en Adam Goldstein Alan Ruttenberg Albert Goldfain Barry Smith Bjoern Peters Carlo Torniai Chris Mungall Chris Stoeckert Christian A. Boelling Clint Dowland Daniel Welch Darren Natale David Osumi-Sutherland Gwen Frishkoff Holger Stenzhorn James A. Overton James Malone Jennifer Fostel Jie Zheng John W. Judkins Jonathan Rees Larisa Soldatova Lawrence Hunter Mathias Brochhausen Matt Brush Matthew Diller Melanie Courtot Michel Dumontier Paolo Ciccarese Pat Hayes Philippe Rocca-Serra Randy Dipert Ron Rudnicki S. Clint Dowland Sam Smith Sarah Bost Satya Sahoo Selja Seppälä Sivaram Arabandi Werner Ceusters William D. Duncan William Duncan William Hogan Yongqun (Oliver) He Yongqun He Amanda Hicks Mathias Brochhausen Shariq Tariq Swetha Garimalla William Hogan The Information Artifact Ontology (IAO) is an ontology of information entities, originally driven by work by the OBI digital entity and realizable information entity branch. The Ontology for Modeling and Representation of Social Entities (OMRSE) is an OBO Foundry ontology that represents the various entities that arise from human social interactions, such as social acts, social roles, social groups, and organizations. Information Artifact Ontology (IAO) Ontology for Modeling and Representation of Social Entities Cui Tao, PhD Kirk Roberts, PhD Licong Cui, PhD Tuan Amith, Xubing Hao, and Licong Cui Tuan Amith, PhD Xubing Hao, PhD Natural Conversation Ontology (NCO) is based on knowledge derived from the Natural Conversation Framework (Moore and Arar), as well as, the amalgamation of theories of conversation analysis. The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies. An ontology describing the domain space of conversation analysis https://creativecommons.org/licenses/by/4.0/ https://creativecommons.org/licenses/by-nc-nd/4.0/ Natural Conversation Ontology OBO Relations Ontology An information artifact is, loosely, a dependent continuant or its bearer that is created as the result of one or more intentional processes. Examples: uniprot, the english language, the contents of this document or a printout of it, the temperature measurements from a weather balloon. For more information, see the project home page at https://github.com/information-artifact-ontology/IAO This ontology grew out of efforts to represent the reality underlying the demographic information required by the US federal government's "meaningful use" criteria for electronic medical records and a presentation by Dr. William Hogan at the Electronic Health Record of the Future conference in Buffalo, NY http://ontology.buffalo.edu/EHR/Demographics_Hogan_Buffalo_2010_09_22.ppt IDs allocated to related efforts: PNO: IAO_0020000-IAO_0020999, D_ACTS: IAO_0021000-IAO_0021999 IDs allocated to subdomains of IAO. pno.owl: IAO_0020000-IAO_0020999, d-acts.owl: IAO_0021000-IAO_0021999 https://github.com/ProfTuan/NCO 2025-12-02 2024-11-25 2025-03-05 prototype 2022-11-07 https://github.com/oborel/obo-relations/ 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 term The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> editor preferred label editor preferred term editor preferred term example of usage A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> example of usage example of usage has curation status PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot has curation status definition The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. 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.obofoundry.org/obo/obi> editor note term editor Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition editor definition editor term editor alternative label A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like. OBO Operations committee PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related). alternative label 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 curator note An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg curator note term tracker item the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ An IRI or similar locator for a request or discussion of an ontology term. Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg The 'tracker item' can associate a tracker with a specific ontology term. term tracker item imported from For external terms/classes, the ontology from which the term was imported PERSON:Alan Ruttenberg PERSON:Melanie Courtot GROUP:OBI:<http://purl.obolibrary.org/obo/obi> imported from expand expression to ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones Chris Mungall expand expression to OBO foundry unique label An alternative name for a class or property which is unique across the OBO Foundry. The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . PERSON:Alan Ruttenberg PERSON:Bjoern Peters PERSON:Chris Mungall PERSON:Melanie Courtot GROUP:OBO Foundry <http://obofoundry.org/> OBO foundry unique label elucidation person:Alan Ruttenberg Person:Barry Smith Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms elucidation 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 assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. temporal interpretation temporal interpretation 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 http://purl.obolibrary.org/obo/ro/docs/shortcut-relations/ A logical macro assertion whose domain is an IRI for a property logical macro assertion on a property Used to annotate object properties to describe a logical meta-property or characteristic of the object property. logical macro assertion on an object property part-of is homeomorphic for independent continuants. R is homemorphic for C iff (1) there exists some x,y such that x R y, and x and y instantiate C and (2) for all x, if x is an instance of C, and there exists some y some such that x R y, then it follows that y is an instance of C. 2018-10-21T19:46:34Z R homeomorphic-for C expands to: C SubClassOf R only C. Additionally, for any class D that is disjoint with C, we can also expand to C DisjointWith R some D, D DisjointWith R some C. is homeomorphic for example utterance disease characteristic (MONDO:0021125) has cross-reference (http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NCIT:C41009"^^xsd:string An annotation property that links an ontology entity or a statement to a prefixed identifier or URI. 2024-03-18 database_cross_reference has cross-reference An alternative label for a class or property which has the exact same meaning than the preferred name/primary label. https://github.com/information-artifact-ontology/ontology-metadata/issues/20 has exact synonym has_exact_synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/20 An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct. https://github.com/information-artifact-ontology/ontology-metadata/issues/21 has related synonym has_related_synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/21 in_subset is defined by label The range of skos:altLabel is the class of RDF plain literals. skos:prefLabel, skos:altLabel and skos:hiddenLabel are pairwise disjoint properties. alternative label An alternative lexical label for a resource. Acronyms, abbreviations, spelling variants, and irregular plural/singular forms may be included among the alternative labels for a concept. Mis-spelled terms are normally included as hidden labels (see skos:hiddenLabel). change note A note about a modification to a concept. definition A statement or formal explanation of the meaning of