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IDMP-535 - Merge branch 'master' of https://github.com/edmcouncil/idmp
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…into IDMP-535 and address conflicts

Signed-off-by: Elisa Kendall <ekendall@thematix.com>
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ElisaKendall committed Dec 14, 2023
2 parents 352201c + ecf3e8d commit 34257b7
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47 changes: 47 additions & 0 deletions .github/workflows/spellcheck_run.yml
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# This workflow will run spellchecking for IDMP project

name: IDMP Spellcheck Test

on:
push:
pull_request:
branches: ["master"]

permissions:
contents: read

jobs:
spellcheck:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- name: Set up Python 3.10
uses: actions/setup-python@v3
with:
python-version: "3.10"
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install -r etc/testing/spelling/requirements.txt
- name: Install robot
run: |
sudo wget --no-verbose -m -nH -nd -P /usr/bin https://raw.githubusercontent.com/ontodev/robot/master/bin/robot
sudo wget --no-verbose -m -nH -nd -P /usr/bin https://github.com/ontodev/robot/releases/latest/download/robot.jar
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
- 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
if [ $? != 0 ];
then
exit $?
fi
- name: Archive logfile
uses: actions/upload-artifact@v3
if: always()
with:
name: logifle
path: spellcheck_log.log

5 changes: 1 addition & 4 deletions .github/workflows/unit_tests_run.yml
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Expand Up @@ -93,10 +93,7 @@ jobs:
done
- name: Combine GSRS with IDMP
run: |
sudo wget --no-verbose -m -nH -nd https://idmp-datasets.s3.eu-central-1.amazonaws.com/GSRS/gsrs-active-moiety.ttl
sudo wget --no-verbose -m -nH -nd https://idmp-datasets.s3.eu-central-1.amazonaws.com/GSRS/gsrs-dct-identifier.ttl
sudo wget --no-verbose -m -nH -nd https://idmp-datasets.s3.eu-central-1.amazonaws.com/GSRS/gsrs-skos-altLabel.ttl
source_files=(gsrs-transformed.ttl AboutIDMPDev-ReferenceIndividuals.ttl gsrs-active-moiety.ttl gsrs-dct-identifier.ttl gsrs-skos-altLabel.ttl)
source_files=(gsrs-transformed.ttl AboutIDMPDev-ReferenceIndividuals.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
Expand Down
24 changes: 21 additions & 3 deletions AboutIDMPDev-ReferenceIndividuals.rdf
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Expand Up @@ -40,7 +40,6 @@
<owl:imports rdf:resource="https://www.omg.org/spec/Commons/Classifiers/"/>
<owl:imports rdf:resource="https://www.omg.org/spec/Commons/CodesAndCodeSets/"/>
<owl:imports rdf:resource="https://www.omg.org/spec/Commons/Collections/"/>
<owl:imports rdf:resource="https://www.omg.org/spec/Commons/RolesAndCompositions/"/>
<owl:imports rdf:resource="https://www.omg.org/spec/Commons/ContextualDesignators/"/>
<owl:imports rdf:resource="https://www.omg.org/spec/Commons/ContextualIdentifiers/"/>
<owl:imports rdf:resource="https://www.omg.org/spec/Commons/DatesAndTimes/"/>
Expand All @@ -61,6 +60,7 @@
<owl:imports rdf:resource="https://www.omg.org/spec/Commons/QuantitiesAndUnits/"/>
<owl:imports rdf:resource="https://www.omg.org/spec/Commons/RegistrationAuthorities/"/>
<owl:imports rdf:resource="https://www.omg.org/spec/Commons/RegulatoryAgencies/"/>
<owl:imports rdf:resource="https://www.omg.org/spec/Commons/RolesAndCompositions/"/>
<owl:imports rdf:resource="https://www.omg.org/spec/Commons/StatisticalMeasures/"/>
<owl:imports rdf:resource="https://www.omg.org/spec/Commons/StructuredCollections/"/>
<owl:imports rdf:resource="https://www.omg.org/spec/Commons/TextDatatype/"/>
Expand Down Expand Up @@ -90,6 +90,7 @@
///////////////////////////////////////////////////////////////////////////////////////
-->

