http://orcid.org/0000-0002-4366-3088 https://orcid.org/0000-0001-8815-0078 David Osumi-Sutherland Jie Zheng Pier Luigi Buttigieg Ramona Walls The Population and Community Ontology (PCO) describes material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include community health care, plant pathology, behavioral studies, sociology, and ecology. Population and Community Ontology http://creativecommons.org/publicdomain/zero/1.0/ The Population and Community Ontology (PCO) is licensed under a Creative Commons zero (CC0) license - http://creativecommons.org/publicdomain/zero/1.0/. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. We ask that anyone using this ontology follow the standards of the scientific ontology community by re-using ontology identifiers whenever possible and properly citing the ontology and its creators. editor preferred label editor preferred label editor preferred term editor preferred term editor preferred term~editor preferred label The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> editor preferred label editor preferred label editor preferred term editor preferred term editor preferred term~editor preferred label example example of usage A phrase describing how a 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 OBI_0000281 has curation status has curation status definition definition textual definition The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition definition textual definition editor note An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. PERSON:Daniel Schober GROUP:OBI:<http://purl.obfoundry.org/obo/obi> GROUP:OBI:<http://purl.obofoundry.org/obo/obi> IAO:0000116 uberon editor_note true editor_note editor note 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 term editor alternative term An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> alternative term definition source Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 PERSON:Daniel Schober Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition source definition source has obsolescence reason Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. PERSON:Alan Ruttenberg PERSON:Melanie Courtot has obsolescence reason curator note An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg curator note term tracker item the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ An IRI or similar locator for a request or discussion of an ontology term. Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg The 'tracker item' can associate a tracker with a specific ontology term. term tracker item 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 If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL is a defining property chain axiom If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R. is a defining property chain axiom where second argument is reflexive an alternative term used for STATO statistical ontology and ISA team Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra STATO alternative term has_alternative_id database_cross_reference has_exact_synonym has_related_synonym in_subset label label is part of my brain is part of my body (continuant parthood, two material entities) my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) this day is part of this year (occurrent parthood) a core relation that holds between a part and its whole Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. part_of part of http://www.obofoundry.org/ro/#OBO_REL:part_of has part my body has part my brain (continuant parthood, two material entities) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has_part has part realized in this disease is realized in this disease course this fragility is realized in this shattering this investigator role is realized in this investigation is realized by realized_in [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realized in realizes this disease course realizes this disease this investigation realizes this investigator role this shattering realizes this fragility to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realizes preceded by x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by http://www.obofoundry.org/ro/#OBO_REL:preceded_by preceded by precedes x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. precedes occurs in b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t occurs_in unfolds in unfolds_in Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant occurs in site of [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant contains process This document is about information artifacts and their representations A (currently) primitive relation that relates an information artifact to an entity. 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. person:Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy is about obsolete has member of true inheres in this fragility inheres in this vase this red color inheres in this apple a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence A dependent inheres in its bearer at all times for which the dependent exists. inheres_in inheres in bearer of this apple is bearer of this red color this vase is bearer of this fragility a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. bearer_of is bearer of bearer of participates in this blood clot participates in this blood coagulation this input material (or this output material) participates in this process this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process participates_in participates in has participant this blood coagulation has participant this blood clot this investigation has participant this investigator this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. is concretized as A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. concretizes this catalysis function is a function of this enzyme a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. function_of is function of function of this red color is a quality of this apple a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence A quality inheres in its bearer at all times for which the quality exists. is quality of quality_of quality of this investigator role is a role of this person a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. is role of role_of role of this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. has_function has function this apple has quality this red color a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. has_quality has quality this person has role this investigator role (more colloquially: this person has this role of investigator) a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. has_role has role 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 disposition of this cell derives from this parent cell (cell division) this nucleus derives from this parent nucleus (nuclear division) a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. derives_from derives from this parent cell derives into this cell (cell division) this parent nucleus derives into this nucleus (nuclear division) a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. derives_into derives into is location of my head is the location of my brain this cage is the location of this rat a relation between two independent continuants, the location and the target, in which the target is entirely within the location Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime location_of location of located in my brain is located in my head this rat is located in this cage a relation between two independent continuants, the target and the location, in which the target is entirely within the location Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime located_in http://www.obofoundry.org/ro/#OBO_REL:located_in located in This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. the surface of my skin is a 2D boundary of my body a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. 