a concept. editorial note A note for an editor, translator or maintainer of the vocabulary. example An example of the use of a concept. The range of skos:hiddenLabel is the class of RDF plain literals. skos:prefLabel, skos:altLabel and skos:hiddenLabel are pairwise disjoint properties. hidden label A lexical label for a resource that should be hidden when generating visual displays of the resource, but should still be accessible to free text search operations. history note A note about the past state/use/meaning of a concept. note A general note, for any purpose. This property may be used directly, or as a super-property for more specific note types. A resource has no more than one value of skos:prefLabel per language tag, and no more than one value of skos:prefLabel without language tag. The range of skos:prefLabel is the class of RDF plain literals. skos:prefLabel, skos:altLabel and skos:hiddenLabel are pairwise disjoint properties. preferred label The preferred lexical label for a resource, in a given language. scope note A note that helps to clarify the meaning and/or the use of a concept. is part of my brain is part of my body (continuant parthood, two material entities) my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) this day is part of this year (occurrent parthood) a core relation that holds between a part and its whole Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ 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 https://wiki.geneontology.org/Part_of has part my body has part my brain (continuant parthood, two material entities) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ 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 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 to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realizes preceded by x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by http://www.obofoundry.org/ro/#OBO_REL:preceded_by preceded by precedes x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. precedes This document is about information artifacts and their representations A (currently) primitive relation that relates an information artifact to an entity. 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. person:Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy is about A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named. A primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically 2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. g denotes r =def r is a portion of reality there is some c that is a concretization of g every c that is a concretization of g specifically denotes r person:Alan Ruttenberg Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan denotes inverse of the relation 'denotes' Person: Jie Zheng, Chris Stoeckert, Mike Conlon denoted by has_specified_output has_specified_output The inverse property of is_specified_output_of PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Courtot has_specified_output is_specified_output_of is_specified_output_of A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters is_specified_output_of is_specified_output_of inheres in this fragility is a characteristic of this vase this red color is a characteristic of this apple a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. inheres_in Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. characteristic of bearer of this apple is bearer of this red color this vase is bearer of this fragility Inverse of characteristic_of A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. bearer_of is bearer of bearer_of has characteristic participates in this blood clot participates in this blood coagulation this input material (or this output material) participates in this process this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process participates_in participates in has participant this blood coagulation has participant this blood clot this investigation has participant this investigator this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant http://www.obofoundry.org/ro/#OBO_REL:has_participant http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant has_participant A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a generically dependent continuant and a specifically dependent continuant or process, in which the generically dependent continuant depends on some independent continuant or process in virtue of the fact that the specifically dependent continuant or process also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants or processes. is concretized as concretizes A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. A relationship between a specifically dependent continuant or process and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant or process also depends on that same independent continuant. Multiple specifically dependent continuants or processes can concretize the same generically dependent continuant. http://purl.obolibrary.org/obo/obi.owl concretizes A part of relation that applies only between occurrents. occurrent part of 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. 2017-05-24T09:49:21Z has component process David Osumi-Sutherland X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after 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 https://wiki.geneontology.org/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 'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair')) heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation') x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a "canonical" heart, which participates in blood circulation. Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from) TODO: add homeomorphy axiom This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants. has prototype mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) osteoclast SubClassOf 'capable of' some 'bone resorption' A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. has function realized in For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". capable of c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. has function in capable of part of 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 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 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. consumes has input https://wiki.geneontology.org/Has_input q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. Because part_of is transitive, inheres in is a sub-relation of characteristic of part of inheres in part of characteristic of part of A mereological relationship or a topological relationship Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships mereotopologically related to a particular instances of akt-2 enables some instance of protein kinase activity c enables p iff c is capable of p and c acts to execute p. catalyzes executes has is catalyzing is executing This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. enables https://wiki.geneontology.org/Enables A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. This is a grouping relation that collects relations used for the purpose of connecting structure and function functionally related to inverse of enables enabled by https://wiki.geneontology.org/Enabled_by inverse of has input input of relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. 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. 