None Cohort Ontology 2026-05-19 editor preferred term The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> editor preferred term example of usage A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> example of usage in branch An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet. GROUP:OBI OBI_0000277 in branch has curation status PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot has curation status definition The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition definition editor note An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. PERSON:Daniel Schober GROUP:OBI:<http://purl.obofoundry.org/obo/obi> editor note term editor Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> term editor alternative label A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like. OBO Operations committee PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related). alternative label 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 PERSON:Daniel Schober Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition source has obsolescence reason Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. PERSON:Alan Ruttenberg PERSON:Melanie Courtot has obsolescence reason curator note An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg curator note term tracker item the URL for an ontology term tracker issue, such as https://github.com/monarch-initiative/mondo/issues/7588 A URL for a request or discussion of an ontology term. Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg The 'tracker item' can associate a tracker with a specific ontology term. term tracker item ontology term requester The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg The 'term requester' can credit the person, organization or project who request the ontology term. ontology term requester is denotator type Relates an class defined in an ontology, to the type of it's denotator In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type') Alan Ruttenberg is denotator type imported from For external terms/classes, the ontology from which the term was imported PERSON:Alan Ruttenberg PERSON:Melanie Courtot GROUP:OBI:<http://purl.obolibrary.org/obo/obi> imported from expand expression to ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones Chris Mungall expand expression to expand assertion to ObjectProperty: RO??? Label: spatially disjoint from Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom. Chris Mungall expand assertion to first order logic expression PERSON:Alan Ruttenberg first order logic expression antisymmetric property part_of antisymmetric property xsd:true Use boolean value xsd:true to indicate that the property is an antisymmetric property Alan Ruttenberg antisymmetric property OBO foundry unique label An alternative name for a class or property which is unique across the OBO Foundry. The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . PERSON:Alan Ruttenberg PERSON:Bjoern Peters PERSON:Chris Mungall PERSON:Melanie Courtot GROUP:OBO Foundry <http://obofoundry.org/> OBO foundry unique label has ID digit count Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits) Person:Alan Ruttenberg has ID digit count has ID range allocated Datatype: idrange:1 Annotations: 'has ID range allocated to': "Chris Mungall" EquivalentTo: xsd:integer[> 2151 , <= 2300] Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms Person:Alan Ruttenberg has ID range allocated to has ID policy for Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" Relating an ontology used to record id policy to the ontology namespace whose policy it manages Person:Alan Ruttenberg has ID policy for has ID prefix Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created. Person:Alan Ruttenberg has ID prefix elucidation person:Alan Ruttenberg Person:Barry Smith Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms elucidation has associated axiom(nl) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom associated with a term expressed using natural language has associated axiom(nl) has associated axiom(fol) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom expressed in first order logic using CLIF syntax has associated axiom(fol) is allocated id range Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999" PERSON:Alan Ruttenberg Add as annotation triples in the granting ontology is allocated id range has ontology root term Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root. Nicolas Matentzoglu has ontology root term may be identical to A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged. David Osumi-Sutherland #40 VFB Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance. may be identical to scheduled for obsoletion on or after Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date. Chris Mungall, Jie Zheng https://github.com/geneontology/go-ontology/issues/15532 https://github.com/information-artifact-ontology/ontology-metadata/issues/32 GO ontology scheduled for obsoletion on or after has axiom id Person:Alan Ruttenberg Person:Alan Ruttenberg A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI has axiom label term replaced by Use on obsolete terms, relating the term to another term that can be used as a substitute Person:Alan Ruttenberg Person:Alan Ruttenberg Add as annotation triples in the granting ontology term replaced by This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL. OBO Operations call logical characteristic of object property 'part disjoint with' 'defined by construct' """ PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX : <http://example.org/ CONSTRUCT { [ a owl:Restriction ; owl:onProperty :part_of ; owl:someValuesFrom ?a ; owl:disjointWith [ a owl:Restriction ; owl:onProperty :part_of ; owl:someValuesFrom ?b ] ] } WHERE { ?a :part_disjoint_with ?b . } Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation. defined by construct The property is intended to be used exclusively on synonym assertions, to express that the synonym in question is the preference of a specific community. For example, one community may prefer to say call a disease "A" and another one "B" (but they are the same thing). A provenance property that denotes a synonym to be the preferred one for a specific community. 