2D_boundary_of boundary of is 2D boundary of is boundary of 2D boundary of my body has 2D boundary the surface of my skin a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. has boundary has_2D_boundary has 2D boundary dos 2017-09-17T13:52:24Z Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. directly regulated by Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. GOC:dos Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. dos 2017-09-17T13:52:38Z directly negatively regulated by Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. GOC:dos Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. dos 2017-09-17T13:52:47Z directly positively regulated by Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. GOC:dos David Osumi-Sutherland X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after David Osumi-Sutherland starts_at_end_of X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately preceded by David Osumi-Sutherland ends_at_start_of meets X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) immediately precedes x overlaps y if and only if there exists some z such that x has part z and z part of y http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) overlaps process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit Chris Mungall David Hill Tanya Berardini GO Regulation precludes parthood; the regulatory process may not be within the regulated process. regulates (processual) false regulates Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. Chris Mungall negatively regulates (process to process) negatively regulates Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. Chris Mungall positively regulates (process to process) positively regulates mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) osteoclast SubClassOf 'capable of' some 'bone resorption' A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. Chris Mungall has function realized in For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". capable of c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. Chris Mungall has function in capable of part of Chris Mungall Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporally related to p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. Chris Mungall consumes has input A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. acts upstream of A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. affects acts upstream of or within cjm holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect cjm holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y causally upstream of, negative effect A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297) Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6 Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions ecologically related to A mereological relationship or a topological relationship Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships mereotopologically related to a particular instances of akt-2 enables some instance of protein kinase activity Chris Mungall catalyzes executes has is catalyzing is executing This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. enables A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. Chris Mungall This is a grouping relation that collects relations used for the purpose of connecting structure and function functionally related to this relation holds between c and p when c is part of some c', and c' is capable of p. Chris Mungall false 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 Chris Mungall actively involved in enables part of involved in inverse of enables Chris Mungall enabled by inverse of regulates Chris Mungall regulated by (processual) regulated by inverse of negatively regulates Chris Mungall negatively regulated by inverse of positively regulates Chris Mungall positively regulated by An organism that is a member of a population of organisms is member of is a mereological relation between a item and a collection. is member of member part of SIO member of has member is a mereological relation between a collection and an item. SIO has member inverse of has input Chris Mungall input of inverse of upstream of Chris Mungall causally downstream of Chris Mungall immediately causally downstream of This relation groups causal relations between material entities and causal relations between processes This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causally related to p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain Chris Mungall causally upstream of p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. Chris Mungall immediately causally upstream of p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 Chris Mungall influences (processual) affects causally upstream of or within inverse of causally upstream of or within Chris Mungall causally downstream of or within c involved in regulation of p if c is involved in some p' and p' regulates some p Chris Mungall involved in regulation of c involved in regulation of p if c is involved in some p' and p' positively regulates some p Chris Mungall involved in positive regulation of c involved in regulation of p if c is involved in some p' and p' negatively regulates some p Chris Mungall involved in negative regulation of c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p OWL does not allow defining object properties via a Union Chris Mungall involved in or reguates involved in or involved in regulation of A protein that enables activity in a cytosol. c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. Chris Mungall executes activity in enables activity in is active in true c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. GOC:cjm GOC:dos A relationship that holds between two entities in which the processes executed by the two entities are causally connected. Considering relabeling as 'pairwise interacts with' This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. Chris Mungall Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. in pairwise interaction with interacts with http://purl.obolibrary.org/obo/MI_0914 https://github.com/oborel/obo-relations/wiki/InteractionRelations An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. Chris Mungall binds molecularly binds with molecularly interacts with http://purl.obolibrary.org/obo/MI_0915 Axiomatization to GO to be added later Chris Mungall An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. phosphorylates 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. Chris Mungall Vasundra Touré molecularly controls 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. Chris Mungall Vasundra Touré directly inhibits molecularly decreases activity of 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. Chris Mungall Vasundra Touré directly activates molecularly increases activity of directly positively regulates activity of Chris Mungall This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. helper property (not for use in curation) p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. Chris Mungall has part that occurs in Chris Mungall 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 of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between processes The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between entities Chris Mungall causally influenced by (entity-centric) causally influenced by Chris Mungall interaction relation helper property https://github.com/oborel/obo-relations/wiki/InteractionRelations Chris Mungall 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). Chris Mungall Vasundra Touré causally influences (entity-centric) causally influences Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. Chris Mungall directly regulates (processual) directly regulates gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p Chris Mungall has part structure that is capable of A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. Chris Mungall causal relation between material entity and a process pyrethroid -> growth Holds between c and p if and only if c is capable of some activity a, and a regulates p. capable of regulating Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. capable of negatively regulating renin -> arteriolar smooth muscle contraction Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. capable of positively regulating Inverse of 'causal agent in process' process has causal agent Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. directly positively regulates (process to process) directly positively regulates Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. directly negatively regulates (process to process) directly negatively regulates Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. cjm 2018-01-25T23:20:13Z enables