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CARO to Uberon term replacement for #695 #722

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merged 10 commits into from
Jun 12, 2023
Merged

CARO to Uberon term replacement for #695 #722

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a606ce4
Add OBI as source for organism
ddooley May 27, 2023
a053792
CARO to UBERON term replacement
ddooley May 27, 2023
c3d3906
makefile simplification
ddooley May 27, 2023
ce9c721
Update src/ontology/catalog-v001.xml
ddooley May 29, 2023
58e8278
Update src/ontology/catalog-v001.xml
ddooley May 29, 2023
828a744
Update src/ontology/ro-edit.owl
ddooley May 29, 2023
a5bdcb7
Update src/ontology/ro-edit.owl
ddooley May 29, 2023
5fbe5e1
extra slash
ddooley May 29, 2023
204cd05
drops neuron projection bundle parenting to UBERON_0001062
ddooley Jun 1, 2023
3f18a41
Update catalog-v001.xml
matentzn Jun 12, 2023
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41 changes: 20 additions & 21 deletions src/ontology/Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -109,7 +109,7 @@ all_main: $(MAIN_FILES)
# ----------------------------------------


IMPORTS = omo pato cl envo go caro other orcidio uberon
IMPORTS = omo pato cl envo go other orcidio uberon obi

IMPORT_ROOTS = $(patsubst %, $(IMPORTDIR)/%_import, $(IMPORTS))
IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl)
Expand Down Expand Up @@ -360,16 +360,6 @@ $(IMPORTDIR)/go_import.owl: $(MIRRORDIR)/go.owl $(IMPORTDIR)/go_terms_combined.t
remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) -T $(IMPORTDIR)/go_terms_combined.txt --select complement --select "classes individuals annotation-properties" \
$(ANNOTATE_CONVERT_FILE); fi

## Module for ontology: caro

$(IMPORTDIR)/caro_import.owl: $(MIRRORDIR)/caro.owl $(IMPORTDIR)/caro_terms_combined.txt
if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \
extract -T $(IMPORTDIR)/caro_terms_combined.txt --copy-ontology-annotations true --force true --method BOT \
remove --base-iri $(URIBASE)/CARO --axioms external --preserve-structure false --trim false \
query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru \
remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) -T $(IMPORTDIR)/caro_terms_combined.txt --select complement --select "classes individuals annotation-properties" \
$(ANNOTATE_CONVERT_FILE); fi

## Module for ontology: other

$(IMPORTDIR)/other_import.owl:
Expand All @@ -394,6 +384,16 @@ $(IMPORTDIR)/uberon_import.owl: $(MIRRORDIR)/uberon.owl $(IMPORTDIR)/uberon_term
query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \
$(ANNOTATE_CONVERT_FILE); fi

## Module for ontology: obi

$(IMPORTDIR)/obi_import.owl: $(MIRRORDIR)/obi.owl $(IMPORTDIR)/obi_terms_combined.txt
if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \
extract -T $(IMPORTDIR)/obi_terms_combined.txt --copy-ontology-annotations true --force true --method BOT \
remove --base-iri $(OBOBASE)/OBI --axioms external --preserve-structure false --trim false \
remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) -T $(IMPORTDIR)/obi_terms_combined.txt --select complement \
query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \
$(ANNOTATE_CONVERT_FILE); fi


.PHONY: refresh-imports
refresh-imports:
Expand Down Expand Up @@ -512,16 +512,6 @@ mirror-go: | $(TMPDIR)
mv $@.tmp.owl $(TMPDIR)/$@.owl; fi


## ONTOLOGY: caro
.PHONY: mirror-caro
.PRECIOUS: $(MIRRORDIR)/caro.owl
mirror-caro: | $(TMPDIR)
if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/caro.owl --create-dirs -o $(MIRRORDIR)/caro.owl --retry 4 --max-time 200 &&\
$(ROBOT) convert -i $(MIRRORDIR)/caro.owl -o $@.tmp.owl && \
$(ROBOT) remove -i $@.tmp.owl --base-iri $(URIBASE)/CARO --axioms external --preserve-structure false --trim false -o $@.tmp.owl &&\
mv $@.tmp.owl $(TMPDIR)/$@.owl; fi


## ONTOLOGY: other
## You have configured your default mirror type to no_mirror.

Expand All @@ -543,6 +533,15 @@ mirror-uberon: | $(TMPDIR)
mv $@.tmp.owl $(TMPDIR)/$@.owl; fi


## ONTOLOGY: obi
.PHONY: mirror-obi
.PRECIOUS: $(MIRRORDIR)/obi.owl
mirror-obi: | $(TMPDIR)
if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/obi.owl --create-dirs -o $(MIRRORDIR)/obi.owl --retry 4 --max-time 200 &&\
$(ROBOT) convert -i $(MIRRORDIR)/obi.owl -o $@.tmp.owl &&\
mv $@.tmp.owl $(TMPDIR)/$@.owl; fi