<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 @@ -122,6 +123,20 @@
<owl:imports rdf:resource="https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO21090-HarmonizedDatatypes/"/>
<owl:imports rdf:resource="https://spec.pistoiaalliance.org/idmp/ontology/ISO/MedicalDictionaryForRegulatoryActivities/"/>


<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Informative Semantic Publishing and Referencing (SPAR) Ontology Imports
//
///////////////////////////////////////////////////////////////////////////////////////
-->

<owl:imports rdf:resource="http://purl.org/orb/1.0/"/>
<owl:imports rdf:resource="http://purl.org/spar/deo"/>
<owl:imports rdf:resource="http://purl.org/spar/doco"/>


<!--
///////////////////////////////////////////////////////////////////////////////////////
//
Expand All @@ -130,14 +145,17 @@
///////////////////////////////////////////////////////////////////////////////////////
-->

<owl:imports rdf:resource="https://spec.pistoiaalliance.org/idmp/ontology/EXT/Extensions/DocumentComponents/"/>
<owl:imports rdf:resource="https://spec.pistoiaalliance.org/idmp/ontology/EXT/Extensions/UnifiedCodeForUnitsOfMeasure/"/>
<owl:imports rdf:resource="https://spec.pistoiaalliance.org/idmp/ontology/EXT/Examples/AmlodipineExample/"/>
<owl:imports rdf:resource="https://spec.pistoiaalliance.org/idmp/ontology/EXT/Examples/CellCeptExample/"/>
<owl:imports rdf:resource="https://spec.pistoiaalliance.org/idmp/ontology/EXT/Examples/EuropeanUnionClinicalTrialsRegister/"/>
<owl:imports rdf:resource="https://spec.pistoiaalliance.org/idmp/ontology/EXT/Examples/InfanrixHexaExample/"/>
<owl:imports rdf:resource="https://spec.pistoiaalliance.org/idmp/ontology/EXT/Examples/QlairaExample/"/>
<owl:imports rdf:resource="https://spec.pistoiaalliance.org/idmp/ontology/EXT/Examples/TerlipressinExample/"/>
<owl:versionIRI rdf:resource="https://spec.pistoiaalliance.org/idmp/ontology/20230901/AboutIDMPDev-ReferenceIndividuals/"/>

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


</owl:Ontology>

</rdf:RDF>
7 changes: 4 additions & 3 deletions AboutIDMPDev.rdf
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Expand Up @@ -40,7 +40,6 @@
<owl:imports rdf:resource="https://www.omg.org/spec/Commons/Classifiers/"/>
<owl:imports rdf:resource="https://www.omg.org/spec/Commons/CodesAndCodeSets/"/>
<owl:imports rdf:resource="https://www.omg.org/spec/Commons/Collections/"/>
<owl:imports rdf:resource="https://www.omg.org/spec/Commons/RolesAndCompositions/"/>
<owl:imports rdf:resource="https://www.omg.org/spec/Commons/ContextualDesignators/"/>
<owl:imports rdf:resource="https://www.omg.org/spec/Commons/ContextualIdentifiers/"/>
<owl:imports rdf:resource="https://www.omg.org/spec/Commons/DatesAndTimes/"/>
Expand All @@ -61,6 +60,7 @@
<owl:imports rdf:resource="https://www.omg.org/spec/Commons/QuantitiesAndUnits/"/>
<owl:imports rdf:resource="https://www.omg.org/spec/Commons/RegistrationAuthorities/"/>
<owl:imports rdf:resource="https://www.omg.org/spec/Commons/RegulatoryAgencies/"/>
<owl:imports rdf:resource="https://www.omg.org/spec/Commons/RolesAndCompositions/"/>
<owl:imports rdf:resource="https://www.omg.org/spec/Commons/StatisticalMeasures/"/>
<owl:imports rdf:resource="https://www.omg.org/spec/Commons/StructuredCollections/"/>
<owl:imports rdf:resource="https://www.omg.org/spec/Commons/TextDatatype/"/>
Expand Down Expand Up @@ -89,6 +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 @@ -118,8 +119,8 @@
<owl:imports rdf:resource="https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11615-MedicinalProducts/"/>
<owl:imports rdf:resource="https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11616-PharmaceuticalProducts/"/>
<owl:imports rdf:resource="https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO21090-HarmonizedDatatypes/"/>

