocyte. A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin. myeloid cell differentiation The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of any cell of the myeloid leukocyte, megakaryocyte, thrombocyte, or erythrocyte lineages. secretory granule A small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. Secretory granules move towards the periphery of the cell and upon stimulation, their membranes fuse with the cell membrane, and their protein load is exteriorized. Processing of the contained protein may take place in secretory granules. cell differentiation The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state. neuron differentiation The process in which a relatively unspecialized cell acquires specialized features of a neuron. T cell differentiation The process in which a precursor cell type acquires characteristics of a more mature T-cell. A T cell is a type of lymphocyte whose definin characteristic is the expression of a T cell receptor complex. erythrocyte differentiation The process in which a myeloid precursor cell acquires specializes features of an erythrocyte. megakaryocyte differentiation The process in which a myeloid precursor cell acquires specializes features of a megakaryocyte. monocyte differentiation The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of a monocyte. macrophage differentiation The process in which a relatively unspecialized monocyte acquires the specialized features of a macrophage. chromosome condensation The progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells. apoptotic chromosome condensation The compaction of chromatin during apoptosis. osteoclast differentiation The process in which a relatively unspecialized monocyte acquires the specialized features of an osteoclast. An osteoclast is a specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue. ribonucleoprotein complex A macromolecular complex containing both protein and RNA molecules. cytoplasmic vesicle membrane The lipid bilayer surrounding a cytoplasmic vesicle. secretory granule membrane The lipid bilayer surrounding a secretory granule. granulocyte differentiation The process in which a myeloid precursor cell acquires the specialized features of a granulocyte. Granulocytes are a class of leukocytes characterized by the presence of granules in their cytoplasm. These cells are active in allergic immune reactions such as arthritic inflammation and rashes. This class includes basophils, eosinophils and neutrophils. epithelial cell differentiation The process in which a relatively unspecialized cell acquires specialized features of an epithelial cell, any of the cells making up an epithelium. pancreas development The process whose specific outcome is the progression of the pancreas over time, from its formation to the mature structure. The pancreas is an endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes. endocrine pancreas development The process whose specific outcome is the progression of the endocrine pancreas over time, from its formation to the mature structure. The endocrine pancreas is made up of islet cells that produce insulin, glucagon and somatostatin. organelle membrane A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle. regulation of cellular metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. cytoplasmic vesicle A vesicle formed of membrane or protein, found in the cytoplasm of a cell. vesicle Any small, fluid-filled, spherical organelle enclosed by membrane or protein. membrane-bounded vesicle Any small, fluid-filled, spherical organelle enclosed by a lipid bilayer. multicellular organismal process Any biological process, occurring at the level of a multicellular organism, pertinent to its function. developmental process A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. secretion by cell The controlled release of a substance by a cell. macromolecular complex A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which the constituent parts function together. immunoglobulin V(D)J recombination The process in which immunoglobulin gene segments are recombined within a single locus utilizing the conserved heptamer and nonomer recombination signal sequences (RSS). For immunoglobulin heavy chains V, D, and J gene segments are joined, and for immunoglobulin light chains V and J gene segments are joined. homotypic cell-cell adhesion The attachment of a cell to a second cell of the identical type via adhesion molecules. response to monosaccharide Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a monosaccharide stimulus. detection of monosaccharide stimulus The series of events in which a stimulus from a monosaccharide is received and converted into a molecular signal. cellular nitrogen compound metabolic process The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells. cellular macromolecule biosynthetic process The chemical reactions and pathways resulting in the formation of a macromolecule, any 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, carried out by individual cells. protein modification process The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications). Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification). ghrelin secretion The regulated release of ghrelin from a cell. Ghrelin is a 28 amino acid hunger-stimulating peptide hormone. regulation of molecular function, epigenetic Any heritable epigenetic process that modulates the frequency, rate or extent of protein function by self-perpetuating conformational conversions of normal proteins in healthy cells. This is distinct from, though mechanistically analogous to, disease states associated with prion propagation and amyloidogenesis. A single protein, if it carries a glutamine/asparagine-rich ('prion') domain, can sometimes stably exist in at least two distinct physical states, each associated with a different phenotype; propagation of one of these traits is achieved by a self-perpetuating change in the protein from one form to the other, mediated by conformational changes in the glutamine/asparagine-rich domain. Prion domains are both modular and transferable to other proteins, on which they can confer a heritable epigenetic alteration of function; existing bioinformatics data indicate that they are rare in non-eukarya, but common in eukarya. 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 activation The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific. melanosome A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells. 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. DNA polymerase complex A protein complex that possesses DNA polymerase activity and is involved in template directed synthesis of DNA. azurophil granule Primary lysosomal granule found in neutrophil granulocytes. Contains a wide range of hydrolytic enzymes and is released into the extracellular fluid. zymogen granule membrane The lipid bilayer surrounding a zymogen granule. MHC protein complex A transmembrane protein complex composed of an MHC alpha chain and, in most cases, either an MHC class II beta chain or an invariant beta2-microglobin chain, and with or without a bound peptide, lipid, or polysaccharide antigen. MHC class II protein complex A transmembrane protein complex composed of an MHC class II alpha and MHC class II beta chain, and with or without a bound peptide or polysaccharide antigen. amide transport The directed movement of an amide, any compound containing one, two, or three acyl groups attached to a nitrogen atom, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. myeloid dendritic cell differentiation The process in which a monocyte acquires the specialized features of a dendritic cell, an immunocompetent cell of the lymphoid and hemopoietic systems and skin. macromolecule metabolic process The chemical reactions and pathways involving macromolecules, any 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. organelle Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane. membrane-bounded organelle Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. intracellular organelle Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. intracellular membrane-bounded organelle Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. intracellular non-membrane-bounded organelle Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes. protein complex Any macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical. receptor complex Any protein complex that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function. macromolecule modification The covalent alteration of one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological macromolecule, resulting in a change in its properties. macromolecule methylation The covalent attachment of a methyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological macromolecule. sequence-specific DNA binding Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding. regulation of DNA methylation Any process that modulates the frequency, rate or extent of the covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine. cellular metabolic process The chemical reactions and pathways by which individual cells transform chemical substances. primary metabolic process The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism. cellular biosynthetic process The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. cellular macromolecule metabolic process The chemical reactions and pathways involving macromolecules, any 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, as carried out by individual cells. cellular protein metabolic process The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification. type B pancreatic cell proliferation The multiplication or reproduction of pancreatic B cells, resulting in the expansion of an pancreatic B cell population. Pancreatic B cell are cells of the pancreas that secrete insulin. organelle part Any constituent part of an organelle, an organized structure of distinctive morphology and function. Includes constituent parts of the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, but excludes the plasma membrane. intracellular part Any constituent part of the living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. membrane part Any constituent part of a membrane, a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. cytoplasmic vesicle part Any constituent part of cytoplasmic vesicle, a vesicle formed of membrane or protein, found in the cytoplasm of a cell. cytoplasmic part Any constituent part of the cytoplasm, all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. intracellular organelle part A constituent part of an intracellular organelle, an organized structure of distinctive morphology and function, occurring within the cell. Includes constituent parts of the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton but excludes the plasma membrane. contractile fiber part Any constituent part of a contractile fiber, a fiber composed of actin, myosin, and associated proteins, found in cells of smooth or striated muscle. plasma membrane part Any constituent part of the plasma membrane, the membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. cell part Any constituent part of a cell, the basic structural and functional unit of all organisms. single-organism process A biological process that involves only one organism. single organism reproductive process A biological process that directly contributes to the process of producing new individuals, involving a single organism. multi-organism reproductive process A biological process that directly contributes to the process of producing new individuals, involving another organism. multi-multicellular organism process A multicellular organism process which involves another multicellular organism of the same or different species. single-multicellular organism process A biological process occurring within a single, multicellular organism. single-organism metabolic process A metabolic process - chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances - which involves a single organism. single-organism cellular process Any process that is carried out at the cellular level, occurring within a single organism. single-organism transport The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore, involving a single organism. single-organism developmental process A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition, involving only one organism. innate immune response Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens. leukocyte activation A change in morphology and behavior of a leukocyte resulting from exposure to a specific antigen, mitogen, cytokine, cellular ligand, or soluble factor. fat cell differentiation The process in which a relatively unspecialized cell acquires specialized features of an adipocyte, an animal connective tissue cell specialized for the synthesis and storage of fat. regulation of T cell differentiation Any process that modulates the frequency, rate or extent of T cell differentiation. regulation of cell differentiation Any process that modulates the frequency, rate or extent of cell differentiation, the process in which relatively unspecialized cells acquire specialized structural and functional features. regulation of lymphocyte differentiation Any process that modulates the frequency, rate or extent of lymphocyte differentiation. heterocycle metabolic process The chemical reactions and pathways involving heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings). lymphocyte activation A change in morphology and behavior of a lymphocyte resulting from exposure to a specific antigen, mitogen, cytokine, chemokine, cellular ligand, or soluble factor. hormone secretion The regulated release of hormones, substances with a specific regulatory effect on a particular organ or group of cells. secretion The controlled release of a substance by a cell or a tissue. somatic stem cell division The self-renewing division of a somatic stem cell, a stem cell that can give rise to cell types of the body other than those of the germ-line. cell development The process whose specific outcome is the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate. oogenesis The complete process of formation and maturation of an ovum or female gamete from a primordial female germ cell. Examples of this process are found in Mus musculus and Drosophila melanogaster. multicellular organismal reproductive process The process, occurring above the cellular level, that is pertinent to the reproductive function of a multicellular organism. This includes the integrated processes at the level of tissues and organs. anatomical structure development The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome. stem cell differentiation The process in which a relatively unspecialized cell acquires specialized features of a stem cell. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells. cellular developmental process A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition. cell motility Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another. catecholamine secretion The regulated release of catecholamines by a cell. The catecholamines are a group of physiologically important biogenic amines that possess a catechol (3,4-dihydroxyphenyl) nucleus and are derivatives of 3,4-dihydroxyphenylethylamine. regulation of immune response Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus. regulation of biological process Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. regulation of developmental process Any process that modulates the frequency, rate or extent of development, the biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). regulation of cellular process Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. regulation of T cell activation Any process that modulates the frequency, rate or extent of T cell activation. regulation of body fluid levels Any process that modulates the levels of body fluids. multicellular organismal movement Any physiological process involved in changing the position of a multicellular organism or an anatomical part of a multicellular organism. response to stimulus Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism. regulation of DNA metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving DNA. regulation of nitrogen compound metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds. localization Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported to or maintained in a specific location. establishment of localization The directed movement of a cell, substance or cellular entity, such as a protein complex or organelle, to a specific location. regulation of lymphocyte activation Any process that modulates the frequency, rate or extent of lymphocyte activation. chromosome organization A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome. detection of glucose The series of events in which a glucose stimulus is received by a cell and converted into a molecular signal. multi-organism process A biological process which involves another organism of the same or different species. catecholamine transport The directed movement of catecholamines, a group of physiologically important biogenic amines that possess a catechol (3,4-dihydroxyphenyl) nucleus and are derivatives of 3,4-dihydroxyphenylethylamine. cardiac muscle cell differentiation The process in which a cardiac muscle precursor cell acquires specialized features of a cardiac muscle cell. Cardiac muscle cells are striated muscle cells that are responsible for heart contraction. heart contraction The multicellular organismal process in which the heart decreases in volume in a characteristic way to propel blood through the body. regulation of macromolecule metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any 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. transdifferentiation The conversion of a differentiated cell of one fate into a differentiated cell of another fate without first undergoing cell division or reversion to a more primitive or stem cell-like fate. chondroblast differentiation The process in which a mesenchymal cell, acquires specialized structural and/or functional features of a chondroblast. Differentiation includes the processes involved in commitment of a cell to a chondroblast fate. A chondroblast is a precursor cell to chondrocytes. endocrine hormone secretion The regulated release of a hormone into the circulatory system. biological regulation Any process that modulates a measurable attribute of any biological process, quality or function. regulation of biological quality Any process that modulates a qualitative or quantitative trait of a biological quality. A biological quality is a measurable attribute of an organism or part of an organism, such as size, mass, shape, color, etc. glucagon secretion The regulated release of glucagon from secretory granules in the A (alpha) cells of the pancreas (islets of Langerhans). somatostatin secretion The regulated release of somatostatin from secretory granules in the D cells of the pancreas. leukocyte aggregation The adhesion of one leukocyte to one or more other leukocytes via adhesion molecules. organelle assembly The aggregation, arrangement and bonding together of a set of components to form an organelle. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. organic substance transport The directed movement of organic substances into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore. An organic substance is a molecular entity that contains carbon. organic substance metabolic process The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon. nitrogen compound transport The directed movement of nitrogen-containing compounds into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. extracellular exosome assembly The aggregation, arrangement and bonding together of a set of components to form an extracellular vesicular exosome, a membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. regulation of primary metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism involving those compounds formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism. nucleic acid metabolic process Any cellular metabolic process involving nucleic acids. single organism cell adhesion The attachment, via cell adhesion molecules, of a cell to either another cell of the same organism, or to an underlying substrate of the same organism such as the extracellular matrix. organic cyclic compound metabolic process The chemical reactions and pathways involving organic cyclic compound. organic substance biosynthetic process The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon. regulation of leukocyte differentiation Any process that modulates the frequency, rate or extent of leukocyte differentiation. catalytic complex A protein complex which is capable of catalytic activity. single-organism localization A localization which involves only one organism. single-organism organelle organization An organelle organization which involves only one organism. regulation of hemopoiesis Any process that modulates the frequency, rate or extent of hemopoiesis. regulation of multicellular organismal development Any process that modulates the frequency, rate or extent of multicellular organismal development. measurement unit label 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. A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure. Examples of measurement unit labels are liters, inches, weight per volume. PERSON: Alan Ruttenberg PERSON: Melanie Courtot measurement unit label objective specification 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? In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction. OBI Plan and Planned Process/Roles Branch OBI_0000217 PERSON: Alan Ruttenberg PERSON: Barry Smith PERSON: Bjoern Peters PERSON: Jennifer Fostel 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. goal specification objective specification action specification Alan Ruttenberg OBI Plan and Planned Process branch Pour the contents of flask 1 into flask 2 a directive information entity that describes an action the bearer will take action specification datum label 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. 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 GROUP: IAO datum label http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n software GROUP: OBI PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Chris Stoeckert PERSON: Melanie Courtot Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit. see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178 software data item 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. 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ 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. Data items include counts of things, analyte concentrations, and statistical summaries. 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 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. data data item symbol 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). An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. PERSON: James A. Overton PERSON: Jonathan Rees a serial number such as "12324X" a stop sign a written proper name such as "OBI" based on Oxford English Dictionary symbol information content entity 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ). A generically dependent continuant that is about some thing. Examples of information content entites include journal articles, data, graphical layouts, and graphs. OBI_0000142 PERSON: Chris Stoeckert information content entity 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. scalar measurement datum 1 1 10 feet. 3 ml. 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form PERSON: Alan Ruttenberg PERSON: Melanie Courtot 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. a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label. scalar measurement datum directive information entity 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 An information content entity whose concretizations indicate to their bearer how to realize them in a process. PERSON: Alan Ruttenberg PERSON: Bjoern Peters 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 directive information entity algorithm A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata. OBI_0000270 PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies. Philippe Rocca-Serra PlanAndPlannedProcess Branch adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg) algorithm curation status specification Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) GROUP:OBI:<http://purl.obolibrary.org/obo/obi> OBI_0000266 PERSON:Bill Bug 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. curation status specification data set 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. 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. Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). OBI_0000042 data set group:OBI person:Allyson Lister person:Chris Stoeckert 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. OBI_0000030 group:OBI image person:Alan Ruttenberg person:Allyson person:Chris Stoeckert data about an ontology part Person:Alan Ruttenberg data about an ontology part data about an ontology part is a data item about a part of an ontology, for example a term plan specification 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 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. 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. Alan Ruttenberg Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved OBI Plan and Planned Process branch OBI_0000344 PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice. plan specification measurement datum 2/2/2009 is_specified_output of some assay? A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. 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,}. OBI_0000305 group:OBI measurement datum person:Chris Stoeckert obsolescence reason specification PERSON: Alan Ruttenberg PERSON: Melanie Courtot The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. obsolescence reason specification textual entity 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 Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities text textual entity figure An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something. Any picture, diagram or table PERSON: Lawrence Hunter figure document A collection of information content entities intended to be understood together as a whole A journal article, patent application, laboratory notebook, or a book PERSON: Lawrence Hunter document publication A document that has been accepted by a publisher A journal article or book PERSON: Lawrence Hunter publication publication about an investigation A publication that is about an investigation Most scientific journal articles PERSON: Lawrence Hunter publication about an investigation scientific publication time measurement datum 2009/09/28 Alan Ruttenberg. Fucoidan-use-case A scalar measurement datum that is the result of measuring a temporal interval Person:Alan Ruttenberg time measurement datum email address Alan Ruttenberg 1/3/2012 - Provisional id, see issue at http://code.google.com/p/information-artifact-ontology/issues/detail?id=130&thanks=130&ts=1325636583 Person:Alan Ruttenberg Person:Chris Stoeckart email address documenting 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 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. documenting wikipedia http://en.wikipedia.org/wiki/Documenting centrally registered identifier symbol A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry. CRID symbol Original proposal from Bjoern, discussions at IAO calls PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot 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. centrally registered identifier symbol centrally registered identifier CRID 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. An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs. 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. Original proposal from Bjoern, discussions at IAO calls PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot 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. centrally registered identifier centrally registered identifier registry 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. CRID registry Original proposal from Bjoern, discussions at IAO calls PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot PubMed is a CRID registry. It has a dataset of PubMed identifiers associated with journal articles. 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 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. http://code.google.com/p/information-artifact-ontology/issues/detail?id=114 written name obese a status with body weight that is grossly above the average, acceptable or desirable weight, usually due to accumulation of excess fat tissue in the body chewing "The process of biting and mashing food with the teeth prior to swallowing." [NBO:GVG] Mus musculus Mus musculus Rattus Rattus Rattus norvegicus Rattus norvegicus Viruses Viruses Euteleostomi Euteleostomi Bacteria Bacteria Archaea Archaea Eukaryota Eukaryota Euarchontoglires Euarchontoglires Teleostei Teleostei Amniota Amniota Sauria Sauria Murinae Murinae Vertebrata <Metazoa> Vertebrata <Metazoa> Gnathostomata <vertebrate> Gnathostomata <vertebrate> Danio rerio Danio rerio Serpentes Serpentes Aves Aves Homo sapiens Homo sapiens Extraction of Differential Gene Expression software Storey J.D. (2007) The optimal discovery procedure: A new approach to simultaneous significance testing, Journal of the Royal Statistical Society, Series B, 69: 347-368. Storey J.D., Dai J.Y., and Leek J.T. (2007) The optimal discovery procedure for large-scale significance testing, with applications to comparative microarray experiments, Biostatistics, 8: 414-432. Leek J.T,. Monsen E.C., Dabney A.R., and Storey J.D. (2006) EDGE: Extraction and analysis of differential gene expression, Bioinformatics, 22: 507-508. Storey J.D., Xiao W., Leek J.T., Tompkins R.G., and Davis R.W. (2005) Significance analysis of time course microarray experiments, Proceedings of the National Academy of Sciences, 102: 12837-12842. EDGE Elisabetta Manduchi Beta Cell Biology Consortium A software that is used for the differential gene expression significance analysis of DNA microarray experiments for both standard and time course experiments. The outputs consist of bothe p-values and q-values. Patterns from Gene Expression software The input consists of (replicated) intensities from a collection of array experiments from two or more conditions (or from a collection of direct comparisons on 2-channel arrays). The output consists of patterns, one for each row identifier in the data file. One condition is used as a reference to which the other types are compared. The length of a pattern equals the number of non-reference sample types. The symbols in the patterns are integers, where positive integers represent up-regulation as compared to the reference sample type and negative integers represent down-regulation. The patterns are based on the false discovery rates for each position in the pattern, so that the number of positive and negative symbols that appear in each position of the pattern is as descriptive as the data variability allows. The patterns generated are easily interpretable in that integers are used to represent different levels of up- or down-regulation as compared to the reference sample type. A software that can be used to produce lists of differentially expressed genes with confidence measures attached. These lists are generated via a False Discovery Rate (FDR) method of controlling the false positives. Patterns from Gene Expression (PaGE) is more than a differential expression analysis tool. PaGE is a tool to attach descriptive, dependable, and easily interpretable expression patterns to genes across multiple conditions, each represented by a set of replicated array experiments. Elisabetta Manduchi PaGE PMID:15797908 Grant G.R., Liu J., Stoeckert C.J.Jr. (2005) A practical false discovery rate approach to identifying patterns of differential expression in microarray data, Bioinformatics, 21(11): 2684-2690. Beta Cell Biology Consortium GLobal Identifier of Target Regions software Beta Cell Biology Consortium GLITR Elisabetta Manduchi, Jie Zheng A software that is used to identify transcription factor binding sites in a genome that have been enriched with aligned reads generated from ChIP-Seq technology. PMID:19553195 Tuteja G., White P., Schug J., Kaestner K.H. (2009) Extracting transcription factor targets from ChIP-Seq data. Nucleic Acids Res., 37(17): e113. doi: 10.1093/nar/gkp536. peak calling Jie Zheng http://en.wikipedia.org/wiki/Peak_calling A data transformation to identify protein-binding regions in a genome sequence from the data generated from a ChIP-sequencing or ChIP-chip experiment. When the protein is a transcription factor, the region is a transcription factor binding site (TFBS). planned process '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.) 6/11/9: Edited at workshop. Used to include: is initiated by an agent Bjoern Peters Injecting mice with a vaccine in order to test its efficacy 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. branch derived A processual entity that realizes a plan which is the concretization of a plan specification. This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) planned process biological feature identification objective Biological_feature_identification_objective is an objective role carried out by the proposition defining the aim of a study designed to examine or characterize a particular biological feature. Jennifer Fostel biological feature identification objective material supplier role Jackson Labs is an organization which provide mice as experimental material Supplier role is a special kind of service, e.g. biobank material provider role supplier PERSON:Jennifer Fostel a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation. material supplier role reference substance role reference substance Calibration standard, positive control substance, vehicle Good Laboratory Practices: Questions and Answers - Test Control and Reference Substance Characterization http://www.epa.gov/enforcement/monitoring/programs/fifra/glpqanda-character.html OBI Person:Jennifer Fostel a role inhering in a material entity that is realized when characteristics or responses elicited by the substance are used for comparison or reference. reference substance role waiting BP: I have doubts about the utility of this. OBI branch derived PERSON:Alan Ruttenberg We need a better handling/modeling of time (January 2008) not actively doing anything to a material for a duration of time. waiting 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 mass spectrometer A mass spectrometer is an instrument which is used to measure the mass to charge ratio of ions. All mass spectrometers consist of three basic parts: an ion source, a mass analyzer, and a detector system. The stages within the mass spectrometer are: 1. Production of ions from the sample 2. Separation of ions with different masses 3. Detection of the number of ions of each mass produced 4.Collection of data to generate the mass spectrum Frank Gibson LCQ Fleet Ion Trap MSn manufactured by thermo fisher scientific http://en.wikipedia.org/wiki/Mass_spectrometry mass spectrometer microarray platform OBI Instrument branch OBI Instrument branch A microarray platform is a platform that contains the instruments, software and reagents needed to perform a microarray protocol. definition_source: OBI. microarray platform software optimization objective Jennifer Fostel Software_optimization is a software_testing_objective role describing a study designed to identify the best software or parameters of the software. software optimization objective investigation Could add specific objective specification Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation study Bjoern Peters 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 OBI branch derived a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). investigation evaluant role Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. GROUP: Role Branch OBI 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) 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 evaluant role examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected") reporting party role MO:submitter mapped to this term. So, alternative term 'submitter' was added. Person who prepares microarray data in MAGE-TAB format and submits to a database, such as ArrayExpress. reporting party submitter Jennifer Fostel OBI The first section has been pre-designated as the 'Reporting Party' section and should be filled with the Reporting Party's personal information. http://www.mercedsheriff.com/SelfReporting.htm a study personnel role played by a party who reports the outcome of a study component reporting party role assay Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house. any method study assay 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. A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies. OBI branch derived PlanAndPlannedProcess Branch assay measuring scientific observation diagnosis textual entity Jennifer Fostel diagnosis is an assessment of a disease or injury, its likely prognosis and treatment. diagnosis textual entity culture medium 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. A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008 OBI Person: Jennifer Fostel, Jie Zheng culture medium reagent role 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. PERSON:Matthew Brush reagent (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). 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. Buffer, dye, a catalyst, a solvating agent. PERSON:Matthew Brush reagent role material processing A cell lysis, production of a cloning vector, creating a buffer. PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca Serra A planned process which results in physical changes in a specified input material OBI branch derived PERSON: Bjoern Peters material processing material transformation protocol testing objective Jennifer Fostel Protocol_testing_objective is a methodology_testing_objective role describing a study designed to examine the effects of using different protocols. protocol testing objective participant under investigation role 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. 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. OBI 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. 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 GROUP: Role Branch participant under investigation role measured expression level OBI Data Transformation branch A measurement datum that is the outcome of the quantification of an assay for the activity of a gene, or the number of RNA transcripts. Examples are quantified data from an expression microarray experiment, PCR measurements, etc. measured expression level person:Chris Stoeckert biological vector role 6/12/2009 Alan made this a material to be added role, because it was, and because this speeded up reasoning Feb 20, 2009. The material transmitted can be genetic information (as in cloning vector) or a pathogen (as in a disease vector) GROUP: Role Branch OBI and Wikipedia a biological vector role is a material to be added role that is realized by the process of transmitting material to the organism that is the target of the transmission. 1983 Sci. Amer. Jan. 58/2 Plasmids are routinely used as vectors for introducing foreign DNA into bacteria. Some epidemiological aspects and vector role of tick infestation on layers in the Faisalabad district (Pakistan). http://journals.cambridge.org/action/displayAbstract;jsessionid=0373164489D00868AEEF2C556EB4FD29.tomcat1?fromPage=online&aid=624280 biological vector role specimen role 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. GROUP: Role Branch 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. OBI 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 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. specimen role sequence feature identification objective Jennifer Fostel Sequence_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features exhibited at the level of a macromolecular sequence, e.g. nucleic acid, protein, polysaccharide. sequence feature identification objective intervention design An intervention design is a study design in which a controlled process applied to the subjects (the intervention) serves as the independent variable manipulated by the experimentalist. The treatment (perturbation or intervention) defined can be defined as a combination of values taken by independent variable manipulated by the experimentalists are applied to the recruited subjects assigned (possibly by applying specific methods) to treatment groups. The specificity of intervention design is the fact that independent variables are being manipulated and a response of the biological system is evaluated via response variables as monitored by possibly a series of assays. OBI branch derived PMID: 18208636.Br J Nutr. 2008 Jan 22;:1-11.Effect of vitamin D supplementation on bone and vitamin D status among Pakistani immigrants in Denmark: a randomised double-blinded placebo-controlled intervention study. Philppe Rocca-Serra intervention design worker role "executes the study plan" includes the suppliers and manufacturers of reagents and other materials used in the study worker OBI Person:Jennifer Fostel 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 worker role gene list group:OBI A data set of the names or identifiers of genes that are the outcome of an analysis or have been put together for the purpose of an analysis. Gene lists may arise from analysis to determine differentially expressed genes, may be collected from the literature for involvement in a particular process or pathway (e.g., inflammation), or may be the input for gene set enrichment analysis. gene list kind of report. (alan) need to be careful to distinguish from output of a data transformation or calculation. A gene list is a report when it is published as such? Relates to question of whether report is a whole, or whether it can be a part of some other narrative object. person:Chris Stoeckert molecular feature identification objective Jennifer Fostel Molecular_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features of a biological system, e.g. expression profiling, copy number of molecular components, epigenetic modifications. molecular feature identification objective hardware testing objective Hardware_testing_objective is a methodology_testing_objective role describing a study designed to examine the effects of using different hardware, e.g. scanner. Jennifer Fostel hardware testing objective complete nutrient role A nutrient role that inheres in a material entity and is realized in the use of that material entity by an organism to provide all needed nourishment. complete nutrient Person: Jennifer Fostel Rat chow; RPMI medium + serum; use example: CNS17 (Complete Nutrient System) Grow 3-2-4, http://www.kalyx.com/store/proddetail.cfm/ItemID/552307/CategoryID/12000/SubCatID/2755/file.htm complete nutrient role cDNA library GROUP: PSI Mixed population of cDNAs (complementaryDNA) made from mRNA from a defined source, usually a specific cell type. This term should be associated only to nucleic acid interactors not to their proteins product. For instance in 2h screening use living cells (MI:0349) as sample process. ALT DEF (PRS):: a cDNA library is a collection of host cells, typically E.Coli cells but not exclusively. modified by transfer of plasmid DNA molecule used as vector containing a fragment or totality of cDNA molecule (the insert) . cDNA library may have an array of role and applications. PERSON: Luisa Montecchi PERSON: Philippe Rocca-Serra PMID:6110205. collection of cDNA derived from mouse splenocytes. PRS: 22022008. class moved under population, modification of definition and replacement of biomaterials in previous definition with 'material' addition of has_role restriction cDNA library population 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 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 adapted from Oxford English Dictionnary population rem1: collection somehow always involve a selection process imaging assay An imaging assay is an assay to produce a picture of an entity. definition_source: OBI. OBI branch derived PlanAndPlannedProcess Branch imaging assay protocol optimization objective Jennifer Fostel Protocol_optimization is a protocol_testing_objective role describing a study designed to identify the best protocol. This may be carried out by comparing different protocols or by modifying the parameters used within a single protocol. protocol optimization objective biological replicate role a reference participant role realized by equivalent treatment of participants biological replicate A member of a dose-time group; a patient in a given arm of a trial OBI Person:Jennifer Fostel biological replicate role investigation agent role Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. 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. investigation agent role investigator study person role 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. GROUP: Role Branch 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) 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) OBI The person perform microarray experiments and submit microarray results (including raw data, processed data) with experiment description to ArrayExpress. nutrient role 19 Feb 2009; old def: A nutrient role is a role played by a substance used in an organism's metabolism which is taken in from the environment and provides nourishment. nutrient GROUP: Role branch Luria broth; vitamin A; A nutrient is a substance used in an organism's metabolism which must be taken in from the environment. Wikipedia. Wikipedia, feb 29, 2008 a role that inheres in a material entity and is realized in the use of that material entity by an organism when it is used in that organism's metabolism and provides nourishment. nutrient role methodology testing objective Jennifer Fostel Methodology_testing_objective is an objective role carried out by a proposition defining the aim of the study is to examine the effect of using different methodologies. methodology testing objective cellular feature identification objective Cellular_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize a biological feature monitored at the cellular level, e.g. stage of cell cycle, stage of differentiation. Jennifer Fostel cellular feature identification objective reference subject role reference participant Jennifer Fostel OBI Saline treated rat; one of three identically-treated subjects a reference subject role which inheres in an organism or entity of organismal origin so that the characteristics or responses of the participant playing the reference participant role are used for comparison or reference reference subject role enzymatic cleavage OBI branch derived PlanAndPlannedProcess Branch Polymorphism R62W results in resistance of CD23 to enzymatic cleavage in cultured cells. Genes Immun. 