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New About files #545

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167e89a
renaming of about files
mereolog Nov 23, 2023
e0c6976
pre-merge change
mereolog Dec 14, 2023
b10af30
pre-merge change
mereolog Dec 14, 2023
3b7918c
pre-merge change
mereolog Dec 14, 2023
5125bb6
merge to master
mereolog Dec 15, 2023
c018bf2
removal of previous about files
mereolog Dec 15, 2023
186d475
two typos in IRIs fixed
mereolog Dec 15, 2023
9b779d9
fixes to merge problems
mereolog Dec 18, 2023
c8b9a14
fixes to merge problems
mereolog Dec 18, 2023
0db9519
Update ISO11615-MedicinalProducts.rdf
mereolog Dec 18, 2023
07505a4
fixes to merge problems
mereolog Dec 18, 2023
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4 changes: 2 additions & 2 deletions .github/workflows/spellcheck_run.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -30,10 +30,10 @@ jobs:
sudo chmod +x /usr/bin/robot
- name: Merge all IDMP ontologies with robot
run: |
robot merge --input AboutIDMPDev-ReferenceIndividuals.rdf --output AboutIDMPDev-ReferenceIndividuals.ttl --catalog /home/runner/work/idmp/idmp/catalog-v001.xml
robot merge --input AboutIDMPOntologiesAndExamples.rdf --output AboutIDMPOntologiesAndExamples.ttl --catalog /home/runner/work/idmp/idmp/catalog-v001.xml
- name: Run spellchecker
run: |
python etc/testing/spelling/onto_spellchecker.py --ontology /home/runner/work/idmp/idmp/AboutIDMPDev-ReferenceIndividuals.ttl --spell etc/testing/spelling/domain_specific_spellings.json --filter spec.pistoiaalliance.org
python etc/testing/spelling/onto_spellchecker.py --ontology /home/runner/work/idmp/idmp/AboutIDMPOntologiesAndExamples.ttl --spell etc/testing/spelling/domain_specific_spellings.json --filter spec.pistoiaalliance.org
if [ $? != 0 ];
then
exit $?
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6 changes: 3 additions & 3 deletions .github/workflows/unit_tests_run.yml
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Expand Up @@ -35,7 +35,7 @@ jobs:
- name: Run unit tests using Apache Jena
run: |
java -Xmx5G -jar etc/unit_tests/target/unit-test-runner-1.0.jar \
-ontology_location ./AboutIDMPDev-ReferenceIndividuals.ttl \
-ontology_location ./AboutIDMPOntologiesAndExamples.ttl \
-root_folder etc/unit_tests/ \
-cq_source etc/CQ/Example/ \
-config_file configs/idmp_tests_config.yaml
Expand All @@ -48,7 +48,7 @@ jobs:
if: always()
with:
name: merged-ontology
path: AboutIDMPDev-ReferenceIndividuals.ttl
path: AboutIDMPOntologiesAndExamples.ttl
GSRS:
runs-on: ubuntu-latest
env:
Expand Down Expand Up @@ -93,7 +93,7 @@ jobs:
done
- name: Combine GSRS with IDMP
run: |
source_files=(gsrs-transformed.ttl AboutIDMPDev-ReferenceIndividuals.ttl)
source_files=(gsrs-transformed.ttl AboutIDMPOntologiesAndExamples.ttl)
output_file=gsrs-final.ttl
# Loop through the source files and append their contents to the output file
for file in "${source_files[@]}"; do
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126 changes: 0 additions & 126 deletions AboutIDMPDev.rdf
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This file was deleted.

12 changes: 6 additions & 6 deletions AboutIDMPProd-ReferenceIndividuals.rdf → AboutIDMPOntologies.rdf
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Expand Up @@ -2,24 +2,24 @@
<!DOCTYPE rdf:RDF [
<!ENTITY dct "http://purl.org/dc/terms/">
<!ENTITY cmns-av "https://www.omg.org/spec/Commons/AnnotationVocabulary/">
<!ENTITY idmp-prod-ref "https://spec.pistoiaalliance.org/idmp/ontology/AboutIDMPProd-ReferenceIndividuals/">
<!ENTITY idmp-about "https://spec.pistoiaalliance.org/idmp/ontology/AboutIDMPOntologies/">
<!ENTITY owl "http://www.w3.org/2002/07/owl#">
<!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<!ENTITY rdfs "http://www.w3.org/2000/01/rdf-schema#">
<!ENTITY skos "http://www.w3.org/2004/02/skos/core#">
<!ENTITY xsd "http://www.w3.org/2001/XMLSchema#">
]>
<rdf:RDF xml:base="https://spec.pistoiaalliance.org/idmp/ontology/AboutIDMPProd-ReferenceIndividuals/"
<rdf:RDF xml:base="https://spec.pistoiaalliance.org/idmp/ontology/AboutIDMPOntologies/"
xmlns:dct="http://purl.org/dc/terms/"
xmlns:cmns-av="https://www.omg.org/spec/Commons/AnnotationVocabulary/"
xmlns:idmp-prod-ref="https://spec.pistoiaalliance.org/idmp/ontology/AboutIDMPProd-ReferenceIndividuals/"
xmlns:idmp-about="https://spec.pistoiaalliance.org/idmp/ontology/AboutIDMPOntologies/"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:skos="http://www.w3.org/2004/02/skos/core#"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#">

