diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md index 719d4ec1f..e50a76f3d 100644 --- a/.github/pull_request_template.md +++ b/.github/pull_request_template.md @@ -4,16 +4,15 @@ Describe the findings of the discussion in the issue or meeting. ## Type of change (CHANGELOG.md) -### Added +### Add - Added a new class [#](https://github.com/OpenEnergyPlatform/ontology/issues/) -### Updated +### Update - Updated a definition [#](https://github.com/OpenEnergyPlatform/ontology/issues/) -### Removed +### Remove - Removed a broken link [#](https://github.com/OpenEnergyPlatform/ontology/issues/) - ## Workflow checklist ### Automation diff --git a/CHANGELOG.md b/CHANGELOG.md index 3e3f6612f..7ef18db83 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,6 +4,30 @@ All notable changes to this project will be documented in this file. The format is inspired from [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) and the versioning aims to respect [Semantic Versioning](http://semver.org/spec/v2.0.0.html). + +## [2.1.0] - 2023-12-05 + +### Added +- resilience, power system resilience, power system (#1744) +- service product role, service product (#1748) +- region of relevance, study subregion role, study region role, interacting region role, considered region role (#1749) +- import from IAO: time stamped measurement datum, action specification, data format specification, objective specification, study design, software application, software library, software method, software module, software script, document part, journal article, version number, cartesian spatial coordinate datum, one dimensional cartesian spatial coordinate datum, two dimensional cartesian spatial coordinate datum, three dimensional cartesian spatial coordinate datum, has time stamp (#1754) +- fuel blending quota, fuel quota blending value (#1763) +- study report due to legal obligation (#1777) +- market share and market share value (#1779) + +### Changed +- subregion, study region, study subregion, interacting region, considered region (#1749) +- model factsheet (#1751) +- is connected to, has sink, has source (#1762) +- temperature, pressure (#1767) +- carbon capture and storage technology (#1768) +- power rating, power capacity (#1770) +- boiler (#1771) +- B7, E10 (#1774) +- data descriptor (#1775) +- target description, policy instrument, policy (#1778) + ## [2.0.1] - 2023-10-26 ### Changed diff --git a/CITATION.cff b/CITATION.cff index 6a02372b5..08731fde7 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -146,7 +146,7 @@ authors: title: "Open Energy Ontology (OEO)" type: software license: CC0-1.0 -version: 2.0.1 +version: 2.1.0 doi: -date-released: 2023-10-26 +date-released: 2023-12-05 url: "https://github.com/OpenEnergyPlatform/ontology" diff --git a/Makefile b/Makefile index a9f7b496a..0269dad7e 100644 --- a/Makefile +++ b/Makefile @@ -50,12 +50,14 @@ endef .PHONY: all clean base merge directories -all: base merge +all: base merge closure base: | directories $(VERSIONDIR)/catalog-v001.xml build/robot.jar $(OWL_COPY) $(OMN_COPY) $(OMN_TRANSLATE) merge: | $(VERSIONDIR)/oeo-full.omn +closure: | $(VERSIONDIR)/oeo-closure.owl + clean: - $(RM) -r $(VERSIONDIR) $(ROBOT_PATH) @@ -73,7 +75,7 @@ $(VERSIONDIR)/catalog-v001.xml: src/ontology/catalog-v001.xml sed -i -E "s/edits\//modules\//m" $@ build/robot.jar: | build - curl -L -o $@ https://github.com/ontodev/robot/releases/download/v1.4.1/robot.jar + curl -L -o $@ https://github.com/ontodev/robot/releases/download/v1.9.2/robot.jar $(VERSIONDIR)/%.owl: $(VERSIONDIR)/%.omn @@ -105,3 +107,7 @@ $(VERSIONDIR)/oeo-full.owl : | base $(VERSIONDIR)/oeo-full.omn : $(VERSIONDIR)/oeo-full.owl $(call translate_to_omn,$@,$<) $(call replace_owls,$@) + +$(VERSIONDIR)/oeo-closure.owl : $(VERSIONDIR)/oeo-full.owl + $(ROBOT) reason --input $< --reasoner hermit --catalog $(VERSIONDIR)/catalog-v001.xml --axiom-generators "SubClass EquivalentClass DataPropertyCharacteristic EquivalentDataProperties SubDataProperty ClassAssertion EquivalentObjectProperty InverseObjectProperties ObjectPropertyCharacteristic SubObjectProperty ObjectPropertyRange ObjectPropertyDomain" --include-indirect true annotate --ontology-iri http://openenergy-platform.org/ontology/oeo/ --output $@ + $(ROBOT) merge --catalog $(VERSIONDIR)/catalog-v001.xml --input $< --input $@ annotate --ontology-iri http://openenergy-platform.org/ontology/oeo/ --output $@ diff --git a/VERSION b/VERSION index 38f77a65b..7ec1d6db4 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -2.0.1 +2.1.0 diff --git a/src/ontology/edits/catalog-v001.xml b/src/ontology/edits/catalog-v001.xml index 44ae76102..041f7f296 100644 --- a/src/ontology/edits/catalog-v001.xml +++ b/src/ontology/edits/catalog-v001.xml @@ -5,14 +5,11 @@ - - - - - + + diff --git a/src/ontology/edits/oeo-import-edits.owl b/src/ontology/edits/oeo-import-edits.owl index d8517b8f3..f4805e1f7 100644 --- a/src/ontology/edits/oeo-import-edits.owl +++ b/src/ontology/edits/oeo-import-edits.owl @@ -7,8 +7,10 @@ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" + xmlns:prov="http://www.w3.org/ns/prov#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" - xmlns:terms="http://purl.org/dc/terms/"> + xmlns:terms="http://purl.org/dc/terms/" + xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> Open Energy Ontology (imports-edit module) @@ -35,12 +37,24 @@ Currently, it covers the `ro-extracted.owl`-file which is a subset of the Relati + + + + + + + + + + + + @@ -70,35 +84,42 @@ Currently, it covers the `ro-extracted.owl`-file which is a subset of the Relati - + - + + + - - - - - + - + + issue https://github.com/OpenEnergyPlatform/ontology/issues/596 +Pull request https://github.com/OpenEnergyPlatform/ontology/pull/599 +Pull request https://github.com/OpenEnergyPlatform/ontology/pull/603 - +fix duplicate implementation of `Inverse Of` +issue https://github.com/OpenEnergyPlatform/ontology/issues/979 +pull request https://github.com/OpenEnergyPlatform/ontology/pull/1086 + - + - - + + - + - + + + IAO declared "time measurement datum" as range, which is (not yet) imported by OEO. Therefore the range declaration is missing here. + @@ -261,36 +282,6 @@ pull request https://github.com/OpenEnergyPlatform/ontology/pull/1086 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -305,30 +296,13 @@ pull request https://github.com/OpenEnergyPlatform/ontology/pull/1086 - - - - - - - - + - - - - - - - - add bearer axiom to oeo-import-edits -issue: https://github.com/OpenEnergyPlatform/ontology/issues/1305 -pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1485 - + @@ -341,19 +315,6 @@ pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1485 - - - - - - - - - - - - - add bearer axiom to oeo-import-edits issue: https://github.com/OpenEnergyPlatform/ontology/issues/1305 pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1485 @@ -376,14 +337,37 @@ pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1485 - - - - - - Add 'has licence' axiom: issue: https://github.com/OpenEnergyPlatform/ontology/issues/1275 +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1547 +move axiom to oeo-model +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1738 + + + + + + + + + add subclass axiom to report +issue: https://github.com/OpenEnergyPlatform/ontology/issues/1700 +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1754 + IAO provides two parent classes, from which only "report" in imported to OEO. + + + + + + + + + add axiom has copyright license +issue https://github.com/OpenEnergyPlatform/ontology/issues/1061 +pull request https://github.com/OpenEnergyPlatform/ontology/pull/1090 + +Delete axiom has (copyright) licence: +issue: https://github.com/OpenEnergyPlatform/ontology/issues/1275 pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1547 @@ -431,6 +415,12 @@ pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1652 + + + + + @@ -465,6 +455,17 @@ https://github.com/OpenEnergyPlatform/ontology/pull/1741 /////////////////////////////////////////////////////////////////////////////////////// --> + + 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. + http://www.ontobee.org/ontology/IAO?iri=http://purl.obolibrary.org/obo/IAO_0000027 + + + + + 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. + issue: https://github.com/OpenEnergyPlatform/ontology/issues/823 +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/826 + add subset of relation below 'causally related to' issue: https://github.com/OpenEnergyPlatform/ontology/issues/1079 diff --git a/src/ontology/edits/oeo-model.omn b/src/ontology/edits/oeo-model.omn index adfce98eb..460016781 100644 --- a/src/ontology/edits/oeo-model.omn +++ b/src/ontology/edits/oeo-model.omn @@ -539,8 +539,14 @@ Class: Class: +Class: + + Class: + SubClassOf: + OEO_00020188 some OEO_00020187 + Class: @@ -706,14 +712,17 @@ Class: OEO_00000119 Annotations: "A data descriptor is an information content entity that contains additional information about some data.", + "metadata", "issue: https://github.com/OpenEnergyPlatform/ontology/issues/612 - pull request: https://github.com/OpenEnergyPlatform/ontology/pull/724 - move to oeo-shared - issue: https://github.com/OpenEnergyPlatform/ontology/issues/1384 - pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1390 - rework module structure - issue: https://github.com/OpenEnergyPlatform/ontology/issues/1592 - pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1652", +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/724 move to oeo-shared +issue: https://github.com/OpenEnergyPlatform/ontology/issues/1384 +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1390 +rework module structure +issue: https://github.com/OpenEnergyPlatform/ontology/issues/1592 +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1652 +add alternative label \"metadata\" +issue: https://github.com/OpenEnergyPlatform/ontology/issues/1548 +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1775", rdfs:label "data descriptor"@en SubClassOf: @@ -975,12 +984,16 @@ pull request: https://github.com/OpenEnergyPlatform/ontology/pull/577 pull request: https://github.com/OpenEnergyPlatform/ontology/pull/584 issue: https://github.com/OpenEnergyPlatform/ontology/issues/851 -pull request: https://github.com/OpenEnergyPlatform/ontology/pull/854", +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/854 + +Fix SubClassOf axioms: +issue: https://github.com/OpenEnergyPlatform/ontology/issues/1750 +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1751", rdfs:label "model factsheet"@en SubClassOf: - OEO_00000162 - and ( some OEO_00000274) + OEO_00000162, + some OEO_00000274 Class: OEO_00000279 @@ -1799,30 +1812,42 @@ Class: OEO_00020032 "In a study, the spatial focus of the investigation lies on one European country, e.g. Germany. This is the study region. The study region is not modelled as a whole, but several subregions are modelled, e.g. German Federal States. These are study subregions. In the study, a spatial region outside the study region plays a role. E.g. for modelling the electricity transfer between Germany and its neighbouring countries. In this example, the neighbouring countries represent the interacting / external region. -The union of the study region and the interacting/ external region ist the considered region.", - "A study region is a spatial region that is under investigation and consists entirely of one or more subregions.", +The union of the study region and the interacting/ external region ist the considered region."