Yongqun "Oliver" He (YH) 03-11-2018 LifO is a formal ontology that represents the life processes of organisms and related entities and relations. LifO is a general purpose ontology that covers the common features associated with different types of organisms such as unicellular prokaryotes (e.g., E. coli) and multicellular organisms (e.g., humans). OWL-DL LifO: An ontology of the life of an organism LifO: Life Ontology Reference: He Y. Ontology-based vaccine and drug adverse event representation and theory-guided systematic causal network analysis towards integrative pharmacovigilance research. Current Pharmacology Reports. 2016 Jun;2(3):113-128. DOI: 10.1007/s40495-016-0055-0. PMID: 27458549. PMCID: PMC4957564. Vision Release: 1.0.17 Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification. Really of interest to developers only BFO OWL specification label Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 Person:Alan Ruttenberg Really of interest to developers only BFO CLIF specification label 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 A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> example of usage has curation status PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot OBI_0000281 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> 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 http://code.google.com/p/information-artifact-ontology/issues/detail?id=115. 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition editor 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 PERSON:Daniel Schober Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition source definition source curator note An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg IAO:0000232 uberon curator_notes true curator_notes curator note curator note curator notes 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 OBO foundry unique label elucidation person:Alan Ruttenberg Person:Barry Smith Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms elucidation 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) an annotation property that lists keyword(s) useful for literature tagging and retrieval of sentences containing the type (or kind) of entity (e.g., interaction) as shown by the ontology term label and definition. Yongqun He has literature mining keywords synonym An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. temporal interpretation https://github.com/oborel/obo-relations/wiki/ROAndTime An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL. logical macro assertion https://github.com/oborel/obo-relations/wiki/ShortcutRelations A logical macro assertion whose domain is an IRI for a property logical macro assertion on a property logical macro assertion on an object property logical macro assertion on an annotation property relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y The general property hierarchy is: "directly P" SubPropertyOf "P" Transitive(P) Where we have an annotation assertion "directly P" "is direct form of" "P" If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q' Chris Mungall is direct form of relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y Chris Mungall is indirect form of An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class. UBPROP:0000001 uberon external_definition true external_definition This annotation property may be replaced with an annotation property from an external ontology such as IAO external_definition Notes on how similar or equivalent classes are represented in other ontologies. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000012 uberon external_ontology_notes true external_ontology_notes external_ontology_notes A metadata relation between a class and its taxonomic rank (eg species, family) ncbi_taxonomy has_rank Examples of a Contributor include a person, an organisation, or a service. Typically, the name of a Contributor should be used to indicate the entity. An entity responsible for making contributions to the content of the resource. Contributor Contributor Examples of a Creator include a person, an organisation, or a service. Typically, the name of a Creator should be used to indicate the entity. An entity primarily responsible for making the content of the resource. Creator Creator Typically, Date will be associated with the creation or availability of the resource. Recommended best practice for encoding the date value is defined in a profile of ISO 8601 [W3CDTF] and follows the YYYY-MM-DD format. A date associated with an event in the life cycle of the resource. Date Date Description may include but is not limited to: an abstract, table of contents, reference to a graphical representation of content or a free-text account of the content. An account of the content of the resource. Description Description Typically, Format may include the media-type or dimensions of the resource. Format may be used to determine the software, hardware or other equipment needed to display or operate the resource. Examples of dimensions include size and duration. Recommended best practice is to select a value from a controlled vocabulary (for example, the list of Internet Media Types [MIME] defining computer media formats). The physical or digital manifestation of the resource. Format Format The present resource may be derived from the Source resource in whole or in part. Recommended best practice is to reference the resource by means of a string or number conforming to a formal identification system. A reference to a resource from which the present resource is derived. Source Source Typically, a Subject will be expressed as keywords, key phrases or classification codes that describe a topic of the resource. Recommended best practice is to select a value from a controlled vocabulary or formal classification scheme. The topic of the content of the resource. Subject and Keywords Subject and Keywords Typically, a Title will be a name by which the resource is formally known. A name given to the resource. Title Title has_alternative_id has_broad_synonym database_cross_reference has_exact_synonym has_narrow_synonym has_obo_namespace has_related_synonym in_subset shorthand is defined by 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 inheres in at all times accidentally included in BFO 1.2 proposal - should have been BFO_0000062 obsolete preceded by 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 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 has occurrent part has spatial occupant at some time part of occurrent specifically depends on at some time part of continuant at some time has continuant part at some time part of continuant at all times that whole exists has continuant part at all times that part exists 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 role dos 2017-05-24T09:44:33Z A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. has component activity w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. dos 2017-05-24T09:49:21Z has component process A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. dos 2017-09-22T14:14:36Z This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. has effector activity David Osumi-Sutherland <= Primitive instance level timing relation between events before or simultaneous with David Osumi-Sutherland t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) simultaneous with David Osumi-Sutherland t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) before David Osumi-Sutherland Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. during which ends David Osumi-Sutherland di Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. encompasses 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 Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. during which starts David Osumi-Sutherland starts before David Osumi-Sutherland ends_at_start_of meets X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) immediately precedes David Osumi-Sutherland io X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) starts during David Osumi-Sutherland d during X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) happens during David Osumi-Sutherland o overlaps X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). ends during x overlaps y if and only if there exists some z such that x has part z and z part of y http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) overlaps w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. has component 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 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 inverse of starts with Chris Mungall Allen starts inverse of ends with Chris Mungall ends p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. Chris Mungall consumes has input p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p. Chris Mungall produces has output cjm holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect cjm holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y causally upstream of, negative effect q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w. Because part_of is transitive, inheres in is a sub-relation of inheres in part of Chris Mungall inheres in part of 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 Chris Mungall This is a grouping relation that collects relations used for the purpose of connecting structure and function