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 iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. causally upstream of p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 influences (processual) affects causally upstream of or within inverse of causally upstream of or within causally downstream of or within A relationship between a material entity and a process where the material entity has some causal role that influences the process causal agent in process p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. 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 depends on The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between entities A relation that holds between two entities that have the property of being sequences or having sequences. http://www.ncbi.nlm.nih.gov/pubmed/20226267 Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect. The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene. sequentially related to Every CDS has as a start sequence the start codon for that transcript x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence started by http://www.ncbi.nlm.nih.gov/pubmed/20226267 has start sequence inverse of has start sequence starts http://www.ncbi.nlm.nih.gov/pubmed/20226267 is start sequence of inverse of has end sequence ends http://www.ncbi.nlm.nih.gov/pubmed/20226267 is end sequence of x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y. In the SO paper, this was defined as an instance-type relation http://www.ncbi.nlm.nih.gov/pubmed/20226267 is consecutive sequence of The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons) x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y bounds sequence of inverse of bounds sequence of is bound by sequence of x has subsequence y iff all of the sequence parts of y are sequence parts of x contains http://www.ncbi.nlm.nih.gov/pubmed/20226267 has subsequence inverse of has subsequence contained by is subsequence of x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y. overlaps sequence of The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). causally influences (entity-centric) causally influences A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between material entity and a process Inverse of 'causal agent in process' process has causal agent Molecules of DNA are carriers of genetic information. This copy of *War and Peace* is carrier of the novel written by Tolstoy. This hard drive is carrier of these data items. *b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t* [072-ISO] is carrier of Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. TODO: Add homeomorphy axiom ECO:0000041 SO:similar_to sameness similar to correspondence resemblance in similarity relationship with has broader match skos:broadMatch is used to state a hierarchical mapping link between two conceptual resources in different concept schemes. Broader concepts are typically rendered as parents in a concept hierarchy (tree). has broader Relates a concept to a concept that is more general in meaning. By convention, skos:broader is only used to assert an immediate (i.e. direct) hierarchical link between two conceptual resources. has broader transitive skos:broaderTransitive is a transitive superproperty of skos:broader. By convention, skos:broaderTransitive is not used to make assertions. Rather, the properties can be used to draw inferences about the transitive closure of the hierarchical relation, which is useful e.g. when implementing a simple query expansion algorithm in a search application. has close match skos:closeMatch is used to link two concepts that are sufficiently similar that they can be used interchangeably in some information retrieval applications. In order to avoid the possibility of "compound errors" when combining mappings across more than two concept schemes, skos:closeMatch is not declared to be a transitive property. skos:exactMatch is disjoint with each of the properties skos:broadMatch and skos:relatedMatch. has exact match skos:exactMatch is used to link two concepts, indicating a high degree of confidence that the concepts can be used interchangeably across a wide range of information retrieval applications. skos:exactMatch is a transitive property, and is a sub-property of skos:closeMatch. has top concept Relates, by convention, a concept scheme to a concept which is topmost in the broader/narrower concept hierarchies for that scheme, providing an entry point to these hierarchies. is in scheme Relates a resource (for example a concept) to a concept scheme in which it is included. A concept may be a member of more than one concept scheme. These concept mapping relations mirror semantic relations, and the data model defined below is similar (with the exception of skos:exactMatch) to the data model defined for semantic relations. A distinct vocabulary is provided for concept mapping relations, to provide a convenient way to differentiate links within a concept scheme from links between concept schemes. However, this pattern of usage is not a formal requirement of the SKOS data model, and relies on informal definitions of best practice. is in mapping relation with Relates two concepts coming, by convention, from different schemes, and that have comparable meanings has member Relates a collection to one of its members. For any resource, every item in the list given as the value of the skos:memberList property is also a value of the skos:member property. has member list Relates an ordered collection to the RDF list containing its members. has narrower match skos:narrowMatch is used to state a hierarchical mapping link between two conceptual resources in different concept schemes. Narrower concepts are typically rendered as children in a concept hierarchy (tree). has narrower Relates a concept to a concept that is more specific in meaning. By convention, skos:broader is only used to assert an immediate (i.e. direct) hierarchical link between two conceptual resources. has narrower transitive skos:narrowerTransitive is a transitive superproperty of skos:narrower. By convention, skos:narrowerTransitive is not used to make assertions. Rather, the properties can be used to draw inferences about the transitive closure of the hierarchical relation, which is useful e.g. when implementing a simple query expansion algorithm in a search application. skos:related is disjoint with skos:broaderTransitive has related Relates a concept to a concept with which there is an associative semantic relationship. has related match skos:relatedMatch is used to state an associative mapping link between two conceptual resources in different concept schemes. is in semantic relation with Links a concept to a concept related by meaning. This property should not be used directly, but as a super-property for all properties denoting a relationship of meaning between concepts. is top concept in scheme Relates a concept to the concept scheme that it is a top level concept of. been spoken has focus utterance string notation A notation, also known as classification code, is a string of characters such as "T58.5" or "303.4833" used to uniquely identify a concept within the scope of a given concept scheme. By convention, skos:notation is used with a typed literal in the object position of the triple. entity Entity Julius Caesar Verdi’s Requiem the Second World War your body mass index BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) entity continuant