2007 Apr;8(3):215-23. Epub 2007 Feb 15. PMID: 17301828 enzymatic cleavage enzymatic cleavage is a protocol application to digest the fraction of input material that is susceptible to that enzyme hardware optimization objective Hardware_optimization is a hardware_testing_objective describing a study designed to identify the best hardware. Jennifer Fostel hardware optimization objective software testing objective Jennifer Fostel Software_testing_objective is a hardware_optimization role describing a study designed to examine the effects of using different software or software parameters, e.g. data processing software. software testing objective organization GROUP: OBI PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Philippe Rocca-Serra PERSON: Susanna Sansone An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: 1) there are organization_member_roles (president, treasurer, branch editor), with individual persons as bearers 2) there are organization_roles (employer, owner, vendor, patent holder) 3) an organization has a charter / rules / bylaws, which specify what roles there are, how they should be realized, and how to modify the charter/rules/bylaws themselves. It is debatable what the organization itself is (some kind of dependent continuant or an aggregate of people). This also determines who/what the bearer of organization_roles' are. My personal favorite is still to define organization as a kind of 'legal entity', but thinking it through leads to all kinds of questions that are clearly outside the scope of OBI. Interestingly enough, it does not seem to matter much where we place organization itself, as long as we can subclass it (University, Corporation, Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, W3C, University of Oklahoma), and have it play roles. This leads to my proposal: We define organization through the statements 1 - 3 above, but without an 'is a' statement for now. We can leave it in its current place in the is_a hierarchy (material entity) or move it up to 'continuant'. We leave further clarifications to BFO, and close this issue for now. 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. organization feed role a role that inheres in a material entity and is realized in the use of that material entity by lab animal to provide all needed nourishment. feed OBI Person: Jennifer Fostel Purina rat chow; cited use: Control; F = feed (rat chow); W = water; F. g. = feed-ginger concentrate. www.academicjournals.org/AJB/PDF/pdf2007/19Sep/Egwurugwu%20et%20al.pdf - Feb 29, 2008 feed role technical replicate role technical replicate technical replicate role is realized when two portions from one evaluant are used in replicate runs of an assay Aliquots of a tissue subjected to parallel assays Person: Jennifer Fostel technical replicate role DNA extraction A DNA extraction is a nucleic acid extraction where the desired output material is DNA. DNA extraction OBI branch derived PlanAndPlannedProcess Branch organism feature identification objective Jennifer Fostel Organism_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize a biological feature monitored at the level of the organism, e.g. height, weight, stage of development, stage of life cycle. organism feature identification objective protocol study protocol 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. OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29) 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. PlanAndPlannedProcess Branch protocol adding a material entity into a target BP Class was renamed from 'administering substance', as this is commonly used only for additions into organisms. Injecting a drug into a mouse. Adding IL-2 to a cell culture. Adding NaCl into water. branch derived adding a material entity into a target is a process with the objective to place a material entity bearing the 'material to be added role' into a material bearing the 'target of material addition role'. analyte role Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. GROUP: Role Branch Glucose in blood (measured in an assay to determine the concentration of glucose). OBI 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. A 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 analyte role disease stage PERSON: Bjoern peters Stage II breast cancer, The timepoint of recovery from a disease a part of an occurrence of a disease process which is associated with position in the normal progression of the disease disease stage intraperitoneal injection BP is the injection of a material entity (bearing the administered substance role) into the peritoneum (bearing the target role) of an organism using a syringe intraperitoneal injection transcription factor binding site identification OBI Philippe Rocca-Serra JZ: add equivalent axiom for classification add alternative term 'TF binding' which was used in BCBC database TF binding Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms. Funct Integr Genomics. 2007 Oct;7(4):335-45. Epub 2007 Jul 19. PMID: 17638031 a planned process with objective to find DNA region specifically recognized by proteins that function as transcription factors transcription factor binding site identification material to be added role 9 March 09 from discussion with PA branch OBI Role Branch drug added to a buffer contained in a tube; substance injected into an animal; material to be added role material to be added role is a protocol participant role realized by a material which is added into a material bearing the target of material addition role in a material addition process drawing a conclusion based on data Bjoern Peters 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. PERSON: Bjoern Peters PERSON: Jennifer Fostel 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 drawing a conclusion based on data planning 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 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 planning histological sample preparation OBI branch derived PERSON:Bjoern Peters histological sample preparation histological sample preparation is the preparation of an input tissue via slicing and labeling to make tissue microstructure of interest visible in a future histology assay mass analyzer Frank Gibson PERSON: Daniel Schober http://en.wikipedia.org/wiki/Mass_spectrometry#Mass_analyzer A Mass analyzer is a device that separates ions according to their mass-to-charge ratio. All mass spectrometers are based on dynamics of charged particles in electric and magnetic fields in vacuum where the two laws of Lorentz force law and Newton's second law of motion apply. The mass analyzer of the Voyager-DE(tm) STR Biospectrometry Workstation mass analyzer ion source Frank Gibson http://en.wikipedia.org/wiki/Mass_spectrometry#Ion_source An ion source is a device that is part of a mass spectrometer that ionizes the material under analysis. The ions are then transported by magnetic or electric fields to the mass analyzer. Techniques for ionization have been key to determining what types of samples can be analyzed by mass spectrometry. Electron ionization and chemical ionization are used for gases and vapors. In chemical ionization sources, the material is ionized by chemical ion-molecule reactions during collisions in the source. Two techniques often used with liquid and solid biological samples include electrospray ionization (due to John Fenn PMID 2675315.) and matrix-assisted laser desorption/ionization (MALDI, due to M. Karas and F. Hillenkamp (Measuring Mass: From Positive Rays to Proteins by Michael A. Grayson (Editor) (ISBN 0-941901-31-9))). The ion source of a Voyager-DE??? STR Biospectrometry Workstation ion source ion detector Frank Gibson http://en.wikipedia.org/wiki/Mass_spectrometry#Detector An ion detector is a device that measures and records the charge induced or current produced when an ion passes by or hits a surface. In a scanning instrument the signal produced in the detector during the course of the scan versus where the instrument is in the scan (at what m/Q) will produce a mass spectrum, a record of ions as a function of m/Q. The ion detector of the Voyager-DE(tm) STR Biospectrometry Workstation ion detector light emission function Bill Bug Daniel Schober Frank Gibson Melanie Courtot A light emission function is an excitation function to excite a material to a specific excitation state that it emits light. light emission function contain function A syringe, a beaker Bill Bug Daniel Schober Frank Gibson Melanie Courtot A contain function is a function to constrain a material entities location in space contain function heat function Bill Bug Daniel Schober Frank Gibson Melanie Courtot A heat function is a function that increases the internal kinetic energy of a material heat function material separation function Bill Bug Daniel Schober Frank Gibson Melanie Courtot A material separation function is a function that increases the resolution between two or more material entities. The to distinction between the entities is usually based on some associated physical quality. material separation function excitation function Bill Bug Daniel Schober Frank Gibson Melanie Courtot A excitation function is a function to inject energy by bombarding a material with energetic particles (e.g., photons) thereby imbuing internal material components such as electrons with additional energy. These internal, 'excited' particles may lead to the rupturing of covalent chemical bonds or may quickly relax back to there unexcited state with an exponential time course thereby locally emitting energy in the form of photons. excitation function synthesizing function A synthesizing function is a function to assemble new output materials from distinct input materials. The output materials typically consist of chemically distinct monomeric objects or object aggregate polymers. Bill Bug Daniel Schober Frank Gibson Melanie Courtot synthesizing function perturb function Bill Bug Daniel Schober Frank Gibson Melanie Courtot A perturb function is a function that disrupts the normal function of a system induced through either internal or external means. External means of perturbation include: (1) displacement fields in the physical sense - e.g., temperature change, osmotic shock, pressure change; (2) application of small molecules such as drugs or toxins to perturb the function of specific pathways or application of surfactants to perturb the normal function of plasma membrane. Internal means of perturbation include: (1) manipulation of gene function via gene knockout or transcript knockdown via RNAi; (2) directed genetic mutation leading to minimal aa alterations that interfere with peptide function. http://en.wikipedia.org/wiki/Perturbation_biology perturb function filter function Frank Gibson A filter function is a function to prevent the flow of certain entities based on a quality or qualities of the entity while allowing entities which have different qualities to pass through filter function mechanical function Bill Bug Daniel Schober Frank Gibson Melanie Courtot A mechanical function is a function that is realised via mechanical work (through an certain amount of energy transferred by some force). http://en.wikipedia.org/wiki/Mechanical_work mechanical function transfer function Bill Bug Daniel Schober Frank Gibson Melanie Courtot A transfer function is a function to displace a material from one location to another. transfer function ionization function Bill Bug Daniel Schober Frank Gibson Melanie Courtot The ion source in amass spectrometer An ionization function is a function to physically convert an atom or molecule into an ion by adding or removing charged particles such as electrons or other ions. http://en.wikipedia.org/wiki/Ionization ionization function cool function Daniel Schober Frank Gibson Melanie Courtot A cool function is a function to decrease the internal kinetic energy of a material below the initial kinetic energy of that type of material. cool function information processor function Frank Gibson An information processor function is a function that converts information from one form to another, by a lossless process or an extraction process. data processor function information processor function image acquisition function Frank Gibson An image acquisition function is a function to acquire an image of a material image acquisition function image creation device Frank Gibson sep:00096 An image creation device is a device which captures a digitized image of an object image acquisition device image creation device solid support function Daniel Schober Frank Gibson Melanie Courtot Taped, glued, pinned, dried or molecularly bonded to a solid support A solid support function is a function of a device on which an entity is kept in a defined position and prevented in its movement solid support function environment control function Bill Bug Daniel Schober Frank Gibson Melanie Courtot An environmental control function is a function that regulates a contained environment within specified parameter ranges. For example the control of light exposure, humidity and temperature. environment control function sort function Daniel Schober Frank Gibson Melanie Courtot A sort function is a function to distinguish material components based on some associated physical quality or entity and to partition the separate components into distinct fractions according to a defined order. sort function PCR product GROUP: OBI BIomaterial Branch GROUP: OBI BIomaterial Branch PCR products are the results of amplifcation process. Detection of a PCR products is used to detect DNA and RNA. PCR product We are using PCR and not the written out words, as this is the most common used. is double stranded DNA that is the specified output of a polymerase chain reaction nucleic acid template role a model or standard for making comparisons; wordnet.princeton.edu/perl/webwn 19 feb 2009 a reference substance role which inheres in nucleic acid material entity and is realized in the process of using the nucleic acid bearing the template role as a reference during synthesis of a reverse copy. nucleic acid template role cloning vector role PERSON: Helen Parkinson pBluescript plays the role of a cloning vector a vector role played by a small, self-replicating DNA or RNA molecule - usually a plasmid or chromosome - and realized in a process whereby foreign DNA or RNA is inserted into the vector during the process of cloning. cloning vector role polymerase chain reaction OBI Plan adapted from wikipedai Opisthorchis viverrini: Detection by polymerase chain reaction (PCR) in human stool samples. Exp Parasitol. 2008 Sep 9. PMID: 18805413 PCR PCR is the process in which a DNA polymerase is used to amplify a piece of DNA by in vitro enzymatic replication. As PCR progresses, the DNA thus generated is itself used as a template for replication. This sets in motion a chain reaction in which the DNA template is exponentially amplified. polymerase chain reaction cloning insert role Feb 20, 2009. from Wikipedia: cloning of any DNA fragment essentially involves four steps: DNA fragmentation with restriction endonucleases, ligation of DNA fragments to a vector, transfection, and screening/selection. There are multiple processes involved, it is not just "cloning process" GROUP: Role branch OBII and Wikipedia cloning insert role cloning insert role is a role which inheres in DNA or RNA and is realized by the process of being inserted into a cloning vector in a cloning process. reverse transcriptase group:OBI person:Melanie Courtot enzyme and has_function some GO:0003964 (RNA-directed DNA polymerase activity) reverse transcriptase syringe OBI Instrument adapted from Wikipedia Philippe Rocca-Serra Accuracy of oral liquid measuring devices: comparison of dosing cup and oral dosing syringe.Ann Pharmacother. 2008 Jan;42(1):46-52. Epub 2007 Dec 4. PMID: 18056832 a processed material which is used to introduce or draw fluids from a material entity. A syringe is made of a piston and body. the movement of the piston in the body determines the amount/volume of fluid to inject or draw syringe extract GROUP: OBI Biomatrial Branch PERSON: Philippe Rocca-Serra 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 extract extracted material transcription profiling assay OBI Philippe Rocca-Serra transcription profiling An assay which aims to provide information about gene expression and transcription activity using ribonucleic acids collected from a material entity using a range of techniques and instrument such as DNA sequencers, DNA microarrays, Northern Blot Whole genome transcription profiling of Anaplasma phagocytophilum in human and tick host cells by tiling array analysis. BMC Genomics. 2008 Jul 31;9:364. PMID: 18671858 gene expression profiling transcription profiling assay averaging objective Elisabetta Manduchi PERSON: Elisabetta Manduchi A mean calculation which has averaging objective is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the 'center of gravity' for the data set. It is also known as the first moment. An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation. James Malone averaging objective injection OBI Biomaterial Philippe Rocca-Serra Multiple Small-Dose Injections Can Reduce the Passage of Sclerosant Foam into Deep Veins During Foam Sclerotherapy for Varicose Veins. Eur J Vasc Endovasc Surg. 2008 Oct 13. PMID: 18922712 injection injection is process which aims at introducing a compound or a mixture into a material entity (either biological entity or instrument) by relying on devices such as syringe or injector connection, attached or forced into a vascular system (veins of an organism or tubes of a machine) or in a tissue. enzyme GROUP:OBI MC: known issue: enzyme doesn't classify under material entity for now as it isn't stated that anything that has_part some material entity is a material entity. If we add as equivalent classes to material entity has_part some material entity and part_of some material entity (each one in his own necessary and sufficient block) Pellet in P3 doesn't classify any more. person: Melanie Courtot (protein or rna) or has_part (protein or rna) and has_function some GO:0003824 (catalytic activity) enzyme intraperitoneal administration Person:Bjoern Peters Rats were injected intraperitoneally with either rrIL-6 (250 ng/0.5 ml) or equal-volume sterile saline twice within an interval of 24 h The administration of a substance into the peritoneum of an organism intraperitoneal administration plasmid group:OBI person:Melanie Courtot plasmid plasmid = DNA and has_quality circular and has_function (is_realized_as some gene expression) GO:0010467 adding material objective BP creating a mouse infected with LCM virus adding material objective is the specification of an objective to add a material into a target material. The adding is asymmetric in the sense that the target material largely retains its identity genotyping assay OBI Biomaterial Philippe Rocca-Serra SNP analysis High-throughput genotyping of oncogenic human papilloma viruses with MALDI-TOF mass spectrometry. Clin Chem. 2008 Jan;54(1):86-92. Epub 2007 Nov 2.PMID: 17981923 an assay which generates data about a genotype from a specimen of genomic DNA. A variety of techniques and instruments can be used to produce information about sequence variation at particular genomic positions. genotype profiling, SNP genotyping genotyping assay analyte measurement objective PERSON: Bjoern Peters PPPB branch 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 analyte measurement objective assay objective PPPB branch PPPB branch 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) assay objective analyte assay PERSON:Bjoern Peters PERSON:Helen Parkinson PERSON:Philippe Rocca-Serra PERSON:Alan Ruttenberg GROUP:OBI Planned process branch PERSON:Bjoern Peters, Helen Parkinson, Philippe Rocca-Serra, Alan Ruttenberg logical def modified to remove expression below, as some analyte assays report below the level of detection, and therefore not a scalar measurement datum, replaced by measurement datum and ('has measurement unit label' some 'measurement unit label') and ('is quality measurement of' some 'molecular concentration')) 2013-09-23: simplify equivalent axiom An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant. Note: is_realization of some analyte role isn't always true, for example when there is none of the analyte in the evaluant. For the moment we are writing it this way, but when the information ontology is further worked out this will be replaced with a condition discussing the measurement. 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 target of material addition role From Branch discussion with BP, AR, MC -- there is a need for the recipient to interact with the administered material. for example, a tooth receiving a filling was not considered to be a target role. GROUP: Role Branch OBI peritoneum of an animal receiving an interperitoneal injection; solution in a tube receiving additional material; location of absorbed material following a dermal application. target of material addition role is a role realized by an entity into which a material is added in a material addition process target of material addition role normalized data set PERSON: James Malone PERSON: Melanie Courtot A data set that is produced as the output of a normalization data transformation. normalized data set measure function A glucometer measures blood glucose concentration, the glucometer has a measure function. PERSON: Daniel Schober PERSON: Helen Parkinson PERSON: Melanie Courtot PERSON:Frank Gibson 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. measure function consume data function PERSON: Daniel Schober PERSON: Frank Gibson PERSON: Melanie Courtot Process data function is a function that is borne by in a material entity by virtue of its structure. When realized the material entity consumes data. consume data function material transformation objective GROUP: OBI PlanAndPlannedProcess Branch PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra 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. artifact creation objective material transformation objective manufacturing GROUP: OBI PlanAndPlannedProcess Branch Manufacturing implies reproducibility and responsibility AR PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra Manufacturing is a process with the intent to produce a processed material which will have a function for future use. A person or organization (having manufacturer role) is a participant in this process This includes a single scientist making a processed material for personal use. manufacturing manufacturing objective GROUP: OBI PlanAndPlannedProcess Branch PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra is the objective to manufacture a material of a certain function (device) manufacturing objective study design execution 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. a planned process that realizes the concretization of a study design branch derived injecting a mouse with PBS solution, weighing it, and recording the weight according to 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. study design execution reverse transcribed polymerase chain reaction 3/21/10, BP:Modified definition to clarify that this is not the assay, but the material transformation Harmonisation of multi-centre real-time reverse-transcribed PCR results of a candidate prognostic marker in breast cancer: an EU-FP6 supported study of members of the EORTC - PathoBiology Group. Span PN, Sieuwerts AM, Heuvel JJ, Spyratos F, Duffy MJ, Eppenberger-Castori S, Vacher S, O'Brien K, McKiernan E, Pierce A, Vuaroqueaux V, Foekens JA, Sweep FC, Martens JW. Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 Philippe Rocca-Serra RT-PCR reverse transcribe pcr is a process which allow amplification of cDNA during a pcr reaction while the cDNA results from a retrotranscription of messenger RNA isolated from a material entity. reverse transcribed polymerase chain reaction reverse transcription polymerase chain reaction manufacturer role GROUP: Role Branch Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process. OBI With respect to The Accuri C6 Flow Cytometer System, the organization Accuri bears the role manufacturer role. With respect to a transformed line of tissue culture cells derived by a specific lab, the lab whose personnel isolated the cll line bears the role manufacturer role. With respect to a specific antibody produced by an individual scientist, the scientist who purifies, characterizes and distributes the anitbody bears the role manufacturer role. manufacturer role DNA sequencing DNA sequencing DNA sequencing is a sequencing process which uses deoxyribonucleic acid as input and results in a the creation of DNA sequence information artifact using a DNA sequencer instrument. Genomic deletions of OFD1 account for 23% of oral-facial-digital type 1 syndrome after negative DNA sequencing. Thauvin-Robinet C, Franco B, Saugier-Veber P, Aral B, Gigot N, Donzel A, Van Maldergem L, Bieth E, Layet V, Mathieu M, Teebi A, Lespinasse J, Callier P, Mugneret F, Masurel-Paulet A, Gautier E, Huet F, Teyssier JR, Tosi M, Frébourg T, Faivre L. Hum Mutat. 2008 Nov 19. PMID: 19023858 OBI Branch derived Philippe Rocca-Serra nucleotide sequencing DNA methylation profiling assay DNA methylation profiling DNA methylation profiling assay Genome-wide, high-resolution DNA methylation profiling using bisulfite-mediated cytosine conversion. Reinders J, Delucinge Vivier C, Theiler G, Chollet D, Descombes P, Paszkowski J. Genome Res. 2008 Mar;18(3):469-76. Epub 2008 Jan 24. PMID: 18218979 OBI branch derived Philippe Rocca-Serra an assay which aims to provide information about state of methylation of DNA molecules using genomic DNA collected from a material entity using a range of techniques and instrument such as DNA sequencers and often relying on treatment with bisulfites to ensure cytosine conversion. material separation objective PPPB branch PPPB branch 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. material separation objective clustered data set A clustered data set is the output of a K means clustering data transformation AR thinks could be a data item instead PERSON: James Malone PERSON: Monnie McGee data set with assigned discovered class labels A data set that is produced as the output of a class discovery data transformation and consists of a data set with assigned discovered class labels. clustered data set differential expression analysis data transformation A differential expression analysis data transformation is a data transformation that has objective differential expression analysis and that consists of James Malone Melanie Courtot Monnie McGee WEB: differential expression analysis data transformation urine specimen 4/10/2011BP: It seems to me that the editor notes refer to a previous version, and are no longer relevant. This could be instead a kind of collection of secreted stuff. Among secreted stuff there is passive, and active. urine is secreted, passiv. lavage is secreted, active a portion of urine collected from an organism are we happy calling collection of urine a material separation? urine specimen material combination Mixing two fluids. Adding salt into water. Injecting a mouse with PBS. bp bp created at workshop as parent class for 'adding material into target', which is asymmetric, while combination encompasses all addition processes. is a material processing with the objective to combine two or more material entities as input into a single material entity as output. material combination device setting Examples, 300V for 4 hours, 200mvolts, 37degrees.A knob set a 300 V is the device setting, the protocol stating to set the instrument to 300V is a device setting specification PERSON: Frank Gibson a quality inheres_in some device and is concretization of some (device_setting_specification and is_about a quality of the device device setting specimen collection process 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 A planned process with the objective of collecting a specimen. Bjoern Peters 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. 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 specimen collection label changed to 'specimen collection process' on 10/27/2014, details see tracker: http://sourceforge.net/p/obi/obi-terms/716/ 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. error correction data transformation EDITORS Monnie McGee An error correction data transformation is a data transformation that has the objective of error correction, where the aim is to remove (correct for) erroneous contributions from the input to the data transformation. James Malone error correction data transformation sample from organism 5/29: This is a helper class for now a material obtained from an organism in order to be a representative of the whole sample from organism 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. center value PERSON: James Malone PERSON: Monnie McGee median A data item that is produced as the output of a center calculation data transformation and represents the center value of the input data. center value portioning objective A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material. The objective to obtain multiple aliquots of an enzyme preparation. portioning objective average value PERSON: James Malone PERSON: Monnie McGee arithmetic mean A data item that is produced as the output of an averaging data transformation and represents the average value of the input data. average value whole organism preparation A material entity which is the output of a process in which one or more whole organisms are prepared in a way to make it easier to study them, and in which the great majority of organismal parts are maintained does this include injecting a dye to a patient to be able to visualize parts of his brain? If not, we should state that the components of the organism are substantially re-arranged. putting a mouse in the blender. Not: putting a mouse on a scale whole organism preparation separation into different composition objective 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). The objective to obtain cells contained in a sample of blood. 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 A objective specification to obtain a material entity for potential use as an input during an investigation. Bjoern Peters Bjoern Peters The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient. specimen collection objective material combination objective PPPB branch bp is an objective to obtain an output material that contains several input materials. material combination objective 454 Genome Sequence 20 454 Genome Sequence 20 GS 20 PMID: 18946007.Pyrosequencing analysis of the oral microflora of healthy adults. Keijser BJ, Zaura E, Huse SM, van der Vossen JM, Schuren FH, Montijn RC, ten Cate JM, Crielaard W. J Dent Res. 2008 Nov;87(11):1016-20. Philippe Rocca-Serra is a DNA sequencer which is manufactured by 454 Life Science Corporation and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. The fluidics subsystem ensures accurate reagent dispensing. It consists of a reagents cassette (which holds the reagent containers), a sipper manifold, pumps, valves, and debubblers. The fluidics subsystem flows the sequencing reagents across the wells of the PicoTiterPlate device, and moves the spent reagents from the PicoTiterPlate device to the waste receptacle. The optics subsystem consists of a CCD camera and a camera controller. The camera captures the light emitted in the wells of the PicoTiterPlate device during each step of the sequencing cycle, and sends the digital images to the computer subsystem for processing. The computer controls the other Sequencer subsystems, and processes the digital images sent by the camera to extract the DNA sequence information. immunoprecipitation OBI plan and planned process branch PMID: 19419533. Arabidopsis RNA immunoprecipitation. Terzi LC, Simpson GG. Plant J. 2009 Jul;59(1):163-8. Philippe Rocca-Serra immunoprecipitation is a process which realizes a material separation objective by relying on antibodies to specifically binding to material entity ABI 377 automated sequencer ABI 377 automated sequencer Applied Biosystems Philippe Rocca-Serra is a DNA sequencer which is manufactured by Applied Biosystems corporation (formerly Perkin-Elmer). It allows automated chain termination DNA sequencing. It has part polyacrylamide gel electrophoresis system and a laser -based detection system to detect fluorescence intensity emitted by the dyes attached to the dideoxyterminator nucleotides or to the primers. MeDIP-seq assay MeDIP-seq assay Methylated DNA immunoprecipitation sequencing assay PMID: 18612301. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, Gräf S, Johnson N, Herrero J, Tomazou EM, Thorne NP, Bäckdahl L, Herberth M, Howe KL, Jackson DK, Miretti MM, Marioni JC, Birney E, Hubbard TJ, Durbin R, Tavaré S, Beck S. Nat Biotechnol. 2008 Jul;26(7):779-85. Philippe Rocca-Serra adapted from wikipedia is an assay which aims at identifying methylated sites in genomic DNA and determining methylation pattern that affect gene transcription by relying on immunoprecipitation of methylated genomic DNA, creation of a library of corresponding DNA fragments (either single or paired-end fragments) and subsequent sequencing using parallelized sequencing methods. animal feeding Bjoern Peters In an investigation, this will typically be part of an animal care process animal feeding animal feeding is a process in which animals are provided with food branch derived giving crickets to a snake. chain termination sequencing PMID: 271968. DNA sequencing with chain-terminating inhibitors. Sanger F, Nicklen S, Coulson AR. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463-7. Philippe Rocca-Serra Sanger sequencing adapted from wikipedia chain termination sequencing dye terminator sequencing is a DNA sequencing which rely on the use of dideoxynucleotides used in 4 distinct sequencing reaction on the same DNA sample. The dideoxynucleotides, once incorporated in the complementary DNA strand being synthesized by the DNA polymerase prevent any further chain elongation. The newly generated sequences are resolved on a polyacrylamide gel using electrophoresis and labels (either fluorochrome or radioactivity) are used to determine the nucleotide present at a given position AB SOLiD System AB SOLiD System Applied Biosystems PMID: 19336255. RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Wilhelm BT, Landry JR. Methods. 2009 Jul;48(3):249-57. Philippe Rocca-Serra is a DNA sequencer which is manufactured by Applied Biosystems and which enable DNA sequencing by ligation Helicos sequencing Helicos sequencing PMID: 18388294. Single-molecule DNA sequencing of a viral genome. Harris TD, Buzby PR, Babcock H, Beer E, Bowers J, Braslavsky I, Causey M, Colonell J, Dimeo J, Efcavitch JW, Giladi E, Gill J, Healy J, Jarosz M, Lapen D, Moulton K, Quake SR, Steinmann K, Thayer E, Tyurina A, Ward R, Weiss H, Xie Z. Science. 2008 Apr 4;320(5872):106-9. Philippe Rocca-Serra adapted from wikipedia is a DNA sequencing which allows sequence identification of billions of DNA molecules immobilized to a surface by using DNA polymerase and fluorescently labeled nucleotides added one at a time. The sequencing process does not requires amplification step and is typically able to produce reads of 25 base pair length. true single molecule sequencing 454 Genome Sequencer FLX 454 GS FLX 454 Genome Sequencer FLX GS-FLX PMID: 18616967. The Genome Sequencer FLX System--longer reads, more applications, straight forward bioinformatics and more complete data sets. Droege M, Hill B. J Biotechnol. 2008 Aug 31;136(1-2):3-10. Philippe Rocca-Serra adapted from https://www.roche-applied-science.com/servlet/RCProductDisplay?langId=-1&storeId=10202&productId=3.8.8.1.1.3&catalogId=10202&krypto=mgV8a0Sdps6%2BCXU8IoddmzNEyGgjde9j8MOFCiMzRsduELeenAlVZ%2FE1QR%2BxLpzNlqMZPLRHqaI%3D&ddkey=https:RCProductDisplay is a DNA sequencer which is manufactured by 454 Life Science Corporation and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. The fluidics subsystem ensures accurate reagent dispensing. It consists of a reagents cassette (which holds the reagent containers), a sipper manifold, pumps, valves, and debubblers. The fluidics subsystem flows the sequencing reagents across the wells of the PicoTiterPlate device, and moves the spent reagents from the PicoTiterPlate device to the waste receptacle. The optics subsystem consists of a CCD camera and a camera controller. The camera captures the light emitted in the wells of the PicoTiterPlate device during each step of the sequencing cycle, and sends the digital images to the computer subsystem for processing. The computer controls the other Sequencer subsystems, and processes the digital images sent by the camera to extract the DNA sequence information. Illumina Genome Analyzer II Illumina Corporation Illumina Genome Analyzer II PMID: 19336255. RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Wilhelm BT, Landry JR.Methods. 2009 Jul;48(3):249-57. Philippe Rocca-Serra is a DNA sequence which is manufactured by Illumina (Solexa) corporation. it support sequencing of single or paired end clone libraries relying on sequencing by synthesis technology Edman degradation Edman degradation PMID 4773306. Niall HD (1973). "Automated Edman degradation: the protein sequenator". Meth. Enzymol. 27: 942-1010 adapted from Wikipedia (http://en.wikipedia.org/wiki/Edman_degradation) is a process which produces a sequence from an input peptide or protein. In this process, the amino-terminal (N-terminal) residue is labeled and cleaved from the peptide without disrupting the peptide bonds between other amino acid residues. SOLiD sequencing PMID: 19119315. High-resolution analysis of the 5'-end transcriptome using a next generation DNA sequencer. Hashimoto S, Qu W, Ahsan B, Ogoshi K, Sasaki A, Nakatani Y, Lee Y, Ogawa M, Ametani A, Suzuki Y, Sugano S, Lee CC, Nutter RC, Morishita S, Matsushima K. PLoS One. 2009;4(1):e4108. Philippe Rocca-Serra SOLiD sequencing adapted from Wikipedia and Applied Biosystems web site is a DNA sequencing which allows sequence identification by relying on the following steps: 1. Primers hybridize to the P1 adapter sequence within the library template. 2. A set of four fluorescently labeled di-base probes compete for ligation to the sequencing primer. Specificity of the di-base probe is achieved by interrogating every 1st and 2nd base in each ligation reaction. 3. Multiple cycles of ligation, detection and cleavage are performed with the number of cycles determining the eventual read length. 4. Following a series of ligation cycles, the extension product is removed and the template is reset with a primer complementary to the n-1 position for a second round of ligation cycles Li-Cor 4300 DNA Analysis System Li-Cor 4300 DNA Analysis System OBI and Li-Cor Philippe Rocca-Serra is a DNA sequencer which is manufactured by Li-Cor corporation and enable automated chain termination based DNA sequencing library preparation PMID: 19570239. Construction and analysis of cotton (Gossypium arboreum L.) drought-related cDNA library. Zhang L, Li FG, Liu CL, Zhang CJ, Zhang XY. BMC Res Notes. 2009 Jul 2;2:120. Philippe Rocca-Serra is a process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors. library construction library preparation ChIP-seq assay ChIP-seq assay PMID: 19275939 ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. Schmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, Odom DT. Methods. 2009 Jul;48(3):240-8. Epub 2009 Mar 9. Philippe Rocca-Serra adapted from Wikipedia an assay which aims at identifying protein binding sites in genomic DNA and determining how protein may regulate gene transcription by relying on immunoprecipitation of DNA bound protein, creation of a library of corresponding DNA fragments (either single or paired-end fragments) and subsequent sequencing using parallelized sequencing methods. chromatin immunoprecipitation sequencing assay made some modification based on the discussion on 2011/4/4 obi dev call, using DNA sequencing instead of union of some specific DNA sequencing processes HeliScope Single Molecule Sequencer HeliScope Single Molecule Sequencer Philippe Rocca-Serra is a DNA sequencer manufacturer by Helicos Corporation to carry out Single Molecule sequencing using reversible termination chemistry paired-end library PMID: 19339662. Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res. 2009 Apr;19(4):521-32. Fullwood MJ, Wei CL, Liu ET, Ruan Y. Philippe Rocca-Serra adapted from information provided by Solid web site is a collection of short paired tags from the two ends of DNA fragments are extracted and covalently linked as ditag constructs mate-paired library paired-end library paired-end tag (PET) library DNA sequencing by ligation DNA sequencing by ligation PERSON: Philippe Rocca-Serra PMID: 19546169. Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two base encoding. McKernan KJ, Peckham HE, Costa G, McLaughlin S, Tsung E, Fu Y, Clouser C, Dunkan C, Ichikawa J, Lee C, Zhang Z, Sheridan A, Fu H, Ranade S, Dimilanta E, Sokolsky T, Zhang L, Hendrickson C, Li B, Kotler L, Stuart J, Malek J, Manning J, Antipova A, Perez D, Moore M, Hayashibara K, Lyons M, Beaudoin R, Coleman B, Laptewicz M, Sanicandro A, Rhodes M, De La Vega F, Gottimukkala RK, Hyland F, Reese M, Yang S, Bafna V, Bashir A, Macbride A, Aklan C, Kidd JM, Eichler EE, Blanchard AP. Genome Res. 2009 Jun 22. is a DNA sequencing which relies on DNA ligase activity to perform chain extension during the sequencing reaction step. Solexa sequencing PMID: 18987734 Accurate whole human genome sequencing using reversible terminator chemistry. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR, Boutell JM, Bryant J, Carter RJ, Keira Cheetham R, Cox AJ, Ellis DJ, Flatbush MR, Gormley NA, Humphray SJ, Irving LJ, Karbelashvili MS, Kirk SM, Li H, Liu X, Maisinger KS, Murray LJ, Obradovic B, Ost T, Parkinson ML, Pratt MR, Rasolonjatovo IM, Reed MT, Rigatti R, Rodighiero C, Ross MT, Sabot A, Sankar SV, Scally A, Schroth GP, Smith ME, Smith VP, Spiridou A, Torrance PE, Tzonev SS, Vermaas EH, Walter K, Wu X, Zhang L, Alam MD, Anastasi C, Aniebo IC, Bailey DM, Bancarz IR, Banerjee S, Barbour SG, Baybayan PA, Benoit VA, Benson KF, Bevis C, Black PJ, Boodhun A, Brennan JS, Bridgham JA, Brown RC, Brown AA, Buermann DH, Bundu AA, Burrows JC, Carter NP, Castillo N, Chiara E Catenazzi M, Chang S, Neil Cooley R, Crake NR, Dada OO, Diakoumakos KD, Dominguez-Fernandez B, Earnshaw DJ, Egbujor UC, Elmore DW, Etchin SS, Ewan MR, Fedurco M, Fraser LJ, Fuentes Fajardo KV, Scott Furey W, George D, Gietzen KJ, Goddard CP, Golda GS, Granieri PA, Green DE, Gustafson DL, Hansen NF, Harnish K, Haudenschild CD, Heyer NI, Hims MM, Ho JT, Horgan AM, Hoschler K, Hurwitz S, Ivanov DV, Johnson MQ, James T, Huw Jones TA, Kang GD, Kerelska TH, Kersey AD, Khrebtukova I, Kindwall AP, Kingsbury Z, Kokko-Gonzales PI, Kumar A, Laurent MA, Lawley CT, Lee SE, Lee X, Liao AK, Loch JA, Lok M, Luo S, Mammen RM, Martin JW, McCauley PG, McNitt P, Mehta P, Moon KW, Mullens JW, Newington T, Ning Z, Ling Ng B, Novo SM, O'Neill MJ, Osborne MA, Osnowski A, Ostadan O, Paraschos LL, Pickering L, Pike AC, Pike AC, Chris Pinkard D, Pliskin DP, Podhasky J, Quijano VJ, Raczy C, Rae VH, Rawlings SR, Chiva Rodriguez A, Roe PM, Rogers J, Rogert Bacigalupo MC, Romanov N, Romieu A, Roth RK, Rourke NJ, Ruediger ST, Rusman E, Sanches-Kuiper RM, Schenker MR, Seoane JM, Shaw RJ, Shiver MK, Short SW, Sizto NL, Sluis JP, Smith MA, Ernest Sohna Sohna J, Spence EJ, Stevens K, Sutton N, Szajkowski L, Tregidgo CL, Turcatti G, Vandevondele S, Verhovsky Y, Virk SM, Wakelin S, Walcott GC, Wang J, Worsley GJ, Yan J, Yau L, Zuerlein M, Rogers J, Mullikin JC, Hurles ME, McCooke NJ, West JS, Oaks FL, Lundberg PL, Klenerman D, Durbin R, Smith AJ. Nature. 