<owl:Ontology rdf:about="https://spec.pistoiaalliance.org/idmp/ontology/AboutIDMPProd-ReferenceIndividuals/">
<owl:Ontology rdf:about="https://spec.pistoiaalliance.org/idmp/ontology/AboutIDMPOntologies/">
<rdfs:label>About IDMP Production - Reference Individuals</rdfs:label>
<dct:abstract>This ontology is provided for the convenience of IDMP users. It loads the IDMP production ontologies based on the contents of GitHub, rather than those that comprise a specific version, such as a quarterly release. Note that while metadata files and other 'load' files, such as the various subject area specific 'all' files, are intentionally excluded, this version of the 'load' file does include all reference data, such as governments and related jurisdictions required for complete IDMP representation.</dct:abstract>
<dct:issued rdf:datatype="&xsd;dateTime">2023-08-13T18:00:00</dct:issued>
Expand Down Expand Up @@ -88,7 +88,7 @@
//
///////////////////////////////////////////////////////////////////////////////////////
-->

<owl:imports rdf:resource="https://www.omg.org/spec/MVF/ISO1087-TerminologyScience/"/>
<owl:imports rdf:resource="https://www.omg.org/spec/MVF/ISO1087-VocabularyForTermsAndDefinitions/"/>
<owl:imports rdf:resource="https://www.omg.org/spec/MVF/MultipleVocabularyFacility/"/>
Expand All @@ -109,7 +109,7 @@
<owl:imports rdf:resource="https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11615-MedicinalProducts/"/>
<owl:imports rdf:resource="https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO21090-HarmonizedDatatypes/"/>

<owl:versionIRI rdf:resource="https://spec.pistoiaalliance.org/idmp/ontology/20231201/AboutIDMPProd-ReferenceIndividuals/"/>
<owl:versionIRI rdf:resource="https://spec.pistoiaalliance.org/idmp/ontology/20230801/AboutIDMPOntologies/"/>

</owl:Ontology>

Expand Down
12 changes: 6 additions & 6 deletions AboutIDMPDev-ReferenceIndividuals.rdf → AboutIDMPOntologiesAndExamples.rdf
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Original file line number Diff line number Diff line change
Expand Up @@ -2,24 +2,24 @@
<!DOCTYPE rdf:RDF [
<!ENTITY dct "http://purl.org/dc/terms/">
<!ENTITY cmns-av "https://www.omg.org/spec/Commons/AnnotationVocabulary/">
<!ENTITY idmp-dev-ref "https://spec.pistoiaalliance.org/idmp/ontology/AboutIDMPDev-ReferenceIndividuals/">
<!ENTITY idmp-examples-about "https://spec.pistoiaalliance.org/idmp/ontology/AboutIDMPOntologiesAndExamples/">
<!ENTITY owl "http://www.w3.org/2002/07/owl#">
<!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<!ENTITY rdfs "http://www.w3.org/2000/01/rdf-schema#">
<!ENTITY skos "http://www.w3.org/2004/02/skos/core#">
<!ENTITY xsd "http://www.w3.org/2001/XMLSchema#">
]>
<rdf:RDF xml:base="https://spec.pistoiaalliance.org/idmp/ontology/AboutIDMPDev-ReferenceIndividuals/"
<rdf:RDF xml:base="https://spec.pistoiaalliance.org/idmp/ontology/AboutIDMPOntologiesAndExamples/"
xmlns:dct="http://purl.org/dc/terms/"
xmlns:cmns-av="https://www.omg.org/spec/Commons/AnnotationVocabulary/"
xmlns:idmp-dev-ref="https://spec.pistoiaalliance.org/idmp/ontology/AboutIDMPDev-ReferenceIndividuals/"
xmlns:idmp-examples-about="https://spec.pistoiaalliance.org/idmp/ontology/AboutIDMPOntologiesAndExamples/"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:skos="http://www.w3.org/2004/02/skos/core#"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#">

<owl:Ontology rdf:about="https://spec.pistoiaalliance.org/idmp/ontology/AboutIDMPDev-ReferenceIndividuals/">
<owl:Ontology rdf:about="https://spec.pistoiaalliance.org/idmp/ontology/AboutIDMPOntologiesAndExamples/">
<rdfs:label>About IDMP Development - Reference Individuals</rdfs:label>
<dct:abstract>This ontology is provided for the convenience of IDMP users. It loads all of the very latest IDMP production and development ontologies, including reference data and examples based on the contents of GitHub, rather than those that comprise a specific version, such as a quarterly release. Note that while metadata files and other 'load' files, such as the various subject area specific 'all' files, are intentionally excluded, this version of the 'load' file does include all reference data, such as governments and related jurisdictions required for complete IDMP representation.</dct:abstract>
<dct:issued rdf:datatype="&xsd;dateTime">2023-08-18T18:00:00</dct:issued>
Expand Down Expand Up @@ -89,7 +89,7 @@
//
///////////////////////////////////////////////////////////////////////////////////////
-->

<owl:imports rdf:resource="https://www.omg.org/spec/MVF/ISO1087-TerminologyScience/"/>
<owl:imports rdf:resource="https://www.omg.org/spec/MVF/ISO1087-VocabularyForTermsAndDefinitions/"/>
<owl:imports rdf:resource="https://www.omg.org/spec/MVF/MultipleVocabularyFacility/"/>
Expand Down Expand Up @@ -152,7 +152,7 @@
<owl:imports rdf:resource="https://spec.pistoiaalliance.org/idmp/ontology/EXT/Examples/TerlipressinExample/"/>
<owl:imports rdf:resource="https://spec.pistoiaalliance.org/idmp/ontology/EXT/Examples/QlairaExample/"/>

<owl:versionIRI rdf:resource="https://spec.pistoiaalliance.org/idmp/ontology/20231201/AboutIDMPDev-ReferenceIndividuals/"/>
<owl:versionIRI rdf:resource="https://spec.pistoiaalliance.org/idmp/ontology/20231101/AboutIDMPOntologiesAndExamples/"/>


</owl:Ontology>
Expand Down
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