diff --git a/.gitignore b/.gitignore index 7c406fe..74cb5e9 100644 --- a/.gitignore +++ b/.gitignore @@ -7,4 +7,8 @@ semantic.cache bin/ src/ontology/seed.txt src/ontology/target/ -src/ontology/dosdp-tools.log \ No newline at end of file +src/ontology/dosdp-tools.log +src/patterns/imports/seed_sorted.txt +src/ontology/ed_definitions_merged.owl +src/ontology/patterns + diff --git a/.travis.yml b/.travis.yml index 097ad47..a8ff2e9 100644 --- a/.travis.yml +++ b/.travis.yml @@ -6,10 +6,10 @@ services: - docker before_install: - - docker pull obolibrary/osklite + - docker pull obolibrary/odkfull # command to run tests -script: cd src/ontology && ./run.sh make test +script: cd src/ontology && make test #after_success: # coveralls diff --git a/credit.obo b/credit.obo new file mode 100644 index 0000000..6b59039 --- /dev/null +++ b/credit.obo @@ -0,0 +1,210 @@ +format-version: 1.2 +data-version: releases/2018-10-02 +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: (contributor role)\n\nSubClassOf( owl:Thing)\n\n\n) + +[Term] +id: BFO:0000002 +is_a: BFO:0000001 + +[Term] +id: BFO:0000020 +is_a: BFO:0000002 + +[Term] +id: BFO:0000031 +is_a: BFO:0000002 + +[Term] +id: CREDIT:00000000 +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 +is_a: IAO:0000030 + +[Term] +id: IAO:0000030 +is_a: BFO:0000031 + +[Term] +id: IAO:0000078 +is_a: IAO:0000102 + +[Term] +id: IAO:0000102 +is_a: IAO:0000027 + +[Term] +id: IAO:0000225 +is_a: IAO:0000102 + +[Term] +id: IAO:0000409 +is_a: IAO:0000102 + +[Term] +id: Subset +is_a: IAO:0000102 + diff --git a/credit.owl b/credit.owl new file mode 100644 index 0000000..8c76eb9 --- /dev/null +++ b/credit.owl @@ -0,0 +1,362 @@ + + + + + + CRediT ontology + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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. + PERSON: Marijane White + http://dictionary.casrai.org/Contributor_Roles + contributor role + + + + + + + + + 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.obo b/imports/iao_import.obo new file mode 100644 index 0000000..dfec86a --- /dev/null +++ b/imports/iao_import.obo @@ -0,0 +1,218 @@ +format-version: 1.2 +ontology: credit/imports/iao_import +owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\n############################\n# Object Properties\n############################\n\n# Object Property: (part of)\n\nEquivalentObjectProperties( ObjectInverseOf())\n\n# Object Property: (has part)\n\nEquivalentObjectProperties( ObjectInverseOf())\n\n# Object Property: (inheres in)\n\nEquivalentObjectProperties( ObjectInverseOf())\n\n# Object Property: (bearer of)\n\nEquivalentObjectProperties( ObjectInverseOf())\n\n\n############################\n# Classes\n############################\n\n# Class: (curation status specification)\n\nEquivalentClasses( ObjectOneOf( ))\n\n# Class: (obsolescence reason specification)\n\nEquivalentClasses( ObjectOneOf( ))\n\n# Class: (denotator type)\n\nEquivalentClasses( ObjectOneOf( ))\n\n# Class: ()\n\nEquivalentClasses( ObjectOneOf())\n\n\n############################\n# Named Individuals\n############################\n\n# Individual: (metadata complete)\n\n\n# Individual: (organizational term)\n\n\n# Individual: (ready for release)\n\n\n# Individual: (metadata incomplete)\n\n\n# Individual: (uncurated)\n\n\n# Individual: (pending final vetting)\n\n\n# Individual: (placeholder removed)\n\n\n# Individual: (terms merged)\n\n\n# Individual: (term imported)\n\n\n# Individual: (term split)\n\n\n# Individual: (to be replaced with external ontology term)\n\n\n# Individual: (requires discussion)\n\n\n\nDifferentIndividuals( )\nDifferentIndividuals( )\n) + +[Term] +id: BFO:0000001 +name: entity +property_value: BFO:0000179 "entity" xsd:string +property_value: BFO:0000180 "Entity" xsd:string +property_value: IAO:0000112 "Julius Caesar" xsd:string +property_value: IAO:0000112 "the Second World War" xsd:string +property_value: IAO:0000112 "Verdi’s Requiem" xsd:string +property_value: IAO:0000112 "your body mass index" xsd:string +property_value: IAO:0000116 "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" xsd:string +property_value: IAO:0000116 "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" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000004", comment="per discussion with Barry Smith", http://www.w3.org/2000/01/rdf-schema#seeAlso="http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf"} +property_value: IAO:0000600 "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/001-001"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000002 +name: continuant +def: "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." [] +is_a: BFO:0000001 ! entity +property_value: BFO:0000179 "continuant" xsd:string +property_value: BFO:0000180 "Continuant" xsd:string +property_value: IAO:0000116 "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" xsd:string +property_value: IAO:0000116 "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" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000007"} +property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"} +property_value: IAO:0000601 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"} +property_value: IAO:0000601 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"} +property_value: IAO:0000601 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/011-002"} +property_value: IAO:0000602 "(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"} +property_value: IAO:0000602 "(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"} +property_value: IAO:0000602 "(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"} +property_value: IAO:0000602 "(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/011-002"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000020 +name: specifically dependent continuant +def: "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." [] +def: "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])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} +is_a: BFO:0000002 ! continuant +disjoint_from: BFO:0000031 ! generically dependent continuant +property_value: BFO:0000179 "sdc" xsd:string +property_value: BFO:0000180 "SpecificallyDependentContinuant" xsd:string +property_value: IAO:0000112 "of one-sided specifically dependent continuants: the mass of this tomato" xsd:string +property_value: IAO:0000112 "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." xsd:string +property_value: IAO:0000112 "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" xsd:string +property_value: IAO:0000112 "the disposition of this fish to decay" xsd:string +property_value: IAO:0000112 "the function of this heart: to pump blood" xsd:string +property_value: IAO:0000112 "the mutual dependence of proton donors and acceptors in chemical reactions [79" xsd:string +property_value: IAO:0000112 "the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction" xsd:string +property_value: IAO:0000112 "the pink color of a medium rare piece of grilled filet mignon at its center" xsd:string +property_value: IAO:0000112 "the role of being a doctor" xsd:string +property_value: IAO:0000112 "the shape of this hole." xsd:string +property_value: IAO:0000112 "the smell of this portion of mozzarella" xsd:string +property_value: IAO:0000116 "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." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000005", comment="per discussion with Barry Smith"} +property_value: IAO:0000602 "(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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000031 +name: generically dependent continuant +def: "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." [] +def: "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])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} +is_a: BFO:0000002 ! continuant +property_value: BFO:0000179 "gdc" xsd:string +property_value: BFO:0000180 "GenericallyDependentContinuant" xsd:string +property_value: IAO:0000112 "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." xsd:string +property_value: IAO:0000112 "the pdf file on your laptop, the pdf file that is a copy thereof on my laptop" xsd:string +property_value: IAO:0000112 "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule." xsd:string +property_value: IAO:0000602 "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: IAO:0000027 +name: data item +def: "a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements." [] +is_a: IAO:0000030 ! information content entity +property_value: IAO:0000111 "data item" xsd:string +property_value: IAO:0000112 "Data items include counts of things, analyte concentrations, and statistical summaries." xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "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." xsd:string +property_value: IAO:0000116 "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." xsd:string +property_value: IAO:0000116 "2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym." xsd:string +property_value: IAO:0000116 "2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/" xsd:string +property_value: IAO:0000116 "JAR: datum -- well, this will be very tricky to define, but maybe some \ninformation-like stuff that might be put into a computer and that is \nmeant, by someone, to denote and/or to be interpreted by some \nprocess... I would include lists, tables, sentences... I think I might \ndefer to Barry, or to Brian Cantwell Smith\n\nJAR: A data item is an approximately justified approximately true approximate belief" xsd:string +property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string +property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string +property_value: IAO:0000117 "PERSON: Jonathan Rees" xsd:string +property_value: IAO:0000118 "data" xsd:string + +[Term] +id: IAO:0000030 +name: information content entity +def: "A generically dependent continuant that is about some thing." [] +is_a: BFO:0000031 ! generically dependent continuant +relationship: IAO:0000136 BFO:0000001 ! is about entity +property_value: IAO:0000111 "information content entity" xsd:string +property_value: IAO:0000112 "Examples of information content entites include journal articles, data, graphical layouts, and graphs." xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000116 "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)." xsd:string +property_value: IAO:0000116 "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).\n\nPrevious. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity." xsd:string +property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string +property_value: IAO:0000119 "OBI_0000142" xsd:string + +[Term] +id: IAO:0000078 +name: curation status specification +def: "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." [] +is_a: IAO:0000102 ! data about an ontology part +property_value: IAO:0000111 "curation status specification" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)" xsd:string +property_value: IAO:0000117 "PERSON:Bill Bug" xsd:string +property_value: IAO:0000119 GROUP:OBI: xsd:string +property_value: IAO:0000119 "OBI_0000266" xsd:string + +[Term] +id: IAO:0000102 +name: data about an ontology part +def: "data about an ontology part is a data item about a part of an ontology, for example a term" [] +is_a: IAO:0000027 ! data item +property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string + +[Term] +id: IAO:0000225 +name: obsolescence reason specification +def: "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." [] +is_a: IAO:0000102 ! data about an ontology part +property_value: IAO:0000111 "obsolescence reason specification" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology." xsd:string +property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string +property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string + +[Term] +id: IAO:0000409 +name: denotator type +def: "A denotator type indicates how a term should be interpreted from an ontological perspective." [] +is_a: IAO:0000102 ! data about an ontology part +property_value: IAO:0000112 "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." xsd:string +property_value: IAO:0000117 "Alan Ruttenberg" xsd:string +property_value: IAO:0000119 "Barry Smith, Werner Ceusters" xsd:string + +[Term] +id: Subset +is_a: IAO:0000102 ! data about an ontology part + +[Typedef] +id: BFO:0000050 +name: part of +def: "a core relation that holds between a part and its whole" [] +property_value: IAO:0000111 "is part of" xsd:string +property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string +property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string +property_value: IAO:0000116 "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." xsd:string +property_value: IAO:0000116 "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" xsd:string +property_value: IAO:0000116 "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.)\n\nA 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'." xsd:string +property_value: IAO:0000118 "part_of" xsd:string +property_value: RO:0001900 RO:0001901 +property_value: seeAlso http://www.obofoundry.org/ro/#OBO_REL:part_of xsd:string +is_transitive: true +inverse_of: BFO:0000051 ! has part + +[Typedef] +id: BFO:0000051 +name: has part +def: "a core relation that holds between a whole and its part" [] +property_value: IAO:0000111 "has part" xsd:string +property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string +property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string +property_value: IAO:0000116 "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." xsd:string +property_value: IAO:0000116 "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" xsd:string +property_value: IAO:0000116 "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.)\n\nA 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'." xsd:string +property_value: IAO:0000118 "has_part" xsd:string +property_value: RO:0001900 RO:0001901 +is_transitive: true + +[Typedef] +id: IAO:0000136 +name: is about +def: "is_about is a (currently) primitive relation that relates an information artifact to an entity." [] +property_value: IAO:0000112 "This document is about information artifacts and their representations" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of \"mentions\" relation. Weaken the is_about relationship to be primitive. \n\nWe will try to build it back up by elaborating the various subproperties that are more precisely defined.