2008 Nov 6;456(7218):53-9. Philippe Rocca-Serra Solexa sequencing adapted from Wikipedia and Illumina / Solexa web site (SS_DNAsequencing.pdf document available on july 2009) is a DNA sequencing which allows sequence identification by relying on use of DNA polymerase and reversible terminator. The methods requires immobilization of genomic DNA fragment onto a surface and a specific clonal amplification step known as bridge PCR. Reliance on reversible terminator allow cycles of DNA chain extension by DNA polymerase and imaging without the need of electrophoretic separation of newly synthesized DNA fragment as with Sanger sequencing. reversible terminator sequencing host role 30 Mar09 submitted by vaccine community 30Mar09 virus reproducing inside a cell; bacteria causing a disease, host can be harmed or not. we want to avoid a cat sitting on my lap and an animal care technician; these are not examples or hosts; dental cares = on tooth, but part of outer layer of tooth, so covered by "within" in the definition GROUP: Role Branch In biology, a host is an organism that harbors a virus or parasite, or a mutual or commensal symbiont, typically providing nourishment and shelter. http://en.wikipedia.org/wiki/Host_(biology) 30 March 09 OBI host role host role is a role played by an organism and realized by providing nourishment, shelter or a means of reproduction to another organism within the organism playing the host role http://en.wikipedia.org/wiki/Host_(biology) pyrosequencing Philippe Rocca-Serra Pyrosequencing sheds light on DNA sequencing. PMID: 1115661. Ronaghi M. Genome Res. 2001 Jan;11(1):3-11. Review. Wikipedia (http://en.wikipedia.org/wiki/Pyrosequencing) and Roche 454 life science web site is a DNA sequencing which allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step. The template DNA is immobilized, and solutions of A, C, G, and T nucleotides are added and removed after the reaction, sequentially. Light is produced only when the nucleotide solution complements the first unpaired base of the template. The sequence of solutions which produce chemiluminescent signals allows the determination of the sequence of the template. ssDNA template is hybridized to a sequencing primer and incubated with the enzymes DNA polymerase, ATP sulfurylase, luciferase and apyrase, and with the substrates adenosine 5-prime phosphosulfate (APS) and luciferin. pyrosequencing recombinant vector A recombinant vector is created by a recombinant vector cloning process, and contains nucleic acids that can be amplified. It retains functions of the original cloning vector. recombinant vector DNA sequencing by synthesis DNA sequencing by synthesis PERSON: Philippe Rocca-Serra PMID: 18263613. A new class of cleavable fluorescent nucleotides: synthesis and optimization as reversible terminators for DNA sequencing by synthesis. Turcatti G, Romieu A, Fedurco M, Tairi AP. Nucleic Acids Res. 2008 Mar;36(4):e25. is a DNA sequencing which relies on DNA polymerase activity to perform chain extension during the sequencing reaction step. single fragment library Philippe Rocca-Serra fragment library is a collection of short tags from DNA fragments, are extracted and covalently linked as single tag constructs single fragment library cloning vector A cloning vector is an engineered material that is used as an input material for a recombinant vector cloning process to carry inserted nucleic acids. It contains an origin of replication for a specific destination host organism, encodes for a selectable gene product and contains a cloning site. cloning vector material sample role 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. A material sample role is a specimen role borne by a material entity that is the output of a material sampling process. 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. material sample role material sample A material entity that has the material sample role OBI: workshop 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. material sample sample sample population bisulfite sequencing 8/19/09: Chris says that there may used to be a way of doing bisulfite sequencing comparing lengths of restriction fragments, which implies that it is possible to do without DNA sequencing. An assay which allows to determine the methylation status of genomic DNA using DNA sequencing techniques preceded by a bisulfite based chemical modification of genomic DNA at CpG island location. PMID: 19581485. High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Hodges E, Smith A, Kendall J, Xuan Z, Ravi K, Rooks M, Zhang M, Ye K, Battacharjee A, Brizuela L, McCombie WR, Wigler M, Hannon GJ, Hicks J. Genome Res. 2009 Jul 6. Philippe Rocca-Serra adapted from Wikipedia bisulfite sequencing study design independent variable 2009-03-16: work has been done on this term 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 thisdefinition please notify OBI. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Chris Stoeckert Web: http://en.wikipedia.org/wiki/Dependent_and_independent_variables study factor In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, disease status is the independent variable. 2/2/2009 Original definition - In the design of experiments, independent variables are those whose values are controlled or selected by the person experimenting (experimenter) to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled. independent variable In the Philly 2013 workshop the label was chosen to distinguish it from "dependent variable" as used in statistical modelling. See: http://en.wikipedia.org/wiki/Statistical_modeling a directive information entity that is part of a study design. Independent variables are entities whose values are selected to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled experimental factor study design independent variable study design dependent variable 2009-03-16: work has been done on this term 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 thisdefinition please notify OBI. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Chris Stoeckert WEB: http://en.wikipedia.org/wiki/Dependent_and_independent_variables In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, the gene expression is the dependent variable. 2/2/2009 In the design of experiments, independent variables are those whose values are controlled or selected by the person experimenting (experimenter) to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled. In the Philly 2013 workshop the label was chosen to distinguish it from "dependent variable" as used in statistical modelling. See: http://en.wikipedia.org/wiki/Statistical_modeling dependent variable dependent variable specification is part of a study design. The dependent variable is the event studied and expected to change when the independent variable varies. study design dependent variable study design controlled variable 2009-03-16: work has been done on this term 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 thisdefinition please notify OBI. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Chris Stoeckert WEB: http://en.wikipedia.org/wiki/Control_variable In the Philly 2013 workshop the label was chosen to distinguish it from "controlled variable" as used in statistical modelling 2/2/2009 Original definition: Controlled variables are also important to identify in experiments. They are the variables that are kept constant to prevent their influence on the effect of the independent variable on the dependent. Every experiment has a controlling variable, and it is necessary to not change it, or the results of the experiment won't be valid controlled variable In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, age is a controlled variable. Controlled variable specification is a part of a study design. They are the entities that could vary, but are kept constant to prevent their influence on the effect of the independent variable on the dependent. study design controlled variable multiple testing correction objective A multiple testing correction objectives is a data transformation objective where the aim is to correct for a set of statistical inferences considered simultaneously Application of the Bonferroni correction http://en.wikipedia.org/wiki/Multiple_Testing_Correction multiple comparison correction objective multiple testing correction objective transcription factor binding site PLace_holder for sequence ontology term SO:0000235 transcription factor binding site purification objective 10/14/09, BP: This should be linked to the 'purified' 'currently conferred quality BP PERSON:Bjoern Peters The objective to separate a material entity into different compositions of which one or more have are purified fractions that contain higher concentration of a desired component, while others contain impurities and are not of interest isolation objective purification objective the objective to obtain a pure fraction of a specific peptide when running an HPLC on a crude synthesis of peptides. cross linking A process in which bonds are created that link one polymer to another PERSON: Chris Stoeckert cross linking cross linking can be used as a probe to link proteins together, to check protein protein interactions http://en.wikipedia.org/wiki/Cross-link material maintenance objective An objective specification maintains some or all of the qualities of a material over time. PERSON: Bjoern Peters material maintenance objective PERSON: Bjoern Peters amplified DNA Alan Ruttenberg Amplied DNA created by PCR DNA that has been produced in an enzymatic amplification process PERSON: Alan Ruttenberg amplified DNA primary structure of DNA macromolecule BP et al a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues. placeholder for SO primary structure of DNA macromolecule DNA residue methylation DNA residue methylation a quality of a DNA residue that has a methyl group attached to it measurement device A device in which a measure function inheres. A ruler, a microarray scanner, a Geiger counter. GROUP:OBI Philly workshop OBI measurement device high molecular weight DNA extract Extraction of chromosomal DNA from mammalian cells by first isolating nucei OBI PERSON:Chris Stoeckert The output of an extraction process in which DNA molecules above a molecular weight cutoff are purified in order to exclude DNA from organellas. high molecular weight DNA extract 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 primary structure of RNA molecule Person:Bjoern Peters The primary structure of an RNA molecule that is completely defined by the set of its nucleic residue parts and the linear order induced by the peptide bonds that hold them together primary structure of RNA molecule polyA RNA extraction A RNA extraction process typically involving the use of poly dT oligomers in which the desired output material is polyA RNA. Person: Chris Stoeckert Person: Jie Zheng UPenn Group polyA RNA extraction organellar RNA extraction A RNA extraction process in which the desired output material is RNA in the organelle(s). Person: Chris Stoeckert Person: Jie Zheng UPenn Group organellar RNA extraction record of missing knowledge A statement in a journal article indicating that the age of a patient at the onset of disease is not known. A statement indicating that the weight of a mouse was not measured. Bjoern Peters This class should probably end up in IAO. It could be further breaken down to indicate different kinds of lack of knowledge, e.g. inability to determine something vs. no attempt made to determine something vs. no informatino available if it was even attempted to determine something. The design pattern should be generalizable. 'unknown sex' is the first example, and needed immediately. a information content entity created to indicate that information about something is not available to the person recording it. record of missing knowledge total RNA extraction A RNA extraction process in which total cellular and organelle RNA are extracted. Person: Chris Stoeckert Person: Jie Zheng UPenn Group total RNA extraction record of unknown sex A database record indicating that the tissue sample in a microarray experiment came from an organism for which the biological sex is not known to the person who created the record. Bjoern Peters I think the statement is still about the instance of the biological sex quality of an organism. It is also about information available to the person making the statement. a record indicating that the biological sex of an organism is not known. record of unknown sex cytoplasmic RNA extraction A RNA extraction process in which the desired output material is RNA in the cytoplasm. Person: Chris Stoeckert Person: Jie Zheng UPenn Group cytoplasmic RNA extraction nuclear RNA extract A RNA extract that is the output of an extraction process in which RNA molecules found in the nucleus, including mRNA precursors (pre-mRNA), are extracted. Isolation and purification of nuclear RNA from animal cells using Norgen Bioteck corp. cytoplasmic and nuclear RNA purification kit (http://www.norgenbiotek.com/display-product.php?ID=30) PERSON: Chris Stoeckert PERSON: Jie Zheng UPenn Group nuclear RNA extract polyA RNA extract A RNA extract that is the output of an extraction process in which RNA molecules with poly A tail at its 3' end are purified. PERSON: Chris Stoeckert PERSON: Jie Zheng Preparation of polyA RNA by cellulose-bound oligo-dT (Aviv, H., Leder, P. 1972. Purification of biologically active globin messenger RNA by chromatography on oligothymidylic acid-cellulose. Proc. Nat. Acad. Sci. USA 69, 1408-1412.) UPenn Group polyA RNA extract pre-mortem specimen Bjoern Peters a specimen that was taken from a live organism material obtained through a liver biopsy from a human patient pre-mortem specimen MO_705 premortem cytoplasmic RNA extract A RNA extract that is the output of a RNA extraction process in which RNA molecules found in the cytoplasm are extracted. Cytoplasmic RNA extraction from mammalian tissues to create cDNA library (Carninci P, Nakamura M, Sato K, Hayashizaki Y, Brownstein MJ. Cytoplasmic RNA extraction from fresh and frozen mammalian tissues. Biotechniques. 2002;33:306–309.) PERSON: Chris Stoeckert PERSON: Jie Zheng UPenn Group cytoplasmic RNA extract RNA extract Group: UPenn Group PERSON: Chris Stoeckert PERSON: Jie Zheng RNA extract an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen. nuclear RNA extraction A RNA extraction process in which the desired output material is RNA in the nucleus. Person: Chris Stoeckert Person: Jie Zheng UPenn Group nuclear RNA extraction real time polymerase chain reaction assay A laboratory technique based on the PCR, which is used to amplify and simultaneously quantify a specific DNA molecule based on the use of complementary probes/primers. It enables both detection and quantification (as absolute number of copies or relative amount when normalized to DNA input or additional normalizing genes) of one or more specific sequences in a DNA sample. Q-PCR WEB: http://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction kinetic polymerase chain reaction person: Bjoern Peters person: Melanie Courtot qPCR quantitative real time polymerase chain reaction real time PCR real time polymerase chain reaction assay protein extract OBI & wikipedia PMID: 20032479. A bovine whey protein extract stimulates human neutrophils to generate bioactive IL-1Ra through a NF-kappaB- and MAPK-dependent mechanism. Rusu D, Drouin R, Pouliot Y, Gauthier S, Poubelle PE. J Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23. Person: Philippe Rocca-Serra a protein extract is the output of an extraction process from tissues or cell cultures resulting in a solution of cellular and/or organellar proteins in buffer solution used to prevent degradation, protein extract total RNA extract A RNA extract that is the output of an extraction process in which total celluar and organelle RNA molecules are isolated from a specimen. Extraction of total RNA from cells with Qiagen mini RNeasy kit. PERSON: Chris Stoeckert PERSON: Jie Zheng UPenn Group total RNA extract organellar RNA extract A RNA extract that is the output of an extraction process in which RNA molecules found in an organelle, e.g., mitochondrion, ER, or chloroplast, excluding the nucleus, are extracted. Extraction of organellar RNA from plant cells using organellar RNA binding protein. PERSON: Chris Stoeckert PERSON: Jie Zheng UPenn Group organellar RNA extract post mortem specimen Bjoern Peters a specimen that was taken from a dead organism post mortem specimen the spleen taken from a dead mouse MO_416 postmortem sequence feature annotation Bjoern Peters Bjoern Peters Information about a sequence region place holder for sequence ontology term sequence feature annotation labeled DNA extract Group: OBI group Group: OBI group Need to find out if we consider labeled nucleotides still nucleotides. It is after consulting with ChEBI group. Added duirng Mar 1, 2010 dev call a labeled specimen that is the output of a labeling process and has grain labeled DNA to be able to detect DNA in future experiments. labeled DNA extract freezing storage 2010/3/3 Alan Ruttenberg: There is a question of whether we should have a separate objective to "prepare for maintenance" 2014/2/3 OBI dev call: "prepare for maintenance" is a separate process. For example, 'freezing' and 'flash freezing' are defined and can be used to produce frozen material for storage. Updated both textual and logical definition. Both input and output material of freezing storage have quality frozen. A storage process in temperature that maintenance the frozen status of the stored entities. OBI Person: Alan Ruttenberg, Mathias Brochhausen a fozen pellet used for later assay freezing storage MO_481 frozen_storage animal euthanization A process in which is the end of life of animal is brought about in accordance with local regulations on treatment of animal subjects and using a method which causes minimal pain and distress to the animal subject Helen Parkinson and Melissa Haendel Melissa Haendel Rats were euthanized with CO2 animal euthanization animal sacrifice may later be refined with more specific list of organisms labeled RNA extract Group: OBI group Group: OBI group Need to find out if we consider labeled nucleotides still nucleotides. It is after consulting with ChEBI group. Added duirng Mar 1, 2010 dev call a labeled specimen that is the output of a labeling process and has grain labeled RNA to be able to detect RNA in future experiments. labeled RNA extract frozen specimen A specimen that has been frozen in order to store it. Frozen blood plasma MO_610 frozen_sample Person:Alan Ruttenberg frozen specimen labeled specimen A specimen that has been modified in order to be able to detect it in future experiments OBI group added during call 3/1/2010 labeled specimen lyophilization storage PERSON: Chris Stoeckert PERSON: Jie Zheng a storage process with input material entity and output freeze dried material for long time storage can link to freezing-dying equipment, such as freeze-dryer, rotary evaporator, if needed lyophilization storage study intervention GROUP: OBI PERSON: Bjoern Peters study intervention the part of the execution of an intervention design study which is varied between two or more subjects in the study material separation device A device with a separation function realized in a planed process flow cytometer material separation device intramuscular injection intramuscular injection is the injection of a material entity (bearing the administered substance role) into the muscle (bearing the target role) of an organism using a syringe service provider role Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer. PERSON:Helen Parkinson 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 service provider role paraffin specimen MO_990 paraffin_sample PERSON: Chris Stoeckert PERSON: Jie Zheng a specimen that is output of a paraffin storage process in which specimen is embedded in paraffin liver tissue embedded in paraffin paraffin specimen compound treatment design MO_555 compound_treatment_design PERSON: Bjoern Peters This is meant to include all kinds of material administrations, including vaccinations, chemical compounds etc. an intervention design in which the treatment is the administration of a compound compound treatment design processed specimen A specimen that has been intentionally physically modified. Bjoern Peters Bjoern Peters processed specimen A tissue sample that has been sliced and stained for a histology study. 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. subcutaneous injection PERSON: Melanie Courtot is the injection of a material entity (bearing the administered substance role) into the hypodermis (bearing the target role) of an organism using a syringe subcutaneous injection lyophilized specimen MO_589 freeze_dried_sample PERSON: Chris Stoeckert PERSON: Jie Zheng a specimen that is output of a lyophilization storage process in which specimen is lyophilized for storage. freezing dried DNA lyophilized specimen container 03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?) A device that can be used to restrict the location of material entities over time PERSON: Bjoern Peters container device 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. A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. 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. OBI development call 2012-12-17. PERSON: Helen Parkinson device instrument dose specification a directive information entity that describes the dose that will be administered to a target a protocol specifying to administer 1 ml of vaccine to a mouse dose specification fresh specimen MO_730 fresh_sample PERSON: Chris Stoeckert PERSON: Jie Zheng a liver freshly removed from a rat a specimen that is output of a specimen creation process used for an investigation without storage. fresh specimen sequence data A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement. GROUP: OBI Person:Chris Stoeckert example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search. sequence data paraffin storage PERSON: Chris Stoeckert PERSON: Jie Zheng UPenn Group a storage process with input organism or anatomical entity and paraffin and output material embedded in paraffin for long term storage need to specify paraffin or wax is one of specified input of the process paraffin storage agar stab specimen MO_971 agar_stab PERSON: Chris Stoeckert PERSON: Jie Zheng a specimen that is output of a process that cell culture inoculated into agar for long term storage. agar stab specimen growth condition intervention design A study design in which the independent variable is the environmental condition in which the specimen is growing MO_588 growth_condition_design PERSON: Bjoern Peters growth condition intervention design PCR instrument 03/21/2010: Added because it is unclear if the thermal cycler definition is intentionally broader than PCR instrument. Contacted Melanie and Trish about this. Definitions and use of alternative terms need to be made consistent. A device that is used to amplify a single or few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence. PCR instrument intravenous injection PERSON: Melanie Courtot intravenous injection is the injection of a material entity (bearing the administered substance role) into the vein (bearing the target role) of an organism using a syringe administration of material to specimen Bjoern Peters Bjoern Peters Staining cells in a tissue slice with a dye. The directed combination of a material entity with a specimen. administration of material to specimen growth environment OBI group PERSON:Richard Scheuermann, Jie Zheng, Bjoern Peters Right now this may be incomplete. Should also cover e.g. sound, light as well. The collection of material entities and their qualities that are located near a live organism, tissue or cell and can influence its growth. growth environment agar stab storage PERSON: Chris Stoeckert PERSON: Jie Zheng UPenn Group a storage process with input cell culture and agar and output agar stab for long time storage agar stab storage need to specify that agar is one of input for this process image creation A planned process that captures an image of an object. PERSON: Jie Zheng Taking a polaroid picture of a patients skin lesion; Using a digital camera to take a picture of a gel image acquisition image creation 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 feature extraction A planed process with objective of obtaining quantified values from an image. MO_928: feature_extraction PERSON: Jie Zheng feature extraction array image creation An image creation process that generate an image from the array. MO_929: image_acquisition PERSON: Jie Zheng array image acquisition array image creation light emission device A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics) OBI Person:Helen Parkinson a device which has a function to emit light. light emission device perturbation device A homogenizer is a perturbation device. A perturbation device is a device which is designed to perform a perturb function Helen Parkinson OBI Vancouver workshop 2010 PERSON: Helen Parkinson perturbation device environmental control device A growth chamber is an environmental control device. An environmental control device is a device which has the function to control some aspect of the environment such as temperature, or humidity. Helen Parkinson OBI environmental control device DNA extract DNA extract Group: UPenn group Person: Jie Zheng The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas. array manufacturer role a manufacturer role which is played by the person or organization that manufactured the array MO_695 array_manufacturer PERSON: Chris Stoeckert, Jie Zheng array manufacturer role tandem mass spectrometer A mass spectrometer in which ions are subjected to two or more sequential stages of analysis (which may be separated spatially or temporally) according to the quotient mass/charge. PERSON: Erik Segerdell http://goldbook.iupac.org/T06250.html tandem mass spectrometer spike-in quality control role MO_937 spike_quality_control PERSON: Chris Stoeckert, Jie Zheng, Bjoern Peter a reference substance role that is borne by a material entity with a known amount which is mixed into the evaluant of assays for quality control or data normalization purposes spike-in quality control role individual organism identifier PERSON: Chris Stoeckert, Jie Zheng MO_169 Individual a CRID symbol used to distinguish one individual organism from another. individual organism identifier dye swap quality control role MO_524 dye_swap_quality_control PERSON: Chris Stoeckert, Jie Zheng a reference substance role that is borne by a material entity used in a dye swap design experiment for quality control or data normalization purposes dye swap quality control role labeled nucleic acid extract MO_221 labeledExtract Person: Jie Zheng a labeled specimen that is the output of a labeling process and has grain labeled nucleic acid for detection of the nucleic acid in future experiments. labeled extract labeled extract labeled nucleic acid extract binding assay Determination of KD value for an antibody binding a protein using a BIACORE assay. Using plate bound antigen in an ELISA to determine if a mixture of serum antibodies bind the antigen. The following are NOT binding assays, as the desired output is not binding data: RNA microarray experiments to determine levels of gene expression. ChIP experiments to determine where in DNA a transcription factor binds. Using an IL-2 antibody on an ELISA plate to determine presence of IL-2 after stimulating a T cell culture. An assay with the objective to characterize the disposition of two or more material entities to form a complex. PERSON:Bjoern Peters, Randi Vita, Jason Greenbaum binding assay cell culture expansion BP: add it as subclass of 'cell culturing' JZ: No 'cell culturing' in OBI Has term 'cell co-culturing' and 'maintaining cell culture'. Don't think either of it fit. So leave the term under process. MO_758 grow PERSON: Chris Stoeckert, Jie Zheng a processual entity that results in the increase of cell numbers cell culture expansion including grow of yeast and bacteria gene knock out MO_771 gene_knock_out PERSON: Chris Stoeckert, Jie Zheng a genetic transformation that renders a gene non-functional, e.g. due to a point mutation, or the removal of all, or part of, the gene using recombinant methods. gene knock out gene knock in PERSON: Chris Stoeckert, Jie Zheng MO_437 gene_knock_in WEB: http://en.wikipedia.org/wiki/Gene_Knock-in a genetic transformation that involves the insertion of a protein coding cDNA sequence at a particular locus in an organism's chromosome. Typically, this is done in mice since the technology for this process is more refined, and because mouse embryonic stem cells are easily manipulated. The difference between knock-in technology and transgenic technology is that a knock-in involves a gene inserted into a specific locus, and is a "targeted" insertion. gene knock in chromosomal substitution A genetic transformation in which all, or part, of a chromosome from a donor replaces that of the recipient. It does not include chromosome recombination. For single gene insertion, use the term 'gene knock in'. MO_995 chromosomal_substitution PERSON: Chris Stoeckert, Jie Zheng chromosomal substitution genetically modified material GROUP: OBI PERSON: Jie Zheng a material entity, organism or cell, that is the output of a genetic transformation process. genetically modified material term is proposed by BP on Oct 25, 2010 dev call transfection MO_366 transfection PERSON: Chris Stoeckert, Jie Zheng a genetic transformation which relies on the use of physical, electrical and chemical phenomena to introduce DNA or RNA into a cell transfection genetic transformation objective suggested to be added by BP and AR during Oct 25, 2010 dev call Person: Jie Zheng Person: Jie Zheng a material transformation objective aims to create genetically modified organism or cell genetic transformation objective induced mutation MO_564 induced_mutation PERSON: Chris Stoeckert, Jie Zheng a genetic transformation that the modification of the genetic material (either coding or non-coding) of an organism is caused by mutagenic compounds or irradiation. induced mutation age since planting measurement datum An age measurement datum that is the result of the measurement of the age of an organism since planting, the process of placing a plant in media (e.g. soil) to allow it to grow, which excludes sowing. Discussed by Jie and Chris, proposed to combine with different kinds of processes as initial time point. Proposed 'age measurement assay' is proceeded by some process. The process can be any kind of process defined in OBI. Think it is more flexible. However, it is hard to model due to lake of temporal predicates on Nov 15, 2010 dev call. Term proposed by Bjoern on Nov 8, 2010 dev call Supported by Alan on Nov 15, 2010 dev call MO_495 planting PERSON:Chris Stoeckert, Jie Zheng age since planting measurement datum age since hatching measurement datum An age measurement datum that is the result of the measurement of the age of an organism since hatching, the process of emergence from an egg. MO_745 hatching PERSON:Chris Stoeckert, Jie Zheng age since hatching measurement datum age measurement assay An assay that measures the duration of temporal interval of a process that is part of the life of the bearer, where the initial time point of the measured process is the beginning of some transitional state of the bearer such as birth or when planted. OBI group PERSON: Alan Ruttenberg This assay measures time not developmental stage. we recognize that development takes different time periods under different conditions such as media / temperature. For example, age measurement assay of fly age, the output likes 28 days but not mid-life of age at room temperature. age measurement assay age since egg laying measurement datum An age measurement datum that is the result of the measurement of the age of an organism since egg laying, the process of the production of egg(s) by an organism. MO_767 egg laying PERSON:Chris Stoeckert, Jie Zheng age since egg laying measurement datum assay validation objective GROUP: Penn Group PERSON: Chris Stoeckert, Jie Zheng an objective specification to check the accuracy or the quality of the results of an assay by comparison with independent results assay validation objective age since germination measurement datum An age measurement datum that is the result of the measurement of the age of an organism since germination, the process consisting of physiological and developmental changes by a seed, spore, pollen grain (microspore), or zygote that occur after release from dormancy, and encompassing events prior to and including the first visible indications of growth. Definition of germination comes from GO. However, the term is deprecated from GO now because it is a grouping term without biological significance. MO_590 germination PERSON:Chris Stoeckert, Jie Zheng age since germination measurement datum validation by reverse transcription PCR design MO_986 reverse_transcription_PCR_quality_control PERSON: Chris Stoeckert, Jie Zheng a study design in which checks the accuracy or the quality of the result of an assay by comparing with reverse transcription PCR results validation by reverse transcription PCR design age since eclosion measurement datum An age measurement datum that is the result of the measurement of the age of an organism since eclosion, the process of emergence of an adult insect from its pupa or cocoon. MO_876 eclosion PERSON:Chris Stoeckert, Jie Zheng age since eclosion measurement datum age since sowing measurement datum An age measurement datum that is the result of the measurement of the age of an organism since sowing, the process of placing a seed or spore in some media with the intention to invoke germination. MO_748 sowing PERSON:Chris Stoeckert, Jie Zheng age since sowing measurement datum age since coitus measurement datum An age measurement datum that is the result of the measurement of the age of an organism since coitus, the process of copulation that occurs during the process of sexual reproduction. MO_783 coitus PERSON:Chris Stoeckert, Jie Zheng age since coitus measurement datum validation by real time PCR design MO_434 real_time_PCR_quality_control PERSON: Chris Stoeckert, Jie Zheng a study design in which the accuracy or the quality of the result of an assay is checked by comparing with real time PCR results validation by real time PCR design age measurement datum A time measurement datum that is the result of measurement of age of an organism In MageTab file, we use initialTimePoint (a process) + age (a number expected) + TimeUnit (definied in UO, such as year, hour, day, etc.) Now we use the term label indicating the start time point of measuring the age, (number + TimeUnit) are expected instances of the class MO_178 Age PERSON: Alan Ruttenberg, Chris Stoeckert, Jie Zheng discussed on Nov 15, dev call All subtype will be defined by textual definition now. note that we are currently defining subtypes of age measurement datum that specify when the age is relative to, e.g. planting, as we don't have adequate temporal predicates yet. life of bearer doesn't imply organism this assay measures time not developmental stage. we recognize that development can take different time periods under different conditions such as media / temperature age as a quality is dubious; we plan to revisit stages in development are currently handled with controlled vocabulary, such as 2-somite stage age measurement datum age since fertilization measurement datum An age measurement datum that is the result of the measurement of the age of an organism since fertilization, the process of the union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. Definition of fertilization comes from GO. MO_701 fertilization PERSON:Chris Stoeckert, Jie Zheng age since fertilization measurement datum age since birth measurement datum An age measurement datum that is the result of the measurement of the age of an organism since birth, the process of emergence and separation of offspring from the mother. MO_710 birth PERSON:Chris Stoeckert, Jie Zheng age since birth measurement datum reverse transcription polymerase chain reaction assay GROUP: Penn Group PERSON: Chris Stoeckert, Jie Zheng an assay that evaluates the concentration of RNA in a sample in which an RNA strand is first reverse transcribed into its DNA complement (complementary DNA, or cDNA) using the enzyme reverse transcriptase, and the resulting cDNA is amplified using traditional or real-time PCR. reverse transcription polymerase chain reaction assay selective organism creation objective PERSON: Chris Stoeckert, Jie Zheng WEB: wikipedia http://en.wikipedia.org/wiki/Cultivar http://en.wikipedia.org/wiki/Ecotype http://en.wikipedia.org/wiki/Strain_%28biology%29 an objective specification to generate a population or type of organism within species that have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms. selective organism creation objective RNA sequencing BP 12/21:Created based on a request from Melanie Bjoern Peters Bjoern Peters RNA sequencing RNA sequencing is a sequencing process which uses ribonucleic acid as input and results in a the creation of RNA sequence information artifact binding datum A data item that states if two or more material entities have the disposition to form a complex, and if so, how strong that disposition is. Bjoern Peters; Randi Vita binding datum selectively maintained organism An organism that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms Bjoern Peters, Helen Parkinson, Philippe Rocca-Serra, Jie Zheng, Chris Stoeckert MO_9 StrainOrLine, MO_71 Ecotype, MO_124 Cultivar cultivar ecotype strain selectively maintained organism operator variation design Person: Chris Stoeckert, Jie Zheng A study design that assesses the operator performance and relation to data consistency and quality. MO_519 operator_variation_design operator variation design comparative genome hybridization by array design Person: Chris Stoeckert, Jie Zheng A study design that detects genomic copy number variations using microarray technology. MO_856 comparative_genome_hybridization_design comparative genome hybridization by array design in vivo design Person: Chris Stoeckert, Jie Zheng A study design that is conducted entirely in a living organism, e.g. a compound treatment in a mouse model. MO_454 in_vivo_design in vivo design genotyping by high throughput sequencing design MO_560 genotyping_design Person: Chris Stoeckert, Jie Zheng A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs using high througput sequencing techniques. genotyping by high throughput sequencing design innate behavior design Person: Chris Stoeckert, Jie Zheng A study design in which the innate behavior of the organism is examined, e.g. path finding in bees. MO_355 innate_behavior_design innate behavior design cell component comparison design A study design that compares samples from different cell components. Person: Chris Stoeckert, Jie Zheng MO_1019 cell_component_comparison_design cell component comparison design ex vivo design Person: Chris Stoeckert, Jie Zheng A study design where all or part of an organism is removed and studied in vitro, e.g. part of a mouse is removed and cultured in vitro. A cell culture with an established cell line is an in vitro experiment. MO_808 ex_vivo_design ex vivo design normalization testing design Person: Chris Stoeckert, Jie Zheng A study design that tests different normalization procedures. MO_729 normalization_testing_design normalization testing design genetic population background information Group: OBI group Group: OBI group a genetic characteristics information which is a part of genotype information that identifies the population of organisms genetic population background information genotype information 'C57BL/6J Hnf1a+/-' in this case, C57BL/6J is the genetic population background information proposed and discussed on San Diego OBI workshop, March 2011 environmental history design MO_698 environmental_history_design Person: Chris Stoeckert, Jie Zheng A study design in which some aspect of the organism's environmental history is studied, such as exposure to teratogen, radiation, climate etc. environmental history design epigenetic modification identification objective A molecular feature identification objective that aims to detect epigenetic modifications, such as DNA methylation, histone modifications. Chris Stoeckert, Jie Zheng Person: Chris Stoeckert epigenetic modification identification objective transcription profiling by tiling array assay Person: James Malone An assay in which the transcriptome of a biological sample is analysed using a tiling path array. EFO_0002769 transcription profiling by tiling array transcription profiling by tiling array assay transcription profiling by high throughput sequencing design Person: Chris Stoeckert, Jie Zheng A study design in which sequencing technology (e.g. Solexa/454) is used to generate RNA sequence, analyse the transcibed regions of the genome, and/or to quantitate transcript abundance Group: ArrayExpress production team transcription profiling by high throughput sequencing design genotyping by high throughput sequencing assay Person: James Malone An assay in which high througput sequencer is used to detect polymorphisms in DNA samples EFO_0002771: genotyping by high throughput sequencing genotyping by high throughput sequencing assay ChIP-chip assay ChIP-on-chip assay Person: James Malone Philippe Rocca-Serra WEB: http://en.wikipedia.org/wiki/ChIP-on-chip an assay that aims to investigate the interactions between protein and DNA relying on chromatin immunoprecipitation ('ChIP') combined with microarray technology ('chip'). Specially, it allows the identification of protein binding sites on a genome-wide basis. ChIP-chip assay array platform variation design Person: Chris Stoeckert, Jie Zheng A study design in which the array platform is compared, e.g. Agilent versus Affymetrix. MO_899 array_platform_variation_design array platform variation design ChIP-seq design http://en.wikipedia.org/wiki/Chip-Sequencing A study design which aims to identify protein and DNA interactions using a combination of chromatin immunoprecipitation and high throughput sequencing. Massively parallel sequence analyses are used in conjunction with whole-genome sequence databases to analyze the interaction pattern of any protein with DNA, or the pattern of any epigenetic chromatin modifications. ChIP-seq design Person: Chris Stoeckert, Jie Zheng translational bias design Person: Chris Stoeckert, Jie Zheng A study design that characterizes the association of transcripts and translation machinery. MO_939 translational_bias_design translational bias design DNA methylation profiling by high throughput sequencing assay EFO_0002761 methylation profiling by high throughput sequencing Group: ArrayExpress production team, James Malone, Helen Parkinson Philippe Rocca-Serra An assay in which the methylation state of DNA is determined and is compared between samples using sequencing based technology DNA methylation profiling by high throughput sequencing assay RNA-seq assay An assay in which sequencing technology (e.g. Solexa/454) is used to generate RNA sequence, analyse the transcibed regions of the genome, and or to quantitate transcript abundance JZ: should be inferred as 'DNA sequencing'. Will check in the future. EFO_0002770 transcription profiling by high throughput sequencing PERSON: James Malone RNA-seq assay an assay that uses high-throughput sequencing technologies to sequence cDNA in order to get information about a sample's RNA content. RNA-Seq provides researchers with efficient ways to measure transcriptome data experimentally, allowing them to get information such as how different alleles of a gene are expressed, detect post-transcriptional mutations or identify gene fusions. WEB: http://en.wikipedia.org/wiki/RNA-Seq transcription profiling by high throughput sequencing genotyping by array assay Group: ArrayExpress production team An assay in which an array is used to detect polymorphisms in DNA samples EFO_0002767: genotyping by array genotyping by array assay DNA methylation profiling by array design Person: Chris Stoeckert, Jie Zheng A study design in which the methylation state of DNA is determined and is compared between samples using array technology. DNA methylation profiling by array design GROUP: ArrayExpress production team translation profiling assay An assay in which surface-bound, translationally competent ribosome complexes are used to generate a translation profile for mRNA, which mRNA may be a single molecular species, or a combination of species, including complex mixtures such as those found in the set of mRNAs isolated from a cell or tissue. One or more components of the surface-bound ribosome complex may be labeled at specific positions to permit analysis of multiple or single molecules for determination of ribosomal conformational changes and translation kinetics. Translation profiles are used as the basis for comparison of an mRNA or set of mRNA species. The translation profile can be used to determine such characteristics as kinetics of initiation, kinetic of elongation, identity of the polypeptide product, and the like. Analysis of translation profiles may be used to determine differential gene expression, optimization of mRNA sequences for expression, screening drug candidates for an effect on translation. EFO_0001033 translation profiling PERSON: James Malone translation profiling assay in vitro design Person: Chris Stoeckert, Jie Zheng A study design that is done in a test tube or a culture dish, e.g. A bacterial invasion assay in an established cell culture. MO_347 in_vitro_design in vitro design RNAi profiling by array design Person: Chris Stoeckert, Jie Zheng A study design in which experiment double stranded RNA is synthesized with a sequence complementary to a gene(s) of interest and introduced into a cell or organism, where it is recognized as exogenous genetic material and activates the RNAi pathway resulting in knockdown of the transcripts and providing a means to study downstream changes in gene expression. Group: ArrayExpress production team RNAi profiling by array design transcription profiling by array design MO_533 transcript_identification_design Person: Chris Stoeckert, Jie Zheng A study design that identifies forms and abundance of transcripts in the genome using microarray technology. transcription profiling by array design disease state design Person: Chris Stoeckert, Jie Zheng A study design in which the pathological condition of a part, organ, or system of an organism is studied. The etiology may be from infection, genetic defect, or environmental stress. MO_902 disease_state_design disease state design wild type organism genotype information C57BL/6J wild type Group: OBI group Group: OBI group a genotype information about an organism and includes information that there are no known modifications to the genetic background. Generally it is the genotype information of a representative individual from a class of organisms. proposed and discussed on San Diego OBI workshop, March 2011 wild type organism genotype information RNAi profiling by array assay An assay in which double stranded RNA is synthesized with a sequence complementary to a gene(s) of interest and introduced into a cell or organism, where it is recognized as exogenous genetic material and activates the RNAi pathway resulting in knockdown of the transcripts and providing a means to study downstream changes in gene expression. EFO_0001030 RNAi profiling by array PERSON: James Malone RNAi profiling by array assay genotype information Genotype information can