Continuant An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] continuant occurrent Occurrent An entity that has temporal parts and that happens, unfolds or develops through time. BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] occurrent ic IndependentContinuant a chair a heart a leg a molecule a spatial region an atom an orchestra. an organism the bottom right portion of a human torso the interior of your mouth 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] A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. independent continuant 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] An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. process 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 realizable entity quality Quality the ambient temperature of this portion of air the color of a tomato the length of the circumference of your waist the mass of this piece of gold. the shape of your nose the shape of your nostril a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] quality sdc SpecificallyDependentContinuant Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key of one-sided specifically dependent continuants: the mass of this tomato of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. the disposition of this fish to decay the function of this heart: to pump blood the mutual dependence of proton donors and acceptors in chemical reactions [79 the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction the pink color of a medium rare piece of grilled filet mignon at its center the role of being a doctor the shape of this hole. the smell of this portion of mozzarella A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] 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. characteristic specifically dependent continuant https://github.com/OBOFoundry/COB/issues/65 https://github.com/oborel/obo-relations/pull/284 object-aggregate ObjectAggregate a collection of cells in a blood biobank. a swarm of bees is an aggregate of members who are linked together through natural bonds a symphony orchestra an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team) defined by fiat: the aggregate of members of an organization defined through physical attachment: the aggregate of atoms in a lump of granite defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container defined via attributive delimitations such as: the patients in this hospital the aggregate of bearings in a constant velocity axle joint the aggregate of blood cells in your body the nitrogen atoms in the atmosphere the restaurants in Palo Alto your collection of Meissen ceramic plates. An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee). ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] object aggregate 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] 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. generically dependent continuant 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. Elucidation: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] material entity immaterial entity data item Data items include counts of things, analyte concentrations, and statistical summaries. An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief PERSON: Alan Ruttenberg PERSON: Chris Stoeckert PERSON: Jonathan Rees data data item information content entity 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 curation status specification The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) PERSON:Bill Bug GROUP:OBI:<http://purl.obolibrary.org/obo/obi> OBI_0000266 curation status specification data about an ontology part Data about an ontology part is a data item about a part of an ontology, for example a term Person:Alan Ruttenberg data about an ontology part An utterance is an information content entity that is a complete unit of speech in spoken language. Mathias Brochhausen Wikipedia: http://en.wikipedia.org/wiki/Utterance Mathias Brochhausen utterance An attributive collection of qualities inhering in energy when transported through a medium in a wave. Mathias Brochhausen mechanical wave quality portion of energy Energy that is transported in a sound wave. Mathias Brochhausen sound energy Sound energy bearing the concretization of an utterance and being the output of an uttering process. utterance energy Oscillating is a processual that shows repetitive variation, typically in time, of some measured quality about a central value (often a point of equilibrium) or between two or more different states. http://en.wikipedia.org/wiki/Oscillation Mathias Brochhausen oscillating is a planned process of making speech sounds which may or may not have an actual language involved. Mathias Brochhausen http://en.wiktionary.org/wiki/utter Mathias Brochhausen utterance process Homo sapiens human being Homo sapiens planned process planned process Injecting mice with a vaccine in order to test its efficacy A process that realizes a plan which is the concretization of a plan specification. 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process. Bjoern Peters branch derived 6/11/9: Edited at workshop. Used to include: is initiated by an agent This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) planned process organism animal fungus plant virus A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') 13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI. GROUP: OBI Biomaterial Branch WEB: http://en.wikipedia.org/wiki/Organism organism Taking notes on a meeting is an example in which the concretization relation is newly established, since the SDCs that concretize the GDCs come into existence as the notes are written. In contrast, using slides prepared by someone else in order to convey information during a presentation is a case of using a concretization in which the performer neither brings the concretizing SDCs into existence nor is responsible for their standing in the concretization relation to the relevant GDCs. A nonlinguistic example is drawing the logo of one’s favorite brand, in which one creates a pattern that concretizes a GDC that is also concretized by patterns on products of the brand. Process in which some participant utilizes some specifically dependent continuant as a concretization of some generically dependent continuant. S. Clint Dowland Matthew Diller Sarah Bost William R. Hogan Instances include any process that brings it about that some specifically dependent continuant begins to stand in a concretization relation to some generically dependent continuant, as well as any process in which someone makes use of a pre-established concretization relation. To be clear, instances do not include using concretizations of words or letters for purposes that do not make use of the concretization relations in which they stand (for example, hanging up a sign in a foreign language as a decoration because one likes the colors, despite having no idea what the sign says). Instances include, but are not limited to, processes that bring about cognitive concretizations. concretization-utilization process For example, reading a text message that says, “It is raining outside,” and inferring that the words on the screen are meant to convey information about the weather. The pattern on the screen that corresponds to the words is the SDC, and the ICE about the rain is the GDC. Or, hearing your spouse say, “Can you come to the kitchen?” and then knowing that your spouse wants you