subfunction cjm 2018-01-26T23:49:30Z acts upstream of or within, positive effect cjm 2018-01-26T23:49:51Z acts upstream of or within, negative effect c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive cjm 2018-01-26T23:53:14Z acts upstream of, positive effect c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative cjm 2018-01-26T23:53:22Z acts upstream of, negative effect cjm 2018-03-13T23:55:05Z causally upstream of or within, negative effect cjm 2018-03-13T23:55:19Z causally upstream of or within, positive effect 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. Vasundra Touré regulates activity of q1 decreased_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 decreased_in_magnitude_relative_to This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'. decreased_in_magnitude_relative_to q1 decreased_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. PATOC:CJM 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 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. PATOC:CJM 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 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. PATOC:CJM q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e. quality reciprocal_of There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality. reciprocal_of q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e. PATOC:CJM entity Entity Julius Caesar Verdi’s Requiem the Second World War your body mass index BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) entity Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf per discussion with Barry Smith An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) continuant Continuant An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] continuant Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] occurrent Occurrent An entity that has temporal parts and that happens, unfolds or develops through time. BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] occurrent Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. per discussion with Barry Smith Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] ic IndependentContinuant a chair a heart a leg a molecule a spatial region an atom an orchestra. an organism the bottom right portion of a human torso the interior of your mouth A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] independent continuant (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities. obsolete dependent continuant true spatial region process Process a process of cell-division, \ a beating of the heart a process of meiosis a process of sleeping the course of a disease the flight of a bird the life of an organism your process of aging. An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] process p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] disposition realizable RealizableEntity the disposition of this piece of metal to conduct electricity. the disposition of your blood to coagulate the function of your reproductive organs the role of being a doctor the role of this boundary to delineate where Utah and Colorado meet A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. https://orcid.org/0000-0001-8815-0078 To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] realizable entity 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] quality sdc SpecificallyDependentContinuant Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key of one-sided specifically dependent continuants: the mass of this tomato of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. the disposition of this fish to decay the function of this heart: to pump blood the mutual dependence of proton donors and acceptors in chemical reactions [79 the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction the pink color of a medium rare piece of grilled filet mignon at its center the role of being a doctor the shape of this hole. the smell of this portion of mozzarella A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] specifically dependent continuant b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. per discussion with Barry Smith (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] role Role John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. the priest role the role of a boundary to demarcate two neighboring administrative territories the role of a building in serving as a military target the role of a stone in marking a property boundary the role of subject in a clinical trial the student role A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] role b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] object-aggregate ObjectAggregate a collection of cells in a blood biobank. a swarm of bees is an aggregate of members who are linked together through natural bonds a symphony orchestra an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team) defined by fiat: the aggregate of members of an organization defined through physical attachment: the aggregate of atoms in a lump of granite defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container defined via attributive delimitations such as: the patients in this hospital the aggregate of bearings in a constant velocity axle joint the aggregate of blood cells in your body the nitrogen atoms in the atmosphere the restaurants in Palo Alto your collection of Meissen ceramic plates. An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee). ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] object aggregate An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] site Site Manhattan Canyon) a hole in the interior of a portion of cheese a rabbit hole an air traffic control region defined in the airspace above an airport the Grand Canyon the Piazza San Marco the cockpit of an aircraft the hold of a ship the interior of a kangaroo pouch the interior of the trunk of your car the interior of your bedroom the interior of your office the interior of your refrigerator the lumen of your gut your left nostril (a fiat part – the opening – of your left nasal cavity) b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] site b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] gdc GenericallyDependentContinuant The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. the pdf file on your laptop, the pdf file that is a copy thereof on my laptop the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] generically dependent continuant 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 material MaterialEntity a flame a forest fire a human being a hurricane a photon a puff of smoke a sea wave a tornado an aggregate of human beings. an energy wave an epidemic the undetached arm of a human being An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] material entity A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] immaterial ImmaterialEntity BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10 immaterial entity Anatomical structure that is an individual member of a clade and, at some point in its life-cycle, consists of more than one cell. multicellular organism Melissa Haendel 9/18/11 MH: Can't define this class based on 2 or more cells because most multi cellular organisms (if not all) have only a single cell at some point in life history. MH: sexual subtypes should probably be logically defined based on sexual processes or sex qualities. multicellular organism Material anatomical entity that is a member of an individual species or is a viral or viroid particle. organism or virus Melissa Haendel 9/18/11 organism or virus or viroid An individual member of a clade. organism mah 7.16.2011 A general term for organism that is agnostic about single cell vs multi-cellular. Note that this is a subclass of 'anatomical structure', meaning that an organism must be a connected structure. So, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms. organism heterotroph that acquires nutrition from a symbiont http://orcid.org/0000-0002-2908-3327 symbiotroph A symbiotroph that reduces the fitness, survival, or growth of its symbiont, often called a host http://orcid.org/0000-0002-2908-3327 https://www.wikidata.org/entity/Q10253316 parasite A self-contained constructed feature used by one or more households as a home, such as a house, apartment, mobile home, houseboat or other 'substantial' structure. A dwelling typically