functionally related to 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 inverse of has input Chris Mungall input of inverse of has output Chris Mungall output of 'protein catabolic process' SubClassOf has_direct_input some protein p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. Chris Mungall directly consumes This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate' has direct input translation SubClassOf has_direct_output some protein p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c. Chris Mungall directly produces obsolete has direct output true inverse of upstream of Chris Mungall causally downstream of Chris Mungall immediately causally downstream of p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q Chris Mungall directly positively regulates directly activates (process to process) directly activates p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q Chris Mungall indirectly positively regulates indirectly activates Chris Mungall directly negatively regulates directly inhibits (process to process) directly inhibits Chris Mungall indirectly negatively regulates indirectly inhibits 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 p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit Chris Mungall directly provides input for (process to process) directly provides input for transitive form of directly_provides_input_for Chris Mungall This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'directly provides input for' (which may later be relabeled simply to 'provides input for') transitively provides input for (process to process) transitively provides input for 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 p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between processes Chris Mungall depends on Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. Chris Mungall directly regulates (processual) directly regulates A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. related via dependence to 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 BFO:0000001 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 BFO:0000002 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 BFO:0000003 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 BFO:0000004 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 true true BFO:0000006 s-region SpatialRegion BFO 2 Reference: Spatial regions do not participate in processes. Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] spatial region BFO:0000008 t-region TemporalRegion Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] temporal region BFO:0000015 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 BFO:0000016 disposition Disposition an atom of element X has the disposition to decay to an atom of element Y certain people have a predisposition to colon cancer children are innately disposed to categorize objects in certain ways. the cell wall is disposed to filter chemicals in endocitosis and exocitosis the cell wall is disposed to filter chemicals in endocytosis and exocytosis BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type [89 BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] disposition BFO:0000017 realizable RealizableEntity the disposition of this piece of metal to conduct electricity. the disposition of your blood to coagulate the function of your reproductive organs the role of being a doctor the role of this boundary to delineate where Utah and Colorado meet A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] realizable entity BFO:0000019 quality Quality the ambient temperature of this portion of air the color of a tomato the length of the circumference of your waist the mass of this piece of gold. the shape of your nose the shape of your nostril a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] quality BFO:0000020 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 relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] specifically dependent continuant BFO:0000023 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 BFO:0000028 3d-s-region ThreeDimensionalSpatialRegion a cube-shaped region of space a sphere-shaped region of space, A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] three-dimensional spatial region BFO:0000029 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 BFO:0000030 object Object atom cell cells and organisms engineered artifacts grain of sand molecule organelle organism planet solid portions of matter star BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting. BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below). BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47 BFO 2 Reference: an object is a maximal causally unified material entity BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74 b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) object BFO:0000031 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 BFO:0000034 function Function the function of a hammer to drive in nails the function of a heart pacemaker to regulate the beating of a heart through electricity the function of amylase in saliva to break down starch into sugar BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] function BFO:0000038 1d-t-region OneDimensionalTemporalRegion the temporal region during which a process occurs. BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks). A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] one-dimensional temporal region BFO:0000040 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 BFO:0000141 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 BFO:0000144 process-profile ProcessProfile On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance. The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on. b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] process profile BFO:0000145 r-quality RelationalQuality John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. a marriage bond, an instance of love, an obligation between one person and another. b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] relational quality BFO:0000148 0d-t-region ZeroDimensionalTemporalRegion a temporal region that is occupied by a process boundary right now the moment at which a child is born the moment at which a finger is detached in an industrial accident the moment of death. temporal instant. A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] zero-dimensional temporal region Small guide RNAs employed for sequence-specific interference with invading nucleic acids by bacteria. PMID:27672148 chebi_ontology crRNA CHEBI:134528 CRISPR RNA CHEBI:134528 High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms. CHEBI:13302 CHEBI:21123 CHEBI:33698 CHEBI:4291 CAS:9007-49-2 KEGG:C00039 Deoxyribonucleic acid deoxyribonucleic acids chebi_ontology (Deoxyribonucleotide)m (Deoxyribonucleotide)n (Deoxyribonucleotide)n+m DNA DNAn DNAn+1 DNS Desoxyribonukleinsaeure deoxyribonucleic acids desoxyribose nucleic acid thymus nucleic acid CHEBI:16991 deoxyribonucleic acid CHEBI:16991 A single-stranded RNA molecule containing about 70-90 nucleotides, folded by intrastrand base pairing into a characteristic secondary ('cloverleaf') structure that carries a specific amino acid and matches it to its corresponding codon on an mRNA during protein synthesis. C10H17O10PR2(C5H8O6PR)n CHEBI:10652 CHEBI:15145 CHEBI:15163 CHEBI:15164 CHEBI:15165 CAS:9014-25-9 KEGG:C00066 transfer RNA chebi_ontology RNA, transfer tRNA CHEBI:17843 transfer RNA CHEBI:17843 RNA molecules which are essential structural and functional components of ribosomes, the subcellular units responsible for protein synthesis. C15H25O16P2R3 CHEBI:10636 CHEBI:15010 Ribosomal RNA ribosomal RNA chebi_ontology rRNA CHEBI:18111 ribosomal RNA CHEBI:18111 A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid. nucleic acids chebi_ontology NA Nukleinsaeure Nukleinsaeuren acide nucleique acides nucleiques acido nucleico acidos nucleicos CHEBI:33696 nucleic acid CHEBI:33696 High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins. CAS:63231-63-0 ribonucleic acid ribonucleic acids chebi_ontology RNA RNS Ribonukleinsaeure pentosenucleic acids ribonucleic acids ribose nucleic acid yeast nucleic acid CHEBI:33697 ribonucleic acid CHEBI:33697 An RNA molecule that transfers the coding information for protein synthesis from the chromosomes to the ribosomes mRNA is formed from a DNA template by transcription. It may be a copy of a single gene or of several adjacent genes (polycistronic mRNA). On the ribosome, the sequence is converted into the programmed amino acid sequence through translation. messenger RNA chebi_ontology mRNA template RNA CHEBI:33699 messenger RNA CHEBI:33699 C10H17O8PR2(C5H8O5PR)n.C10H17O7PR2(C5H8O6PR)n KEGG:C00434 Double-stranded DNA chebi_ontology CHEBI:4705 double-stranded DNA CHEBI:4705 A class of small RNA molecules which are comprised of approximately 150 nucleotides and which are found within the nucleus of eukaryotic cells. PMID:22907602 PMID:23070852 PMID:23190533 PMID:23348838 PMID:23394998 PMID:23426875 PMID:23727230 PMID:23740936 Wikipedia:Small_nuclear_RNA chebi_ontology U-RNA U-RNAs small nuclear RNAs small nuclear ribonucleic acid small nuclear ribonucleic acids snRNA snRNAs CHEBI:74035 small nuclear RNA CHEBI:74035 C10H19O14P3R2(C5H8O5PR)n KEGG:C00271 Single-stranded DNA chebi_ontology CHEBI:9160 single-stranded DNA CHEBI:9160 CL:0000000 cell cell PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .." A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. cell cell A material entity which determines an environmental system. ENVO ENVO:00002297 A material entity determines an environmental system when its removal would cause the collapse of that system. For example, a seamount determines a seamount environment, acting as its 'hub'. This class is currently being aligned to the Basic Formal Ontology. Following this alignment, its definition and the definitions of its subclasses will be revised. environmental feature ENVO:00002297 ENVO:00010483 A portion of environmental material is a fiat object which forms the medium or part of the medium of an environmental system. portion of environmental material Everything under this parent must be a mass noun. All subclasses are to be understood as being composed primarily of the named entity, rather than restricted to that entity. For example, "ENVO:water" is to be understood as "environmental material composed primarly of some CHEBI:water". This class is currently being aligned to the Basic Formal Ontology. Following this alignment, its definition and the definitions of its subclasses will be revised. environmental material ENVO:01000254 A system which has the disposition to environ one or more material entities. 