2025-06-02 preferred label for community CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation) A synonym type for describing abbreviations or initialisms 2023-03-03 abbreviation A synonym type for describing ambiguous synonyms 2023-03-03 ambiguous synonym A synonym type for describing dubious synonyms 2023-03-03 dubious synonym EFO:0006346 (severe cutaneous adverse reaction) has an exact synonym (scar), which is of the type OMO:0003003 (layperson synonym) A synonym type for describing layperson or colloquial synonyms 2023-03-03 layperson synonym CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form) A synonym type for describing pluralization synonyms 2023-03-03 plural form CHEBI:16189 (sulfate) has an exact synonym (sulphate), which is of the type OMO:0003005 (UK spelling synonym) A synonym type for describing UK spelling variants 2023-03-03 UK spelling synonym A synonym type for common misspellings 2023-03-03 misspelling A synonym type for misnomers, i.e., a synonym that is not technically correct but is commonly used anyway 2023-03-03 misnomer MAPT, the gene that encodes the Tau protein, has a previous name DDPAC. Note: in this case, the name type is more specifically the gene symbol. A synonym type for names that have been used as primary labels in the past. 2023-07-25 previous name The legal name for Harvard University (https://ror.org/03vek6s52) is President and Fellows of Harvard College A synonym type for the legal entity name 2023-07-27 legal name CHEBI:46195 has been assigned the english International Nonproproprietary Name (INN) "paracetamol". In some cases such as this one, the INN might be the same as the ontology's primary label The International Nonproprietary Name (INN) is a standardize name for a pharmaceutical drug or active ingredient issued by the World Health Organization (WHO) meant to address the issues with country- or language-specific brand names. These are issued in several languages, including English, Latin, French, Russian, Spanish, Arabic, and Chinese. 2023-09-30 INN International Nonproprietary Name nasopharynx (UBERON:0001728) has the latin name "pars nasalis pharyngis A synonym type for describing Latin term synonyms. 2023-10-12 latin term NASA is an word acronym for the US National Aeronautics and Space Administration because the acronym is pronounced. FBI is an initialism (also known as alphabetism) for the US Federal Bureau of Investigation since the letters are pronounced one at a time. JPEG is an acronym for Joint Photographic Experts Group but does not count as a word acronym nor an initialism since it is mixed how it is pronounced. A synonym type for describing abbreviations that are a part of the full name's words, such as initialisms or alphabetisms. 2023-11-01 acronym The Developing Mouse Brain Atlas Ontology (DBMA) ontology uses part-of in its hierarchy, so this would correspond to the following turtle: `<https://purl.brain-bican.org/ontology/dmbao/dmbao.owl> a owl:Ontology; OMO:0003014 rdfs:subClassOf, BFO:0000050`. Relates an ontology to predicates/properties that should be used by user interfaces to render the hierarchical structure of the ontology. Typically, this is rdfs:subClassOf, but in ontologies that are partonomies, this might also include BFO:0000050 (part of). Tools like OLS can use predicates annotated with this property for rendering the ontology class hierarchy. There can be more than one hierarchical property. In the absence of any, it should be assumed that it is rdfs:subClassOf. 2025-09-17 has ontology hierarchical property A serial number such as "12324X"; a stop sign; a written proper name such as "OBI An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. 2024-03-25 has symbol EGA_subset GWAS_subset MetaboLight_subset PRIDE_subset subset property subset_property An alternative label for a class or property which has a more general meaning than the preferred name/primary label. https://github.com/information-artifact-ontology/ontology-metadata/issues/18 has broad synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/18 disease characteristic (MONDO:0021125) has cross-reference (http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NCIT:C41009"^^xsd:string An annotation property that links an ontology entity or a statement to a prefixed identifier or URI. 2024-03-18 database_cross_reference has cross-reference xRef An alternative label for a class or property which has the exact same meaning than the preferred name/primary label. https://github.com/information-artifact-ontology/ontology-metadata/issues/20 has exact synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/20 An alternative label for a class or property which has a more specific meaning than the preferred name/primary label. https://github.com/information-artifact-ontology/ontology-metadata/issues/19 has narrow synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/19 An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct. https://github.com/information-artifact-ontology/ontology-metadata/issues/21 has related synonym has_related_synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/21 in subset in_subset a core relation that holds between a part and its whole part of a core relation that holds between a whole and its part has part x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. preceded by x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. precedes a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. characteristic of Inverse of characteristic_of has characteristic a relation between a continuant and a process, in which the continuant is somehow involved in the process participates in a relation between a process and a continuant, in which the continuant is somehow involved in the process has participant 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 a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence quality of a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence role of 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 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 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 a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence has disposition inverse of has disposition disposition of a relation between two independent continuants, the location and the target, in which the target is entirely within the location location of a relation between two independent continuants, the target and the location, in which the target is entirely within the location located in A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. has regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. has negative regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. has positive regulatory component activity has component activity w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. has component process directly regulated by Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. directly negatively regulated by Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. directly positively regulated by Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. has effector activity A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. ends after immediately preceded by immediately precedes x overlaps y if and only if there exists some z such that x has part z and z part of y overlaps w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. has component p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. regulates p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. negatively regulates p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. positively regulates 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. capable of c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. capable of part of temporally related to p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. has input c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. acts upstream of c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. affects acts upstream of or within p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. causally upstream of, positive effect p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. causally upstream of, negative effect q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. characteristic of part of A mereological relationship or a topological relationship mereotopologically related to c enables p iff c is capable of p and c acts to execute p. enables A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. functionally related to this relation holds between c and p when c is part of some c', and c' is capable of p. part of structure that is capable of c involved_in p if and only if c enables some process p', and p' is part of p involved in inverse of enables enabled by inverse of regulates regulated by inverse of negatively regulates negatively regulated by inverse of positively regulates positively regulated by inverse of has input input of x spatially_coextensive_with y if and inly if x and y have the same location spatially coextensive with inverse of upstream of causally downstream of immediately causally downstream of p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. indirectly positively regulates p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. indirectly negatively regulates relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. causally related to relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. https://en.wikipedia.org/wiki/Causality p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. causally upstream of p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. immediately causally upstream of p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. affects causally upstream of or within inverse of causally upstream of or within causally downstream of or within c involved in regulation of p if c is involved in some p' and p' regulates some p involved in regulation of c involved in regulation of p if c is involved in some p' and p' positively regulates some p involved in positive regulation of c involved in regulation of p if c is involved in some p' and p' negatively regulates some p involved in negative regulation of c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p involved in or involved in regulation of A relationship that holds between two entities in which the processes executed by the two entities are