From 40a7b31e94c8b87a0171242f68b957dce8f57325 Mon Sep 17 00:00:00 2001 From: marijane white Date: Tue, 2 Oct 2018 16:26:08 -0700 Subject: [PATCH] Prepare ontology release --- credit.obo | 165 ++++++++++++++++++- credit.owl | 240 +++++++++++++++++++++++++++- imports/iao_import.owl | 185 +++++++++++++++++++-- src/ontology/imports/iao_import.owl | 185 +++++++++++++++++++-- 4 files changed, 739 insertions(+), 36 deletions(-) diff --git a/credit.obo b/credit.obo index 0eaab21..6b59039 100644 --- a/credit.obo +++ b/credit.obo @@ -1,9 +1,9 @@ format-version: 1.2 data-version: releases/2018-10-02 -remark: CRediT Ontology +remark: CRediT ontology import: http://purl.obolibrary.org/obo/credit/imports/iao_import.owl ontology: credit -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\n############################\n# Classes\n############################\n\n# Class: (entity)\n\nSubClassOf( owl:Thing)\n\n# Class: (credit)\n\nSubClassOf( owl:Thing)\n\n\n) +owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\n############################\n# Classes\n############################\n\n# Class: (entity)\n\nSubClassOf( owl:Thing)\n\n# Class: (contributor role)\n\nSubClassOf( owl:Thing)\n\n\n) [Term] id: BFO:0000002 @@ -19,7 +19,166 @@ is_a: BFO:0000002 [Term] id: CREDIT:00000000 -name: credit +name: contributor role +def: "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." [] +property_value: IAO:0000111 "contributor role" xsd:string +property_value: IAO:0000114 http://purl.obolibrary.org/obo/IAO_0000120 xsd:string +property_value: IAO:0000117 "PERSON: Marijane White" xsd:string +property_value: IAO:0000119 http://dictionary.casrai.org/Contributor_Roles xsd:string + +[Term] +id: CREDIT:00000001 +name: conceptualization role +def: "Ideas; formulation or evolution of overarching research goals and aims." [] +xref: 8b73531f-db56-4914-9502-4cc4d4d8ed73 +is_a: CREDIT:00000000 ! contributor role +property_value: IAO:0000111 "conceptualization role" xsd:string +property_value: IAO:0000114 http://purl.obolibrary.org/obo/IAO_0000120 xsd:string +property_value: IAO:0000117 "PERSON: Marijane White" xsd:string +property_value: IAO:0000119 http://dictionary.casrai.org/Contributor_Roles/Conceptualization xsd:string + +[Term] +id: CREDIT:00000002 +name: data curation role +def: "Management activities to annotate (produce metadata), scrub data and maintain research data (including software code, where it is necessary for interpreting the data itself) for initial use and later re-use." [] +xref: f93e0f44-f2a4-4ea1-824a-4e0853b05c9d +is_a: CREDIT:00000000 ! contributor role +property_value: IAO:0000111 "data curation role" xsd:string +property_value: IAO:0000114 http://purl.obolibrary.org/obo/IAO_0000120 xsd:string +property_value: IAO:0000117 "PERSON: Marijane White" xsd:string +property_value: IAO:0000119 http://dictionary.casrai.org/Contributor_Roles/Data_curation xsd:string + +[Term] +id: CREDIT:00000003 +name: formal analysis role +def: "Application of statistical, mathematical, computational, or other formal techniques to analyse or synthesize study data." [] +xref: 95394cbd-4dc8-4735-b589-7e5f9e622b3f +is_a: CREDIT:00000000 ! contributor role +property_value: IAO:0000111 "formal analysis role" xsd:string +property_value: IAO:0000114 http://purl.obolibrary.org/obo/IAO_0000120 xsd:string +property_value: IAO:0000117 "PERSON: Marijane White" xsd:string +property_value: IAO:0000119 http://dictionary.casrai.org/Contributor_Roles/Formal_analysis xsd:string + +[Term] +id: CREDIT:00000004 +name: funding acquisition role +def: "Acquisition of the financial support for the project leading to this publication." [] +xref: 34ff6d68-132f-4438-a1f4-fba61ccf364 +is_a: CREDIT:00000000 ! contributor role +property_value: IAO:0000111 "funding acquisition role" xsd:string +property_value: IAO:0000114 http://purl.obolibrary.org/obo/IAO_0000120 xsd:string +property_value: IAO:0000117 "PERSON: Marijane