be: Mus musculus wild type (in this case the genetic population background information is Mus musculus), C57BL/6J Hnf1a+/- (in this case, C57BL/6J is the genetic population background information and Hnf1a+/- is the allele information Group: OBI group Group: OBI group a genetic characteristics information that is about the genetic material of an organism and minimally includes information about the genetic background and can in addition contain information about specific alleles, genetic modifications, etc. discussed on San Diego OBI workshop, March 2011 genotype information RNA stability design Person: Chris Stoeckert, Jie Zheng A study design that examines the stability and/or decay of RNA transcripts. MO_553 RNA_stability_design RNA stability design tiling microarray EFO_0002704: tiling array Person: Helen Parkinson a DNA microarray which has short fragments of nucleic acid immobilized on a substrate. These are designed to cover the whole genome of the target species. Tiling arrays are used to determine genome binding in ChIP assays or to identify transcribed regions. genome tiling array tiling microarray species comparison design A study design that assays differences between distinct species. Person: Chris Stoeckert, Jie Zheng MO_675 species_design species comparison design transcription profiling by RT-PCR design Person: Chris Stoeckert, Jie Zheng A study design which aims to examine the transcriptome of a biological sample by reverse transcription PCR (RT-PCR). Group: ArrayExpress production team transcription profiling by RT-PCR design proteomic profiling by array assay Person: James Malone An assay that proteins in a sample are detected, quantified or otherwise analysed, e.g. antibody profiling using an array based technology EFO_0002765 proteomic profiling by array proteomic profiling by array assay microRNA profiling by array design Person: Chris Stoeckert, Jie Zheng A study design in which a microRNA array is used to analyse the microRNA component of the transcriptome. Group: ArrayExpress production team microRNA profiling by array design organism development design Person: Chris Stoeckert, Jie Zheng A study design that assays events associated with development. Development applies to organism(s) acquiring a mature state. MO_892 development_or_differentiation_design organism development design family history design Person: Chris Stoeckert, Jie Zheng A study design in which the family history such as traits, characteristics, susceptibility to disease is studied. MO_544 family_history_design family history design transcription profiling identification objective A molecular feature identification objective that aims to characterize the abundance of transcripts Group: Penn Group Person: Chris Stoeckert, Jie Zheng transcription profiling identification objective DNA methylation profiling by array assay Person: James Malone Philippe Rocca-Serra An assay in which the methylation state of DNA is determined and is compared between samples using array technology DNA methylation profiling by array assay EFO_0002759 methylation profiling by array microRNA profiling by array assay An assay in which a microRNA array is used to analyse the microRNA component of the transcriptome. EFO_0000753 microRNA profiling by array PERSON: James Malone microRNA profiling by array assay quality control testing design Person: Chris Stoeckert, Jie Zheng A study design in which some aspects of the experiment is quality controlled for the purposes of quality assurance. MO_981 quality_control_testing_design quality control testing design clinical history design Person: Chris Stoeckert, Jie Zheng A study design that the organism's clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc. is studied. MO_832 clinical_history_design clinical history design allele information MO_58 Allele Person: Chris Stoeckert, Jie Zheng a genetic alteration information that about one of two or more alternative forms of a gene or marker sequence and differing from other alleles at one or more mutational sites based on sequence. Polymorphisms are included in this definition. allele information discussed on San Diego OBI workshop, March 2011 genotype information 'C57BL/6J Hnf1a+/-' in this case, Hnf1a+/- is the allele information post-transcriptional modification design Person: Chris Stoeckert, Jie Zheng A study design in which a modification of the transcriptome, proteome (not genome) is made, for example RNAi, antibody targeting. MO_392 cellular_modification_design post transcription modification design? or more clear RNAi design / antibody targeting design? need to check the use cases post-transcriptional modification design transcription profiling by RT-PCR assay An assay in which the transcriptome of a biological sample is analysed by reverse transcription PCR (RT-PCR) EFO_0002943: transcription profiling by RT-PCR Person: Anna Farne transcription profiling by RT-PCR assay genetic alteration information Group: OBI group Group: OBI group a genetic characteristics information that is about known changes or the lack thereof from the genetic background, including allele information, duplication, insertion, deletion, etc. genetic alteration information proposed and discussed on San Diego OBI workshop, March 2011 cellular process design Person: Chris Stoeckert, Jie Zheng A study design that aims to study the processes that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. MO_810 cellular_process_design cellular process design wild type allele information MO_605 genotype Person: Chris Stoeckert, Jie Zheng an allele information that is about the allele found most frequently in natural populations, or in standard laboratory stocks for a given organism. discussed on San Diego OBI workshop, March 2011 wild type allele information injury design Person: Chris Stoeckert, Jie Zheng A study design in which the response of an organism(s) to injury or damage is studied. MO_726 injury_design injury design organism status comparison design Person: Chris Stoeckert, Jie Zheng A study design that compares samples from live and dead organisms. MO_841 organism_status_design organism status comparison design genotyping by array design MO_560 genotyping_design Person: Chris Stoeckert, Jie Zheng A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs using microarray technology. genotyping by array design comparative genomic hybridization by array assay Philippe Rocca-Serra An assay in which changes in DNA sequence copy number are analysed using a microarray. For example the analysis of LOH in tumor cells vs a non diseased sample or the comparison of clinical isolated of disease causing bacteria. EFO_0000749: comparative genomic hybridization by array Person: James Malone array CGH comparative genomic hybridization by array assay stimulus or stress design Person: Chris Stoeckert, Jie Zheng A study design in which the response of an organism(s) to the stress or stimulus is studied, e.g. osmotic stress, heat shock, radiation exposure, behavioral treatment etc. MO_568 stimulus_or_stress_design stimulus or stress design protein and DNA interaction identification objective A sequence feature identification objective that aims to characterize the interactions between protein and DNA which includes identification of transcription factor binding sites. MO_933 binding_site_identification_design Person: Chris Stoeckert, Jie Zheng protein and DNA interaction identification objective protocol optimization design Person: Chris Stoeckert, Jie Zheng A study design where different protocols or protocol parameters are compared aims to find an optimized protocol MO_934 optimization_design protocol optimization design ChIP-chip design ChIP-on-chip design A study design which aims to identify protein binding sites in genomic DNA by a combination of chromatin immunoprecipitation and DNA microarray (chip) assays. ChIP-chip design MO_933 binding_site_identification_design Person: Chris Stoeckert, Jie Zheng genetic characteristics information MO definition: The genotype of the individual organism from which the biomaterial was derived. Individual genetic characteristics include polymorphisms, disease alleles, and haplotypes. examples in ArrayExpress wild_type MutaMouse (CD2F1 mice with lambda-gt10LacZ integration) AlfpCre; SNF5 flox/knockout p53 knock out C57Bl/6 gp130lox/lox MLC2vCRE/+ fer-15; fem-1 df/df pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) MO_66 IndividualGeneticCharacteristics Person: Chris Stoeckert, Jie Zheng a data item that is about genetic material including polymorphisms, disease alleles, and haplotypes. genetic characteristics information imprinting design Person: Chris Stoeckert, Jie Zheng A study design where differences in genetic imprinting of maternally- and paternally-inherited chromosomes (e.g., due to in vivo differences in chemical modification and/or chromatin structure) are compared. MO_914 imprinting_design imprinting design cell cycle design Person: Chris Stoeckert, Jie Zheng A study design that assays events that occur in relation to the cell cycle, which is the period between the formation of a cell, by division of its mother cell and the time when the cell itself divides to form two daughter cells. MO_822 cell_cycle_design cell cycle design translation profiling design Person: Chris Stoeckert, Jie Zheng A study design in which surface-bound, translationally competent ribosome complexes are used to generate a translation profile for mRNA, where mRNA may be a single molecular species, or a combination of species, including complex mixtures such as those found in the set of mRNAs isolated from a cell or tissue. One or more components of the surface-bound ribosome complex may be labeled at specific positions to permit analysis of multiple or single molecules for determination of ribosomal conformational changes and translation kinetics. Translation profiles are used as the basis for comparison of an mRNA or set of mRNA species. The translation profile can be used to determine such characteristics as kinetics of initiation, kinetic of elongation, identity of the polypeptide product, and the like. Analysis of translation profiles may be used to determine differential gene expression, optimization of mRNA sequences for expression, screening drug candidates for an effect on translation. Group: ArrayExpress production team translation profiling design cell type comparison design Person: Chris Stoeckert, Jie Zheng A study design that compares cells of different type, for example different cell lines. MO_764 cell_type_comparison_design cell type comparison design ChIP-chip by tiling array design Group: ArrayExpress production team Person: Chris Stoeckert, Jie Zheng A study design which aims to identify protein binding sites in genomic DNA by a combination of chromatin immunoprecipitation and tiling microarray (chip) assays. ChIP-chip by tiling array design dose response design Person: Chris Stoeckert, Jie Zheng A study design that examines the relationship between the size of the administered dose and the extent of the response. MO_485 dose_response_design dose response design ChIP-chip by tiling array assay Group: ArrayExpress production team An assay where chromatin immunoprecipitation (ChIP) is used in combination with tiling microarray technology ChIP-chip by tiling array assay EFO_0002762 ChIP-chip by tiling array organism part comparison design A study design that compares tissues, regions, organs within or between organisms Person: Chris Stoeckert, Jie Zheng MO_953 organism_part_comparison_design organism part comparison design protein binding site identification design A study design that investigates protein binding sites on nucleic acids. MO_933 binding_site_identification_design Person: Chris Stoeckert, Jie Zheng protein binding site identification design sex comparison design A study design that assays differences associated with an organism's sex, gender or mating type. Person: Chris Stoeckert, Jie Zheng MO_575 sex_design sex comparison design transcription profiling by tiling array design MO_507 tiling_path_design Person: Chris Stoeckert, Jie Zheng A study design in which gene expression on a genome-wide basis is evaluated, without bias toward coding or noncoding regions, using tiling arrays containing oligonucleotides that are either overlapping or spaced at regular intervals. transcription profiling by tiling array design cell differentiation design Person: Chris Stoeckert, Jie Zheng A study design that assays events associated with cell development or differentiation. MO_892 development_or_differentiation_design cell differentiation design transcription profiling design A study design that identifies forms and abundance of transcripts in the genome. MO_533 transcript_identification_design Person: Chris Stoeckert, Jie Zheng transcription profiling design operon identification design Person: Chris Stoeckert, Jie Zheng A study design that identifies locations and members of operons in a genome. MO_772 operon_identification_design operon identification design DNA methylation profiling by high throughput sequencing design Person: Chris Stoeckert, Jie Zheng A study design in which the methylation state of DNA is determined and is compared between samples using high throughput sequencing technology. DNA methylation profiling by high throughput sequencing design GROUP: ArrayExpress production team all pairs design Person: Chris Stoeckert, Jie Zheng A study design in which all specimens are compared to every other specimen. MO_565 all_pairs all pairs design proteomic profiling by array design Person: Chris Stoeckert, Jie Zheng A study design in which proteins in a sample are detected, quantified or otherwise analysed, e.g. antibody profiling using an array based technology Group: ArrayExpress production team proteomic profiling by array design genotyping design Person: Chris Stoeckert, Jie Zheng A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs. MO_560 genotyping_design genotyping design individual genetic characteristics comparison design Person: Chris Stoeckert, Jie Zheng A study design where genotype, haplotype, or other individual genetic characteristics are compared. MO_527 individual_genetic_characteristics_design individual genetic characteristics comparison design pathogenicity design Person: Chris Stoeckert, Jie Zheng A study design in which an infective agent such as a bacterium, virus, protozoan, fungus etc. infects a host organism(s) and the infective agent is assayed. MO_807 pathogenicity_design pathogenicity design genetic modification design Person: Chris Stoeckert, Jie Zheng A study design in which an organism(s) is studied that has had genetic material removed, rearranged, mutagenized or added, such as in a knock out. MO_447 genetic_modification_design genetic modification design transcription profiling by array assay An assay in which the transcriptome of a biological sample is analysed using array technology. Person: James Malone EFO_0002768: transcription profiling by array transcription profiling by array assay strain comparison design Person: Chris Stoeckert, Jie Zheng A study design that assays differences between multiple strains, cultivars, serovars, isolates, lines from organisms of a single species. MO_462 strain_or_line_design strain comparison design cell specimen A specimen primarily composed of cells collected from a multicellular organism or a cell culture MO_612 cell PERSON: Chris Stoeckert, Jie Zheng cell specimen specimen with known storage state A specimen for which it is known whether it has been subjected to storage of a specified type. MO_95 BiosourceType PERSON: Chris Stoeckert, Jie Zheng specimen with known storage state lowess group transformation A lowess transformation where a potentially different normalization curve is generated and used for two or more groups (delineated by some criteria); criteria could include blocks (e.g. print-tip groups) on an array, or the day on which mass spectrometry was performed. MO_861 lowess_group_normalization Person: Elisabetta Manduchi lowess group transformation lowess transformation A data transformation of normalizing ratio data by using a locally weighted polynomial regression (typically after a log transformation). The regression can be performed on log ratios resulting from the relation of two data sets versus the average log intensity data from the same two data sets or it can be performed on raw or log transformed values from one data set versus values from another. The goal could be to remove intensity-dependent dye-specific effects from the set of pair wise ratios. This method can be applied globally, or limited by one or more specified criteria. MO_720 lowess_normalization Person: Elisabetta Manduchi lowess transformation tissue specimen 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). MO_954 organism_part PERSON: Chris Stoeckert, Jie Zheng tissue specimen lowess global transformation A lowess transformation where the same normalization curve is used for all members of the data set; e.g. Features on an array, picked spots on a gel, or measured metabolites in a sample. MO_692 lowess_global_normalization Person: Elisabetta Manduchi lowess global transformation cell collecting A planned process that collects cells from culture. MO_982 harvest PERSON: Chris Stoeckert, Jie Zheng cell collecting linear amplification An enzymatic amplification which amplifies nucleic acid sequence by making many copies off the same template. An example is the use of the T7 promoter for amplification by transcribing many RNA copies. MO_997 linear_amplification PERSON: Chris Stoeckert, Jie Zheng linear amplification atmosphere A growth environment pertaining to the atmospheric conditions that is used to culture or grow an organism. MO_219 atmosphere PERSON: Chris Stoeckert, Jie Zheng atmosphere dissection A planned process that separates and isolates tissues for surgical purposes, or for the analysis or study of their structures. EFO_0003856 dissection MO_374 dissect PERSON: Chris Stoeckert, Jie Zheng dissection purification A planned process to separate a material entity into different compositions of which one or more have are purified fractions that contain higher concentration of a desired component, while others contain impurities and are not of interest MO_406 purify PERSON: Chris Stoeckert, Jie Zheng purification specimen with pre- or post-mortem status A specimen that has been established to be taken from a live (pre-mortem) or dead (post-mortem) organism. MO_84 OrganismStatus PERSON: Chris Stoeckert, Jie Zheng organizational term, used in description of specimen that is created from known pre- or post-mortem status specimen with pre- or post-mortem status sampling time measurement datum A time measurement datum when an observation is made or a sample is taken from a material as measured from some reference point. MO_738 timepoint Person: Chris Stoeckert sampling time measurement datum time point DNA sequence data 8/29/11 call: This is added after a request from Melanie and Yu. They should review it further. This should be a child of 'sequence data', and as of the current definition will infer there. A sequence data item that is about the primary structure of DNA DNA sequence data OBI call; Bjoern Peters OBI call; Melanie Courtout The part of a FASTA file that contains the letters ACTGGGAA binding 9/28/11 BP: The disposition referenced is the one of the ligand to bind the molecule. This along with binding as a function / process needs to be figured out with GO which is inconsistent at this point. A peptide binding to an MHC molecule to form a complex. IEDB PERSON: Bjoern Peters, Randi Vita The process of material entities forming complexes. binding PubMed ID NIAID GSCID-BRC Publication Citation A CRID symbol that is sufficient to look up a citation from the PubMed, a literature database of life sciences and biomedical information. PMID Person: Chris Stoeckert, Jie Zheng PubMed ID PubMed Identifier Website: http://en.wikipedia.org/wiki/Wikipedia:PMID cap analysis of gene expression 5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing. Takahashi H, Lassmann T, Murata M, Carninci P. Nat Protoc. 2012 Feb 23;7(3):542-61. doi: 10.1038/nprot.2012.005. PMID: 22362160 An assay which aims at monitoring RNA transcript abundances in biological samples by extracting 5' ends of capped transcripts, RTPCR and sequence those. Copy numbers of CAGE tags provide a way of quantification and provide a measure of expression of the transcriptome CAGE PERSON:Philippe Rocca-Serra; Marcus Chibucos PMID:14663149 cap analysis of gene expression immunoprecipitation assay An assay with the objective to determine presence of an analyte by mixing a solution of antigen and antibody and separating out bound antigen:antibody complexes using immunoprecipitation. Either the antibody has known specificy, and the antigen mixture is tested for the presence of a specific antigen, or the antigen solution is well defined and the antibody solution is tested for the presence of antigen specific antibodies. Determining if a cell is producing a protein using a protein specific antibody to immunoprecipitate the cell lysate. Determining if the serum of a patient contains antibodies against HBV core protein by immunoprecipitating purified HBV core protein with the patients serum. IEDB PERSON:Bjoern Peters, Randi Vita immunoprecipitation assay chromatin interaction analysis by paired-end tag sequencing ChIA-PET assay An assay that incorporates chromatin immunoprecipitation (ChIP)-based enrichment, chromatin proximity ligation, Paired-End Tags, and high-throughput sequencing to determine de novo long-range chromatin interactions genome-wide. ENCODE project Person: Venkat Malladi, Chris Stoeckert, Jie Zheng Zhang, et al. ChIA-PET analysis of transcriptional chromatin interactions. Methods. 2012 Nov;58(3):289-99. [PMID:22926262] ChIA-PET chromatin interaction analysis by paired-end tag sequencing http://en.wikipedia.org/wiki/ChIA-PET structural analysis by paired-end tag sequencing Yao, et al. Long Span DNA Paired-End-Tag (DNA-PET) Sequencing Strategy for the Interrogation of Genomic Structural Mutations and Fusion-Point-Guided Reconstruction of Amplicons. PLoS One. 2012;7(9):e46152 [PMID:23029419] ENCODE project An assay that incorporates Paired-End Tags and sequencing technology to determine structural variants. DNA-PET Yao, et al. Long Span DNA Paired-End-Tag (DNA-PET) Sequencing Strategy for the Interrogation of Genomic Structural Mutations and Fusion-Point-Guided Reconstruction of Amplicons. PLoS One. 2012;7(9):e46152 [PMID:23029419] DNA-PET assay Person: Venkat Malladi, Chris Stoeckert, Jie Zheng structural analysis by paired-end tag sequencing transcript analysis by paired-end tag sequencing An assay that incorporates Paired-End Tags and sequencing technology to determine transcripts, gene structures, and gene expressions. RNA-PET RNA-PET assay Person: Venkat Malladi, Chris Stoeckert, Jie Zheng ENCODE project Ruan, et al. Genome wide full-length transcript analysis using 5' and 3' paired-end-tag next generation sequencing (RNA-PET). Methods Mol Biol. 2012;809:535-62. [PMID:22113299] Ruan, et al. Genome wide full-length transcript analysis using 5' and 3' paired-end-tag next generation sequencing (RNA-PET). Methods Mol Biol. 2012;809:535-62. [PMID:22113299] transcript analysis by paired-end tag sequencing transcription start site identification objective A transcription profiling identification objective that aims to characterize the transcription start sites of genes. Person: Chris Stoeckert, Jie Zheng Penn Group transcription start site identification objective paired-end library preparation ENCODE project Person: Venkat Malladi, Jie Zheng A library preparation that results in the creation of a library of the 5' and 3' ends of DNA or cDNA fragments using adaptors and endonucleases. The preparation may or may not include cloning process. Venkat Malladi, Jie Zheng paired-end library preparation DNase I hypersensitive sites sequencing assay DNase-seq assay DNase-seq Person: Venkat Malladi, Chris Stoeckert, Jie Zheng ENCODE project DNase I hypersensitive sites sequencing assay Sabo, et al. Discovery of functional noncoding elements by digital analysis of chromatin structure. Proc Natl Acad Sci U S A. 2004 Nov 30;101(48):16837-42. [PMID:15550541] http://en.wikipedia.org/wiki/DNase-Seq An assay to identify the location of regulatory regions, based on the genome-wide sequencing of regions super sensitive to cleavage by DNase I. protein and RNA interaction identification objective JZ: Term added for ENCODE project requested assays. Definition adapted from 'protein and DNA interaction identification objective'. A sequence feature identification objective that aims to characterize the interactions between protein and RNA. Person: Jie Zheng Jie Zheng protein and RNA interaction identification objective RNP (ribonuclear particle) immunoprecipitation high- throughput sequencing assay Zhao et al. Genome-wide identification of polycomb-associated RNAs by RIP-seq. Molecular Cell (2010) vol. 40 (6) pp. 939-53 [PMID:21172659] RIP-seq Person: Venkat Malladi, Chris Stoeckert, Jie Zheng Zhao et al. Genome-wide identification of polycomb-associated RNAs by RIP-seq. Molecular Cell (2010) vol. 40 (6) pp. 939-53 [PMID:21172659] RIP-seq assay An assay that combines immunoprecipitation of an RNA-binding protein and RNA-seq to identify mRNAs associated with selected RNA binding proteins (RBPs). ENCODE project RNP (ribonuclear particle) immunoprecipitation high- throughput sequencing assay cross-linking immunoprecipitation high-throughput sequencing assay CLIP-seq assay ENCODE project CLIP-seq Person: Venkat Malladi, Chris Stoeckert, Jie Zheng Licatalosi et al. HITS-CLIP yields genome-wide insights into brain alternative RNA processing. Nature. 2008 Nov 27 456: 464-469 [PMID:18978773] HITS-CLIP An assay that employs UV-crosslinking between RNA and the protein, followed by immunoprecipitation with antibodies for the protein, fragmentation, and high-throughput used for screening for RNA sequences that interact with a particular RNA-binding protein. Heulga et al. Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins. Cell Rep. 2012 Feb 23;1(2):167-78. [PMID:22574288] cross-linking immunoprecipitation high-throughput sequencing assay formaldehyde-assisted isolation of regulatory elements assay An assay to determine the sequences of those DNA regions in the genome associated with regulatory activity. Giresi, et al. FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Research 17 (6): 877–85. [PMID:17179217] http://en.wikipedia.org/wiki/FAIRE-Seq ENCODE project FAIRE-seq Person: Venkat Malladi, Chris Stoeckert, Jie Zheng FAIRE-seq assay formaldehyde-assisted isolation of regulatory elements assay methylation-sensitive restriction enzyme sequencing assay Maunakea et al. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature. 2010 Jul 8;466(7303):253-7. [PMID:20613842] MRE-seq assay An assay that identifies unmethylated CpGs by use of methylation sensitive restriction enzymes to fragment DNA. MRE-seq Maunakea et al. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature. 2010 Jul 8;466(7303):253-7. [PMID:20613842] Person: Venkat Malladi, Chris Stoeckert, Jie Zheng ENCODE project methylation-sensitive restriction enzyme sequencing assay reduced representation bisulfite sequencing assay reduced representation bisulfite-seq ENCODE project RRBS A bisulfite sequencing assay that identifies genomic methylation patterns by using a bisulfite based protocol that enriches CG-rich parts of the genome. Meissner et al. Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res. 2005; 33(18): 5868–5877. [PMCID: PMC1258174] Meissner et al. Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res. 2005; 33(18): 5868–5877. [PMCID: PMC1258174] Person: Venkat Malladi, Chris Stoeckert, Jie Zheng RRBS assay reduced representation bisulfite sequencing assay shotgun bisulfite-seq assay Cokus et al. Shotgun bisulfite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature. 2008 Mar 13;452(7184):215-9. [PMID:18278030]. A bisulfite sequencing assay that identifies methylated cytosines across the genome using high throughput sequencing. WGSBS Person: Venkat Malladi, Chris Stoeckert, Jie Zheng ENCODE project whole genome bisulfite sequencing WGBS Shotgun bisulfite sequencing Cokus et al. Shotgun bisulfite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature. 2008 Mar 13;452(7184):215-9. [PMID:18278030] shotgun bisulfite-seq assay whole-genome shotgun bisulfite sequencing RNA Annotation and Mapping of Promoters for the Analysis of Gene Expression assay ENCODE project Person: Venkat Malladi, Chris Stoeckert, Jie Zheng Batut et al. High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression. Genome Research. 2013 Jan;23(1):169-80. [PMID:22936248] An assay that identifies transcription start sites (TSS), the quantification of their expression and the characterization of their transcripts using high throughput sequencing. RAMPAGE Batut et al. High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression. Genome Research. 2013 Jan;23(1):169-80. [PMID:22936248] RNA Annotation and Mapping of Promoters for the Analysis of Gene Expression assay assay array Penn Group PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg A device made to be used in an analyte assay for immobilization of substances that bind the analyte at regular spatial positions on a surface. assay array secondary cultured cell A cultured cell that has been passaged or derives from a cell that has been passaged in culture. A secondary cultured cell has been passaged in culture or is a descendant of such a cell that is derived through propagation in culture. PERSON: Matthew Brush The term 'secondary cell culture' is generally used in biological texts/protocols to refer to any culture following an initial passage. We include it here because there are often a number of passages between a primary culture and the establishment of a stable, homogenous cell line. Such cultures are considered to be 'secondary cultures' but not 'cell lines' during this intermediate passaging/selection period between their derivation from a 'primary cell culture' and derivation into a 'cell line', which is a more specific type of secondary culture. secondary cultured cell Person: Matthew Brush establishing cell line a process whereby a new type of cell line is created, either through passaging of a primary cell culture to relative genetic stability and compositional homogeneity, or through some experimental modification of an existing cell line to produce a new line with novel characteristics (e.g. immortalization or some other stable genetic modification, or selection of some defined subset). Person: Matthew Brush establishing cell line 2013-4-20 MHB: For cases of initial establilshment of a line from a primary culture, successive passaging and/or selection processes can confer increasing degrees of genetic stability and compositional homogeneity as compared to the input primary culture. Historically, many texts consider the first passage as the clearest point to define the beginning of a line. However, in practice it is more often that case that more than one passage, and possibly additional selective techniques, may be required before a culture is deemed to have sufficient stability and homogeneity to be considered cell line. This is the view taken in OBI. Regardless, what is important is that some intentional, experimental step has been taken to establish a more homogenous and stable culture that can be characterized and progatated over time. PERSON:Matthew Brush secondary cultured cell population secondary cultured cell population The concept of a 'secondary cultured cell population' covers cell lines as well as cultured cell populations more immediately derived from a primary culture which have yet to achieve adequate genetic stability and compositional homogeneity to be considered a cell line. The extent of the collection of cells in a 'secondary cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). Secondary cultured cell populations can be under active culture, stored in a quiescent state for future use, or applied experimentally. PERSON:Matthew Brush A cultured cell population that is derived through one or more passages in culture. PERSON:Matthew Brush secondary cell culture sample The term 'secondary cell culture' is generally used in biological texts/protocols to refer to any culture of cells following an initial passage. We include it here because there are often a number of passages between a primary culture and the establishment of a stable, homogenous cell line. Such cultures are considered to be 'secondary cultures' but not 'cell lines' during this intermediate passaging/selection period between their derivation from a 'primary cell culture' and derivation into a 'cell line', which is a more specific type of secondary culture. conclusion based on data An information content entity that is inferred from data. Group:2013 Philly Workshop group Group:2013 Philly Workshop group conclusion based on 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. 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". 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 multiplex ligation-mediated amplification Multiplex ligation-dependent probe amplification Chris Stoeckert, Jie Zheng A polymerase chain reaction that amplifies multiple targets with a single primer pair mediated by hybridization of a primer with its target sequence using ligation. MLPA LMA multiplex ligation-mediated amplification web: http://en.wikipedia.org/wiki/Multiplex_Ligation-dependent_Probe_Amplification Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ DNA replication identification objective A molecular feature identification objective that aims to examine charateristics of DNA replication, such as replication time. DNA replication identification objective Group: Penn Group Chris Stoeckert, Jie Zheng chromosome conformation identification objective Chris Stoeckert, Jie Zheng A molecular feature identification objective that aims to determine spatial organization of chromatin. Group: Penn Group chromosome conformation identification objective Carbon-copy chromosome conformation capture assay An assay that is used to analyze the organization of chromosomes at the genome-wide scale. 5C Venkat Malladi, Chris Stoeckert, Jie Zheng ENCODE project 5C assay "Dostie et al. Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res. 2006 October; 16(10):1299-309.[PMID:16954542]" Carbon-copy chromosome conformation capture assay van Berkum et al. Determining spatial chromatin organization of large genomic regions using 5C technology. Methods Mol Biol (2009) vol. 567 pp. 189-213 [PMID:19588094] DNA replication timing by sequencing assay Hansen et al. Sequencing newly replicated DNA reveals widespread plasticity in human replication timing. Proc Natl Acad Sci U S A. 2010 January 5; 107(1): 139–144. [PMID:19966280] Repli-seq ENCODE project Venkat Malladi, Chris Stoeckert, Jie Zheng An assay in which timing of DNA replication is quantified as a function of genome position based on genome-wide sequencing. DNA replication timing by sequencing assay Hansen et al. Sequencing newly replicated DNA reveals widespread plasticity in human replication timing. Proc Natl Acad Sci U S A. 2010 January 5; 107(1): 139–144. [PMID:19966280] Repli-seq assay microRNA profiling by high throughput sequencing assay Person: Venkat Malladi, Chris Stoeckert, Jie Zheng miRNA-seq microRNA-seq assay A RNA-seq assay in which high throughput sequencing technology is used to analyse the microRNA component of the transcriptome. ENCODE project microRNA profiling by high throughput sequencing assay http://www.ebi.ac.uk/efo/EFO_0002896 microRNA-seq Juhlia et al. MicroRNA expression profiling reveals miRNA families regulating specific biological pathways in mouse frontal cortex and hippocampus. PLoS One. 2011;6(6). [PMID: 21731767] protein sequencing by tandem mass spectrometry assay Person: Venkat Malladi, Chris Stoeckert, Jie Zheng protein sequencing by tandem mass spectrometry assay A sequencing assay in which amino acid sequences of proteins is determined using multiple rounds of mass spectrometry and molecule fragmentation. ENCODE project Taylor et al.Implementation and uses of automated de novo peptide sequencing by tandem mass spectrometry. Anal Chem. 2001 Jun;73(11):2594-604. [PMID:11403305] Hunt et al. Protein sequencing by tandem mass spectrometry. Proc Natl Acad Sci U S A. 1986;83(17): 6233–6237. [PMID:3462691] micrococcal nuclease digestion followed by high throughput sequencing assay micrococcal nuclease digestion followed by high throughput sequencing assay ENCODE project Johnson et al. Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin. Genome Res. 2006 Dec;16(12):1505-16. [PMID:17038564] JZ: should be inferred as 'DNA sequencing'. Will check in the future. MNase-seq Cui et al.Genome-wide approaches to determining nucleosome occupancy in metazoans using MNase-Seq. Methods Mol Biol. 2012;833:413-9. [PMID:22183607] MNase-seq assay Person: Venkat Malladi, Chris Stoeckert, Jie Zheng An assay to identify nucleosome positioning by genome wide sequencing of regions senstative to digestion by micrococal nuclease chromatin immunoprecipitation with exonuclease sequencing assay A ChIP-seq assay to identify protein binding sites using an exonuclease to provide greater binding resolution of immunoprecipitation assay by genome wide sequencing. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng Rhee et al. Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution. Cell. 2011 Dec;147(6):1408-19. [PMID:22153082] ENCODE project ChIP-exo assay chromatin immunoprecipitation with exonuclease sequencing assay Rhee et al. Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution. Cell. 2011 Dec;147(6):1408-19. [PMID:22153082] microRNA profiling assay microRNA profiling assay ENCODE project microRNA expression assay A transcription profiling assay in which aims to quantify the microRNA species within a biological sample. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng Kolbert et al. Multi-Platform Analysis of MicroRNA Expression Measurements in RNA from Fresh Frozen and FFPE Tissues. PLoS One. 2013;8(1):e52517 [PMID: 23382819] miRNA expression assay scalar value specification 1 1 scalar value specification A value specification that consists of two parts: a numeral and a unit label PERSON:Bjoern Peters value specification 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. The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass. value specification PERSON:Bjoern Peters An information content entity that specifies a value within a classification scheme or on a quantitative scale. molecular-labeled material PERSON:Matthew Brush OBI developer call, 3-12-12 a material entity that is the specified output of an addition of molecular label process that aims to label some molecular target to allow for its detection in a detection of molecular label assay molecular-labeled material assay using chromatin immunoprecipitation PERSON: Philippe Rocca-Serra an assay which uses immunoprecipitation and which produces data about protein-DNA interaction or DNA epigenetic modification as per user (pployd) request and proposal by Alan Ruttenberg http://sourceforge.net/p/obi/obi-terms/707/ assay using chromatin immunoprecipitation http://www.lifetechnologies.com/uk/en/home/life-science/epigenetics-noncoding-rna-research/chromatin-remodeling/chromatin-immunoprecipitation-chip.html hardware testing design Person: Jie Zheng MO_734 hardware_variation_design A study design that aims to compare different types of hardware for performance, reproducibility, accuracy and precision. hardware testing design systematic review study design systematic review study design Red blood cell transfusion in patients with traumatic brain injury: a systematic review protocol. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4090399/ A study design for identifying in the literature prior studies of a pre-determined phenomenon or set of related phenomena according to certain criteria, extracting findings from these studies, and summarizing these findings and/or attempting to draw new conclusions from them which were not justified by any of the individual, prior studies. Many systematic reviews also assess the quality of the studies so reviewed. PERSON: Bill Hogan The effect of moderate gestational alcohol consumption during pregnancy on speech and language outcomes in children: a systematic review. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3892059/ taxonomic diversity assessment by targeted gene survey OBI PERSON:Philippe Rocca-Serra environmental gene survey http://www.ncbi.nlm.nih.gov/pubmed/20679230 http://www.ncbi.nlm.nih.gov/pubmed/25367129 is an assay which aims to provide information about taxonomic information and community diversity by mean of sequencing specific genomic regions used as marker of identity or diversity. targeted gene survey targeted gene survey DNA barcoding taxonomic diversity assessment by targeted gene survey decision-theoretic analysis objective The best action to take is typically defined as the one that maximizes expected utility. An objective specification which what includes a description of two or more alternative actions to take in a particular situation and a metric that enables comparisons of the two actions. The objective specified is achieved in a planned process which includes a data transformation, the output of which is an identification of the 'best' choice according to the metric. decision-theoretic analysis objective PERSON: Bill Hogan decision analysis objective PERSON: Bill Hogan decision analysis study design a study design that has a decision analysis objective specification as part PERSON: Bill Hogan decision analysis study design PERSON: Bill Hogan biodiversity assessment objective PERSON:Philippe Rocca-Serra PRS for OBI biodiversity assessment objective biodiversity assessment objective is an objective of a planned process aimed at producing data item whose interpretation should provide insight about variety of biological species found in a biological sample at macroscopic or microscopic level DNA methylation profiling by ChIP-chip assay Beta Cell Biology Consoritum A ChIP-chip assay that identifies sites of DNA methylation. DNA methylation ChIP-chip Penn group Person: Chris Stoeckert, Jie Zheng DNA methylation profiling by ChIP-chip assay transcription profiling by MPSS assay expression MPSS Person: Chris Stoeckert, Jie Zheng Beta Cell Biology Consoritum An assay in which the transcriptome of a biological sample is analysed using Massive Parallel Signature Sequencing (MPSS). transcription profiling by MPSS assay http://en.wikipedia.org/wiki/Massively_parallel_signature_sequencing histone modification identification by ChIP-chip assay histone modification identification by ChIP-chip assay Penn group Beta Cell Biology Consoritum histone modification ChIP-chip A ChIP-chip assay to identify regions containing specific histones and their modifications. Person: Chris Stoeckert, Jie Zheng histone modification identification by ChIP-Seq assay Penn group histone modification ChIP-Seq histone modification identification by ChIP-Seq assay Person: Chris Stoeckert, Jie Zheng A ChIP-seq assay to identify regions containing specific histones and their modifications. Beta Cell Biology Consoritum transcription factor binding site identification by ChIP-chip assay A ChIP-chip assay to identify binding sites for transcription factors. Penn group Beta Cell Biology Consoritum TF Binding ChIP-chip Person: Chris Stoeckert, Jie Zheng transcription factor binding site identification by ChIP-chip assay transcription factor binding site identification by ChIP-Seq assay TF Binding ChIP-Seq Beta Cell Biology Consoritum Person: Chris Stoeckert, Jie Zheng transcription factor binding site identification by ChIP-Seq assay A ChIP-seq assay to identify binding sites for transcription factors. Penn group epigenetic modification assay Penn group Person: Chris Stoeckert, Jie Zheng Beta Cell Biology Consoritum An assay that identifies epigenetic modification including histone modifications, open chromatin, and DNA methylation. epigenetic modification assay NextSeq 500 Person: Venkat Malladi, Chris Stoeckert, Jie Zheng NextSeq 500 http://systems.illumina.com/systems/nextseq-sequencer.html ENCODE project A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. Illumina NextSeq 500 translation-associated transcript leader sequencing Janos Demeter, Chris Stoeckert pmid:23580730 Saccharomyces Genome Database (SGD) TATL-seq An RNA-seq assay that combines TL-seq with polysome fractionation pmid:23580730 translation-associated transcript leader sequencing Details see tracker: https://sourceforge.net/p/obi/obi-terms/725/ transcript leader sequencing pmid:23580730 transcript leader sequencing An RNA-seq assay combining enzymatic capture of m(7)G-capped mRNA 5' ends with high-throughput sequencing. Details see tracker: https://sourceforge.net/p/obi/obi-terms/725/ TL-seq Janos Demeter, Chris Stoeckert pmid:23580730 Saccharomyces Genome Database (SGD) ribosomal profiling by sequencing assay Ingolia, Nicholas T. (28 January 2014). "Ribosome profiling: new views of translation, from single codons to genome scale". Nature Reviews Genetics 15 (3): 205-213. doi:10.1038/nrg3645. PMID 24468696. ribosomal profiling Ribo-seq ENCODE project ribosomal profiling by sequencing assay Aspden et al., (August 2014). "Extensive translation of small open reading frames revealed by poly-ribo-seq." eLIFE 2014;3:e03528 A RNA-seq assay to sequence only mRNA protected by the ribosome during translation. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng Ribo-seq assay self-transcribing active regulatory region sequencing assay Person: Venkat Malladi, Chris Stoeckert, Jie Zheng STARR-seq assay self-transcribing active regulatory region sequencing Arnold et al. (January 2013). "Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq". Science 339 (6123): 1074-7. ENCODE project A RNA-seq assay to identify the sequences that act as transcriptional enhancers in a direct, quantitative, and genome-wide manner from sheared genomic DNA. STARR-seq self-transcribing active regulatory region sequencing assay Bohla et al., (September 2014). "A functional insulator screen identifies NURF and dREAM components to be required for enhancer-blocking." PLoS One 9(9):e107765. doi: 10.1371/journal.pone.0107765. carbon-copy chromosome conformation capture assay followed by sequencing assay Lieberman-Aiden E, et al. (2009). Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326: 289-293. A carbon-copy chromosome conformation capture assay to analyze the organization of chromosomes in an unbiased, genome-wide manner using high throughput sequening following carbon-copy chromosome conformation capture. HiC Fudenberg et al., (November 2014). "High order chromatin architecture shapes the landscape of chromosomal alterations in cancer." Nat Biotechol 29(12):1109-13. doi: 10.1038/nbt.2049. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng carbon-copy chromosome conformation capture assay followed by sequencing assay Carbon-copy chromosome conformation capture assay followed by sequencing ENCODE project HiC assay individual-nucleotide resolution cross-linking and immunoprecipitation sequencing assay König et al., (18 January 2012). "Protein-RNA interactions: new genomic technologies and perspectives". Nature Reviews Genetics 13 (2): 77-83. doi:10.1038/nrg3141 iCLIP A cross-linking immunoprecipitation high-throughput sequencing assay to identify protein-RNA interactions by using UV light to covalently bind proteins and RNA molecules, allowing for a very stringent purification of the linked protein-RNA complexes. Huppertz et al., (February 2014). "iCLIP: protein-RNA interactions at nucleotide resolution.". Methods (San Diego, Calif.) 65 (3): 274-87. doi:10.1016/j.ymeth.2013.10.011 individual-nucleotide resolution cross-linking and immunoprecipitation sequencing assay individual-nucleotide resolution cross-linking and immunoprecipitation Person: Venkat Malladi, Chris Stoeckert, Jie Zheng ENCODE project iCLIP assay RNA Bind-n-Seq assay A RNA-seq assay that comprehensively characterizes sequence and structural specificity of RNA binding proteins (RBPs) ENCODE project RNA Bind-n-Seq assay RNA Bind-n-Seq Lambert et al., (June 2014). "RNA Bind-n-Seq: quantitative assessment of the sequence and structural binding specificity of RNA binding proteins." Mol Cell. 2014 Jun 5;54(5):887-900. doi: 10.1016/j.molcel.2014.04.016 RBNS Person: Venkat Malladi, Chris Stoeckert, Jie Zheng RNBS assay poly(A)-site sequencing assay Person: Venkat Malladi, Chris Stoeckert, Jie Zheng A RNA-seq assay for quantitatively profiling RNA polyadenylation at the transcriptome level. poly(A)-site sequencing assay Wu et al., (July 2014). "Genome-wide determination of poly(A) sites in Medicago truncatula: evolutionary conservation of alternative poly(A) site choice. BMC Genomics. 2014 Jul 21;15:615. doi: 10.1186/1471-2164-15-615. ENCODE project PAS-seq assay PAS-seq Shepard et al., (April 2011). "Complex and dynamic landscape of RNA polyadenylation revealed by PAS-Seq." RNA. 2011 Apr;17(4):761-72. doi: 10.1261/rna.2581711 Poly(A)-site sequencing organism organism 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. 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. 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. E.g Drosophila melanogaster Drosophila melanogaster EFO_URI: http://www.ebi.ac.uk/efo/EFO_0000634 GROUP: OBI Biomaterial Branch James Malone Jie Zheng MO_508 NIFSTD:birnlex_376 Tomasz Adamusiak 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. WEB: http://en.wikipedia.org/wiki/Organism animal fungus organism plant virus specimen Biobanking of blood taken and stored in a freezer for potential future investigations stores 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. PERSON: James Malone PERSON: Philippe Rocca-Serra A material entity that has the specimen role. GROUP: OBI Biomaterial Branch specimen cultured cell population A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history. PERSON:Matthew Brush 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 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. cell culture sample 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). organ section GROUP: OBI Biomaterial Branch PERSON: Philippe Rocca-Serra A liver slice used in a perfusion experiment. Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ section study with long-term functional evaluation. Clin Otolaryngol Allied Sci. 1995 Apr;20(2):145-9. PMID: 7634521 A processed material which derives from an organ and results from a process of dissection or histological sample preparation a portion(formerly an organ section is portion of an organ removed from the context of the organ) GROUP: CEBS PERSON: Helen Parkinson organ section data transformation Philippe Rocca-Serra The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value. A planned process that produces output data from input data. Branch editors Elisabetta Manduchi Helen Parkinson James Malone Melanie Courtot Richard Scheuermann Ryan Brinkman Tina Hernandez-Boussard data analysis data processing data transformation feature extraction objective Elisabetta Manduchi A feature extraction objective is a data transformation objective where the aim of the data transformation is to generate quantified values from a scanned image. James Malone TERM: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#feature_extraction feature extraction objective linlog transformation Philippe Rocca-Serra A linlog transformation is a data transformation, described in PMID 16646782, whose input is a matrix [y_ik] and whose output is a matrix obtained by applying formula (9) of this paper, where values below an appropriately determined threshold (dependent on the row i) are transformed via a polynomial of degree 1, and values above this threshold are transformed via a logarithm. Elisabetta Manduchi PMID: 16646782 This can be used for microarray normalization, e.g. to normalize the data from a two-channel expression microarray assay, as described in PMID 16646782. linlog transformation loess global transformation Philippe Rocca-Serra A loess global transformation is a loess transformation where only one loess fitting is performed, utilizing one subset of (or possibly all of) the data points in the input so that there is only one resulting loess curve y=f(x) which is used for the transformation. Elisabetta Manduchi James Malone Melanie Courtot OTHER: Editor's generalization based on MGED Ontology term loess global transformation loess group transformation Philippe Rocca-Serra A loess group transformation is a loess transformation where the input is partitioned into groups and for each group a loess fitting is performed, utilizing a subset of (or possibly all of) the data points in that group. Thus, a collection of loess curves y=f_i(x) is generated, one per group. Each (x, y) in the input is transformed into (x, y-f_i(x)), where f_i(x) is the curve corresponding to the group to which that data point belongs. Elisabetta Manduchi James Malone Melanie Courtot OTHER: Editor's generalization based on MGED Ontology term loess group transformation loess scale group transformation A loess scale group transformation is a data transformation consisting in the application of a scale adjustment following a loess group transformation, to render the group variances for the second variable (y) similar. Has objective scaling. Elisabetta Manduchi James Malone Melanie Courtot OTHER: Editor's generalization based on MGED Ontology term loess scale group transformation total intensity transformation single Philippe Rocca-Serra A total intensity transformation single is a data transformation that takes as input an n-dimensional (real) vector and multiplies each component of this vector by a coefficient, where the coefficient is obtained by taking the sum of the input components or of a subset of these, multiplied by a constant of choice. Elisabetta Manduchi Helen Parkinson James Malone Melanie Courtot Note that if the word "sum" is replaced by the word "mean" in the definition, the resulting definition is equivalent. OTHER: Adjusted from MGED Ontology This can be used as a simple normalization method for expression microarray assays. For example, each intensity from a one-channel microarray assay is multiplied by a constant so that the output mean intensity over the microarray equals a desired target T (the multiplicative constant in this case is the T/(mean intensity)). total intensity transformation single total intensity transformation paired Philippe Rocca-Serra A total intensity transformation paired is a data transformation that takes as input two n-dimensional (real) vectors and multiplies each component of the first vector by a coefficient, where the coefficient is obtained by taking the ratio of the sum of the second input components or of a subset of these by the sum of the first input components or of a subset of these (the same subset is used for the two vectors). Elisabetta Manduchi Note that if the word "sum" is replaced by the word "mean" in the definition, the resulting definition is equivalent. OTHER: Adjusted from MGED Ontology This can be used as a simple normalization method for the two channels from a two-channel expression microarray assay or from two related one-channel expression microarray assays. total intensity transformation paired quantile transformation A quantile transformation is a data transformation that takes as input a collection of data sets, where each can be thought as an n-dimensional (real) vector, and which transforms each data set so that the resulting output data sets have equal quantiles. Elisabetta Manduchi PERSON: Elisabetta Manduchi This can be used for expression microarray assay normalization and it is referred to as "quantile normalization", according to the procedure described e.g. in PMID 12538238. quantile transformation differential expression analysis objective A differential expression analysis objective is a data transformation objective whose input consists of expression levels of entities (such as transcripts or proteins), or of sets of such expression levels, under two or more conditions and whose output reflects which of these are likely to have different expression across such conditions. Analyses implemented by the SAM (http://www-stat.stanford.edu/~tibs/SAM), PaGE (www.cbil.upenn.edu/PaGE) or GSEA (www.broad.mit.edu/gsea/) algorithms and software Elisabetta Manduchi PERSON: Elisabetta Manduchi differential expression analysis objective dye swap merge A dye swap merge is a replicate analysis which takes as input data from paired two-channel microarray assays where the sample labeled with one dye in the first assay is labeled with the other dye in the second assay and vice versa. The output for each reporter is obtained by combining its (raw or possibly pre-processed) M values in the two assays, where the M value in an assay is defined as the difference of the log intensities in the two channels. This can be used as a normalization step, when appropriate assumptions are met. Elisabetta Manduchi James Malone PERSON: Elisabetta Manduchi PERSON: James Malone dye swap merge moving average Philippe Rocca-Serra A moving average is a data transformation in which center calculations, usually mean calculations, are performed on values within a sliding window across the input data set. Elisabetta Manduchi Helen Parkinson PERSON: Elisabetta Manduchi PERSON: Helen Parkinson The moving average is often used to handle data from tiling arrays. moving average replicate analysis A replicate analysis is a data transformation in which data from replicates are combined, e.g. through descriptive statistics calculations, and the results might be utilized for a variety of purposes, like assessing reproducibility, identifying outliers, normalizing, etc. Elisabetta Manduchi Helen Parkinson PERSON: Helen Parkinson PERSON:Elisabetta Manduchi Replicate analysis can be used in microarray analysis to identify and potentially exclude low quality data. replicate analysis loess transformation Philippe Rocca-Serra A loess transformation is a data transformation that takes as input a collection of real number pairs (x, y) and, after performing (one or more) loess fittings, utilizes the resulting curves to transform each (x, y) in the input into (x, y-f(x)) where f(x) is one of the fitted curves. Elisabetta Manduchi James Malone Melanie Courtot OTHER: Editor's generalization based on MGED Ontology term loess transformation multiple testing correction method A multiple testing correction method is a hypothesis test performed simultaneously on M > 1 hypotheses. Multiple testing procedures produce a set of rejected hypotheses that is an estimate for the set of false null hypotheses while controlling for a suitably define Type I error rate Monnie McGee PAPER: Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 9-10. multiple testing correction method multiple testing procedure data transformation objective Modified definition in 2013 Philly OBI workshop An objective specification to transformation input data into output data James Malone PERSON: James Malone data transformation objective normalize objective data normalization objective Elisabetta Manduchi Helen Parkinson PERSON: Elisabetta Manduchi PERSON: Helen Parkinson A normalization objective is a data transformation objective where the aim is to remove systematic sources of variation to put the data on equal footing in order to create a common base for comparisons. James Malone PERSON: James Malone Quantile transformation which has normalization objective can be used for expression microarray assay normalization and it is referred to as "quantile normalization", according to the procedure described e.g. in PMID 12538238. data normalization objective correction objective PERSON: James Malone PERSON: Melanie Courtot A correction objective is a data transformation objective where the aim is to correct for error, noise or other impairments to the input of the data transformation or derived from the data transformation itself James Malone Type I error correction correction objective normalization data transformation James Malone A normalization data transformation is a data transformation that has objective normalization. PERSON: James Malone normalization data transformation averaging data transformation James Malone An averaging data transformation is a data transformation that has objective averaging. PERSON: James Malone averaging data transformation class discovery data transformation James Malone clustering data transformation unsupervised classification data transformation A class discovery data transformation (sometimes called unsupervised classification) is a data transformation that has objective class discovery. PERSON: James Malone class discovery data transformation center calculation objective PERSON: James Malone A center calculation objective is a data transformation objective where the aim is to calculate the center of an input data set. A mean calculation which has center calculation objective is a data transformation in which the center of the input data is discovered through the calculation of a mean average. James Malone center calculation objective class discovery objective PERSON: Elisabetta Manduchi PERSON: James Malone clustering objective A class discovery objective (sometimes called unsupervised classification) is a data transformation objective where the aim is to organize input data (typically vectors of attributes) into classes, where the number of classes and their specifications are not known a priori. Depending on usage, the class assignment can be definite or probabilistic. James Malone class discovery objective discriminant analysis objective unsupervised classification objective center calculation data transformation James Malone A center calculation data transformation is a data transformation that has objective of center calculation. PERSON: James Malone center calculation data transformation scaling objective Person:Helen Parkinson Scaling gene expression data for cross platform analysis http://www.springerprotocols.com/Abstract/doi/10.1007/978-1-59745-454-4_13 is a data transformation objective where all, or some of a data set is adjusted by some data transformation according to some scale, for example a user defined minimum or maximum Awaiting English definition from Monnie McGee James Malone scaling objective scaling data transformation A scaling data transformation is a data transformation that has objective scaling. James Malone PERSON: James Malone scaling data transformation error correction objective Application of a multiple testing correction method PERSON: James Malone An error correction objective is a data transformation objective where the aim is to remove (correct for) erroneous contributions arising from the input data, or the transformation itself. James Malone, Helen Parkinson error correction objective sequential design Any design in which the decision as to whether to enroll the next patient, pair of patients, or block of patients is determined by whether the cumulative treatment difference for all previous patients is within specified limits. Enrollment is continued if the difference does not exceed the limits. It is terminated if it does MUSC PMID: 17710740.Pharm Stat. 2007 Aug 20.Sequential design approaches for bioequivalence studies with crossover designs. Philippe Rocca-Serra Provenance: OCI sequential design observation design OBI branch derived PMID: 12387964.Lancet. 2002 Oct 12;360(9340):1144-9.Deficiency of antibacterial peptides in patients with morbus Kostmann: an observation study. Philippe Rocca-Serra observation design observation design is a study design in which subjects are monitored in the absence of any active intervention by experimentalists. pool of specimens GROUP: CEBS PERSON: Jennifer Fostel A pool of specimens is a mixture of a population of samples which have been gathered from one or more sample populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish. check with advisors as to how to represent multiple instances of any class? a set of specimens which have been gathered from one or more sample_populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish pool of specimens genetically modified organism PERSON: Philippe Rocca-Serra A protocol for removal of antibiotic resistance cassettes from human embryonic stem cells genetically modified by homologous recombination or transgenesis. Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 OBI Biomaterial an organism that is the output of a genetic transformation process genetically modified organism extraction A material separation in which a desired component of an input material is separated from the remainder Person:Bjoern Peters Philippe Rocca-Serra nucleic acid extraction using phenol chloroform 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. extraction centrifugation Philippe Rocca-Serra adapted from http://www.fao.org/DOCREP/003/X3910E/X3910E06.htm PMID: 18428461.Purification of oligodendrocytes and their progenitors using immunomagnetic separation and Percoll gradient centrifugation. Curr Protoc Neurosci. 2001 May;Chapter 3:Unit 3.12. centrifugation centrifugation is a process separating molecules by size or density using centrifugal forces generated by a spinning rotor. G-forces of several hundred thousand times gravity are generated in ultracentrifugation staining Philippe Rocca-Serra adapted from Wikipedia: http://en.wikipedia.org/wiki/Staining PMID: 18540298. Role of modified bleach method in staining of acid-fast bacilli in lymph node aspirates. Acta Cytol. 2008 May-Jun;52(3):325-8. Staining is a process which results in the addition a class-specific (DNA, proteins, lipids, carbohydrates) dye to a substrate to qualify or quantify the presence of a specific compound. staining washing OBI-Branch Philippe Rocca-Serra PMID: 6874122. Dialysis leucopenia--no correction after prolonged washing of the membrane. Int J Artif Organs. 1983 May;6(3):113-4. washing washing is a process by which a material entity acting as contaminant (e.g. excess staining reagent) is removed by application of one or more cycles of solution in flow. irradiation Philippe Rocca-Serra adapted from wikipedia (http://en.wikipedia.org/wiki/Irradiation) PMID: 18563778.Histological and modeling study of skin thermal injury to 2.0 mum laser irradiation.Lasers Surg Med. 2008 Jun 18;40(5):358-370. irradiation irradiation is a process by which a material entity is exposed to radiative energy, which could be ionizing radiation (such as gamma rays or X-rays) or not such as UV light or microwaves enzymatic ligation OBI-Branch Philippe Rocca-Serra An enzymatic ligation is a planned process in which molecules are joined by covalent bonds through the action of an material entity with a ligase activity PMID: 17853876. Enzymatic ligation assisted by nucleases: simultaneous ligation and digestion promote the ordered assembly of DNA. Nat Protoc. 2007;2(9):2198-202. enzymatic ligation storage OBI-Branch Philippe Rocca-Serra 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 PMID: 18550121.Total Prostate Specific Antigen Stability Confirmed After Long-Term Storage of Serum at -80C. J Urol. 2008 Jun 10. storage cell lysis BP, JG, RV: There is also a need for the unplanned cell lysis, which is probably not in the scope of OBI, but should be linked to from this process. Philippe Rocca-Serra adapted from wikipedia [http://en.wikipedia.org/wiki/Lysis] PMID: 18484276.Cell lysis with dimethyl sulphoxide produces stable homogeneous solutions in the dichlorofluorescein oxidative stress assay. Free Radic Res. 2008 May;42(5):435-41. cell lysis cell lysis is a process by which cell membrane integrity of live cells is compromised and leads to cell death. Cell lysis may be achieved by means of viral action or osmotic shock. immobilization OBI-Branch Philippe Rocca-Serra PMID: 18562258. The immobilization of proteins on biodegradable fibers via biotin-streptavidin bridges.Acta Biomater. 2008 May 23. immbolization is a process by which material entity become (possibly covalently but not necessarily) attached to the surface of another material entity used a substratum. immobilization nucleic acid hybridization Philippe Rocca-Serra adapted from wikipedia [http://en.wikipedia.org/wiki/Nucleic_acid_hybridization] hybridization assay PMID: 18555787.Quantitative analysis of DNA hybridization in a flowthrough microarray for molecular testing. Anal Biochem. 2008 May 27. a planned process by which totally or partially complementary, single-stranded nucleic acids are combined into a single molecule called heteroduplex or homoduplex to an extent depending on the amount of complementarity. nucleic acid hybridization flow cell flow_cell Aparatus in the fluidic subsystem where the sheath and sample meet. Can be one of several types; jet-in-air, quartz cuvette, or a hybrid of the two. The sample flows through the center of a fluid column of sheath fluid in the flow cell. Biofilm Flow Cell Person:John Quinn flow cell http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm flow cytometer A flow_cytometer is an instrument for counting, examining and sorting microscopic particles in suspension. It allows simultaneous multiparametric analysis of the physical and/or chemical characteristics of single cells flowing through an optical and/or electronic detection apparatus. A flow cytometer is an instrument that can be used to quantitatively measure the properties of individual cells in a flowing medium. FACS Calibur John Quinn flow cytometer http://en.wikipedia.org/wiki/Flow_cytometer light source A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics). Light sources may include one of a variety of lamps (e.g., xenon, halogen, mercury). Most light sources are operated from line power, but some may be powered from batteries. They are mostly used in endoscopic, microscopic, and other examination and/or in surgical procedures. The light source is part of the optical subsystem. In a flow cytometer the light source directs high intensity light at particles at the interrogation point. The light source in a flow cytometer is usually a laser. Elizabeth M. Goralczyk John Quinn Olga Tchuvatkina Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 light source obscuration bar Flow Cytometry: First Principles, by Alice Longobardi Givan, ISBN-10: 0471382248, ISBN-13: 978-0471382249 An obscuration bar is a an optical subsystem which is a strip of metal or other material that serves to block out direct light from the illuminating beam. The obscuration bar prevents the bright light scattered in the forward directions from burning out the collection device. Daniel Schober John Quinn obscuration bar obscuration bar in a flow cytometer optical filter 720 LP filter, 580/30 BP filter An optical filter is an optical subsystem that selectively transmits light having certain properties (often, a particular range of wavelengths, that is, range of colours of light), while blocking the remainder. They are commonly used in photography, in many optical instruments, and to colour stage lighting Optical filters can be arranged to segregate and collect light by wave length. John Quinn http://en.wikipedia.org/wiki/Optical_filter optical filter photodetector A photodetector is a device used to detect and measure the intensity of radiant energy through photoelectric action. In a cytometer, photodetectors measure either the number of photons of laser light scattered on impact with a cell (for example), or the flourescence emitted by excitation of a fluorescent dye. A photomultiplier tube, a photo diode John Quinn http://einstein.stanford.edu/content/glossary/glossary.html photodetector flow cytometer sorter A flow_cytometer_sorter is a flow_cytometer that analyzes and separates or sorts particles passing through (based on properties measured during analysis) to collect cells of interest. BioSorter2000, LSR2 John Quinn Melanie Courtot flow cytometer sorter http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm DNA sequencer A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences. ABI 377 DNA Sequencer, ABI 310 DNA Sequencer DNA sequencer MO Trish Whetzel array scanner GROUP: MGED Ontology An processed material which acquires images of fluorescence (induced with lasers) from labeled molecules on the surface of the microarray chip GenePix 4200A, GenePix4000B Trish Whetzel array scanner arrayer BioRobotics Microgrid II TAS, Affymetrix GMS 417 MO_697 arrayer Trish Whetzel a device which deposits biological material onto a substrate in a defined pattern. arrayer centrifuge A device with a rapidly rotating container that applies centrifugal force to its contents Person: Jennifer Fostel Melanie Courtot Trish Whetzel centrifuge http://en.wikipedia.org/wiki/Centrifuge computer A computer is an instrument which manipulates (stores, retrieves, and processes) data according to a list of instructions. Apple PowerBook, Dell OptiPlex Melanie Courtot Trish Whetzel computer http://en.wikipedia.org/wiki/Computer heating block A heating block is an instrument or part of an instrument which raises or maintains the temperature of a sample to a defined constant temperature during certain parts of an assay An instrument used to heat and/or maintain material at a set temperature. Daniel Schober MO heating block homogenizer A homogenizer is an instrument for the homogenization of various types of material, such as tissue, plant, food, soil, and many others. Melanie Courtot Trish Whetzel homogenizer http://en.wikipedia.org/wiki/Homogenizer mortar, blender hybridization chamber A device which is used to maintain constant contact of a liquid on an array. This can be either a glass vial or slide. Glass Array Hybridization Cassette MO_563 hybridization_chamber Trish Whetzel hybridization chamber hybridization station A device which is used to maintain the temperature of one or more hybridization_chamber(s) at a defined, constant temperature. Labnet Problot12 MO_497 hybridization station Trish Whetzel hybridization station liquid handler Beckman BioMek 2000 DS: Is this class justified? Its a unnamed class. If so, put a fluidic_system and the fluidic_subsystem as subclasses. TW: This is required by MO. FG & DS: Capture as function. All: Needs to be reviewed, according to query use case. If we keep it its kept as unnamed owl class. The liquid handling class remains but as an undefined class with are unlikely to have children. It is expected that the reasoner would classifiy appropriate classes under this class that meet the have the liquid_handling function relation. DS: Is this class justified? Its a unnamed class. If so, put a fluidic_system and the fluidic_subsystem as subclasses. TW: This is required by MO. FG: Or as function. MO_868 liquid_handler a device that is used for automated liquid transfer and handling. liquid handler liquid_handling_instrument oligonucleotide synthesizer An instrument used to chemically synthesize oligonucleotides. Automated Multiplex Oligonucleotide Synthesizer MO Trish Whetzel oligonucleotide synthesizer sonicator A device that converts a variable electrical current to mechanical vibration of a metallic probe. The device is used for the lysis of cells, the mixing of compounds or solutions, to framgent molecules of DNA, or to create emulsions. MO Sonicator 3000 Trish Whetzel sonicator spectrophotometer A spectrophotometer is an instrument that measures the intensity of light as a function of the color, or more specifically, the wavelength of light, transmitted by a substance. Helios Gamma Spectrophotometer MO Melanie Courtot Trish Whetzel spectrophotometer thermal cycler An instrument that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. DNA_amplifier MO Melanie Courtot PCR_machine Piko(tm) 96-well Thermal Cycler Polymerase_Chain_Reaction_ machine Trish Whetzel thermal cycler thermocycler vortexer A vortexer is an instrument that mixes small vials of liquid by creating a rotation of the liquid around its own center. It consists of an electric motor with the drive shaft oriented vertically and attached to a cupped rubber piece mounted slightly off-center. As the motor runs the rubber piece oscillates rapidly in a circular motion. When a test tube or other appropriate container is pressed into the rubber cup (or touched to its edge) the motion is transmitted to the liquid inside and a vortex is created. Melanie Courtot Trish Whetzel VWR Genie 2 http://en.wikipedia.org/wiki/Vortex_mixer vortex_mixer vortexer microarray wash station ArrayIt(r) Microarray Wash Station MO_626 wash_station Trish Whetzel a device that is used to wash Affymetrix-type arrays. microarray wash station temperature control bath Alan Ruttenburg Daniel Schober Frank Gibson OBI Instrument branch A temperature_control_bath is a device that has the function to regulate the temperature of a material, the function to contain fluid and the function to vary and maintain the temperature of the contained fluid. Heat exchange (energy transfer) between the material and the heating element is facilitated via the contained fluid. A temperature_control_bath is composed of a container, a heating element and/or a cooling element and a means to adjust the needed temperature. In most cases also a timer and a means to stir the fluid is provided as well. DS: This was heated_bath. It was renamed to reflect the possability that the same bath can be used for cooling. We can now define the temperature variables and based on that infer if it is a cooling device or a heating device (also quite relative to surrounding temperature). VWR Signature Deep-Chamber Heated Water Bath. A water bath is used for temperatures up to 100 degrees C. An oil bath is employed for temperatures over 100 degrees C. temperature control bath cytometer A cytometer is an instrument for counting and measuring cells. Melanie Courtot cytometer http://medical.merriam-webster.com/medical/cytometer microarray An affymetrix U133 array is a microarray. Microarrays include 1 and 2-color arrays, custom and commercial arrays (e.g, Affymetrix, Agilent, Nimblegen, Illumina, etc.) for expression profiling, DNA variant detection, protein binding, and other genomic and functional genomic assays. PERSON: Chris Stoeckert A processed material that is made to be used in an analyte assay. It consists of a physical immobilisation matrix in which substances that bind the analyte are placed in regular spatial position. Daniel Schober microarray DNA microarray PERSON: Frank Gibson Web:<http://en.wikipedia.org/wiki/DNA_microarray>@2008/03/03 A DNA-microarray is a microarray that is used as a physical 2D immobilisation matrix for DNA sequences. DNA microarray-bound DNA fragments are used as targets for a hybridising probed sample. DNA Chip DNA microarray DNA-array Moran G, Stokes C, Thewes S, Hube B, Coleman DC, Sullivan D (2004). "Comparative genomics using Candida albicans DNA microarrays reveals absence and divergence of virulence-associated genes in Candida dubliniensis". Microbiology 150: 3363-3382. doi:10.1099/mic.0.27221-0. PMID 15470115 PERSON: Daniel Schober protein microarray PERSON: Daniel Schober A protein-microarray is a microarray, ususlly a piece of glass, on which different molecules of protein have been affixed at separate locations in an ordered manner. These are used to identify protein-protein or protein-small molecule interactions. Daniel Schober The most common protein microarray is the antibody microarray, where antibodies are spotted onto the protein chip and are used as capture molecules to detect proteins from cell lysate solutions. protein microarray droplet sorter OBI Instrument branch OBI Instrument branch A droplet sorter is part_of a flow cytometer sorter that converts the carrier fluid stream into individual droplets, and these droplets are directed into separate locations for recovery (enriching the original sample for particles of interest based on qualities determined by gating) or disposal. droplet sorter water bath Daniel Schober PERSON: Daniel Schober A water bath is a temperature control bath in which a water acts as contact medium enabling temperature transfer from the heating element or cooling element to the sample. The temperature can be controlled in the 0 to 100 degree centigrade range (under normal pressure). A water bath was used to allow for cell incubation at 38 degree centigrade for 8 hours. water bath microtome PERSON: Daniel Schober PERSON: Phillippe Rocca-Serra A microtome is a mechanical instrument used to cut biological specimens into very thin segments for further treatment (e.g. ISH) and ultimately microscopic or histologic examination. Most microtomes provide cooling facilities (cryo-microtome) and use a steel blade to cut a slice of defined thickness. Some are automatic, and some are driven by hand. PMID: 9974145.Serial sectioning of thick tissue with a novel vibrating blade microtome. Brain Res Brain Res Protoc. 1999 Jan;3(3):302-7. microtome 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 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. experimental design rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol. study design clinical study design Clinical Research Glossary Version 4.0 CDICS glossary group PMID: 17655677.J Cardiovasc Electrophysiol. 2007 Aug;18(9):965-71.Biventricular versus right ventricular pacing in patients with AV block (BLOCK HF): clinical study design and rationale. Plan for the precise procedure to be followed in a clinical trial, including planned and actual timing of events, choice of control group, method of allocating treatments, blinding methods; assigns a subject to pass through one or more epochs in the course of a trial. Specific design elements, e.g., crossover, parallel; dose-escalation [Modified from Pocock, Clinical Trials: A Practical Approach] PlanAndPlannedProcess Branch The definition needs to be extended to other things than simply patients clinical study design repeated measure design PMID: 10959922.J Biopharm Stat. 2000 Aug;10(3):433-45.Equivalence in test assay method comparisons for the repeated-measure, matched-pair design in medical device studies: statistical considerations. PlanAndPlannedProcess Branch a study design which use the same individuals and exposure them to a set of conditions. The effect of order and practice can be confounding factor in such designs http://www.holah.karoo.net/experimentaldesigns.htm repeated measure design cross over design (source: http://www.sbu.se/Filer/Content0/publikationer/1/literaturesearching_1993/glossary.html) PMID: 17601993-Objective: HIV-infected patients with lipodystrophy (HIV-lipodystrophy) are insulin resistant and have elevated plasma free fatty acid (FFA) concentrations. We aimed to explore the mechanisms underlying FFA-induced insulin resistance in patients with HIV-lipodystrophy. Research Design and Methods: Using a randomized placebo-controlled cross-over design, we studied the effects of an overnight acipimox-induced suppression of FFA on glucose and FFA metabolism by using stable isotope labelled tracer techniques during basal conditions and a two-stage euglycemic, hyperinsulinemic clamp (20 mU insulin/m(2)/min; 50 mU insulin/m(2)/min) in nine patients with nondiabetic HIV-lipodystrophy. All patients received antiretroviral therapy. Biopsies from the vastus lateralis muscle were obtained during each stage of the clamp. Results: Acipimox treatment reduced basal FFA rate of appearance by 68.9% (52.6%-79.5%) and decreased plasma FFA concentration by 51.6 % (42.0%-58.9%), (both, P < 0.0001). Endogenous glucose production was not influenced by acipimox. During the clamp the increase in glucose-uptake was significantly greater after acipimox treatment compared to placebo (acipimox: 26.85 (18.09-39.86) vs placebo: 20.30 (13.67-30.13) mumol/kg/min; P < 0.01). Insulin increased phosphorylation of Akt (Thr(308)) and GSK-3beta (Ser(9)), decreased phosphorylation of glycogen synthase (GS) site 3a+b and increased GS-activity (I-form) in skeletal muscle (P < 0.01). Acipimox decreased phosphorylation of GS (site 3a+b) (P < 0.02) and increased GS-activity (P < 0.01) in muscle. Conclusion: The present study provides direct evidence that suppression of lipolysis in patients with HIV-lipodystrophy improves insulin-stimulated peripheral glucose-uptake. The increased glucose-uptake may in part be explained by increased dephosphorylation of GS (site 3a+b) resulting in increased GS activity. Philippe Rocca-Serra a repeated measure design which ensures that experimental units receive, in sequence, the treatment (or the control), and then, after a specified time interval (aka *wash-out periods*), switch to the control (or treatment). In this design, subjects (patients in human context) serve as their own controls, and randomization may be used to determine the ordering which a subject receives the treatment and control cross over design n-to-1 design Adapted from http://www.childrens-mercy.org/stats/definitions/crossover.htm and source:http://symptomresearch.nih.gov/chapter_6/sec1/csss1pg1.htm) N-of-1 design is a cross-over design in which the same patient is repeatedly randomised to receive either the experimental treatment or its control (Senn, 1993). Philippe Rocca-Serra n-to-1 design matched pairs design A matched pair design is a study design which use groups of individuals associated (hence matched) to each other based on a set of criteria, one member going to one treatment, the other member receiving the other treatment. PMID: 17288613-BSTRACT: BACKGROUND: Physicians in Canadian emergency departments (EDs) annually treat 185,000 alert and stable trauma victims who are at risk for cervical spine (C-spine) injury. However, only 0.9% of these patients have suffered a cervical spine fracture. Current use of radiography is not efficient. The Canadian C-Spine Rule is designed to allow physicians to be more selective and accurate in ordering C-spine radiography, and to rapidly clear the C-spine without the need for radiography in many patients. The goal of this phase III study is to evaluate the effectiveness of an active strategy to implement the Canadian C-Spine Rule into physician practice. Specific objectives are to: 1) determine clinical impact, 2) determine sustainability, 3) evaluate performance, and 4) conduct an economic evaluation. METHODS: We propose a matched-pair cluster design study that compares outcomes during three consecutive 12-months before, after, and decay periods at six pairs of intervention and control sites. These 12 hospital ED sites will be stratified as teaching or community hospitals, matched according to baseline C-spine radiography ordering rates, and then allocated within each pair to either intervention or control groups. During the after period at the intervention sites, simple and inexpensive strategies will be employed to actively implement the Canadian C-Spine Rule. The following outcomes will be assessed: 1) measures of clinical impact, 2) performance of the Canadian C-Spine Rule, and 3) economic measures. During the 12-month decay period, implementation strategies will continue, allowing us to evaluate the sustainability of the effect. We estimate a sample size of 4,800 patients in each period in order to have adequate power to evaluate the main outcomes. DISCUSSION: Phase I successfully derived the Canadian C-Spine Rule and phase II confirmed the accuracy and safety of the rule, hence, the potential for physicians to improve care. What remains unknown is the actual change in clinical behaviors that can be affected by implementation of the Canadian C-Spine Rule, and whether implementation can be achieved with simple and inexpensive measures. We believe that the Canadian C-Spine Rule has the potential to significantly reduce health care costs and improve the efficiency of patient flow in busy Canadian EDs. Philippe Rocca-Serra http://www.holah.karoo.net/experimentaldesigns.htm matched pairs design parallel group design A parallel group design or independent measure design is a study design which uses unique experimental unit each experimental group, in other word no two individuals are shared between experimental groups, hence also known as parallel group design. Subjects of a treatment group receive a unique combination of independent variable values making up a treatment PMID: 17408389-Purpose: Proliferative vitreoretinopathy (PVR) is the most important reason for blindness following retinal detachment. Presently, vitreous tamponades such as gas or silicone oil cannot contact the lower part of the retina. A heavier-than-water tamponade displaces the inflammatory and PVR-stimulating environment from the inferior area of the retina. The Heavy Silicone Oil versus Standard Silicone Oil Study (HSO Study) is designed to answer the question of whether a heavier-than-water tamponade improves the prognosis of eyes with PVR of the lower retina. Methods: The HSO Study is a multicentre, randomized, prospective controlled clinical trial comparing two endotamponades within a two-arm parallel group design. Patients with inferiorly and posteriorly located PVR are randomized to either heavy silicone oil or standard silicone oil as a tamponading agent. Three hundred and fifty consecutive patients are recruited per group. After intraoperative re-attachment, patients are randomized to either standard silicone oil (1000 cSt or 5000 cSt) or Densiron((R)) as a tamponading agent. The main endpoint criteria are complete retinal attachment at 12 months and change of visual acuity (VA) 12 months postoperatively compared with the preoperative VA. Secondary endpoints include complete retinal attachment before endotamponade removal, quality of life analysis and the number of retina affecting re-operation within 1 year of follow-up. Results: The design and early recruitment phase of the study are described. Conclusions: The results of this study will uncover whether or not heavy silicone oil improves the prognosis of eyes with PVR. Philippe Rocca-Serra http://www.holah.karoo.net/experimentaldesigns.htm independent measure design parallel group design randomized complete block design A randomized complete block design is_a study design which assigns randomly treatments to block. The number of units per block equals the number of treatment so each block receives each treatment exactly once (hence the qualifier 'complete'). The design was originally devised from field trials used in agronomy and agriculture. The analysis assumes that there is no interaction between block and treatment. The method was then used in other settings So The randomised complete block design is a design in which the subjects are matched according to a variable which the experimenter wishes to control. The subjects are put into groups (blocks) of the same size as the number of treatments. The members of each block are then randomly assigned to different treatment groups. Philippe Rocca-Serra http://www.stats.gla.ac.uk/steps/glossary/anova.html,(A researcher is carrying out a study of the effectiveness of four different skin creams for the treatment of a certain skin disease. He has eighty subjects and plans to divide them into 4 treatment groups of twenty subjects each. Using a randomised blocks& design, the subjects are assessed and put in blocks of four according to how severe their skin condition is; the four most severe cases are the first block, the next four most severe cases are the second block, and so on to the twentieth block. The four &members of each block are then randomly assigned, one to each of the four treatment groups. http://www.stats.gla.ac.uk/steps/glossary/anova.html#rbd)) http://www.tufts.edu/~gdallal/ranblock.htm randomized complete block design balanced incomplete block design PMID: 7622388.Health Educ Q. 1995 May;22(2):201-10.Balanced incomplete block design: description, case study, and implications for practice. Philippe Rocca-Serra balanced incomplete block design balanced incomplete block design is a kind of factorial design where all treatment pairs occur together within a block an equal number ?? times. ??ii' is the number of times treatment i occurs with i' http://en.wikipedia.org/wiki/Block_design and http://www.stat.psu.edu/~jglenn/stat503/05_factorial/02_factorial_IBD.html loop design A loop experiment design is where labeled extracts are compared in consecutive pairs. synonym: circular design