to come to the kitchen. You have interpreted the patterns of the sound as concretizing a GDC about what your spouse wants. Or, seeing a drawing of a basketball player and inferring—perhaps incorrectly—that it is of Michael Jordan. Process in which some participant infers that some particular specifically dependent continuant stands in the concretization relation to some particular generically dependent continuant. S. Clint Dowland Matthew Diller Sarah Bost William R. Hogan The interpretation need not be accurate. It may even be the case that the specifically dependent continuant has not previously concretized anything. concretization-interpretation process A process in which some participant shares some generically dependent continuant with some other participant. The former utilizes some specifically dependent continuant that concretizes the generically dependent continuant intended to be shared, while the latter interprets that specifically dependent continuant to concretize some particular generically dependent continuant, aiming to accurately infer the other participant’s intent. S. Clint Dowland Mathias Brochhausen Matthew Diller William R. Hogan For example, if you tell someone, “It is raining,” you produce sounds that have patterns that concretize information about the weather. Your utilization of that concretization is part of the communication. When the other person hears you, they interpret those patterns to concretize something, which may or may not be the same as what you intended to convey. In other words, they interpret the sounds you produce to have meanings associated with them, and that interpretation process is another part of the communication. If a process does not have a part of each type, it is not a communication. The interpretation need not correspond exactly to what was intended by the other participant. The term 'participant' in the definition need not refer to a human agent. communication quality pressure Any entity that is ordered in discrete units along a linear axis. sequentially ordered entity Any individual unit of a collection of like units arranged in a linear order An individual unit can be a molecular entity such as a base pair, or an abstract entity, such as the abstraction of a base pair. sequence atomic unit Conversational patterns involving methods to connect or discconect with participants conversation level management A pattern involving "methodically and collaboratively close down the encounter...using the activities of opening and closing to mark the boundaries between this conversation and the next one." (Moore and Arar, 2019) closing A pattern involving "disengagements [that] may be temporary or terminal. Besides the user or agent simply failing to continue, users may ask to be transferred to a human, or users may start talking to someone else in the room, agents may refuse to continue talking, and more." (Moore and Arar, 2019) disengaging "secur[ing] the attention of the intended recipient and establish that we are talking to each other." (Moore and Arar, 2019). This is pattern is initiated by the agent opening by agent "secur[ing] the attention of the intended recipient and establish that we are talking to each other." (Moore and Arar, 2019). This is pattern is initiated by the user opening by user A pattern involving "talk[ing] to the agent about what it can do. For a virtual agent to be intelligent and conversational, it must be able to talk about what it can and cannot do." (Moore and Arar, 2019) capabilities closing offer disaffirmed closing offer affirmed closing success check reopened closing success check disaffirmed closing success check affirmed closing name request by agent closing appreciation by organizational closing farewell by user pre-closing by user last topic check by user last topic check by agent offense complaint by user offense complaint by agent recipient correction transfer aborted transfer successful opening greeting by agent opening self-identification by agent opening name request by agent opening direct address by agent opening welfare check by agent opening organization offer of help by agent opening authentication by agent organizational problem request by agent greeting by user summons by user welfare check by user displaced welfare check by user general capability check capability expansion specific capability check utterance suggestion "Sequence-level management involves repairing a previous utterance in order to complete a sequence, closing a sequence, or aborting a sequence." (Moore and Arar, 2019) sequence level management This pattern is "enable users to indicate that they are done with a sequence or activity and ready to move on. Sequence closers include several intents, including acknowledgments (e.g., okay, ok, all right, got it), appreciations (e.g., thank you, thanks, ok thanks), laughter tokens (e.g., haha, ha ha, lol), positive assessments (e.g., great!, excellent, awesome!), or negative assessments (e.g., too bad, oh well, that sucks)." (Moore and Arar, 2019) sequence closer This pattern is repair that involves multiple turns beyond the SPP. extended repair This pattern "referr[s] specifically to the repeating and paraphrasing of prior utterances or parts of them." (Moore and Arar, 2019) This pattern can be initiated by the user repair by user This pattern "referr[s] specifically to the repeating and paraphrasing of prior utterances or parts of them." (Moore and Arar, 2019) This pattern can be initiated by the agent repair by agent This pattern involving "abandon[ing] a failing sequence without completing or closing it, with phrases like 'nevermind', 'nvm', 'forget it', 'I give up', etc. This might be done when the agent fails to understand the user or to return the desired information and the user wishes to stop trying" (Moore and Arar, 2019) sequence abort sequence closer - repaired sequence closer appreciation - not helped sequence closer appreciation - helped sequence closer - not helped sequence closer - helped sequence-closing thirds self correction misunderstanding report other hearing check and mishearing report other correction A type of conversation navigation that "elicit repeats of all or part of the agent's utterances" (Moore and Arar, 2019) repeat request repeat request default partial repeat request hearing check confirmed hearing check correction paraphrase request paraphrase request default definition request repair definition request default definition request standalone example request example request default understanding check confirmed understanding check disconfirmed understanding check (agent) paraphrase request (agent) subsequent paraphrase requests agent continuor no answer account repeat acknowledgement sequence abort capability offer accept sequence abort capability offer declined "handle the main business of the conversation: what services the agent provides and what the user is trying to accomplish." (Moore and Arar, 2019) conversational activities The "pattern may involve closed or open inquiries and different third-position checks by the agent to determine if the agent heard the user correctly or if the user has more to say. The agent inquiry pattern is especially useful for interviewing users or eliciting their opinions, where you wish to elicit and preserve the exact words of the user." (Moore and Arar, 2019) inquiry by agent agent inquiry "patterns can also be combined in