@en, + "A study region is a region of relevance that has the study region role and consists entirely of one or more subregions."@en, "issue: https://github.com/OpenEnergyPlatform/ontology/issues/475 pull request: https://github.com/OpenEnergyPlatform/ontology/pull/585 rework module structure issue: https://github.com/OpenEnergyPlatform/ontology/issues/1592 -pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1652", +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1652 + +relocated, made equivalent +issue: https://github.com/OpenEnergyPlatform/ontology/issues/1745 +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1749", rdfs:label "study region"@en + EquivalentTo: + OEO_00360020 + and ( some OEO_00360021) + SubClassOf: - + OEO_00360020 Class: OEO_00020033 Annotations: - "A subregion is a spatial region that is a part of spatial region.", + "A subregion is a region of relevance that is in every respect a component of a region of relevance, but never encompasses the entire extent of a region of relevance."@en, "issue: https://github.com/OpenEnergyPlatform/ontology/issues/475 -pull request: https://github.com/OpenEnergyPlatform/ontology/pull/585", +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/585 + +changed definition, relocated +issue: https://github.com/OpenEnergyPlatform/ontology/issues/1745 +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1749", rdfs:label "subregion"@en SubClassOf: - + OEO_00360020 Class: OEO_00020034 @@ -1831,12 +1856,20 @@ Class: OEO_00020034 "In a study, the spatial focus of the investigation lies on one European country, e.g. Germany. This is the study region. The study region is not modelled as a whole, but several subregions are modelled, e.g. German Federal States. These are study subregions. In the study, a spatial region outside the study region plays a role. E.g. for modelling the electricity transfer between Germany and its neighbouring countries. In this example, the neighbouring countries represent the interacting / external region. -The union of the study region and the interacting/ external region ist the considered region.", - "A study subregion is a subregion of a study region.", +The union of the study region and the interacting/ external region ist the considered region."@en, + "A study subregion is a subregion that has the study subregion role."@en, "issue: https://github.com/OpenEnergyPlatform/ontology/issues/475 -pull request: https://github.com/OpenEnergyPlatform/ontology/pull/585", +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/585 + +relocated, made equivalent +issue: https://github.com/OpenEnergyPlatform/ontology/issues/1745 +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1749", rdfs:label "study subregion"@en + EquivalentTo: + OEO_00020033 + and ( some OEO_00360024) + SubClassOf: OEO_00020033 @@ -1847,18 +1880,26 @@ Class: OEO_00020035 "In a study, the spatial focus of the investigation lies on one European country, e.g. Germany. This is the study region. The study region is not modelled as a whole, but several subregions are modelled, e.g. German Federal States. These are study subregions. In the study, a spatial region outside the study region plays a role. E.g. for modelling the electricity transfer between Germany and its neighbouring countries. In this example, the neighbouring countries represent the interacting / external region. -The union of the study region and the interacting/ external region ist the considered region.", - "A considered region is a spatial region that is used in an analysis.", +The union of the study region and the interacting/ external region ist the considered region."@en, + "A considered region is a region of relevance that has the considered region role."@en, "issue: https://github.com/OpenEnergyPlatform/ontology/issues/475 pull request: https://github.com/OpenEnergyPlatform/ontology/pull/585 rework module structure issue: https://github.com/OpenEnergyPlatform/ontology/issues/1592 -pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1652", +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1652 + +relocated, made equivalent +issue: https://github.com/OpenEnergyPlatform/ontology/issues/1745 +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1749", rdfs:label "considered region"@en + EquivalentTo: + OEO_00360020 + and ( some OEO_00360022) + SubClassOf: - + OEO_00360020 Class: OEO_00020036 @@ -1867,15 +1908,23 @@ Class: OEO_00020036 "In a study, the spatial focus of the investigation lies on one European country, e.g. Germany. This is the study region. The study region is not modelled as a whole, but several subregions are modelled, e.g. German Federal States. These are study subregions. In the study, a spatial region outside the study region plays a role. E.g. for modelling the electricity transfer between Germany and its neighbouring countries. In this example, the neighbouring countries represent the interacting / external region. -The union of the study region and the interacting/ external region ist the considered region.", - "An interacting region is a spatial region that interacts with a study region. It is part of a considered region, but not a study region.", +The union of the study region and the interacting/ external region ist the considered region."@en, + "An interacting region is a region of relevance that has the interacting region role."@en, "external region", "issue: https://github.com/OpenEnergyPlatform/ontology/issues/475 -pull request: https://github.com/OpenEnergyPlatform/ontology/pull/585", +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/585 + +relocated, made equivalent +issue: https://github.com/OpenEnergyPlatform/ontology/issues/1745 +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1749", rdfs:label "interacting region"@en + EquivalentTo: + OEO_00360020 + and ( some OEO_00360023) + SubClassOf: - + OEO_00360020 Class: OEO_00020072 @@ -1966,13 +2015,17 @@ pull request: https://github.com/OpenEnergyPlatform/ontology/pull/882", Class: OEO_00020093 Annotations: - "A target description is an information content entity that contains statements about a desired future state of a system that a person or organisation commits to in a legally binding way.", + "A target description is an objective specification that contains statements about a desired future state of a system that a person or organisation commits to in a legally binding way.", "issue: https://github.com/OpenEnergyPlatform/ontology/issues/28 -pull request: https://github.com/OpenEnergyPlatform/ontology/pull/881", +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/881 + +reclassify +issue: https://github.com/OpenEnergyPlatform/ontology/issues/1684 +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1778", rdfs:label "target description"@en SubClassOf: - + Class: OEO_00020097 @@ -2333,7 +2386,8 @@ pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1652", rdfs:label "reference role"@en SubClassOf: - + , + OEO_00010121 some OEO_00360020 Class: OEO_00020314 @@ -2435,6 +2489,19 @@ pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1707", OEO_00020352 +Class: OEO_00020373 + + Annotations: + "A study report due to legal obligation is a study report that is created beacause of a legal obligation."@en, + "legally mandatory study report"@en, + "issue: https://github.com/OpenEnergyPlatform/ontology/issues/1641 +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1777", + rdfs:label "study report due to legal obligation"@en + + SubClassOf: + OEO_00020012 + + Class: OEO_00030007 Annotations: @@ -3009,6 +3076,82 @@ pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1711", OEO_00010252 +Class: OEO_00360020 + + Annotations: + "A region of relevance is a spatial region that is used in a study or analysis."@en, + "issue: https://github.com/OpenEnergyPlatform/ontology/issues/1745 +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1749", + rdfs:label "region of relevance"@en + + SubClassOf: + + + +Class: OEO_00360021 + + Annotations: + "In a study, the spatial focus of the investigation lies on one European country, e.g. Germany. This is the study region. +The study region is not modelled as a whole, but several subregions are modelled, e.g. German Federal States. These are study subregions. +In the study, a spatial region outside the study region plays a role. E.g. for modelling the electricity transfer between Germany and its neighbouring countries. In this example, the neighbouring countries represent the interacting / external region. +The union of the study region and the interacting/ external region ist the considered region."@en, + "A study region role is a role of a region of relevance that is under investigation and consists entirely of one or more subregions."