Christian Hauschke Christoph Lange Michael Conlon Philip Strömert _WIP - NOT READY FOR PRODUCTION_ The Academic Event Ontology (AEON) is used to represent information regarding academic events. The ontology supports the identification, development, management, evaluation, and impact assessment of events, components of events and event series, as well as identification and reuse of works presented or developed at events. The ontology is independent of knowledge, creative domain, or topics related to events. AEON is focused on events and assumes the representation of many entities associated with events such as attendees, locations, academic works, datetimes, and processes are defined in compatible ontologies. Academic Event Ontology AEON is being developed as a part of the ConfIDent project (https://projects.tib.eu/confident). 2022-06-27 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 term example of usage A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> example of usage in branch An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet. GROUP:OBI OBI_0000277 in branch has curation status PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot has curation status definition The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition definition editor note An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. PERSON:Daniel Schober GROUP:OBI:<http://purl.obofoundry.org/obo/obi> editor note term editor Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> term editor alternative label alternative term 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. An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) 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 has obsolescence reason Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. PERSON:Alan Ruttenberg PERSON:Melanie Courtot has obsolescence reason curator note An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg curator note term tracker item the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ An IRI or similar locator for a request or discussion of an ontology term. Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg The 'tracker item' can associate a tracker with a specific ontology term. term tracker item ontology term requester The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg The 'term requester' can credit the person, organization or project who request the ontology term. ontology term requester is denotator type Relates an class defined in an ontology, to the type of it's denotator In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type') Alan Ruttenberg is denotator type imported from For external terms/classes, the ontology from which the term was imported PERSON:Alan Ruttenberg PERSON:Melanie Courtot GROUP:OBI:<http://purl.obolibrary.org/obo/obi> imported from expand expression to ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones Chris Mungall expand expression to expand assertion to ObjectProperty: RO??? Label: spatially disjoint from Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom. Chris Mungall expand assertion to first order logic expression PERSON:Alan Ruttenberg first order logic expression antisymmetric property part_of antisymmetric property xsd:true Use boolean value xsd:true to indicate that the property is an antisymmetric property Alan Ruttenberg antisymmetric property OBO foundry unique label An alternative name for a class or property which is unique across the OBO Foundry. The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . PERSON:Alan Ruttenberg PERSON:Bjoern Peters PERSON:Chris Mungall PERSON:Melanie Courtot GROUP:OBO Foundry <http://obofoundry.org/> OBO foundry unique label has ID digit count Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits) Person:Alan Ruttenberg has ID digit count has ID range allocated Datatype: idrange:1 Annotations: 'has ID range allocated to': "Chris Mungall" EquivalentTo: xsd:integer[> 2151 , <= 2300] Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms Person:Alan Ruttenberg has ID range allocated to has ID policy for Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" Relating an ontology used to record id policy to the ontology namespace whose policy it manages Person:Alan Ruttenberg has ID policy for has ID prefix Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created. Person:Alan Ruttenberg has ID prefix elucidation person:Alan Ruttenberg Person:Barry Smith Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms elucidation has associated axiom(nl) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom associated with a term expressed using natural language has associated axiom(nl) has associated axiom(fol) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom expressed in first order logic using CLIF syntax has associated axiom(fol) is allocated id range Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999" PERSON:Alan Ruttenberg Add as annotation triples in the granting ontology is allocated id range has ontology root term Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root. Nicolas Matentzoglu has ontology root term may be identical to A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged. David Osumi-Sutherland #40 VFB Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance. may be identical to scheduled for obsoletion on or after Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date. Chris Mungall, Jie Zheng https://github.com/geneontology/go-ontology/issues/15532 https://github.com/information-artifact-ontology/ontology-metadata/issues/32 GO ontology scheduled for obsoletion on or after has axiom id Person:Alan Ruttenberg Person:Alan Ruttenberg A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI has axiom label term replaced by Use on obsolete terms, relating the term to another term that can be used as a substitute Person:Alan Ruttenberg Person:Alan Ruttenberg Add as annotation triples in the granting ontology term replaced by This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL. OBO Operations call logical characteristic of object property 'part disjoint with' 'defined by construct' """ PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX : <http://example.org/ CONSTRUCT { [ a owl:Restriction ; owl:onProperty :part_of ; owl:someValuesFrom ?a ; owl:disjointWith [ a owl:Restriction ; owl:onProperty :part_of ; owl:someValuesFrom ?b ] ] } WHERE { ?a :part_disjoint_with ?b . } Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation. defined by construct 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. Philip Strömert 2020-10-14T15:31:27Z maps to description license title An alternative label for a class or property which has a more general meaning than the preferred name/primary label. https://github.com/information-artifact-ontology/ontology-metadata/issues/18 has broad synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/18 An alternative label for a class or property which has the exact same meaning than the preferred name/primary label. https://github.com/information-artifact-ontology/ontology-metadata/issues/20 has exact synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/20 An alternative label for a class or property which has a more specific meaning than the preferred name/primary label. https://github.com/information-artifact-ontology/ontology-metadata/issues/19 has narrow synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/19 An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct. https://github.com/information-artifact-ontology/ontology-metadata/issues/21 has related synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/21 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/ Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. part_of part of http://www.obofoundry.org/ro/#OBO_REL:part_of has part my body has part my brain (continuant parthood, two material entities) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has_part has part realized in this disease is realized in this disease course this fragility is realized in this shattering this investigator role is realized in this investigation is realized by realized_in [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realized in realizes this disease course realizes this disease this investigation realizes this investigator role this shattering realizes this fragility to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realizes occurs in b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t occurs_in unfolds in unfolds_in Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant occurs in site of [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant contains process This document is about information artifacts and their representations A (currently) primitive relation that relates an information artifact to an entity. 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. person:Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy is about 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 A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. PERSON: Alan Ruttenberg 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 inheres in this fragility inheres in this vase this fragility is a characteristic of this vase this red color inheres in this apple 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. a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence A dependent inheres in its bearer at all times for which the dependent exists. inheres_in 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 inheres in bearer of this apple is bearer of this red color this vase is bearer of this fragility Inverse of characteristic_of a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. bearer_of is bearer of bearer of 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 has participant this investigator role is a role of this person a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. is role of role_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. role of this person has role this investigator role (more colloquially: this person has this role of investigator) a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. has_role has role A part of relation that applies only between occurrents. occurrent part of Chris Mungall Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporally related to inverse of starts with Chris Mungall Allen starts 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 inverse of ends with Chris Mungall ends x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. Chris Mungall finished by ends with p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. Chris Mungall produces has output An organism that is a member of a population of organisms is member of is a mereological relation between a item and a collection. is member of member part of SIO member of has member is a mereological relation between a collection and an item. SIO has member inverse of has output Chris Mungall output of "has ocurrent part" is a relation that holds between a whole occurrent (process) and its part. has occurrent part A relation obtaining between an 'academic event type specification' and an 'academic event', in which the former is used to descibe the sociocultural format of the latter. A set of possible common academic event type specification is provided in AEON as named individuals. https://orcid.org/0000-0002-1595-3213 specifies academic event format of https://github.com/tibonto/aeon/issues/139 A relation obtaining between an 'academic event' and an 'academic event format specification' that specifies the sociocultrural format of the 'academic event'. https://orcid.org/0000-0002-1595-3213 has academic event format https://github.com/tibonto/aeon/issues/139 has DID A relation obtaining between an entity and a distributed identifier document (DID) that is used to denote the verifiable, decentralized digital identity of an entity. https://orcid.org/0000-0002-1595-3213 has distributed identifier has DID A relation obtaining between an 'academic event' and an academic field descriptor that is used to describe the scientific subject of the planned process according to some controlled vocabulary or thesaurus. https://orcid.org/0000-0002-1595-3213 has academic field descriptor A relation obtaining between a obi:'planned process' and an 'event topic descriptor' that is used to descibe the theme of the planned process. https://orcid.org/0000-0002-1595-3213 has event topic decriptor A relation obtaining between a obi:'planned process' and an 'event fee specification'. https://orcid.org/0000-0002-1595-3213 has event fee specification 'has contributor' is a relation obtaining between a planned process and a person or organization that holds a contributor role which is being realized by the planned process. A contribution to a planned process takes place when someone works on the planning or realization of a planned process. https://orcid.org/0000-0002-1595-3213 has contributor A relation obtaining between a planned process and a person that holds an attendee role which is being realized by the planned process. https://orcid.org/0000-0002-1595-3213 {"wikidata": {"uri": "https://www.wikidata.org/wiki/Property:P710", "label": "participantLabel"}} has attendee A relation obtaining between a planned process and a person that holds a moderator role which is being realized by the planned process. https://orcid.org/0000-0002-1595-3213 has moderator A relation obtaining between a planned process and a person or organization that holds an organizer role which is being realized by the planned process. https://orcid.org/0000-0002-1595-3213 {"wikidata": {"uri": "https://www.wikidata.org/wiki/Property:P664", "label": "organizerLabel"}, "openresearch": {"uri": "https://www.openresearch.org/wiki/Property:Has_organizer", "label": "Has_organizer"},"crossref": {"api_proceedings_endpoint_uri": "https://api.crossref.org/types/proceedings/works?select=event", "json_api_key": {"event": "sponsor"}}} has organizer A relation obtaining between a planned process and a person that holds a reviewer role which is being realized by the planned process. https://orcid.org/0000-0002-1595-3213 has reviewer A relation obtaining between a planned process and a person that holds a presenter role which is being realized by the planned process. https://orcid.org/0000-0002-1595-3213 {"wikidata": {"uri": "https://www.wikidata.org/wiki/Property:P823", "label": "speaker"}} has presenter A relation obtaining between a planned process and a person or organization that holds a sponsor role which is being realized by the planned process. https://orcid.org/0000-0002-1595-3213 has sponsor A relation obtaining between a planned process and a person that holds a committee member role which is being realized by the planned process. https://orcid.org/0000-0002-1595-3213 has committee member A relation obtaining between a planned process and a person that holds a contact person role which is being realized by the planned process. https://orcid.org/0000-0002-1595-3213 has contact person A relation between a planned process and a person that holds a keynote speaker role which is being realized by the planned process. https://orcid.org/0000-0002-1595-3213 has keynote speaker A relation obtaining between a planned process and a person that holds a committee chair role which is being realized by the planned process. https://orcid.org/0000-0002-1595-3213 has committee chair see inverse relation 'has deadline Given the fact that deadlines are specified in various planned processes this term should probably be regarded as a placeholder which ought to be defined in a broader ontology, maybe something like IAO? https://orcid.org/0000-0002-1595-3213 2021-07-19T11:29:50Z specifies deadline of a relation between a planned process and a deadline specification Given the fact that deadlines are specified in various planned processes this term should probably be regarded as a placeholder which ought to be defined in a broader ontology, maybe something like IAO? https://orcid.org/0000-0002-1595-3213 2021-07-19T11:30:01Z has deadline A relation obtaining between a digital iao:information content entity and its corresponding ISO 26324 conform digital object identifier. https://orcid.org/0000-0002-1595-3213 has DOI A relation obtaining between an entity and the 'GND identifier' used by the German national library to denote this entity. https://orcid.org/0000-0002-1595-3213 {"wikidata": {"uri": "https://www.wikidata.org/wiki/Property:P227", "label": "GND_ID"}, "gnd": {"uri": "https://d-nb.info/standards/elementset/gnd#gndIdentifier", "label": "GND-Identifier"}} has GND identifier A relation obtaining between a person or organization and the 'international standard name identifier' used to denote the person or organization in the ISNI database. https://orcid.org/0000-0002-1595-3213 has ISNI A relation obtaining between a person and the 'ORCID' used to denote the person in the ORCID database. https://orcid.org/0000-0002-1595-3213 has ORCID A relation obtaining between a person and the 'ROR identifier' used to denote the entity in the ROR database. https://orcid.org/0000-0002-1595-3213 https://ror.org/ has ROR A relation obtaining between an entity and the Wikidata identifier used to denote this entity in the Wikidata database. https://orcid.org/0000-0002-1595-3213 has Wikidata QID {"wikidata": {"uri": null, "label": "itemID"}, "openresearch": {"uri": "https://www.openresearch.org/wiki/Property:Wikidataid", "label": "Wikidataid"}} has QID A relation obtaining between an academic event series and an academic event. It is used to express that the academic event series has a specific academic event as its part. academic event series of https://orcid.org/0000-0002-1595-3213 collocated event of see also inverse property: A relation obtaining between an academic event and another academic event. A joint event is an event that shares some of the planning and organizing logistics with another academic event, but is otherwise independent from it. https://orcid.org/0000-0002-1595-3213 joint event of A relation obtaining between an academic event and an academic event series. It is used to express that the academic event is part of a specific event series. https://orcid.org/0000-0002-1595-3213 {"wikidata": {"uri": "https://www.wikidata.org/wiki/Property:P179", "label": "part_of_the_seriesLabel"}, "openresearch": {"uri": "https://www.openresearch.org/wiki/Property:Event_in_series", "label": "Event_in_series"}} part of academic event series see also inverse property: A relation obtaining between an academic event and another academic event or event series. An umbrelle event/series is a superordinate event/series that combines several smaller academic events/series at the same time. https://orcid.org/0000-0002-1595-3213 umbrella event of A relation obtaining between a bfo:occurent and the country in which it occurs. https://orcid.org/0000-0002-1595-3213 {"wikidata": {"uri": "https://www.wikidata.org/wiki/Property:P17", "label": "countryLabel"}, "openresearch": {"uri": "https://www.openresearch.org/wiki/Property:Has_location_country", "label": "Has_location_country"}} occurs in country https://github.com/tibonto/aeon/issues/142 A relation obtaining between a bfo:occurent and the city in which it occurs. https://orcid.org/0000-0002-1595-3213 {"wikidata": {"uri": "https://www.wikidata.org/wiki/Property:P276", "label": "locationLabel"}, "openresearch": {"uri": "https://www.openresearch.org/wiki/Property:Has_location_city", "label": "Has_location_city"}, "gnd": {"uri": "https://d-nb.info/standards/elementset/gnd#placeOfConferenceOrEvent", "label": "Place of conference or event"}} occurs in city https://github.com/tibonto/aeon/issues/142 A relation obtaining between a bfo:occurent and the province in which it occurs. https://orcid.org/0000-0002-1595-3213 {"wikidata": {"uri": "https://www.wikidata.org/wiki/Property:P131", "label": "located_in_the_administrative_territorial_entityLabel"}, "openresearch": {"uri": "https://www.openresearch.org/wiki/Property:Has_location_state", "label": "Has_location_state"}} occurs in province https://github.com/tibonto/aeon/issues/142 A relation obtaining between a bfo:occurent and the event venue in which it occurs. https://orcid.org/0000-0002-1595-3213 occurs in event venue see also inverse property: A relation obtaining between an 'academic field descriptor' and a obi:'planned process', in which the former is used to descibe the scientific subject of the latter according to some controlled vocabulary or thesaurus. https://orcid.org/0000-0002-1595-3213 describes academic field A relation obtaining between a person and a planned process, in which the person holds an attendee role that is being realized by the planned process the moment the person is actually a member of the audience of said planned process. https://orcid.org/0000-0002-1595-3213 attends at planned process A relation obtaining between a person and a planned process, in which the person holds a committee chair role that is being realized by the planned process. https://orcid.org/0000-0002-1595-3213 is committee chair in A relation obtaining between a person and a planned process, in which the person holds a committee member role that is being realized by the planned process. https://orcid.org/0000-0002-1595-3213 is committee member in A relation obtaining between a person and a planned process, in which the person holds the role of being the designated contact person and that role is being realized by the planned process. https://orcid.org/0000-0002-1595-3213 is contact person of A relation obtaining between a person or organization and a planned process, in which the person or organization holds a contributor role that is being realized by the planned process. https://orcid.org/0000-0002-1595-3213 contributes to planned process A relation obtaining between an 'academic event' or 'academic event series' and the WikiCFP identifier used to denote this 'academic event' or 'academic event series' in the wikiCFP database. https://orcid.org/0000-0002-1595-3213 http://www.wikicfp.com/cfp/ {"wikidata": {"uri": "https://www.wikidata.org/wiki/Property:P5127", "label": "WikiCFP_conference_series_ID"}} has WikiCFP identifier A relation obtaining between an academic event and another academic event. A collocated event is an event that takes place at the same location and time as another academic event. https://orcid.org/0000-0002-1595-3213 has collocated event A relation obtaining between an academic event and another academic event. A joint event is an event that shares some of the planning and organizing logistics with another academic event, but is otherwise independent from it. https://orcid.org/0000-0002-1595-3213 has joint event A relation obtaining between an academic event and another academic event or event series. An umbrelle event is a superordinate event that combines several smaller academic events at the same time. To say p 'has umbrella event' d =def. there exists an academic event d that is a superordinate event of p and that there must be other academic events that have the same relation. https://orcid.org/0000-0002-1595-3213 has umbrella event A relation between a person and a planned process, in which the person holds a keynote speaker role that is being realized by the planned process. https://orcid.org/0000-0002-1595-3213 holds keynote speech at A relation obtaining between a person and a planned process, in which the person holds a moderator role that is being realized by the planned process. https://orcid.org/0000-0002-1595-3213 moderates at A relation obtaining between a person or organization and a planned process, in which the person or organization holds an organizer role that is being realized by the planned process. https://orcid.org/0000-0002-1595-3213 organizes A relation between a person and a planned process, in which the person holds a reviewer role that is being realized by the planned process. https://orcid.org/0000-0002-1595-3213 reviews at A relation obtaining between a person and a planned process, in which the person holds a presenter role that is being realized by the planned process. https://orcid.org/0000-0002-1595-3213 presents at A relation obtaining between an 'event fee specification' and a obi:'planned process'. https://orcid.org/0000-0002-1595-3213 2021-06-28T12:48:49Z specifies event fee of A relation obtaining between a person or organization and a planned process, in which the person or organization holds a sponsor role that is being realized by the planned process. https://orcid.org/0000-0002-1595-3213 sponsors see also inverse property: A relation obtaining between an 'event topic descriptor' and a obi:'planned process', in which the former is used to descibe the theme of the latter. https://orcid.org/0000-0002-1595-3213 describes event topic has representation 12th arrondissement of Paris 20g I feel sick to my stomach every Tuesday 'has representation' is a data property that attaches between an information content entity and a value that contains linguistically or computationally coded text. Further processing may enable the value to be represented in a component data structure such as an OBI value specification. Damion Dooley Mark Miller 2019-07-14T07:05:50Z has representation A data property which is intended to be used for the literal representation of a deadline specification in the xsd:dateTimeStamp format https://orcid.org/0000-0002-1595-3213 2021-07-19T13:49:58Z deadline datetime value A shortend representation of a planned process name that has been formed from the initial components of a planned process name representation, usually using individual initial letters. https://orcid.org/0000-0002-1595-3213 2021-09-13T08:55:02Z planned process acronym CORE ranking acceptance rate accepted papers accepted short papers contact@academic-event.org This data property associates an email adress with a contributor. It needs to be discussed, if we need this information to be modeled more finegrained using e.g. iao:'email address' (see alsohttps://github.com/information-artifact-ontology/IAO/issues/130). For now it seems sufficient to have a data property. email address value 0049 176 123456 This data property associates a telephone number with a contributor It needs to be discussed, if we need this information to be modeled more finegrained using e.g. iao:'email address' (see also https://github.com/information-artifact-ontology/IAO/issues/130). For now it seems sufficient to have a data property. phone number value coordinates {"wikidata": {"uri": "https://www.wikidata.org/wiki/Property:P2047", "label": "duration"}, "gnd": {"uri": "https://d-nb.info/standards/elementset/gnd#dateOfConferenceOrEvent", "label": "Date of conference or event"}} duration A data property to provide the planned end date of an academic event in the xsd:dateTimeStamp format. https://orcid.org/0000-0002-1595-3213 {"wikidata": {"uri": "https://www.wikidata.org/wiki/Property:P582", "label": "end_time"}, "openresearch": {"uri": "https://www.openresearch.org/wiki/Property:End_date", "label": "End_date"},"crossref": {"api_proceedings_endpoint_uri": "https://api.crossref.org/types/proceedings/works?select=event", "json_api_key": {"event": "end"}}} planned end date The event frequency is the literal value of the number of month until the next