causally connected. interacts with An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. molecularly interacts with phosphorylates The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. directly regulates activity of The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. directly negatively regulates activity of The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. directly positively regulates activity of helper property (not for use in curation) is kinase activity A relationship between a material entity and a process where the material entity has some causal role that influences the process causal agent in process p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. causal relation between processes depends on causal relation between entities causally influenced by interaction relation helper property molecular interaction relation helper property The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). causally influences p directly regulates q iff p is immediately causally upstream of q and p regulates q. directly regulates s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p has part structure that is capable of A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. causal relation between material entity and a process Holds between c and p if and only if c is capable of some activity a, and a regulates p. capable of regulating Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. capable of negatively regulating Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. capable of positively regulating Inverse of 'causal agent in process' process has causal agent p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. directly positively regulates p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. directly negatively regulates Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. enables subfunction acts upstream of or within, positive effect acts upstream of or within, negative effect c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive acts upstream of, positive effect c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative acts upstream of, negative effect causally upstream of or within, negative effect causally upstream of or within, positive effect The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. regulates activity of p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. indirectly causally upstream of p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. indirectly regulates X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y. device utilizes material A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C. regulates characteristic A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C. positively regulates characteristic A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C. negatively regulates characteristic hasCohort hasSubCohort has_data_collection_location isSubCohortOf GAZ:00000457 Africa GAZ:00000465 Asia GAZ:00000463 Australia GAZ:00002942 Austria GAZ:00003750 Bangladesh GAZ:00002938 Belgium GAZ:00002828 Brazil GAZ:00000905 Burkina Faso GAZ:00002560 Canada GAZ:00000588 Central Africa GAZ:00002891 Central America GAZ:00002845 China GAZ:00002901 Costa Rica GAZ:00002719 Croatia GAZ:00002635 Denmark GAZ:00000556 Eastern Africa GAZ:00002471 Eastern Asia GAZ:00002959 Estonia GAZ:00000567 Ethiopia GAZ:00000464 Europe GAZ:00002937 Finland GAZ:00002940 France GAZ:00002646 Germany GAZ:00000908 Ghana GAZ:00002945 Greece GAZ:00000843 Iceland GAZ:00002839 India GAZ:00002650 Italy GAZ:00002747 Japan GAZ:00001101 Kenya GAZ:00000459 Latin America and the Caribbean GAZ:00005860 Melanesia GAZ:00002852 Mexico GAZ:00005862 Micronesia GAZ:00001549 Netherlands GAZ:00000555 Northern Africa GAZ:00000458 Northern America GAZ:00002699 Norway GAZ:00000468 Oceania GAZ:00005246 Pakistan GAZ:00002932 Peru GAZ:00002939 Poland GAZ:00005861 Polynesia GAZ:00003923 Singapore GAZ:00000559 South-Eastern Asia GAZ:00000459 South America GAZ:00000553 South Africa GAZ:00002472 South Asia GAZ:00000553 Southern Africa GAZ:00000591 Spain GAZ:00002729 Sweden GAZ:00005341 Taiwan GAZ:00002637 United Kingdom GAZ:00002459 United States GAZ:00000554 Western Africa 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. continuant An entity that has temporal parts and that happens, unfolds or develops through time. occurrent 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]) independent continuant spatial region 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]) process disposition 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. realizable entity quality b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) specifically dependent continuant 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. role function An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. material entity immaterial entity A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. gene product or complex activity molecular_function A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. GOC:pdt A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. Wikipedia:Biological_process single organism process single-organism process biological process biological_process A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. GOC:pdt true Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. Reactome:R-HSA-6788855 Reactome:R-HSA-6788867 kinase activity Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. ISBN:0198506732 Reactome:R-HSA-6788855 FN3KRP phosphorylates PsiAm, RibAm Reactome:R-HSA-6788867 FN3K phosphorylates ketosamines data entity