@en, + "issue: https://github.com/OpenEnergyPlatform/ontology/issues/1745 +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1749", + rdfs:label "study region role"@en + + SubClassOf: + , + OEO_00010121 some OEO_00360020 + + +Class: OEO_00360022 + + Annotations: + "In a study, the spatial focus of the investigation lies on one European country, e.g. Germany. This is the study region. +The study region is not modelled as a whole, but several subregions are modelled, e.g. German Federal States. These are study subregions. +In the study, a spatial region outside the study region plays a role. E.g. for modelling the electricity transfer between Germany and its neighbouring countries. In this example, the neighbouring countries represent the interacting / external region. +The union of the study region and the interacting/ external region ist the considered region."@en, + "A considered region role is the role of a region of relevance that is used in an analysis."@en, + "issue: https://github.com/OpenEnergyPlatform/ontology/issues/1745 +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1749", + rdfs:label "considered region role"@en + + SubClassOf: + , + OEO_00010121 some OEO_00360020 + + +Class: OEO_00360023 + + Annotations: + "In a study, the spatial focus of the investigation lies on one European country, e.g. Germany. This is the study region. +The study region is not modelled as a whole, but several subregions are modelled, e.g. German Federal States. These are study subregions. +In the study, a spatial region outside the study region plays a role. E.g. for modelling the electricity transfer between Germany and its neighbouring countries. In this example, the neighbouring countries represent the interacting / external region. +The union of the study region and the interacting/ external region ist the considered region."@en, + "An interacting region role is a role of a region of relevance that interacts with a region of relevance that has the study region role. It is part of a region of relevance that has the considered region role, but not a study region role."@en, + "issue: https://github.com/OpenEnergyPlatform/ontology/issues/1745 +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1749", + rdfs:label "interacting region role"@en + + SubClassOf: + , + OEO_00010121 some OEO_00360020 + + +Class: OEO_00360024 + + Annotations: + "A study subregion role is a study region role that refers to a subregion."@en, + "issue: https://github.com/OpenEnergyPlatform/ontology/issues/1745 +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1749", + rdfs:label "study subregion role"@en + + SubClassOf: + OEO_00360021, + OEO_00010121 some OEO_00020033 + + Individual: OEO_00000049 Annotations: diff --git a/src/ontology/edits/oeo-physical.omn b/src/ontology/edits/oeo-physical.omn index 793ba3afb..1cc1e0581 100644 --- a/src/ontology/edits/oeo-physical.omn +++ b/src/ontology/edits/oeo-physical.omn @@ -277,9 +277,12 @@ ObjectProperty: OEO_00000525 ObjectProperty: OEO_00000526 Annotations: - "A relation that holds between two nodes in a graph that are connected to each other through an edge.", + "A relation that holds between two neighbouring grid nodes in a supply grid.", "issue: https://github.com/OpenEnergyPlatform/ontology/issues/66 -pull requests: https://github.com/OpenEnergyPlatform/ontology/pull/478", +pull requests: https://github.com/OpenEnergyPlatform/ontology/pull/478 + +issue: https://github.com/OpenEnergyPlatform/ontology/issues/1116 +pull requests: https://github.com/OpenEnergyPlatform/ontology/pull/1762", rdfs:label "is connected to"@en SubPropertyOf: @@ -288,13 +291,22 @@ pull requests: https://github.com/OpenEnergyPlatform/ontology/pull/478", Characteristics: Symmetric + Domain: + OEO_00000296 + + Range: + OEO_00000296 + ObjectProperty: OEO_00000527 Annotations: - "A relation that holds between a directed graph and a node in that graph that has edges ending but not starting there.", + "A relation that holds between a supply grid g and a grid node n, in which n is part of g and n works as an extraction point of the supply system.", "issue: https://github.com/OpenEnergyPlatform/ontology/issues/66 -pull requests: https://github.com/OpenEnergyPlatform/ontology/pull/478", +pull requests: https://github.com/OpenEnergyPlatform/ontology/pull/478 + +issue: https://github.com/OpenEnergyPlatform/ontology/issues/1116 +pull requests: https://github.com/OpenEnergyPlatform/ontology/pull/1762", rdfs:label "has sink"@en SubPropertyOf: @@ -303,13 +315,22 @@ pull requests: https://github.com/OpenEnergyPlatform/ontology/pull/478", DisjointWith: OEO_00000528 + Domain: + OEO_00000200 + + Range: + OEO_00000296 + ObjectProperty: OEO_00000528 Annotations: - "A relation that holds between a directed graph and a node in that graph that has edges starting but not ending there.", + "A relation that holds between a supply grid g and a grid node n, in which n is part of g and n works as entry point to the supply system.", "issue: https://github.com/OpenEnergyPlatform/ontology/issues/66 -pull requests: https://github.com/OpenEnergyPlatform/ontology/pull/478", +pull requests: https://github.com/OpenEnergyPlatform/ontology/pull/478 + +issue: https://github.com/OpenEnergyPlatform/ontology/issues/1116 +pull requests: https://github.com/OpenEnergyPlatform/ontology/pull/1762", rdfs:label "has source"@en SubPropertyOf: @@ -318,6 +339,12 @@ pull requests: https://github.com/OpenEnergyPlatform/ontology/pull/478", DisjointWith: OEO_00000527 + Domain: + OEO_00000200 + + Range: + OEO_00000296 + ObjectProperty: OEO_00000529 @@ -654,6 +681,14 @@ Class: Class: + Annotations: + "move axiom to oeo-physical +issue: https://github.com/OpenEnergyPlatform/ontology/issues/1738 +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1776" + + SubClassOf: + OEO_00140002 some OEO_00020143 + Class: @@ -6646,17 +6681,21 @@ pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1486", Class: OEO_00010257 Annotations: - "A power capacity is a maximum value of a generator or power generating unit to generate power.", + "A power capacity is a power rating of a generator or power generating unit to generate power.", "issue: https://github.com/OpenEnergyPlatform/ontology/issues/1092 pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1155 Fix 'quantity value of' axiom: issue: https://github.com/OpenEnergyPlatform/ontology/issues/1223 -pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1235", +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1235 + +Restructure 'power rating' and 'power capacity': +issue: https://github.com/OpenEnergyPlatform/ontology/issues/1492 +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1770", rdfs:label "power capacity"@en SubClassOf: - OEO_00010256, + OEO_00230001, OEO_00020056 some (OEO_00000188 or OEO_00000334), OEO_00040010 some @@ -8379,29 +8418,39 @@ pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1723", Class: OEO_00010447 Annotations: - "E10 is a gasoline fuel that consists of (fossil) gasoline and up to 10 % ethanol."@en, + "E10 is a gasoline fuel that consists of (fossil) gasoline and up to 10 % ethanol and that is liquid."@en, "issue: https://github.com/OpenEnergyPlatform/ontology/issues/1504 -pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1723", +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1723 + +Make liquid fuel: +issue: https://github.com/OpenEnergyPlatform/ontology/issues/1764 +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1774", rdfs:label "E10"@en SubClassOf: OEO_00010241, ( some OEO_00000183) - and ( some OEO_00010446) + and ( some OEO_00010446), + OEO_00000529 value OEO_00000256 Class: OEO_00010448 Annotations: - "B7 is a diesel fuel that consists of fossil diesel fuel and up to 7 % biodiesel."@en, + "B7 is a diesel fuel that consists of fossil diesel fuel and up to 7 % biodiesel and that is liquid."@en, "issue: https://github.com/OpenEnergyPlatform/ontology/issues/1504 -pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1723", +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1723 + +Make liquid fuel: +issue: https://github.com/OpenEnergyPlatform/ontology/issues/1764 +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1774", rdfs:label "B7"@en SubClassOf: OEO_00010242, ( some OEO_00000071) - and ( some OEO_00000183) + and ( some OEO_00000183), + OEO_00000529 value OEO_00000256 Class: OEO_00010449 @@ -8434,6 +8483,73 @@ pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1727", and ( some OEO_00140003)) +Class: OEO_00010451 + + Annotations: + "A fuel blending quota is a quality of a blended fuel that indicates the share of liquid renewable fuel or liquid biofuel mixed into fossil fuel."@en, + "issue: https://github.com/OpenEnergyPlatform/ontology/issues/1413 +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1763", + rdfs:label "fuel blending quota"@en + + SubClassOf: + + + +Class: OEO_00010452 + + Annotations: + "A fuel blending quota value is a fraction value that quantifies a fuel blending quota."@en, + "issue: https://github.com/OpenEnergyPlatform/ontology/issues/1413 +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1763", + rdfs:label "fuel quota blending value"@en + + SubClassOf: + OEO_00140127, + some OEO_00010451 + + +Class: OEO_00010453 + + Annotations: + "Temperature is a quality representing the driving force for the flow of heat energy and is a measure of the heat content of a material entity."@en, + "issue: https://github.com/OpenEnergyPlatform/ontology/issues/1505 +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1767", + rdfs:label "temperature"@en + + SubClassOf: + , + OEO_00010121 some + + +Class: OEO_00010454 + + Annotations: + "A pressure is a quality representing the force per unit area that its bearer exerts on itself or on a surface that bounds its bearer.", + "issue: https://github.com/OpenEnergyPlatform/ontology/issues/1505 +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1767", + rdfs:label "pressure"@en + + SubClassOf: + , + OEO_00010121 some + + +Class: OEO_00010455 + + Annotations: + "A carbon capture and storage technology is a technology that describes how to combine artificial objects and a carbon capture and storage process in a specific way to permanently store CO2."