event in a certain takes place. {"wikidata": {"uri": "https://www.wikidata.org/wiki/Property:P2257", "label": "event_interval_inmonths"}} event frequency The ordinal number of an academic event, if it is a part of an event series. {"crossref": {"api_proceedings_endpoint_uri": "https://api.crossref.org/types/proceedings/works?select=event", "json_api_key": {"event": "number"}}} event number as scheduled canceled delayed planned postponed maps_to: DataCite:dateType --- allowed value mapping ConfIDent → DataCite scheduled → valid postponed → updated cancled → withdrawn event status event type other The year in which an event takes place. event year 150.00 The literal, numerical (decimal) value of an event fee that is specified in an event fee specification. https://orcid.org/0000-0002-1595-3213 event fee value EUR USD The literal string value of an event fee currency that is specified in an event fee specification. https://orcid.org/0000-0002-1595-3213 This data property should have a value from the controlled list defined by the ISO_4217 standard (https://en.wikipedia.org/wiki/ISO_4217). event fee currency This data property should be used to provide the language that is officially spoken at an event . The allowed string should preferrably be encoded in the ISO 639-1 standard (e.g. German would be "de"). It needs to be discussed, if a data property is sufficient for our use case, or if it might be better to model the officially spoken language of an academic event as a generically dependent continuant that participates in this planned process as sugessted by the developers of the language ontology (https://github.com/vivo-ontologies/language-ontology/wiki/Usage). https://orcid.org/0000-0002-1595-3213 {"wikidata": {"uri": "https://www.wikidata.org/wiki/Property:P2936", "label": "language_usedLabel"}} event language location logo meeting URL metric {"openresearch": {"uri": "https://www.openresearch.org/wiki/Property:Attendees", "label": "Attendees"}} number of attendess number of tracks A data property to provide the previously planned end date of an academic event in the xsd:dateTimeStamp format, when the planned end date has been rescheduled. https://orcid.org/0000-0002-1595-3213 previously planned end date A data property to provide the previously planned start date of an academic event in the xsd:dateTimeStamp format, when the planned start date has been rescheduled. https://orcid.org/0000-0002-1595-3213 previously planned start date proceeding cite count {"wikidata": {"uri": "https://www.wikidata.org/wiki/Property:P856", "label": "official_website"}, "openresearch": {"uri": "https://www.openresearch.org/wiki/Property:Homepage", "label": "Homepage"}} process website series cite count sponsor type A data property to provide the planned end date of an academic event in the xsd:dateTimeStamp format. https://orcid.org/0000-0002-1595-3213 {"wikidata": {"uri": "https://www.wikidata.org/wiki/Property:P580", "label": "start_time"}, "openresearch": {"uri": "https://www.openresearch.org/wiki/Property:Start_date", "label": "Start_date"},"crossref": {"api_proceedings_endpoint_uri": "https://api.crossref.org/types/proceedings/works?select=event", "json_api_key": {"event": "start"}}} planned start date state submitted papers summary summary licence venue venue website root node creating a data set A planned process that has a data set as its specified output. William R. Hogan data set creation dataset creation dataset creating entity Entity Julius Caesar Verdi’s Requiem the Second World War your body mass index BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) entity Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf per discussion with Barry Smith An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) continuant Continuant An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] continuant Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] occurrent Occurrent An entity that has temporal parts and that happens, unfolds or develops through time. BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] occurrent Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. per discussion with Barry Smith Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] ic IndependentContinuant a chair a heart a leg a molecule a spatial region an atom an orchestra. an organism the bottom right portion of a human torso the interior of your mouth A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] independent continuant 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] s-region SpatialRegion BFO 2 Reference: Spatial regions do not participate in processes. Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] spatial region Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. per discussion with Barry Smith A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] t-region TemporalRegion Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] temporal region Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional per discussion with Barry Smith A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] 2d-s-region TwoDimensionalSpatialRegion an infinitely thin plane in space. the surface of a sphere-shaped part of space A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] two-dimensional spatial region A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] st-region SpatiotemporalRegion the spatiotemporal region occupied by a human life the spatiotemporal region occupied by a process of cellular meiosis. the spatiotemporal region occupied by the development of a cancer tumor A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) Every spatiotemporal region occupies_spatiotemporal_region itself. Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] spatiotemporal region A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] process Process a process of cell-division, \ a beating of the heart a process of meiosis a process of sleeping the course of a disease the flight of a bird the life of an organism your process of aging. An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] process p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] disposition Disposition an atom of element X has the disposition to decay to an atom of element Y certain people have a predisposition to colon cancer children are innately disposed to categorize objects in certain ways. the cell wall is disposed to filter chemicals in endocytosis and exocytosis BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] disposition b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] realizable RealizableEntity the disposition of this piece of metal to conduct electricity. the disposition of your blood to coagulate the function of your reproductive organs the role of being a doctor the role of this boundary to delineate where Utah and Colorado meet A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] realizable entity 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] 0d-s-region ZeroDimensionalSpatialRegion A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] zero-dimensional spatial region A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] quality 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 (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] 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]) sdc SpecificallyDependentContinuant Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key of one-sided specifically dependent continuants: the mass of this tomato of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. the disposition of this fish to decay the function of this heart: to pump blood the mutual dependence of proton donors and acceptors in chemical reactions [79 the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction the pink color of a medium rare piece of grilled filet mignon at its center the role of being a doctor the shape of this hole. the smell of this portion of mozzarella A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] specifically dependent continuant b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. per discussion with Barry Smith (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] role Role John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. the priest role the role of a boundary to demarcate two neighboring administrative territories the role of a building in serving as a military target the role of a stone in marking a property boundary the role of subject in a clinical trial the student role A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] role b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] fiat-object-part FiatObjectPart or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29 the FMA:regional parts of an intact human body. the Western hemisphere of the Earth the division of the brain into regions the division of the planet into hemispheres the dorsal and ventral surfaces of the body the upper and lower lobes of the left lung BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] fiat object part b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] 1d-s-region OneDimensionalSpatialRegion an edge of a cube-shaped portion of space. A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] one-dimensional spatial region A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] object-aggregate ObjectAggregate a collection of cells in a blood biobank. a swarm of bees is an aggregate of members who are linked together through natural bonds a symphony orchestra an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team) defined by fiat: the aggregate of members of an organization defined through physical attachment: the aggregate of atoms in a lump of granite defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container defined via attributive delimitations such as: the patients in this hospital the aggregate of bearings in a constant velocity axle joint the aggregate of blood cells in your body the nitrogen atoms in the atmosphere the restaurants in Palo Alto your collection of Meissen ceramic plates. An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee). ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] object aggregate An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] 3d-s-region ThreeDimensionalSpatialRegion a cube-shaped region of space a sphere-shaped region of space, A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] three-dimensional spatial region A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] site Site Manhattan Canyon) a hole in the interior of a portion of cheese a rabbit hole an air traffic control region defined in the airspace above an airport the Grand Canyon the Piazza San Marco the cockpit of an aircraft the hold of a ship the interior of a kangaroo pouch the interior of the trunk of your car the interior of your bedroom the interior of your office the interior of your refrigerator the lumen of your gut your left nostril (a fiat part – the opening – of your left nasal cavity) b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] site b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] object Object atom cell cells and organisms engineered artifacts grain of sand molecule organelle organism planet solid portions of matter star BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting. BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below). BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47 BFO 2 Reference: an object is a maximal causally unified material entity BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74 b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) object b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) gdc GenericallyDependentContinuant The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. the pdf file on your laptop, the pdf file that is a copy thereof on my laptop the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] generically dependent continuant b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] function Function the function of a hammer to drive in nails the function of a heart pacemaker to regulate the beating of a heart through electricity the function of amylase in saliva to break down starch into sugar BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] function A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] p-boundary ProcessBoundary the boundary between the 2nd and 3rd year of your life. p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] process boundary p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] 1d-t-region OneDimensionalTemporalRegion the temporal region during which a process occurs. BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks). A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] one-dimensional temporal region A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] material MaterialEntity a flame a forest fire a human being a hurricane a photon a puff of smoke a sea wave a tornado an aggregate of human beings. an energy wave an epidemic the undetached arm of a human being An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] material entity A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] cf-boundary ContinuantFiatBoundary b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions. BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29 Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. Every continuant fiat boundary is located at some spatial region at every time at which it exists (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] continuant fiat boundary b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] immaterial ImmaterialEntity BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10 