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48 situation module (#57)
* Add situation module * Add situation module * change prefix * Fix namespaces * add gfo-core module * add gfo-situation-simple pattern * update gfo-situation-simple pattern * update update gfo-situation-simple pattern * add gfo-situation-object pattern * add gfo-situation-object-extended pattern * Update gfo-core module * update gfo-core module * add gfo-presentic module * add gfo-presentic module * update gfo-core module * add gfo-timeExtended module * add gfo-connector-presentic-timeExtended module * delete gfo-base * Add situation patterns+examples from JAO paper * Corrections * Add new files to CI workflow * Fix import resolution * Remove CI test step for deleted ontology * Specify profile for reasoning tests * Update documentation * Replace robot `reason` calls with `report` * Disable report for gfo-light.owl again This file will be replaced in another pull request * Add some labels * Update import statement of gfo.owl * Add gfo.owl to tested files * Remove unnecessary prefixes * Merge imports of some modules before reporting * Add labels to examples * Add rdfs:labels to individuals * Correct auto generated labels that start with a number * Remove module files from PR * Remove module tests from PR * Temporarily reinstitute gfo-base.owl * Fix import * replace gfo-core by gfo-base * replace risk_sit_1_timespan by 10_months_timespan --------- Co-authored-by: auciteli <auciteli@imise.uni-leipzig.de> Co-authored-by: AlexU75 <65653151+AlexU75@users.noreply.github.com> Co-authored-by: Christoph Beger <ChristophB@users.noreply.github.com>
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‎.github/workflows/test.yml

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steps:
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- uses: actions/checkout@v4
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- run: check-rdfxml gfo.owl
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- run: check-rdfxml gfo-light.owl
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- run: check-rdfxml modules/gfo-base.owl
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# - run: check-rdfxml modules/gfo-core.ttl
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# - run: check-rdfxml modules/gfo-presentic.ttl
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# - run: check-rdfxml modules/gfo-timeExtended.ttl
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# - run: check-rdfxml modules/gfo-connector-presentic-timeExtended.ttl
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- run: check-rdfxml modules/situation/gfo-situation.ttl
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- run: check-rdfxml modules/situation/gfo-situation-object-extended.ttl
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- run: check-rdfxml modules/situation/gfo-situation-object.ttl
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- run: check-rdfxml modules/situation/gfo-situation-presentic-object-reified-presentic-attributives.ttl
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- run: check-rdfxml modules/situation/gfo-situation-presentic-object-reified-presentic-objects.ttl
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- run: check-rdfxml modules/situation/gfo-situation-presentic-object.ttl
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- run: check-rdfxml modules/situation/gfo-situation-presentic-simple.ttl
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- run: check-rdfxml modules/situation/gfo-situation-simple.ttl
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- run: check-rdfxml modules/situation/gfo-situation-time-extended.ttl
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- run: check-rdfxml modules/situation/examples/gfo-situation-object-example.ttl
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- run: check-rdfxml modules/situation/examples/gfo-situation-object-extended-example.ttl
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- run: check-rdfxml modules/situation/examples/gfo-situation-presentic-object-example.ttl
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- run: check-rdfxml modules/situation/examples/gfo-situation-presentic-object-reified-presentic-attributives-example.ttl
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- run: check-rdfxml modules/situation/examples/gfo-situation-presentic-object-reified-presentic-objects-example.ttl
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- run: check-rdfxml modules/situation/examples/gfo-situation-presentic-simple-example.ttl
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- run: check-rdfxml modules/situation/examples/gfo-situation-simple-example.ttl
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- run: check-rdfxml modules/situation/examples/gfo-situation-time-extended-example.ttl
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- run: robot reason --input gfo-light.owl
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- run: robot reason --input modules/gfo-base.owl
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- run: robot report --profile qc_report/profile.txt -i gfo.owl
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# - run: robot report --profile qc_report/profile.txt -i gfo-light.owl
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# - run: robot report --profile qc_report/profile.txt -i modules/gfo-core.ttl
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# - run: robot report --profile qc_report/profile.txt -i modules/gfo-presentic.ttl
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# - run: robot report --profile qc_report/profile.txt -i modules/gfo-timeExtended.ttl
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- run: robot report --profile qc_report/profile.txt -i modules/situation/gfo-situation.ttl
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- run: robot report --profile qc_report/profile.txt -i modules/situation/gfo-situation-object-extended.ttl
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- run: robot report --profile qc_report/profile.txt -i modules/situation/gfo-situation-object.ttl
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- run: robot report --profile qc_report/profile.txt -i modules/situation/gfo-situation-presentic-object-reified-presentic-attributives.ttl
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- run: robot report --profile qc_report/profile.txt -i modules/situation/gfo-situation-presentic-object-reified-presentic-objects.ttl
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- run: robot report --profile qc_report/profile.txt -i modules/situation/gfo-situation-presentic-object.ttl
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- run: robot report --profile qc_report/profile.txt -i modules/situation/gfo-situation-presentic-simple.ttl
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- run: robot report --profile qc_report/profile.txt -i modules/situation/gfo-situation-simple.ttl
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- run: robot report --profile qc_report/profile.txt -i modules/situation/gfo-situation-time-extended.ttl
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# - run: robot report --input gfo-light.owl --profile qc_report/profile.txt
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- run: robot report --input modules/gfo-base.owl --profile qc_report/profile.txt
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# - run: robot merge --collapse-import-closure true -i modules/gfo-connector-presentic-timeExtended.ttl report --profile qc_report/profile.txt
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- run: robot merge --collapse-import-closure true -i modules/situation/examples/gfo-situation-object-example.ttl report --profile qc_report/profile.txt
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- run: robot merge --collapse-import-closure true -i modules/situation/examples/gfo-situation-object-extended-example.ttl report --profile qc_report/profile.txt
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- run: robot merge --collapse-import-closure true -i modules/situation/examples/gfo-situation-presentic-object-example.ttl report --profile qc_report/profile.txt
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- run: robot merge --collapse-import-closure true -i modules/situation/examples/gfo-situation-presentic-object-reified-presentic-attributives-example.ttl report --profile qc_report/profile.txt
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- run: robot merge --collapse-import-closure true -i modules/situation/examples/gfo-situation-presentic-object-reified-presentic-objects-example.ttl report --profile qc_report/profile.txt
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- run: robot merge --collapse-import-closure true -i modules/situation/examples/gfo-situation-presentic-simple-example.ttl report --profile qc_report/profile.txt
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- run: robot merge --collapse-import-closure true -i modules/situation/examples/gfo-situation-simple-example.ttl report --profile qc_report/profile.txt
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- run: robot merge --collapse-import-closure true -i modules/situation/examples/gfo-situation-time-extended-example.ttl report --profile qc_report/profile.txt