data entity information content entity information content entity curation status specification The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) PERSON:Bill Bug GROUP:OBI:<http://purl.obolibrary.org/obo/obi> OBI_0000266 curation status specification data about an ontology part Data about an ontology part is a data item about a part of an ontology, for example a term Person:Alan Ruttenberg data about an ontology part obsolescence reason specification The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. PERSON: Alan Ruttenberg PERSON: Melanie Courtot obsolescence reason specification denotator type The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. A denotator type indicates how a term should be interpreted from an ontological perspective. Alan Ruttenberg Barry Smith, Werner Ceusters denotator type ontology module I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it. ontology file This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology. ontology module base ontology module An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies. base ontology module editors ontology module An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users. source ontology module editors ontology module main release ontology module An ontology module that is intended to be the primary release product and the one consumed by the majority of tools. TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module main release ontology module bridge ontology module An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module. bridge ontology module import ontology module A subset ontology module that is intended to be imported from another ontology. TODO: add axioms that indicate this is the output of a module extraction process. import file import ontology module subset ontology module An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms. ontology slim subset ontology subset ontology module curation subset ontology module A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation. curation subset ontology module analysis ontology module An ontology module that is intended for usage in analysis or discovery applications. analysis subset ontology module single layer ontology module A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint. ribbon subset single layer subset ontology module exclusion subset ontology module A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes. antislim exclusion subset ontology module external import ontology module An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach. external import external import ontology module species subset ontology module A subset ontology that is crafted to either include or exclude a taxonomic grouping of species. taxon subset species subset ontology module reasoned ontology module An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available. reasoned ontology module generated ontology module An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV. TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process generated ontology module template generated ontology module An ontology module that is automatically generated from a template specification and fillers for slots in that template. template generated ontology module taxonomic bridge ontology module taxonomic bridge ontology module ontology module subsetted by expressivity ontology module subsetted by expressivity obo basic subset ontology module A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools. Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses). An ontology is OBO Basic if and only if it has the following characteristics: DAG Unidirectional No Dangling Clauses Fully Asserted Fully Labeled No equivalence axioms Singly labeled edges No qualifier lists No disjointness axioms No owl-axioms header No imports obo basic subset ontology module ontology module subsetted by OWL profile ontology module subsetted by OWL profile EL++ ontology module EL++ ontology module Geographic Area Conceptual Entity Country A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities quality A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities PATOC:GVG A group of individuals grouped together based on a shared characteristic or property of interest. EFO:0004445 NCIT:C61512 cohort 2 A study, project or consortium that compares multiple cohorts. cohort aggregation 1000G 1000 Genomes 1000G ANM AddNeuroMed AddNeuroMed Cohort ANM AddNeuroMed APC APC Trail Adenoma Prevention with Celecoxib Adenoma Prevention with Celecoxib trail APC APC Trail Adenoma Prevention with Celecoxib ASAP Advanced Study of Aortic Pathology ASAP AWI-Gen Africa Wits-INDEPTH partnership for Genomics studies AWI-Gen arcOGEN Arthritis Research UK Osteoarthritis Genetics arcOGEN ACP Asian Cancer Project ACP AAA Aspirin for Asymptomatic Atherosclerosis Study AAA AEGS1 AtheroExpress AEGS1 ARIC Atherosclerosis Risk in Communities Study ARIC ADRN Atopic Dermatitis Research Network ADRN ACS Australia Cancer Study ACS AOCS Australian Ovarian Cancer Study AOCS ATR Australian Twin Registry ATR ALSPAC AMC-PAS Avon Longitudinal Study of Parents and Children ALSPAC AMC-PAS BFM Berlin_Frankfurt_Munster trials BFM BCPP Bladder Cancer Prognosis Programme BCPP Brazil Brazilian Cohort Brazil BCAC Breast Cancer Association Consortium BCAC BRUNECK Bruneck study BRUNECK CALGB Cancer and Leukemia Group B CALGB TCGA Cancer Genome Atlas TCGA CPS Cancer Prevention Study CPS CAPS Cancer Prostate in Sweden CAPS CHARM Candesartan in Heart failure Assessment of Reduction in