immaterial entity 1d-cf-boundary OneDimensionalContinuantFiatBoundary The Equator all geopolitical boundaries all lines of latitude and longitude the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin. the median sulcus of your tongue a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] one-dimensional continuant fiat boundary a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] process-profile ProcessProfile On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance. The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on. b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] process profile b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] r-quality RelationalQuality John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. a marriage bond, an instance of requited love, an obligation between one person and another. b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] relational quality b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] 2d-cf-boundary TwoDimensionalContinuantFiatBoundary a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] two-dimensional continuant fiat boundary a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] 0d-cf-boundary ZeroDimensionalContinuantFiatBoundary the geographic North Pole the point of origin of some spatial coordinate system. the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] zero-dimensional continuant fiat boundary zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. requested by Melanie Courtot a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] 0d-t-region ZeroDimensionalTemporalRegion a temporal region that is occupied by a process boundary right now the moment at which a child is born the moment at which a finger is detached in an industrial accident the moment of death. temporal instant. A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] zero-dimensional temporal region A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] history History A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) history A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) contributor role http://purl.obolibrary.org/obo/IAO_0000120 A high-level classification of the diverse roles performed in the work leading to a published research output in the sciences. Its purpose to provide transparency in contributions to scholarly published work, to enable improved systems of attribution, credit, and accountability. https://orcid.org/0000-0001-5059-4132 http://dictionary.casrai.org/Contributor_Roles 9dbb95f4-55ed-4e43-9301-a9f0e3e17afe contributor role Coordination of research dissemination through popular media and the press, as well as community outreach and liaising of project directly to the community. Similar to vivo:OutreachProviderRole? communication role outreach role 2018-09-14T19:51:26Z marketing and communication role A role in which a person participates in the transfer of knowledge and skills, through teaching, development of educational materials or curriculum, through program development or other means. educational role 2018-09-14T19:55:45Z education and training role Policy development generally involves research, analysis, consultation and synthesis of information to produce recommendations for action by an individual or an organization. It should also involve an evaluation of options against a set of criteria used to assess each option. 2018-09-14T20:04:29Z policy development role Manage regulatory and compliance issues for the research project. regulatory administration role 2018-09-14T20:05:56Z regulatory and compliance role A person that is responsible for usage of instrumentation, such as equipment or devices, or instruments like a survey or questionnaire. 2018-09-14T20:06:00Z instrumentation role Coordination of diverse team members, often across different disciplines and locations. 2018-09-14T20:06:26Z team management role An educational role in which a person develops educational or training materials that are intended to transfer knowledge, for use in a classroom, indpendent learning or other settings. educational material development role 2018-09-14T20:15:18Z training material role An educational role in which a person participates in the development of an educational program, designed for learners to achieve a set of compentencies around a given topic or area of focus. educational program development role 2018-09-14T20:15:23Z training program development role An educational role in which knowledge and skills are transferred through teaching. This may be equivalent to vivo:Teacher Role. educational instruction role educational training role teaching role 2018-09-14T20:15:29Z instruction role An educational role in which knowledge and skills are transferred through teaching. https://www.wikidata.org/wiki/Q8434 An information technology systems role that specifically focuses on the computer hardware, the physical components of a computer system. hardware systems role 2018-09-14T20:17:16Z hardware role An information technology systems role that specifically focuses on the computer hardware, the physical components of a computer system. https://www.wikidata.org/wiki/Q3966 A software systems role that involves maintenance and operation of a computer system and/or network. sysadmin role systems administration role 2018-09-14T20:17:32Z system administrator role A software systems role that involves maintenance and operation of a computer system and/or network. https://www.wikidata.org/wiki/Q327353 A methodology role that involves creation of a detailed plan of a scientific or medical experiment, treatment, or procedure. protocol development role 2018-09-14T20:19:56Z protocol creation role A methodology role that involves creation of a detailed plan of a scientific or medical experiment, treatment, or procedure. https://www.merriam-webster.com/dictionary/protocol A person that is responsible for operating equipment or instrumentation and/or that ensures equipment is well-maintained, properly configured, and safely functional. instrument technician role 2018-09-14T20:23:44Z equipment technician role A person that is responsible for operating equipment or instrumentation and/or that ensures equipment is well-maintained, properly configured, and safely functional. https://en.wikipedia.org/wiki/Biomedical_equipment_technician Creation or refinement of a survey or questionnaire, a list of questions aimed at extracting specific data from a particular group of people. 2018-09-14T20:23:49Z survey and questionnaire development role Creation or refinement of a survey or questionnaire, a list of questions aimed at extracting specific data from a particular group of people. https://www.wikidata.org/wiki/Q7257997 Planning, management, and monitoring of projects. 2018-09-14T20:25:55Z project management role Contribution to the basic, underlying framework or features of a system or organization. 2018-10-01T20:48:11Z infrastructure role Contribution to the basic, underlying framework or features of a system or organization. https://www.dictionary.com/browse/infrastructure Evaluation is a systematic method for collecting, analyzing, and using information to answer questions about projects, policies and programs, particularly about their effectiveness and efficiency. 2018-10-01T20:48:24Z project, policy or program evaluation role Evaluation is a systematic method for collecting, analyzing, and using information to answer questions about projects, policies and programs, particularly about their effectiveness and efficiency. https://en.wikipedia.org/wiki/Program_evaluation The organization of the different elements needed to implement a study. 2018-10-01T20:49:10Z coordination role The organization of the different elements needed to implement a study. https://learn.nursing.jhu.edu/face-to-face/courses/research-coordinator/index.html A communication role which involves the dynamic relational process that facilitates communication, interaction, involvement, and exchange between an organization and a community for a range of social and organizational outcomes. 2018-10-01T20:55:22Z community engagement role A communication role which involves the dynamic relational process that facilitates communication, interaction, involvement, and exchange between an organization and a community for a range of social and organizational outcomes. Johnston, K. A. (2018). Toward a theory of social engagement. In K. A. Johnston & M. Taylor (Eds.), The Handbook of Communication Engagement (pp. 19-32). Hoboken, NJ: Wiley. A communication role that involves development or production of materials, such as brochures, websites, flyers, presentations, etc., for the purposes of promotion of a entity, like a project, group or organization. 2018-10-01T20:56:18Z outreach materials development role The person or organization that provides money for a particular purpose, such as a grant to perform research. funder role funding source role The person or organization that provides money for a particular purpose, such as a grant to perform research. https://www.lexico.com/en/definition/funder Oral presentation intended to present information or teach people about a particular subject, such as a talk or poster presentation at a conference. lecture role lecturer role presentation role speaker role presenter role Oral presentation intended to present information or teach people about a particular subject, such as a talk or poster presentation at a conference. https://www.wikidata.org/wiki/Q603773 Evaluation of scientific, academic, or professional work, such as manuscripts or grants by others working in the same field. manuscript review role peer review role Evaluation of scientific, academic, or professional work, such as manuscripts or grants by others working in the same field. https://www.lexico.com/en/definition/peer_review A role that involves giving advice in a particular field. https://orcid.org/0000-0001-8420-5254 advisory role advisory role https://www.lexico.com/en/definition/adviser A role that is realized through the act of formally accepting an artifact for inclusion in some larger resource (e.g. database, registry, collection, etc.) https://orcid.org/0000-0002-1048-5019 An agent accepting an artifact possesses the authority to decide if it belongs in a particular resource or collection. This agent may or may not also have directly evaluated it themselves - but if they did, an 'evaluator role' could additionally be captured. acceptor role A role that is realized through the act of formally accepting an artifact for inclusion in some larger resource (e.g. database, registry, collection, etc.) https://orcid.org/0000-0002-1048-5019 A role that is realized through the act of formally submitting or depositing an artifact to be included in some larger resource (e.g. database, registry, collection, etc.) depositor role https://orcid.org/0000-0002-1048-5019 An agent submitting an artifact may or may not also have contributed to its creation. If they did, and additional ‘creator role’ can be applied. submitter role A role that is realized through the act of formally submitting or depositing an artifact to be included in some larger resource (e.g. database, registry, collection, etc.) https://orcid.org/0000-0002-1048-5019 A role that is realized through the review and evaluation of an artifact - generally to assess its quality, completeness, relevance, or other characteristics. assessor role reviewer role https://orcid.org/0000-0002-1048-5019 Evaluating an artifact does not involve modification of the assessed artifact - however the suggestion of alterations can be a separate outcome of an evaluation. If the artifact is modified by the agent during or subsequent to the evaluation, a 'modifier role' should additionally be applied. evaluator role A role that is realized through the review and evaluation of an artifact - generally to assess its quality, completeness, relevance, or other characteristics. https://orcid.org/0000-0002-1048-5019 FTT:1242 FTT:1252 FTT:15 FTT:16 FTT:18 FTT:19 FTT:21 FTT:22 FTT:23 FTT:24 FTT:25 FTT:26 FTT:27 FTT:28 FTT:29 FTT:37 SWEETRealm:AdministrativeRegion TGN:80001 TGN:81099 TGN:81123 https://en.wikipedia.org/wiki/Administrative_region administrative area administrative division administrative entity boundary region civil area district free trade zone governed place leased area (government) leased zone (government) neutral zone (political) prefecture protectorate sheikdom sultanate trade zone administrative region administrative area ADL:FTT administrative division ADL:FTT administrative division Getty:TGN administrative entity Getty:TGN boundary region ADL:FTT civil area ADL:FTT district ADL:FTT free trade zone ADL:FTT governed place ADL:FTT leased area (government) ADL:FTT leased zone (government) ADL:FTT neutral zone (political) ADL:FTT prefecture ADL:FTT protectorate ADL:FTT sheikdom ADL:FTT sultanate ADL:FTT trade zone ADL:FTT A primary administrative division of a country, such as a state in the United States. FTT:414 FTT:569 Geonames:A.ADM1 TGN:81100 ENVO countries, 1st order division first level subdivision first-order administrative division ENVO:00000005 first-order administrative region A primary administrative division of a country, such as a state in the United States. Geonames:http://www.geonames.org/export/codes.html countries, 1st order division ADL:FTT first level subdivision Getty:TGN first-order administrative division Geonames:feature A political association with effective dominion over a geographic area. FTT:424 FTT:566 FTT:567 FTT:571 SWEETRealm:Country SWEETRealm:State TGN:80006 TGN:81010 TGN:81011 TGN:81102 https://en.wikipedia.org/wiki/Nation nation