\n\nSome 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." xsd:string +property_value: IAO:0000117 "person:Alan Ruttenberg" xsd:string +property_value: IAO:0000119 "Smith, Ceusters, Ruttenberg, 2000 years of philosophy" xsd:string +domain: IAO:0000030 ! information content entity + +[Typedef] +id: RO:0000052 +name: inheres in +def: "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" [] +property_value: IAO:0000111 "inheres in" xsd:string +property_value: IAO:0000112 "this fragility inheres in this vase" xsd:string +property_value: IAO:0000112 "this red color inheres in this apple" xsd:string +property_value: IAO:0000116 "A dependent inheres in its bearer at all times for which the dependent exists." xsd:string +property_value: IAO:0000118 "inheres_in" xsd:string +property_value: RO:0001900 RO:0001901 +inverse_of: RO:0000053 ! bearer of + +[Typedef] +id: RO:0000053 +name: bearer of +def: "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" [] +property_value: IAO:0000111 "bearer of" xsd:string +property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string +property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string +property_value: IAO:0000116 "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." xsd:string +property_value: IAO:0000118 "bearer_of" xsd:string +property_value: IAO:0000118 "is bearer of" xsd:string +property_value: RO:0001900 RO:0001901 +range: BFO:0000020 ! specifically dependent continuant + diff --git a/imports/iao_import.owl b/imports/iao_import.owl new file mode 100644 index 0000000..3514e58 --- /dev/null +++ b/imports/iao_import.owl @@ -0,0 +1,1030 @@ + + + + + + + + + + + + + + + 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 + + + + + + + + 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.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 + + + + + + + + + + + + + + + + + + + + + + + + + + is part of + my brain is part of my body (continuant parthood, two material entities) + my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) + this day is part of this year (occurrent parthood) + a core relation that holds between a part and its whole + Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime + Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) + +A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. + part_of + + part of + http://www.obofoundry.org/ro/#OBO_REL:part_of + + + + + + + + + + + + + + has part + my body has part my brain (continuant parthood, two material entities) + my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) + this year has part this day (occurrent parthood) + a core relation that holds between a whole and its part + Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime + Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) + +A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. + has_part + + has part + + + + + + + + + This document is about information artifacts and their representations + + is_about is a (currently) primitive relation that relates an information artifact to an entity. + 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. + +We will try to build it back up by elaborating the various subproperties that are more precisely defined. + +Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. + person:Alan Ruttenberg + Smith, Ceusters, Ruttenberg, 2000 years of philosophy + is about + + + + + + + + + + + + + + inheres in + this fragility inheres in this vase + this red color inheres in this apple + a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence + A dependent inheres in its bearer at all times for which the dependent exists. + inheres_in + + inheres in + + + + + + + + + + + + + + bearer of + this apple is bearer of this red color + this vase is bearer of this fragility + a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence + A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. + bearer_of + is bearer of + + bearer of + + + + + + + + + + + + + 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 + + + + + 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 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]) + + + + + + + + + + + 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] + + + + + + + + + + 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] + + + + + + + + + + data item + Data items include counts of things, analyte concentrations, and statistical summaries. + + a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. + 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. + 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. + 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. + 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ + JAR: datum -- well, this will be very tricky to define, but maybe some +information-like stuff that might be put into a computer and that is +meant, by someone, to denote and/or to be interpreted by some +process... I would include lists, tables, sentences... I think I might +defer to Barry, or to Brian Cantwell Smith + +JAR: A data item is an approximately justified approximately true approximate belief + PERSON: Alan Ruttenberg + PERSON: Chris Stoeckert + PERSON: Jonathan Rees + data + data item + + + + + + + + + + + + + + + information content entity + Examples of information content entites include journal articles, data, graphical layouts, and graphs. + + A generically dependent continuant that is about some thing. + 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ). + information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). + +Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. + PERSON: Chris Stoeckert + OBI_0000142 + information content entity + + + + + + + + + + + + + + + + + + + + + + + + curation status specification + + The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. + Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) + PERSON:Bill Bug + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + OBI_0000266 + curation status specification + + + + + + + + + data about an ontology part is a data item about a part of an ontology, for example a term + Person:Alan Ruttenberg + data about an ontology part + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + example to be eventually removed + + + + + + + + + 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 + + + + + + + + + Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. + metadata complete + + + + + + + + + term created to ease viewing/sort terms for development purpose, and will not be included in a release + organizational term + + + + + + + + + Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." + ready for release + + + + + + + + + Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. + metadata incomplete + + + + + + + + + Nothing done yet beyond assigning a unique class ID and proposing a preferred term. + uncurated + + + + + + + + + All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. + pending final vetting + + + + + + + + + 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 + core + + + + + + + + + placeholder removed + + + + + + + + + An editor note should explain what were the merged terms and the reason for the merge. + terms merged + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason. + We expect to be able to mine these new reasons and add instances as required. + other + true + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + Terms with this status should eventually replaced with a term from another ontology. + Alan Ruttenberg + group:OBI + to be replaced with external ontology term + + + + + + + + + A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. + Alan Ruttenberg + group:OBI + requires discussion + + + + + + + + + +## Elucidation + +This is used when the statement/axiom is assumed to hold true 'eternally' + +## How to interpret (informal) + +First the "atemporal" FOL is derived from the OWL using the standard +interpretation. This axiom is temporalized by embedding the axiom +within a for-all-times quantified sentence. The t argument is added to +all instantiation predicates and predicates that use this relation. + +## Example + + Class: nucleus + SubClassOf: part_of some cell + + forall t : + forall n : + instance_of(n,Nucleus,t) + implies + exists c : + instance_of(c,Cell,t) + part_of(n,c,t) + +## Notes + +This interpretation is *not* the same as an at-all-times relation + + + axiom holds for all times + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/ontology/Makefile b/src/ontology/Makefile index 8cadca3..2e20232 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -22,11 +22,12 @@ DOSDP_SCHEMA=http:// # change to PURL when ready. PATTERN_TESTER=simple_pattern_tester.py DOSDPT=dosdp-tools + # ---------------------------------------- # Top-level targets # ---------------------------------------- -all: all_imports sparql_test patterns $(ONT).owl $(ONT).obo +all: all_imports sparql_test patterns $(ONT).owl $(ONT).obo test: sparql_test all prepare_release: all cp $(ONT).owl $(ONT).obo $(RELEASEDIR) &&\ @@ -37,7 +38,7 @@ prepare_release: all git add $(RELEASEDIR)/imports/*.owl &&\ (test -f subsets/*owl && cp subsets/* $(RELEASEDIR)/subsets && git add $(RELEASEDIR)/subsets/* || echo "no subsets") &&\ echo "Release files are now in $(RELEASEDIR) - now you should commit, push and make a release on github" - + # ---------------------------------------- # Main release targets # ---------------------------------------- @@ -45,9 +46,9 @@ prepare_release: all # by default we use Elk to perform a reason-relax-reduce chain # after that we annotate the ontology with the release versionInfo $(ONT).owl: $(SRC) - $(ROBOT) reason -i $< -r ELK