Mortality and morbidit CHARM CAGE Cardio-metabolic Genome Epidemiology Study CAGE CARDIOGENICS Cardiogenics Study CARDIOGENICS CARDIoGRAMplusC4D CHANCE Carolina Head and Neck Cancer Epidemiology CHANCE CARTaGENE CARTaGENE cohort (CHU Sainte-Justine, Quebec, Canada) CARTaGENE CART Center for Autism Research and Treatment CART CADD Center on Antisocial Drug Dependence CADD CEPH Centre dEtude du Polymorphisme Humain CEPH CNG Centre National de G_notypage CNG CAG Chicago Asthma Genetics CAG BAMSE Children, Allergy, Milieu, Stockholm, Epidemiology BAMSE CAP Cholesterol and Atherosclerosis Pharmacogenetics CAP Cilento Cilento study Cilento COIN COIN-B CORSA Colorectal Cancer Study of Austria CORSA CLEAR Consortium for the Longitudinal Evaluation of African Americans with Early Rheumatoid Arthritis CLEAR COMPASS Consortium of Minority Population Genome-Wide Association Studies of Stroke COMPASS KORA Cooperative Health Research in the Region of Augsburg KORA CHB Copenhagen BB Copenhagen Hospital Biobank CHB Copenhagen BB CROATIA-KORCULA CROATIA-Korcula Study CROATIA-KORCULA DGC Danish Glostrup Cohort DGC DGP Diabetes Genetics in Pakistan DGP DMS Diabetes in Mexico Study DMS DPP Diabetes Prevention Program DPP DREAM Diabetes Reduction Assessment with Ramipril and Rosiglitazone Medication DREAM DIRECT Diabetes Research on Patient Stratification DIRECT DHS Dortmund Health Study DHS DCC Duke Cognition Cohort DCC DUNDEE DDS Durban Diabetes Study DDS NELSON Dutch and Belgian Lung Cancer Screening Trial NELSON DMP Dutch Microbiome Project DMP ESS Edinburgh Stroke Study ESS ENGAGE ENGAGE_AF-TIMI_48 ENGAGE AF-TIMI 48 ENGAGE ENGAGE_AF-TIMI_48 EPIGEN ERF Erasmus Rucphen Family Study ERF EB Estonian Biobank EB EPIC European Prospective Investigation into Cancer EPIC EPIC-Norfolk European Prospective Investigation of Cancer-Norfolk EPIC-Norfolk EuroTARGET EuroTARGET project EuroTARGET ELGAN Extremely Low Gestational Age Newborns ELGAN FAS Fatty Acid Sensor Study FAS FTC Finnish Twin Cohort Study FTC FINRISK FGFP Flemish Gut Flora Project FGFP GAS Gabriel Advanced Survey GAS GCAT GCAT. Genomes For Life. GCAT GENESIS GAMS Genetic Analysis of Multiple Sclerosis GAMS GCAN Genetic Consortium for Anorexia Nervosa GCAN CRA Genetic Epidemiology of Asthma in Costa Rica CRA GOMAP Genetic Overlap between Metabolic and Psychiatric traits GOMAP PROFILE Genetic Prostate cancer risk stratification for targeted screening PROFILE GRIso Genetic Research in Isolated GRIso GoDARTS Genetics of diabetes Audit and Research GoDARTS GEHA Genetics of Healthy Aging GEHA GenomeAsia100K GenomeAsia 100K project GenomeAsia100K GMMG German Multiple Myeloma Study Group GMMG GPS Ghana Prostate Study GPS GIST Glaucoma Inheritance Study in Tasmania GIST HELIC Greece Hellenic Isolated Cohorts HELIC HRS Health and Retirement Study HRS Health2000 Health2000 Study Health2000 HPS Heart Protection Study HPS DCS Hoorn Diabetes Care System DCS HDR Hospital Discharge Register Sweden HDR HGI Human Genetics Initiative HGI HCS Hunter Community Study HCS ICR Icelandic Cancer Registry ICR IMPACT Identification of Men with a genetic predisposition to ProstAte Cancer IMPACT IIBDGC IIBDGC genotyped CD study IIBDGC ISS Indiana Sisters Study ISS INMA INfancia y Medio Ambiente Project INMA ICGC International Cancer Genome Consortium-Chronic Lymphocytic Leukemia ICGC IHGC International Headache Genetics Consortium IHGC IMSGC International Multiple Sclerosis Genetics Consortium IMSGC ISC International Schizophrenia Consortium ISC INGI Italian Network on Genetic Isolates Studies INGI LMC Leeds Melanoma Cohort LMC LLS Leiden Longevity Study LLS LifeLines Living-Biobank Living Biobank Living-Biobank CARE Los Angeles component of The Womens Contraceptive and Reproductive Experiences Study CARE LBC Lothian Birth Cohort LBC LSR Lund Stroke Register LSR MARTHA Marseille Thrombosis Association Marseille Thrombosis Association Study MARTHA Marseille Thrombosis Association MXBB Mexican Biobank MXBB MIRAGE MGS Molecular Genetics of Schizophrenia Collaboration MGS MORGAM MOnica Risk, Genetics, Archiving and Monograph MORGAM MONICA Monitoring of Trends and Determinants in Cardiovascular Disease MONICA MESA Multi-Ethnic Study of Atherosclerosis MESA MFS Multicenter Family Study MFS MEC Multiethnic Cohort Study of Diet and Health MEC MEGA Multiple Environmental and Genetic Assessment of Risk Factors for Venous Thrombosis MEGA NHSBT National Health Service Blood and Transplant NHSBT NSCCG National Study of Colorectal Cancer Genetics NSCCG NTR Netherlands Twin Registry NTR NECC New England-based Case-Control Study of Ovarian Cancer NECC NIDDK NBS Nijmegen Biomedical Study NBS NICOLA Northern Ireland Cohort for Longitudinal Study of Ageing NICOLA NSPHS Northern Sweden Population Health Study NSPHS MOBA MoBa Norwegian Mother and Child Cohort study MOBA MoBa ORCADES Orkney Complex Disease Study ORCADES ORIGIN Outcome Reduction With Initial Glargine Intervention Outcome Reduction With Initial Glargine Intervention Trial ORIGIN Outcome Reduction With Initial Glargine Intervention OCAC Ovarian Cancer Association Consortium OCAC OCS Ovarian Cancer Study OCS OBB Oxford Biobank OBB PCL PanCareLIFE PCL PEG Parkinson Environment and Gene PEG PoBI People of the British Isles PoBI PANIC Physical Activity and Nutrition in Children Study PANIC PopCol Population-based Colonoscopy study PopCol PROCARDIS Precocious Coronary Artery Disease Study PROCARDIS PAMELA Pressioni Arteriose Monitorate E Loro Associazionie PAMELA PIVUS Prospective Investigation of the