White" xsd:string +property_value: IAO:0000119 http://dictionary.casrai.org/Contributor_Roles/Funding_acquisition xsd:string + +[Term] +id: CREDIT:00000005 +name: investigation role +def: "Conducting a research and investigation process, specifically performing the experiments, or data/evidence collection." [] +xref: 2451924d-425e-4778-9f4c-36c848ca70c2 +is_a: CREDIT:00000000 ! contributor role +property_value: IAO:0000111 "investigation role" xsd:string +property_value: IAO:0000114 http://purl.obolibrary.org/obo/IAO_0000120 xsd:string +property_value: IAO:0000117 "PERSON: Marijane White" xsd:string +property_value: IAO:0000119 http://dictionary.casrai.org/Contributor_Roles/Investigation xsd:string + +[Term] +id: CREDIT:00000006 +name: methodology role +def: "Development or design of methodology; creation of models." [] +xref: f21e2be9-4e38-4ab7-8691-d6f72d5d5843 +is_a: CREDIT:00000000 ! contributor role +property_value: IAO:0000111 "methodology role" xsd:string +property_value: IAO:0000114 http://purl.obolibrary.org/obo/IAO_0000120 xsd:string +property_value: IAO:0000117 "PERSON: Marijane White" xsd:string +property_value: IAO:0000119 http://dictionary.casrai.org/Contributor_Roles/Methodology xsd:string + +[Term] +id: CREDIT:00000007 +name: project administration role +def: "Management and coordination responsibility for the research activity planning and execution." [] +xref: a693fe76-ea33-49ad-9dcc-5e4f3ac5f938 +is_a: CREDIT:00000000 ! contributor role +property_value: IAO:0000111 "project administration role" xsd:string +property_value: IAO:0000114 IAO:0000120 +property_value: IAO:0000117 "PERSON: Marijane White" xsd:string +property_value: IAO:0000119 http://dictionary.casrai.org/Contributor_Roles/Project_administration xsd:string + +[Term] +id: CREDIT:00000008 +name: resources role +def: "Provision of study materials, reagents, materials, patients, laboratory samples, animals, instrumentation, computing resources, or other analysis tools." [] +xref: ebd781f0-bf79-492c-ac21-b31b9c3c990c +is_a: CREDIT:00000000 ! contributor role +property_value: IAO:0000111 "resources role" xsd:string +property_value: IAO:0000114 IAO:0000120 +property_value: IAO:0000117 "PERSON: Marijane White" xsd:string +property_value: IAO:0000119 http://dictionary.casrai.org/Contributor_Roles/Resources xsd:string + +[Term] +id: CREDIT:00000009 +name: software role +def: "Programming, software development; designing computer programs; implementation of the computer code and supporting algorithms; testing of existing code components." [] +xref: f89c5233-01b0-4778-93e9-cc7d107aa2c8 +is_a: CREDIT:00000000 ! contributor role +property_value: IAO:0000111 "software role" xsd:string +property_value: IAO:0000114 IAO:0000120 +property_value: IAO:0000117 "PERSON:Marijane White" xsd:string +property_value: IAO:0000119 http://dictionary.casrai.org/Contributor_Roles/Software xsd:string + +[Term] +id: CREDIT:00000010 +name: supervision role +def: "Oversight and leadership responsibility for the research activity planning and execution, including mentorship external to the core team." [] +xref: 0c8ca7d4-06ad-4527-9cea-a8801fcb8746 +is_a: CREDIT:00000000 ! contributor role +property_value: IAO:0000111 "supervision role" xsd:string +property_value: IAO:0000114 http://purl.obolibrary.org/obo/IAO_0000120 xsd:string +property_value: IAO:0000117 "PERSON: Marijane White" xsd:string +property_value: IAO:0000119 http://dictionary.casrai.org/Contributor_Roles/Supervision xsd:string + +[Term] +id: CREDIT:00000011 +name: validation role +def: "Verification, whether as a part of the activity or separate, of the overall replication/reproducibility of results/experiments and other research outputs." [] +xref: 4b1bf348-faf2-4fc4-bd66-4cd3a84b9d44 +is_a: CREDIT:00000000 ! contributor role +property_value: IAO:0000111 "validation role" xsd:string +property_value: IAO:0000114 http://purl.obolibrary.org/obo/IAO_0000120 