2013-09-23T16:04:08Z EcoLexicon:environment environment In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised. environmental system ENVO:01001110 An environmental system which includes both living and non-living components. This class will be primarily filled by inference, any environmental system which necessarily includes living parts should be autoclassified here. ecosystem The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms. GO:0019952 GO:0050876 Wikipedia:Reproduction reproductive physiological process biological_process GO:0000003 reproduction GO:0000003 A change in the morphology or behavior of a cell resulting from exposure to an activating factor such as a cellular or soluble ligand. biological_process GO:0001775 cell activation GO:0001775 An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory). Wikipedia:Adaptive_immune_system acquired immune response immune memory response biological_process GO:0002250 This term was added by GO_REF:0000022. adaptive immune response GO:0002250 A multicellular organismal process carried out by any of the organs or tissues in an organ system. An organ system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a biological objective. organ system process biological_process GO:0003008 system process GO:0003008 A organ system process carried out at the level of a muscle. Muscle tissue is composed of contractile cells or fibers. biological_process muscle physiological process GO:0003012 muscle system process GO:0003012 A organ system process carried out by any of the organs or tissues of the circulatory system. The circulatory system is an organ system that moves extracellular fluids to and from tissue within a multicellular organism. Wikipedia:Circulatory_system biological_process GO:0003013 circulatory system process GO:0003013 A organ system process carried out by any of the organs or tissues of the renal system. The renal system maintains fluid balance, and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products. In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels; in other species, the renal system may comprise related structures (e.g., nephrocytes and malpighian tubules in Drosophila). excretory system process biological_process kidney system process GO:0003014 renal system process GO:0003014 A system process carried out by the organs and tissues of the respiratory system. The respiratory system is an organ system responsible for respiratory gaseous exchange. GO:0010802 respiratory gaseous exchange by respiratory system biological_process GO:0003016 respiratory system process GO:0003016 The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together. GO:0008372 NIF_Subcellular:sao-1337158144 NIF_Subcellular:sao1337158144 cell or subcellular entity cellular component cellular_component subcellular entity GO:0005575 Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. Note that when this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this. cellular_component GO:0005575 A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. NIF_Subcellular:sao1702920020 Wikipedia:Cell_nucleus cell nucleus horsetail nucleus cellular_component GO:0005634 nucleus GO:0005634 All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. Wikipedia:Cytoplasm cellular_component GO:0005737 cytoplasm GO:0005737 A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. NIF_Subcellular:sao1860313010 Wikipedia:Mitochondrion mitochondria cellular_component GO:0005739 Some anaerobic or microaerophilic organisms (e.g. Entamoeba histolytica, Giardia intestinalis and several Microsporidia species) do not have mitochondria, and contain mitochondrion-related organelles (MROs) instead, called mitosomes or hydrogenosomes, very likely derived from mitochondria. To annotate gene products located in these mitochondrial relics in species such as Entamoeba histolytica, Giardia intestinalis or others, please use GO:0032047 'mitosome' or GO:0042566 'hydrogenosome'. (See PMID:24316280 for a list of species currently known to contain mitochondrion-related organelles.) mitochondrion GO:0005739 The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances. energy pathways biological_process intermediary metabolism metabolic energy generation GO:0006091 generation of precursor metabolites and energy GO:0006091 The cellular synthesis of RNA on a template of DNA. GO:0006350 GO:0061018 GO:0061022 cellular transcription transcription Wikipedia:Transcription_(genetics) DNA-dependent transcription cellular transcription, DNA-dependent transcription, DNA-dependent biological_process transcription regulator activity GO:0006351 transcription, DNA-templated GO:0006351 The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome. GO:0006416 GO:0006453 GO:0043037 Reactome:REACT_100338 Reactome:REACT_100851 Reactome:REACT_101045 Reactome:REACT_101324 Reactome:REACT_1014 Reactome:REACT_103420 Reactome:REACT_105544 Reactome:REACT_29980 Reactome:REACT_33559 Reactome:REACT_77710 Reactome:REACT_79784 Reactome:REACT_81734 Reactome:REACT_81833 Reactome:REACT_82171 Reactome:REACT_83429 Reactome:REACT_83530 Reactome:REACT_86996 Reactome:REACT_95535 Reactome:REACT_96394 Wikipedia:Translation_(genetics) protein anabolism protein biosynthesis protein biosynthetic process protein formation protein synthesis protein translation biological_process GO:0006412 translation GO:0006412 The chemical reactions and pathways resulting in the formation of ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0006758 GO:0006759 Reactome:REACT_102219 Reactome:REACT_104315 Reactome:REACT_105384 Reactome:REACT_106830 Reactome:REACT_109466 Reactome:REACT_190 Reactome:REACT_28537 Reactome:REACT_31626 Reactome:REACT_33014 Reactome:REACT_78557 Reactome:REACT_86305 Reactome:REACT_88682 Reactome:REACT_90150 Reactome:REACT_92655 Reactome:REACT_96844 Reactome:REACT_991 ATP anabolism ATP biosynthesis ATP formation ATP synthesis ATP regeneration biological_process GO:0006754 ATP biosynthetic process GO:0006754 The directed, self-propelled movement of a cell or subcellular component without the involvement of an external agent such as a transporter or a pore. cellular component motion cellular component movement biological_process cell movement GO:0006928 Note that in GO cellular components include whole cells (cell is_a cellular component). movement of cell or subcellular component GO:0006928 The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis). Wikipedia:Chemotaxis taxis in response to chemical stimulus biological_process GO:0006935 chemotaxis GO:0006935 Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. biological_process GO:0006955 This term was improved by GO_REF:0000022. It was redefined and moved. immune response GO:0006955 Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. Wikipedia:Cell_signaling biological_process GO:0007154 cell communication GO:0007154 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. janelomax 2012-09-20T14:06:08Z GO:0044708 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 GO:0007610 Any process in an organism in which a relatively long-lasting adaptive behavioral change occurs as the result of experience. Wikipedia:Learning biological_process GO:0007612 learning GO:0007612 Behavior associated with the intake of food. Wikipedia:List_of_feeding_behaviours behavioral response to food behavioural response to food feeding behaviour drinking eating biological_process GO:0007631 See also the biological process term 'behavior ; GO:0007610'. feeding behavior GO:0007631 biological_process Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end. janelomax 2012-09-19T15:05:24Z GO:0000004 GO:0007582 GO:0044699 Wikipedia:Biological_process biological process physiological process biological_process single organism process single-organism process GO:0008150 Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. Note that 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 ND, no data, is used to indicate