<owl:versionIRI rdf:resource="https://spec.pistoiaalliance.org/idmp/ontology/20230901/AboutIDMPDev/"/>
<owl:imports rdf:resource="https://spec.pistoiaalliance.org/idmp/ontology/ISO/MedicalDictionaryForRegulatoryActivities/"/>
<owl:versionIRI rdf:resource="https://spec.pistoiaalliance.org/idmp/ontology/20231201/AboutIDMPDev/"/>
</owl:Ontology>

</rdf:RDF>
5 changes: 3 additions & 2 deletions AboutIDMPProd-ReferenceIndividuals.rdf
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Expand Up @@ -40,7 +40,6 @@
<owl:imports rdf:resource="https://www.omg.org/spec/Commons/Classifiers/"/>
<owl:imports rdf:resource="https://www.omg.org/spec/Commons/CodesAndCodeSets/"/>
<owl:imports rdf:resource="https://www.omg.org/spec/Commons/Collections/"/>
<owl:imports rdf:resource="https://www.omg.org/spec/Commons/RolesAndCompositions/"/>
<owl:imports rdf:resource="https://www.omg.org/spec/Commons/ContextualDesignators/"/>
<owl:imports rdf:resource="https://www.omg.org/spec/Commons/ContextualIdentifiers/"/>
<owl:imports rdf:resource="https://www.omg.org/spec/Commons/DatesAndTimes/"/>
Expand All @@ -61,6 +60,7 @@
<owl:imports rdf:resource="https://www.omg.org/spec/Commons/QuantitiesAndUnits/"/>
<owl:imports rdf:resource="https://www.omg.org/spec/Commons/RegistrationAuthorities/"/>
<owl:imports rdf:resource="https://www.omg.org/spec/Commons/RegulatoryAgencies/"/>
<owl:imports rdf:resource="https://www.omg.org/spec/Commons/RolesAndCompositions/"/>
<owl:imports rdf:resource="https://www.omg.org/spec/Commons/StatisticalMeasures/"/>
<owl:imports rdf:resource="https://www.omg.org/spec/Commons/TextDatatype/"/>

Expand Down Expand Up @@ -89,6 +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 All @@ -108,7 +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/20230801/AboutIDMPProd-ReferenceIndividuals/"/>
<owl:versionIRI rdf:resource="https://spec.pistoiaalliance.org/idmp/ontology/20231201/AboutIDMPProd-ReferenceIndividuals/"/>

</owl:Ontology>

Expand Down
5 changes: 3 additions & 2 deletions AboutIDMPProd.rdf
Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,6 @@
<owl:imports rdf:resource="https://www.omg.org/spec/Commons/Classifiers/"/>
<owl:imports rdf:resource="https://www.omg.org/spec/Commons/CodesAndCodeSets/"/>
<owl:imports rdf:resource="https://www.omg.org/spec/Commons/Collections/"/>
<owl:imports rdf:resource="https://www.omg.org/spec/Commons/RolesAndCompositions/"/>
<owl:imports rdf:resource="https://www.omg.org/spec/Commons/ContextualDesignators/"/>
<owl:imports rdf:resource="https://www.omg.org/spec/Commons/ContextualIdentifiers/"/>
<owl:imports rdf:resource="https://www.omg.org/spec/Commons/DatesAndTimes/"/>
Expand All @@ -54,6 +53,7 @@
<owl:imports rdf:resource="https://www.omg.org/spec/Commons/QuantitiesAndUnits/"/>
<owl:imports rdf:resource="https://www.omg.org/spec/Commons/RegistrationAuthorities/"/>
<owl:imports rdf:resource="https://www.omg.org/spec/Commons/RegulatoryAgencies/"/>
<owl:imports rdf:resource="https://www.omg.org/spec/Commons/RolesAndCompositions/"/>
<owl:imports rdf:resource="https://www.omg.org/spec/Commons/StatisticalMeasures/"/>
<owl:imports rdf:resource="https://www.omg.org/spec/Commons/TextDatatype/"/>

Expand Down Expand Up @@ -81,6 +81,7 @@
///////////////////////////////////////////////////////////////////////////////////////
-->