independent nation independent political entity independent sovereign nation ENVO country political entity state ENVO:00000009 national geopolitical entity A political association with effective dominion over a geographic area. https://en.wikipedia.org/wiki/State nation ADL:FTT independent nation Getty:TGN independent political entity Getty:TGN independent sovereign nation Getty:TGN country ADL:FTT political entity ADL:FTT Place or area with clustered or scattered buildings and a permanent human population. place FTT:1097 FTT:33 Geonames:P.PPL Geonames:P.PPLS TGN:22201 TGN:83002 https://en.wikipedia.org/wiki/Populated_place inhabited place populated place populated places settlement ENVO inhabited region populated locality ENVO:00000062 populated place Place or area with clustered or scattered buildings and a permanent human population. USGS:http://mapping.usgs.gov/www/ti/GNIS/gnis_users_guide_appendixc.html place USGS:SDTS inhabited place Getty:TGN populated place Geonames:feature populated places Geonames:feature settlement USGS:SDTS A geographical region whose affairs and population are administered by an authority. FTT:1093 Geonames:A.PCL TGN:80002 political entity political entity A geographical region whose affairs and population are administered by an authority. MA:ma political entity Geonames:feature Incorporated populated place. urban area EcoLexicon:city FTT:430 FTT:483 FTT:484 FTT:485 SWEETRealm:City TGN:83020 TGN:83040 TGN:83043 https://en.wikipedia.org/wiki/City ENVO ENVO:00000856 city Incorporated populated place. ADL:FTT urban area ADL:FTT A site which has its extent determined by the presence or influence of one or more components of an environmental system or the processes occurring therein. environmental area envoPolar Formerly, this class was an experimental class and a subclass of "environmental feature". It is now aligned to BFO. The class was not obsoleted as the core semantics maintained their stability through its transition. environmental zone A settlement with a high density of buildings and inhabitants. See also: http://www.ecotope.org/anthromes/v1/guide/urban/12_dense_settlements/default.aspx The thresholds for what makes a settlment "dense" can be determined as needed. If there is a specific threshold that should be added to ENVO, please make a new class request. dense settlement conditional specification A directive information entity that specifies what should happen if the trigger condition is fulfilled. PlanAndPlannedProcess Branch OBI branch derived OBI_0000349 conditional specification objective specification In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction. A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed." 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that. Answers the question, why did you do this experiment? PERSON: Alan Ruttenberg PERSON: Barry Smith PERSON: Bjoern Peters PERSON: Jennifer Fostel goal specification OBI Plan and Planned Process/Roles Branch OBI_0000217 objective specification Pour the contents of flask 1 into flask 2 A directive information entity that describes an action the bearer will take. Alan Ruttenberg OBI Plan and Planned Process branch action specification 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 symbol a serial number such as "12324X" a stop sign a written proper name such as "OBI" An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. 20091104, MC: this needs work and will most probably change 2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154). PERSON: James A. Overton PERSON: Jonathan Rees based on Oxford English Dictionary symbol 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 An information content entity whose concretizations indicate to their bearer how to realize them in a process. 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it. 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan PERSON: Alan Ruttenberg PERSON: Bjoern Peters directive information entity rule example to be added A rule is an executable which guides, defines, restricts actions. MSI PRS OBI_0500021 PRS rule 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 set Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction. person:Allyson Lister person:Chris Stoeckert OBI_0000042 group:OBI data set 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 plan specification PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice. A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. 2014-03-31: A plan specification can have other parts, such as conditional specifications. Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved Alan Ruttenberg OBI Plan and Planned Process branch OBI_0000344 2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them plan specification obsolescence reason specification The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. PERSON: Alan Ruttenberg PERSON: Melanie Courtot obsolescence reason specification document A journal article, patent application, laboratory notebook, or a book A collection of information content entities intended to be understood together as a whole PERSON: Lawrence Hunter document publication journal article, newspaper story, book, etc. A document that is the output of a publishing process. PERSON: Chris Stoeckert PERSON: Jie Zheng PERSON: Lawrence Hunter published document Revisit the term in Octorber 2020. Improve the defintion. publication denotator type The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. A denotator type indicates how a term should be interpreted from an ontological perspective. Alan Ruttenberg Barry Smith, Werner Ceusters denotator type A planned process of making information, such as literature, music, and software etc., available to the public for sale or for free. Person: Jie Zheng https://en.wikipedia.org/wiki/Publishing VEuPathDB publishing process The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed. A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry. PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot CRID symbol Original proposal from Bjoern, discussions at IAO calls centrally registered identifier symbol The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed. An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs. 2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records'). Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation. Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered. PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot CRID Original proposal from Bjoern, discussions at IAO calls centrally registered identifier PubMed is a CRID registry. It has a dataset of PubMed identifiers associated with journal articles. A CRID registry is a dataset of CRID records, each consisting of a CRID symbol and additional information which was recorded in the dataset through a assigning a centrally registered identifier process. PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot CRID registry Original proposal from Bjoern, discussions at IAO calls centrally registered identifier registry identifier An identifier is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity. identifier ontology module I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it. ontology file This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology. ontology module base ontology module An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies. base ontology module editors ontology module An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users. source ontology module editors ontology module main release ontology module An ontology module that is intended to be the primary release product and the one consumed by the majority of tools. TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module main release ontology module bridge ontology module An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module. bridge ontology module import ontology module A subset ontology module that is intended to be imported from another ontology. TODO: add axioms that indicate this is the output of a module extraction process. import file import ontology module subset ontology module An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms. ontology slim subset ontology subset ontology module curation subset ontology module A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation. curation subset ontology module analysis ontology module An ontology module that is intended for usage in analysis or discovery applications. analysis subset ontology module single layer ontology module A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint. ribbon subset single layer subset ontology module exclusion subset ontology module A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes. antislim exclusion subset ontology module external import ontology module An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach. external import external import ontology module species subset ontology module A subset ontology that is crafted to either include or exclude a taxonomic grouping of species. taxon subset species subset ontology module reasoned ontology module An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available. reasoned ontology module generated ontology module An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV. TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process generated ontology module template generated ontology module An ontology module that is automatically generated from a template specification and fillers for slots in that template. template generated ontology module taxonomic bridge ontology module taxonomic bridge ontology module ontology module subsetted by expressivity ontology module subsetted by expressivity obo basic subset ontology module A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools. Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses). An ontology is OBO Basic if and only if it has the following characteristics: DAG Unidirectional No Dangling Clauses Fully Asserted Fully Labeled No equivalence axioms Singly labeled edges No qualifier lists No disjointness axioms No owl-axioms header No imports obo basic subset ontology module ontology module subsetted by OWL profile ontology module subsetted by OWL profile EL++ ontology module EL++ ontology module An organization that is operated without the principal goal of making a financial profit. Yongqun He nonprofit organization An organization which has the principle goal of earning financial profit. Yongqun He profit organization Homo sapiens human human being man 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 organization PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods. An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: 1) there are organization_member_roles (president, treasurer, branch editor), with individual persons as bearers 2) there are organization_roles (employer, owner, vendor, patent holder) 3) an organization has a charter / rules / bylaws, which specify what roles there are, how they should be realized, and how to modify the charter/rules/bylaws themselves. It is debatable what the organization itself is (some kind of dependent continuant or an aggregate of people). This also determines who/what the bearer of organization_roles' are. My personal favorite is still to define organization as a kind of 'legal entity', but thinking it through leads to all kinds of questions that are clearly outside the scope of OBI. Interestingly enough, it does not seem to matter much where we place organization itself, as long as we can subclass it (University, Corporation, Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, W3C, University of Oklahoma), and have it play roles. This leads to my proposal: We define organization through the statements 1 - 3 above, but without an 'is a' statement for now. We can leave it in its current place in the is_a hierarchy (material entity) or move it up to 'continuant'. We leave further clarifications to BFO, and close this issue for now. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Philippe Rocca-Serra PERSON: Susanna Sansone GROUP: OBI organization 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 The 19th International Semantic Web Conference (ISWC2020) is an academic event. An academic event is a planned process that refers to a gathering of researchers (not necessarily academics), in which these researches have the chance to present and discuss their work and possible future collaborations according to a certain sociocultural format. At the moment a general differentiation between some academic events, such as conference, colloquium, forum and symposium, is not as clear as it should be from an ontologist perspektive, as the use of these terms varies significantly throughout different sociocultural contexts. However, as ConfIDent tries to shed light on the culture of academic events, understanding them simply as synonyms would be too broad at the moment. Hence they are defined here rather adhoc with the reference to a specific academic event type specification that specifies its sociocultural format. These specific plan specifications are provided in AEON as named individuals for the purpose of automatically classifying academic events within the application of the ConfIDent project. It is the intention of the ConfIDent project to collect and analyse a large body of empirical data on academic events and series, especially with regard to the inherent academic event plan specifications, so that an evidence based diffirentiation might be possible. This means that the subclasses of academic event in question are prone to be edited in the future. TODO: * It needs to be discussed, if we need the "process boundary" class to describe the start and end of an academic event or event series. * It needs to be discussed, if we need the "temporal region" and "spatiotemporal region" classes to describe the duration and manifestation in spacetime of an academic event or event series. https://orcid.org/0000-0002-1595-3213 {"wikidata": {"uri": "https://www.wikidata.org/wiki/Q1656682", "label": "eventLabel"}, "openresearch": {"uri": "https://www.openresearch.org/wiki/Category:Event", "label": "Event"}, "gnd": {"uri": "https://d-nb.info/standards/elementset/gnd#ConferenceOrEvent", "label": "Conference or Event"}} academic event International Semantic Web Conference (ISWC) series An academic event series is a planned process that is the set of all recurring academic events of a destinct identity. This destinct identity is usually demarked by a shared name that only differs with regard to some ordnial symbol, such as 1st or the year of the academic event. {"wikidata": {"uri": "https://www.wikidata.org/wiki/Q15900647", "label": "conference_seriesLabel"}, "openresearch": {"uri": "https://www.openresearch.org/wiki/Category:Event_series", "label": "Event_series"}, "gnd": {"uri": "https://d-nb.info/standards/elementset/gnd#SeriesOfConferenceOrEvent", "label": "Series of conference or event"}} academic event series An internal identifier is an iao:identifier that is only meant to be used inside the reference system, such as an application, in which it is declared. The alternative term "ConfIDent ID" is used here, as the ontology is being developed by the ConfIDent project (https://projects.tib.eu/en/confident) to be used in its service. Thus the internal identifier is called "ConfIDent ID". You will probably want to change that in your implementation. https://orcid.org/0000-0002-1595-3213 internal identifier event type An academic event format specification is a plan specification that classifies a planned gathering of people in an academic context according to some sociocultural format, which provides implicit and explicit details on how this gathing is to be carried out by its participants in terms of achieving certain objectives, fulfiling certain conditions and performing certain actions. It needs to be discussed whether this class should be expanded to also describe the format of an 'academic event series', e.g. conference series. At the moment it is assumed that an 'academic event series', understood as a obi:'planned process', has no destinct format itself. Since this process is defined as the set of all recurring academic events of a destinct identity, the event series type would also only be the set of the academic event types of the academic events in this series. https://orcid.org/0000-0002-1595-3213 event type academic event format specification The contributor role inheres in a person or organization that participates in a planned process by somehow contributing to it. https://orcid.org/0000-0002-1595-3213 2020-09-28T12:51:02Z aeon contributor role https://github.com/tibonto/aeon/issues/144 The organizer role inheres in a person or organization that contributes to a planned process by planning and managing its realization. https://orcid.org/0000-0002-1595-3213 organizer role https://github.com/tibonto/aeon/issues/144 The 'committee member role' inheres in a person who contributes to a planned process by somehow realizing the function of the committe he is a member of. https://orcid.org/0000-0002-1595-3213 event committee member role https://github.com/tibonto/aeon/issues/144 The 'committee chair role' inheres in a person who contributes to a planned process by somehow realizing the function of the committee he is a chair of. https://orcid.org/0000-0002-1595-3213 event committee chair role https://github.com/tibonto/aeon/issues/144 The contact person role inheres in a person that contributes to a planned process by functioning as the addressee of the planned process who answers general inquiries and redirects more complex inqueries to a more appropriate addressee. https://orcid.org/0000-0002-1595-3213 contact person role https://github.com/tibonto/aeon/issues/144 The attendee role inheres in a person that contributes to a planned process by attending it. https://orcid.org/0000-0002-1595-3213 attendee role https://github.com/tibonto/aeon/issues/144 The moderating role inheres in a person that contributes to a planned process by facilitating the communication. https://orcid.org/0000-0002-1595-3213 moderator role https://github.com/tibonto/aeon/issues/144 Evaluation of scientific, academic, or professional work, such as manuscripts or grants by others working in the same field. The reviewer role inheres in a person that contributes to a planned process by reviewing something of interest in a planned process. ToDo: use CRO IRI http://purl.obolibrary.org/obo/CRO_0000101 https://orcid.org/0000-0002-1595-3213 manuscript review role reviewer role https://github.com/tibonto/aeon/issues/144 The presenter role inheres in a person that contributes to a planned process by presenting something of interest at a planned process. https://orcid.org/0000-0002-1595-3213 invited speaker role http://purl.obolibrary.org/obo/CRO_0000100 aeon presenter role https://github.com/tibonto/aeon/issues/144 The keynote speaker role inheres in a person that contributes to a planned process by holding a keynote speech at a planned process. https://orcid.org/0000-0002-1595-3213 keynote speaker role https://github.com/tibonto/aeon/issues/144 The sponsor role inheres in a person or organization that contributes to a planned process by providing the financial or material ressources needed to realize a planned process. PS 2-9-2020: For me there is still the open question on how to best model the different sponsor types (e.g. gold, silver, bronze...). As the possible sponsor types can have various schemes, it seems best to have named individuals of the aeon:Sponsor class at the moment. https://orcid.org/0000-0002-1595-3213 sponsor role https://github.com/tibonto/aeon/issues/144 DOI A digital object identifier (DOI) is an iao:identifier that persitently denotes a digital object acording to the ISO standard 26324. https://orcid.org/0000-0002-1595-3213 digital object identifier https://www.doi.org/ DOI A 'GND identifier' is a iao:'centrally registered identifier' that denotes an entity in "The Integrated Authority File (GND)" of the German national library. https://orcid.org/0000-0002-1595-3213 https://d-nb.info/standards/elementset/gnd#gndIdentifier GND ID An 'ISNI' (International Standard Name Identifier) is a iao:'centrally registered identifier' that denotes persons and organizations in the ISNI database. https://orcid.org/0000-0002-1595-3213 International Standard Name Identifier https://isni.org/page/what-is-isni/ ISNI An 'ORCID' is a iao:'centrally registered identifier' that denotes authors and contributors of scholarly communication in the ORCID database. https://orcid.org/0000-0002-1595-3213 Open Researcher and Contributor ID https://en.wikipedia.org/wiki/ORCID ORCID A 'ROR identifier' is a iao:'centrally registered identifier' that denotes an organization in the ROR database. https://orcid.org/0000-0002-1595-3213 ROR ID research organization registry identifier https://ror.org/ ROR ID QID A 'Wikidata QID identifier' is a iao:'centrally registered identifier' that denotes an entity in the Wikidata database. https://orcid.org/0000-0002-1595-3213 q number wikidata q number https://www.wikidata.org/wiki/Q43649390 "https://www.wikidata.org/wiki/"^^ xsd:anyURI Wikidata QID replaced by ENVO:00000856 DEPRECATED city https://github.com/tibonto/aeon/issues/142 true replaced by ENVO term DEPRECATED country https://github.com/tibonto/aeon/issues/142 true replaced by ENVO term DEPRECATED province https://github.com/tibonto/aeon/issues/142 true An event venue is a site where an event takes place. https://orcid.org/0000-0002-1595-3213 event venue DDC 410 Linguistics, OECD 6.02 Languages and literature, ... An 'academic field desciptor' is a data item that contextualizes a obi:'planned process' by providing a reference to a controlled vocalulary, which codifies the subdevision of knowledge taught and researched at the college or university level. https://orcid.org/0000-0002-1595-3213 academic discipline category academic field descriptor "AI, knowledge graphs, cloud computing" could be a set of keywords that denote the main topics covered by a specific conference. "The future of knowlegde graphs in the humanities" could be a 'topic' of an interdisciplinary oriented computer sciences conference. An 'event topic descriptor' is a data item that describes the central theme of a planned process. https://orcid.org/0000-0002-1595-3213 event theme description The instances of this class can be terms from a controlled vocabulary or thesaurus, phrases or just keywords. event topic descriptor The Zoom room in which an online conference is being held is a virtual location, that exists as long as the IT infrastructure on which it runs (is being realized) is not failing or turned off by an agent with the capability to do so. The service Twitter provides is a virtual location, in which the Twitter users can communicate with each other in a mostly text-based mode. A virtual location is a realizable entity that provides a digital space for humans and computers to interact with one another in various digital modes (e.g. text, audio, video, tactile). It specifically depends on the IT infrastructure that is used to realize the virtual location in the planned process of running certain code on certain computers. virtual site 2020-10-14T15:31:27Z virtual location 1 1 An event fee specification is a conditional specification that, as part of a plan specification, specifies the currency and the amount of money that has to be paid by participants of an event depending on their role in that event. https://orcid.org/0000-0002-1595-3213 event fee specification DID A 'decentralized identifier document' (DID) is an iao:identifier that denotes a verifiable, decentralized digital identity of an entity. https://orcid.org/0000-0002-1595-3213 DID https://www.w3.org/TR/did-core/Overview.html 2020-11-20T17:31:33Z decentralized identifier document An academic event committee is a body of one or more persons (object aggregate) that is responsible for the realization of a certain task or aspect in an academic event. Academic event committees are usually formed in the planning process of those academic events that need to subdevide and delegate the tasks that need to be carried out for the realization of the academic event.. academic event committee A deadline specification is a conditional specification that, as part of an action specification, defines until when a specified action has to be carried out. Given the fact that deadlines are specified in various planned processes this term should probably be regarded as a placeholder which ought to be defined in a broader ontology, maybe something like IAO? https://orcid.org/0000-0002-1595-3213 2021-07-19T08:50:13Z deadline specification An abstract deadline is a submission deadline that, as part of a call for abstracts of an academic event, specifies the date until which a contribution to a planned process in form of an abstract has to be submitted. https://orcid.org/0000-0002-1595-3213 2021-07-19T09:55:44Z abstract deadline A camera-ready deadline is a submission deadline that, as part of a call for papers of an academic event, specifies the date until which a contribution to a planned process that is ready for publishing has to be submitted. https://orcid.org/0000-0002-1595-3213 2021-07-19T09:55:44Z camera-ready deadline A demo deadline is a submission deadline that, as part of a call for papers of an academic event, specifies the date until which a contribution to a planned process in form of a demonstration has to be submitted. https://orcid.org/0000-0002-1595-3213 2021-07-19T09:55:44Z demo deadline A notification deadline is a deadline specification that specifies until when a participant of a planned process has to inform another participant of that process about something concering the plan of the process. Given the fact that notification deadlines are specified in various planned processes this term should probably be regarded as a placeholder which ought to be defined in a broader ontology, maybe something like IAO? https://orcid.org/0000-0002-1595-3213 2021-07-19T09:55:44Z notification deadline A paper deadline is a submission deadline that, as part of a call for papers of an academic event, specifies the date until which a contribution to a planned process in form of a paper has to be submitted. https://orcid.org/0000-0002-1595-3213 2021-07-19T09:55:44Z paper deadline A poster deadline is a submission deadline that, as part of a call for papers of an academic event, specifies the date until which a contribution to a planned process in form of a poster has to be submitted. https://orcid.org/0000-0002-1595-3213 2021-07-19T09:55:44Z poster deadline A conditional specification that, as part of an academic event type specification, specifies the date until which contributions that answer the call for papers of an academic event have to be submitted. Given the fact that submission deadlines are specified in various planned processes this term should probably be regarded as a placeholder which ought to be defined in a broader ontology, maybe something like IAO? https://orcid.org/0000-0002-1595-3213 2021-07-19T09:55:44Z submission deadline A tutorial deadline is a submission deadline that, as part of a call for papers of an academic event, specifies the date until which