this. biological_process GO:0008150 The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. janelomax 2012-10-17T15:46:40Z GO:0044710 Wikipedia:Metabolism metabolism metabolic process resulting in cell growth metabolism resulting in cell growth biological_process single-organism metabolic process GO:0008152 Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions. metabolic process GO:0008152 The directed movement of a motile cell or organism in response to physical parameters involved in energy generation, such as light, oxygen, and oxidizable substrates. energytaxis taxis in response to energy source biological_process GO:0009453 energy taxis GO:0009453 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an external stimulus. response to environmental stimulus biological_process GO:0009605 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. response to external stimulus GO:0009605 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus arising within the organism. biological_process GO:0009719 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. response to endogenous stimulus GO:0009719 Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. janelomax 2012-12-11T16:56:55Z GO:0008151 GO:0044763 GO:0050875 cell physiology cellular physiological process cell growth and/or maintenance biological_process single-organism cellular process GO:0009987 cellular process GO:0009987 A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. Wikipedia:Biological_membrane cellular_component GO:0016020 membrane GO:0016020 The process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present. GO:0048591 cellular growth growth of cell biological_process cell expansion metabolic process resulting in cell growth metabolism resulting in cell growth non-developmental cell growth non-developmental growth of a unicellular organism GO:0016049 cell growth GO:0016049 A physical, chemical, or biochemical process carried out by living organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism. biological_process GO:0022600 digestive system process GO:0022600 The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state. Wikipedia:Cellular_differentiation biological_process GO:0030154 cell differentiation GO:0030154 The regrowth of a lost or destroyed body part, such as an organ or tissue. This process may occur via renewal, repair, and/or growth alone (i.e. increase in size or mass). Wikipedia:Regeneration_(biology) biological_process GO:0031099 regeneration GO:0031099 Any biological process, occurring at the level of a multicellular organism, pertinent to its function. janelomax 2012-09-19T16:07:47Z GO:0044707 GO:0050874 organismal physiological process biological_process single-multicellular organism process GO:0032501 multicellular organismal process GO:0032501 A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. janelomax 2012-12-19T12:21:31Z GO:0044767 development biological_process single-organism developmental process GO:0032502 developmental process GO:0032502 The increase in size or mass of an organ. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that function together as to perform a specific function. biological_process GO:0035265 organ growth GO:0035265 The increase in size or mass of an entire organism, a part of an organism or a cell. GO:0048590 biological_process growth pattern non-developmental growth GO:0040007 See also the biological process term 'cell growth ; GO:0016049'. growth GO:0040007 Self-propelled movement of a cell or organism from one location to another. biological_process GO:0040011 locomotion GO:0040011 The directed movement of a motile cell or organism in response to an external stimulus. Wikipedia:Taxis directed movement in response to stimulus biological_process GO:0042330 taxis GO:0042330 The specific behavior of an organism relating to the intake of food, any substance (usually solid) that can be metabolized by an organism to give energy and build tissue. eating behaviour biological_process GO:0042755 eating behavior GO:0042755 The specific behavior of an organism relating to the intake of liquids, especially water. drinking behaviour biological_process GO:0042756 drinking behavior GO:0042756 Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane. NIF_Subcellular:sao1539965131 Wikipedia:Organelle cellular_component GO:0043226 organelle GO:0043226 Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. cellular_component GO:0043229 intracellular organelle GO:0043229 Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. intracellular membrane-enclosed organelle cellular_component GO:0043231 intracellular membrane-bounded organelle GO:0043231 The environmental space outside of an organism; this may be a host organism in the case of parasitic and symbiotic organisms. cellular_component GO:0043245 extraorganismal space GO:0043245 The space within a host but external to the plasma membrane of host cells, e.g. within host bloodstream. host extracellular space cellular_component GO:0043655 extracellular space of host GO:0043655 The chemical reactions and pathways by which individual cells transform chemical substances. cellular metabolism biological_process intermediary metabolism GO:0044237 cellular metabolic process GO:0044237 Any constituent part of the extracellular region, the space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers constituent parts of the host cell environment outside an intracellular parasite. NIF_Subcellular:sao9117790637 cellular_component extracellular structure GO:0044421 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. extracellular region part GO:0044421 Any constituent part of the living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. cellular_component GO:0044424 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. intracellular part GO:0044424 Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens. GO:0002226 Reactome:REACT_101086 Reactome:REACT_108180 Reactome:REACT_110518 Reactome:REACT_31297 Reactome:REACT_32992 Reactome:REACT_6802 Reactome:REACT_78575 Reactome:REACT_81815 Reactome:REACT_81962 Reactome:REACT_86987 Reactome:REACT_88681 Reactome:REACT_90618 Reactome:REACT_90753 Reactome:REACT_94451 Reactome:REACT_95471 Reactome:REACT_95642 Reactome:REACT_99610 Wikipedia:Innate_immune_system innate immunity nonspecific immune response biological_process GO:0045087 This term was improved by GO_REF:0000022. It was moved. innate immune response GO:0045087 The increase in size or mass of an entire organism, a part of an organism or a cell, where the increase in size or mass has the specific outcome of the progression of the organism over time from one condition to another. biological_process GO:0048589 developmental growth GO:0048589 A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition. biological_process GO:0048869 cellular developmental process GO:0048869 Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another. cell locomotion movement of a cell biological_process cell movement GO:0048870 cell motility GO:0048870 A organ system process carried out by any of the organs or tissues of neurological system. neurological system process neurophysiological process biological_process pan-neural process GO:0050877 Discussion of class label and synonyms: https://github.com/geneontology/go-ontology/issues/13824 nervous system process GO:0050877 The process that involves the secretion of or response to endocrine hormones. An endocrine hormone is a hormone released into the circulatory system. endocrine physiological process endocrine physiology biological_process GO:0050886 endocrine process GO:0050886 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism. GO:0051869 physiological response to stimulus biological_process GO:0050896 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. response to stimulus GO:0050896 Any process that modulates a measurable attribute of any biological process, quality or function. regulation biological_process GO:0065007 biological regulation GO:0065007 IAO:0000027 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 IAO:0000030 information content entity Examples of information content entites include journal articles, data, graphical layouts, and graphs. A generically dependent continuant that is about some thing. 