<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 @@ -100,7 +101,7 @@
<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/20230801/AboutIDMPProd/"/>
<owl:versionIRI rdf:resource="https://spec.pistoiaalliance.org/idmp/ontology/20231201/AboutIDMPProd/"/>

</owl:Ontology>

Expand Down
38 changes: 38 additions & 0 deletions CMNS/AsianJurisdiction/catalog-v001.xml
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@@ -0,0 +1,38 @@
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<catalog xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog" prefer="public">
<uri id="8ed7afe9-aef5-41cc-b33c-9a84bc027fdb" name="https://www.omg.org/spec/Commons/AnnotationVocabulary/" uri="../AnnotationVocabulary.rdf" />
<uri id="d4d02968-0f5e-4c32-ac56-2fd8b47111bf" name="https://www.omg.org/spec/Commons/AsianJurisdiction/WesternAsiaGovernmentEntitiesAndJurisdictions/" uri="../AsianJurisdiction/WesternAsiaGovernmentEntitiesAndJurisdictions.rdf" />
<uri id="15a1efae-4df1-4736-9b8a-adf3e392fe3d" name="https://www.omg.org/spec/Commons/Classifiers/" uri="../Classifiers.rdf" />
<uri id="9a8379a1-2ec9-477c-b4a6-0cf746afacc8" name="https://www.omg.org/spec/Commons/CodesAndCodeSets/" uri="../CodesAndCodeSets.rdf" />
<uri id="479347ac-ee5e-4ac2-9565-65285dece0ca" name="https://www.omg.org/spec/Commons/Collections/" uri="../Collections.rdf" />
<uri id="User Entered Import Resolution" name="https://www.omg.org/spec/Commons/RolesAndCompositions/" uri="../RolesAndCompositions.rdf"/>
<uri id="236fa49c-2305-4cee-b3b4-8b11932b69b4" name="https://www.omg.org/spec/Commons/ContextualDesignators/" uri="../ContextualDesignators.rdf" />
<uri id="97fe73fd-23ac-499f-aa10-9ffd83db1220" name="https://www.omg.org/spec/Commons/ContextualIdentifiers/" uri="../ContextualIdentifiers.rdf" />
<uri id="c7507de1-ae84-4bb5-b5a8-ff4a1f5e751b" name="https://www.omg.org/spec/Commons/DatesAndTimes/" uri="../DatesAndTimes.rdf" />
<uri id="242453c2-c0b3-4fba-ab3b-8d5291b5d3f2" name="https://www.omg.org/spec/Commons/Designators/" uri="../Designators.rdf" />
<uri id="9ceda4c2-d336-4fab-9322-ba57bbcf7404" name="https://www.omg.org/spec/Commons/Documents/" uri="../Documents.rdf" />
<uri id="db68eaba-d238-4b68-bbeb-a5abec6f5b0c" name="https://www.omg.org/spec/Commons/EuropeanJurisdiction/EasternEuropeGovernmentEntitiesAndJurisdictions/" uri="../EuropeanJurisdiction/EasternEuropeGovernmentEntitiesAndJurisdictions.rdf" />
<uri id="21804c88-6b93-429c-9300-bd3b5bf257e5" name="https://www.omg.org/spec/Commons/EuropeanJurisdiction/EUGovernmentEntitiesAndJurisdictions/" uri="../EuropeanJurisdiction/EUGovernmentEntitiesAndJurisdictions.rdf" />
<uri id="64667615-dbf3-4d11-9402-f72777c3579e" name="https://www.omg.org/spec/Commons/EuropeanJurisdiction/NorthernEuropeGovernmentEntitiesAndJurisdictions/" uri="../EuropeanJurisdiction/NorthernEuropeGovernmentEntitiesAndJurisdictions.rdf" />
<uri id="16ef2be4-e665-4b35-b495-257874fab707" name="https://www.omg.org/spec/Commons/EuropeanJurisdiction/SouthernEuropeGovernmentEntitiesAndJurisdictions/" uri="../EuropeanJurisdiction/SouthernEuropeGovernmentEntitiesAndJurisdictions.rdf" />