MO_912 PMID: 12933549 Philippe Rocca-Serra on behalf of MO loop design reference design A reference experiment design type is where all samples are compared to a common reference. MO_699 PMID: 12933549 Philippe Rocca-Serra on behalf of MO reference design latin square design Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and Latin square design is_a study design which allows in its simpler form controlling 2 levels of nuisance variables (also known as blocking variables).he 2 nuisance factors are divided into a tabular grid with the property that each row and each column receive each treatment exactly once. PMID: 17582121-Our objective was to examine the effects of dietary cation-anion difference (DCAD) with different concentrations of dietary crude protein (CP) on performance and acid-base status in early lactation cows. Six lactating Holstein cows averaging 44 d in milk were used in a 6 x 6 Latin square design with a 2 x 3 factorial arrangement of treatments: DCAD of -3, 22, or 47 milliequivalents (Na + K - Cl - S)/100 g of dry matter (DM), and 16 or 19% CP on a DM basis. Linear increases with DCAD occurred in DM intake, milk fat percentage, 4% fat-corrected milk production, milk true protein, milk lactose, and milk solids-not-fat. Milk production itself was unaffected by DCAD. Jugular venous blood pH, base excess and HCO3(-) concentration, and urine pH increased, but jugular venous blood Cl- concentration, urine titratable acidity, and net acid excretion decreased linearly with increasing DCAD. An elevated ratio of coccygeal venous plasma essential AA to nonessential AA with increasing DCAD indicated that N metabolism in the rumen was affected, probably resulting in more microbial protein flowing to the small intestine. Cows fed 16% CP had lower urea N in milk than cows fed 19% CP; the same was true for urea N in coccygeal venous plasma and urine. Dry matter intake, milk production, milk composition, and acid-base status did not differ between the 16 and 19% CP treatments. It was concluded that DCAD affected DM intake and performance of dairy cows in early lactation. Feeding 16% dietary CP to cows in early lactation, compared with 19% CP, maintained lactation performance while reducing urea N excretion in milk and urine. Philippe Rocca-Serra latin square design graeco latin square design Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and Greco-Latin square design is a study design which relates to Latin square design PMID: 6846242-Beaton et al (Am J Clin Nutr 1979;32:2546-59) reported on the partitioning of variance in 1-day dietary data for the intake of energy, protein, total carbohydrate, total fat, classes of fatty acids, cholesterol, and alcohol. Using the same food intake data and the expanded National Heart, Lung and Blood Institute food composition data base, these analyses of sources of variance have been expanded to include classes of carbohydrate, vitamin A, vitamin C, thiamin, riboflavin, niacin, calcium, iron, total ash, caffeine, and crude fiber. The analyses relate to observed intakes (replicated six times) of 30 adult males and 30 adult females obtained under a paired Graeco-Latin square design with sequence of interview, interviewer, and day of the week as determinants. Neither sequence nor interviewer made consistent contribution to variance. In females, day of the week had a significant effect for several nutrients. The major partitioning of variance was between interindividual variation (between subjects) and intraindividual variation (within subjects) which included both true day-to-day variation in intake and methodological variation. For all except caffeine, the intraindividual variability of 1-day data was larger than the interindividual variability. For vitamin A, almost all of the variance was associated with day-to-day variability. One day data provide a very inadequate estimate of usual intake of individuals. In the design of nutrition studies it is critical that the intended use of dietary data be a major consideration in deciding on methodology. There is no ideal dietary method. There may be preferred methods for particular purposes. Philippe Rocca-Serra graeco latin square design only 2 articles in pubmed ->probably irrelevant hyper graeco latin square design Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and PRS to do Philippe Rocca-Serra hyper graeco latin square design no example found in pubmed->not in use in the community factorial design PMID: 17582121-Our objective was to examine the effects of dietary cation-anion difference (DCAD) with different concentrations of dietary crude protein (CP) on performance and acid-base status in early lactation cows. Six lactating Holstein cows averaging 44 d in milk were used in a 6 x 6 Latin square design with a 2 x 3 factorial arrangement of treatments: DCAD of -3, 22, or 47 milliequivalents (Na + K - Cl - S)/100 g of dry matter (DM), and 16 or 19% CP on a DM basis. Linear increases with DCAD occurred in DM intake, milk fat percentage, 4% fat-corrected milk production, milk true protein, milk lactose, and milk solids-not-fat. Milk production itself was unaffected by DCAD. Jugular venous blood pH, base excess and HCO3(-) concentration, and urine pH increased, but jugular venous blood Cl- concentration, urine titratable acidity, and net acid excretion decreased linearly with increasing DCAD. An elevated ratio of coccygeal venous plasma essential AA to nonessential AA with increasing DCAD indicated that N metabolism in the rumen was affected, probably resulting in more microbial protein flowing to the small intestine. Cows fed 16% CP had lower urea N in milk than cows fed 19% CP; the same was true for urea N in coccygeal venous plasma and urine. Dry matter intake, milk production, milk composition, and acid-base status did not differ between the 16 and 19% CP treatments. It was concluded that DCAD affected DM intake and performance of dairy cows in early lactation. Feeding 16% dietary CP to cows in early lactation, compared with 19% CP, maintained lactation performance while reducing urea N excretion in milk and urine. Philippe Rocca-Serra factorial design factorial design is_a study design which is used to evaluate two or more factors simultaneously. The treatments are combinations of levels of the factors. The advantages of factorial designs over one-factor-at-a-time experiments is that they are more efficient and they allow interactions to be detected. In statistics, a factorial design experiment is an experiment whose design consists of two or more factors, each with discrete possible values or levels, and whose experimental units take on all possible combinations of these levels across all such factors. Such an experiment allows studying the effect of each factor on the response variable, as well as the effects of interactions between factors on the response variable. http://www.stats.gla.ac.uk/steps/glossary/anova.html#facdes And from wikipedia (01/03/2007): http://en.wikipedia.org/wiki/Factorial_experiment) 2x2 factorial design 2x2 factorial design PMID: 17561240 PMID: 17561240-The present experiment evaluates the effects of intermittent exposure to a social stimulus on ethanol and water drinking in rats. Four groups of rats were arranged in a 2x2 factorial design with 2 levels of Social procedure (Intermittent Social vs Continuous Social) and 2 levels of sipper Liquid (Ethanol vs Water). Intermittent Social groups received 35 trials per session. Each trial consisted of the insertion of the sipper tube for 10 s followed by lifting of the guillotine door for 15 s. The guillotine door separated the experimental rat from the conspecific rat in the wire mesh cage during the 60 s inter-trial interval. The Continuous Social groups received similar procedures except that the guillotine door was raised during the entire duration of the session. For the Ethanol groups, the concentrations of ethanol in the sipper [3, 4, 6, 8, 10, 12, 14, and 16% (vol/vol)] increased across sessions, while the Water groups received 0% ethanol (water) in the sipper throughout the experiment. Both Social procedures induced more intake of ethanol than water. The Intermittent Social procedure induced more ethanol intake at the two highest ethanol concentration blocks (10-12% and 14-16%) than the Continuous Social procedure, but this effect was not observed with water. Effects of social stimulation on ethanol drinking are discussed. Philippe Rocca-Serra a factorial design which has 2 experimental factors (aka independent variables) and 2 factor levels per experimental factors fractional factorial design A fractional factorial design is_a study design in which only an adequately chosen fraction of the treatment combinations required for the complete factorial experiment is selected to be run Philippe Rocca-Serra fractional factorial design http://www.itl.nist.gov/div898/handbook/pri/section3/pri334.htm From ASQC (1983) Glossary & Tables for Statistical Quality Control dye swap design An experiment design type where the label orientations are reversed. exact synonym: flip dye, dye flip MO_858 PMID: 17411393-Dye-specific bias effects, commonly observed in the two-color microarray platform, are normally corrected using the dye swap design. This design, however, is relatively expensive and labor-intensive. We propose a self-self hybridization design as an alternative to the dye swap design. In this design, the treated and control samples are labeled with Cy5 and Cy3 (or Cy3 and Cy5), respectively, without dye swap, along with a set of self-self hybridizations on the control sample. We compare this design with the dye swap design through investigation of mouse primary hepatocytes treated with three peroxisome proliferator-activated receptor-alpha (PPARalpha) agonists at three dose levels. Using Agilent's Whole Mouse Genome microarray, differentially expressed genes (DEG) were determined for both the self-self hybridization and dye swap designs. The DEG concordance between the two designs was over 80% across each dose treatment and chemical. Furthermore, 90% of DEG-associated biological pathways were in common between the designs, indicating that biological interpretations would be consistent. The reduced labor and expense for the self-self hybridization design make it an efficient substitute for the dye swap design. For example, in larger toxicogenomic studies, only about half the chips are required for the self-self hybridization design compared to that needed in the dye swap design. Philippe Rocca-Serra on behalf of MO dye swap design replicate design A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments. MO_885 Philippe Rocca-Serra on behalf of MO replicate design self vs self design A study design that investigates variance and error estimates in the experimental system, and is where the same extract is compared. MO_490 PMID: 17411393-Dye-specific bias effects, commonly observed in the two-color microarray platform, are normally corrected using the dye swap design. This design, however, is relatively expensive and labor-intensive. We propose a self-self hybridization design as an alternative to the dye swap design. In this design, the treated and control samples are labeled with Cy5 and Cy3 (or Cy3 and Cy5), respectively, without dye swap, along with a set of self-self hybridizations on the control sample. We compare this design with the dye swap design through investigation of mouse primary hepatocytes treated with three peroxisome proliferator-activated receptor-alpha (PPARalpha) agonists at three dose levels. Using Agilent's Whole Mouse Genome microarray, differentially expressed genes (DEG) were determined for both the self-self hybridization and dye swap designs. The DEG concordance between the two designs was over 80% across each dose treatment and chemical. Furthermore, 90% of DEG-associated biological pathways were in common between the designs, indicating that biological interpretations would be consistent. The reduced labor and expense for the self-self hybridization design make it an efficient substitute for the dye swap design. For example, in larger toxicogenomic studies, only about half the chips are required for the self-self hybridization design compared to that needed in the dye swap design. Philippe Rocca-Serra on behalf of MO self vs self design time series design Groups of assays that are related as part of a time series. MO_887 PMID: 14744830-Microarrays are powerful tools for surveying the expression levels of many thousands of genes simultaneously. They belong to the new genomics technologies which have important applications in the biological, agricultural and pharmaceutical sciences. There are myriad sources of uncertainty in microarray experiments, and rigorous experimental design is essential for fully realizing the potential of these valuable resources. Two questions frequently asked by biologists on the brink of conducting cDNA or two-colour, spotted microarray experiments are 'Which mRNA samples should be competitively hybridized together on the same slide?' and 'How many times should each slide be replicated?' Early experience has shown that whilst the field of classical experimental design has much to offer this emerging multi-disciplinary area, new approaches which accommodate features specific to the microarray context are needed. In this paper, we propose optimal designs for factorial and time course experiments, which are special designs arising quite frequently in microarray experimentation. Our criterion for optimality is statistical efficiency based on a new notion of admissible designs; our approach enables efficient designs to be selected subject to the information available on the effects of most interest to biologists, the number of arrays available for the experiment, and other resource or practical constraints, including limitations on the amount of mRNA probe. We show that our designs are superior to both the popular reference designs, which are highly inefficient, and to designs incorporating all possible direct pairwise comparisons. Moreover, our proposed designs represent a substantial practical improvement over classical experimental designs which work in terms of standard interactions and main effects. The latter do not provide a basis for meaningful inference on the effects of most interest to biologists, nor make the most efficient use of valuable and limited resources. Philippe Rocca-Serra on behalf of MO time series design tumor grading Compiled by Helen Parkinson for Transcriptomics thanks to Adam Witney Determination of the grade (severity/stage) of a tumor sample, used in cancer biology to describe abnormalities/qualities of tumor cells or tissues. Values can be described by terms from NCI Thesaurus. OBI branch derived; submitted by MO grading of tumor tumor grading collecting specimen from organism IEDB PERSON:Bjoern Peters a process with the objective to obtain a material entity that was part of an organism for potential future use in an investigation 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 killing Philippe Rocca-Serra A protocol application in which an organism is intentionally put to death CEBS, Biomaterial_branch Jennifer Fostel Terminal sacrifice of animals by cervical dislocation at the end of an investigation. death status type difficult to place this properly - JG. Death process (e.g. unscheduled death) is out of scope but should be added somewhere. All killings have death process as a part, but not all death processes are part of a killing. euthanisia killing life termination sacrifice administering substance in vivo 1 2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893050&group_id=177891&atid=886178 A process by which a substance is intentionally given to an organism resulting in exposure of the organism to that substance. Balb/c mice received an intracameral or subconjunctival injection of trinitrophenylated spleen cells Person:Bjoern Peters Bjoern Peters Different routes and means of administration should go as children underneath this IEDB Update the definition based on the discussion. Details see the tracker: https://sourceforge.net/p/obi/obi-terms/738/ administering substance in vivo injecting mice with 10 ug morphine intranasally, a patient taking two pills of 1 mg aspirin orally needs roles such as perturber and perturbee (children of input role). Perturb is too strong. Host might be the name for one role. Others considered: Doner, Donated, Acceptor. exposure of material to environment Alan says there will be problmes, e.g. with selection by survival Bjoern Peters IEDB Putting cells in a freezer at -80C. Cy5-labeled DNA is irradiated with a laser to excite the fluorophore. Inducing a phase transition in a material by putting it in an environment with a specific temperature. Oxygen deprivation in a chamber. a planned process in which an input material is exposed to a defined set of conditions in a controlled environment. The environment is a specified input. exposure of material to environment acclimatization A protocol application in which an object is left in an environment for some period of time, until some qualities of interest are in equilibrium with that environment. CEBS, Biomaterial_branch Jennifer Fostel acclimatization placing mice in animal facility for 2 weeks prior to an experiment to accustom them to their environment, reducing stress material component separation Bjoern Peters IEDB 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 material component separation pooling specimens 2 OBI branch derived PlanAndPlannedProcess Branch http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=104564; Combining spleens of 20 mice, Combining supernatant from a cell culture obtained at different time points like' is one of the things that you should be controling for in a well-designed experiment. The instances of material need to have the same class. physical combination of several instances of like material pooling specimens sample pooling material portioning OBI branch derived PERSON:Bjoern Peters a material processing in which the input substance is partitioned into a number of portions that are similar in composition. aliquoting apportioning material portioning pouring 50 mL aliquots of fetal calf serum into conical tubes from a 500 mL stock histology PRS:20090901: addition of alternative term = histopathology histopathology OBI branch derived PERSON:Compiled by Helen Parkinson for Transcriptomics thanks to Adam Witney histology need to incorporate parts\n---\nThis is a very vague term, it should be in the same place as transcriptomics, proteomics metaboloimcs. It is the 'study' of tissues, not the process of studying tissues\n the counting of the number of cells with fluorescent label at their surface to determine the percentage of the population which was activated the visual examination of cells or tissue (or images of them) with an assessment regarding a quality of the cells or tissue. Parts are: staining, imaging, judgement excision Alan Ruttenberg, Kevin Clancy Cutting out the portion of a gel which contains a DNA fragment excision the use physical means to remove a portion of a substance from the rest www.crohnsresource.com/glossary.jsp (via google define:resection) non specific enzymatic cleavage OBI branch derived PERSON:Kevin Clancy The use of agarase to digest an agar gel a protocol application to digest the fraction of input material that is susceptible to that enzyme non specific enzymatic cleavage maintaining cell culture OBI branch derived PlanAndPlannedProcess Branch 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 maintaining cell culture artificially induced reverse transcription It could also be added that the reverse transcriptase is bearer of a GO:0003964 RNA-directed DNA polymerase activity, which is realized in this process. OBI branch derived PERSON:Kevin Clancy The use of M-MLV reverse transcriptase from the Moloney murine leukemia virus to transcribe an RNA sample into cDNA We need to indicate the relationship between the cDNA generated and the RNA that was used as a template. This may be outside of the OBI scope a protocol with the objective to transcribe single-stranded RNA into complementary DNA (cDNA) artificially induced reverse transcription cell permeabilization A protocol application to permeabilize cell membranes, allowing molecules to more easily pass through the membrane than was possible prior to the protocol application Electroporation of HeLa cells to allow transfection with pUC19. OBI branch derived PERSON:Bjoern Peters cell permeabilization definition blessed by Jay, Alan, Randi need to add output cell has_quality permeable establishing cell culture PERSON:Matthew Brush 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). establishing cell culture 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. PERSON:Matthew Brush cell culture splitting cell culture passaging An active cell culture is typically split when it has grown to confluence in its culture dish. Cell culture splitting of a cell culture sample results in an increase in its passage number, which measures how long a sample has been propagated in vitro, and therefore how many selective or genetic changes it is likely to have undergone. OBI branch derived PlanAndPlannedProcess Branch The act of taking a cell culture of high density, counting the cells, removing part of the cells, and re-seeding a select number of the cells into new flasks with fresh tissue culture media. The act of taking part of a homogeneous cell culture and creating one or more additional separate cultures of similar qualities. input: cell_culture, output cell_culture min cardinality 2. part of cell culturing cell culture splitting addition of molecular label labeling OBI developer call, 3-12-12 PERSON:Matthew Brush The addition of phycoerytherin label to an anti-CD8 antibody, to label all antibodies. The addition of anti-CD8-PE to a population of cells, to label the subpopulation cells that are CD8+. a material processing technique intended to add a molecular label to some input material entity, to allow detection of the molecular target of this label in a detection of molecular label assay addition of molecular label concentrate Evaporation of the solution containing DNA to increase the concentration of the DNA molecules OBI branch derived PERSON:Kevin Clancy a protocol application to create an output material with an increased density of a material of interest that is part of the input material by separating other parts of the input material concentrate genetic transformation OBI branch derived PERSON:Kevin Clancy The transduction of E. coli through the introduction of a plasmid encoding for M. avium p35 genetic modification genetic transformation the introduction. alteration or integration of genetic material into a cell or organism sequencing assay OBI branch derived PlanAndPlannedProcess Branch The use of the Sanger method of DNA sequencing to determine the order of the nucleotides in a DNA template has_output should be sequence of input; we don't have sequence well defined yet sequencing assay the use of a chemical or biochemical means to infer the sequence of a biomaterial vector mediated amplification E coli expressing the gene for M avium p35 were cultured in order to produce p35. OBI branch derived PERSON:Kevin Clancy The process of creating a copy of some biological entity in cell culture vector mediated amplification specific enzymatic cleavage OBI branch derived PERSON:Kevin Clancy The use of a protease to digest a protein into peptides a protocol application to digest the fraction of input material that is susceptible to that enzyme specific enzymatic cleavage protease cleavage OBI branch derived PlanAndPlannedProcess Branch enzymatic digestion protease cleavage protease cleavage is an enzymatic cleavage which relies on enzyme with protease activity to act on proteins and produce polypeptides (protein fragments). the use of trypsin to cleave pepsin into peptide fragments enzymatic amplification OBI branch derived PERSON:Kevin Clancy enzymatic amplification the use of a polymerase chain reaction to amplify a fragment of DNA the use of enzymes to increase the number of molecules of a biomaterial recombinant vector cloning molecular cloning OBI branch derived a planned process with the objective to insert genetic material into a cloning vector for future replication of the inserted material pa_branch (Alan, Randi, Kevin, Jay, Bjoern) recombinant vector cloning RNA extraction A RNA extraction is a nucleic acid extraction where the desired output material is RNA OBI branch derived PlanAndPlannedProcess Branch RNA extraction requested by Helen Parkinson for MO nucleic acid extraction OBI branch derived 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. PlanAndPlannedProcess Branch a material separation to recover the nucleic acid fraction of an input material nucleic acid extraction requested by Helen Parkinson for MO. Could be defined class phage display library PERSON: Bjoern Peters PERSON: Philippe Rocca-Serra PMID: 15905471.Nucleic Acids Res. 2005 May 19;33(9):e81.Oligonucleotide-assisted cleavage and ligation: a novel directional DNA cloning technology to capture cDNAs. Application in the construction of a human immune antibody phage-display library. [Phage display library encoding fragments of human antibodies. m-rna library encoding for 9-mer peptides] PRS: 22022008. class moved under population, modification of definition and replacement of biomaterials in previous definition with 'material' addition of has_role restriction WEB: http://www.immuneepitope.org/home.do a phage display library is a collection of materials in which a mixture of genes or gene fragments is expressed and can be individually selected and amplified. display library phage display library cell lysate The effect of vaccination with the lysate of heat-shocked tumor cells on nitric oxide production in BALB/c mice with fibrosarcoma tumor. Cell Biol Int. 2008 Jul;32(7):835-40. PMID: 18455932 lysed material GROUP: PSI PERSON: Susanna Sansone PRS:22-02-2008: is a material which has output_role during lysis protocol-application. old defintion: A mixture (collection) of cell components created by rupturing of the cell wall resulting from a lysis process a cell lysate is a material entity which is output of a cell lysis process cell lysate lysate assay bead A globular or round particle of defined physicochemical properties and size which can be exploited as either the primary substance for detection or as a secondary solid platform for the attachment of bioactive molecules. DS: Probably better modeled as a role. Dynabeads are commercially available magnetic beads which are precoated with antibodies specific for select cellular receptors and are used to separate cell populations. OBI assay bead bead infection IEDB IEDB infection the detrimental process in which an infectious agent colonizes or replicates in a host environment adaptive immune receptor IEDB IEDB adaptive immune receptor is a receptor produced by cells of the adaptive immune system with the purpose of binding epitopes. obsolete_disease 1 http://purl.obolibrary.org/obo/OGMS_0000031 IEDB IEDB obsolete_disease placeholder to be imported from disease ontology disposition to infect an organism IEDB IEDB Is a role borne by an agent, and realized when in contact with or inside another organism in which it is capable of replicating and causing disease disposition to infect an organism material to be added 10/26/09: This defined class is used as a 'macro expression' to reduce the size of the IEDB export 2010/02/24 Alan Ruttenberg: I think this might generate confusion as the common use of the term would consider something to be a specimen during the realization of the role, not only if it bears it. However having this class as a probe, or for display, or as a macro might be useful. Ideally we would mark or segregate such classes A mixture of peptides that is being added into a cell culture. IEDB a material that is added to another one in a material combination process material to be added target of material addition 10/26/09: This defined class is used as a 'macro' to reduce the size of the IEDB export. A cell culture into which a mixture of peptides is being added. A material entity into which another is being added in a material combinatino process IEDB target of material addition pathologic process IEDB IEDB abnormal, harmful processes caused by or associated with a disease pathologic process clinical history A series of statements representing health-relevant qualities of a patient and of a patient's family. phenotype A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species. disease A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. disease course The totality of all processes through which a given disease instance is realized. treatment A processual entity whose completion is hypothesized (by a healthcare provider) to alleviate the signs and symptoms associated with a disorder quality A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities. PATO:0000001 PATO:0000072 quality trait age A time quality inhering in a bearer by virtue of how long the bearer has existed. PATO:0000011 quality composition A single physical entity inhering in an bearer by virtue of the bearer's quantities or relative ratios of subparts. For example calcium composition (which may inhere in bone), haemoglobin composition (which may inhere in blood). PATO:0000025 PATO:0002015 compositionality content quality structure, composition concentration of A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance. PATO:0000033 concentration quality biological sex 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. PATO:0000047 quality morphology A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. PATO:0000051 quality shape A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc). PATO:0000052 PATO:0001647 Shapes are invariant on size transformations. Shapes can be subdivided into 2D and 3D shapes, We can also make a distinction between shapes of complete self-connected objects, and shapes of parts of objects. quality relational shape quality qualitative PATO:0000068 TODO: define this or obsolete it and move children somewhere else. quality deviation(from_normal) A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average. PATO:0000069 quality size A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude. PATO:0000117 quality structure A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form. PATO:0000141 PATO:0001452 quality relational structural quality temperature A physical quality of the thermal energy of a system. PATO:0000146 quality time A quality in which events occur in sequence. PATO:0000165 quality viability An organismal quality inhering in a bearer or a population by virtue of the bearer's disposition to survive and develop normally or the number of surviving individuals in a given population. PATO:0000169 quality maturity A quality of a single physical entity which is held by a bearer when the latter exhibits complete growth, differentiation, or development. PATO:0000261 quality female A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes. PATO:0000383 quality male A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes. PATO:0000384 quality circular A shape quality inhering in a bearer by virtue of the bearer's being such that every part of the surface or the circumference is equidistant from the center. PATO:0000411 quality round rounded normal A quality inhering in a bearer by virtue of the bearer's exhibiting no deviation from normal or average. PATO:0000461 average quality increased size A size quality which is relatively high. PATO:0000586 PATO:0001202 big enlarged expanded great large quality elliptic A spheroid quality inhering in a bearer by virtue of the bearer's being oval with two axes of symmetry, as produced by a conical section. PATO:0000947 ellipse-shaped ellipsoid elliptical oval ovoid quality physical quality A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. PATO:0001018 PATO:0002079 Wikipedia:Physical_property quality relational physical quality physical object quality A quality which inheres in a continuant. PATO:0001237 PATO:0001238 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. monadic quality of a continuant monadic quality of an object monadic quality of continuant multiply inhering quality of a physical entity quality quality of a continuant quality of a single physical entity quality of an object quality of continuant snap:Quality bacterial mating type A mating type that indicates whether the F plasmid has integrated into the chromosome. PATO:0001335 quality yeast mating type A yeast mating type. PATO:0001337 quality mixed sex A biological sex quality inhering in a population of multiple sexes. For example a mixture of females and male or males and hermaphrodites. PATO:0001338 quality biomaterial purity A composition quality inhering in an bearer by virtue of the bearer's homogeneity of a biomaterial. PATO:0001339 quality hermaphrodite A biological sex quality inhering in an organism or a population with both male and female sexual organs in one individual. PATO:0001340 intersex quality a mating type (yeast) A S. cerevisiae mating type cells that secrete a pheromone that in alpha haploids stimulates processes that lead to mating. PATO:0001341 a quality Saccharomyces cerevisiae mating type A S. cerevisiae mating type. PATO:0001342 quality Schizosaccharomyces pombe mating type A S. pombe mating type determined by the gene configuration on the mat1 locus. PATO:0001343 quality alpha mating type (yeast) A S. cerevisiae mating type cells that secrete a pheromone that stimulates a haploids. PATO:0001344 alpha quality h minus A S. pombe mating type determined by the mat1-Mc and mat1-Mi on the mat1 locus. M PATO:0001345 h - quality h plus A S. pombe mating type determined by the mat1-Pc and mat1-Pi on the mat1 locus. P PATO:0001346 h+ quality F mating type A bacterial mating type indicating the presence of F plasmid in a bacterial cell. PATO:0001347 quality F minus mating type A bacterial mating type indicating the absence of F plasmid in a bacterial cell. F- PATO:0001348 quality ploidy A cellular quality inhering in a bearer by virtue of the bearer's number of homologous sets of chromosomes in the nucleus or primary chromosome-containing compartment of the cell, each set essentially coding for all the biological traits of the organism. PATO:0001374 quality haploid A ploidy quality inhering in a bearer by virtue of the bearer's containing a single set of homologous chromosomes. PATO:0001375 quality polyploid A ploidy quality inhering in a bearer by virtue of the bearer's containing more than two homologous sets of chromosomes. PATO:0001377 quality aneuploid A ploidy quality inhering in a bearer by virtue of the bearer's containing a non-integral multiple of the monoploid number, due to extra or missing chromosomes. PATO:0001385 quality euploid A ploidy quality inhering in a bearer by virtue of the bearer's containing an integral multiple of the monoploid number, possibly excluding the sex-determining chromosomes. PATO:0001393 quality diploid A ploidy quality inhering in a bearer by virtue of the bearer's having two copies (homologs) of each chromosome, usually one from the mother and one from the father. PATO:0001394 The exact number may be one or two different from the 2n number and still be classified as diploidy (although with aneuploidy). Nearly all mammals are diploid organisms, although all individuals have some small fracton of cells that are polyploidy. quality cellular quality A monadic quality of continuant that exists at the cellular level of organisation. PATO:0001396 quality cellular potency A cellular quality that arises by virtue of whether the bearer's disposition to differentiate into one or more mature cell types. PATO:0001397 quality unipotent A cellular potency that is the capacity to produce only one differentiated cell type. PATO:0001400 Unipotent cells have the quality of self-renewal which distinguishes them from non-stem cells. quality oligopotent A cellular potency that is the capacity to form multiple differentiated cell types of a specific lineage and lack self renewing capacity. Less potent than multipotent, often thought of as precursor or progenitor cell status. PATO:0001401 quality multipotent A cellular potency that is the capacity to form multiple differentiated cell types. PATO:0001402 quality nucleate quality A cellular quality inhering in a bearer by virtue of bearer's number of nuclei. PATO:0001404 quality anucleate A nucleate quality inhering in a bearer by virtue of the bearer's having no nucleus. PATO:0001405 quality mononucleate A nucleate quality inhering in a bearer by virtue of the bearer's having one nucleus. PATO:0001407 quality striated A shape quality inhering in a bearer by virtue of the bearer's being marked by narrow lines or grooves, usually parallel. PATO:0001410 quality alive A viability quality inhering in a bearer by virtue of the bearer's condition before death. PATO:0001421 quality dead A viability quality inhering in a bearer by virtue of the cessation of the bearer's life. PATO:0001422 quality immature A quality inhering in a bearer by virtue of the bearer's lacking complete growth, differentiation, or development. PATO:0001501 quality underdeveloped mature A quality inhering in a bearer by virtue of the bearer's exhibiting complete growth, differentiation, or development. PATO:0001701 quality concave A shape quality in a bearer by virtue of the bearer's curving inward. PATO:0001857 quality cylindrical A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a consistently-sized round cross section. PATO:0001203 PATO:0001873 quality rod-like rod-shaped tubulate discoid A shape quality inhering in a bearer by virtue of the bearer's being cylindrical, in which the height is less than the diameter. PATO:0001874 disc-shaped disk-shaped quality phenotypic sex PATO:0001894 quality mating type A biological sex quality inhering in an individual or a population that undergo sexual reproduction. PATO:0001895 quality frozen A quality inhering in a bearer by virtue of the bearer's being kept below its freezing point. PATO:0001985 quality organismal quality A quality that inheres in an entire organism or part of an organism. PATO:0001995 quality population quality A quality that inheres in an entire population or part of a population. PATO:0002003 quality concavity PATO:0002005 Surface shape that refers to the inward or outward curvature of the surface. quality 2-D shape 2-D projection A shape that inheres in a 2 dimensional entity, such as a cross section or projection of a 3 dimensional entity. PATO:0002006 cross-sectional quality convex 3-D shape A complete three dimensional shape in which for every line connecting pair of points on the object is within the object. Or: a shape lacking cavities. Contrast: concave. Image:http://upload.wikimedia.org/wikipedia/commons/0/06/Convex_polygon_illustration1.png PATO:0002007 Use this term or an is_a child of this term when the entire shape of the object is known. quality biconcave A concave quality inhering in a bearer by virtue of the bearer's curving inward on both sides or surfaces. PATO:0002039 quality affinity 2009-09-18T01:16:16Z A molecular quality that arises from the molecular attraction exerted between two atoms or compounds. George Gkoutos PATO:0002070 quality basophilic 2009-10-05T12:05:23Z An affinity inhering in a tissue constituent by virtue of the bearer exhibiting a molecular interaction for basic dyes under specific ph conditions. PATO:0002094 george quality molecular quality 2010-03-10T03:18:15Z A quality which inheres in a molecular entity, a single molecule, atom, ion, radical etc. George Gkoutos PATO:0002061 PATO:0002182 quality relational molecular quality 3-D shape 2010-10-05T12:31:16Z A shape that inheres in a 3 dimensional entity. PATO:0002266 george quality increased quality 2011-06-16T06:39:43Z A quality that has a value that is increased compared to normal or average. George Gkoutos PATO:0002300 quality increased object quality 2011-06-16T06:54:01Z A quality of an object that has a value that is increased compared to normal or average. George Gkoutos PATO:0002305 quality superelliptic 2011-10-12T12:45:16Z A shape constituting a transition between a rectangle and a circle; a closed curve, of which the circle and ellipse are special cases, whose parametric equation is x = a.cos2/rt, y = b.cos2/rt George Gkoutos Lamé curve PATO:0002318 quality transversely striated 2013-09-15T12:29:15Z A shape quality inhering in a bearer by virtue of the bearer's being marked by narrow lines or grooves, usually parallel, that are oriented transversely relative to the long axis of the bearer. PATO:0002478 gkoutos quality protein An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA. CD19 molecule A protein that is a translation product of the human CD19 gene or a 1:1 ortholog thereof. It is composed of an N-terminal extracellular domain containing two Ig-like C2-type (immunoglobulin-like) domains, followed by a single-pass transmembrane segment and a cytoplasmic C-terminal tail. CD19 expression is restricted to members of the B cell lineage. It functions as a co-receptor for B-cell antigen receptor (BCR), regulating signal transduction. CD34 molecule A protein that is a translation product of the human CD34 gene or a 1:1 ortholog thereof. It is a leukocyte membrane protein expressed specifically by lymphohematopoietic progenitor cells. It contains a single-pass transmembrane domain and that show distinct expression on early hematopoietic precursors and vascular-associated tissue. Acts as a scaffold that presents selectin carbohydrate ligands in a clustered, tissue specific manner to allow for higher avidity interactions between leukocytes and endothelial cells during the inflammatory process. In common with related sialomucins (endoglycan and podocalyxin), the extracellular region is dominated by an N-terminal mucin-like domain, which is densely substituted with sialylated O-linked carbohydrates. The mucin-like region is followed by a cysteine-containing and presumably globular domain. This domain may fold into an immunoglobulin-like structure as the positions of 2 of the cysteines are conserved in the C2 set of the immunoglobulin superfamily. The cytoplasmic domain is around 73-76 residues long and highly conserved. CD4 molecule A protein that is a translation product of the human CD4 gene or a 1:1 ortholog thereof. CD4 is an accessory protein for MHC class-II antigen/T-cell receptor interaction. It is the primary receptor for HIV-1. CD4 has four immunoglobulin-like domains in its extracellular region that share the same structure, but can differ in sequence. receptor-type tyrosine-protein phosphatase C A protein that is a translation product of the human PTPRC gene or a 1:1 ortholog thereof. It is composed of an extracellular domain, a single transmembrane segment and two tandem intracytoplasmic protein-tyrosine phosphatase domains. Contains 1 to 3 copies of the Fibronectin type III domain (Pfam:PF00041) followed by two copies of the Protein-tyrosine phosphatase (Pfam:PF00102) domain. Receptor-type tyrosine-protein phosphatase C (CD45) regulates signal transduction and lymphocyte activation by specific association with receptor molecules on T and B cells. Multiple isoforms of CD45 (180-235 kDa) can be generated asa result of alternative splicing of three variable exons 4(A), 5(B) and 6(C), encoding sequences at the N-terminal extracellular domain of the molecule. integrin alpha-M An integrin alpha with A domain that is a translation product of the human ITGAM gene or a 1:1 ortholog thereof. They constitute subunits of the integrin alpha-M/beta-2 receptor. This receptor is implicated in various adhesive interactions of monocytes, macrophages and granulocytes as well as in mediating the uptake of complement-coated particles. It is also a receptor for fibrinogen, factor X and ICAM1. receptor-type tyrosine-protein phosphatase C isoform CD45RA A receptor-type tyrosine-protein phosphatase C that is a translation product of a mature transcript of the PTPRC gene, that includes the region encoded by the variable exon 4(A), and lacks the region encoded by exons 5(B) and 6(C). CD3 epsilon A CD3 subunit that is a translation product of the human CD3E gene or a 1:1 ortholog thereof. neural cell adhesion molecule 1 A neural cell adhesion molecule NCAM that is a translation product of the human NCAM1 gene or a 1:1 ortholog thereof. CD2 molecule A protein that is a translation product of the human CD2 gene or a 1:1 ortholog thereof. T-cell surface glycoprotein CD8 alpha chain A protein that is a translation product of the human CD8A gene or a 1:1 ortholog thereof. CD8 is a transmembrane that is a co-receptor for MHC class-I antigen/T-cell receptor interaction. The most common form of CD8 is composed of a CD8 alpha and a CD8 beta chain. chemokine receptor CCR1/3/1L A rhodopsin-like G-protein coupled receptor that is a translation product of the CCR1, CCR3, or CCR1L1 genes (the last found so far only in mouse). C-C chemokine receptor type 1 A chemokine receptor CCR1/3/1L that is a translation product of the human CCR1 gene or a 1:1 ortholog thereof. C-C chemokine receptor type 3 A chemokine receptor CCR1/3/1L that is a translation product of the human CCR3 gene or a 1:1 ortholog thereof. membrane-spanning 4-domains subfamily A member 1 A protein that is a translation product of the human MS4A1 gene or a 1:1 ortholog thereof. CD44 molecule A protein that is a translation product of the human CD44 gene or a 1:1 ortholog thereof. carcinoembryonic antigen-related cell adhesion molecule 8 A protein that is a translation product of the human CEACAM8 gene or a 1:1 ortholog thereof. CD69 molecule A protein that is a translation product of the human CD69 gene or a 1:1 ortholog thereof. A type II transmembrane protein with a C-type lectin binding domain in the extracellular portion of the molecule. Involved in lymphocyte proliferation and functions as a signal transmitting receptor in lymphocytes, natural killer (NK) cells, and platelets. ectonucleotide pyrophosphatase/phosphodiesterase family member 3 A protein that is a translation product of the human ENPP3 gene or a 1:1 ortholog thereof. endoglin A protein that is a translation product of the human ENG gene or a 1:1 ortholog thereof. immunoglobulin gamma Fc receptor II/III/IV A protein with a core domain architecture consisting of an extracellular domain containing two copies of the Immunoglobulin domain (Pfam:PF00047), followed by a single-pass transmembrane region and a small intracellular domain. The active protein is a low affinity receptor for immunoglobulin gamma chain Fc region. Human II-a, II-b, and II-c represent a recent gene expansion and are equally related to mouse II, III, and IV. Human III-A and III-B are closely related and closer to mouse IV than to mouse III. interleukin-2 receptor subunit beta A protein that is a translation product of the human IL2RB gene or a 1:1 ortholog thereof. ADP-ribosyl cyclase 1 An ADP-ribosyl cyclase that is a translation product of the human CD38 gene or a 1:1 ortholog thereof. cadherin-5 A cadherin that is a translation product of the human CDH5 gene or a 1:1 ortholog thereof. alpha-(1,3)-fucosyltransferase FUT4 A fucosyltransferase that is a translation product of the human FUT4 gene or a 1:1 ortholog thereof. low affinity immunoglobulin gamma Fc region receptor II An immunoglobulin gamma Fc receptor II/III/IV that is a translation product of the mouse Fcgr2 gene or a 1:1 ortholog thereof. low affinity immunoglobulin gamma Fc region receptor III An immunoglobulin gamma Fc receptor II/III/IV that is a translation product of the mouse Fcgr3 gene or a 1:1 ortholog thereof. epithelial cell adhesion molecule A tumor-associated calcium signal transducer that is a translation product of the human EPCAM gene or a 1:1 ortholog thereof. prominin-1 A prominin that is a translation product of the human PROM1 gene or a 1:1 ortholog thereof. 