includes nearby outbuildings, sheds etc. within the curtilage of the property, excluding any 'open fields beyond'. It has significance in relation to search and seizure, conveyancing of real property, burglary, trespass, and land use planning. See https://github.com/EnvironmentOntology/envo/issues/264 for discussion. This definition needs a lot of clean up and links to household and related classes must be made to form logical definitions for inference to work. Subclasses will be added by inference. human dwelling A self-contained constructed feature used by one or more households as a home, such as a house, apartment, mobile home, houseboat or other 'substantial' structure. A dwelling typically includes nearby outbuildings, sheds etc. within the curtilage of the property, excluding any 'open fields beyond'. It has significance in relation to search and seizure, conveyancing of real property, burglary, trespass, and land use planning. https://en.wikipedia.org/wiki/Dwelling accessed 11/25/2015 A shrubland biome which is densely vegetated by dwarf or short mangroves (and associates) that are generally less than 6 meters in height, is tidally influenced, is located in tropical or subtropical areas. CMECS:577 https://cmecscatalog.org/cmecs/classification/unit/577.html envoCmecs envoMarine This class aligns to the Coastal and Marine Ecological Classification Standard (CMECS). In ENVO, we may adapt the definition for consistency, but the semantics (meaning) of the term should be unaffected. Please consult the CMECS catalogue (https://cmecscatalog.org/) for authoritative and semantically unconstrained definitions. CMECS provides the following notes: "Commonly found on intertidal mud flats along the shores of estuaries. Tidal mangrove shrublands may include immature stands or stunted mature trees that indicate a harsh growing environment. Areas characterized by tall mangroves (> 6 meters) are placed in the Tidal Mangrove Forest Biotic Group. Where tidal amplitude is relatively low, the vegetation forms narrow bands along the coastal plains, and it rarely penetrates inland more than several kilometers along rivers. Where tidal amplitude is greater, mangroves extend further inland along river courses, forming extensive stands in the major river deltas. Also, mangrove cays may occur within the lagoon complex of barrier reefs. The list of biotic communities for this group is long: a few examples are provided below, and the complete list is available in Appendix F" tidal mangrove shrubland molecular process molecular_function catalytic activity The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity. jl 2012-09-20T14:06:08Z GO:0023032 GO:0044708 GO:0044709 Wikipedia:Behavior behavioral response to stimulus behaviour behavioural response to stimulus biological_process single-organism behavior GO:0007610 1. Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation reviews. 2. While a broader definition of behavior encompassing plants and single cell organisms would be justified on the basis of some usage (see PMID:20160973 for discussion), GO uses a tight definition that limits behavior to animals and to responses involving the nervous system, excluding plant responses that GO classifies under development, and responses of unicellular organisms that has general classifications for covering the responses of cells in multicellular organisms (e.g. cell chemotaxis). behavior The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity. GOC:ems GOC:jl ISBN:0395448956 PMID:20160973 A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. jl 2012-09-19T15:05:24Z GO:0000004 GO:0007582 GO:0044699 Wikipedia:Biological_process biological process physiological process biological_process single organism process single-organism process GO:0008150 Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. biological_process A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. GOC:pdt true kinase activity transferase activity transferase activity, transferring phosphorus-containing groups Behavior directed towards society, or taking place between members of the same species. Occurs predominantly, or only, in individuals that are part of a group. Wikipedia:Social_behavior social behaviour biological_process cooperative behavior GO:0035176 Behavior such as predation which involves members of different species is not social. Communication between members of different species is also not social behavior. social behavior Behavior directed towards society, or taking place between members of the same species. Occurs predominantly, or only, in individuals that are part of a group. GOC:jh2 PMID:12848939 Wikipedia:Social_behavior Any process evolved to enable an interaction with an organism of a different species. https://github.com/geneontology/go-ontology/issues/20191 interaction with another species interspecies interaction interspecies interaction between organisms interspecies interaction with other organisms biological_process GO:0044419 biological process involved in interspecies interaction between organisms Any process evolved to enable an interaction with an organism of a different species. GOC:cc Any process in which an organism has an effect on an organism of the same species. https://github.com/geneontology/go-ontology/issues/20191 intraspecies interaction between organisms intraspecies interaction with other organisms biological_process GO:0051703 biological process involved in intraspecies interaction between organisms Any process in which an organism has an effect on an organism of the same species. GOC:ai A biological process which involves another organism of the same or different species. GO:0051706 interaction between organisms physiological interaction between organisms physiological interaction with other organism biological_process GO:0051704 multi-organism process A biological process which involves another organism of the same or different species. GOC:jl data item Data items include counts of things, analyte concentrations, and statistical summaries. a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief PERSON: Alan Ruttenberg PERSON: Chris Stoeckert PERSON: Jonathan Rees data data item information content entity 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 measurement datum Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}. A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. 2/2/2009 is_specified_output of some assay? person:Chris Stoeckert OBI_0000305 group:OBI measurement datum 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 GC_ID:1 ncbi_taxonomy Vira Viridae viruses Viruses Vira Viridae viruses GC_ID:1 ncbi_taxonomy Teleostomi NCBITaxon:40673 GC_ID:1 bony vertebrates ncbi_taxonomy Euteleostomi bony vertebrates GC_ID:1 charophyte/embryophyte group ncbi_taxonomy Charophyta/Embryophyta group Streptophytina charophyte/embryophyte group Charophyta/Embryophyta group GC_ID:1 ncbi_taxonomy biota cellular organisms biota GC_ID:1 ncbi_taxonomy Dipnotetrapodomorpha GC_ID:1 PMID:11743200 PMID:11791233 ncbi_taxonomy Boreotheria Boreoeutheria Boreotheria GC_ID:1 ncbi_taxonomy Acrogymnospermae GC_ID:11 PMID:10425795 PMID:10425796 PMID:10425797 PMID:10490293 PMID:10843050 PMID:10939651 PMID:10939673 PMID:10939677 PMID:11211268 PMID:11321083 PMID:11321113 PMID:11411719 PMID:11540071 PMID:11542017 PMID:11542087 PMID:11760965 PMID:12054223 PMID:2112744 PMID:270744 PMID:7520741 PMID:8123559 PMID:8186100 PMID:8590690 PMID:9103655 PMID:9336922 eubacteria ncbi_taxonomy Monera Procaryotae Prokaryota Prokaryotae bacteria prokaryote prokaryotes Bacteria eubacteria Monera Procaryotae Prokaryota Prokaryotae bacteria prokaryote prokaryotes GC_ID:1 ncbi_taxonomy Homo/Pan/Gorilla group Homininae Homo/Pan/Gorilla group GC_ID:11 PMID:10425795 PMID:10425796 PMID:10425797 PMID:10490293 PMID:10843050 PMID:10939651 PMID:10939673 PMID:10939677 PMID:11211268 PMID:11321083 PMID:11321113 PMID:11411719 PMID:11540071 PMID:11541975 PMID:11542064 PMID:11542149 PMID:11760965 PMID:12054223 PMID:2112744 PMID:25527841 PMID:270744 PMID:8123559 PMID:8590690 PMID:9103655 PMID:9336922 ncbi_taxonomy Archaebacteria Mendosicutes Metabacteria Monera Procaryotae Prokaryota Prokaryotae archaea prokaryote prokaryotes Archaea Archaebacteria Mendosicutes Metabacteria Monera Procaryotae Prokaryota Prokaryotae