a variety of ways to support pedagogical activities, such as tutoring. For example, the extended telling pattern can be combined with the quiz pattern to teach the user new material and test his or her retention" (Moore and Arar, 2019) teaching tutoring A pattern that "handles requests for information initiated by the user, for example in question-and-answer (Q&A) scenarios. Like all conversational UX patterns, the pattern itself is separate from the content. In other words, agents may answer inquiries about health insurance, travel policies, movie trivia, small talk, and much more. For example, the agent may answer inquiries about computer history" (Moore and Arar, 2019). This is pattern is initiated by the user. inquiry by user user inquiry A pattern where "the user makes a request, for example in customer service conversations. It handles sets of related requests, or topics, that require entity extraction and agent elicitations (a.k.a. "slot filling"). Multiple entities are captured, even when no request type is recognized, and preserved as context across the set of unique requests (i.e., intents).... [may] require a little more context design than standalone requests or 'slotted intents'. They require a context variable for the topic that is relevant across multiple requests or intents." (Moore and Arar, 2019) open request A pattern where "activities that typically require more than one turn to complete. Such extended tellings may be initiated by the user with requests like, "tell me about Key West," "tell me all the things you can do," "tell me a story," "how do I meditate?," "how do I do that?," etc. The telling is then produced interactionally in the following way: the teller gives the first part of the telling and then waits for an indication from the recipient to continue the telling" (Moore and Arar, 2019) extended telling "the quiz pattern involves the agent asking the user questions and evaluating the answers. The user can get the answer right, wrong, initiate a repair, or give up. The quiz is a basic conversation pattern that is used in pedagogical interactions, as well as for fun. The ordinary question-answer joke uses the quiz pattern, as do trivia games. In its simplest form, the quiz pattern is initiated by the user, who then answers the question correctly" (Moore and Arar, 2019) quiz "the customer or service seeker presents a problem to the representative or agent of the organization and requests a solution. The agent may need to probe the user�s situation with a series of diagnostic questions in order to determine the likely cause of the problem and the appropriate solution. The agent may then talk the user through a set of instructions for solving the problem. Troubleshooting can therefore be supported by combining the open request and extended telling patterns." (Moore and Arar, 2019). Initiated by the user troubleshooting user-initiated inquiry by agent extended answer inquiry by agent completion check inquiry by agent hearing disconfirmed inquiry by agent hearing confirmed inquiry by agent open inquiry by user confirmation inquiry by user disconfirmation inquiry by user repairs open request nonverbal open request continuer open request screening open request agent detail request open request user detail request open request summary warrant request and refusal open request summary with artifacts open request incremental open request series open request repairs extended telling abort extended telling with repair quiz incorrect quiz repairs quiz user-initiated quiz agent-initiated A theortical framework for natural conversational design; Core application ontology concept framing natural language framework natural conversation model "conversational actions for getting around the conversation space that are easy for users to remember" (Moore and Arar, 2019) conversation navigation expandable sequences, like an accordion [Moore et al. 2016, Moore 2018]. Compact sequences are common, but each sequence can be expanded by either party as needed. interaction model Style and presentation of the content of an utterance content format "formal structures or patterns of human talk-in-interaction" (Moore and Arar, 2019) pattern language repeat request A type of conversation navigation that "to close their interaction with the system. This is similar to closing an application or logging out of a system" (Moore and Arar, 2019) conversation closing sequence abort A type of conversation navigation that to assess by way of conversation to find out the capabilities of the agent. capability check sequence closer An utterance expressed in one sentence or smaller unit short content format An autterance presented in a multiple sentence utterance or document-like format long content format story telling A sequence involving an FPP and SPP. "An adjacency pair is composed of two utterances by two speakers, one after the other. The speaking of the first utterance (the first-pair part, or the first turn) provokes a responding utterance (the second-pair part, or the second turn)" (Wikipedia) adjacency pair base sequence; action pair A type of TCU that initaties an adjacency pair first pair part fpp A type of TCU that closes an adjacency pair second pair part spp Smallest unit of speech utterance action type design type preferred response dispreferred response "fundamental segment of speech in a conversation...pieces of conversation which may comprise an entire speaking turn by a speaker. A turn is created through certain forms or units that listeners can recognize and count on, called turn construction units (TCUs), and speakers and listeners will know that such forms can be a word or a clause, and use that knowledge to predict when a speaker is finished so that others can speak, to avoid or minimize both overlap and silence." (Wikipedia) turn conversational unit something expressed by an individual that not only presents information but performs an action as well (Wikipedia) speech acts basic element of language that carries meaning, can be used on its own, and is uninterruptible (Wikipedia) words "group of words or singular word acting as a grammatical unit." (Wikipedia) phrases constituent or phrase that comprises a semantic predicand (expressed or not) and a semantic predicate. A typical clause consists of a subject and a syntactic predicate, the latter typically a verb phrase composed of a verb with or without any objects and other modifiers. (Wikipedia) clauses string of words that expresses a complete thought, or as a unit consisting of a subject and predicate (Wikipedia) sentence "Sequences are general patterns that, like tools or devices, can be used and reused in all kinds of different situations and settings, for all kinds of different purposes. " (Moore and Arar, 2019) sequence sequence of utterances that elaborates on the base interaction for additional information. Helps in mutual understanding between parties. sequence expansion a type of sequence expansion that occurs after the base sequence interaction post expansion Conversational sequence with the the goal of rectifying misunderstanding or miscommunication during a conversation. "Repairs consist of a redoing of all or part of a previous utterance, either by the speaker or a recipient, where that utterance poses difficulty in speaking, hearing, or understanding and thereby prevents the conversation from moving forward" (Moore and Arar, 