a contribution to a planned process in form of a tutorial has to be submitted. https://orcid.org/0000-0002-1595-3213 2021-07-19T09:55:44Z tutorial deadline A workshop deadline is a submission deadline that, as part of a call for papers of an academic event, specifies the date until which a contribution to a planned process in form of a workshop has to be submitted. https://orcid.org/0000-0002-1595-3213 2021-07-19T09:55:44Z workshop deadline A call for papers is an action specification in which the organizers of an academic event describe to prospective presenters the broad theme of the event, list the event's topics and formalities such as what kind of paper has to be submitted, to whom, and by what deadline. https://orcid.org/0000-0002-1595-3213 CFP https://en.wikipedia.org/wiki/Academic_conference#Organizing_an_academic_conference 2021-07-19T10:06:59Z call for papers CFP A call for abstracts is an action specification in which the organizers of an academic event describe to prospective presenters the broad theme of the event, list the event's topics and formalities such as what kind of abstract has to be submitted, to whom, and by what deadline. https://orcid.org/0000-0002-1595-3213 https://en.wikipedia.org/wiki/Academic_conference#Organizing_an_academic_conference 2021-07-19T11:24:02Z call for abstracts An identifier that is a proper name identifying a planned process. TODO: request term from IAO https://orcid.org/0000-0002-1595-3213 2021-09-13T08:55:02Z planned process name An academic event format specification that classifies an academic event as a colloquium. https://orcid.org/0000-0002-1595-3213 colloquium plan specification https://github.com/tibonto/aeon/issues/139 An academic event whose sociocultural format is determined in an academic event type specification that classifies the academic event as a colloquium. https://orcid.org/0000-0002-1595-3213 A possible definition could be the following, where one can also see how the definition depends on certain planned objectives, conditions and actions: A colloquium is an academic event that usually lasts only a few hours and serves to discuss a specific topic. Colloquia are usually part of the academic exchange in everyday university life with only one speaker, but can also take place on special occasions (anniversaries, start or end of the lecture phase, etc.) and can have more than one speaker. academic colloquium An academic event format specification that classifies an academic event as a conference. https://orcid.org/0000-0002-1595-3213 conference plan specification https://github.com/tibonto/aeon/issues/139 An academic event whose sociocultural format is determined in an academic event type specification that classifies the academic event as a conference. https://orcid.org/0000-0002-1595-3213 A possible literature based definition could be the following, where one can also see how the definition depends on certain planned objectives, conditions and actions: A conference is an academic event that lasts up to several days and serves as a forum for presentations on a specific topic or subject area. In addition to subject-specific conferences, there are also interdisciplinary conferences which allow both a broader focus and more specific questions on a particular (academic) problem. Conferences often have a highly formalized structure of parallel, clearly defined sessions with several short presentations and plenary sessions with invited (keynote) speakers who are considered multipliers in their (research) field. Ideally, the selection of the speakers and their contributions is subject to a review process. academic conference A possible literature based definition could be the following, where one can also see how the definition depends on certain planned objectives, conditions and actions: A conference is an academic event that lasts up to several days and serves as a forum for presentations on a specific topic or subject area. In addition to subject-specific conferences, there are also interdisciplinary conferences which allow both a broader focus and more specific questions on a particular (academic) problem. Conferences often have a highly formalized structure of parallel, clearly defined sessions with several short presentations and plenary sessions with invited (keynote) speakers who are considered multipliers in their (research) field. Ideally, the selection of the speakers and their contributions is subject to a review process. Casserly, P. (2019). Symposium vs. conference, what’s the difference? A symposium versus a conference. What’s the actual difference? And how does it affect organising or submitting to one? Ex Ordo. https://www.exordo.com/blog/symposium-vs-conference/ Hansen, Thomas Trøst; Pedersen, David Budtz; Foley, Carmel (PRE-PRINT). Academic Event: an empirically-grounded typology and their academic impact. DOI: https://doi.org/10.3727/152599519X15506259856598. An academic event format specification that classifies an academic event as a forum. https://orcid.org/0000-0002-1595-3213 forum plan specification https://github.com/tibonto/aeon/issues/139 An academic event whose sociocultural format is determined in an academic event type specification that classifies the academic event as a forum. https://orcid.org/0000-0002-1595-3213 A forum is an academic event that usually is public and involves audience discussion. academic forum A forum is an academic event that usually is public and involves audience discussion. https://www.merriam-webster.com/dictionary/forum An academic event format specification that classifies an academic event as a hackathon. https://orcid.org/0000-0002-1595-3213 hackathon plan specification https://github.com/tibonto/aeon/issues/139 An academic event in which computer programmers and others involved in software development, including graphic designers, interface designers, project managers, domain experts, and others collaborate intensively in a design sprint-like manner on software projects. https://orcid.org/0000-0002-1595-3213 Briscoe, G., & Mulligan, C. (2014). Digital innovation: the hackathon phenomenon (Creativeworks London). https://qmro.qmul.ac.uk/xmlui/handle/123456789/11418 https://en.wikipedia.org/wiki/Hackathon academic hackathon An academic event format specification that classifies an academic event as a seminar. https://orcid.org/0000-0002-1595-3213 seminar plan specification https://github.com/tibonto/aeon/issues/139 An academic event that has the function to instruct a small group or small groups, often for recurring meetings, on some particular subject, in which everyone present is usually encouraged to participate. https://orcid.org/0000-0002-1595-3213 https://en.wikipedia.org/wiki/Seminar academic seminar An academic event format specification that classifies an academic event as a session. https://orcid.org/0000-0002-1595-3213 session plan specification https://github.com/tibonto/aeon/issues/139 An academic event that is a clearly defined part of a larger academic event, such as an academic conference or track, in which a small number of presenters (usually 2-5) focus on a specific topic. A session is usually formally accompanied by a session chair, who assumes the function of a moderator. https://orcid.org/0000-0002-1595-3213 academic event session An academic event format specification that classifies an academic event as a symposium. https://orcid.org/0000-0002-1595-3213 symposium plan specification https://github.com/tibonto/aeon/issues/139 An academic event whose sociocultural format is determined in an academic event type specification that classifies the academic event as a symposium. https://orcid.org/0000-0002-1595-3213 A possible literature based definition could be the following: A symposium is a specific type of conference with a narrower thematic focus, with fewer participants and of shorter duration. The degree of structuring lies between a classic conference and a workshop, allows more discussion than the larger conference, but is usually more formalized than the workshop. academic symposium A possible literature based definition could be the following: A symposium is a specific type of conference with a narrower thematic focus, with fewer participants and of shorter duration. The degree of structuring lies between a classic conference and a workshop, allows more discussion than the larger conference, but is usually more formalized than the workshop. Canadian Institute for Knowledge Development (CIKD). (2019). Difference between scientific events. NCM Conferences blog. https://ncmconferences.com/difference-between-scientific-events/ Casserly, P. (2019). Symposium vs. conference, what’s the difference? A symposium versus a conference. What’s the actual difference? And how does it affect organising or submitting to one? Ex Ordo. https://www.exordo.com/blog/symposium-vs-conference/ Hansen, Thomas Trøst; Pedersen, David Budtz; Foley, Carmel (PRE-PRINT). Academic Event: an empirically-grounded typology and their academic impact. DOI: https://doi.org/10.3727/152599519X15506259856598. An academic event format specification that classifies an academic event as a keynote speech. https://orcid.org/0000-0002-1595-3213 keynote plan specification https://github.com/tibonto/aeon/issues/139 A keynote speech is a special talk that has the function to set the underlying tone and summarize the core message or most important revelation off the academic at which it is given. https://orcid.org/0000-0002-1595-3213 keynote keynote lecture https://en.wikipedia.org/wiki/Keynote academic keynote speech An academic event format specification that classifies an academic event as a track. https://orcid.org/0000-0002-1595-3213 track plan specification https://github.com/tibonto/aeon/issues/139 An academic event that, as a part of a larger academic event, has the function to group even smaller parts of the academic event, like sessions and talks, according to a shared theme or topic. It usually has dedicated chairs and program committees. https://orcid.org/0000-0002-1595-3213 stream https://www.conftool.net/ctforum/index.php/topic,99.0.html academic event track An academic event format specification that classifies an academic event as a tutorial. https://orcid.org/0000-0002-1595-3213 tutorial plan specification https://github.com/tibonto/aeon/issues/139 An academic event that has the function to educate the audience on a certain topic. A tutorial is often realized as an academic event talk or academic event session. https://orcid.org/0000-0002-1595-3213 https://en.wikipedia.org/wiki/Tutorial academic tutorial An academic event format specification that classifies an academic event as a workshop. https://orcid.org/0000-0002-1595-3213 workshop plan specification https://github.com/tibonto/aeon/issues/139 A smaller academic event that serves to exchange information on a specific topic or problem. It usually last one or two days and offers space for discussion and the development of content and solutions. Group work is often part of the event concept. https://orcid.org/0000-0002-1595-3213 Alston, J. M. (2019). What's the difference between a conference, a seminar, a workshop and a symposium? Conference Monkey Insights. https://conferencemonkey.org/insight/whats-the-difference-between-a-conference-a-seminar-a-workshop-and-a-symposium-1075915 Canadian Institute for Knowledge Development (CIKD). (2019). Difference between scientific events. NCM Conferences blog. https://ncmconferences.com/difference-between-scientific-events/ academic workshop An academic event format specification that classifies an academic event as a congress. https://orcid.org/0000-0002-1595-3213 congress plan specification https://github.com/tibonto/aeon/issues/139 Academic event whose sociocultural format is determined in an academic event type specification that classifies the academic event as a congress. It usually is a larger type of conference with regard to the number of participants and organizers. https://orcid.org/0000-0002-1595-3213 A possible literature based definition could be the following: A congress is a conference that is characterised by a larger number of participants (often several hundred) and is oftentimes organised jointly by large, established (e.g. specialised societies) and/or several institutions. Congresses have a broader thematic focus than simple conferences, take place in certain cycles, but can still target an exclusive group of participants (e.g. representatives of a single discipline). academic congress A possible literature based definition could be the following: A congress is a conference that is characterised by a larger number of participants (often several hundred) and is oftentimes organised jointly by large, established (e.g. specialised societies) and/or several institutions. Congresses have a broader thematic focus than simple conferences, take place in certain cycles, but can still target an exclusive group of participants (e.g. representatives of a single discipline). Canadian Institute for Knowledge Development (CIKD). (2019). Difference between scientific events. NCM Conferences blog. https://ncmconferences.com/difference-between-scientific-events/ Hansen, Thomas Trøst; Pedersen, David Budtz; Foley, Carmel (PRE-PRINT). Academic Event: an empirically-grounded typology and their academic impact. DOI: https://doi.org/10.3727/152599519X15506259856598. An academic event format specification that classifies an academic event as a talk. https://orcid.org/0000-0002-1595-3213 talk plan specification https://github.com/tibonto/aeon/issues/139 presentation An academic event that is a unit of a larger academic event, such as an academic