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ). information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. PERSON: Chris Stoeckert OBI_0000142 information content entity IAO:0000078 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 IAO:0000102 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 IAO:0000109 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 IDO:0000586 infection A part of an extended organism that itself has as part a population of one or more infectious agents and that (1) exists as a result of processes initiated by members of the infectious agent population and is (2) clinically abnormal in virtue of the presence of this infectious agent population, or (3) has a disposition to bring clinical abnormality to immunocompetent organisms of the same Species as the host (the organism corresponding to the extended organism) through transmission of a member or offspring of a member of the infectious agent population. infection INO:0000001 A process that includes at least two associated interactions. If the interaction is physical and molecular, the interaction network is molecular interactions usually found in cells. YH, ZX http://en.wikipedia.org/wiki/Interaction_network interaction network process INO:0000002 A process that has two or more participants (i.e., interactors) that have an effect upon one another. YH, ZX https://en.wikipedia.org/wiki/Interaction interact, interacted, interacting, interaction, interaction, interactor, interactors, interacts, participates; plays a role, contribute, contributed, contributes, contributing, engagement, engagements, engages, engaging, involve, involved, involves, involving, act, acted, acting, acts interaction INO:0000003 an interaction network process that includes at least two related interactions together to achieve one specific task(s). A pathway process has a start point(s) and an end point(s). YH, ZX pathway process INO:0000004 an interaction network model that is represented by a probabilistic graphical model (a type of statistical model) that represents a set of random variables and their conditional dependencies via a directed acyclic graph (DAG). YH, ZX WEB: http://en.wikipedia.org/wiki/Bayesian_network Bayesian network INO:0000005 an regulator role that is borne by a material entity that regulates an interaction. YH regulator role INO:0000009 an interactor role that is borne by a material entity that acts as an input of an interaction. YH, ZX interaction input role input interactor role INO:0000010 an interactor role that is borne by a material entity that acts as an output of an interaction. YH, ZX interaction output role output interactor role INO:0000012 an interaction network model that is represented by at least two mutual information interactions. YH, ZX WEB: http://en.wikipedia.org/wiki/Mutual_information mutual information network INO:0000013 a node is an object that represents an interactor in a graph of an interaction or interaction network. YH, ZX is node equal to interactor?? (YL) node INO:0000014 an edge is an object that represents a graphic line that links two interactors in an interaction. YH, ZX edge INO:0000015 a role that is borne by a material entity to act as a participant in an interaction process. YH, ZX interactor role INO:0000147 an input interactor role that is borne by an entity that motivates a life process. Oliver He https://en.wikipedia.org/wiki/Motivation#Herzberg's_two-factor_theory motivator role INO:0000150 an input interactor role that is borne by an entity (e.g. status, job security, salary and fringe benefits) that does not motivate if present, but, if absent, results in demotivation. Oliver He https://en.wikipedia.org/wiki/Motivation#Herzberg's_two-factor_theory hygiene factor role INO:0000157 A regulation represents a regulatory interaction between two interactors. YH, ZX, AO, JH regulate, regulated, regulates, regulating, regulation, regulator, modulate, modulated, modulates, modulating, modulation, mediate, mediated, mediates, mediating, influence, influenced, influences, influencing, affect, affected, affecting, affects, impact, impacted, impacting, impacts, effect, effected, effecting, effects, require, required, requires, requiring, respond, responded, responding, responds, responsive, change, changed, changes, changing, alter, altered, altering, alters, modified, modifies, modify, modifying, depend, depended, depending, depends, direct, directed, directing, directs, drive, driven, drives, driving, cause, caused, causes, causing, lead, leading, leads, led, target, targeted, targeting, targets, dependent, essential for regulation GO: GO_0065007 INO:0000158 An information content entity that models interaction network https://en.wikipedia.org/wiki/Interactome interaction network model LifO:0000001 An integrative interaction network process of an organism that starts from the moment when the first cell forms, has its blueprint stored in the genotype, and performs its dynamic process by interacting with its environment to achieve its survival and other motivations. Oliver He OneNet life He Y. Ontology-based vaccine and drug adverse event representation and theory-guided systematic causal network analysis towards integrative pharmacovigilance research. Current Pharmacology Reports. 2016 Jun;2(3):113-128. DOI: 10.1007/s40495-016-0055-0. PMID: 27458549. PMCID: PMC4957564. http://www.hegroup.org/onenettheory.html https://en.wikipedia.org/wiki/Life life LifO:0000002 A material entity that is the part (DNA sequence) of the genetic makeup of an cell or organism which determines a specific characteristic (phenotype) of that cell or organism. Oliver He genotype LifO:0000003 a genotype that exists in a prokaryotic organism (bacterium or archaeon). Oliver He prokaryotic genotype LifO:0000004 a genotype that exists in an eukaryotic organism (e.g., human). Oliver He eukaryotic genotype LifO:0000005 An organism is an individual entity that exhibits the properties of life, including reproduction, growth and development, maintenance, and response to stimuli. All organisms are composed of one or more cells. Oliver He https://en.wikipedia.org/wiki/Organism An organism may be either a prokaryote or a eukaryote. Prokaryotes are represented by two separate domains—bacteria and archaea. Eukaryotic organisms are characterized by the presence of a membrane-bound cell nucleus and contain additional membrane-bound compartments called organelles. Viruses are not typically considered to be organisms because they are incapable of autonomous reproduction, growth or metabolism. organism LifO:0000006 A time point when the first cell of a multicellular organism or the cell of a single cell organism just forms. This is the time when the OneNet life process of an organism just starts based on the OneNet theory of life. Oliver He OneNet life start time the first cell formation moment LifO:0000009 A process that is performed by a life organism or a component of the life organism. Oliver He https://en.wikipedia.org/wiki/Life life process LifO:0000010 a life process that motivates or stimulates an individual to an action to accomplish a goal or motive. Oliver He https://en.wikipedia.org/wiki/Motivation life motivation LifO:0000011 a realizable entity that represents a need, desire, or drive within an organism that motivates the organism to action. Oliver He https://en.wikipedia.org/wiki/Motivation life motive LifO:0000012 A life motive to survive. This is the most basic motive of life. Oliver He motive to survive LifO:0000014 A society is a group of people who have persistent social interactions , share the same geographical or social territory, and have common motivations. Oliver He https://en.wikipedia.org/wiki/Society society LifO:0000015 Oliver He a social motive that is made by a society to achieve. society motive LifO:0000017 A life motive to physiological need such as hunger, thirst, and sleep. Oliver He https://en.wikipedia.org/wiki/Maslow%27s_hierarchy_of_needs physiological need LifO:0000018 A life motive for interpersonal and involves feelings of belongingness. Oliver He https://en.wikipedia.org/wiki/Maslow%27s_hierarchy_of_needs motive for social belonging LifO:0000019 A life motive for an organism to realize and achieve its full potential. Oliver He https://en.wikipedia.org/wiki/Maslow%27s_hierarchy_of_needs motive for self-actualization LifO:0000020 A life motive for an organism to realize and achieve some higher goal outside oneself, in altruism and spirituality, which is essentially the desire to reach infinite. Oliver He https://en.wikipedia.org/wiki/Maslow%27s_hierarchy_of_needs motive for self-transcendence LifO:0000021 A life motive for an organism to achieve a desire to be accepted and valued by others. Oliver He https://en.wikipedia.org/wiki/Maslow%27s_hierarchy_of_needs motive for self-esteem LifO:0000022 A life motive for safety. Oliver He https://en.wikipedia.org/wiki/Maslow%27s_hierarchy_of_needs safety need LifO:0000023 A safety need that is on an organism's physical safety. Oliver He https://en.wikipedia.org/wiki/Maslow%27s_hierarchy_of_needs physical safety need LifO:0000024 A safety need that is on an organism's economical situation Oliver He https://en.wikipedia.org/wiki/Maslow%27s_hierarchy_of_needs economical safety need LifO:0000025 A safety need to maintain one's health and well-being Oliver He https://en.wikipedia.org/wiki/Maslow%27s_hierarchy_of_needs health need LifO:0000026 A physiological need for sleep. Oliver He https://en.wikipedia.org/wiki/Maslow%27s_hierarchy_of_needs sleep need LifO:0000027 A physiological need for food. Oliver He https://en.wikipedia.org/wiki/Maslow%27s_hierarchy_of_needs food need LifO:0000028 A physiological need for water or against thirst. Oliver He https://en.wikipedia.org/wiki/Maslow%27s_hierarchy_of_needs water need LifO:0000029 A physiological need for air and breathing. Oliver He https://en.wikipedia.org/wiki/Maslow%27s_hierarchy_of_needs breathing need LifO:0000030 A physiological need for clothing. Oliver He https://en.wikipedia.org/wiki/Maslow%27s_hierarchy_of_needs clothing need LifO:0000031 A physiological need for shelter. Oliver He https://en.wikipedia.org/wiki/Maslow%27s_hierarchy_of_needs shelter need LifO:0000032 A physiological need for sexual instinct. Oliver He https://en.wikipedia.org/wiki/Maslow%27s_hierarchy_of_needs sexual instinct need LifO:0000033 A social