archaea prokaryote prokaryotes GC_ID:1 PMID:23020233 PMID:30257078 eucaryotes eukaryotes ncbi_taxonomy Eucarya Eucaryotae Eukarya Eukaryotae eukaryotes Eukaryota eucaryotes eukaryotes Eucarya Eucaryotae Eukarya Eukaryotae eukaryotes GC_ID:1 PMID:23020233 green algae ncbi_taxonomy Chlorophycota Chlorophyta sensu Bremer 1985 algae green algae Chlorophyta green algae Chlorophycota Chlorophyta sensu Bremer 1985 algae green algae GC_ID:1 PMID:11214319 PMID:12082125 PMID:12878460 PMID:15522813 ncbi_taxonomy Euarchontoglires GC_ID:1 ncbi_taxonomy Anthropoidea Simiiformes Anthropoidea GC_ID:1 ape apes ncbi_taxonomy Hominoidea ape apes GC_ID:1 higher plants land plants plants ncbi_taxonomy land plants Embryophyta higher plants land plants plants land plants GC_ID:1 tetrapods ncbi_taxonomy Tetrapoda tetrapods GC_ID:1 amniotes ncbi_taxonomy Amniota amniotes GC_ID:1 Theria ncbi_taxonomy Theria <mammals> Theria GC_ID:1 PMID:16248873 PMID:30257078 Chlorophyta/Embryophyta group chlorophyte/embryophyte group green plants ncbi_taxonomy Chlorobionta Chloroplastida green plants Viridiplantae Chlorophyta/Embryophyta group chlorophyte/embryophyte group green plants Chlorobionta Chloroplastida green plants GC_ID:1 ncbi_taxonomy Fungi/Metazoa group opisthokonts Opisthokonta Fungi/Metazoa group opisthokonts GC_ID:1 metazoans multicellular animals ncbi_taxonomy Animalia animals Metazoa metazoans multicellular animals Animalia animals GC_ID:1 ncbi_taxonomy Bilateria GC_ID:1 deuterostomes ncbi_taxonomy Deuterostomia deuterostomes GC_ID:1 PMID:25249442 angiosperms flowering plants ncbi_taxonomy Angiospermae Magnoliophyta flowering plants Magnoliopsida angiosperms flowering plants Angiospermae Magnoliophyta flowering plants GC_ID:1 ncbi_taxonomy Streptophyta GC_ID:1 ncbi_taxonomy Haplorrhini GC_ID:1 mammals ncbi_taxonomy mammals Mammalia mammals mammals GC_ID:1 PMID:11062127 PMID:12684019 ncbi_taxonomy Mycota fungi Fungi Mycota fungi fungi GC_ID:1 vascular plants ncbi_taxonomy vascular plants Tracheophyta vascular plants vascular plants GC_ID:1 seed plants ncbi_taxonomy seed plants Spermatophyta seed plants seed plants GC_ID:1 ncbi_taxonomy Eumetazoa GC_ID:1 chordates ncbi_taxonomy chordates Chordata chordates chordates GC_ID:1 Vertebrata vertebrates ncbi_taxonomy vertebrates Vertebrata <vertebrates> Vertebrata vertebrates vertebrates GC_ID:1 Gnathostomata jawed vertebrates ncbi_taxonomy Gnathostomata <vertebrates> Gnathostomata jawed vertebrates GC_ID:1 euphyllophytes ncbi_taxonomy Euphyllophyta euphyllophytes GC_ID:1 ncbi_taxonomy Sarcopterygii GC_ID:1 Craniata ncbi_taxonomy Craniata <chordates> Craniata GC_ID:1 eutherian mammals placental mammals placentals ncbi_taxonomy Placentalia placentals Eutheria eutherian mammals placental mammals placentals Placentalia placentals GC_ID:1 primate ncbi_taxonomy Primata primates Primates primate Primata primates GC_ID:1 ncbi_taxonomy Catarrhini GC_ID:1 great apes ncbi_taxonomy Pongidae Hominidae great apes Pongidae GC_ID:1 humans ncbi_taxonomy Homo humans GC_ID:1 human man ncbi_taxonomy Homo sapiens human man A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities quality (PATO) PATO:0000072 quality PATO:0000001 quality A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities PATOC:GVG quality PATO:0000068 TODO: define this or obsolete it and move children somewhere else. qualitative A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average. quality PATO:0000069 deviation (from_normal) A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average. PATOC:GVG The number of entities of this type that are part of the whole organism. PATO:0000053 PATO:0000071 PATO:0001169 PATO:0001226 presence or absence in organism quantitative quality count in organism number presence PATO:0000070 This term was originally named "presence". It has been renamed to reduce ambiguity. Consider annotating with the reciprocal relation,PATO:0001555, has_number_of. For example, rather than E=fin ray Q=count in organism C=10, say E=organism Q=has number of E2= fin ray C=10. amount The number of entities of this type that are part of the whole organism. PATOC:GVG A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time. quality PATO:0000161 rate A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time. PATOC:melissa A quality inhering in a bearer by virtue of the bearer's exhibiting no deviation from normal or average. quality average PATO:0000461 normal A quality inhering in a bearer by virtue of the bearer's exhibiting no deviation from normal or average. PATOC:GVG A quality inhering in a bearer by virtue of the bearer's existence. quality present in organism PATO:0000467 present A quality inhering in a bearer by virtue of the bearer's existence. PATOC:GVG An amount which is relatively high. PATO:0000420 PATO:0000650 increased number present in greater numbers in organism supernumerary quality accessory increased PATO:0000470 increased amount An amount which is relatively high. PATOC:GVG A rate which is relatively low. slow rate quality PATO:0000911 decreased rate A rate which is relatively low. PATO:GVG A rate which is relatively high. fast rate high rate quality PATO:0000912 increased rate A rate which is relatively high. PATO:GVG A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. PATO:0002079 Wikipedia:Physical_property relational physical quality quality PATO:0001018 physical quality A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. PATOC:GVG A physical quality which inheres in a bearer by virtue of some influence is exerted by the bearer's mass per unit size. quality density PATO:0001019 mass density A physical quality which inheres in a bearer by virtue of some influence is exerted by the bearer's mass per unit size. WordNet:WordNet A physical quality which inheres in a bearer by virtue of the bearer's exhibiting density. quality PATO:0001164 dense A physical quality which inheres in a bearer by virtue of the bearer's exhibiting density. PATOC:GVG A quality which inheres in an process. PATO:0001239 PATO:0001240 quality of a process quality of occurrent quality of process relational quality of occurrent quality PATO:0001236 See comments of relational quality of a physical entity. process quality A quality which inheres in an process. PATOC:GVG A quality which inheres in a continuant. PATO:0001237 PATO:0001238 snap:Quality monadic quality of a continuant multiply inhering quality of a physical entity quality of a continuant quality of a single physical entity quality of an object quality of continuant monadic quality of an object monadic quality of continuant quality PATO:0001241 Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles. physical object quality A quality which inheres in a continuant. PATOC:GVG A biological sex quality inhering in a population of multiple sexes. quality PATO:0001338 For example a mixture of females and male or males and hermaphrodites. mixed sex A biological sex quality inhering in a population of multiple sexes. MGED:MGED A quality inhering in a population by virtue of the proportion of its members that are ill at a given time. quality PATO:0001415 morbidity A quality inhering in a population by virtue of the proportion of its members that are ill at a given time. PATOC:GVG The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts. OBO_REL:has_part extra or missing physical or functional parts has or lacks parts of type mereological quality number of quality cardinality number PATO:0001555 has number of The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts. PATOC:CJM A density which is higher relative to the normal or average. high density quality PATO:0001788 increased mass density A density which is higher relative to the normal or average. PATOC:GVG A density which is lower relative to the normal or average. low density quality PATO:0001790 decreased mass density A density which is lower relative to the normal or average. PATOC:GVG An amount which is relatively low. PATO:0000419 PATO:0000468 decreased number present in fewer numbers in organism quality decreased reduced subnumerary PATO:0001997 decreased amount An amount which is relatively low. PATOC:GVG A quality that inheres in an entire population or part of a population. quality PATO:0002003 population quality A quality that inheres in an entire population