‎CONTRIBUTING.md

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@@ -24,9 +24,9 @@ If you want to contribute changes, please do so by:
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Edit the ontology files using a suitable ontology editor or text editor.
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Adhere to the GFO's existing coding style and conventions.
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Ensure your changes are well-documented and understandable.
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You can run the following command with docker to check your changes locally (in this case `modules/gfo-base.owl` is checked):
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You can run the following command with docker to check your changes locally (in this case `modules/gfo-core.owl` is checked):
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docker run -it -v .:/gfo -w /gfo obolibrary/odklite robot report --input modules/gfo-base.owl --profile qc_report/profile.txt
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docker run -it -v .:/gfo -w /gfo obolibrary/odklite robot report --input modules/gfo-core.owl --profile qc_report/profile.txt
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4. Commit and push all changes.
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5. Create a [pull request](https://github.com/Onto-Med/GFO/pulls).

‎catalog-v001.xml

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<?xml version="1.0" encoding="UTF-8" standalone="no"?>
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<catalog prefer="public" xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog">
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<uri id="gfo-core" name="https://w3id.org/gfo/core/" uri="modules/gfo-core.ttl"/>
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</catalog>

‎gfo.owl

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<owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2024-11-18</owl:versionInfo>
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<owl:versionIRI rdf:resource="https://w3id.org/gfo/release/2024-11-18" />
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<owl:priorVersion rdf:resource="https://w3id.org/gfo/release/2024-07-05" />
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<owl:imports rdf:resource="https://w3id.org/gfo/base/" />
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<owl:imports rdf:resource="https://w3id.org/gfo/base" />
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<dc:title xml:lang="en">General Formal Ontology (GFO)</dc:title>
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<rdfs:label xml:lang="en">General Formal Ontology (GFO)</rdfs:label>
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<dc:description xml:lang="en">The General Formal Ontology is a top-level ontology for conceptual