5'-nucleotidase A protein that is a translation product of the human NT5E gene or a 1:1 ortholog thereof. CD59-like glycoprotein A protein that is a translation product of the CD59 or closely related gene. This gene is present as a single copy in human and has undergone a lineage-specific duplication in mouse. CD59 antigen has a core architecture consisting of one UPAR/Ly-6 domain (Pfam:PF00021), a small domain of about 70 amino acids and containing 5 conserved disulfide bonds. It is both N- and O-glycosylated and is a GPI-anchored protein that releases soluble forms in some tissues. CD7 molecule A protein that is a translation product of the human CD7 gene or a 1:1 ortholog thereof. T-cell surface glycoprotein CD5 A protein that is a translation product of the human CD5 gene or a 1:1 ortholog thereof. Thy-1 membrane glycoprotein A protein that is a translation product of the human THY1 gene or a 1:1 ortholog thereof. interleukin-3 receptor class 2 alpha chain A protein that is a translation product of the human IL3RA gene or a 1:1 ortholog thereof. interleukin-5 receptor subunit alpha A protein that is a translation product of the human IL5RA gene or a 1:1 ortholog thereof. interleukin-7 receptor subunit alpha A protein that is a translation product of the human IL7R gene or a 1:1 ortholog thereof. KLRB1-like protein A protein that is a translation product of the KLRB1 gene or its closely related paralogs (KLRB1A-F). There are lineage-specific expansions in mouse and rat. leukosialin A protein that is a translation product of the human SPN gene or a 1:1 ortholog thereof. CD14 molecule A protein that is a translation product of the human CD14 gene or a 1:1 ortholog thereof. CD33 molecule A protein that is a translation product of the human CD33 gene or a 1:1 ortholog thereof. neprilysin A protein that is a translation product of the human MME gene or a 1:1 ortholog thereof. paired box protein PAX-5 A protein that is a translation product of the human PAX5 gene or a 1:1 ortholog thereof. signal transducer CD24 A protein that is a translation product of the human CD24 gene or a 1:1 ortholog thereof. transcription factor PU.1 A protein that is a translation product of the human SPI1 gene or a 1:1 ortholog thereof. transferrin receptor protein 1 A protein that is a translation product of the human TFRC gene or a 1:1 ortholog thereof. tumor necrosis factor ligand superfamily member 5 A protein that is a translation product of the human CD40LG gene or a 1:1 ortholog thereof. urokinase plasminogen activator surface receptor A protein that is a translation product of the human PLAUR gene or a 1:1 ortholog thereof. mast/stem cell growth factor receptor A CSF-1/PDGF receptor-type tyrosine-protein kinase that is a translation product of the human KIT gene or a 1:1 ortholog thereof. vascular endothelial growth factor receptor 2 A vascular endothelial growth factor receptor that is a translation product of the human KDR gene or a 1:1 ortholog thereof. lymphocyte antigen 6G A ly-6-like protein that is a translation product of the mouse Ly6g gene or a 1:1 ortholog thereof. lymphocyte antigen 76 A protein that is a translation product of the mouse Ly76 gene or a 1:1 ortholog thereof. CD9 molecule A tetraspanin that is a translation product of the human CD9 gene or a 1:1 ortholog thereof. CCAAT/enhancer-binding protein alpha A protein that is a translation product of the human CEBPA gene or a 1:1 ortholog thereof. DNA nucleotidylexotransferase A protein that is a translation product of the human DNTT gene or a 1:1 ortholog thereof. high affinity immunoglobulin epsilon receptor subunit alpha An immunoglobulin gamma Fc receptor II/III/IV that is a translation product of the human FCER1A gene or a 1:1 ortholog thereof. hepatocyte nuclear factor 3-alpha A protein that is a translation product of the human FOXA1 gene or a 1:1 ortholog thereof. hepatocyte nuclear factor 3-beta A protein that is a translation product of the human FOXA2 gene or a 1:1 ortholog thereof. erythroid transcription factor A protein that is a translation product of the human GATA1 gene or a 1:1 ortholog thereof. endothelial transcription factor GATA-2 A protein that is a translation product of the human GATA2 gene or a 1:1 ortholog thereof. glucagon A protein that is a translation product of the human GCG gene or a 1:1 ortholog thereof. hepatocyte nuclear factor 1-alpha A protein that is a translation product of the human HNF1A gene or a 1:1 ortholog thereof. hepatocyte nuclear factor 4-alpha A protein that is a translation product of the human HNF4A gene or a 1:1 ortholog thereof. insulin A protein that is a translation product of the human INS gene or a 1:1 ortholog thereof. insulinoma-associated protein 1 A protein that is a translation product of the human INSM1 gene or a 1:1 ortholog thereof. insulin gene enhancer protein ISL-1 A protein that is a translation product of the human ISL1 gene or a 1:1 ortholog thereof. transcription factor MafA A protein that is a translation product of the human MAFA gene or a 1:1 ortholog thereof. neurogenic differentiation factor 1 A protein that is a translation product of the human NEUROD1 gene or a 1:1 ortholog thereof. neurogenin-3 A protein that is a translation product of the human NEUROG3 gene or a 1:1 ortholog thereof. homeobox protein Nkx-2.2 A protein that is a translation product of the human NKX2-2 gene or a 1:1 ortholog thereof. homeobox protein Nkx-6.1 A protein that is a translation product of the human NKX6-1 gene or a 1:1 ortholog thereof. hepatocyte nuclear factor 6 A protein that is a translation product of the human ONECUT1 gene or a 1:1 ortholog thereof. pancreas/duodenum homeobox protein 1 A protein that is a translation product of the human PDX1 gene or a 1:1 ortholog thereof. pancreas transcription factor 1 subunit alpha A protein that is a translation product of the human PTF1A gene or a 1:1 ortholog thereof. recombining binding protein suppressor of hairless A protein that is a translation product of the human RBPJ gene or a 1:1 ortholog thereof. recombining binding protein suppressor of hairless-like protein A protein that is a translation product of the human RBPJL gene or a 1:1 ortholog thereof. transcription factor SOX-17 A protein that is a translation product of the human SOX17 gene or a 1:1 ortholog thereof. T-cell acute lymphocytic leukemia protein 1 A protein that is a translation product of the human TAL1 gene or a 1:1 ortholog thereof. DNA ligase A protein that is a translation product of the Escherichia coli K-12 ligA gene or a 1:1 ortholog thereof. antibody reagent molecular label role a reagent role inhering in a molecular entity intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay. molecular label a molecular reagent intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay cancer cell a cell that is the output of some malignant cell transformation process whereby a cell in vivo becomes capable of causing cancer in an organism. Such cells are typically able to proliferate indefinitely if cultured in vitro. monoclonal antibody An antibody reagent produced by clonal hybridoma cells deriving from the fusion of a single activasted B-cell with a neoplastic cell, such that antibodies isolated from such cells are monospecific for a single epitope. A collection of such antibodies has specificity for a single epitopes on its target antigen - versus a collection of 'polyclonal antibodies', which recognize various different epitopes. But at the structural level of the individual molecular reagent, there is of course no distinction between mono- and poly-clonal antibodies. polyclonal antibody an antibody reagent that is output from an antibody production process that yields a heterogenous collection of antibodies that are not mono-specific (ie individual antibodies in the collection may recognize different epitopes becasue they arise from more than one clone of B-lymphocyte cells). Polyclonal antibodies are typically manufactured through an antibody production technique in which a host organism is immunized with a specific immunogen and antibodies purified from serum collected following the induced immune response. A collection of such antibodies has specificity for various different epitopes on its target antigen - versus a collection of 'monoclonal antibodies', which all recognize a single epitope. But at the structural level of the individual molecular reagent, there is of course no distinction between mono- and poly-clonal antibodies. ICR 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. polypeptide A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation. sequence_feature Any extent of continuous biological sequence. read A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine. enhancer A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter. miRNA Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene (or the product of other non coding RNA genes. Micro RNAs are produced from precursor molecules (SO:0000647) that can form local hairpin structures, which ordinarily are processed (usually via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors. pseudogene A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their "normal" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its "normal" paralog). polymer_attribute An attribute to describe the kind of biological sequence. pseudogenic_region A non-functional descendant of a functional entity. SRP_RNA The signal recognition particle (SRP) is a universally conserved ribonucleoprotein. It is involved in the co-translational targeting of proteins to membranes. The eukaryotic SRP consists of a 300-nucleotide 7S RNA and six proteins: SRPs 72, 68, 54, 19, 14, and 9. Archaeal SRP consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54 proteins. In most eubacteria, the SRP consists of a 4.5S RNA and the Ffh protein (a homologue of the eukaryotic SRP54 protein). Eukaryotic and archaeal 7S RNAs have very similar secondary structures, with eight helical elements. These fold into the Alu and S domains, separated by a long linker region. Eubacterial SRP is generally a simpler structure, with the M domain of Ffh bound to a region of the 4.5S RNA that corresponds to helix 8 of the eukaryotic and archaeal SRP S domain. Some Gram-positive bacteria (e.g. Bacillus subtilis), however, have a larger SRP RNA that also has an Alu domain. The Alu domain is thought to mediate the peptide chain elongation retardation function of the SRP. The universally conserved helix which interacts with the SRP54/Ffh M domain mediates signal sequence recognition. In eukaryotes and archaea, the SRP19-helix 6 complex is thought to be involved in SRP assembly and stabilizes helix 8 for SRP54 binding. ncRNA An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product. transcript An RNA synthesized on a DNA or RNA template by an RNA polymerase. gene A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions. QTL A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci. gene_member_region A region of a gene. transgene A transgene is a gene that has been transferred naturally or by any of a number of genetic engineering techniques from one organism to another. circular A quality of a nucleotide polymer that has no terminal nucleotide residues. BAC_end A region of sequence from the end of a BAC clone that may provide a highly specific marker. protein_coding_gene ncRNA_gene miRNA_gene scRNA_gene snoRNA_gene snRNA_gene tRNA_gene biological_region A region defined by its disposition to be involved in a biological process. YAC_end A region of sequence from the end of a YAC clone that may provide a highly specific marker. heritable_phenotypic_marker A biological_region characterized as a single heritable trait in a phenotype screen. The heritable phenotype may be mapped to a chromosome but generally has not been characterized to a specific gene locus. rRNA_gene A gene that encodes for ribosomal RNA. RNase_P_RNA_gene A gene that encodes an RNase P RNA. RNase_MRP_RNA_gene A gene that encodes a RNase_MRP_RNA. lincRNA_gene A gene that encodes large intervening non-coding RNA. telomerase_RNA_gene A telomerase RNA gene is a non coding RNA gene the RNA product of which is a component of telomerase. pseudogenic_gene_segment A gene segment which when incorporated by somatic recombination in the final gene transcript results in a nonfunctional product. gene_segment A gene component region which acts as a recombinational unit of a gene whose functional form is generated through somatic recombination. uterine cervix Lower, narrow portion of the uterus where it joins with the top end of the vagina. uterine cervix islet of Langerhans islet of Langerhans the clusters of hormone-producing cells that are scattered throughout the pancreas pituitary gland The pituitary gland is an endocrine gland that secretes hormones that regulate many other glands [GO]. An endocrine gland located ventral to the diencephalon and derived from mixed neuroectodermal and non neuroectodermal origin [ZFIN]. pituitary gland zone of skin Any portion of the organ that covers that body and consists of a layer of epidermis and a layer of dermis. zone of skin endocrine pancreas The part of the pancreas that is part of the endocrine system and is made up of islet cells, which produce insulin, glucagon and somatostatin. endocrine pancreas exocrine pancreas The part of the pancreas that is part of the exocrine system and which produces and store zymogens of digestive enzymes, such as chymotrypsinogen and trypsinogen in the acinar cells [GO]. exocrine pancreas sense organ An organ that is capable of transducing sensory stimulus to the nervous system. sense organ tube Any hollow cylindrical anatomical structure containing a lumen through which substances are transported. tube lymph node Any of the rounded masses of lymphoid tissue that are surrounded by a capsule of connective tissue, are distributed along the lymphatic vessels, and contain numerous lymphocytes which filter the flow of lymph. lymph node head The head is the anterior-most division of the body [GO]. head serous membrane multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer. serous membrane dorsal root ganglion * Sensory ganglia located on the dorsal spinal roots within the vertebral column. The spinal ganglion cells are pseudounipolar. The single primary branch bifurcates sending a peripheral process to carry sensory information from the periphery and a central branch which relays that information to the spinal cord or brain. (MSH) * ganglion found on the posterior root of each spinal nerve, composed of the unipolar nerve cell bodies of the sensory neurons of the nerve. (CSP) dorsal root ganglion ganglion A biological tissue mass, most commonly a mass of nerve cell bodies. ganglion duct A tubular structure that transports or secretes substances. duct large intestine A subdivision of the digestive tract that connects the small intestine to the cloaca or anus. Lacks or has few villi[Kardong]. large intestine anatomical structure Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. anatomical structure organ Anatomical structure that performs a specific function or group of functions [WP]. organ organ segment 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 eyeball[FMA]. organ segment organ part Anatomical structure which has as its direct parts two or more types of tissue and is continuous with one or more anatomical structures likewise constituted by two or more portions of tissues distinct from those of their complement. Examples: osteon, cortical bone, neck of femur, bronchopulmonary segment, left lobe of liver, anterior right side of heart, interventricular branch of left coronary artery, right atrium, mitral valve, head of pancreas[FMA]. organ part respiratory tract Anatomical structure that is part of the respiratory system. In mammals consists of upper and lower tracts respiratory tract embryo stage A life cycle stage that starts with fertilization and ends with the fully formed embryo. embryo stage segment of respiratory tract An organ segment that is part of a respiratory tract [Automatically generated definition]. segment of respiratory tract mixed endoderm/mesoderm-derived structure An anatomical structure that develops from the endoderm and the mesoderm. mixed endoderm/mesoderm-derived structure mixed ectoderm/mesoderm/endoderm-derived structure An anatomical structure that develops from the ectoderm, mesoderm and endoderm. mixed ectoderm/mesoderm/endoderm-derived structure post-embryonic stage post-embryonic stage stage succeeding embryo, including mature structure life cycle stage A spatiotemporal region encompassing some part of the life cycle of an organism. life cycle stage sexually immature stage sexually immature stage post-juvenile adult stage The stage of being a sexually mature adult animal. post-juvenile adult stage lung epithelium The epithelial layer of the lung. lung epithelium respiratory tube A tube in the respiratory system. Examples: bronchus, bronchiole, trachea. respiratory tube neuron projection bundle A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses. neuron projection bundle intestine Segment of the alimentary canal extending from the stomach to the anus and, in humans and other mammals, consists of two segments, the small intestine and the large intestine. intestine segment of colon An organ segment that is part of a colon [Automatically generated definition]. segment of colon blood Circulating body substance which consists of blood plasma and hemoglobin-carrying red blood cells. Excludes blood analogues (see UBERON:0000179 haemolymphatic fluid). blood gyrus A ridge on the cerebral cortex. It is generally surrounded by one or more sulci . gyrus preputial gland A aired, lobulated, modified sebaceous glands located in the inguinal region adjacent to the penis and vagina, with pheromonal functions in male rodents; in males, the preputial gland empties into the preputial cavity and in females, the preputial (aka clitoral) gland duct empties into the clitoral fossa. preputial gland prefrontal cortex The anterior part of the frontal lobes of the brain, lying in front of the motor and premotor areas.nnThis brain region has been implicated in planning complex cognitive behaviors, personality expression, decision making and moderating correct social behavior. The basic activity of this brain region is considered to be orchestration of thoughts and actions in accordance with internal goals.nnThe most typical psychological term for functions carried out by the pre-frontal cortex area is executive function. Executive function relates to abilities to differentiate among conflicting thoughts, determine good and bad, better and best, same and different, future consequences of current activities, working toward a defined goal, prediction of outcomes, expectation based on actions, and social 'control' (the ability to suppress urges that, if not suppressed, could lead to socially-unacceptable outcomes).nnMany authors have indicated an integral link between a person's personality and the functions of the prefrontal cortex. - definition adapted from Wikipedia prefrontal cortex 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. organism substance material anatomical entity Anatomical entity that has mass. material anatomical entity multicellular organism Anatomical structure that is an individual member of a species and consists of more than one cell. multicellular organism compound organ component Multi-tissue structure that is part of a compound organ. compound organ component testis A gonad of a male animal. A gonad produces and releases sperm. testis organism subdivision 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. organism subdivision anatomical cluster Anatomical group that has its parts adjacent to one another. anatomical cluster extraembryonic structure A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis. extraembryonic structure tissue Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. tissue multi-tissue structure Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types. multi-tissue structure epithelium Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO]. epithelium simple columnar epithelium Unilaminar epithelium, which consists of a single layer of columnar cells. Examples: ciliated columnar epithelium, gastric epithelium, microvillus columnar epithelium.[FMA] simple columnar epithelium simple squamous epithelium Unilaminar epithelium which consists of a single layer of squamous cells. Examples: pulmonary alveolar epithelium, endothelium.[FMA] simple squamous epithelium cavitated compound organ Compound organ that contains one or more macroscopic anatomical spaces. cavitated compound organ unilaminar epithelium Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA] unilaminar epithelium embryo Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. embryo germ layer A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm. germ layer ectoderm Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. ectoderm endoderm Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. endoderm mesoderm The middle germ layer of the embryo, between the endoderm and ectoderm. mesoderm stomach An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium. stomach aorta The main trunk of the systemic arterial system that carries blood from the heart to all the organs and other structures of the body, bringing oxygenated blood to all parts of the body in the systemic circulation aorta heart A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ. heart brain The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP]. brain cerebral cortex The thin layer of gray matter on the surface of the cerebral hemisphere that develops from the telencephalon. It consists of the neocortex (6 layered cortex or isocortex), the hippocampal formation and the olfactory cortex. cerebral cortex retina The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates. retina eye An organ that detects light. eye femur Endochondral longbone connecting the pelvic girdle with posterior zeugopodium skeleton.[VSAO, modified]. femur skeletal joint Anatomical cluster that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO]. skeletal joint pons Brainstrem structure that has as its parts the pontine tegmentum and basal part of pons[FMA]. pons gonad Reproductive organ that produces and releases eggs (ovary) or sperm (testis). gonad female gonad female gonad the gonad of a female organism which contains germ cells uterus the female muscular organ of gestation in which the developing embryo or fetus is nourished until birth uterus vagina A fibromuscular tubular tract leading from the uterus to the exterior of the body in female placental mammals and marsupials, or to the cloaca in female birds, monotremes, and some reptiles[WP]. vagina seminal vesicle Either of a pair of glandular pouches that lie one on either side of the male reproductive tract and in the human male secrete a sugar- and protein-containing fluid into the ejaculatory duct. seminal vesicle skin epidermis The outer layer of the skin[WP]. cellular, multilayered epithelium derived from the ectoderm[ZFA]. skin epidermis adipose tissue Portion of connective tissue composed of adipocytes enmeshed in areolar tissue adipose tissue axon tract A group of axons linking two or more neuropils and having a common origin, termination[FBbt]. axon tract yolk sac A sac-like expansion of the ventral wall of the intestine, narrowed into a yolk stalk near the body[Hyman's]. Membranous sac attached to an embryo, providing early nourishment in the form of yolk in bony fishes, sharks, reptiles, birds, and primitive mammals. It functions as the developmental circulatory system of the human embryo, before internal circulation begins. In the mouse, the yolk sac is the first site of blood formation, generating primitive macrophages and erythrocytes[WP]. yolk sac saliva-secreting gland saliva-secreting exocrine glands of the oral cavity[GO] saliva-secreting gland anatomical entity Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. anatomical entity ventral pancreatic duct A duct joining the pancreas to the common bile duct to supply pancreatic juices which aid in digestion provided by the exocrine pancreas. The pancreatic duct joins the common bile duct just prior to the ampulla of Vater, after which both ducts perforate the medial side of the second portion of the duodenum at the major duodenal papilla. ventral pancreatic duct urine Excretion that is the output of a kidney urine calcareous tooth Organ with a cavity which consist of dentine surrounded by enamel. Examples: incisor, molar. calcareous tooth diaphragm A thin musculomebranous barrier that separates the abdominal and thoracic cavities. Often used for breathing control diaphragm parathyroid gland The parathyroid gland is an endocrine gland for secretion of parathyroid hormone, usually found as a pair, embedded in the connective tissue capsule on the posterior surface of the thyroid gland. Parathyroid regulates calcium and phosphorous metabolism. parathyroid gland cardiac muscle tissue Muscle composed of cardiac muscle cells that is part of the heart[ZFA]. involuntary striated muscle found in the walls of the heart, specifically the myocardium[Wikipedia]. Tissue which consists of cardiac myocytes surrounded by cardiac endomysium. Examples: Cardiac muscle tissue proper, conducting tissue of heart[FMA]. cardiac muscle tissue skeletal muscle tissue Muscle tissue that consists primarily of skeletal muscle fibers. skeletal muscle tissue smooth muscle tissue Muscle tissue which is unstriated, composed primarily of smooth muscle fibers surrounded by a reticulum of collagen and elastic fibers. Smooth muscle differs from striated muscle in the much higher actin/myosin ratio, the absence of conspicuous sarcomeres and the ability to contract to a much smaller fraction of its resting length[GO]. Tissue which consists of smooth muscle . Examples: Arrector muscle of hair, Muscularis mucosae. smooth muscle tissue caecum A pouch in the digestive tract that connects the ileum with the ascending colon of the large intestine. It is separated from the ileum by the ileocecal valve, and is the beginning of the large intestine. It is also separated from the colon by the cecocolic junction. caecum vermiform appendix A blind-ended tube connected to the cecum, from which it develops embryologically[WP]. vermiform appendix colon Last portion of the large intestine before it becomes the rectum. colon ascending colon Segment of the colon which is continuous with the cecum proximally and the transverse colon distally.[FMA,modified] ascending colon sigmoid colon The part of the large intestine that is closest to the rectum and anus. It forms a loop that averages about 40 cm. in length, and normally lies within the pelvis, but on account of its freedom of movement it is liable to be displaced into the abdominal cavity. sigmoid colon pyloric antrum pyloric antrum the area at the bottom of the stomach on the caudal side of the pyloric canal that contains gastrin-producing G cells, which stimulate acid production, and the luminal pH-sensitive population of somatostatin-producing D cells adrenal cortex adrenal cortex the thick outer layer of the adrenal gland that produces and secretes steroid hormones such as corticosterone, estrone and aldosterone urinary bladder distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion[MP]. urinary bladder pancreatic acinus The secretory units of the exocrine pancreas, where fluid containing digestive enzymes is produced; consists of a group of secretory cells surrounding a luminal space that connects to the pancreatic duct. pancreatic acinus pancreas An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes[GO]. pancreas myometrium myometrium the smooth muscle coat of the uterus, which forms the main mass of the organ and surrounds and supports the endometrium epididymis epididymis the elongated structure connected to the posterior surface of the testis that transports, stores, and matures spermatozoa between testis and vas deferens seminiferous tubule of testis seminiferous tubule of testis the tubules in the testes where spermatogenesis occurs white adipose tissue Connective tissue consisting of fat-storing cells and arranged in lobular groups or along minor blood vessels[MP,modified] white adipose tissue brown adipose tissue A thermogenic form of adipose tissue that is composed of brown adipocytes[MP,modified] brown adipose tissue gastrocnemius The most superficial muscle of the triceps surae group, in the posterior portion of the lower hindleg. gastrocnemius soleus muscle A deep muscle of the triceps surae group, in the superficial posterior compartment of the leg. soleus muscle bone element Skeletal element that is composed of bone tissue. bone element knee joint The knee joint joins the thigh with the leg and consists of two articulations: one between the femur and tibia, and one between the femur and patella. It is the largest and most complicated joint in the human body. The knee is a mobile trocho-ginglymus (i.e. a pivotal hinge joint), which permits flexion and extension as well as a slight medial and lateral rotation[WP,unvetted]. knee joint thoracic aorta the part of the aorta that extends from the origin at the heart to the diaphragm, and from which arises numerous branches that supply oxygenated blood to the chest cage and the organs within the chest thoracic aorta abdominal aorta Abdominal part of aorta: the distal part of the descending aorta, which is the continuation of the thoracic part and gives rise to the inferior phrenic, lumbar, median sacral, superior and inferior mesenteric, middle suprarenal, renal, and testicular or ovarian arteries, and celiac trunk[BTO]. The abdominal aorta is the largest artery in the abdominal cavity. As part of the aorta, it is a direct continuation of descending aorta(of the thorax). [WP,unvetted]. abdominal aorta lower respiratory tract The segment of respiratory tract from the trachea to the lungs[WP,modified] lower respiratory tract muscle organ Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO]. Nonparenchymatous organ that primarily consists of skeletal muscle tissue aggregated into macroscopic fasciculi by connective tissue; together with other muscles, it constitutes the muscular system. Examples: biceps, diaphragm, masseter, right third external intercostal muscle, external oblique, levator ani, serratus anterior[FMA]. muscle organ artery An epithelial tube or tree of tibes that transports blood away from the heart[modified from AEO definition]. artery vein Any of the tubular branching vessels that carry blood from the capillaries toward the heart. vein mandible A dentary bone that is the only bone in one of the lateral halves of the lower jaw skeleton. mandible tongue A muscular organ in the floor of the mouth. tongue submandibular gland Either of the paired compound tubuloalveolar (aka tubuloacinar) major salivary glands composed of both serous and mucous secretory cells and situated beneath the mandible. submandibular gland autonomic ganglion autonomic ganglion ganglion that has dendrites that form a junction between autonomic nerves originating from the central nervous system and autonomic nerves innervating their target organs in the periphery. There are two subtypes, sympathetic ganglion and parasympathetic ganglion. sympathetic ganglion A ganglion of the sympathetic nervous system. Examples: paravertebral and the prevertebral ganglia, which include the sympathetic chain ganglia, the superior, middle, and inferior cervical ganglia, and the aorticorenal, celiac, and stellate ganglia sympathetic ganglion paravertebral ganglion Trunk ganglion which is part of a bilaterally paired set of sympathetic ganglia located anterior and lateral to the spinal cord. paravertebral ganglion parasympathetic ganglion Ganglion containing neurons that receive innervation from parasympathetic neurons in the central nervous system and subserves parasympathetic functions through innervation of smooth muscle, cardiac muscle and glands. parasympathetic ganglion lacrimal gland The lacrimal glands are paired almond-shaped glands, located in or near the orbital region, that secrete the aqueous layer of the tear film.[WP]. lacrimal gland sebaceous gland A holocrine gland that secretes sebum into the hair follicles, or in hairless areas into ducts.[MP]. sebaceous gland major salivary gland One of the three largest glands of the oral cavity that secrete most of the saliva, including the parotid, submandibular, and sublingual glands. major salivary gland parotid gland The parotid gland is the largest of the salivary glands. It is found wrapped around the mandibular ramus, and it secretes saliva through Stensen's duct into the oral cavity, to facilitate mastication and swallowing. [WP,unvetted]. parotid gland frontal cortex Anterior portion of the neocortex, lying anterior to the central sulcus in humans. It is bounded by the parietal cortex posteriorly and the temporal cortex laterally[NIFSTD,modified]. frontal cortex parietal lobe Upper central part of the cerebral hemisphere. (MSH) parietal lobe caudate nucleus Subcortical nucleus of telecephalic origin consisting of an elongated gray mass lying lateral to and bordering the lateral ventricle. It is divided into a head, body and tail in some species. caudate nucleus globus pallidus Subcortical nucleus, functionally part of the basal ganglia, which consists of two segments the external (or lateral) and internal (or medial) separated by the medial medullary lamina in primates. In rodents, The globus pallidus lateral is separated from the medial segment by the fibers of the internal capsule/cerebral peduncle. globus pallidus amygdala Subcortical brain region lying anterior to the hippocampal formation in the temporal lobe and anterior to the temporal horn of the lateral ventricle in some species. It is usually subdivided into several groups. Functionally, it is not considered a unitary structure (MM). amygdala midbrain Organ component of neuraxis that has as its parts the tectum, cerebral peduncle, midbrain tegmentum and cerebral aqueduct[FMA]. The brain region between the forebrain anteriorly and the hindbrain posteriorly, including the tectum dorsally and the midbrain tegmentum ventrally[ZFA]. The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)[GO]. midbrain medulla oblongata Organ component of neuraxis that has as its parts the medullary reticular formation, inferior olivary complex and cochlear nuclear complex, among other structures[FMA]. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate[GO]. medulla oblongata dorsal plus ventral thalamus Subcortical brain region consisting of paired gray matter bodies in the dorsal diencephalon and forming part of the lateral wall of the third ventricle of the brain. The thalamus represents the major portion of the diencephalon and is commonly divided into cellular aggregates known as nuclear groups.(MeSH). The dorsal topographic division of the interbrain. The macrodissected adult human thalamus was clearly illustrated by Vesalius in 1543 and the term as defined here was introduced by His in 1893. It includes the traditional epithalamus, dorsal thalamus, and ventral thalamus of Herrick (1910, pp. 494, 498). Also see Kuhlenbeck (1927, Ch. 9) and Jones (1985, p. 87). dorsal plus ventral thalamus hypothalamus A specialized brain region of the ventral diencephalon arising near the end of the segmentation period; the embryonic hypothalamic region will give rise to the posterior pituitary gland as well as a number of brain nuclei. [ZFA]. One of the most important functions of the hypothalamus is to link the nervous system to the endocrine system via the pituitary gland (hypophysis).[Wikipedia]. hypothalamus subthalamic nucleus The subthalamic nucleus is the lens-shaped nucleus located in the ventral part of the subthalamus on the inner aspect of the internal capsule that is concerned with the integration of somatic motor function[GO]. subthalamic nucleus mammary gland A specialized accessory gland of the skin of mammals that secretes milk. The gland is typically only developed in females, and regresses in males. mammary gland endothelium of artery An endothelium that is part of an artery [Automatically generated definition]. endothelium of artery preoptic area Area of the forebrain anterior to the posterior tuberculum and the hypothalamus and ventral to the ventral thalamus[ZFA]. preoptic area Ammon's horn A part of the brain consisting of a three layered cortex located in the forebrain bordering the medial surface of the lateral ventricle. The term hippocampus is often used synonymously with hippocampal formation which consists of the hippocampus proper or Cornu Ammonis, the dentate gyrus and the subiculum. Ammon's horn blood vessel A vessel through which blood circulates in the body. blood vessel endothelium A layer of epithelium that lines the heart, blood vessels (endothelium, vascular), lymph vessels (endothelium, lymphatic), and the serous cavities of the body[MESH]. Simple squamous epithelium which lines blood and lymphatic vessels and the heart[FMA] endothelium placenta organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin[GO]. The fetal portion of the placenta is known as the villous chorion. The maternal portion is known as the decidua basalis. The two portions are held together by anchoring villi that are anchored to the decidua basalis by the cytotrophoblastic shell. placenta superior cervical ganglion Trunk ganglion which is bilaterally paired and located at the anterior end of the sympathetic ganglion chain. superior cervical ganglion olfactory epithelium A sensory epithelium inside the nasal cavity that is responsible for detecting odors[WP]. olfactory epithelium gray matter A nervous system structure composed primarily of nerve cell bodies (somas). May also include dendrites and the initial unmyelinated portion of axons. gray matter hindbrain The most posterior of the three principal regions of the brain. In mammals and birds the hindbrain is divided into a rostral metencephalon and a caudal myelencephalon. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata (From: Neuroanatomy of the Zebrafish Brain)[ZFA]. Organ component of neuraxis that has as its parts the pons, cerebellum and medulla oblongata[FMA]. hindbrain epithelium of bronchus An epithelium that is part of a bronchus [Automatically generated definition]. epithelium of bronchus striated muscle tissue Tissue which consists of striated muscle fibers surrounded by endomysium. Examples: Skeletal muscle tissue, Cardiac muscle tissue[FMA]. striated muscle tissue cerebellum Part of the metencephalon that lies in the posterior cranial fossa behind the brain stem. It is concerned with the coordination of movement[MESH]. A large dorsally projecting part of the brain concerned especially with the coordination of muscles and the maintenance of bodily equilibrium, situated between the brain stem and the back of the cerebrum , and formed in humans of two lateral lobes and a median lobe[BTO]. Brain structure derived from the anterior hindbrain, and perhaps including posterior midbrain. The cerebellum plays a role in somatic motor function, the control of muscle tone, and balance[ZFA]. cerebellum thyroid gland A two-lobed endocrine gland found in all vertebrates, located in front of and on either side of the trachea in humans, and producing various hormones, such as triiodothyronine and calcitonin[BTO]. thyroid gland lung Respiration organ that develops as an oupocketing of the esophagus. lung embryonic structure Anatomical structure that is part of an embryo. embryonic structure ciliary ganglion The ciliary ganglion is a parasympathetic ganglion located in the posterior orbit. It measures 1P2 millimeters in diameter and contains approximately 2,500 neurons (adapted from Wikipedia) ciliary ganglion umbilical vein The umbilical vein is a blood vessel present during fetal development that carries oxygenated blood from the placenta to the growing fetus. [WP,unvetted]. umbilical vein hypodermis Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP]. hypodermis viscus An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen. viscus spleen spleen the organ that functions to filter blood and to store red corpuscles and platelets liver An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO]. liver small intestine Subdivision of digestive tract that connects the stomach to the large intestine and is where much of the digestion and absorption of food takes place (with the exception of ruminants). The mammalian small intestine is long and coiled and can be differentiated histologically into: duodenum, jejunem, ileum[WP,cjm,Kardong]. small intestine gall bladder An organ that aids digestion and stores bile produced by the liver[WP]. gall bladder kidney A paired organ of the urinary tract which has the production of urine as its primary function. kidney duodenum The first part of the small intestine. At the junction of the stomach and the duodenum the alimentary canal is inflected. The duodenum first goes anteriorly for a short distance, turns dorsally, and eventually caudally, thus it is a U-shaped structure with two horizontal sections (a ventral and a dorsal one). duodenum ileum ileum the portion of the small intestine that extends from the jejunum to the colon medulla of thymus Medullary portion of thymus. The reticulum is coarser than in the cortex, the lymphoid cells are relatively fewer in number, and there are found peculiar nest-like bodies, the concentric corpuscles of Hassall. These concentric corpuscles are composed of a central mass, consisting of one or more granular cells, and of a capsule formed of epithelioid cells. They are the remains of the epithelial tubes, which grow out from the third branchial pouches of the embryo to form the thymus. Each follicle is surrounded by a vascular plexus, from which vessels pass into the interior, and radiate from the periphery toward the center, forming a second zone just within the margin of the medullary portion. In the center of the medullary portion there are very few vessels, and they are of minute size. medulla of thymus bronchus bronchus the upper conducting airways of the lung; these airways arise from the terminus of the trachea spinal cord Part of the central nervous system located in the vertebral canal continuous with and caudal to the brain; demarcated from brain by plane of foramen magnum. It is composed of an inner core of gray matter in which nerve cells predominate, and an outer layer of white matter in which myelinated nerve fibers predominate, and surrounds the central canal. (CUMBO) spinal cord vomeronasal organ An organ thought to supplement the olfactory system in receiving pheromonic communication. The sensory part of the organ is in two long, thin sacs, situated on either side of the nasal septum at its base. vomeronasal organ olfactory bulb A bulbous anterior projection of the olfactory lobe that is the place of termination of the olfactory nerves and is especially well developed in lower vertebrates (as fishes)[BTO]. olfactory bulb telencephalic ventricle A brain ventricle that is part of a telencephalon. In mammals and species with an evaginated telencephalon, this is one of a pair of lateral structures, one in each hemisphere telencephalic ventricle nucleus of brain A neural nucleus that is part of the brain. nucleus of brain umbilical cord The connecting cord from the developing embryo to the placenta. umbilical cord corpus callosum White matter structure containing massive numbers of commissural fibers connecting cortical areas in the two cerebral hemispheres.it is subdivided into a genu, a rostrum, a body, and a splenium. (MM) corpus callosum neural crest 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]. neural crest atrioventricular node Subdivision of conducting system of heart which is located in the muscular part of the interatrial septum that is continuous with the atrioventricular bundle.