From f5c7b85f07b65803bc9b78701a2cfd0b49c40833 Mon Sep 17 00:00:00 2001 From: matentzn Date: Sun, 5 Apr 2026 06:10:08 +0000 Subject: [PATCH] Integrate MGI MP-HP lexical mappings into build (#1013) https://claude.ai/code/session_01ChK2mm7BcsKrL7Hwjksw4f --- .gitignore | 1 + src/ontology/Makefile | 12 +++++++++--- 2 files changed, 10 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index f8cfb6a0..54347507 100644 --- a/.gitignore +++ b/.gitignore @@ -323,3 +323,4 @@ src/ontology/reports/xrefs.tsv src/ontology/imports/*.json /src/metadata src/mappings/*.owl +.claude/ diff --git a/src/ontology/Makefile b/src/ontology/Makefile index 2c7e73df..ea62d076 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -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) @@ -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) @@ -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 @@ -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 # ----------------------------------------