Merge pull request #252 from obophenotype/swisslipid-import

Add Swisslipid import to OBA

.gitignore

@@ -60,3 +60,5 @@ src/ontology/run.sh.env
 /oba-baseplus.*
 *.db
 *.gz
+src/ontology/imports/lipidmaps_import.owl
+src/ontology/imports/swisslipids_import.owl

docs/editors-guide.md

@@ -99,6 +99,13 @@ When creating new OBA terms using DOSDP patterns for example the [entity-attribu
 
 Sometimes, a new term you are using in a DOSDP pattern is *not yet* in a slim. So you will have to *refresh* the slim first. 
 
+### Refresh LIPID Maps
+
+LIPID map is currently (03.06.2023) not imported, but curated manually, because https://www.lipidmaps.org/resources/sparql does not work. To update the LIPID maps imports, you have to
+
+- Add a LIPID term to https://github.com/obophenotype/bio-attribute-ontology/blob/master/src/templates/external.tsv
+- When refreshing the imports in the usual way, this TSV file (a ROBOT template) is built in place of a proper LIPID MAPS mirror.
+
 ### Refresh PRO Slim:
 
 *Note*: you will need at least 32 GB RAM for this

docs/odk-workflows/RepositoryFileStructure.md

@@ -32,6 +32,8 @@ These are the current imports in OBA
 | so | http://purl.obolibrary.org/obo/so.owl | None |
 | po | http://purl.obolibrary.org/obo/po.owl | None |
 | bfo | http://purl.obolibrary.org/obo/bfo.owl | None |
+| swisslipids | http://purl.obolibrary.org/obo/swisslipids.owl | None |
+| lipidmaps | http://purl.obolibrary.org/obo/lipidmaps.owl | None |
 
 ## Components
 Components, in contrast to imports, are considered full members of the ontology. This means that any axiom in a component is also included in the ontology base - which means it is considered _native_ to the ontology. While this sounds complicated, consider this: conceptually, no component should be part of more than one ontology. If that seems to be the case, we are most likely talking about an import. Components are often not needed for ontologies, but there are some use cases:

src/ontology/Makefile

@@ -1,7 +1,7 @@
 # ----------------------------------------
 # Makefile for oba
 # Generated using ontology-development-kit
-# ODK Version: v1.4
+# ODK Version: v1.4.1
 # ----------------------------------------
 # IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use oba.Makefile instead
 
@@ -44,7 +44,7 @@ REPORT_PROFILE_OPTS =       --profile $(ROBOT_PROFILE)
 OBO_FORMAT_OPTIONS =        
 SPARQL_VALIDATION_CHECKS =  equivalent-classes owldef-self-reference 
 SPARQL_EXPORTS =            basic-report 
-ODK_VERSION_MAKEFILE =      v1.4
+ODK_VERSION_MAKEFILE =      v1.4.1
 
 TODAY ?=                    $(shell date +%Y-%m-%d)
 OBODATE ?=                  $(shell date +'%d:%m:%Y %H:%M')
@@ -114,7 +114,7 @@ all_main: $(MAIN_FILES)
 # ----------------------------------------
 
 
-IMPORTS =  ro chebi goplus go pato omo hp mondo ncbitaxon uberon cl nbo pr so po bfo
+IMPORTS =  ro chebi goplus go pato omo hp mondo ncbitaxon uberon cl nbo pr so po bfo swisslipids lipidmaps
 
 IMPORT_ROOTS =  $(IMPORTDIR)/merged_import
 IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl)
@@ -506,8 +506,10 @@ mirror-uberon: | $(TMPDIR)
 .PHONY: mirror-cl
 .PRECIOUS: $(MIRRORDIR)/cl.owl
 mirror-cl: | $(TMPDIR)
-	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/cl/cl-base.owl --create-dirs -o $(MIRRORDIR)/cl.owl --retry 4 --max-time 200 &&\
-		$(ROBOT) convert -i $(MIRRORDIR)/cl.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
+	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/cl.owl --create-dirs -o $(MIRRORDIR)/cl.owl --retry 4 --max-time 200 &&\
+		$(ROBOT) convert -i $(MIRRORDIR)/cl.owl -o $@.tmp.owl && \
+		$(ROBOT) remove -i $@.tmp.owl --base-iri $(URIBASE)/CL --axioms external --preserve-structure false --trim false -o $@.tmp.owl &&\
+		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
 
