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Add mechanism to retrieve missing CHEBI ids and include them in build #106

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merged 9 commits into from
Jan 30, 2025
Merged

Add mechanism to retrieve missing CHEBI ids and include them in build #106

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5155650
Add target to get missing_phenio_nodes.tsv
caufieldjh Jan 16, 2025
4853c7f
Add target to include new terms in chebi_terms import
caufieldjh Jan 16, 2025
63ba7c6
Include add_chebi_ids target when building PHENIO base
caufieldjh Jan 16, 2025
e1632bf
Put CHEBI terms from Monarch in their own list
caufieldjh Jan 17, 2025
ac2b990
Add target for chebi_terms_combined
caufieldjh Jan 17, 2025
7e10f50
Restructure the /%_terms_combined.txt target
caufieldjh Jan 23, 2025
601a37c
chebi_terms_combined -> chebi
caufieldjh Jan 23, 2025
8ca769f
Restructure terms_combined target again to make it if-else
caufieldjh Jan 23, 2025
00f1a3c
Change CHEBI CURIEs to URIs
caufieldjh Jan 24, 2025
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10 changes: 7 additions & 3 deletions src/ontology/Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -360,9 +360,13 @@ ANNOTATION_PROPERTIES=rdfs:label IAO:0000115
# This pattern uses ROBOT to generate an import module

# Should be able to drop this if robot can just take a big messy list of terms as input.
$(IMPORTDIR)/%_terms_combined.txt: $(IMPORTSEED) $(IMPORTDIR)/%_terms.txt
if [ $(IMP) = true ]; then cat $^ | grep -v ^# | sort | uniq > $@; fi

$(IMPORTDIR)/%_terms_combined.txt: $(IMPORTSEED) $(IMPORTDIR)/%_terms.txt $(TMPDIR)/monarch_chebi_terms.txt
if [ $(IMP) = true ] && [ "$*" = "chebi" ]; then \
echo "Processing chebi terms"; \
cat $(word 1,$^) $(word 3,$^) | grep -v ^# | sort | uniq > $@; \
elif [ $(IMP) = true ]; then \
cat $(word 1,$^) $(word 2,$^) | grep -v ^# | sort | uniq > $@; \
fi

ALL_TERMS_COMBINED = $(patsubst %, $(IMPORTDIR)/%_terms_combined.txt, $(IMPORTS))
$(IMPORTDIR)/merged_terms_combined.txt: $(ALL_TERMS_COMBINED)
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10 changes: 10 additions & 0 deletions src/ontology/phenio.Makefile
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Expand Up @@ -60,6 +60,16 @@ mirror-hgnc: | $(TMPDIR)

endif

# Retrieve list of node IDs expected to be in PHENIO by downstream consumers
# Specifically Monarch
missing_phenio_nodes.tsv: | $(TMPDIR)
curl -L https://data.monarchinitiative.org/monarch-kg-dev/latest/qc/missing_phenio_nodes.tsv --create-dirs --retry 4 --max-time 400 > $@

# Just get the CHEBI IDs
# and change them to URIs
$(TMPDIR)/monarch_chebi_terms.txt: missing_phenio_nodes.tsv
cat $^ | grep CHEBI | cut -f 1 | sed 's/CHEBI:/http:\/\/purl.obolibrary.org\/obo\/CHEBI_/' > $@
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no need for this, ROBOT can deal with CURIEs just fine

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Great, I thought it should be able to handle CURIEs.


################################################################
#### Release files #############################################
################################################################
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