@en, + "CCS technology"@en, + "issue: https://github.com/OpenEnergyPlatform/ontology/issues/1760 +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1768", + rdfs:label "carbon capture and storage technology"@en + + SubClassOf: + OEO_00000407, + some + (OEO_00000061 + and ( some OEO_00010141)) + + Class: OEO_00020001 Annotations: @@ -11751,7 +11867,7 @@ pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1486", Class: OEO_00230001 Annotations: - "Power rating is a power capacity stating the maximum power an energy converting component can convert.", + "A power rating is a maximum value stating the maximum power an energy converting component can convert.", Annotations: "issue: https://github.com/OpenEnergyPlatform/ontology/issues/256 pull request: https://github.com/OpenEnergyPlatform/ontology/pull/779" @@ -11768,11 +11884,15 @@ https://github.com/OpenEnergyPlatform/ontology/pull/993 Make subclass of 'power capacity': issue: https://github.com/OpenEnergyPlatform/ontology/issues/1092 -pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1155", +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1155 + +Restructure 'power rating' and 'power capacity': +issue: https://github.com/OpenEnergyPlatform/ontology/issues/1492 +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1770", rdfs:label "power rating"@en SubClassOf: - OEO_00010257, + OEO_00010256, OEO_00020056 some OEO_00000011, OEO_00040010 some @@ -12588,9 +12708,18 @@ Class: OEO_00310013 Annotations: "A boiler is a heater that increases the thermal energy of fluids.", "issue: https://github.com/OpenEnergyPlatform/ontology/issues/1254 -pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1432", +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1432 + +issue: https://github.com/OpenEnergyPlatform/ontology/issues/1570 +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1771", rdfs:label "boiler"@en + EquivalentTo: + OEO_00000210 + and ( some + (OEO_00010248 + and ( some OEO_00140116))) + SubClassOf: OEO_00000210, OEO_00000503 some OEO_00140116 @@ -14305,6 +14434,47 @@ pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1722", +Class: OEO_00360015 + + Annotations: + "Resilience is a disposition of a system that represents the capacity of a system to absorb disturbance and reorganize so as to retain essentially the same function, structure, and feedbacks."@en, + "B. Walker, C. S. Holling, S. R. Carpenter, and A. Kinzig, “Resilience, adaptability and transformability in social–ecological systems,” Ecol. Soc., vol. 9, no. 2, 2004, Art. no. 5", + "issue: https://github.com/OpenEnergyPlatform/ontology/issues/1550 +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1744", + rdfs:label "resilience"@en + + SubClassOf: + , + OEO_00010121 some + + +Class: OEO_00360016 + + Annotations: + "Power system resilience is the resilience of a power system that represents the ability to limit the extent, system impact, and duration of degradation in order to sustain critical services following an extraordinary event."@en, + "A. M. Stanković et al., \"Methods for Analysis and Quantification of Power System Resilience,\" in IEEE Transactions on Power Systems, vol. 38, no. 5, pp. 4774-4787, Sept. 2023, doi: 10.1109/TPWRS.2022.3212688.", + "issue: https://github.com/OpenEnergyPlatform/ontology/issues/1550 +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1744", + rdfs:comment "Key enablers for a resilient response include the capacity to anticipate, absorb, rapidly recover from, adapt to, and learn from such an event. Extraordinary events for the power system may be caused by natural threats, accidents, equipment failures, and deliberate physical or cyber-attacks."@en, + rdfs:label "power system resilience"@en + + SubClassOf: + OEO_00360015, + OEO_00010121 some OEO_00360017 + + +Class: OEO_00360017 + + Annotations: + "A power system is an energy system covering the generation, transportation, distribution and consumption of electrical energy."@en, + "issue: https://github.com/OpenEnergyPlatform/ontology/issues/1550 +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1744", + rdfs:label "power system"@en + + SubClassOf: + OEO_00030024 + + Individual: OEO_00000182 Annotations: diff --git a/src/ontology/edits/oeo-shared-axioms.omn b/src/ontology/edits/oeo-shared-axioms.omn index c3498cff9..ba6a32573 100644 --- a/src/ontology/edits/oeo-shared-axioms.omn +++ b/src/ontology/edits/oeo-shared-axioms.omn @@ -363,6 +363,14 @@ Class: Class: + Annotations: + "add bearer axiom to oeo-import-edits +issue: https://github.com/OpenEnergyPlatform/ontology/issues/1305 +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1485 +move bearer axiom to oeo-shared +issue: https://github.com/OpenEnergyPlatform/ontology/issues/1738 +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1776" + Class: @@ -643,6 +651,9 @@ Class: OEO_00020072 some OEO_00000367 +Class: OEO_00020093 + + Class: OEO_00020121 @@ -803,6 +814,12 @@ Class: OEO_00140139 Class: OEO_00140149 +Class: OEO_00140150 + + SubClassOf: + some OEO_00020093 + + Class: OEO_00140151 diff --git a/src/ontology/edits/oeo-shared.omn b/src/ontology/edits/oeo-shared.omn index 5f5df5ef1..5bf6544ce 100644 --- a/src/ontology/edits/oeo-shared.omn +++ b/src/ontology/edits/oeo-shared.omn @@ -10,8 +10,8 @@ Prefix: xsd: Ontology: +Import: Import: -Import: Import: Import: Import: @@ -121,15 +121,6 @@ Pull request https://github.com/OpenEnergyPlatform/ontology/pull/603" ObjectProperty: - Annotations: - "issue https://github.com/OpenEnergyPlatform/ontology/issues/596 -Pull request https://github.com/OpenEnergyPlatform/ontology/pull/599 -Pull request https://github.com/OpenEnergyPlatform/ontology/pull/603 - -fix duplicate implementation of `Inverse Of` -issue https://github.com/OpenEnergyPlatform/ontology/issues/979 -pull request https://github.com/OpenEnergyPlatform/ontology/pull/1086" - ObjectProperty: @@ -1010,6 +1001,9 @@ Class: Class: + SubClassOf: + OEO_00010121 some + Class: @@ -1019,6 +1013,10 @@ Class: Class: + SubClassOf: + OEO_00010121 some + (OEO_00000150 or ) + Class: @@ -1049,25 +1047,9 @@ Class: Class: - Annotations: - - Annotations: "issue: https://github.com/OpenEnergyPlatform/ontology/issues/823 -pull request: https://github.com/OpenEnergyPlatform/ontology/pull/826" - "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.", - "http://www.ontobee.org/ontology/IAO?iri=http://purl.obolibrary.org/obo/IAO_0000027" - Class: - Annotations: - "add axiom has copyright license -issue https://github.com/OpenEnergyPlatform/ontology/issues/1061 -pull request https://github.com/OpenEnergyPlatform/ontology/pull/1090 - -Delete axiom has (copyright) licence: -issue: https://github.com/OpenEnergyPlatform/ontology/issues/1275 -pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1547" - Class: diff --git a/src/ontology/edits/oeo-social.omn b/src/ontology/edits/oeo-social.omn index e1cd01cc5..f51459a7b 100644 --- a/src/ontology/edits/oeo-social.omn +++ b/src/ontology/edits/oeo-social.omn @@ -361,6 +361,9 @@ Class: Class: +Class: + + Class: @@ -1948,7 +1951,7 @@ pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1652", Class: OEO_00140150 Annotations: - "A policy is a specifically dependent continuant that is a deliberate system of principles, rules and guidelines, adopted by an organisation to guide decision making with respect to particular situations and implemented to achieve stated goals.", + "A policy is a plan specification that is a deliberate system of principles, rules and guidelines, adopted by an organisation to guide decision making with respect to particular situations and implemented to achieve stated goals.", "policies and measures", "issue: https://github.com/OpenEnergyPlatform/ontology/issues/444 pull request: https://github.com/OpenEnergyPlatform/ontology/pull/797 @@ -1959,11 +1962,15 @@ pull request: https://github.com/OpenEnergyPlatform/ontology/pull/853 alternative label issue: https://github.com/OpenEnergyPlatform/ontology/issues/1329 -pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1614", +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1614 + +reclassify and add axiom to target description +issue: https://github.com/OpenEnergyPlatform/ontology/issues/1684 +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1778", rdfs:label "policy"@en SubClassOf: - , + , OEO_00010121 some OEO_00030022, some OEO_00140151 @@ -1986,11 +1993,15 @@ pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1614 rework module structure issue: https://github.com/OpenEnergyPlatform/ontology/issues/1592 -pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1652", +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1652 + +reclassify +issue: https://github.com/OpenEnergyPlatform/ontology/issues/1684 +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1778", rdfs:label "policy instrument"@en SubClassOf: - , + , Annotations: "issue: https://github.com/OpenEnergyPlatform/ontology/issues/444 pull request: https://github.com/OpenEnergyPlatform/ontology/pull/853" @@ -2192,6 +2203,34 @@ pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1698"@en, (OEO_00000323 or OEO_00030022) +Class: OEO_00360018 + + Annotations: + "A service product role is the role of an immaterial entity that is the result of a service process, and whose value is determined by the value and the costs of the service."@en, + "issue: https://github.com/OpenEnergyPlatform/ontology/issues/1584 +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1748", + rdfs:label "service product role"@en + + SubClassOf: + + + +Class: OEO_00360019 + + Annotations: + "A service product is an immaterial entity that has the service product role."