relax reduce -r ELK annotate -V $(BASE)/releases/`date +%Y-%m-%d`/$(ONT).owl -o $@ + $(ROBOT) reason -i $< -r ELK -e none relax reduce -r ELK annotate -V $(BASE)/releases/`date +%Y-%m-%d`/$(ONT).owl -o $@ $(ONT).obo: $(ONT).owl - $(ROBOT) convert -i $< -f obo -o $(ONT).obo.tmp && mv $(ONT).obo.tmp $@ + $(ROBOT) convert --check false -i $< -f obo -o $(ONT).obo.tmp && mv $(ONT).obo.tmp $@ # ---------------------------------------- # Import modules @@ -88,7 +89,7 @@ imports/%_import.obo: imports/%_import.owl $(ROBOT) convert --check false -i $< -f obo -o $@.tmp && mv $@.tmp $@ # clone remote ontology locally, perfoming some excision of relations and annotations -mirror/%.owl: $(SRC) +mirror/%.owl: $(ROBOT) convert -I $(OBO)/$*.owl -o $@ .PRECIOUS: mirror/%.owl @@ -161,7 +162,7 @@ pattern_schema_checks: ../patterns/imports/%_import.owl: mirror/%.owl ../patterns/imports/seed_sorted.txt $(ROBOT) extract -i $< -T ../patterns/imports/seed_sorted.txt --method BOT -O mirror/$*.owl annotate --ontology-iri $(OBO)/$(ONT)/patterns/imports/$*_import.owl -o $@ -patterns: $(PATTERN_IMPORTS) +.PHONY: patterns $(PATTERN_IMPORTS) pattern_files := $(wildcard ../patterns/*.yaml) pattern_tsv_files := $(wildcard ../patterns/*.tsv) @@ -177,12 +178,4 @@ $(IMS)/patterns/%.ofn: ../patterns/%.yaml ../patterns/%.tsv $(ONT)-edit.owl pattern_modules := $(patsubst %.yaml, $(IMS)/patterns/%.ofn, $(notdir $(wildcard ../patterns/*.yaml))) ../patterns/definitions.owl: $(pattern_modules) - $(ROBOT) merge $(addprefix -i , $(pattern_modules)) annotate --ontology-iri $(OBO)/$(ONT)/patterns/defintions.owl -o $@ - - - - - - - - + $(ROBOT) merge $(addprefix -i , $(pattern_modules)) annotate --ontology-iri $(OBO)/$(ONT)/patterns/definitions.owl -o $@ diff --git a/src/ontology/imports/catalog-v001.xml b/src/ontology/imports/catalog-v001.xml deleted file mode 100644 index 76102d3..0000000 --- a/src/ontology/imports/catalog-v001.xml +++ /dev/null @@ -1,6 +0,0 @@ - - - - - - diff --git a/src/ontology/imports/iao_import.owl b/src/ontology/imports/iao_import.owl index 14cba22..3514e58 100644 --- a/src/ontology/imports/iao_import.owl +++ b/src/ontology/imports/iao_import.owl @@ -3,12 +3,11 @@ xml:base="http://purl.obolibrary.org/obo/credit/imports/iao_import.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:dc="http://purl.org/dc/elements/1.1/"> + xmlns:foaf="http://xmlns.com/foaf/0.1/"> @@ -26,31 +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 + @@ -91,77 +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 + - + - - - - - - - - - 2018-09-18T22:13:32Z - database_cross_reference - + @@ -318,12 +404,6 @@ Some currently missing phenomena that should be considered "about" are entity - - - - An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - - @@ -332,6 +412,12 @@ Some currently missing phenomena that should be considered "about" are per discussion with Barry Smith + + + + An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) + + @@ -355,24 +441,6 @@ Some currently missing phenomena that should be considered "about" are 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]) - - @@ -409,6 +477,24 @@ Some currently missing phenomena that should be considered "about" are (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] + + + + 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]) + + @@ -861,6 +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 + + + + + + + + + + + diff --git a/src/patterns/definitions.owl b/src/patterns/definitions.owl index 7fd7523..e22ab1a 100644 --- a/src/patterns/definitions.owl +++ b/src/patterns/definitions.owl @@ -1,6 +1,6 @@ - - + diff --git a/src/patterns/imports/seed.txt b/src/patterns/imports/seed.txt index 7c495d8..e69de29 100644 --- a/src/patterns/imports/seed.txt +++ b/src/patterns/imports/seed.txt @@ -1,18 +0,0 @@ -term -http://www.w3.org/2002/07/owl#ObjectProperty -http://purl.obolibrary.org/obo/PATO_0000460 -http://purl.obolibrary.org/obo/RO_0002573 -http://www.w3.org/2002/07/owl#Restriction -http://purl.obolibrary.org/obo/BFO_0000051 -http://www.w3.org/2002/07/owl#Class -http://www.w3.org/1999/02/22-rdf-syntax-ns#nil -http://www.w3.org/2002/07/owl#Ontology -http://purl.obolibrary.org/obo/BFO_0000001 -http://purl.obolibrary.org/obo/RO_0000052 -http://www.w3.org/2002/07/owl#AnnotationProperty -http://purl.obolibrary.org/obo/PATO_0000001 -http://purl.oboibrary.org/obo/upheno/patterns/abnormal -urn:unnamed:ontology#ont1 -http://www.geneontology.org/formats/oboInOwl#hasExactSynonym -http://purl.org/dc/terms/title -http://purl.obolibrary.org/obo/IAO_0000115 diff --git a/src/patterns/pattern.owl b/src/patterns/pattern.owl new file mode 100644 index 0000000..cb0341a --- /dev/null +++ b/src/patterns/pattern.owl @@ -0,0 +1,11 @@ +Prefix(:=) +Prefix(owl:=) +Prefix(rdf:=) +Prefix(xml:=) +Prefix(xsd:=) +Prefix(rdfs:=) + + +Ontology( + +)