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CARO to Uberon term replacement for #695 (#722)
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* Add OBI as source for organism

Will switch to COB once it has OBI:0100026

* CARO to UBERON term replacement

Note a number of object property domain and range get switched.

* makefile simplification

* Update src/ontology/catalog-v001.xml

Co-authored-by: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>

* Update src/ontology/catalog-v001.xml

Co-authored-by: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>

* Update src/ontology/ro-edit.owl

Co-authored-by: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>

* Update src/ontology/ro-edit.owl

Co-authored-by: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>

* extra slash

* drops neuron projection bundle parenting to UBERON_0001062

* Update catalog-v001.xml

---------

Co-authored-by: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>
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@ddooley @matentzn
ddooley and matentzn authored Jun 12, 2023
1 parent e4c555b commit 9e6b6e5
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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 @@ -354,16 +354,6 @@ $(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 @@ -388,6 +378,16 @@ $(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 @@ -506,16 +506,6 @@ 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 @@ -537,6 +527,15 @@ 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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Original file line number Diff line number Diff line change
@@ -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>
<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/uberon_import.owl" uri="imports/uberon_import.owl"/>
<uri name="http://purl.obolibrary.org/obo/ro/imports/obi_import.owl" uri="imports/obi_import.owl"/>
<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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