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Merge pull request #5 from berkeleybop/ncit-clip
Pruned NCIT and OBI
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‎docs/odk-workflows/RepoManagement.md‎

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There are a large number of options that can be set to configure your ODK, but we will only discuss a few of them here.
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NOTE for Windows users:
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You may get a cryptic failure such as `Set Illegal Option -` if the update script located in `src/scripts/update_repo.sh`
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was saved using Windows Line endings. These need to change to unix line endings. In Notepad++, for example, you can
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click on Edit->EOL Conversion->Unix LF to change this.
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## Managing imports
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You can use the update repository worflow described on this page to perform the following operations to your imports:

‎docs/odk-workflows/components.md‎

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# Adding components to an ODK repo
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For details on what components are, please see component section of [repository file structure document](../odk-workflows/RepositoryFileStructure.md).
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To add custom components to an ODK repo, please follow the following steps:
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1) Locate your odk yaml file and open it with your favourite text editor (src/ontology/bero-odk.yaml)
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2) Search if there is already a component section to the yaml file, if not add it accordingly, adding the name of your component:
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```
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components:
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products:
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- filename: your-component-name.owl
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```
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3) Add the component to your catalog file (src/ontology/catalog-v001.xml)
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```
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<uri name="http://purl.obolibrary.org/obo/bero/components/your-component-name.owl" uri="components/your-component-name.owl"/>
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```
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4) Add the component to the edit file (src/ontology/bero-edit.obo)
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for .obo formats:
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```
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import: http://purl.obolibrary.org/obo/bero/components/your-component-name.owl
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```
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for .owl formats:
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```
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Import(<http://purl.obolibrary.org/obo/bero/components/your-component-name.owl>)
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```
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5) Refresh your repo by running `sh run.sh make update_repo` - this should create a new file in src/ontology/components.
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6) In your custom makefile (src/ontology/bero.Makefile) add a goal for your custom make file. In this example, the goal is a ROBOT template.
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```
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$(COMPONENTSDIR)/your-component-name.owl: $(SRC) ../templates/your-component-template.tsv
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$(ROBOT) template --template ../templates/your-component-template.tsv \
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annotate --ontology-iri $(ONTBASE)/$@ --output $(COMPONENTSDIR)/your-component-name.owl
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```
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(If using a ROBOT template, do not forget to add your template tsv in src/templates/)
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7) Make the file by running `sh run.sh make components/your-component-name.owl`
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‎src/ontology/Makefile‎

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‎src/ontology/bero-odk.yaml‎

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- id: omo
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- id: ecocore
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use_base: TRUE
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- id: obi
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make_base: TRUE
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- id: to
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make_base: TRUE
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- id: chebi
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- id: mesh
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mirror_from: https://raw.githubusercontent.com/cmungall/mesh2owl/master/mesh-obo.obo
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module_type: custom
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- id: obi
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make_base: TRUE
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module_type: custom
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robot_java_args: '-Xmx20G'
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robot_report:

‎src/ontology/bero.Makefile‎

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#changes here rather than in the main Makefile
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MESH_TERMS_FILE = imports/mesh_terms.txt
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NCIT_TERMS_FILE = imports/ncit_terms.txt
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MAIN_FILES_RELEASE = $(foreach n,$(MAIN_FILES), ../../$(n))
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$(ONT)-full.owl: $(SRC) $(OTHER_SRC) $(IMPORT_FILES)
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$(IMPORTDIR)/ncit_import.owl: $(MIRRORDIR)/ncit.owl $(IMPORTDIR)/ncit_terms_combined.txt
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if [ $(IMP) = true ]; then $(ROBOT) remove -i $< \
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if [ $(IMP) = true ]; then $(ROBOT) extract -i $< \
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--method MIREOT \
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--branch-from-terms $(NCIT_TERMS_FILE) \
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remove \
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--term oboInOwl:hasExactSynonym \
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query --update ../sparql/preprocess-module.ru --update ../sparql/inject-subset-declaration.ru --update ../sparql/postprocess-module.ru \
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annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@; fi
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query --update ../sparql/preprocess-module.ru --update ../sparql/inject-subset-declaration.ru --update ../sparql/postprocess-module.ru \
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annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@; fi
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$(IMPORTDIR)/obi_import.owl: $(MIRRORDIR)/obi.owl $(IMPORTDIR)/obi_terms_combined.txt
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if [ $(IMP) = true ]; then $(ROBOT) remove -i $< \
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--term OBI:0000011 \
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--select "self descendants" \
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--select "owl:deprecated='true'^^xsd:boolean" \
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--signature true \
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query --update ../sparql/preprocess-module.ru --update ../sparql/inject-subset-declaration.ru --update ../sparql/postprocess-module.ru \
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annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@; fi
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deploy_release:
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@test $(GHVERSION)
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ls -alt $(MAIN_FILES_RELEASE)