2019) repair elicit an insertion sequence emerged out of the base adjacency pair (between the FPP and SPP). insert expansion repeat a type of sequence expansion that occurs before the base sequence interaction, specifically before the FPP. They consist of their own sequence pairs pre-expansion pre sequences screen Occurs after the SPP of the base pair, and an extension of SPP where the SPP is the FPP of another SPP, essentially stretching the base pair. non-minimal post expansion An additional turn sequence after the base sequence pair. Designed not to emphasize the base sequence, and typically a closing sequence. minimal post expansion an insertion sequence emerging after the FPP post first pair part insert expansion an insertion sequence emerging before the SPP pre second pair part insert expansion "Pre-requests... checks on the availability of the time to be asked for" (Sidell, 2015) pre request Pre-invitation often check on the availability of the intended invitee (Sidnell, 2015) pre-invitation Sometimes prefaces announcements or stories. "[T]ypicall check on a condition for the successful accomplishment of the base first pair part... often takes the form of question about what the recipient knows" (Sidnell, 2015) pre-announcement "A next turn repair initiator is an utterance, used in the turn after a repairable item, that prompts for a third turn repair in the next turn." https://glossary.sil.org/term/next-turn-repair-initiator next turn repair initiator ntri "constative is the expression of a belief, together with the expression of an intention that the hearer form (or continue to hold) a like belief." (Bach and Harnish, 1979) constatives "They express, perfunctorily if not genuinely, certain feelings toward the hearer. These feelings and their expression are appropriate to particular sorts of occasions...Because acknowledgments are expected on particular occasions, they are often issued not so much to express a genuine feeling as to satisfy the social expectation that such a feeling be expressed." (Bach and Harnish, 1979) acknowledgements Commissives are acts of obligating oneself or of proposing to obligate oneself to do something specified in the propositional content, which may also specify conditions under which the deed is to be done or does not have to be done. (Bach and Harnish, 1979) commissives "Directives express the speaker's attitude toward some prospective action by the hearer." (Bach and Harnish, 1979) directives in uttering e, S asserts that P if S expresses: i. the belief that P, and ii. the intention that H believe that P. (Bach and Harnish, 1979) affirming assert; allege; aver; avow; claim; declare; deny; incate; maintain; propound; say; state; submit alleging announcing In uttering e, S responds that P if S expresses: i. the belief that P, which H has inquired about, and ii. the intention that H believe that P. (Bach and Harnish, 1979) answering answer; reply; respond; retort In uttering e, S ascribes F to 0 if S expresses: i. the belief that F applies to 0, and ii. the intention that H believe that F applies to o. (Bach and Harnish, 1979) attributing ascribe; attribute; predicate claiming In uttering e, S describes 0 as F if S expresses: i. the belief that 0 is F, and ii. the intention that H believe that 0 is F. (Bach and Harnish, 1979) classifying appraise; assess; call; categorize; characterize; classify; date; describe; diagnosie; evaluate; grade; identify; portray; rank In uttering e, S assents to the claim that P if S expresses: i. the belief that P, as claimed by H (or as otherwise under discussion), and ii. the intention (perhaps already fulfilled) that H believe that P. (Bach and Harnish, 1979) concurring accept; agree; assent; concur In uttering e, S confirms (the claim) that P if S expresses: i. the belief that P, based on some truth-seeking procedure, and ii. the intention that H believe that P because S has support for P. (Bach and Harnish, 1979) confirming appraise; assess; bear witness; certify; conclude; confirm; corroborate; diagnose; find; judge; substantiate; testify; validate; verify; vouch for In uttering e, S suggests that P if S expresses: i. the belief that there is reason, but not sufficient reason, to believe that P, and ii. the intention that H believe that there is reason, but not sufficient reason, to believe that P. (Bach and Harnish, 1979) conject uring conjecture; guess; hypothesize; speculate; suggest denying In uttering e, S dissents from the claim that P if S expresses: i. the disbelief that P, contrary to what was claimed by H (or was otherwise under discussion), and ii. the intention that H disbelieve that P (Bach and Harnish, 1979) diagreeing differ; disagree; dissent; reject disclosing In uttering e, S disputes the claim that P if S expresses: i. the belief that there is reason not to believe that P, contrary to what was claimed by H (or was otherwise under discussion), and ii. the intention that H believe that there is reason not to believe that P (Bach and Harnish, 1979) disputing demur; dispute; object; protest; question identifying In uttering e, S informs H that P if S expresses: i. the belief that P, and ii. the intention that H form the belief that P. (Bach and Harnish, 1979) informing advise; annouce; appraise; disclose; inform; insist; notify; point out; report; reveal; tell; testify insisting In uttering e, S predicts that P if S expresses: i. the belief that it will be the case that P, and ii. the intention that H believe that it will be the case that P. (Bach and Harnish, 1979) predicting forecast; prophesy ranking In uttering e, S retrodicts that P if S expresses: i. the belief that it was the case that P, and ii. the intention that H believe that it was the case that P. (Bach and Harnish, 1979) reporting recount; report; retrodictives stating In uttering e, S supposes that P if S expresses: i. the belief that it is worth considering the consequences of P, and ii. the intention that H believe that it is worth considering the consequences of P. (Back and Harnish, 1979) stipulating assume; hypothesize; posturlate; stipulate; suppose; theorize In uttering e, S apologizes to H for D if S expresses: i. regret for having done D to H, and ii. the intention that H believe that S regrets having done D to H, or i. the intention that his utterance satisfy the social expectation that one express regret for having done something regrettable like D, and ii. the intention that H take S's utterance as satisfying this expectation. (Bach and Harnish, 1979) apologizing In uttering e, S condoles H for (misfortune) D if S expresses: i. sympathy with H's having (or suffering) D, and ii. the intention that H believe that S sympathizes with H's having D, or i. the intention that his utterance satisfy the social expectation that one express sympathy for misfortunes like D, and ii. the intention that H take S's utterance as satisfying this expectation. (Bach and Harish, 1979) condoling commiserate; condole In uttering e, S congratulates H for D if S expresses: i. gladness for H's having D(-ed), and ii. the intention that H believe that S is glad that H has D(-ed), or i. the intention that his utterance satisfy the social expectation that one express gladness for good fortunes like D( -ing), and ii. the intention that H take S's utterance as satisfying this expectation (Bach and Harnish, 1979) congratulating compliment; congratulate; felicitate