[FMA] atrioventricular node peritoneum A serous membrane that lines the peritoneal cavity[VHOG,modified]. peritoneum exocrine gland A gland that secretes products (excluding hormones and other chemical messengers) into ducts (duct glands) which lead directly into the external environment[WP]. Typical exocrine glands include sweat glands, salivary glands, mammary glands, stomach, liver, pancreas exocrine gland prostate gland The prostate gland is a partly muscular, partly glandular body that is situated near the base of the mammalian male urethra and secretes an alkaline viscid fluid which is a major constituent of the ejaculatory fluid. prostate gland endocrine gland Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified]. endocrine gland adrenal gland Either of a pair of complex endocrine organs near the anterior medial border of the kidney consisting of a mesodermal cortex that produces glucocorticoid, mineralocorticoid, and androgenic hormones and an ectodermal medulla that produces epinephrine and norepinephrine[BTO]. adrenal gland thymus Anatomical structure of largely lymphoid tissue that functions in cell-mediated immunity by being the site where T cells develop. thymus bone marrow bone marrow the soft tissue that fills the cavities of bones tonsil either of the two small almond-shaped masses of lymph tissue found on either side of the oropharynx tonsil connective tissue Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance. connective tissue muscle tissue Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO]. muscle tissue bile duct Any of the ducts that form the biliary tree, carrying bile from the liver to the small intestine. bile duct immune system Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies. immune system pericardium The combination of pericardial sac (a double-walled sac containing the heart and the roots of the great vessels) plus fibrous pericardium. pericardium skin gland A gland that is part of a skin of body [Automatically generated definition]. skin gland basal ganglion An individual member of a collection of basal ganglia. Basal ganglia are subcortical masses of gray matter in the forebrain and midbrain that are richly interconnected and so viewed as a functional system. The nuclei usually included are the caudate nucleus (caudoputamen in rodents), putamen, globus pallidus, substantia nigra (pars compacta and pars reticulata) and the subthalamic nucleus. Some also include the nucleus accumbens and ventral pallidum[NIF,modified]. basal ganglion limb bone A bone that is part of a limb [Automatically generated definition]. limb bone striatum A region of the forebrain consisting of the caudate nucleus, putamen and fundus striati.[GO]. striatum endochondral bone Replacement bone that forms within cartilage. endochondral bone gland an organ that functions as a secretory or excretory organ gland digit A subdivision of the autopod that has as part a series of phalanges together with associated vasculature, musculature, integument and nerves. It is continuous with the metapodial subdivision of the autopod, but does not include the metapodials. In species such as humans, fully formed digits are distinct, whereas in other species the digits may be connected by interdigital webbing, or may be completely unseparated (for example, in cetaceans). digit regional part of brain Anatomical divisons of the brain according to one or more criteria, e.g. cytoarchitectural, gross anatomy. Parts may be contiguous in 3D or not, e.g., basal ganglia. Regions of brain across multiple species are contained within this category. regional part of brain cerebral peduncle Synonym for macrodissected adult human tegmentum (Vicq d'Azyr, 1784; Swanson, 2000); pp. 555-556. Later used thus by for example His (1893b, p. 178), Herrick (1915, p. 160), Strong & Elwyn (1943, p. 17), Carpenter (1976, p. 367), Williams & Warwick (1980, p. 935). cerebral peduncle ventral tegmental area Unpaired midbrain region situated in the ventromedial portion of the reticular formation. The VTA is medial to the substantia nigra and ventral to the red nucleus, and extends caudally from the posterior hypothalamus in the diencephalon. The VTA contains dopamine neurons that project to various limbic and cortical areas and is a critical component of the brain's reward circuitry. ventral tegmental area cingulate gyrus One of the convolutions on the medial surface of the cerebral hemisphere. It surrounds the rostral part of the brain and interhemispheric commissure and forms part of the limbic system. (MSH) One of three essential structures comprising the limbic lobe, the other two being the hippocampus and parahippocampal gyrus. (CSP) cingulate gyrus surface structure Anatomical structure that overlaps the outer epithelial layer and is adjacent to the space surrounding the organism. surface structure compound organ Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types. compound organ trachea The trachea is the portion of the airway that attaches to the bronchi as it branches [GO:dph]. trachea skull Anatomical structure that is part of the head consisting entirely of cranium and mandible[WP]. skull reproductive organ An organ involved in reproduction reproductive organ endoderm of foregut An endoderm that is part of a foregut [Automatically generated definition]. endoderm of foregut mesentery of oesophagus A mesentery that is part of a esophagus [Automatically generated definition]. mesentery of oesophagus gland of diencephalon Any gland that is part of the diencephalon. Examples: pineal gland, neurohypophysis. gland of diencephalon gland of integumental system A gland that is part of a integumental system [Automatically generated definition]. gland of integumental system gland of gut A gland that is part of a digestive tract [Automatically generated definition]. gland of gut head bone A bone that is part of a head [Automatically generated definition]. head bone facial bone A bone that is part of a facial skeleton [Automatically generated definition]. facial bone hindlimb bone A bone that is part of a hindlimb region. Examples: any pes phalanx, femur. Counter-examples: ischium, pubis (they are part of the pelvic girdle) hindlimb bone respiratory system artery An artery that is part of a respiratory system [Automatically generated definition]. respiratory system artery arterial blood vessel A blood vessel that is part of the arterial system. Includes artery, arteriole and aorta. arterial blood vessel brain gray matter A gray matter that is part of a brain [Automatically generated definition]. brain gray matter limb long bone A long bone that is part of a limb [Automatically generated definition]. limb long bone hindlimb long bone A long bone that is part of a hindlimb [Automatically generated definition]. hindlimb long bone respiratory system arterial blood vessel An arterial blood vessel that is part of a respiratory system [Automatically generated definition]. respiratory system arterial blood vessel limb joint Any joint that is part of a (free) limb. limb joint mouth mucosa A mucous membrane that lines the mouth. mouth mucosa fallopian tube Initial section of the oviduct through which the ova pass from the ovary to the uterus fallopian tube tooth-like structure hard bony, calcareous, or chitinous organ found in the mouth or pharynx of an animal and used in procuring or masticating food. tooth-like structure epithelial tube Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system. epithelial tube endothelial tube Any endothelium that has the quality of being cylindrical [Automatically generated definition]. endothelial tube pancreatic epithelial bud The embryonic pancreas develops from two separate anlagen in the foregut epithelium, one dorsal and two ventral pancreatic buds[PMID]. pancreatic epithelial bud ventral pancreatic bud pancreatic bud that gives rise to the major pancreatic duct. ventral pancreatic bud digestive system duct A duct that is part of a digestive system [Automatically generated definition]. digestive system duct sex gland Any of the organized aggregations of cells that function as secretory or excretory organs and are associated with reproduction. sex gland brain ventricle/choroid plexus The brain ventricles or their associated choroid plexuses brain ventricle/choroid plexus brain ventricle brain ventricle one of the system of communicating cavities in the brain that are continuous with the central canal of the spinal cord, that like it are derived from the medullary canal of the embryo, that are lined with an epithelial ependyma, and that contain a serous fluid anatomical conduit Any tube, opening or passage that connects two distinct anatomical spaces. anatomical conduit endoderm-derived structure An anatomical structure that develops (entirely or partially) from the endoderm. endoderm-derived structure mesoderm-derived structure An anatomical structure that develops (entirely or partially) from the mesoderm. mesoderm-derived structure ectoderm-derived structure An anatomical structure that develops (entirely or partially) from the ectoderm. ectoderm-derived structure hemopoietic organ Organ that is part of the hematopoietic system. hemopoietic organ hindlimb zeugopod muscle A muscle organ that is part of a hindlimb zeugopod (lower leg) [Automatically generated definition]. hindlimb zeugopod muscle pharyngeal arch artery One of a series of paired embryological vascular structures formed within a pharyngeal arch; in the adult, some of these vessels give rise to the great vessels[MP] pharyngeal arch artery bone of free limb or fin A bone that is part of an appendage [Automatically generated definition]. bone of free limb or fin cavity lining cavity lining blood vessel endothelium An endothelium that lines the blood vasculature. Other endothelia may line lymph vessels, the heart blood vessel endothelium arterial system endothelium An endothelium that is part of an arterial system [Automatically generated definition]. arterial system endothelium dentary The dentary is a dermal bone that forms the antero-lateral part of the lower jaw in fishes and amphibians, extending to the whole lower jaw in mammals[VHOG,modified]. dentary dermal skeletal element dermal skeletal element dermis-derived entity that is made of skeletal tissue. skeletal element Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. skeletal element bone of lower jaw Any bone that is part of the lower jaw skeleton. This includes (when present): the dentary/mandible, the articular, the splenial, the suprangular bone of lower jaw respiratory tract epithelium respiratory tract epithelium the pseudostratified ciliated epithelium that lines much of the conducting portion of the airway, including part of the nasal cavity and larynx, the trachea, and bronchi respiratory system epithelium An epithelium that is part of a respiratory system [Automatically generated definition]. respiratory system epithelium lower respiratory tract epithelium An epithelium that is part of a lower respiratory tract [Automatically generated definition]. lower respiratory tract epithelium aorta endothelium aorta endothelium the thin layer of flat cells that line the aorta and form a barrier between circulating blood in the lumen and the rest of the vessel wall cardiovascular system endothelium An endothelium that is part of the cardiovascular system. cardiovascular system endothelium subdivision of digestive tract A proximal-distal subdivision of the digestive tract. subdivision of digestive tract organ component layer A part of a wall of an organ that forms a layer. organ component layer mucosa of tongue A mucosa that is part of a tongue [Automatically generated definition]. mucosa of tongue immune organ An organ that is part of a immune system [Automatically generated definition]. immune organ reproductive structure An anatomical structure that is part of the reproductive system. reproductive structure multi cell part structure A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part. multi cell part structure abdomen element An organ or element that is in the abdomen. Examples: spleen, intestine, kidney, abdominal mammary gland. abdomen element trunk region element An organ or element that part of the trunk region. The trunk region can be further subdividied into thoracic (including chest and thoracic cavity) and abdominal (including abdomen and pelbis) regions. trunk region element thoracic segment organ An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions. thoracic segment organ embryonic tissue A portion of tissue that is part of an embryo. embryonic tissue male preputial gland One of the sebaceous glands of the corona and neck of the glans penis. male preputial gland nasal cavity epithelium An epithelium that lines the nasal cavity. nasal cavity epithelium male reproductive gland A sex gland that is part of a male reproductive system. male reproductive gland cerebral hemisphere gray matter A gray matter that is part of a cerebral hemisphere. cerebral hemisphere gray matter definitive endoderm definitive endoderm extraembryonic membrane Intrinsic membrane that arises from embryonic germ layers and grow to surround the developing embryo. extraembryonic membrane segment of aorta Any portion of the aorta including the ascending and descending aorta, and aortic arch or a portion of the aortic orifice of the left ventricle. segment of aorta occipital region Anatomical cluster that is located in the posterior region of the cranium and forms the margin of the foramen magnum and occipital condyles. occipital region duct of male reproductive system Any of the ducts that are part of a male reproductive system. duct of male reproductive system endo-epithelium Epithelium that derives from the endoderm. Examples: urothelium, transitional epithelium of ureter, epithelium of prostatic gland.[FMA] endo-epithelium integumentary adnexa Anatomical structure embedded in or located in the integument that is part of the integumental system. Examples: hair, follicles, skin glands, claws, nails, feathers. integumentary adnexa glandular epithelium An epithelium that is composed primarily of secretory cells. glandular epithelium adrenal/interrenal gland This gland can either be a discrete structure located bilaterally above each kidney, or a cluster of cells in the head kidney that perform the functions of the adrenal gland. In either case, this organ consists of two cells types, aminergic chromaffin cells and steroidogenic cortical cells[GO] adrenal/interrenal gland squamous epithelium An epithelium characterised by its most superficial layer consisting of squamous epithelial cells. squamous epithelium digestive gland A gland, such as the liver or pancreas, that secretes into the alimentary canal substances necessary for digestion. digestive gland primary circulatory organ A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified]. primary circulatory organ tracheobronchial tree The structure from the trachea, bronchi, and bronchioles that forms the airways that supply air to the lungs. The lining of the tracheobronchial tree consists of ciliated columnar epithelial cells. tracheobronchial tree pancreatic duct A duct that is part of the pancreas and connected to the duodenum. pancreatic duct outer epithelium The epidermis is the entire outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species[GO]. outer epithelium epithelial sac An epithelial tube that is open at one end only. epithelial sac ciliated columnar epithelium Simple columnar epithelium in which the luminal side of the cells bears cilia. Examples: epithelium of trachea, epithelium of uterine tube.[FMA] ciliated columnar epithelium external nose External part of the olfactory apparatus. external nose dermal bone Skeletal element that forms superficially in the organism, usually in association with the ectoderm[VSAO]. dermal bone telencephalic nucleus A nucleus of brain that is part of a telencephalon. telencephalic nucleus glandular acinus The many-lobed berry cluster of cells that is the terminous of a gland where the secretion is produced is acinar in form. glandular acinus digestive tract diverticulum Branch or outpocketing of the digestive tract. digestive tract diverticulum sac sac multicellular anatomical structure An anatomical structure that has more than one cell as a part. multicellular anatomical structure oral gland Gland of the epithelium lining the oral cavity. The most common are the salivary glands. oral gland male accessory sex gland Any gland, other than the gonad, associated with the genital tract, such as the ampulla of the ductus deferens and the bulbourethral, prostate and vesicular glands of the male. male accessory sex gland neural crest-derived structure An anatomical structure that develops from the neural crest. neural crest-derived structure structure with developmental contribution from neural crest An anatomical structure that has some part that develops from the neural crest. structure with developmental contribution from neural crest germ layer / neural crest germ layer / neural crest endochondral element A skeletal element that has the potential to participate in endochondral ossification, and may participate in intramembranous ossification. endochondral element ecto-epithelium Epithelium that derives from the ectoderm. Examples: epithelium of acinus of lactiferous duct, subscapular lens epithelium, epithelium of posterior surface of cornea. ecto-epithelium pseudostratified ciliated columnar epithelium Epithelium composed of a single layer of cells, appearing as layered because the column-shaped cells vary in height so the nuclei are at different levels. The basal portions of all the cells are in contact with the basement membrane. It lines the respiratory system and the male reproductive tract. The cilia in the respiratory tract are motile, while the stereocilia in the male reproductive tract are immobile. pseudostratified ciliated columnar epithelium bone of appendage girdle complex A bone that is part of an appendage girdle complex (i.e. any bone in a limb, fin or girdle). bone of appendage girdle complex synovial limb joint Any synovial joint that is part of a (free) limb. synovial limb joint central nervous system cell part cluster A multi cell part structure that is part of a central nervous system. central nervous system cell part cluster gray matter of telencephalon A portion of gray matter that is part of a telencephalon. gray matter of telencephalon meso-epithelium Epithelium that derives from the mesoderm. [Automatically generated definition]. meso-epithelium bone of jaw A bone element that is part of a jaw region. bone of jaw hemopoietic tissue Blood-forming tissue, consisting of reticular fibers and cells. Also known as hemopoietic tissue hemopoietic tissue subdivision of uterine tube subdivision of uterine tube subdivision of tube subdivision of tube exocrine pancreas epithelium Epithelium lining the exocrine pancreas. exocrine pancreas epithelium digestive system element Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements. digestive system element embryoid body Embryoid bodies (EBs) are three-dimensional aggregates of pluripotent stem cells. embryoid body skeletal muscle organ A muscle organ that consists of skeletal muscle tissue ensheathed in epimysium, that develops from myotome and that is innervated by some somatic motor neuron. Skeletal muscles are typically attached (via a tendon) to a bone but there are exceptions (e.g. intrinsic tongue muscles). skeletal muscle organ hindlimb endochondral element A hindlimb bone or its cartilage or pre-cartilage precursor. hindlimb endochondral element limb endochondral element A limb bone or its cartilage or pre-cartilage precursor. limb endochondral element lateral structure Any structure that is placed on one side of the left-right axis of a bilaterian. lateral structure upper respiratory conduit Any anatomical conduit which is part of the upper respiratory tract upper respiratory conduit lobe of cerebral hemisphere Subdivision of telencephalon which is one of a number of subdivisions of each hemisphere separated by both real landmarks (sulci and fissures) and arbitrary boundaries[FMA,modified]. lobe of cerebral hemisphere abdominal viscera A viscus that is part of a abdomen. abdominal viscera bladder organ A membranous sac in animals that serves as the receptacle of a liquid or contains gas. bladder organ nose epithelium nose epithelium exocrine gland of integumental system An exocrine gland that is part of a integumental system. exocrine gland of integumental system lymphomyeloid tissue lymphomyeloid tissue multi organ part structure An multicellular anatomical structure that has subparts of multiple organs as a part. multi organ part structure cell cluster A cluster of cells, largely surrounded by a morphological boundary. cell cluster length unit A unit which is a standard measure of the distance between two points. length unit mass unit A unit which is a standard measure of the amount of matter/energy of a physical object. mass unit time unit A unit which is a standard measure of the dimension in which events occur in sequence. time unit temperature unit A unit which is a standard measure of the average kinetic energy of the particles in a sample of matter. temperature unit substance unit A unit which is a standardised quantity of an element or compound with uniform composition. substance unit meter A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second. meter kilogram A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France. kilogram second A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom. second kelvin A thermodynamic temperature unit which is equal to the fraction 1/273.16 of the thermodynamic temperature of the triple point of water. kelvin mole A substance unit which is equal to the amount of substance of a molecular system which contains as many elementary entities as there are atoms in 0.012 kilogram of carbon 12. mole centimeter A length unit which is equal to one hundredth of a meter or 10^[-2] m. centimeter millimeter A length unit which is equal to one thousandth of a meter or 10^[-3] m. millimeter micrometer A length unit which is equal to one millionth of a meter or 10^[-6] m. micrometer nanometer A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m. nanometer gram A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg. gram milligram A mass unit which is equal to one thousandth of a gram or 10^[-3] g. milligram microgram A mass unit which is equal to one millionth of a gram or 10^[-6] g. microgram nanogram A mass unit which is equal to one thousandth of one millionth of a gram or 10^[-9] g. nanogram picogram A mass unit which is equal to 10^[-12] g. picogram degree Celsius A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K. degree Celsius millisecond A time unit which is equal to one thousandth of a second or 10^[-3] s. millisecond microsecond A time unit which is equal to one millionth of a second or 10^[-6] s. microsecond minute A time unit which is equal to 60 seconds. minute hour A time unit which is equal to 3600 seconds or 60 minutes. hour day A time unit which is equal to 24 hours. day week A time unit which is equal to 7 days. week month A time unit which is approximately equal to the length of time of one of cycle of the moon's phases which in science is taken to be equal to 30 days. month year A time unit which is equal to 12 months which is science is taken to be equal to 365.25 days. year micromole A substance unit equal to a millionth of a mol or 10^[-6] mol. micromole nanomole A substance unit equal to one thousandth of one millionth of a mole or 10^[-9] mol. nanomole picomole A substance unit equal to 10^[-12] mol. picomole femtomole A substance unit equal to 10^[-15] mol. femtomole attomole A substance unit equal to 10^[-18] mol. attomole base unit A unit which is one of a particular measure to which all measures of that type can be related. base unit concentration unit A unit which represents a standard measurement of how much of a given substance there is mixed with another substance. concentration unit mass density unit A density unit which is a standard measure of the mass of a substance in a given volume. mass density unit unit of molarity A concentration unit which is a standard measure of the number of moles of a given substance per liter of solution. unit of molarity molar A unit of concentration which expresses a concentration of 1 mole of solute per liter of solution (mol/L). molar millimolar A unit of molarity which is equal to one thousandth of a molar or 10^[-3] M. millimolar micromolar A unit of molarity which is equal to one millionth of a molar or 10^[-6] M. micromolar picomolar A unit of molarity which is equal to 10^[-12] M. picomolar volume unit A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas. volume unit cubic centimeter A volume unit which is equal to one millionth of a cubic meter or 10^[-9] m^[3], or to 1 ml. cubic centimeter milliliter A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter. milliliter liter A volume unit which is equal to one thousandth of a cubic meter or 10^[-3] m^[3], or to 1 decimeter. liter microliter A volume unit which is equal to one millionth of a liter or 10^[-6] L. microliter nanoliter A volume unit which is equal to one thousandth of one millionth of a liter or 10^[-9] L. nanoliter picoliter A volume unit which is equal to 10^[-12] L. picoliter femtoliter A volume unit which is equal to 10^[-15] L. femtoliter radiation unit A unit which is a standard measure of the amount of radiation emitted by a given radiation source as well as the amount of radiation absorbed or deposited in a specific material by a radiation source. radiation unit activity (of a radionuclide) unit A unit which is a standard measure of the transformation (disintegration) rate of a radioactive substance. activity (of a radionuclide) unit curie An activity (of a radionuclide) unit which is equal to the activity of a quantity of radioactive material in which there are 3.7 x 10^[10] atom disintegration per second (dps). curie roentgen An exposure unit which is equal to the amount of radiation required to liberate positive and negative charges of one electrostatic unit of charge in 1 cm^[3] of air at standard temperature and pressure (STP). This corresponds to the generation of approximately 2.0810^[9] ion pairs. roentgen Roentgen equivalent man A dose equivalent unit which when multiplied by hundred is equal to one sievert or 1 Sv. 1 Sv is equal to 100 rem. Roentgen equivalent man disintegrations per minute An activity (of a radionuclide) unit which is equal to the activity of a quantity of radioactive material in which one nucleus decays per minute or there is one atom disintegration per minute. disintegrations per minute counts per minute An activity (of a radionuclide) unit which is equal to the number of light emissions produced by ionizing radiation in one minute. counts per minute light unit A unit which is a standard measure of the intensity of light. light unit mass percentage A dimensionless concentration unit which denotes the mass of a substance in a mixture as a percentage of the mass of the entire mixture. mass percentage mass volume percentage A dimensionless concentration unit which denotes the mass of the substance in a mixture as a percentage of the volume of the entire mixture. mass volume percentage volume percentage A dimensionless concentration unit which denotes the volume of the solute in mL per 100 mL of the resulting solution. volume percentage gram per liter A mass unit density which is equal to mass of an object in grams divided by the volume in liters. gram per liter milligram per milliliter A mass unit density which is equal to mass of an object in milligrams divided by the volume in milliliters. milligram per milliliter dimensionless unit A unit which is a standard measure of physical quantity consisting of only a numerical number without any units. dimensionless unit percent A dimensionless ratio unit which denotes numbers as fractions of 100. percent count unit A dimensionless unit which denotes a simple count of things. count unit degree Fahrenheit A temperature unit which is equal to 5/9ths of a kelvin. Negative 40 degrees Fahrenheit is equal to negative 40 degrees Celsius. degree Fahrenheit pH A dimensionless concentration notation which denotes the acidity of a solution in terms of activity of hydrogen ions (H+). pH volume per unit volume A dimensionless concentration unit which denotes the given volume of the solute in the total volume of the resulting solution. volume per unit volume milliliter per liter A volume per unit volume unit which is equal to one millionth of a liter of solute in one liter of solution. milliliter per liter gram per deciliter A mass density unit which is equal to mass of an object in grams divided by the volume in deciliters. gram per deciliter deciliter A volume unit which is equal to one tenth of a liter or 10^[-1] L. deciliter colony forming unit per milliliter A colony forming unit which a measure of viable bacterial numbers in one milliliter. colony forming unit per milliliter bit An information unit which refers to a digit in the binary numeral system, which consists of base 2 digits (ie there are only 2 possible values: 0 or 1). bit islet of Langerhans morphology trait Any measurable or observable characteristic related to the shape, structure, color or pattern of the cellular masses consisting of several to several hundred cells in the interstitial tissue of the pancreas; they are composed of five different cell types that make up the endocrine portion of the pancreas. acute lymphoblastic leukemia A leukemia/lymphoma found predominately in children and adolescents and characterized by a high number of lymphoblasts and solid tumor lesions. Frequent sites involve LYMPH NODES, skin, and bones. It most commonly presents as leukemia. A neoplasm characterized by abnormalities of the lymphoid cell precursors leading to excessive lymphoblasts in the marrow and other organs. It is the most common cancer in children and accounts for the vast majority of all childhood leukemias. Leukemia with an acute onset, characterized by the presence of lymphoblasts in the bone marrow and the peripheral blood. It includes the acute B lymphoblastic leukemia and acute T lymphoblastic leukemia. Leukemia with an acute onset, characterized by the presence of lymphoblasts in the bone marrow and the peripheral blood. It includes the precursor B lymphoblastic leukemia and precursor T lymphoblastic leukemia. When the disease process is confined to a mass lesion with no or minimal evidence of blood and less than 25% marrow involvement, the diagnosis is lymphoblastic lymphoma; with blood and greater than 25% marrow involvement, ALL is the appropriate term. acute myeloid leukemia Clonal expansion of myeloid blasts in bone marrow, blood, and other tissue. Myeloid leukemias develop from changes in cells that normally produce NEUTROPHILS; BASOPHILS; EOSINOPHILS; and MONOCYTES. acute promyelocytic leukemia An acute myeloid leukemia (AML) in which abnormal promyelocytes predominate. It is characterized by the t(15;17)(q22;q12) translocation. There are two variants: the typical and micro granular (hypo granular) variant. This AML is particularly sensitive to treatment with all trans-retinoic acid and has a favorable prognosis. (WHO, 2001) -- 2003 An acute myeloid leukemia (AML) in which abnormal promyelocytes predominate. It is characterized by the t(15;17)(q22;q12) translocation. There are two variants: the typical and microgranular variant. This AML is particularly sensitive to treatment with all trans-retinoic acid and has a favorable prognosis. (WHO, 2001) asthma A bronchial disease that is characterized by chronic inflammation and narrowing of the airways, which is caused by a combination of environmental and genetic factors resulting in recurring periods of wheezing (a whistling sound while breathing), chest tightness, shortness of breath, mucus production and coughing. The symptoms appear due to a variety of triggers such as allergens, irritants, respiratory infections, weather changes, excercise, stress, reflux disease, medications, foods and emotional anxiety. A chronic respiratory disease manifested as difficulty breathing due to the narrowing of bronchial passageways. A form of bronchial disorder with three distinct components: airway hyper-responsiveness (RESPIRATORY HYPERSENSITIVITY), airway INFLAMMATION, and intermittent AIRWAY OBSTRUCTION. It is characterized by spasmodic contraction of airway smooth muscle, WHEEZING, and dyspnea (DYSPNEA, PAROXYSMAL). Tendency of the smooth muscle of the tracheobronchial tree to contract more intensely in response to a given stimulus than it does in the response seen in normal individuals. This condition is present in virtually all symptomatic patients with asthma. The most prominent manifestation of this smooth muscle contraction is a decrease in airway caliber that can be readily measured in the pulmonary function laboratory. Burkitts lymphoma A form of undifferentiated malignant LYMPHOMA usually found in central Africa, but also reported in other parts of the world. It is commonly manifested as a large osteolytic lesion in the jaw or as an abdominal mass. B-cell antigens are expressed on the immature cells that make up the tumor in virtually all cases of Burkitt lymphoma. The Epstein-Barr virus (HERPESVIRUS 4, HUMAN) has been isolated from Burkitt lymphoma cases in Africa and it is implicated as the causative agent in these cases; however, most non-African cases are EBV-negative. cancer A malignant neoplasm in which new abnormal tissue grow by excessive cellular division and proliferation more rapidly than normal and continues to grow after the stimuli that initiated the new growth cease. chronic myelogenous leukemia Clonal hematopoetic disorder caused by an acquired genetic defect in PLURIPOTENT STEM CELLS. It starts in MYELOID CELLS of the bone marrow, invades the blood and then other organs. The condition progresses from a stable, more indolent, chronic phase (LEUKEMIA, MYELOID, CHRONIC PHASE) lasting up to 7 years, to an advanced phase composed of an accelerated phase (LEUKEMIA, MYELOID, ACCELERATED PHASE) and BLAST CRISIS. colorectal adenocarcinoma A malignant tumor usually arising from the epithelium lining the large intestinal mucosa. Colon carcinoma is one of the most common malignancies in both males and females, and is especially common in North America and Europe. Grossly, most colon carcinomas are polypoid or ulcerating lesions. Microscopically, adenocarcinoma is the most frequently seen morphologic subtype. Prognosis depends on the stage of the disease (depth of invasion, metastasis to regional/distal lymph nodes or other anatomic sites). -- 2004 An adenocarcinoma arising from the colon. It is more frequently seen in populations with a Western type diet and in patients with a history of chronic inflammatory bowel disease. Signs and symptoms include intestinal bleeding, anemia, and change in bowel habits. According to the degree of cellular differentiation, colonic adenocarcinomas are divided into well differentiated, moderately, and poorly differentiated. Morphologic variants include the mucinous adenocarcinoma and signet-ring adenocarcinoma. Lymphatic or hematogenous spread can occur early in the process and lead to systemic disease. Tumors or cancer of the COLON or the RECTUM or both. Risk factors for colorectal cancer include chronic ULCERATIVE COLITIS; FAMILIAL POLYPOSIS COLI; exposure to ASBESTOS; and irradiation of the CERVIX UTERI. compound based treatment A treatment process in which a chemical compound is administered to the subject under investigation. diabetes mellitus A heterogeneous group of disorders characterized by HYPERGLYCEMIA and GLUCOSE INTOLERANCE. A metabolic disorder characterized by abnormally high blood sugar levels due to diminished production of insulin or insulin resistance/desensitization. family history Family history is a form of clinicaly history specifically about relevant aspects of genetic preconditions or family member's clinical history. insulinoma A benign tumor of the PANCREATIC BETA CELLS. Insulinoma secretes excess INSULIN resulting in HYPOGLYCEMIA. A usually benign, well circumscribed neoplasm arising from the beta cells of the pancreas. Patients exhibit symptoms related to hypoglycemia due to inappropriate secretion of insulin. leukemia A cancer that affects the blood or bone marrow characterized by an abnormal proliferation of blood cells. A malignant (clonal) hematologic disorder, involving hematopoietic stem cells and characterized by the presence of primitive or atypical myeloid or lymphoid cells in the bone marrow and the blood. Leukemias are classified as acute or chronic based on the degree of cellular differentiation and the predominant cell type present. Leukemia is usually associated with anemia, fever, hemorrhagic episodes, and splenomegaly. Common leukemias include acute myeloid leukemia, chronic myelogenous leukemia, acute lymphoblastic or precursor lymphoblastic leukemia, and chronic lymphocytic leukemia. Treatment is vital to patient survival; untreated, the natural course of acute leukemias is normally measured in weeks or months, while that of chronic leukemias is more often measured in months or years. A progressive, malignant disease of the blood-forming organs, characterized by distorted proliferation and development of leukocytes and their precursors in the blood and bone marrow. Leukemias were originally termed acute or chronic based on life expectancy but now are classified according to cellular maturity. Acute leukemias consist of predominately immature cells; chronic leukemias are composed of more mature cells. (From The Merck Manual, 2006) neoplasm A benign or malignant tissue growth resulting from uncontrolled cell proliferation. Benign neoplastic cells resemble normal cells without exhibiting significant cytologic atypia, while malignant cells exhibit overt signs such as dysplastic features, atypical mitotic figures, necrosis, nuclear pleomorphism, and anaplasia. Representative examples of benign neoplasms include papillomas, cystadenomas, and lipomas; malignant neoplasms include carcinomas, sarcomas, lymphomas, and leukemias. experiment performer An individual who does some experimental process. type I diabetes mellitus A subtype of DIABETES MELLITUS that is characterized by INSULIN deficiency. It is manifested by the sudden onset of severe HYPERGLYCEMIA, rapid progression to DIABETIC KETOACIDOSIS, and DEATH unless treated with insulin. The disease may occur at any age, but is most common in childhood or adolescence. An autoimmune disease of endocrine system and is_a diabetes mellitus that results from autoimmune destruction of insulin-producing beta cells of the pancreas. Diabetes mellitus characterized by insulin deficiency, sudden onset, severe hyperglycemia, rapid progression to ketoacidosis, and death unless treated with insulin. The disease may occur at any age, but is most common in childhood or adolescence. type II diabetes mellitus A subclass of DIABETES MELLITUS that is not INSULIN-responsive or dependent (NIDDM). It is characterized initially by INSULIN RESISTANCE and HYPERINSULINEMIA; and eventually by GLUCOSE INTOLERANCE; HYPERGLYCEMIA; and overt diabetes. Type II diabetes mellitus is no longer considered a disease exclusively found in adults. Patients seldom develop KETOSIS but often exhibit OBESITY. A type of diabetes mellitus that is characterized by insulin resistance or desensitization and increased blood glucose levels. This is a chronic disease that can develop gradually over the life of a patient and can be linked to both environmental factors and heredity. lymphoid neoplasm Malignant lymphoma composed of large B lymphoid cells whose nuclear size can exceed normal macrophage nuclei, or more than twice the size of a normal lymphocyte. The pattern is predominantly diffuse. Most of these lymphomas represent the malignant counterpart of B-lymphocytes at midstage in the process of differentiation. data analyst investigator submitter ethnic group A group of people with a common cultural heritage that sets them apart from others in a variety of social relationships. (MSH); A social group characterized by a distinctive social and cultural tradition maintained from generation to generation, a common history and origin and a sense of identification with the group; members of the group have distinctive features in their way of life, shared experiences and often a common genetic heritage; these features may be reflected in their experience of health and disease. (NCI); Ethnicity - an arbitrary classification of the social group a person belongs to, and either identifies with or is identified with by others, as a result of a complex of cultural, biological, geographical and other factors such as linguistic, dietary and religion traditions; ancestry, background, allegiance, or association; and physical characteristics traditionally associated with race. Increasingly the concept is used synonymously with race but this use trend has a pragmatic basis rather than scientific. (NCI); The concept of ethnic origin is an attempt to classify people, not according to their current ethnicity, but according to where their ancestors came from. Ethnic origin has become a popular classification in statistics, where the concept of race has been largely discarded. (from Wikipedia) (NCI); a group of people with a common cultural heritage that sets them apart from others in a variety of social relationships. (CSP) An ethnic group is a population whose members have a common heritage that is real or presumed such as common culture, language, religion, behaviour or biological trait. myeloid neoplasm INS-1 Pancreatic beta -cell line of rat origin. mouse prenatal NOD mouse Theiler stage 11 Theiler stage 17 Theiler stage 21 Theiler stage 22 Theiler stage 24 Theiler stage 26 Theiler stage 28 Theiler stage 28 is a mouse postnatal stage characterised by postnatal development after a mouse is newly born. fasting Abstaining from food. MIN6 The murine MIN6 cell line derived from in vivo immortalized insulin-secreting pancreatic beta cells. International Unit pancreatic cell mouse postnatal Theiler stage 27 Theiler stage 27 is a newborn mouse. Theiler stage 1 Theiler stage 2 Theiler stage 3 Theiler stage 4 Theiler stage 5 Theiler stage 6 Theiler stage 7 Theiler stage 8 Theiler stage 9 Theiler stage 10 Theiler stage 12 Theiler stage 13 Theiler stage 14 Theiler stage 15 Theiler stage 16 Theiler stage 18 Theiler stage 19 Theiler stage 20 Theiler stage 23 Theiler stage 25 Feature Extraction Software Obsolete Class embryonic day 15.5 15.5 days after fertilization Person: Chris Stoeckert, Jie Zheng embryonic day 16.5 16.5 days after fertilization Person: Chris Stoeckert, Jie Zheng embryonic day 8.5 Person: Chris Stoeckert, Jie Zheng 8.5 days after fertilization embryonic day 17.5 Person: Chris Stoeckert, Jie Zheng 17.5 days after fertilization embryonic day 8.25 8.25 days after fertilization Person: Chris Stoeckert, Jie Zheng embryonic day 18.5 Person: Chris Stoeckert, Jie Zheng 18.5 days after fertilization embryonic day 8 8 days after fertilization Person: Chris Stoeckert, Jie Zheng embryonic day 18 18 days after fertilization Person: Chris Stoeckert, Jie Zheng embryonic day 11.5 Person: Chris Stoeckert, Jie Zheng 11.5 days after fertilization postnatal day 0 Person: Jie Zheng 0 day after birth embryonic day 12.5 12.5 days after fertilization Person: Chris Stoeckert, Jie Zheng postnatal day 4 4 days after birth Person: Jie Zheng embryonic day 9.5 Person: Chris Stoeckert, Jie Zheng 9.5 days after fertilization postnatal day 12 12 days after birth Person: Jie Zheng embryonic day 10.5 Person: Chris Stoeckert, Jie Zheng 10.5 days after fertilization postnatal day 60 Person: Jie Zheng 60 days after birth embryonic day 13.5 Person: Chris Stoeckert, Jie Zheng 13.5 days after fertilization embryonic day 14.5 Person: Chris Stoeckert, Jie Zheng 14.5 days after fertilization postnatal day 1 Person: Jie Zheng 1 day after birth postnatal day 8 Person: Jie Zheng 8 days after birth embryonic day 11.25 11.25 days after fertilization Person: Chris Stoeckert, Jie Zheng age 4 weeks Person: Jie Zheng 4 weeks after birth age 8 weeks Person: Jie Zheng age 8 weeks age 10 weeks age 10 weeks Person: Jie Zheng adult Person: Jie Zheng age of an organism that fully grown or developed. example to be eventually removed example to be eventually removed failed exploratory term Person:Alan Ruttenberg The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job failed exploratory term 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 PERSON:Alan Ruttenberg organizational term term created to ease viewing/sort terms for development purpose, and will not be included in a release 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 placeholder removed placeholder removed terms merged An editor note should explain what were the merged terms and the reason for the merge. terms merged term imported This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. term imported term split This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. term split to be replaced with external ontology term Alan Ruttenberg Terms with this status should eventually replaced with a term from another ontology. 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 Helicos Helicos Philippe Rocca-Serra Roche Philippe Rocca-Serra Roche Illumina Illumina Philippe Rocca-Serra Li-Cor Li-Cor Philippe Rocca-Serra Applied Biosystems Applied Biosystems Philippe Rocca-Serra axiom holds for all times ## 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 relation has no temporal argument ## Elucidation This is used when the first-order logic form of the relation is binary, and takes no temporal argument. ## Example: Class: limb SubClassOf: develops_from some lateral-plate-mesoderm forall t, t2: forall x : instance_of(x,Limb,t) implies exists y : instance_of(y,LPM,t2) develops_from(x,y) To say that each spatiotemporal region s temporally_projects_onto some temporal region t is to say that t is the temporal extension of s. (axiom label in BFO2 Reference: [080-003]) To say that spatiotemporal region s spatially_projects_onto spatial region r at t is to say that r is the spatial extent of s at t. (axiom label in BFO2 Reference: [081-003]) To say that spatiotemporal region s spatially_projects_onto spatial region r at t is to say that r is the spatial extent of s at t. (axiom label in BFO2 Reference: [081-003]) To say that each spatiotemporal region s temporally_projects_onto some temporal region t is to say that t is the temporal extension of s. (axiom label in BFO2 Reference: [080-003]) Person:Alan Ruttenberg