@en, + "issue: https://github.com/OpenEnergyPlatform/ontology/issues/1584 +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1748", + rdfs:label "service product"@en + + EquivalentTo: + + and ( some OEO_00360018) + + SubClassOf: + + + Individual: OEO_00010122 Annotations: @@ -2271,3 +2310,25 @@ pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1724", OEO_00140150 +Class: OEO_00160006 + + Annotations: + "A market share is a quality of a market exchange which quantifies the proportion a good to the total amount of goods traded in that market exchange.", + "issue: https://github.com/OpenEnergyPlatform/ontology/issues/1636 +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1779", + rdfs:label "market share"@en + + SubClassOf: + + + +Class: OEO_00160007 + + Annotations: + "A market share value is a fraction value that quantifies a market share.", + "issue: https://github.com/OpenEnergyPlatform/ontology/issues/1636 +pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1779", + rdfs:label "market share value"@en + + SubClassOf: + OEO_00000350 diff --git a/src/ontology/imports/iao-extracted.owl b/src/ontology/imports/iao-extracted.owl index 90faf7ce9..bb2914dea 100644 --- a/src/ontology/imports/iao-extracted.owl +++ b/src/ontology/imports/iao-extracted.owl @@ -10,7 +10,7 @@ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"> - This file contains externally imported content from the Information Artifact Ontology (IAO) for import into the Open Energy Ontology (OEO). It is automatically extracted using ROBOT. + This file contains externally imported content from the Information Artifact Ontology (IAO) for import into the Open Energy Ontology (OEO). It is automatically extracted using ROBOT from the list of selected terms (iao-extract-w-hierarchy.txt, iao-extract-n-hierarchy.txt) located in the OEO-tools repository. @@ -26,83 +26,6 @@ - - - - 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 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 - - - - - - - - - - - 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 - - - - - @@ -118,43 +41,49 @@ - + 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 - + @@ -170,47 +99,53 @@ example of usage - - - - - - example of usage - + - + A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. - + PERSON:Daniel Schober - + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - + + + + + + + example of usage - + + + + + + + @@ -222,44 +157,44 @@ PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot - + has curation status - + has curation status - + PERSON:Alan Ruttenberg - + PERSON:Bill Bug - + PERSON:Melanie Courtot - + has curation status - + @@ -299,25 +234,25 @@ We also have the outstanding issue of how to aim different definitions to differ - + definition - + - + The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. - + @@ -342,25 +277,31 @@ We don't have definitions of 'meaning' or 'expression' 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 - + @@ -380,43 +321,49 @@ 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.obofoundry.org/obo/obi> - + + + + + + + editor note - + @@ -437,49 +384,55 @@ We also have the outstanding issue of how to aim different definitions to differ - + 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 - + @@ -494,62 +447,62 @@ We also have the outstanding issue of how to aim different definitions to differ PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related). - + alternative label - + alternative label - + - + A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like. - + OBO Operations committee - + PERSON:Daniel Schober - + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - + Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related). - + alternative label - + @@ -570,49 +523,55 @@ We also have the outstanding issue of how to aim different definitions to differ - + 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 - + @@ -631,37 +590,43 @@ We also have the outstanding issue of how to aim different definitions to differ - + curator note - + - + An administrative note of use for a curator but of no use for a user - + PERSON:Alan Ruttenberg - + + + + + + + curator note - + @@ -676,223 +641,285 @@ We also have the outstanding issue of how to aim different definitions to differ Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg The 'tracker item' can associate a tracker with a specific ontology term. - + term tracker item - + term tracker item - + the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ - + - + An IRI or similar locator for a request or discussion of an ontology term. - + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - + The 'tracker item' can associate a tracker with a specific ontology term. - + term tracker item - + - + - - 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 + + ontology term requester + + The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + The 'term requester' can credit the person, organization or project who request the ontology term. + + ontology term requester - + - + - + - elucidation - + ontology term requester + + + + + + + + + + + + The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. + - + - person:Alan Ruttenberg - + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + - + - Person:Barry Smith - + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + - - - 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 - + + + The 'term requester' can credit the person, organization or project who request the ontology term. + - + - elucidation - + ontology term requester + - + - - has associated axiom(nl) - Person:Alan Ruttenberg - Person:Alan Ruttenberg - An axiom associated with a term expressed using natural language + + imported from + + For external terms/classes, the ontology from which the term was imported + PERSON:Alan Ruttenberg + PERSON:Melanie Courtot + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - has associated axiom(nl) + imported from - + - + - + - has associated axiom(nl) - + imported from + + + + + + + + + + + + For external terms/classes, the ontology from which the term was imported + + + + + + PERSON:Alan Ruttenberg + - + - Person:Alan Ruttenberg - + PERSON:Melanie Courtot + - + - Person:Alan Ruttenberg - + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + - - - An axiom associated with a term expressed using natural language - + + + + - + - has associated axiom(nl) - + imported from + - + - - has associated axiom(fol) - Person:Alan Ruttenberg - Person:Alan Ruttenberg - An axiom expressed in first order logic using CLIF syntax - - has associated axiom(fol) + + may be identical to + A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged. + David Osumi-Sutherland + #40 + VFB + Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance. + + may be identical to - - - Person:Alan Ruttenberg - + + + + - - - An axiom expressed in first order logic using CLIF syntax - + + + may be identical to + - - - has associated axiom(fol) - + + + A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged. + - - - - + + + David Osumi-Sutherland + - - - has associated axiom(fol) - + + + #40 + - - - Person:Alan Ruttenberg - + + + VFB + + + + + + Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance. + + + + + + may be identical to + - + - - + + An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. + + temporal interpretation - + - + + + + + + An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. + + + + + + temporal interpretation + @@ -900,13 +927,13 @@ We also have the outstanding issue of how to aim different definitions to differ - + - + @@ -914,13 +941,13 @@ We also have the outstanding issue of how to aim different definitions to differ - + - + @@ -928,29 +955,35 @@ We also have the outstanding issue of how to aim different definitions to differ - + - + - - - + + + + + + + + + - + @@ -969,7 +1002,7 @@ We also have the outstanding issue of how to aim different definitions to differ - + @@ -985,10 +1018,112 @@ We also have the outstanding issue of how to aim different definitions to differ + + + + + has part + my body has part my brain (continuant parthood, two material entities) + my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) + this year has part this day (occurrent parthood) + a core relation that holds between a whole and its part + Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) + +A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. + has_part + + + has part + + + + + + + + + + + + + + + + + has part + + + + + + my body has part my brain (continuant parthood, two material entities) + + + + + + my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) + + + + + + this year has part this day (occurrent parthood) + + + + + + a core relation that holds between a whole and its part + + + + + + Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. + + + + + + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + + + + + + Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) + +A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. + + + + + + has_part + + + + + + + + + + + + has part + + + + + - + This document is about information artifacts and their representations A (currently) primitive relation that relates an information artifact to an entity. @@ -999,38 +1134,38 @@ We will try to build it back up by elaborating the various subproperties that ar 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 - + - - - + + + This document is about information artifacts and their representations - + - + A (currently) primitive relation that relates an information artifact to an entity. - + @@ -1040,25 +1175,74 @@ Some currently missing phenomena that should be considered "about" are 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 - + + + + + + + + + + + relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken + Alan Ruttenberg + + has time stamp + + + + + + + + + + + + + + + + + + + + + + + relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken + + + + + + Alan Ruttenberg + + + + + + has time stamp + @@ -1066,13 +1250,13 @@ Some currently missing phenomena that should be considered "about" are - + - + @@ -1088,108 +1272,191 @@ Some currently missing phenomena that should be considered "about" are - + - - + + + objective specification + In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction. + + A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. + 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed." + 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that. + Answers the question, why did you do this experiment? + PERSON: Alan Ruttenberg + PERSON: Barry Smith + PERSON: Bjoern Peters + PERSON: Jennifer Fostel + goal specification + OBI Plan and Planned Process/Roles Branch + OBI_0000217 + + objective specification - + - + - - - - - - - - - - - - + + + + - - - - - - - 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. - 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 - - - - - + + + objective specification + - - - gdc - + + + In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction. + - - - 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. - + + + A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. + - - - the pdf file on your laptop, the pdf file that is a copy thereof on my laptop - + + + 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed." + - + + + 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that. + + + + + + Answers the question, why did you do this experiment? + + + + + + PERSON: Alan Ruttenberg + + + + + + PERSON: Barry Smith + + + + + + PERSON: Bjoern Peters + + + + + + PERSON: Jennifer Fostel + + + + + + goal specification + + + + + + OBI Plan and Planned Process/Roles Branch + + + + + + OBI_0000217 + + + + + + objective specification + + + + + + + + + + Pour the contents of flask 1 into flask 2 + + A directive information entity that describes an action the bearer will take. + Alan Ruttenberg + OBI Plan and Planned Process branch + + action specification + + + + + + + + + + + + + + + - the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. - + Pour the contents of flask 1 into flask 2 + + + + + + + - + - 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]) - - + A directive information entity that describes an action the bearer will take. + - - - (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] - - + + + Alan Ruttenberg + - - - - + + + OBI Plan and Planned Process branch + - + - generically dependent continuant - + action specification + @@ -1208,81 +1475,158 @@ interpreted by or directly executed by a processing unit. PERSON: Chris Stoeckert PERSON: Melanie Courtot GROUP: OBI - + software - + - + software - + - + Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit. - + see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178 - + PERSON: Alan Ruttenberg - + PERSON: Bjoern Peters - + PERSON: Chris Stoeckert - + PERSON: Melanie Courtot - + GROUP: OBI - + software - + + + + + + + + + journal article + Examples are articles published in the journals, Nature and Science. The content can often be cited by reference to a paper based encoding, e.g. Authors, Title of article, Journal name, date or year of publication, volume and page number. + + A report that is published in a journal. + PERSON: Alan Ruttenberg + PERSON: Chris Stoeckert + OBI_0000159 + group:OBI + + journal article + + + + + + + + + + + journal article + + + + + + Examples are articles published in the journals, Nature and Science. The content can often be cited by reference to a paper based encoding, e.g. Authors, Title of article, Journal name, date or year of publication, volume and page number. + + + + + + + + + + + + A report that is published in a journal. + + + + + + PERSON: Alan Ruttenberg + + + + + + PERSON: Chris Stoeckert + + + + + + OBI_0000159 + + + + + + group:OBI + + + + + + journal article + @@ -1299,74 +1643,74 @@ interpreted by or directly executed by a processing unit. person:Chris Stoeckert OBI_0000058 group:OBI - + programming language - + - + programming language - + R, Perl, Java - + - + A language in which source code is written that is intended to be executed/run by a software interpreter. Programming languages are ways to write instructions that specify what to do, and sometimes, how to do it. - + person:Alan Ruttenberg - + person:Chris Stoeckert - + OBI_0000058 - + group:OBI - + programming language - + @@ -1394,68 +1738,68 @@ JAR: A data item is an approximately justified approximately true approximate be PERSON: Chris Stoeckert PERSON: Jonathan Rees data - + data item - + - + data item - + Data items include counts of things, analyte concentrations, and statistical summaries. - + - + An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. - + 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. - + 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. - + 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. - + 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ - + @@ -1467,37 +1811,37 @@ 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 - + @@ -1517,92 +1861,92 @@ JAR: A data item is an approximately justified approximately true approximate be PERSON: James A. Overton PERSON: Jonathan Rees based on Oxford English Dictionary - + symbol - + - + symbol - + a serial number such as "12324X" - + a stop sign - + a written proper name such as "OBI" - + - + An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. - + 20091104, MC: this needs work and will most probably change - + 2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154). - + PERSON: James A. Overton - + PERSON: Jonathan Rees - + based on Oxford English Dictionary - + symbol - + @@ -1610,7 +1954,6 @@ JAR: A data item is an approximately justified approximately true approximate be - information content entity Examples of information content entites include journal articles, data, graphical layouts, and graphs. @@ -1621,50 +1964,44 @@ JAR: A data item is an approximately justified approximately true approximate be 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 - - - - - - - + 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). - + @@ -1672,25 +2009,25 @@ Previous. An information content entity is a non-realizable information entity t 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 - + @@ -1707,74 +2044,74 @@ Previous. An information content entity is a non-realizable information entity t Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan PERSON: Alan Ruttenberg PERSON: Bjoern Peters - + directive information entity - + - + - + An information content entity whose concretizations indicate to their bearer how to realize them in a process. - + 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. - + 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it. - + 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO - + Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan - + PERSON: Alan Ruttenberg - + PERSON: Bjoern Peters - + directive information entity - + @@ -1791,74 +2128,74 @@ Previous. An information content entity is a non-realizable information entity t PlanAndPlannedProcess Branch OBI_0000270 adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg) - + algorithm - + - + algorithm - + PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies. - + - + A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata. - + Philippe Rocca-Serra - + PlanAndPlannedProcess Branch - + OBI_0000270 - + adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg) - + algorithm - + @@ -1886,44 +2223,44 @@ whole sentence is deleted. PERSON: Melanie Courtot GROUP: OBI OBI_0000099 - + report - + - + report - + Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article. - + - + A document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record). - + @@ -1934,67 +2271,157 @@ that are completed? For example, a progress report is (usually) about something that definitely has *not* been completed, or may include (only) projections. I think the definition would not suffer if the whole sentence is deleted. - + 2009-03-16: this was report of results with definition: A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so. - + 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. - + 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'document'. Alan restored as there are OBI dependencies and this merits further discussion - + disagreement about where reports go. alan: only some gene lists are reports. Is a report all the content of some document? The example of usage suggests that a report may be part of some article. Term needs clarification - + PERSON: Alan Ruttenberg - + PERSON: Chris Stoeckert - + PERSON: Melanie Courtot - + GROUP: OBI - + OBI_0000099 - + report - + + + + + + + + + + data format specification + + A data format specification is the information content borne by the document published defining the specification. +Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file + 2009-03-16: provenance: term imported from OBI_0000187, which had original definition "A data format specification is a plan which organizes +information. Example: The ISO document specifying what encompasses an +XML document; The instructions in a XSD file" + PERSON: Alan Ruttenberg + PlanAndPlannedProcess Branch + OBI branch derived + OBI_0000187 + + data format specification + + + + + + + + + + + + + + + + + data format specification + + + + + + + + + + + + A data format specification is the information content borne by the document published defining the specification. +Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file + + + + + + 2009-03-16: provenance: term imported from OBI_0000187, which had original definition "A data format specification is a plan which organizes +information. Example: The ISO document specifying what encompasses an +XML document; The instructions in a XSD file" + + + + + + PERSON: Alan Ruttenberg + + + + + + PlanAndPlannedProcess Branch + + + + + + OBI branch derived + + + + + + OBI_0000187 + + + + + + data format specification + @@ -2013,86 +2440,86 @@ whole sentence is deleted. person:Chris Stoeckert OBI_0000042 group:OBI - + data set - + - + data set - + Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). - + - + A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. - + 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type - + 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction. - + person:Allyson Lister - + person:Chris Stoeckert - + OBI_0000042 - + group:OBI - + data set - + @@ -2120,7 +2547,7 @@ Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them - + plan specification https://github.com/information-artifact-ontology/IAO/issues/231#issuecomment-1010455131 @@ -2128,85 +2555,85 @@ Request that IAO either clarify these or change definitions not to use them - + - + plan specification - + PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice. - + - + A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. - + 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. - + 2014-03-31: A plan specification can have other parts, such as conditional specifications. - + 2022-01-16 Updated definition to that proposed by Clint Dowloand, IAO Issue 231. - + Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved - + Alan Ruttenberg - + Clint Dowland - + OBI Plan and Planned Process branch - + OBI_0000344 - + @@ -2218,19 +2645,166 @@ Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them - + plan specification - + https://github.com/information-artifact-ontology/IAO/issues/231#issuecomment-1010455131 - + + + + + + + + + + measurement datum + Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}. + + A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. + 2/2/2009 is_specified_output of some assay? + person:Chris Stoeckert + OBI_0000305 + group:OBI + + measurement datum + + + + + + + + + + + + + + + + + measurement datum + + + + + + Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}. + + + + + + + + + + + + A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. + + + + + + 2/2/2009 is_specified_output of some assay? + + + + + + person:Chris Stoeckert + + + + + + OBI_0000305 + + + + + + group:OBI + + + + + + measurement datum + + + + + + + + + + version number + + A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name. + Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version + GROUP: IAO + + version number + + + + + + + + + + + + + + + + + version number + + + + + + + + + + + + A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name. + + + + + + Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version + + + + + + GROUP: IAO + + + + + + version number + @@ -2247,74 +2821,74 @@ Request that IAO either clarify these or change definitions not to use themMC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities. PERSON: Lawrence Hunter text - + textual entity - + - + textual entity - + Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities - + - + A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc. - + AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc. - + MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities. - + PERSON: Lawrence Hunter - + text - + textual entity - + @@ -2328,147 +2902,826 @@ Request that IAO either clarify these or change definitions not to use them A collection of information content entities intended to be understood together as a whole PERSON: Lawrence Hunter - + document - + - + document - + A journal article, patent application, laboratory notebook, or a book - + - + A collection of information content entities intended to be understood together as a whole - + PERSON: Lawrence Hunter - + document - + - + - - - written name - "Bill Clinton" - "The Eiffel Tower" - "United States of America" - - A textual entity that denotes a particular in reality. - PERSON: Bill Hogan - https://github.com/information-artifact-ontology/IAO/issues/114 - The qualifier "written" is to set it apart from spoken names. Also, note the restrictions to particulars. We are not naming universals. We could however, be naming, attributive collections which are particulars, so "All people located in the boundaries of the city of Little Rock, AR on June 18, 2011 at 9:50a CDT" would be a name. - + + + document part + An abstract, introduction, method or results section. + + An information content entity that is part of a document. + PERSON: Lawrence Hunter + + document part + + + + + + + + + + + + + + + + + document part + + + + + + An abstract, introduction, method or results section. + + + + + + + + + + + + An information content entity that is part of a document. + + + + + + PERSON: Lawrence Hunter + + + + + + document part + + + + + + + + + + + A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude + 2009-08-18 Alan Ruttenberg - question to BFO list about whether the BFO sense of the lower dimensional regions is that they are always part of actual space (the three dimensional sort) http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617 + Alan Ruttenberg + AR notes: We need to discuss whether it should include site. + + cartesian spatial coordinate datum + http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617 + + + + + + + + + + + + + + + + + + + + + + + A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude + + + + + + 2009-08-18 Alan Ruttenberg - question to BFO list about whether the BFO sense of the lower dimensional regions is that they are always part of actual space (the three dimensional sort) http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617 + + + + + + Alan Ruttenberg + + + + + + AR notes: We need to discuss whether it should include site. + + + + + + cartesian spatial coordinate datum + + + + + + http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617 + + + + + + + + + + + A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region + Alan Ruttenberg + + one dimensional cartesian spatial coordinate datum + + + + + + + + + + + + + + + + + + + + + + + A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region + + + + + + Alan Ruttenberg + + + + + + one dimensional cartesian spatial coordinate datum + + + + + + + + + + + A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region + Alan Ruttenberg + + two dimensional cartesian spatial coordinate datum + + + + + + + + + + + + + + + + + + + + + + + A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region + + + + + + Alan Ruttenberg + + + + + + two dimensional cartesian spatial coordinate datum + + + + + + + + + + + A cartesion spatial coordinate datum that uses three values to specify a position within a three dimensional spatial region + Alan Ruttenberg + + three dimensional cartesian spatial coordinate datum + + + + + + + + + + + + + + + + + + + + + + + A cartesion spatial coordinate datum that uses three values to specify a position within a three dimensional spatial region + + + + + + Alan Ruttenberg + + + + + + three dimensional cartesian spatial coordinate datum + + + + + + + + + + + + time stamped measurement datum + + + + + + + + + + + + + + + + + + + + + + + time stamped measurement datum + + + + + + + + + + written name + "Bill Clinton" + "The Eiffel Tower" + "United States of America" + + A textual entity that denotes a particular in reality. + PERSON: Bill Hogan + https://github.com/information-artifact-ontology/IAO/issues/114 + The qualifier "written" is to set it apart from spoken names. Also, note the restrictions to particulars. We are not naming universals. We could however, be naming, attributive collections which are particulars, so "All people located in the boundaries of the city of Little Rock, AR on June 18, 2011 at 9:50a CDT" would be a name. + written name - + - + written name - + "Bill Clinton" - + "The Eiffel Tower" - + "United States of America" - + - + A textual entity that denotes a particular in reality. - + PERSON: Bill Hogan - + https://github.com/information-artifact-ontology/IAO/issues/114 - + The qualifier "written" is to set it apart from spoken names. Also, note the restrictions to particulars. We are not naming universals. We could however, be naming, attributive collections which are particulars, so "All people located in the boundaries of the city of Little Rock, AR on June 18, 2011 at 9:50a CDT" would be a name. - + written name - + + + + + + + + + + + A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task. + PERSON: Melanie Courtot + PERSON: Michel Dumontier + https://github.com/information-artifact-ontology/IAO/issues/80 + + software method + + + + + + + + + + + + + + + + + + + + + + + A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task. + + + + + + PERSON: Melanie Courtot + + + + + + PERSON: Michel Dumontier + + + + + + https://github.com/information-artifact-ontology/IAO/issues/80 + + + + + + software method + + + + + + + + + + + A software module is software composed of a collection of software methods. + PERSON: Melanei Courtot + PERSON: Michel Dumontier + https://github.com/information-artifact-ontology/IAO/issues/80 + + software module + + + + + + + + + + + + + + + + + + + + + + + A software module is software composed of a collection of software methods. + + + + + + PERSON: Melanei Courtot + + + + + + PERSON: Michel Dumontier + + + + + + https://github.com/information-artifact-ontology/IAO/issues/80 + + + + + + software module + + + + + + + + + + + A software library is software composed of a collection of software modules and/or software methods in a form that can be statically or dynamically linked to some software application. + PERSON: Melanie Courtot + PERSON: Michel Dumontier + https://github.com/information-artifact-ontology/IAO/issues/80 + + software library + + + + + + + + + + + + + + + + + + + + + + + A software library is software composed of a collection of software modules and/or software methods in a form that can be statically or dynamically linked to some software application. + + + + + + PERSON: Melanie Courtot + + + + + + PERSON: Michel Dumontier + + + + + + https://github.com/information-artifact-ontology/IAO/issues/80 + + + + + + software library + + + + + + + + + + + A software application is software that can be directly executed by some processing unit. + PERSON: Melanie Courtot + PERSON: Michel Dumontier + https://github.com/information-artifact-ontology/IAO/issues/80 + + software application + + + + + + + + + + + + + + + + + + + + + + + A software application is software that can be directly executed by some processing unit. + + + + + + PERSON: Melanie Courtot + + + + + + PERSON: Michel Dumontier + + + + + + https://github.com/information-artifact-ontology/IAO/issues/80 + + + + + + software application + + + + + + + + + + + A software script is software whose instructions can be executed using a software interpreter. + PERSON: Melanie Courtot + PERSON: Michel Dumontier + https://github.com/information-artifact-ontology/IAO/issues/80 + + software script + + + + + + + + + + + + + + + + + + + + + + + A software script is software whose instructions