Merge pull request #122 from monarch-initiative/foodon_for_mic

Add FOODON partial import for MIC food terms

Author: kevinschaper

docs/odk-workflows/RepositoryFileStructure.md

@@ -33,6 +33,7 @@ These are the current imports in PHENIO
 | pato | http://purl.obolibrary.org/obo/pato.owl | slme |
 | mpath | http://purl.obolibrary.org/obo/mpath.owl | slme |
 | nbo | http://purl.obolibrary.org/obo/nbo.owl | slme |
+| foodon | http://purl.obolibrary.org/obo/foodon.owl | slme |
 | upheno-bridge | https://raw.githubusercontent.com/obophenotype/upheno/refs/heads/master/src/ontology/components/upheno-bridge.owl | slme |
 | upheno-alignments | https://raw.githubusercontent.com/obophenotype/upheno/refs/heads/master/src/ontology/components/upheno-alignments.owl | slme |
 ## Components

src/ontology/Makefile

@@ -10,7 +10,7 @@
 # More information: https://github.com/INCATools/ontology-development-kit/
 
 # Fingerprint of the configuration file when this Makefile was last generated
-CONFIG_HASH=                54f36db115c6c77e8be9f3c4ce65dc2c04c59ba8bda026bc48bf5607dc7e4345
+CONFIG_HASH=                8a1e7113eb999f6d8e09c96cc08cc2dcec13f87d8e4d4ef643c332d1fa5da07b
 
 
 # ----------------------------------------
@@ -196,7 +196,7 @@ all_main: $(MAIN_FILES)
 # ----------------------------------------
 
 
-IMPORTS =  monochrom ncbigene hgnc so bspo wbls zfs fbdv chebi pr eco bfo ro ncbitaxon-taxslim pato mpath nbo upheno-bridge upheno-alignments
+IMPORTS =  monochrom ncbigene hgnc so bspo wbls zfs fbdv chebi pr eco bfo ro ncbitaxon-taxslim pato mpath nbo foodon upheno-bridge upheno-alignments
 
 IMPORT_ROOTS =  $(IMPORTDIR)/merged_import
 IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl)
@@ -1123,6 +1123,14 @@ mirror-nbo: | $(TMPDIR)
 	$(ROBOT) remove -i $(TMPDIR)/nbo-download.owl --base-iri http://purl.obolibrary.org/obo/NBO_ --axioms external --preserve-structure false --trim false -o $(TMPDIR)/$@.owl
 
 
+## ONTOLOGY: foodon
+.PHONY: mirror-foodon
+.PRECIOUS: $(MIRRORDIR)/foodon.owl
+mirror-foodon: | $(TMPDIR)
+	curl -L $(OBOBASE)/foodon.owl --create-dirs -o $(TMPDIR)/foodon-download.owl --retry 4 --max-time 400 && \
+	$(ROBOT) remove -i $(TMPDIR)/foodon-download.owl --base-iri http://purl.obolibrary.org/obo/FOODON_ --axioms external --preserve-structure false --trim false -o $(TMPDIR)/$@.owl
+
+
 ## ONTOLOGY: upheno-bridge
 .PHONY: mirror-upheno-bridge
 .PRECIOUS: $(MIRRORDIR)/upheno-bridge.owl

src/ontology/imports/foodon_import.owl

@@ -0,0 +1,14 @@
+<?xml version="1.0"?>
+<rdf:RDF
+     xml:base="http://purl.obolibrary.org/obo/"
+     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+     xmlns:owl="http://www.w3.org/2002/07/owl#"
+     xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"
+     xmlns:xml="http://www.w3.org/XML/1998/namespace"
+     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
+     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
+     xmlns:obo="http://purl.obolibrary.org/obo/">
+    <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/phenio/imports/foodon_import.owl"/>
+
+    <!-- This is a placeholder, it will be regenerated when makefile is first executed -->
+</rdf:RDF>

src/ontology/imports/foodon_terms.txt

@@ -0,0 +1,54 @@
+FOODON:00001001
+FOODON:00001040
+FOODON:00001041
+FOODON:00001082
+FOODON:00001088
+FOODON:00001123
+FOODON:00001164
+FOODON:00001169
+FOODON:00001172
+FOODON:00001175
+FOODON:00001240
+FOODON:00001257
+FOODON:00001264
+FOODON:00001274
+FOODON:00001275
+FOODON:00001564
+FOODON:00001620
+FOODON:00001666
+FOODON:00001687
+FOODON:00001895
+FOODON:00001997
+FOODON:00002050
+FOODON:00002055
+FOODON:00002075
+FOODON:00002255
+FOODON:00002269
+FOODON:00002320
+FOODON:00002323
+FOODON:00002479
+FOODON:00002644
+FOODON:00002668
+FOODON:00002669
+FOODON:00002923
+FOODON:00003029
+FOODON:00003094
+FOODON:00003205
+FOODON:00003208
+FOODON:00003429
+FOODON:00003443
+FOODON:00003521
+FOODON:00003523
+FOODON:00003534
+FOODON:00003600
+FOODON:00004387
+FOODON:00004697
+FOODON:02020157
+FOODON:02020913
+FOODON:03301410
+FOODON:03301415
+FOODON:03304999
+FOODON:03306867
+FOODON:03306936
+FOODON:03411116
+FOODON:03411222

src/ontology/phenio-odk.yaml

@@ -125,7 +125,11 @@ import_group:
       make_base: TRUE
       base_iris:
         - http://purl.obolibrary.org/obo/NBO_
-    
+    - id: foodon
+      make_base: TRUE
+      base_iris:
+        - http://purl.obolibrary.org/obo/FOODON_
+
     # Bridge Ontologies (Phenotypes) - we import these as import modules to only get the bridging axioms relevant to PHENIO
     - id: upheno-bridge
       mirror_from: https://raw.githubusercontent.com/obophenotype/upheno/refs/heads/master/src/ontology/components/upheno-bridge.owl

src/ontology/phenio.Makefile

@@ -116,7 +116,6 @@ phenio-full.owl: $(TMPDIR)/$(ONT)-full-unreasoned.owl $(MAPPINGDIR)/cl.sssom.tsv
 		remove --select "<http://purl.obolibrary.org/obo/PCO_*>" \
 		remove --select "<hhttps://purl.brain-bican.org/ontology/mbao/MBA_*>" \
 		remove --select "<http://purl.obolibrary.org/obo/CLM_*>" \
-		remove --select "<http://purl.obolibrary.org/obo/FOODON_*>" \
 		remove --select "<http://purl.obolibrary.org/obo/PO_*>" \
 		remove --select "<http://purl.obolibrary.org/obo/BTO_*>" \
 		remove --select "<http://purl.obolibrary.org/obo/RnorDv_*>" \