event session, at which a specific topic is being presented in a rather short way often as a part of a larger academic event such as a session, conference or workshop. https://orcid.org/0000-0002-1595-3213 presentation speech academic event talk An academic event format specification that classifies an academic event as a poster session. https://orcid.org/0000-0002-1595-3213 poster session plan specification https://github.com/tibonto/aeon/issues/139 A poster session is a session at which poster papers are presented. https://orcid.org/0000-0002-1595-3213 https://en.wikipedia.org/wiki/Poster_session academic poster session An attendance fee specification is an event fee specification that, as part of a plan specification, defines the currency and amount of money a person has to pay to attend an event. https://orcid.org/0000-0002-1595-3213 2021-07-05T10:14:06Z attendance fee specification Philip Strömert is an attendee of PIDapalooza 2021. An attendee is a contributer that holds an attendee role which is being realized in a planned process. The general assumption is that the attendee role is being realized the moment someone shows up to an event which she is expected to participate in as part of an audience. Someone who plans to attend some academic event but never shows up during this event, would not be considered an attendee of the event. Defining 'attendee' is not trivial, as the expectations of what an attendee must do, can differ from community to community and from event type to event type. For some an attendee must have been accredited by some official organizer and might only get a certificate of attendence at the end of it, when a certain amount of participation (e.g. visited sessions, completed workshops) has been achieved. For others it might suffice to simple be present. We need this concept of an attendee in order to be able to properly quantify the participation in a planned process. For this we would also need to have an action specification that is the conretizaion of the attendee role. https://orcid.org/0000-0002-1595-3213 A person who participates actively or passively in an event. attendee https://github.com/tibonto/aeon/issues/144 A committee chair is a committee member that holds a committee chair role which is being realized in a planned process. https://orcid.org/0000-0002-1595-3213 A committee chair is a committe member that is expected to speak on behalf of and to be responsible for the committee. The person who is in charge of a committee with primary responsibility for carrying out the committee's duties. event committee chair https://github.com/tibonto/aeon/issues/144 A committee member is an organizer that holds a committee member role which is being realized in a planned process. https://orcid.org/0000-0002-1595-3213 event committee member https://github.com/tibonto/aeon/issues/144 A contact person is an organizer that holds a contact person role which is being realized in a planned process. https://orcid.org/0000-0002-1595-3213 A contact peron is defined by its role to be the person who answers general questions about a planned process and who forwards any further inquiries to the appropriate recipiant. contact person https://github.com/tibonto/aeon/issues/144 All organizers and participants of the academic event called PIDapalooza 2020 are contributors of that particular event.. TODO: There needs to be an ICE branch in AEON covering the action and objective specifications which the various contributors have to concretize when realizing their roles. The concretization of these specification calsses needs to be axiomized here and in the various contributor roles. A contributor is a person or organization that holds a contributor role which is being realized in a planned process. An academic conference is being realized by the contributions of different kinds of people and organizations. The organizers plan the program and manage the needed logistics. The sponsors provide the resources and funds needed for the realization. The speakers contribute by presenting their academic work. The reviewers make sure the submitted work is worth to be presented. The moderators make sure that the mode of communication is caried out as planned by the organizer. The attendees contribute by being there as the audience, providing feedback and by making up the pool of possible future collaborators. This class and its children should be defined in an ontology that covers the domain of contributorship in the sciences. The contributor ontology (CRO - http://purl.obolibrary.org/obo/cro.owl) seems to be the best place. However at the moment CRO only covers "the diverse roles performed in the work leading to a published research output in the sciences." An academic event or event series should ot be understood as a published research output, as they are procceses (occurents) and not ICEs. https://orcid.org/0000-0002-1595-3213 A person or organization can only be considered a contributor of some planned process, if and only if the act of contributing has been fulfilled. The contributor role is being realized, when the task (objective specification) attached to this role has been achieved somehow. It can thus be possible for a person or organization to hold multiple roles either in the same or in different planned processes. contributor https://github.com/tibonto/aeon/issues/144 The finance committee is an academic event committee that has the task of monitoring and managing the budget of an academic event. PERSON: Philip Strömert event finance committee The general or steering committee is an academic event committee that is responsible for the entire conceptual design of an academic event. This entails decisions on the content focus, budget, size, choice of venue and time, selection of other responsible persons, etc. steering committee general committee A 'keynote speaker' is a presenter that holds a keynote speaker role which is being realized in a planned process. https://orcid.org/0000-0002-1595-3213 An invited person - often a multiplier in his or her (research) field - responsible for delivering a keynote speech. keynote speaker https://github.com/tibonto/aeon/issues/144 The local committee is an academic event committee that is in charge of planning, organizing and carrying out an academic event on site. This entails being in charge of managing the venue, registration, supply, accommodations etc. local committee A moderator is a contributer that holds a moderating role which is being realized in a planned process. https://orcid.org/0000-0002-1595-3213 A person responsible for facilitating a session at an academic event. moderator https://github.com/tibonto/aeon/issues/144 DataCite is an organizer of PIDapalooza 2020. Organizers of academic events or event series are often organizations that form special taks forces, or event committees, in order to plan and manage all aspects related to the realization of the event or event series. An organizer is a contributer that holds an organizing role which is being realized in a planned process. https://orcid.org/0000-0002-1595-3213 A person or organization that is responsible for the planning and realization of a planned process. organizer https://github.com/tibonto/aeon/issues/144 The programme committee is an academic event committee that is responsible for planning what body of work is to be presented at an academic event. This entails making a call to the scientifiy community to submit their work, to review these submissions and to invite presenters that will fit to the academic event according to its planned scope. program committee The publication committee is an academic event committee that is responsible for the publication of the proceedings of an academic event. publication committee The publicity committee is an academic event committee that is responsible for the external communication of an academic event. This entails the promotion, (social) media relations, web presence, further releases, etc. publicity committee The reviewer of a conference who reviews the submitted papers. A reviewer is a contributer that holds a reviewer role which is being realized in a planned process. https://orcid.org/0000-0002-1595-3213 reviewer https://github.com/tibonto/aeon/issues/144 A presenter is a person who's role it is to present some body of work to an audience. Philip Strömert is a presenter at PIDapalooza 2021. A presenter is a contributer that holds a presenter role which is being realized in a planned process. https://orcid.org/0000-0002-1595-3213 speaker presenter https://github.com/tibonto/aeon/issues/144 An organization or person that promises to fund an academic event is a sponsor of that event the moment the promised funds have been recieved by the organizers of the event. A sponsor is a contributer that holds a sponsor role which is being realized in a planned process. Philip Strömert 2-9-2020: For me there is still the open question on how to best model the different sponsor types (e.g. gold, silver, bronze...), as there are various schemes. At the moment any sponsor type other than gold, silver or bronze can be further specified by using the data property "sponsor_type". We could also reuse the "event type a SKOS:concept" pattern here. But it seems best to have a clear definition of each sponsor type, in order to be able to subclass them here and add the corresponding roles and properties. https://orcid.org/0000-0002-1595-3213 sponsor https://github.com/tibonto/aeon/issues/144 A sponsor fee specification is an event fee specification that, as part of a plan specification, defines the currency and amount of money a sponsor has to pay to sponsor an event. https://orcid.org/0000-0002-1595-3213 2021-07-05T10:15:52Z sponsor fee specification The sponsorship committee ia an academic event committee that is responsible for aquireing and managing the sponsorships of an academic event. sponsorship committee The technical committee ia an academic event committee that is responsible for the technical needs associated with the realization of an academic event. technical committee A 'wikiCFP identifier' is a iao:'centrally registered identifier' that denotes an 'academic event' or 'academic event series' in the wikiCFP database. https://orcid.org/0000-0002-1595-3213 wikiCFP ID http://www.wikicfp.com/cfp/ wikiCFP identifier methodology role http://purl.obolibrary.org/obo/IAO_0000120 Development or design of methodology; creation of models. https://orcid.org/0000-0001-5059-4132 http://dictionary.casrai.org/Contributor_Roles/Methodology http://purl.org/credit/ontology f21e2be9-4e38-4ab7-8691-d6f72d5d5843 methodology role software role Programming, software development; designing computer programs; implementation of the computer code and supporting algorithms; testing of existing code components. https://orcid.org/0000-0001-5059-4132 software systems role http://dictionary.casrai.org/Contributor_Roles/Software http://purl.org/credit/ontology f89c5233-01b0-4778-93e9-cc7d107aa2c8 software role example to be eventually removed example to be eventually removed failed exploratory term The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job Person:Alan Ruttenberg failed exploratory term metadata complete Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. metadata complete organizational term Term created to ease viewing/sort terms for development purpose, and will not be included in a release organizational term ready for release Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." ready for release metadata incomplete Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. metadata incomplete uncurated Nothing done yet beyond assigning a unique class ID and proposing a preferred term. uncurated pending final vetting All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. pending final vetting Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes. PERSON: Alan Ruttenberg PERSON: Melanie Courtot obsolete_core true placeholder removed placeholder removed terms merged An editor note should explain what were the merged terms and the reason for the merge. terms merged term imported This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. term imported term split This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. term split universal Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. Alan Ruttenberg A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf universal defined class A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. Alan Ruttenberg defined class named class expression A named class expression is a logical expression that is given a name. The name can be used in place of the expression. named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions Alan Ruttenberg named class expression to be replaced with external ontology term Terms with this status should eventually replaced with a term from another ontology. Alan Ruttenberg group:OBI to be replaced with external ontology term requires discussion A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. Alan Ruttenberg group:OBI requires discussion The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not. This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease. https://github.com/information-artifact-ontology/ontology-metadata/issues/77 https://orcid.org/0000-0001-5208-3432 out of scope _VIVO2020_speaker1 2020-06-18T19:00:00Z 2020-06-16T09:00:00Z _VIVO2020 _VIVO2020_format VIVO 2020 https://www.wikidata.org/wiki/Q108430463 _VIVO2020_name VIVO Conference 2020 11th Annual International VIVO Conference 2020 _VIVO2020_speaker1_role _VIVO_series _VIVO2020_ConfIDentID _0000-0002-1595-3213 _VIVO2020_QID _VIVO_series_QID