belonging motive for friendship. Oliver He https://en.wikipedia.org/wiki/Maslow%27s_hierarchy_of_needs motive for friendship LifO:0000034 A social belonging motive for friendship. Oliver He https://en.wikipedia.org/wiki/Maslow%27s_hierarchy_of_needs motive for intimacy LifO:0000035 A social belonging motive for family. Oliver He https://en.wikipedia.org/wiki/Maslow%27s_hierarchy_of_needs motive for family LifO:0000037 a life motivation that is motivated by intrinsic self-desire to seek out new things and new challenges, to analyze one's capacity, to observe, or to gain knowledge. It is driven by an interest or enjoyment in the task itself, and exists within the individual rather than relying on external pressures or a desire for consideration. Oliver He https://en.wikipedia.org/wiki/Motivation#Intrinsic_motivation The phenomenon of intrinsic motivation was first acknowledged within experimental studies of animal behavior. In these studies, it was evident that the organisms would engage in playful and curiosity driven behaviors in the absence of reward. intrinsic motivation LifO:0000041 Common extrinsic motivations are rewards (for example money or grades) for showing the desired behavior, and the threat of punishment following misbehavior. Competition is an extrinsic motivator because it encourages the performer to win and to beat others, not simply to enjoy the intrinsic rewards of the activity. A cheering crowd and the desire to win a trophy are also extrinsic incentives. a life motivation that is motivated by influences outside of the individual. The performance aims to attain a desired outcome. It is the opposite of intrinsic motivation. Oliver He https://en.wikipedia.org/wiki/Motivation#Extrinsic_motivation extrinsic motivation LifO:0000042 A zero-dimensional temporal region that indicates a specific time point in one organism's life. Oliver He OneNet life start time life time point LifO:0000043 a process profile that represents a process’s capability to produce an effect. Oliver He http://fusion.isif.org/proceedings/fusion12CD/html/pdf/313_146.pdf https://en.wikipedia.org/wiki/Effectiveness effectiveness LifO:0000044 an effectiveness that represents a process’s capability to get a thing done, or meet a target or desire. Oliver He https://en.wikipedia.org/wiki/Efficacy efficiency LifO:0000045 an effectiveness that represents a process’s capability to do a "right" thing, i.e., setting a right target to achieve an overall goal (the effect). Oliver He https://en.wikipedia.org/wiki/Correctness_(computer_science) correctness LifO:0000046 an effectiveness that represents a process’s capability to do a thing in the most economical way. Oliver He https://en.wikipedia.org/wiki/Correctness_(computer_science) efficiency LifO:0000047 A recurrent and patterned process that involves the interactions or responses of indivdiuals to one antoher wihch have attained statiblity. Oliver He https://www.slideshare.net/annaloucanete7/chapter10-social social process LifO:0000048 A society that exists to promote an academic discipline, profession, or a group of related disciplines such as the arts. Oliver He https://en.wikipedia.org/wiki/Learned_society scholarly society LifO:0000049 A society in which individuals are confronted with personal decisions as opposed to a magical or tribal or collectivist society. Oliver He https://en.wikipedia.org/wiki/Open_society open society LifO:0000050 A society process that changes or reconstructs the cultural concept of a society Oliver He repositioning of culture https://en.wikipedia.org/wiki/Culture_change cultural change LifO:0000051 A behavior among two or more organisms in a society. Oliver He https://en.wikipedia.org/wiki/Social_behavior social behavior LifO:0000052 A social behavior that involves the coordinated behavior of large groups of similar animals as well as emergent properties of these groups. Oliver He https://en.wikipedia.org/wiki/Social_behavior collective animal behavior LifO:0000053 A consciousness shared by individuals within a society. Oliver He https://en.wikipedia.org/wiki/Social_consciousness social consciousness LifO:0000054 A social behavior that can potentially cause or threaten physical or emotional harm. Oliver He https://en.wikipedia.org/wiki/Social_behavior aggressive social behavior LifO:0000055 An aggressive social behavior that involves one bullying another. Oliver He bullying behavior https://en.wikipedia.org/wiki/Social_behavior bullying social behavior LifO:0000056 An aggressive social behavior that involves violent actions among individuals. Oliver He violent behavior https://en.wikipedia.org/wiki/Social_behavior violent social behavior LifO:0000057 the quality in a society that arises from a concern for what is regarded as excellent in arts, letters, manners, scholarly pursuits, etc. Oliver He http://www.dictionary.com/browse/culture culture LifO:0000058 Oliver He An incentive or drive resulting from a sociocultural influence that initiates behavior toward a particular goal. https://medical-dictionary.thefreedictionary.com/social+motivation social motive LifO:0000059 A social process that is driven by a social motive. Oliver He https://www.slideshare.net/annaloucanete7/chapter10-social social motivation LifO:0000060 A social motivation that is driven by a society motive. Oliver He https://www.slideshare.net/annaloucanete7/chapter10-social society motivation LifO:0000061 An interaction between two or more individuals or populations in a society. Social interaction is a building block of society. Oliver He https://courses.lumenlearning.com/boundless-sociology/chapter/understanding-social-interaction/ social interaction LifO:0000062 a realizable entity, such as norm, law, regulation, that is realized in social behavior. Oliver He https://en.wikipedia.org/wiki/Social_rule_system_theory social rule LifO:0000063 informal understanding that governs the behavior of the members of a society Oliver He https://en.wikipedia.org/wiki/Social_norm social norm LifO:0000064 a social rule that is created and enforced through social or governmental institutions to regulate behavior in a society. Oliver He https://en.wikipedia.org/wiki/Law law LifO:0000065 A time point when a life organism just dies. Oliver He life death moment LifO:0000159 A science branch that analyzes the mechanisms of dynamic interactions among different participants and their associated pathways and networks in a life organism. Oliver He OneNet life dynamics life dynamics MFOEM:000001 An emotion process is a complex mental process that is a synchronized aggregate of constituent mental processes including an appraisal process as part, and which gives rise to an action tendency. occurrent emotion short-term emotion emotion process MF:0000008 A mental process that creates, modifies or has as participant some cognitive representation. cognitive process GO:0050890, cognition, defined as `The operation of the mind by which an organism becomes aware of objects of thought or perception; it includes the mental activities associated with thinking, learning, and memory.' MF:0000017 Consciousness is an inseparable part of all mental processes. It is that part of the mental process that: a) confers a subjective perspective, a phenomenology, an experience of the mental process of which it is a part; and b) intends the object or event that the mental process is about, should such exist; i.e., it confers intentionality on the mental process. Note that while there are different modes of consciousness corresponding to the different senses, the whole of conscious experience at any one time is largely experienced as a unity, that is, as a fused whole. Mental processes which are simultaneously ongoing are separable only in fiat, not in essence. consciousness MF:0000019 a mental process which is a) produced by a causal process (for example involving light rays or air vibrations) involving a part of the environment of the organism, and b) is experienced by the organism as being so caused, and c) in which the relevant part of the environment is thereby represented to the organism perception MF:0000020 A mental process is a bodily process that is of a type such that it can of itself be conscious. Examples include thinking, feeling pain, remembering and emotion as occurrent experiences. Valence is a process profile of an emotion, mood, or affective bodily feeling (such as pleasure and pain). Valence can be positive or negative, with different strengths in both directions. For example, pleasure is positively valenced while pain is negatively valenced. A bodily process which brings into being, sustains or modifies a cognitive representation or a beahvior inducing state. mental process GO:0050890, cognition, defined as `The operation of the mind by which an organism becomes aware of objects of thought or perception; it includes the mental activities associated with thinking, learning, and memory.' MF:0000030 A dependent continuant which is about a portion of reality. http://www.jbiomedsem.com/content/1/1/10 representation MF:0000031 A representation which specifically depends on an anatomical structure in the cognitive system of an organism. http://www.jbiomedsem.com/content/1/1/10 cognitive representation MF:0000032 A bodily disposition is a disposition that inheres in some extended organism. Examples