 
 ## ONTOLOGY: nbo
@@ -556,6 +558,20 @@ mirror-bfo: | $(TMPDIR)
 		$(ROBOT) remove -i $@.tmp.owl --base-iri $(URIBASE)/BFO --axioms external --preserve-structure false --trim false -o $@.tmp.owl &&\
 		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
 
+
+## ONTOLOGY: swisslipids
+.PHONY: mirror-swisslipids
+.PRECIOUS: $(MIRRORDIR)/swisslipids.owl
+$(MIRRORDIR)/swisslipids.owl: 
+	echo "ERROR: You have configured your default mirror type to be custom; this behavior needs to be overwritten in oba.Makefile!" && false
+
+
+## ONTOLOGY: lipidmaps
+.PHONY: mirror-lipidmaps
+.PRECIOUS: $(MIRRORDIR)/lipidmaps.owl
+$(MIRRORDIR)/lipidmaps.owl: 
+	echo "ERROR: You have configured your default mirror type to be custom; this behavior needs to be overwritten in oba.Makefile!" && false
+
 ALL_MIRRORS = $(patsubst %, $(MIRRORDIR)/%.owl, $(IMPORTS))
 MERGE_MIRRORS = true
 
@@ -667,7 +683,7 @@ DOSDP_PATTERN_NAMES_DEFAULT = $(strip $(patsubst %.tsv,%, $(notdir $(wildcard $(
 $(DOSDP_OWL_FILES_DEFAULT): $(EDIT_PREPROCESSED) $(DOSDP_TSV_FILES_DEFAULT) $(ALL_PATTERN_FILES)
 	if [ $(PAT) = true ] && [ "${DOSDP_PATTERN_NAMES_DEFAULT}" ]; then $(DOSDPT) generate --catalog=catalog-v001.xml \
     --infile=$(PATTERNDIR)/data/default/ --template=$(PATTERNDIR)/dosdp-patterns --batch-patterns="$(DOSDP_PATTERN_NAMES_DEFAULT)" \
-    --ontology=$< --obo-prefixes=true --outfile=$(PATTERNDIR)/data/default; fi
+    --ontology=$< --obo-prefixes=true --prefixes=config/prefixes.yaml --outfile=$(PATTERNDIR)/data/default; fi
 
 
 # Generate template file seeds

src/ontology/components/obsoletes.owl

@@ -7,8 +7,8 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/oba/components/obsoletes.owl>
-<http://purl.obolibrary.org/obo/oba/releases/2023-06-16/components/obsoletes.owl>
-Annotation(owl:versionInfo "2023-06-16")
+<http://purl.obolibrary.org/obo/oba/releases/2023-06-23/components/obsoletes.owl>
+Annotation(owl:versionInfo "2023-06-23")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/OBA_0000037>))
 Declaration(Class(<http://purl.obolibrary.org/obo/OBA_0000039>))

src/ontology/components/synonyms.owl

@@ -7,8 +7,8 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/oba/components/synonyms.owl>
-<http://purl.obolibrary.org/obo/oba/releases/2023-06-16/components/synonyms.owl>
-Annotation(owl:versionInfo "2023-06-16")
+<http://purl.obolibrary.org/obo/oba/releases/2023-06-23/components/synonyms.owl>
+Annotation(owl:versionInfo "2023-06-23")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/OBA_0002546>))
 Declaration(Class(<http://purl.obolibrary.org/obo/OBA_0002565>))

src/ontology/config/prefixes.yaml

@@ -0,0 +1,2 @@
+LM: "https://bioregistry.io/lipidmaps:"
+SLM: "https://swisslipids.org/rdf/SLM_"

src/ontology/imports/lipidmaps_terms.txt

@@ -0,0 +1,3 @@
+LM:LMST03020077
+LM:LMPK12010207
+LM:LMSP00000010