or part of a population. PATOC:GVG george 2009-06-05T09:16:46Z quality PATO:0002062 physical quality of a process A quality that has a value that is increased compared to normal or average. George Gkoutos 2011-06-16T06:39:43Z quality PATO:0002300 increased quality A quality that has a value that is increased compared to normal or average. PATOC:GVG A quality that has a value that is decreased compared to normal or average. George Gkoutos 2011-06-16T06:40:15Z quality PATO:0002301 decreased quality A quality that has a value that is decreased compared to normal or average. PATOC:GVG A quality of a process that has a value that is decreased compared to normal or average. George Gkoutos 2011-06-16T06:50:59Z quality PATO:0002302 decreased process quality A quality of a process that has a value that is decreased compared to normal or average. PATOC:GVG A quality of an object that has a value that is decreased compared to normal or average. George Gkoutos 2011-06-16T06:51:54Z quality PATO:0002303 decreased object quality A quality of an object that has a value that is decreased compared to normal or average. PATOC:GVG A quality of a process that has a value that is increased compared to normal or average. George Gkoutos 2011-06-16T06:53:08Z quality PATO:0002304 increased process quality A quality of a process that has a value that is increased compared to normal or average. PATOC:GVG A quality of an object that has a value that is increased compared to normal or average. George Gkoutos 2011-06-16T06:54:01Z quality PATO:0002305 increased object quality A quality of an object that has a value that is increased compared to normal or average. PATOC:GVG 2 Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family. A material entity that consists of two or more organisms, viruses, or viroids. group of organism organism collection May be of the same or different species. collection of organisms This a general term that can include every organism of a species living in an area or any subset of them. Subclasses can be more specific as needed. A collection of organisms, all of the same species, that live in the same place. ISBN:0878932739 It is sometimes difficult to define the physical boundaries of a population. In the case of sexually reproducing organisms, the individuals within a population have the potential to reproduce with one another during the course of their lifetimes. 'Community', as often used to describe a group of humans, is a type of population of organisms. Classes for population already exist in IDO ('organism population', IDO_0000509) and OBI ('population', OBI_0000181). The definitions should be standardized across OBO Foundry ontologies and only one term used. population of organisms A multi-species collection of organisms of at least two different species, living in a particular area. Must have at least two populations of different species as members. multispecies community ISBN:0865423504 Ecological community is defined broadly here, but includes both ecological interactions (inherited from parent term community) and spatial co-existence. It may be used to describe every organisms living in an area, but is often used to refer only to organisms of a particular taxon or guild (e.g., the plant community, the insect community, the herbivore community). The word community, as it often used to describe a group of humans living together, is a type of single-species collection of organisms, not an ecological community. ecological community A quality that inheres in a population of organisms. See Chris's comments on population qualities at: http://code.google.com/p/popcomm-ontology/issues/detail?id=4. These may not belong under BFO:quality. May be better to call them population characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2. This class is used only for qualities of PCO:population of organsism, while PATO:population quality can inhere in either a population of organisms or an ecological community. Includes qualities like population size, population growth rate, carrying capacity, immigration rate, emigration rate, fecundity, and death rate. A population quality may depend on the qualities of individual organisms in the population, but cannot be measured or described for a single organism. This term may be replaced by a PATO term. quality of a population A quality that inheres in a community. These may not belong under BFO:quality. May be better to call them community characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2. Includes qualities like diversity, species richness, stability, resilience, community structure, number of trophic levels. A community quality may depend on the qualities of individual organism in the community, but cannot be measured or described for a single individual. quality of an ecological community A process that has as primary participant a population. Includes processes such as population growth, extinction, evolution, selection, and adaptation. Population processes may depend on the processes of individual organisms {e.g., population growth reflects the cumulative multicellular organism reproduction (GO:0032504) and death (GO:0016265) of all individuals in a population}, but cannot be described for an individual organism. Some of these processes (e.g., evolution, extinction) can also occur at the species level, so PCO distinguishes between, for example, population extinction and species extinction. The GO has the terms 'multi-organism process' (GO:0051704) and 'intraspecies interactions between organisms' (GO:0051703), but these categories are only defined for interactions between two individuals. It is unclear at this point if 'biological process' (GO:0008150) encompasses population processes. population process The rate of birth of a population of organisms. population birth rate The rate of death of a population of organsisms. population death rate The rate of growth of a population. population growth rate The maximum number of individuals that can be supported in a population that is growing according to logistic growth. Carrying capacity is better defined as a quality of the environment in which a population lives. This term will be deprecated from PCO and moved to ecoCORE. ISBN:0878932739 obsolete carrying capacity true The number of different species represented in an ecological community. This is a quality of an ecological community (PCO_0000002). If your metric includes the abundances of species (evenness) as well as the number, you should use community species diversity (PCO_0000019). adapted from http://en.wikipedia.org/wiki/Species_richness community species richness A process that leads to a change in the number of individuals (positive or negative) in a population. population growth A population process that leads to an increase in the numbers of individuals in a population following a logistic (S-shaped) curve. Generally occurs when the population has a carrying capacity in a particular habitat. logistic population growth A population growth process that leads to an exponential increase in the number of individuals in a population. exponential population growth Interactions are now covered in EcoCore ontology. obsolete predator role true true Interactions are now covered in EcoCore ontology. obsolete prey role true true Interactions are now covered in EcoCore ontology. obsolete symbiont role true true A collection of organisms that has as members every organism of given species and no organisms of any other species. A collection of organisms that has as parts every organism of a species and no organisms of any other species. At the moment there is no way to specify in an OWL axiom that the collection includes every individual of a species. This should be added, if possible. taxonomic group This term is neutral with respect to which organisms are included in a species. Membership will depend on the species concept and the taxonomic assertions used to define the species. These criteria must be specified by the user. species as a collection of organisms A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species. collection of organisms of the same species single-species collection of organisms The number of different species that are represented in a given community, weighted by their abundance. Community