Vasculature in Uppsala Seniors PIVUS PAGE Psoriasis Association Genetics Extension PAGE PGC Psychiatric GWAS Consortium PGC Radar Research on Adolescent Development and Relationships Radar RS Rotterdam Study RS SLSJ Saguenay-Lac-Saint-Jean asthma study SLSJ SAHLSIS Sahlgrenska Academy Study on Ischemic Stroke SAHLSIS SardiNIA SardiNIA Study of Aging SardiNIA SDR Scania Diabetes Registry SDR Shanghai Shanghai Study Shanghai SCOT Short Course Oncology Treatment trial SCOT SSC Simons Simplex Collection SSC SCH Singapore Chinese Study SCH SORCE Spit Spit for Science Spit SWEBIC Sweden Bipolar Disorder Cohort SWEBIC STR Swedish Twin Registry STR TDS Taiwan Type 2 Diabetes Study TDS TEENAGE TEENs of Attica: Genes and Environment TEENAGE ELSA The English Longitudinal Study of Ageing ELSA Fenland The Fenland Study Fenland HGF The Helmholtz-Gemeinschaft Deutscher Forschungszentren HGF MANOLIS The MANOLIS cohort MANOLIS Netherlands The Netherlands AAA GWAS dataset Netherlands NBM The Norwegian Biobank for Myeloma NBM PROMIS The Pakistan Risk Of Myocardial Infarction Study PROMIS SMART The Secondary Manifestations of ARTerial disease study SMART HSIEA THISEAS The Hellenic study of Interactions between SNPs & Eating in Atherosclerosis The Hellenic study of Interactions between Single nucleotide polymorphisms and Eating in Atherosclerosis Susceptibility HSIEA THISEAS The Hellenic study of Interactions between SNPs & Eating in Atherosclerosis TNT Treating to New Targets TNT TEDS Twins Early Development Study TEDS T1DGC Type 1 Diabetes Genetics Consortium T1DGC TwinsUK UK Adult Twin Register TwinsUK UKB UK Biobank UKB UKBEC UK Brain Expression Consortium UKBEC UKCCS UK Childhood Cancer Study UKCCS UKHLS UK Household Longitudinal Study UKHLS UKIBD Genetics Consortium UKIBDGC UK Inflammatory Bowel Disease Genetics Consortium UKIBD Genetics Consortium UKIBDGC VIKING Viking Health Study VIKING WTCCC Wellcome Trust Case Control Consortium WTCCC BCC Basquecolon cohort BCC INTERVAL study CONVERGE GENIE Gene-Environmental Interaction and phenotype study GENIE CAS China Atherosclerosis Study CAS DIPP Diabetes Prediction and Prevention DIPP FGENTCARD Functional genomic diagnostic tools for coronary artery disease FGENTCARD GCKD German Chronic Kidney Disease Study GCKD GLS German Longevity Study GLS GRACE_Genetics Global Registry of Acute Coronary Events GRACE_Genetics TwinGene TwinGene Study TwinGene ULSAM Uppsala Longitudinal Study of Adult Men ULSAM BLSA Baltimore Longitudinal Study of Ageing BLSA MNDA Motor Neuron Disease Biobank study MNDA DC Diabetic Cohort DC Ely Ely Study Ely GASP Genetic Asthma Susceptibility to Indoor Pollution in Peru GASP PPMI Parkinson's Progression Markers Initiative PPMI PEC Psychosis Endophenotype Consortium PEC SHIP Study of Health in Pomerania SHIP CHRIS The Cooperative Health Research in South Tyrol CHRIS HEALS The Health Effects of Arsenic Longitudinal Study HEALS TwinGene Registry temporary unclassified WWF:AA1310 https://www.worldwildlife.org/ecoregions/aa1310 Western Australian Mulga Shrublands Ecoregion https://www.worldwildlife.org/biomes/deserts-and-xeric-shrublands Australasia Ecoregion WWF:AA1309 https://www.worldwildlife.org/ecoregions/aa1309 Tirari-Sturt Stony Desert Ecoregion WWF:AA1308 https://www.worldwildlife.org/ecoregions/aa1308 Simpson Desert Region WWF:AA1307 https://www.worldwildlife.org/ecoregions/aa1307 Pilbara Shrublands Ecoregion WWF:AA1301 https://www.worldwildlife.org/ecoregions/aa1301 Carnarvon Xeric Shrublands Ecoregion WWF:AA1302 https://www.worldwildlife.org/ecoregions/aa1302 Central Ranges Xeric Shrub Ecoregion WWF:AA1303 https://www.worldwildlife.org/ecoregions/aa1303 Gibson Desert Ecoregion WWF:AA1304 https://www.worldwildlife.org/ecoregions/aa1304 The Great Sandy-Tanami Desert Ecoregion WWF:AA1305 https://www.worldwildlife.org/ecoregions/aa1305 Great Victoria Desert Ecoregion WWF:AA1306 https://www.worldwildlife.org/ecoregions/aa1306 Nullarbor Plains Xeric Shrubland Ecoregion https://www.worldwildlife.org/biomes/deserts-and-xeric-shrublands Afrotropical Ecoregion WWF:AT1322 https://www.worldwildlife.org/ecoregions/at1322 Succulent Karoo Ecoregion WWF:AT1321 https://www.worldwildlife.org/ecoregions/at1321 Yemen and Saudi Arabia Ecoregion WWF:AT1320 https://www.worldwildlife.org/ecoregions/at1320 Yemen, Saudi Arabia, and Oman Ecoregion WWF:AT1319 https://www.worldwildlife.org/ecoregions/at1319 Somali Montane Xeric Woodland Ecoregion WWF:AT1318 https://www.worldwildlife.org/ecoregions/at1318 Socotran Archipelago Ecoregion WWF:AT1317 https://www.worldwildlife.org/ecoregions/at1317 Red Sea Coastal Desert Ecoregion WWF:AT1316 https://www.worldwildlife.org/ecoregions/at1316 Namibian Savanna Woodland Ecoregion WWF:AT1315 https://www.worldwildlife.org/ecoregions/at1315 Namib Desert Ecoregion WWF:AT1314 https://www.worldwildlife.org/ecoregions/at1314 Nama Karoo Ecoregion WWF:AT1313 https://www.worldwildlife.org/ecoregions/at1313 Masai Xeric Grasslands and Shrublands Ecoregion WWF:AT1312 https://www.worldwildlife.org/ecoregions/at1312 Madagascar Succulent Woodlands Ecoregion WWF:AT1311 https://www.worldwildlife.org/ecoregions/at1311 Madagascar Spiny Thickets Ecoregion WWF:AT1310 https://www.worldwildlife.org/ecoregions/at1310 Kaokoveld Desert Ecoregion WWF:AT1309 https://www.worldwildlife.org/ecoregions/at1309 Kalahari Xeric Savanna Ecoregion WWF:AT1308 https://www.worldwildlife.org/ecoregions/at1308 Ile Europa and Bassas da India Ecoregion WWF:AT1307 https://www.worldwildlife.org/ecoregions/at1307 Hobyo Grassland