$(MIRRORDIR)/%.owl: mirror-% | $(MIRRORDIR)
if [ $(IMP) = true ] && [ $(MIR) = true ] && [ -f $(TMPDIR)/mirror-$*.owl ]; then if cmp -s $(TMPDIR)/mirror-$*.owl $@ ; then echo "Mirror identical, ignoring."; else echo "Mirrors different, updating." &&\
cp $(TMPDIR)/mirror-$*.owl $@; fi; fi
Expand Down
42 changes: 17 additions & 25 deletions src/ontology/catalog-v001.xml
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@@ -1,28 +1,20 @@
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<catalog prefer="public" xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog">
<group id="Folder Repository, directory=, recursive=false, Auto-Update=false, version=2" prefer="public" xml:base="">


<uri name="http://purl.obolibrary.org/obo/ro/imports/omo_import.owl" uri="imports/omo_import.owl"/>
<uri name="http://purl.obolibrary.org/obo/ro/imports/pato_import.owl" uri="imports/pato_import.owl"/>
<uri name="http://purl.obolibrary.org/obo/ro/imports/cl_import.owl" uri="imports/cl_import.owl"/>
<uri name="http://purl.obolibrary.org/obo/ro/imports/envo_import.owl" uri="imports/envo_import.owl"/>
<uri name="http://purl.obolibrary.org/obo/ro/imports/orcidio_import.owl" uri="imports/orcidio_import.owl"/>
<uri name="http://purl.obolibrary.org/obo/ro/imports/go_import.owl" uri="imports/go_import.owl"/>
<uri name="http://purl.obolibrary.org/obo/ro/imports/caro_import.owl" uri="imports/caro_import.owl"/>

<uri name="http://purl.obolibrary.org/obo/ro/components/core.owl" uri="components/core.owl"/>

<uri name="http://purl.obolibrary.org/obo/ro/components/el-constraints.owl" uri="components/el-constraints.owl"/>

<uri name="http://purl.obolibrary.org/obo/ro/components/generated-axioms.owl" uri="components/generated-axioms.owl"/>

<uri name="http://purl.obolibrary.org/obo/ro/imports/other_import.owl" uri="imports/other_import.owl"/>

<uri name="http://purl.obolibrary.org/obo/ro/components/rohom.owl" uri="components/rohom.owl"/>

<uri name="http://purl.obolibrary.org/obo/ro/components/temporal-intervals.owl" uri="components/temporal-intervals.owl"/>


</group>
<uri id="Imports Wizard Entry" name="http://purl.obolibrary.org/obo/ro/imports/uberon_import.owl" uri="imports/uberon_import.owl"/>
<uri id="Imports Wizard Entry" name="http://purl.obolibrary.org/obo/ro/imports/obi_import.owl" uri="imports/obi_import.owl"/>
<group id="Folder Repository, directory=, recursive=false, Auto-Update=false, version=2" prefer="public" xml:base="">
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<uri name="http://purl.obolibrary.org/obo/ro/imports/omo_import.owl" uri="imports/omo_import.owl"/>
<uri name="http://purl.obolibrary.org/obo/ro/imports/pato_import.owl" uri="imports/pato_import.owl"/>
<uri name="http://purl.obolibrary.org/obo/ro/imports/cl_import.owl" uri="imports/cl_import.owl"/>
<uri name="http://purl.obolibrary.org/obo/ro/imports/envo_import.owl" uri="imports/envo_import.owl"/>
<uri name="http://purl.obolibrary.org/obo/ro/imports/orcidio_import.owl" uri="imports/orcidio_import.owl"/>
<uri name="http://purl.obolibrary.org/obo/ro/imports/go_import.owl" uri="imports/go_import.owl"/>
<uri name="http://purl.obolibrary.org/obo/ro/imports/caro_import.owl" uri="imports/caro_import.owl"/>
<uri name="http://purl.obolibrary.org/obo/ro/components/core.owl" uri="components/core.owl"/>
<uri name="http://purl.obolibrary.org/obo/ro/components/el-constraints.owl" uri="components/el-constraints.owl"/>
<uri name="http://purl.obolibrary.org/obo/ro/components/generated-axioms.owl" uri="components/generated-axioms.owl"/>
<uri name="http://purl.obolibrary.org/obo/ro/imports/other_import.owl" uri="imports/other_import.owl"/>
<uri name="http://purl.obolibrary.org/obo/ro/components/rohom.owl" uri="components/rohom.owl"/>
<uri name="http://purl.obolibrary.org/obo/ro/components/temporal-intervals.owl" uri="components/temporal-intervals.owl"/>
</group>
</catalog>
112 changes: 0 additions & 112 deletions src/ontology/imports/caro_import.owl
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6 changes: 0 additions & 6 deletions src/ontology/imports/caro_terms.txt
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