species diversity can be calculated in different ways, but consists of two components: species richness and species evenness. If your metric does not include the abundances of different species, but rather just the numer of species, you should use community species richness (PCO_0000010). More specific subclasses or instances of this class may be created to describe specific ways of measuring diversity. adapted from http://en.wikipedia.org/wiki/Species_diversity The Shannon Index and Simpson Index are examples of ways in which species diversity is quantified. community species diversity A domestic group, or a number of domestic groups linked through descent (demonstrated or stipulated) from a common ancestor, marriage, or adoption. Needs axioms for family relationships. http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25173 Family membership through marriage or adoption apply primarily to human families. In most species, family membership is defined by common anscestry. family A population process that ultimately leads to the death of all individuals in a population. population extinction A process that ultimately leads to the death of all individuals in a population. species extinction If there are 40 foxes, and 1000 dogs, the community is not very even, but if there are 40 foxes and 42 dogs, the community is quite even. A quality of an ecological community that reflects how close in abundance all species in a community are. adapted from http://en.wikipedia.org/wiki/Species_evenness community species evenness 1 An organismal entity that consists of one or more people who live in the same dwelling and also share at meals or living accommodation, and may consist of a single family or some other grouping of people. WEB: http://en.wikipedia.org/wiki/Household household This is an example population added to demonstrate the modeling pattern for collections of organisms. obsolete red population true An example class added to demonstrate the design pattern for collections of organism. Red organism should be automatically classified as a member of red population when the reasoner is synchronized using a DL query. obsolete red organism true 2 A collection of organisms of the same species that has as members only humans. human community human population collection of humans A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other. Biological or social relations are covered by RO_0002437 (biotically interacts with), but that relations does provide an easy way to specify that two entities are interacting with each other (participating in the same interaction). Until that axiom is specified, the logical definition of this term is incomplete. These relations can include shared values, occupying the same spatial regkion. A community be be a single species collection of organsisms (as in a human community, which is also a type of population) or a or multi-species collection of organisms (as in an ecological community). obsolete community true 2 A collection of organisms that consists of two or more organisms from at least two species. Need to add axiom to specify that it has at a mimum members of two different species, but not sure how to specify that. Can't say "('has member' only ('member of' min 2 'species as a collection of organisms'))". multi-species collection of organisms A household in which the majority of the income of its members is derived from agricultural activities. This is a more narrow definition in which the majority of income of a house comes from agricultural activities, as opposed to the broad definition in which any income comes from agricultural activities. The narrow definition was chosen to be consistent with the SDGIO (UN Sustainable Development Goals) which requested this term. agricultural household A material entity that is one or more organisms, viruses or viroids. organismal entity A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other. genealogical family Matthew Brush, as part of http://datamodel.clinicalgenome.org/interpretation/ biological family A type of social behavior in which a collection of humans intentionally gathers together on a temporary basis to engage socially. Intented to replace http://purl.obolibrary.org/obo/GENEPIO_0001029 GenEpiO curators human social gathering activity A human social event in which humans living in the same area or neighborhood gather to carry out activiites relevent to the people living in the area. Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001034 GenEpio curators human community event A human social gathering in which the intention is to have a good time. Often the intention is to celebrate something like a birthday, anniversary, or holiday, but there is not always a purpose. Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001030 GenEpiO curators party A human social gathering at which each participant is expected to bring food to share. A potluck also can be party, a social meal, or some other type of social gathering. Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001033 GenEpio curators potluck A human social gathering at which two people are married. May include a legal or social ceremony. Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001031 GenEpio curators wedding A human social gathering at which the key participant is an expectant parent and other guests bring presents for the soon to be born baby. Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001032 GenEpiO curators baby shower An ecological community which is composed primarily of dwarf or short mangroves, often populations of Laguncularia racemosa, Avicennia germinans, Sarcocornia pacifica, or Batis maritima. https://orcid.org/0000-0002-4366-3088 https://cmecscatalog.org/cmecs/classification/unit/577.html mangrove community tidal shrubland community tidal mangrove shrubland community A physical object quality that is inhered in a material entity that is too small to be viewed by the unaided eye. should move to PATO invisible to unaided eye microbial organism microbe 2 A collection of organisms consisting of two or more microbes. https://orcid.org/0000-0001-8815-0078 collection of microbial organisms A multi-species collection of organisms that consists of two or more microbes from at least two species. https://orcid.org/0000-0001-8815-0078 multi-species collection of microbes 1 2 A single-species collection of organisms that consists of two or more microbes of the same species and no members of any other species. https://orcid.org/0000-0001-8815-0078 single species collection of microbes A population of organisms consisting of only microbes of the same species, that live in the same place. https://orcid.org/0000-0001-8815-0078 microbiota microbial population A count data item of the number of steps in the line of descent from a common ancestor for a multicellular organism. number of generations number of generations of multicellular organism A count data item of the number of steps in the line of descent from a common ancestor for a multicellular organism. An increased mass density of a population of organisms such that the density of organisms in an area is increased beyond sustainable levels. increased density of population overcrowded population A quality of a human population such that the density humans in an area is increased beyond sustainable levels. overcrowded human population A collection of organisms that has as members every organism of a taxon and no organisms of any other equal or higher ranked taxon. The taxon may be at any level. If the taxon is species, then this is the same as the class species as a collection of organisms. When defining a taxon, it is generally understood that members include both living organisms and dead organisms that are known through specimens or observations. This term is neutral with respect to which organisms are included in a taxon. Membership will depend on the taxon concept and the assertions used to define the taxon. These criteria must be specified by the user. The best practice is to refer to a formal taxon description, rather than informal names "Genus species" without an authority. taxon as collection of organisms An organism or virus or viroid that is a microbe and a parasite. microbial parasite A microbial population of parasites that is defined by