‎modules/situation/examples/catalog-v001.xml

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<?xml version="1.0" encoding="UTF-8" standalone="no"?>
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<catalog prefer="public" xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog">
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<uri id="Imports Wizard Entry" name="https://w3id.org/gfo/pattern/situation/simple" uri="../gfo-situation-simple.ttl"/>
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<uri id="Imports Wizard Entry" name="https://w3id.org/gfo/pattern/situation/time-extended" uri="../gfo-situation-time-extended.ttl"/>
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<uri id="Imports Wizard Entry" name="https://w3id.org/gfo/pattern/situation/object" uri="../gfo-situation-object.ttl"/>
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<uri id="Imports Wizard Entry" name="https://w3id.org/gfo/pattern/situation/object-extended" uri="../gfo-situation-object-extended.ttl"/>
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<uri id="Imports Wizard Entry" name="https://w3id.org/gfo/pattern/situation/presentic-simple" uri="../gfo-situation-presentic-simple.ttl"/>
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<uri id="Imports Wizard Entry" name="https://w3id.org/gfo/pattern/situation/presentic-object" uri="../gfo-situation-presentic-object.ttl"/>
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<uri id="Imports Wizard Entry" name="https://w3id.org/gfo/pattern/situation/presentic-object-reified-presentic-attributives" uri="../gfo-situation-presentic-object-reified-presentic-attributives.ttl"/>
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<uri id="Imports Wizard Entry" name="https://w3id.org/gfo/pattern/situation/presentic-object-reified-presentic-objects" uri="../gfo-situation-presentic-object-reified-presentic-objects.ttl"/>
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<uri id="Imports Wizard Entry" name="https://w3id.org/gfo/pattern/situation/simple-example" uri="gfo-situation-simple-example.ttl"/>
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<uri id="Imports Wizard Entry" name="https://w3id.org/gfo/pattern/situation/time-extended-example" uri="gfo-situation-time-extended-example.ttl"/>
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<uri id="Imports Wizard Entry" name="https://w3id.org/gfo/pattern/situation/object-example" uri="gfo-situation-object-example.ttl"/>
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<uri id="Imports Wizard Entry" name="https://w3id.org/gfo/pattern/situation/object-extended-example" uri="gfo-situation-object-extended-example.ttl"/>
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<uri id="Imports Wizard Entry" name="https://w3id.org/gfo/pattern/situation/presentic-simple-example" uri="gfo-situation-presentic-simple-example.ttl"/>
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<uri id="Imports Wizard Entry" name="https://w3id.org/gfo/pattern/situation/presentic-object-example" uri="gfo-situation-presentic-object-example.ttl"/>
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<uri id="Imports Wizard Entry" name="https://w3id.org/gfo/pattern/situation/presentic-object-reified-presentic-attributives-example" uri="gfo-situation-presentic-object-reified-presentic-attributives-example.ttl"/>
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<uri id="Imports Wizard Entry" name="https://w3id.org/gfo/pattern/situation/presentic-object-reified-presentic-objects-example" uri="gfo-situation-presentic-object-reified-presentic-objects-example.ttl"/>
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<group id="Folder Repository, directory=, recursive=true, Auto-Update=true, version=2" prefer="public" xml:base=""/>
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</catalog>