In uttering e, S greets H if S expresses: i. pleasure at seeing (or meeting) H, and ii. the intention that H believe that S is pleased to see (or meet) H, or i. the intention that his utterance satisfy the social expectation that one express pleasure at seeing (or meeting) someone, and ii. the intention that H take S's utterance as satisfying this expectation. (Bach and Harnish, 1979) greeting In uttering e, S thanks H for D if S expresses: i. gratitude to H for D, and ii. the intention that H believe that S is grateful to H for D, or i. the intention that his utterance satisfy the social expectation that one express gratitude at being benefited, and ii. the intention that H take S' s utterance as satisfying this expectation. "No thanks": S thanks H for offering D and rejects the offer (Bach and Harnish, 1979) thanking In uttering e, S accepts H's acknowledgment if S expresses: i. appreciation for H's . acknowledgment, and ii. the intention that H believe that S appreciates H's acknowledgment, or i. the intention that his utterance satisfy the social expectation that one express appreciation of an acknowledgment, and ii. the intention that H take S's utterance as satisfying this expectation. "You're welcome": S accepts H's thanks (Bach and Harnish, 1979) accepting (acknowledging an acknowledgement) contract: Sand H make mutually conditional promises; fulfillment of each is conditional on the fulfillment of the other (Bach and Harnish, 1979) agreeing guarantee that: S affirms (constative) the quality of something, x, and promises to make repairs or restitution if x is relevantly defective. guarantee x: S promises to make repairs or restitution if x is defective in some relevant respect. (Bach and Harnish, 1979) guaranteeing S requests (directive) H's presence and promises acceptance of his presence. (Bach and Harnish, 1979) inviting In uttering e, S offers A to H if S expresses: i. the belief that S's utterance obligates him to A on condition that H indicates he wants S to A, ii. the intention to A on condition that H indicates he wants S to A, and iii. the intention that H believe that S's utterance obligates S to A and that S intends to A, on condition that H indicates he wants S to A. (Bach and Harnish, 1979) offering offer; propose In uttering e, S promises H to A if S expresses: i. the belief that his utterance obligates him to A, ii. the intention to A, and iii. the intention that H believe that S's utterance obligates S to A and that S intends to A. (Bach and Harnish, 1979) promising promise; swear; vow swear that: S asserts (constative) that P and promises that he is telling the truth. (Bach and Harnish, 1979) swearing S offers his services. (Bach and Harnish, 1979) volunteering In uttering e, S advises H to A if S expresses: i. the belief that there is (sufficient) reason for H to A, and ii. the intention thatH take S's belief as (sufficient) reason for him to A. (Bach and Harnish, 1979) advising admonish; advise; caution; counsel; propose; recommend; suggest; urge; warn admonishing In uttering e, S questions H as to whether or not P if S expresses: i. the desire that H tell S whether or not P, and ii. the intention that H tell S whether or not P because of S's desire. (Bach and Harnish, 1979) asking ask; inquire; interrogate; query; question; quiz In uttering e, S requests H to A if S expresses: i. the desire that H do A, and ii. the intention that H do A because (at least partly) of S's desire. (Bach and Harnish, 1979) begging ask; beg; beseech; implore; insiste; invite; petition; plead; pray; request; solicit; summon; supplicate; tell; urge dismissing execusing In uttering e, S prohibits H from A-ing if S expresses: i. the belief that his utterance, in virtue of his authority over H, constitutes sufficient reason for H not to A, and ii. the intention that because of S's utterance H not do A. (Bach and Harnish, 1979) forbidding enjoin; forbid; prohibit; proscribe; restrict instructing In uttering e, S requires H to A if S expresses: i. the belief that his utterance, in virtue of his authority over H, constitutes sufficient reason for H to A, and ii. the intention that H do A because of S's utterance. (Bach and Harnish, 1979) ordering bid; charge; command; demand; dictate; direct; enjoin; instruct; order; prescribe; require In uttering e, S permits H to A if S expresses: i. the belief that his utterance, in virtue of his authority over H, entitles H to A, and ii. the intention that H believe that S's utterance entitles him to A. (Bach and Harnish, 1979) permitting agree to; allow; authorize; bless; consent to; dismiss; execuse; exempt; forgive; grant; license; pardon; release; sanction requesting requiring suggesting urging warning An artifical autonomous system agent software agent A human participant in an interaction (e.g.conversation) with a machine user human user Merriam-Webster. (n.d.). Uncommunicative. In Merriam-Webster.com dictionary. Retrieved December 2, 2025, from https://www.merriam-webster.com/dictionary/uncommunicative not disposed to talk or impart information uncommunicative An utterance expressed by entity that is a machine machine utterance a type of utterance that is expressed by human human utterance Collection A meaningful collection of concepts. Labelled collections can be used where you would like a set of concepts to be displayed under a 'node label' in the hierarchy. Concept An idea or notion; a unit of thought. Concept Scheme A set of concepts, optionally including statements about semantic relationships between those concepts. Thesauri, classification schemes, subject heading lists, taxonomies, 'folksonomies', and other types of controlled vocabulary are all examples of concept schemes. Concept schemes are also embedded in glossaries and terminologies. A concept scheme may be defined to include concepts from different sources. Ordered Collection An ordered collection of concepts, where both the grouping and the ordering are meaningful. Ordered collections can be used where you would like a set of concepts to be displayed in a specific order, and optionally under a 'node label'. example to be eventually removed example to be eventually removed metadata complete Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. metadata complete organizational term Term created to ease viewing/sort terms for development purpose, and will not be included in a release organizational term ready for release Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." ready for release metadata incomplete Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. metadata incomplete uncurated Nothing done yet beyond assigning a unique class ID and proposing a preferred term. uncurated pending final vetting All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. pending final vetting to be replaced with external ontology term Terms with this status should eventually replaced with a term from another ontology. Alan Ruttenberg group:OBI to be replaced with external ontology term requires discussion A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. Alan Ruttenberg group:OBI requires discussion ## Elucidation This is used when the statement/axiom is assumed to hold true &apos;eternally&apos; ## How to interpret (informal) First the &quot;atemporal&quot; 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 bioinformatics researcher Christopher J. Mungall researcher David Osumi-Sutherland