are: my disposition to catch a cold when exposed to a virus, my ability to speak the English language. bodily disposition MF:0000033 A mental disposition is a bodily disposition that is realized in a mental process. mental disposition Interaction between molecules that may participate in formation of one, but possibly more, physical complexes. Often describes a set of molecules that are co-purified in a single pull-down or coimmunoprecipitation but might participate in formation of distinct physical complexes sharing a common bait. PSI-MI MI:0914 association MI:0914 NCBITaxon:10090 NCBITaxon:85055 GC_ID:1 house mouse mouse ncbi_taxonomy Mus muscaris mice C57BL/6xCBA/CaJ hybrid Mus musculus NCBITaxon:1224 GC_ID:11 PMID:11321122 PMID:11542017 PMID:11837318 PMID:16280474 PMID:26654112 purple bacteria purple bacteria and relatives purple non-sulfur bacteria purple photosynthetic bacteria purple photosynthetic bacteria and relatives ncbi_taxonomy Alphaproteobacteraeota proteobacteria Proteobacteria NCBITaxon:1773 GC_ID:11 ncbi_taxonomy Bacillus tuberculosis Bacterium tuberculosis Mycobacterium tuberculosis typus humanus Mycobacterium tuberculosis var. hominis Mycobacterium tuberculosis NCBITaxon:2 Bacteria eubacteria GC_ID:11 PMID:10425795 PMID:10425796 PMID:10425797 PMID:10490293 PMID:10843050 PMID:10939651 PMID:10939673 PMID:10939677 PMID:11211268 PMID:11321083 PMID:11321113 PMID:11411719 PMID:11540071 PMID:11542017 PMID:11542087 PMID:11760965 PMID:12054223 PMID:2112744 PMID:270744 PMID:8123559 PMID:8590690 PMID:9103655 PMID:9336922 eubacteria ncbi_taxonomy Monera Procaryotae Prokaryota Prokaryotae bacteria not Bacteria Haeckel 1894 prokaryote prokaryotes Bacteria NCBITaxon:2157 Archaea GC_ID:11 PMID:10425795 PMID:10425796 PMID:10425797 PMID:10490293 PMID:10843050 PMID:10939651 PMID:10939673 PMID:10939677 PMID:11211268 PMID:11321083 PMID:11321113 PMID:11411719 PMID:11540071 PMID:11541975 PMID:11542064 PMID:11542149 PMID:11760965 PMID:12054223 PMID:2112744 PMID:25527841 PMID:270744 PMID:8123559 PMID:8590690 PMID:9103655 PMID:9336922 ncbi_taxonomy Archaebacteria Mendosicutes Metabacteria Monera Procaryotae Prokaryota Prokaryotae archaea prokaryote prokaryotes Archaea NCBITaxon:235 GC_ID:11 Brucella melitensis bv. Abortus ncbi_taxonomy Bacterium abortus Brucella melitensis biovar Abortus Brucella abortus NCBITaxon:2759 Eukaryota eucaryotes eukaryotes GC_ID:1 PMID:23020233 eucaryotes eukaryotes ncbi_taxonomy Eucarya Eucaryotae Eukarya Eukaryotae eukaryotes Eukaryota NCBITaxon:314146 GC_ID:1 PMID:11214319 PMID:12082125 PMID:12878460 PMID:15522813 ncbi_taxonomy Euarchontoglires NCBITaxon:562 NCBITaxon:1637691 NCBITaxon:662101 NCBITaxon:662104 GC_ID:11 PMID:10319482 E. coli Escherichia/Shigella coli ncbi_taxonomy Bacillus coli Bacterium coli Bacterium coli commune Enterococcus coli Escherchia coli Eschericia coli Escherichia coli NCBITaxon:5791 GC_ID:1 ncbi_taxonomy Physarum polycephalum NCBITaxon:9606 GC_ID:1 human man ncbi_taxonomy Homo sapiens OBI:0000181 population PMID12564891. Environ Sci Technol. 2003 Jan 15;37(2):223-8. Effects of historic PCB exposures on the reproductive success of the Hudson River striped bass population. a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area 1/28/2013, BP, on the call it was raised that we may want to switch to an external ontology for all populatin terms: http://code.google.com/p/popcomm-ontology/ PERSON: Philippe Rocca-Serra adapted from Oxford English Dictionnary rem1: collection somehow always involve a selection process population OBI:0000725 host role In biology, a host is an organism that harbors a virus or parasite, or a mutual or commensal symbiont, typically providing nourishment and shelter. http://en.wikipedia.org/wiki/Host_(biology) 30 March 09 host role is a role played by an organism and realized by providing nourishment, shelter or a means of reproduction to another organism within the organism playing the host role 30Mar09 virus reproducing inside a cell; bacteria causing a disease, host can be harmed or not. we want to avoid a cat sitting on my lap and an animal care technician; these are not examples or hosts; dental cares = on tooth, but part of outer layer of tooth, so covered by "within" in the definition GROUP: Role Branch 30 Mar09 submitted by vaccine community OBI http://en.wikipedia.org/wiki/Host_(biology) host role OBI:0001933 value specification The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass. An information content entity that specifies a value within a classification scheme or on a quantitative scale. This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement. PERSON:Bjoern Peters value specification OBI:1110021 infection process the detrimental process in which an infectious agent colonizes or replicates in a host environment IEDB IEDB infection process OBI:1110093 disposition to infect an organism Is a role borne by an agent, and realized when in contact with or inside another organism in which it is capable of replicating and causing disease IEDB IEDB disposition to infect an organism OBI:1110122 pathologic process abnormal, harmful processes caused by or associated with a disease IEDB IEDB pathologic process OGG:0000000001 A genome is a material entity that represents the entirety of an organism's hereditary information. The genome includes both the genes and the non-coding sequences of the DNA and RNA. Oliver He Book: Eugene Nester, Denise Anderson, C. Evans Roberts, Jr., Microbiology (Companion Site): A Human Perspective, 7th Edition. Mcgraw Hill, October 18, 2011. ISBN-13: 978-0073375311 WEB: http://en.wikipedia.org/wiki/Genome genome OGG:0000000002 A gene is a material entity that represents the entire DNA sequence required for synthesis of a functional protein or RNA molecule. Oliver He WEB: http://www.ncbi.nlm.nih.gov/books/NBK21640/ In addition to the coding regions (exons), a gene includes transcription-control regions and sometimes introns. Although the majority of genes encode proteins, some encode tRNAs, rRNAs, and other types of RNA. gene OGG:0000000003 a disposition that a gene can be used as a blueprint for generating a new form of product such as protein. Yongqun He WEB: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/entrezgene/entrezgene.asn YH: According to NCBI Gene project, there are two gene types: unknown (0) , tRNA (1) , rRNA (2) , snRNA (3) , scRNA (4) , snoRNA (5) , protein-coding (6) , pseudo (7) , transposon (8) , miscRNA (9) , ncRNA (10) , other (255). Therefore, we have generated corresponding gene dispositions. Note that we don't use the term "gene type" here to differentiate the meanings of "type" and "disposition". gene disposition OGMS:0000023 A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2010-07-19T11:13:49Z phenotype OGMS:0000087 An object aggregate consisting of an organism and all material entities located within the organism, overlapping the organism, or occupying sites formed in part by the organism. Albert Goldfain http://code.google.com/p/ogms/issues/detail?id=3 creation date: 2010-01-25T04:51:11Z extended organism An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA. protein PR:000000001 Proteins descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB]. protein PR:000000001 RO:0002577 A material entity consisting of multiple components that are causally integrated. May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43 Chris Mungall http://www.jbiomedsem.com/content/4/1/43 system Anatomical structure that performs a specific function or group of functions [WP]. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4 CARO:0020004 EFO:0000634 EMAPA:35949 ENVO:01000162 FMA:67498 MA:0003001 NCIT:C13018 OpenCyc:Mx4rv5XMb5wpEbGdrcN5Y29ycA OpenCyc:Mx4rwP3iWpwpEbGdrcN5Y29ycA UMLS:C0178784 WBbt:0003760 uberon anatomical unit body organ element UBERON:0000062 organ UBERON:0000062 A multicellular structure that is a part of an organ. currently defined in a very broad sense, may be replaced by more specific classes in the future AAO:0011124 EFO:0000635 FMA:82472 cardinal organ part uberon regional part of organ UBERON:0000064 organ part UBERON:0000064 Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. changed label and definition to reflect CARO2 AAO:0000607 AAO:0010054 AEO:0000043 BILA:0000043 CALOHA:TS-2090 CARO:0000043 EHDAA2:0003043 EMAPA:35868 FBbt:00007003 FMA:9637 HAO:0000043 MA:0003002 MESH:D014024 NCIT:C12801 TAO:0001477 TGMA:0001844 UMLS:C0040300 VHOG:0001757 WBbt:0005729 XAO:0003040 ZFA:0001477 galen:Tissue portion of tissue tissue portion simple tissue uberon UBERON:0000479 tissue UBERON:0000479 Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. AAO:0010841 AEO:0000000 BILA:0000000 CARO:0000000 EHDAA2:0002229 FBbt:10000000 FBbt_root:00000000 FMA:62955 HAO:0000000 MA:0000001 NCIT:C12219 TAO:0100000 TGMA:0001822 UMLS:C1515976 XAO:0000000 ZFA:0100000 uberon UBERON:0001062 anatomical entity UBERON:0001062 An anatomical structure that has more than one cell as a part. CARO:0010000 FBbt:00100313 multicellular structure uberon UBERON:0010000 multicellular anatomical structure UBERON:0010000 owl:Thing example to be eventually removed Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. metadata complete term created to ease viewing/sort terms for development purpose, and will not be included in a release PERSON:Alan