<uri id="5b48c004-5d20-4f82-ae39-3d8fbcb0d103" name="https://www.omg.org/spec/Commons/EuropeanJurisdiction/UKGovernmentEntitiesAndJurisdictions/" uri="../EuropeanJurisdiction/UKGovernmentEntitiesAndJurisdictions.rdf" />
<uri id="cb55761f-309f-49bc-bbf3-e712fe78a723" name="https://www.omg.org/spec/Commons/EuropeanJurisdiction/WesternEuropeGovernmentEntitiesAndJurisdictions/" uri="../EuropeanJurisdiction/WesternEuropeGovernmentEntitiesAndJurisdictions.rdf" />
<uri id="75a31fc7-4cf4-448a-ae66-64c4676ac09c" name="https://www.omg.org/spec/Commons/GovernmentEntities/" uri="../GovernmentEntities.rdf" />
<uri id="7191dd77-8051-4ae4-9cd0-af4568f99584" name="https://www.omg.org/spec/Commons/Identifiers/" uri="../Identifiers.rdf" />
<uri id="2d8323a2-7218-43d7-9551-da62f6cda487" name="https://www.omg.org/spec/Commons/Locations/" uri="../Locations.rdf" />
<uri id="a54c8306-482c-4912-9758-2716a18902d7" name="https://www.omg.org/spec/Commons/MappingDatesAndTimesToOWLTime/" uri="../MappingDatesAndTimesToOWLTime.rdf" />
<uri id="effea865-d2d6-4d72-8d47-88b502301d20" name="https://www.omg.org/spec/Commons/Organizations/" uri="../Organizations.rdf" />
<uri id="a874d4b6-3465-4834-a9db-755fa37784a5" name="https://www.omg.org/spec/Commons/PartiesAndSituations/" uri="../PartiesAndSituations.rdf" />
<uri id="82d1e8a7-ccdf-4c05-a626-d742d0679734" name="https://www.omg.org/spec/Commons/ProductsAndServices/" uri="../ProductsAndServices.rdf" />
<uri id="6be63fb4-fc66-4d02-aaa8-29be076fe3f1" name="https://www.omg.org/spec/Commons/QuantitiesAndUnits/" uri="../QuantitiesAndUnits.rdf" />
<uri id="e720db85-ca87-4e45-a3bd-c802f0d90895" name="https://www.omg.org/spec/Commons/RegistrationAuthorities/" uri="../RegistrationAuthorities.rdf" />
<uri id="b28cc417-03d3-4e1d-b3d3-658e41939d12" name="https://www.omg.org/spec/Commons/RegulatoryAgencies/" uri="../RegulatoryAgencies.rdf" />
<uri id="235b1d04-c09a-45bd-9da7-13683e7b841d" name="https://www.omg.org/spec/Commons/StatisticalMeasures/" uri="../StatisticalMeasures.rdf" />
<uri id="5fc843ca-cf16-4ea0-9977-efdd8a583c9b" name="https://www.omg.org/spec/Commons/StructuredCollections/" uri="../StructuredCollections.rdf" />
<uri id="c9def58c-9ed0-4373-bb55-2fa09eeb620d" name="https://www.omg.org/spec/Commons/TextDatatype/" uri="../TextDatatype.rdf" />
<uri id="9c8fa174-dd64-438c-9cf6-bbfe8ddd41ad" name="https://www.omg.org/spec/LCC/Countries/CountryRepresentation/" uri="../../LCC/Countries/CountryRepresentation.rdf" />
<uri id="7f4f0c9b-1f36-4d38-a8e0-c33721347d77" name="https://www.omg.org/spec/LCC/Countries/ISO3166-1-CountryCodes/" uri="../../LCC/Countries/ISO3166-1-CountryCodes.rdf" />
<uri id="d35f6b37-c010-4be1-9ac1-b8dc70a93e2f" name="https://www.omg.org/spec/LCC/Languages/ISO639-1-LanguageCodes/" uri="../../LCC/Languages/ISO639-1-LanguageCodes.rdf" />
<uri id="41c08e30-7592-46a4-946d-6ee305b7be19" name="https://www.omg.org/spec/LCC/Languages/ISO639-2-LanguageCodes/" uri="../../LCC/Languages/ISO639-2-LanguageCodes.rdf" />
<uri id="33e738ac-35b3-40a5-923b-f85406635ea1" name="https://www.omg.org/spec/LCC/Languages/LanguageRepresentation/" uri="../../LCC/Languages/LanguageRepresentation.rdf" />
</catalog>
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