xsd:string +property_value: IAO:0000117 "PERSON: Marijane White" xsd:string +property_value: IAO:0000119 http://dictionary.casrai.org/Contributor_Roles/Validation xsd:string + +[Term] +id: CREDIT:00000012 +name: visualization role +def: "Preparation, creation and/or presentation of the published work, specifically visualization/data presentation." [] +xref: 76b9d56a-e430-4e0a-84c9-59c11be343ae +is_a: CREDIT:00000000 ! contributor role +property_value: IAO:0000111 "visualization role" xsd:string +property_value: IAO:0000114 http://purl.obolibrary.org/obo/IAO_0000120 xsd:string +property_value: IAO:0000117 "PERSON: Marijane White" xsd:string +property_value: IAO:0000119 http://dictionary.casrai.org/Contributor_Roles/Visualization xsd:string + +[Term] +id: CREDIT:00000013 +name: writing original draft role +def: "Preparation, creation and/or presentation of the published work, specifically writing the initial draft (including substantive translation)." [] +xref: 43ebbd94-98b4-42f1-866b-c930cef228ca +is_a: CREDIT:00000000 ! contributor role +property_value: IAO:0000111 "writing original draft role" xsd:string +property_value: IAO:0000114 http://purl.obolibrary.org/obo/IAO_0000123 xsd:string +property_value: IAO:0000117 "PERSON: Marijane White" xsd:string +property_value: IAO:0000119 http://dictionary.casrai.org/Contributor_Roles/Writing_%E2%80%93_original_draft xsd:string + +[Term] +id: CREDIT:00000014 +name: writing review and editing role +def: "Preparation, creation and/or presentation of the published work by those from the original research group, specifically critical review, commentary or revision – including pre- or post-publication stages." [] +xref: d3aead86-f2a2-47f7-bb99-79de6421164d +is_a: CREDIT:00000000 ! contributor role +property_value: IAO:0000111 "writing review and editing role" xsd:string +property_value: IAO:0000114 http://purl.obolibrary.org/obo/IAO_0000123 xsd:string +property_value: IAO:0000117 "PERSON: Marijane White" xsd:string +property_value: IAO:0000119 http://dictionary.casrai.org/Contributor_Roles/Writing_%E2%80%93_review_%26_editing xsd:string [Term] id: IAO:0000027 diff --git a/credit.owl b/credit.owl index b8eb333..8c76eb9 100644 --- a/credit.owl +++ b/credit.owl @@ -3,18 +3,37 @@ xml:base="http://purl.obolibrary.org/obo/credit.owl" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:owl="http://www.w3.org/2002/07/owl#" + xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" - xmlns:obo="http://purl.obolibrary.org/obo/"> + xmlns:obo="http://purl.obolibrary.org/obo/" + xmlns:foaf="http://xmlns.com/foaf/0.1/"> - CRediT Ontology + CRediT ontology + + + + + + + + + + + + + + + conceptualization role + http://purl.obolibrary.org/obo/IAO_0000120 + Ideas; formulation or evolution of overarching research goals and aims. + PERSON: Marijane White + http://dictionary.casrai.org/Contributor_Roles/Conceptualization + 8b73531f-db56-4914-9502-4cc4d4d8ed73 + conceptualization role + + + + + + + + + data curation role + http://purl.obolibrary.org/obo/IAO_0000120 + Management activities to annotate (produce metadata), scrub data and maintain research data (including software code, where it is necessary for interpreting the data itself) for initial use and later re-use. + PERSON: Marijane White + http://dictionary.casrai.org/Contributor_Roles/Data_curation + f93e0f44-f2a4-4ea1-824a-4e0853b05c9d + data curation role + + + + + + + + + formal analysis role + http://purl.obolibrary.org/obo/IAO_0000120 + Application of statistical, mathematical, computational, or other formal techniques to analyse or synthesize study data. + PERSON: Marijane White + http://dictionary.casrai.org/Contributor_Roles/Formal_analysis + 95394cbd-4dc8-4735-b589-7e5f9e622b3f + formal analysis role + + + + + + + + + funding acquisition role + http://purl.obolibrary.org/obo/IAO_0000120 + Acquisition of the financial support for the project leading to this publication. + PERSON: Marijane White + http://dictionary.casrai.org/Contributor_Roles/Funding_acquisition + 34ff6d68-132f-4438-a1f4-fba61ccf364 + funding acquisition role + + + + + + + + + investigation role + http://purl.obolibrary.org/obo/IAO_0000120 + Conducting a research and investigation process, specifically performing the experiments, or data/evidence collection. + PERSON: Marijane White + http://dictionary.casrai.org/Contributor_Roles/Investigation + 2451924d-425e-4778-9f4c-36c848ca70c2 + investigation role + + + + + + + + + methodology role + http://purl.obolibrary.org/obo/IAO_0000120 + Development or design of methodology; creation of models. + PERSON: Marijane White + http://dictionary.casrai.org/Contributor_Roles/Methodology + f21e2be9-4e38-4ab7-8691-d6f72d5d5843 + methodology role + + + + + + + + + project administration role + + Management and coordination responsibility for the research activity planning and execution. + PERSON: Marijane White + http://dictionary.casrai.org/Contributor_Roles/Project_administration + a693fe76-ea33-49ad-9dcc-5e4f3ac5f938 + project administration role + + + + + + + + + resources role + + Provision of study materials, reagents, materials, patients, laboratory samples, animals, instrumentation, computing resources, or other analysis tools. + PERSON: Marijane White + http://dictionary.casrai.org/Contributor_Roles/Resources + ebd781f0-bf79-492c-ac21-b31b9c3c990c + resources role + + + + + + + + + software role + + Programming, software development; designing computer programs; implementation of the computer code and supporting algorithms; testing of existing code components. + PERSON:Marijane White + http://dictionary.casrai.org/Contributor_Roles/Software + f89c5233-01b0-4778-93e9-cc7d107aa2c8 + software role + + + + + + + + + supervision role + http://purl.obolibrary.org/obo/IAO_0000120 + Oversight and leadership responsibility for the research activity planning and execution, including mentorship external to the core team. + PERSON: Marijane White + http://dictionary.casrai.org/Contributor_Roles/Supervision + 0c8ca7d4-06ad-4527-9cea-a8801fcb8746 + supervision role + + + + + + + + + validation role + http://purl.obolibrary.org/obo/IAO_0000120 + Verification, whether as a part of the activity or separate, of the overall replication/reproducibility of results/experiments and other research outputs. + PERSON: Marijane White + http://dictionary.casrai.org/Contributor_Roles/Validation + 4b1bf348-faf2-4fc4-bd66-4cd3a84b9d44 + validation role + + + + + + + + + visualization role + http://purl.obolibrary.org/obo/IAO_0000120 + Preparation, creation and/or presentation of the published work, specifically visualization/data presentation. + PERSON: Marijane White + http://dictionary.casrai.org/Contributor_Roles/Visualization + 76b9d56a-e430-4e0a-84c9-59c11be343ae + visualization role + + + + + + + + + writing original draft role + http://purl.obolibrary.org/obo/IAO_0000123 + Preparation, creation and/or presentation of the published work, specifically writing the initial draft (including substantive translation). + PERSON: Marijane White + http://dictionary.casrai.org/Contributor_Roles/Writing_%E2%80%93_original_draft + 43ebbd94-98b4-42f1-866b-c930cef228ca + writing original draft role + + + + + + + + + writing review and editing role + http://purl.obolibrary.org/obo/IAO_0000123 + Preparation, creation and/or presentation of the published work by those from the original research group, specifically critical review, commentary or revision – including pre- or post-publication stages. + PERSON: Marijane White + http://dictionary.casrai.org/Contributor_Roles/Writing_%E2%80%93_review_%26_editing + d3aead86-f2a2-47f7-bb99-79de6421164d + writing review and editing role diff --git a/imports/iao_import.owl b/imports/iao_import.owl index 7bf239f..3514e58 100644 --- a/imports/iao_import.owl +++ b/imports/iao_import.owl @@ -6,7 +6,8 @@ xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" - xmlns:obo="http://purl.obolibrary.org/obo/"> + xmlns:obo="http://purl.obolibrary.org/obo/" + xmlns:foaf="http://xmlns.com/foaf/0.1/"> @@ -24,31 +25,63 @@ - + + 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 + + A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + example of usage + - + + has curation status + PERSON:Alan Ruttenberg + PERSON:Bill Bug + PERSON:Melanie Courtot + OBI_0000281 + has curation status + @@ -89,55 +122,132 @@ We also have the outstanding issue of how to aim different definitions to differ - + + editor note + + An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obfoundry.org/obo/obi> + + 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 term + + An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + alternative term + - + + definition source + + formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 + PERSON:Daniel Schober + Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + definition source + + + + + + + - + + 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) + - + + 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 + - + + temporal interpretation + https://github.com/oborel/obo-relations/wiki/ROAndTime + + + + + + + @@ -837,6 +947,51 @@ Previous. An information content entity is a non-realizable information entity t + + + + + +## Elucidation + +This is used when the statement/axiom is assumed to hold true 'eternally' + +## How to interpret (informal) + +First the "atemporal" FOL is derived from the OWL using the standard +interpretation. This axiom is temporalized by embedding the axiom +within a for-all-times quantified sentence. The t argument is added to +all instantiation predicates and predicates that use this relation. + +## Example + + Class: nucleus + SubClassOf: part_of some cell + + forall t : + forall n : + instance_of(n,Nucleus,t) + implies + exists c : + instance_of(c,Cell,t) + part_of(n,c,t) + +## Notes + +This interpretation is *not* the same as an at-all-times relation + + + axiom holds for all times + + + + + + + + + + - + + 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 + + A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + example of usage + - + + has curation status + PERSON:Alan Ruttenberg + PERSON:Bill Bug + PERSON:Melanie Courtot + OBI_0000281 + has curation status + @@ -89,55 +122,132 @@ We also have the outstanding issue of how to aim different definitions to differ - + + editor note + + An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obfoundry.org/obo/obi> + + 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 term + + An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + alternative term + - + + definition source + + formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 + PERSON:Daniel Schober + Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + definition source + + + + + + + - + + 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) + - + + 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 + - + + temporal interpretation + https://github.com/oborel/obo-relations/wiki/ROAndTime + + + + + + + @@ -837,6 +947,51 @@ Previous. An information content entity is a non-realizable information entity t + + + + + +## Elucidation + +This is used when the statement/axiom is assumed to hold true 'eternally' + +## How to interpret (informal) + +First the "atemporal" FOL is derived from the OWL using the standard +interpretation. This axiom is temporalized by embedding the axiom +within a for-all-times quantified sentence. The t argument is added to +all instantiation predicates and predicates that use this relation. + +## Example + + Class: nucleus + SubClassOf: part_of some cell + + forall t : + forall n : + instance_of(n,Nucleus,t) + implies + exists c : + instance_of(c,Cell,t) + part_of(n,c,t) + +## Notes + +This interpretation is *not* the same as an at-all-times relation + + + axiom holds for all times + + + + + + + + + +