can be executed using a software interpreter. + + + + + + PERSON: Melanie Courtot + + + + + + PERSON: Michel Dumontier + + + + + + https://github.com/information-artifact-ontology/IAO/issues/80 + + + + + + software script + + + + + + + + + + study design + A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. + + + study design + + + + + + + + + + + + + + + + + study design + + + + + + A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. + + + + + + + + + + + + study design + diff --git a/src/ontology/imports/omo-extracted.owl b/src/ontology/imports/omo-extracted.owl deleted file mode 100644 index 341776b4e..000000000 --- a/src/ontology/imports/omo-extracted.owl +++ /dev/null @@ -1,905 +0,0 @@ - - - - - This file contains externally imported content from the OBO Metadata Ontology (OMO) for import into the Open Energy Ontology (OEO). It is automatically extracted using ROBOT. - - - - - - - - - - - - - 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 - - - - - - - - - - - editor preferred term - - - - - - - - - - - - The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) - - - - - - PERSON:Daniel Schober - - - - - - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - - - - - editor preferred term - - - - - - - - - example of usage - - A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - example of usage - - - - - - - - - - - A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. - - - - - - PERSON:Daniel Schober - - - - - - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - - - - - example of usage - - - - - - - - - - - - example of usage - - - - - - - - - has curation status - PERSON:Alan Ruttenberg - PERSON:Bill Bug - PERSON:Melanie Courtot - - has curation status - - - - - - - - - - - has curation status - - - - - - PERSON:Alan Ruttenberg - - - - - - PERSON:Bill Bug - - - - - - PERSON:Melanie Courtot - - - - - - has curation status - - - - - - - - - definition - - The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. - 2012-04-05: -Barry Smith - -The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. - -Can you fix to something like: - -A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. - -Alan Ruttenberg - -Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. - -On the specifics of the proposed definition: - -We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. - -Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. - -We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - definition - - - - - - - - - - - definition - - - - - - - - - - - - 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 - - - - - - - - - editor note - - An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obofoundry.org/obo/obi> - - editor note - - - - - - - - - - - editor note - - - - - - - - - - - - An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. - - - - - - PERSON:Daniel Schober - - - - - - GROUP:OBI:<http://purl.obofoundry.org/obo/obi> - - - - - - editor note - - - - - - - - - term editor - - Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people - 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - term editor - - - - - - - - - - - term editor - - - - - - - - - - - - Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people - - - - - - 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. - - - - - - PERSON:Daniel Schober - - - - - - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - - - - - term editor - - - - - - - - - alternative label - - A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like. - OBO Operations committee - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related). - - alternative label - - - - - - - - - - - alternative label - - - - - - - - - - - - A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like. - - - - - - OBO Operations committee - - - - - - PERSON:Daniel Schober - - - - - - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - - - - - Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related). - - - - - - alternative label - - - - - - - - - definition source - - Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 - PERSON:Daniel Schober - Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - definition source - - - - - - - - - - - definition source - - - - - - - - - - - - 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 - - - - - - - - - term tracker item - the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ - - An IRI or similar locator for a request or discussion of an ontology term. - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - The 'tracker item' can associate a tracker with a specific ontology term. - - term tracker item - - - - - - - - - - - term tracker item - - - - - - the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ - - - - - - - - - - - - An IRI or similar locator for a request or discussion of an ontology term. - - - - - - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - - - - - - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - - - - - - The 'tracker item' can associate a tracker with a specific ontology term. - - - - - - term tracker item - - - - - - - - - ontology term requester - - The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - The 'term requester' can credit the person, organization or project who request the ontology term. - - ontology term requester - - - - - - - - - - - ontology term requester - - - - - - - - - - - - The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. - - - - - - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - - - - - - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - - - - - - The 'term requester' can credit the person, organization or project who request the ontology term. - - - - - - ontology term requester - - - - - - - - - may be identical to - A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged. - David Osumi-Sutherland - #40 - VFB - Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance. - - may be identical to - - - - - - - - - - - may be identical to - - - - - - A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged. - - - - - - David Osumi-Sutherland - - - - - - #40 - - - - - - VFB - - - - - - Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance. - - - - - - may be identical to - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - data item - - data item - - - - - - - - - - - - - - - - - data item - - - - - - data item - - - - - - - - - - information content entity - - information content entity - - - - - - - - - - - - - - - - - information content entity - - - - - - information content entity - - - - - - - - - - - - - - - - diff --git a/src/ontology/imports/ro-extracted.owl b/src/ontology/imports/ro-extracted.owl index 142279e7c..2726b95ac 100644 --- a/src/ontology/imports/ro-extracted.owl +++ b/src/ontology/imports/ro-extracted.owl @@ -13,7 +13,7 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - This file contains externally imported content from the Relations Ontology (RO) for import into the Open Energy Ontology (OEO). It is automatically extracted using ROBOT from the list of selected terms (ro-extract-w-hierarchy.txt, ro-extract-n-hierarchy.txt) located in the OEO-repository. + This file contains externally imported content from the Relations Ontology (RO) for import into the Open Energy Ontology (OEO). It is automatically extracted using ROBOT from the list of selected terms (ro-extract-w-hierarchy.txt, ro-extract-n-hierarchy.txt) located in the OEO-repository. @@ -457,90 +457,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An - - - has part - my body has part my brain (continuant parthood, two material entities) - my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) - this year has part this day (occurrent parthood) - a core relation that holds between a whole and its part - Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. - Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) - -A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. - has_part - - has part - - - - - has part - - - - - - my body has part my brain (continuant parthood, two material entities) - - - - - - my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) - - - - - - this year has part this day (occurrent parthood) - - - - - - a core relation that holds between a whole and its part - - - - - - Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. - - - - - - Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - - - - - - Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) - -A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. - - - - - - has_part - - - - - - - - - - - - has part - - + @@ -961,32 +878,32 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. + + this apple has quality this red color - - has_quality + + a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence - - has quality + + A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. - - this apple has quality this red color + + has_quality - - a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence + + has quality @@ -1070,12 +987,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. location of - - - - is location of - - @@ -1118,6 +1029,12 @@ A continuant cannot have an occurrent as part: use 'participates in'. location of + + + + is location of + + @@ -2554,10 +2471,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different A mereological relationship or a topological relationship - mereotopologically related to - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships + + mereotopologically related to @@ -2567,14 +2484,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - mereotopologically related to + + - - + + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships @@ -2585,13 +2502,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships + + mereotopologically related to - + diff --git a/src/ontology/oeo.omn b/src/ontology/oeo.omn index d026c642f..e145c9ff6 100644 --- a/src/ontology/oeo.omn +++ b/src/ontology/oeo.omn @@ -13,13 +13,11 @@ Prefix: xsd: Ontology: -Import: Import: Import: Import: Import: Import: -Import: Annotations: dc:contributor "(0001) Lukas Emele (@l-emele)", @@ -80,4 +78,3 @@ AnnotationProperty: dct:title Datatype: rdf:PlainLiteral -