and Shrubland Ecoregion WWF:AT1306 https://www.worldwildlife.org/ecoregions/at1306 Oman and United Arab Emirates Ecoregion WWF:AT1305 https://www.worldwildlife.org/ecoregions/at1305 Ethiopian Xeric Grasslands and Shrublands Ecoregion WWF:AT1304 https://www.worldwildlife.org/ecoregions/at1304 Eritrean Coastal Desert Ecoregion WWF:AT1303 https://www.worldwildlife.org/ecoregions/at1303 East Saharan Montane Xeric Woodland Ecoregion WWF:AT1302 https://www.worldwildlife.org/ecoregions/at1302 Oman, Yemen, and Saudi Arabia Ecoregion WWF:AT1301 https://www.worldwildlife.org/ecoregions/at1301 Aldabra Island Xeric Scrub Ecoregion Indo-Malay Ecoregion WWF:IM1304 Southern Asia: Western India into Pakistan Thar Desert WWF:IM1303 Southern Asia: Eastern India and western Pakistan Northwestern Thorn Scrub Forests Stellar radiation emitted from Sol. Solar radiation example to be eventually removed example to be eventually removed failed exploratory term The term was initially used in an attempt to structure part of the ontology, but in retrospect failed to do a good job. Terms created as placeholders with the expectation of being permanent should instead be deprecated using the "placeholder removed" (obo:IAO_0000226) justification. Person:Alan Ruttenberg 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 The term was created to ease viewing/sorting terms for development purposes, but will not be included in a release. organizational term ready for release Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." ready for release metadata incomplete Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. metadata incomplete uncurated Nothing done yet beyond assigning a unique class ID and proposing a preferred term. uncurated pending final vetting All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. pending final vetting Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes. PERSON: Alan Ruttenberg PERSON: Melanie Courtot obsolete_core true placeholder removed The term was created to temporarily stand in for a semantic purpose, but is no longer needed, typically due to another permanent term being defined. This reason is appropriate for a temporary term even if no permanent term is defined; for example if the need for the term no longer exists. If a permanent (replacement) term is defined, the deprecated term should reference the replacement with IAO:0100001. If no replacement is defined, it may be appropriate to reference alternative terms with oboInOwl:consider. placeholder removed terms merged The term has been combined with one or more other terms to create a more encompassing (merged) term. The deprecated term should reference the merged term with obo:IAO_0100001. The replacement term should reference the original terms as sources using obo:RO_0001000 (derives_from). An editor note should explain what were the merged terms and the reason for the merge. terms merged term imported The term has been replaced by a term imported from another ontology. This is to be used when the original term has been replaced by a term imported from an other ontology. The deprecated term should reference the imported term with obo:IAO_0100001. term imported term split The term has been split into two or more new terms. 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. The deprecated term should reference the replacement terms with obo:IAO_0100001. term split universal Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. Alan Ruttenberg A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf universal defined class A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. Alan Ruttenberg defined class named class expression A named class expression is a logical expression that is given a name. The name can be used in place of the expression. named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions Alan Ruttenberg named class expression to be replaced with external ontology term Terms with this status should eventually replaced with a term from another ontology. Alan Ruttenberg group:OBI to be replaced with external ontology term requires discussion A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. Alan Ruttenberg group:OBI requires discussion The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not. This obsolesence reason should be used conservatively. Typical valid examples in disease ontologies are: unnecessary class grouping; mistaked creation of a disease associated to a phenotype. https://github.com/information-artifact-ontology/ontology-metadata/issues/77 https://orcid.org/0000-0001-5208-3432 out of scope The term was added to the ontology on the assumption it was a valid domain entity, but it turns out the entity does not exist in reality. This obsolesence reason should be used conservatively. For example: Obsoleting class that describes a breed of cow based on a record in an existing database, that was later retracted as faulty (breed does not exist). Do not use this term to obsolete a historic concept (that was once valid, but not anymore). https://github.com/information-artifact-ontology/ontology-metadata/issues/136 https://orcid.org/0000-0002-4142-7153 domain entity does not exist inferring direct neg reg edge from input to regulatory subfunction inferring direct positive reg edge from input to regulatory subfunction effector input is compound function input Input of effector is input of its parent MF if effector directly negatively regulates X, its parent MF directly negatively regulates X 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).