Ruttenberg organizational term Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." ready for release Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. metadata incomplete Nothing done yet beyond assigning a unique class ID and proposing a preferred term. uncurated All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. pending final vetting Terms with this status should eventually replaced with a term from another ontology. Alan Ruttenberg group:OBI to be replaced with external ontology term A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. Alan Ruttenberg group:OBI requires discussion ## Elucidation This is used when the statement/axiom is assumed to hold true 'eternally' ## How to interpret (informal) First the "atemporal" FOL is derived from the OWL using the standard interpretation. This axiom is temporalized by embedding the axiom within a for-all-times quantified sentence. The t argument is added to all instantiation predicates and predicates that use this relation. ## Example Class: nucleus SubClassOf: part_of some cell forall t : forall n : instance_of(n,Nucleus,t) implies exists c : instance_of(c,Cell,t) part_of(n,c,t) ## Notes This interpretation is *not* the same as an at-all-times relation axiom holds for all times en Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester Alan Ruttenberg Allyson Lister Barry Smith Bill Bug Bjoern Peters Carlo Torniai Chris Mungall Chris Stoeckert Chris Taylor Christian Bolling Cristian Cocos Daniel Rubin Daniel Schober Dawn Field Dirk Derom Elisabetta Manduchi Eric Deutsch Frank Gibson Gilberto Fragoso Helen C. Causton Helen Parkinson Holger Stenzhorn James A. Overton James Malone Jay Greenbaum Jeffrey Grethe Jennifer Fostel Jessica Turner Jie Zheng Joe White John Westbrook Kevin Clancy Larisa Soldatova Lawrence Hunter Liju Fan Luisa Montecchi Matthew Brush Matthew Pocock Melanie Courtot Melissa Haendel Mervi Heiskanen Monnie McGee Norman Morrison Philip Lord Philippe Rocca-Serra Pierre Grenon Richard Bruskiewich Richard Scheuermann Robert Stevens Ryan R. Brinkman Stefan Wiemann Susanna-Assunta Sansone Tanya Gray Tina Hernandez-Boussard Trish Whetzel Yongqun He 2009-07-31 The Ontology for Biomedical Investigations (OBI) is build in a collaborative, international effort and will serve as a resource for annotating biomedical investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. This ontology arose from the Functional Genomics Investigation Ontology (FuGO) and will contain both terms that are common to all biomedical investigations, including functional genomics investigations and those that are more domain specific. OWL-DL An ontology for the annotation of biomedical and functional genomics experiments. Ontology for Biomedical Investigation Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them. 2017-11-07 Vision Release: 1.0.17 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 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 occupies spatial region at some time exists at has disposition at all times has participant at all times This document is about information artifacts and their representations is_about is a (currently) primitive relation that relates an information artifact to an entity. 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. person:Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy is about An object property that represents a relation between a life process and its genetic design stored in the genotype of an organism has life blueprint An object property that represents a relation between a genotype and a phenotype where the genotype is the blueprint of the phenotype. Oliver He blueprint for phenotype An object property that represents a relation between a life process and a life motive. Oliver He motivated by An object property that represents a relation between a living organism and a life motive. Oliver He has motive An object property that represents a relation between a protein and a gene such that the gene codes for the protein. Oliver He protein has gene template An object property that represents a relation between a gene and a RNA such that the gene is transcribed into the RNA. Oliver He transcribed to An object property that represents a relation between a mRNA and a protein such that the mRNA is transcribed into the protein. translated to An object property that represents a relation between a protein and a mRNA such that the mRNA is translated to the protein. protein has mRNA template has value specification A relation between an information content entity and a value specification that specifies its value. PERSON: James A. Overton OBI has value specification 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 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 Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. Chris Mungall started by starts with x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. Chris Mungall finished by ends with BFO 2 Reference: BFO does not claim to be a complete coverage of all entities. It seeks only to provide coverage of those entities studied by empirical science together with those entities which affect or are involved in human activities such as data processing and planning – coverage that is sufficiently broad to provide assistance to those engaged in building domain ontologies for purposes of data annotation [17 BFO 2 Reference: BFO’s treatment of continuants and occurrents – as also its treatment of regions, rests on a dichotomy between space and time, and on the view that there are two perspectives on reality – earlier called the ‘SNAP’ and ‘SPAN’ perspectives, both of which are essential to the non-reductionist representation of reality as we understand it from the best available science [30 BFO 2 Reference: For both terms and relational expressions in BFO, we distinguish between primitive and defined. ‘Entity’ is an example of one such primitive term. Primitive terms in a highest-level ontology such as BFO are terms that 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. Alan Ruttenberg Albert Goldfain Barry Smith Bill Duncan Bjoern Peters Chris Mungall David Osumi-Sutherland Fabian Neuhaus James A. Overton Janna Hastings Jie Zheng Jonathan Bona Larry Hunter Leonard Jacuzzo Ludger Jansen Mark Ressler Mathias Brochhausen Mauricio Almeida Melanie Courtot Pierre Grenon Randall Dipert Robert Rovetto Ron Rudnicki Stefan Schulz Thomas Bittner Werner Ceusters Yongqun "Oliver" He The http://purl.obolibary.org/obo/bfo/classes-only.owl variant of BFO ("bfo_classes_only.owl") includes only the class hierarchy and annotations from the full OWL version of BFO 2: http://purl.obolibary.org/obo/bfo.owl ("bfo.owl"). There are no object properties or logical axioms that use the object properties in bfo_classes_only.owl. As the logical axioms in the bfo_classes_only.owl variant are limited to subclass and disjoint assertions they are much weaker than the logical axioms in bfo.owl. If you plan to use the relations that define BFO 2, you should import bfo.owl instead of bfo_classes_only.owl. To the extent that the relations are used without importing bfo.owl, be mindful that they should be used in a manner consistent with their use in bfo.owl. Otherwise if your ontology is imported by a another ontology that imports bfo.owl there may be inconsistencies. See the BFO 2 release notes for further information about BFO 2. Please note that the current release of bfo.owl uses temporal relations when the subject or object is a continuant, a major change from BFO 1. This is an early version of BFO version 2 and has not yet been extensively reviewed by the project team members. Please see the project site http://code.google.com/p/bfo/ , the bfo2 owl discussion group http://groups.google.com/group/bfo-owl-devel , the bfo2 discussion group http://groups.google.com/group/bfo-devel, the tracking google doc http://goo.gl/IlrEE, and the current version of the bfo2 reference http://purl.obolibrary.org/obo/bfo/dev/bfo2-reference.docx . This ontology is generated from a specification at http://bfo.googlecode.com/svn/trunk/src/ontology/owl-group/specification/ and with the code that generates the OWL version in http://bfo.googlecode.com/svn/trunk/src/tools/. A very early version of BFO version 2 in CLIF is at http://purl.obolibrary.org/obo/bfo/dev/bfo.clif Yongqun "Oliver" He (YH) 03-11-2018 LifO is a formal ontology that represents the life processes of organisms and related entities and relations. LifO is a general purpose ontology that covers the common features associated with different types of organisms such as unicellular prokaryotes (e.g., E. coli) and multicellular organisms (e.g., humans). OWL-DL LifO: An ontology of the life of an organism LifO: Life Ontology Reference: He Y. Ontology-based vaccine and drug adverse event representation and theory-guided systematic causal network analysis towards integrative pharmacovigilance research. Current Pharmacology Reports. 2016 Jun;2(3):113-128. DOI: 10.1007/s40495-016-0055-0. PMID: 27458549. PMCID: PMC4957564. Vision Release: 1.0.17 The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies. OBO Relations Ontology Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 26 Logical Axioms: 0] Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 32 Logical Axioms: 0] https://github.com/oborel/obo-relations/