shared features such as genetic markers reflecting a common origin and distinguishing the population from other related parasite populations. VEuPathDB parasite isolate population A community species diversity metric that accounts for both the abundance and evenness of the species present quantified via the following formula: the negative sum of, the product of the proportion of species i relative to the total number of species (pi) multiplied by the natural logarithm of this proportion (ln pi). Shannon entropy Shannon's diversity index Shannon-Wiener index Shannon diversity index A community species diversity metric that is quantified via the following formula: the reciprocal of the sum of squared proportion of species i relative to the total number of species (pi). Simpson index Simpson diversity index A community species diversity metric that is quantified via the following formula: the sum of squared proportion of species i relative to the total number of species (pi). inverse Simpson diversity index An organism that is part of a polyphyletic group of mostly photosynthetic Eukaryotes encompassing green plants excluding Embriophyta (land plants). Included organisms range from unicellular microalgae, such as Chlorella and diatoms to multicellular forms such as giant kelp. alga algae seaweed alga excluding Cyanobacteria A community species diversity that is the mean species diversity at a site or within a specific habitat. α-diversity alpha diversity A community species diversity that is the ratio between regional and local species diversity. true beta diversity β-diversity beta diversity A community species diversity that is the total species diversity in a landscape. The area or landscape of interest may be of very different sizes in different situations, but it should encompass multiple sites or habitats as measured by alpha diversity. γ-diversity gamma diversity TBD: add logical definition The density of plants in an ecological community or population, often measured as the number of plants per area. plant density The density of seedlings in an ecological community or population, often measured as the number of seedlings per area. TBD: add logical definition seedling density The density of plants in a population or organisms (a single species), often measured as the number of plants per area. TBD: add logical definition plant density of a population The density of plants in an ecological community (multiple species), often measured as the number of plants per area. TBD: add logical definition plant density of an ecological community The density of seedlings in a population or organisms (a single species), often measured as the number of seedlings per area. TBD: add logical definition seedling density of a population The density of seedlings in an ecological community (multiple species), often measured as the number of plants per area. TBD: add logical definition seedling density of an ecological community 2 A collection of organisms that consists of exactly two organism, viruses, or viroids that are interacting with each other. pair of interacting organisms A pair of interacting organisms that consists of exactly two organism, viruses, or viroids of the same species that are interacting with each other. pair of interacting organisms of the same species A population which is participating in a migration process. migratory population A population process during which a population moves from one area to another. https://en.wikipedia.org/wiki/Migration The distance between the areas is not specified here, nor is the minimum distance required for such movements to be considered migrations. population migration A population migration during which a population of humans moves from one area to another with the intention of settling permanently in the new location. https://en.wikipedia.org/wiki/Human_migration The distance between the areas is not specified here, nor is the minimum distance required for such movements to be considered migrations. "Nomadic movements are normally not regarded as migrations as there is no intention to settle in the new place and because the movement is generally seasonal. Only a few nomadic people have retained this form of lifestyle in modern times. Also, the temporary movement of people for the purpose of travel, tourism, pilgrimages, or the commute is not regarded as migration, in the absence of an intention to live and settle in the visited places." - https://en.wikipedia.org/wiki/Human_migration human population migration A migratory population of humans, travelling with the intention of settling in a new area. https://en.wikipedia.org/wiki/Human_migration human migratory population An ecological community which is composed of co-existing populations of microbial organisms that interact, directly or indirectly, such that they impact one another's ecological fitness. A class for a collection of organisms considered "microbial" and an accompanying quality in PATO (e.g. "microscopic") would be useful to better axiomatise this class. See https://github.com/PopulationAndCommunityOntology/pco/issues/22 http://orcid.org/0000-0002-4366-3088 http://dx.doi.org/10.1038/ismej.2009.88 microbiota The definition of a microbial species is deeply debated, however, units of phylogenetic and functional diversity are recognised with respect to their varying roles in an ecosystem. In turn, there exist multiple operational definitions of microbial community, such as local, phenomenological, and indexical communities. This class seeks to capture microbial communities in a very broad sense, as collections of phylogenetically and functionally divergent microbial organisms co-existing, potentially interacting, and competing for niche space in the same ecosystem over a period of time in which their causal footprints overlap one another. microbial community a count of 4 resulting from counting limbs in humans a count is a data item denoted by an integer and represented the number of instances or occurences of an entity Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra STATO count A material entity that is one or more organisms, viruses or viroids. wrong IRI form http://purl.obolibrary.org/obo/PCO_0000031 obsolete organismal entity true An ecological community which is composed primarily of dwarf or short mangroves, often populations of Laguncularia racemosa, Avicennia germinans, Sarcocornia pacifica, or Batis maritima. https://orcid.org/0000-0002-4366-3088 https://cmecscatalog.org/cmecs/classification/unit/577.html mangrove community tidal shrubland community obsolete tidal mangrove shrubland community true A physical object quality that is inhered in a material entity that is too small to be viewed by the unaided eye. should move to PATO obsolete invisible to unaided eye true microbial organism obsolete microbe true A collection of organisms consisting of two or more microbes. https://orcid.org/0000-0001-8815-0078 obsolete collection of microbial organisms true A multi-species collection of organisms that consists of two or more microbes from at least two species. https://orcid.org/0000-0001-8815-0078 obsolete multi-species collection of microbes true A single-species collection of organisms that consists of two or more microbes of the same species and no members of any other species. https://orcid.org/0000-0001-8815-0078 obsolete single species collection of microbes true A population of organisms consisting of only microbes of the same species, that live in the same place. https://orcid.org/0000-0001-8815-0078 microbiota obsolete microbial population true example to be eventually removed example to be eventually removed failed exploratory term The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job Person:Alan Ruttenberg failed exploratory term metadata complete Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. metadata complete organizational term Term created to ease viewing/sort terms for development purpose, and will not be included in a release 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 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 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 true MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z infer input from direct reg '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).