‎src/ontology/imports/ncit_terms.txt‎

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http://purl.obolibrary.org/obo/NCIT_C12913
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http://purl.obolibrary.org/obo/NCIT_C12219
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http://purl.obolibrary.org/obo/NCIT_C20633
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http://purl.obolibrary.org/obo/NCIT_C17828
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http://purl.obolibrary.org/obo/NCIT_C12218
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http://purl.obolibrary.org/obo/NCIT_C20047
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http://purl.obolibrary.org/obo/NCIT_C7057
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http://purl.obolibrary.org/obo/NCIT_C1908
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http://purl.obolibrary.org/obo/NCIT_C22188
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http://purl.obolibrary.org/obo/NCIT_C22187
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http://purl.obolibrary.org/obo/NCIT_C16612
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http://purl.obolibrary.org/obo/NCIT_C26548
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http://purl.obolibrary.org/obo/NCIT_C97325
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http://purl.obolibrary.org/obo/NCIT_C3910
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http://purl.obolibrary.org/obo/NCIT_C14250

‎src/ontology/imports/ncit_terms_combined.txt‎

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http://purl.obolibrary.org/obo/BERO_0000000
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http://purl.obolibrary.org/obo/NCIT_C12218
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http://purl.obolibrary.org/obo/NCIT_C12219
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http://purl.obolibrary.org/obo/NCIT_C12913
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http://purl.obolibrary.org/obo/NCIT_C14250
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http://purl.obolibrary.org/obo/NCIT_C16612
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http://purl.obolibrary.org/obo/NCIT_C17828
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http://purl.obolibrary.org/obo/NCIT_C1908
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http://purl.obolibrary.org/obo/NCIT_C20047
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http://purl.obolibrary.org/obo/NCIT_C20633
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http://purl.obolibrary.org/obo/NCIT_C22187
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http://purl.obolibrary.org/obo/NCIT_C22188
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http://purl.obolibrary.org/obo/NCIT_C26548
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http://purl.obolibrary.org/obo/NCIT_C3910
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http://purl.obolibrary.org/obo/NCIT_C7057
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http://purl.obolibrary.org/obo/NCIT_C97325
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http://purl.obolibrary.org/obo/bero.owl
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http://purl.org/dc/terms/description
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http://purl.org/dc/terms/license

‎src/ontology/run.sh‎

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# See README-editors.md for more details.
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IMAGE=${IMAGE:-odkfull}
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ODK_JAVA_OPTS=-Xmx20G
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ODK_DEBUG=${ODK_DEBUG:-no}
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TIMECMD=
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if [ x$ODK_DEBUG = xyes ]; then
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# If you wish to change the format string, take care of using
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# non-breaking spaces (U+00A0) instead of normal spaces, to
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# prevent the shell from tokenizing the format string.
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echo "Running ${IMAGE} with ${ODK_JAVA_OPTS} of memory for ROBOT and Java-based pipeline steps."
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TIMECMD="/usr/bin/time -f ### DEBUG STATS ###\nElapsed time: %E\nPeak memory: %M kb"
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fi
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docker run -v $PWD/../../:/work -w /work/src/ontology -e ROBOT_JAVA_ARGS='-Xmx20G' -e JAVA_OPTS='-Xmx20G' --rm -ti obolibrary/$IMAGE $TIMECMD "$@"
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docker run -v $PWD/../../:/work -w /work/src/ontology -e ROBOT_JAVA_ARGS="$ODK_JAVA_OPTS" -e JAVA_OPTS="$ODK_JAVA_OPTS" --rm -ti obolibrary/$IMAGE $TIMECMD "$@"
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case "$@" in
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*update_repo*|*release*)
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echo "Please remember to update your ODK image from time to time: https://oboacademy.github.io/obook/howto/odk-update/."
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;;
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esac

‎src/scripts/update_repo.sh‎

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mkdir -p $ROOTDIR/.github/workflows
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cp -n target/$OID/.github/workflows/qc.yml $ROOTDIR/.github/workflows/qc.yml
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cp -n target/$OID/.github/workflows/docs.yml $ROOTDIR/.github/workflows/docs.yml
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cp target/$OID/.github/workflows/docs.yml $ROOTDIR/.github/workflows/docs.yml
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cp -n target/$OID/mkdocs.yaml $ROOTDIR/
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echo "WARNING: These files should be manually migrated: mkdocs.yaml, .gitignore, src/ontology/catalog.xml (if you added a new import or component)"
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echo "Update successfully completed."
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echo "WARNING: Your QC workflows have not been updated automatically. Please update the ODK version number(s) in .github/workflows/qc.yml."
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echo "Ontology repository update successfully completed."

‎src/sparql/inject-synonymtype-declaration.ru‎

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PREFIX : <http://www.test.com/ns/test#>
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PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
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PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
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INSERT { ?y rdfs:subPropertyOf <http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty> . }
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WHERE {
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?x <http://www.geneontology.org/formats/oboInOwl#hasSynonymType> ?y .
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FILTER(isIRI(?y))
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FILTER(regex(str(?y),"^(http://purl.obolibrary.org/obo/)") || regex(str(?y),"^(http://www.ebi.ac.uk/efo/)") || regex(str(?y),"^(https://w3id.org/biolink/)"))
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}

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