‎modules/situation/examples/gfo-situation-object-example.ttl

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@prefix : <https://w3id.org/gfo/situation/> .
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@prefix dc: <http://purl.org/dc/elements/1.1/> .
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@prefix owl: <http://www.w3.org/2002/07/owl#> .
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@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
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@prefix rio: <https://w3id.org/rio/> .
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@prefix xml: <http://www.w3.org/XML/1998/namespace> .
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@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
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@prefix bibo: <http://purl.org/ontology/bibo/> .
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@prefix doap: <http://usefulinc.com/ns/doap#> .
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@prefix foaf: <http://xmlns.com/foaf/0.1/> .
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@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
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@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
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@prefix vann: <http://purl.org/vocab/vann/> .
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@prefix terms: <http://purl.org/dc/terms/> .
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@prefix rio-ex: <https://w3id.org/rio/example/> .
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@prefix gfo-core: <https://w3id.org/gfo/core/> .
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@base <https://w3id.org/gfo/situation/> .
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<https://w3id.org/gfo/pattern/situation/object-example> rdf:type owl:Ontology ;
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owl:versionIRI <https://w3id.org/gfo/pattern/situation/object-example/release/2024-12-19> ;
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owl:imports <https://w3id.org/gfo/pattern/situation/object> ;
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dc:created "2024-12-11" ;
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dc:creator "Alexandr Uciteli" ,
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"Christoph Beger" ,
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"Frank Löbe" ,
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"Franz Matthies" ,
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"Heinrich Herre" ,
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"Konrad Höffner" ,
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"Patryk Burek" ,
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"Ralph Schäfermeier" ;
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dc:description "GFO-object-situation-example is an example for the object design pattern for modeling object situations."@en ;
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dc:modified "2024-12-11" ;
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dc:title "General Formal Ontology (object situation pattern example)"@en ;
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terms:license <http://creativecommons.org/licenses/by/4.0/> ;
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bibo:doi <https://zenodo.org/doi/10.5281/zenodo.5205419> ;
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vann:preferredNamespacePrefix "gfo-object-situation-example" ;
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vann:preferredNamespaceURI "https://w3id.org/gfo/pattern/situation/object-example" ;
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doap:repository <https://github.com/Onto-Med/GFO> ;
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rdfs:label "GFO object situation pattern example"@en ;
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owl:versionInfo "2024-12-11" ;
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foaf:homepage "https://github.com/Onto-Med/GFO" .
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#################################################################
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# Annotation properties
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#################################################################
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### http://purl.org/dc/elements/1.1/created
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dc:created rdf:type owl:AnnotationProperty .
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### http://purl.org/dc/elements/1.1/creator
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dc:creator rdf:type owl:AnnotationProperty .
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### http://purl.org/dc/elements/1.1/description
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dc:description rdf:type owl:AnnotationProperty .
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### http://purl.org/dc/elements/1.1/modified
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dc:modified rdf:type owl:AnnotationProperty .
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### http://purl.org/dc/elements/1.1/title
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dc:title rdf:type owl:AnnotationProperty .
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### http://purl.org/dc/terms/license
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terms:license rdf:type owl:AnnotationProperty .
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### http://purl.org/ontology/bibo/doi
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bibo:doi rdf:type owl:AnnotationProperty .
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### http://purl.org/vocab/vann/preferredNamespacePrefix
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vann:preferredNamespacePrefix rdf:type owl:AnnotationProperty .
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### http://purl.org/vocab/vann/preferredNamespaceURI
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vann:preferredNamespaceURI rdf:type owl:AnnotationProperty .
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### http://usefulinc.com/ns/doap#repository
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doap:repository rdf:type owl:AnnotationProperty .
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### http://www.w3.org/2000/01/rdf-schema#comment
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rdfs:comment rdf:type owl:AnnotationProperty .
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### http://www.w3.org/2002/07/owl#versionInfo
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owl:versionInfo rdf:type owl:AnnotationProperty .
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### http://www.w3.org/2004/02/skos/core#altLabel
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skos:altLabel rdf:type owl:AnnotationProperty .
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### http://www.w3.org/2004/02/skos/core#definition
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skos:definition rdf:type owl:AnnotationProperty .
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### http://www.w3.org/2004/02/skos/core#example
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skos:example rdf:type owl:AnnotationProperty .
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### http://xmlns.com/foaf/0.1/homepage
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foaf:homepage rdf:type owl:AnnotationProperty .
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#################################################################
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# Classes
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#################################################################
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### https://w3id.org/rio/Patient
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rio:Patient rdf:type owl:Class ;
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rdfs:subClassOf gfo-core:Object ,
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[ rdf:type owl:Restriction ;
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owl:onProperty gfo-core:hasQuality ;
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owl:someValuesFrom rio:PatientAge
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] ,
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[ rdf:type owl:Restriction ;
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owl:onProperty gfo-core:participatesIn ;
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owl:someValuesFrom rio:RiskSituation
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] ;
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rdfs:label "Patient"@en .
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### https://w3id.org/rio/PatientAge
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rio:PatientAge rdf:type owl:Class ;
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rdfs:subClassOf gfo-core:Quality ;
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rdfs:label "Patient age"@en .
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### https://w3id.org/rio/RiskSeverity
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rio:RiskSeverity rdf:type owl:Class ;
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rdfs:subClassOf gfo-core:Quality ;
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rdfs:label "Risk severity"@en .
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### https://w3id.org/rio/RiskSituation
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rio:RiskSituation rdf:type owl:Class ;
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rdfs:subClassOf :Situation ,
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[ rdf:type owl:Restriction ;
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owl:onProperty gfo-core:hasParticipantQuality ;
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owl:someValuesFrom rio:PatientAge
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] ;
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rdfs:label "Risk situation"@en .
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#################################################################
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# Individuals
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#################################################################
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### https://w3id.org/rio/example/highly_severe
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rio-ex:highly_severe rdf:type owl:NamedIndividual ,
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rio:RiskSeverity ;
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rdfs:label "highly_severe"@en .
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### https://w3id.org/rio/example/patient_1
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rio-ex:patient_1 rdf:type owl:NamedIndividual ,
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rio:Patient ;
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gfo-core:hasQuality <https://w3id.org/rio/example/10_months> ;
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gfo-core:participatesIn rio-ex:risk_sit1 ;
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rdfs:label "patient_1"@en .
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### https://w3id.org/rio/example/risk_sit1
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rio-ex:risk_sit1 rdf:type owl:NamedIndividual ,
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rio:RiskSituation ;
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gfo-core:hasParticipantQuality <https://w3id.org/rio/example/10_months> ;
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gfo-core:hasQuality rio-ex:highly_severe ;
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rdfs:label "risk_sit1"@en .
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### https://w3id.org/rio/example/10_months
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<https://w3id.org/rio/example/10_months> rdf:type owl:NamedIndividual ,
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rio:PatientAge ;
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rdfs:label "10_months"@en .
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### Generated by the OWL API (version 4.5.29.2024-05-13T12:11:03Z) https://github.com/owlcs/owlapi

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