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Integrate MGI MP-HP lexical mappings into build (#1013) #1020

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Integrate MGI MP-HP lexical mappings into build (#1013) #1020

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1 change: 1 addition & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -323,3 +323,4 @@ src/ontology/reports/xrefs.tsv
src/ontology/imports/*.json
/src/metadata
src/mappings/*.owl
.claude/
12 changes: 9 additions & 3 deletions src/ontology/Makefile
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Expand Up @@ -70,7 +70,7 @@ PATTERN_RELEASE_FILES= $(PATTERNDIR)/definitions.owl $(PATTERNDIR)/pattern.
MAPPINGDIR= ../mappings
MAPPING_TESTER= sssom validate
SSSOMPY= sssom
MAPPINGS= apo-go apo-oba apo-pato upheno-species-independent upheno-species-independent-eq upheno-species-independent-manual upheno-lexical upheno-cross-species nbo-go uberon
MAPPINGS= apo-go apo-oba apo-pato upheno-species-independent upheno-species-independent-eq upheno-species-independent-manual upheno-lexical upheno-cross-species nbo-go uberon mp-hp-mgi-lex
MAPPING_RELEASE_FILES= $(foreach n,$(MAPPINGS), $(MAPPINGDIR)/$(n).sssom.tsv)


Expand Down Expand Up @@ -233,7 +233,7 @@ all_subsets: $(SUBSET_FILES)
# ----------------------------------------


MAPPINGS = apo-go apo-oba apo-pato upheno-species-independent upheno-species-independent-eq upheno-species-independent-manual upheno-lexical upheno-cross-species nbo-go uberon
MAPPINGS = apo-go apo-oba apo-pato upheno-species-independent upheno-species-independent-eq upheno-species-independent-manual upheno-lexical upheno-cross-species nbo-go uberon mp-hp-mgi-lex


MAPPING_FILES = $(foreach p, $(MAPPINGS), $(MAPPINGDIR)/$(p).sssom.tsv)
Expand Down Expand Up @@ -595,11 +595,13 @@ $(COMPONENTSDIR)/upheno-manual-curation.owl: $(TEMPLATEDIR)/phenotypes-without-p
$(ANNOTATE_CONVERT_FILE)
.PRECIOUS: $(COMPONENTSDIR)/upheno-manual-curation.owl

$(COMPONENTSDIR)/upheno-bridge.owl: $(MAPPINGDIR)/upheno-species-independent.sssom.tsv $(TMPDIR)/stamp-component-upheno-bridge.owl | all_robot_plugins
$(COMPONENTSDIR)/upheno-bridge.owl: $(MAPPINGDIR)/upheno-species-independent.sssom.tsv $(MAPPINGDIR)/mp-hp-mgi-lex.sssom.tsv $(TMPDIR)/stamp-component-upheno-bridge.owl | all_robot_plugins
$(ROBOT) --add-prefix 'sssom: https://w3id.org/sssom/' \
--add-prefix 'semapv: http://w3id.org/semapv/vocab/' \
sssom:inject --sssom $(MAPPINGDIR)/upheno-species-independent.sssom.tsv \
--create --direct \
sssom:inject --sssom $(MAPPINGDIR)/mp-hp-mgi-lex.sssom.tsv \
--direct \
$(ANNOTATE_CONVERT_FILE)
.PRECIOUS: $(COMPONENTSDIR)/upheno-bridge.owl

Expand Down Expand Up @@ -1063,6 +1065,10 @@ $(MAPPINGDIR)/nbo-go.sssom.tsv:
$(MAPPINGDIR)/uberon.sssom.tsv:
test -f $@

# MGI MP-HP lexical mappings, updated weekly from https://github.com/mapping-commons/mh_mapping_initiative
$(MAPPINGDIR)/mp-hp-mgi-lex.sssom.tsv:
wget -O $@ https://raw.githubusercontent.com/mapping-commons/mh_mapping_initiative/master/mappings/mp_hp_mgi_lex.tsv

# ----------------------------------------
# Release artefacts: export formats
# ----------------------------------------
Expand Down