Build the “composite“ life stages ontology directly in Uberon

.gitignore

@@ -197,7 +197,9 @@ composite-metazoan.*
 composite-metazoan-basic.*
 composite-vertebrate.*
 composite-vertebrate-basic.*
+composite-lifestages.*
 collected-metazoan.*
+collected-lifestages.*
 ext.json
 ext.obo
 ext.owl

src/ontology/Makefile

@@ -1,7 +1,7 @@
 # ----------------------------------------
 # Makefile for uberon
 # Generated using ontology-development-kit
-# ODK Version: v1.5.2
+# ODK Version: v1.5.4
 # ----------------------------------------
 # IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use uberon.Makefile instead
 
@@ -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=                60e47a069bd32a71a48c480dcf88b75d116c5eef7d1f9a55073500ff79968b28
+CONFIG_HASH=                2280340b1810b2a972296e0c511d5e87711793855300136263ac0b8801de9cf3
 
 
 # ----------------------------------------
@@ -47,7 +47,7 @@ REPORT_PROFILE_OPTS =       --profile $(ROBOT_PROFILE)
 OBO_FORMAT_OPTIONS =        
 SPARQL_VALIDATION_CHECKS =  equivalent-classes owldef-self-reference illegal-annotation-property taxon-range orcid-contributor obsolete-replaced_by xrefs-mesh-pattern label-synonym-polysemy id-format 
 SPARQL_EXPORTS =            basic-report 
-ODK_VERSION_MAKEFILE =      v1.5.2
+ODK_VERSION_MAKEFILE =      v1.5.4
 
 TODAY ?=                    $(shell date +%Y-%m-%d)
 OBODATE ?=                  $(shell date +'%d:%m:%Y %H:%M')
@@ -65,13 +65,13 @@ PATTERN_RELEASE_FILES=      $(PATTERNDIR)/definitions.owl $(PATTERNDIR)/pattern.
 MAPPINGDIR=                 ../mappings
 MAPPING_TESTER=             sssom validate
 SSSOMPY=                    sssom
-MAPPINGS=                   fbbt cl biomappings uberon-local uberon import-corrections 
+MAPPINGS=                   fbbt cl sslso biomappings uberon-local uberon import-corrections 
 MAPPING_RELEASE_FILES=      $(foreach n,$(MAPPINGS), $(MAPPINGDIR)/$(n).sssom.tsv)
 
 
 FORMATS = $(sort  owl obo json owl)
 FORMATS_INCL_TSV = $(sort $(FORMATS) tsv)
-RELEASE_ARTEFACTS = $(sort $(ONT)-base $(ONT)-full $(ONT)-simple $(ONT)-basic collected-metazoan composite-metazoan composite-metazoan-basic composite-vertebrate composite-vertebrate-basic common-anatomy )
+RELEASE_ARTEFACTS = $(sort $(ONT)-base $(ONT)-full $(ONT)-simple $(ONT)-basic collected-metazoan composite-metazoan composite-metazoan-basic composite-vertebrate composite-vertebrate-basic collected-lifestages composite-lifestages common-anatomy )
 
 ifeq ($(ODK_DEBUG),yes)
 ODK_DEBUG_FILE = debug.log
@@ -154,7 +154,7 @@ $(ROBOT_PLUGINS_DIRECTORY)/%.jar:
 # Specific rules for supplementary plugins defined in configuration
 
 $(ROBOT_PLUGINS_DIRECTORY)/uberon.jar:
-	curl -L -o $@ https://github.com/gouttegd/uberon-robot-plugin/releases/download/uberon-robot-plugin-0.3.1/uberon.jar
+	curl -L -o $@ https://github.com/gouttegd/uberon-robot-plugin/releases/download/uberon-robot-plugin-0.3.2/uberon.jar
 
 
 # ----------------------------------------
@@ -202,7 +202,7 @@ all_subsets: $(SUBSET_FILES)
 # ----------------------------------------
 
 
-MAPPINGS =  fbbt cl biomappings uberon-local uberon import-corrections
+MAPPINGS =  fbbt cl sslso biomappings uberon-local uberon import-corrections
 
 MAPPING_FILES = $(patsubst %, $(MAPPINGDIR)/%.sssom.tsv, $(MAPPINGS))
 
@@ -756,6 +756,10 @@ $(MAPPINGDIR)/fbbt.sssom.tsv:
 $(MAPPINGDIR)/cl.sssom.tsv:
 	test -f $@
 
+# This mappingset is manually curated, so we only check that the file actually exists.
+$(MAPPINGDIR)/sslso.sssom.tsv:
+	test -f $@
+
 # This mappingset is manually curated, so we only check that the file actually exists.
 $(MAPPINGDIR)/biomappings.sssom.tsv:
 	test -f $@
@@ -836,6 +840,18 @@ composite-vertebrate-basic.json: composite-vertebrate-basic.owl
 	$(ROBOT) annotate --input $< --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
 		convert --check false -f json -o [email protected] &&\
 		mv [email protected] $@
+collected-lifestages.obo: collected-lifestages.owl
+	$(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o [email protected] && grep -v ^owl-axioms [email protected] > $@ && rm [email protected]
+collected-lifestages.json: collected-lifestages.owl
+	$(ROBOT) annotate --input $< --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
+		convert --check false -f json -o [email protected] &&\
+		mv [email protected] $@
+composite-lifestages.obo: composite-lifestages.owl
+	$(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o [email protected] && grep -v ^owl-axioms [email protected] > $@ && rm [email protected]
+composite-lifestages.json: composite-lifestages.owl
+	$(ROBOT) annotate --input $< --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
+		convert --check false -f json -o [email protected] &&\
+		mv [email protected] $@
 common-anatomy.obo: common-anatomy.owl
 	$(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o [email protected] && grep -v ^owl-axioms [email protected] > $@ && rm [email protected]
 common-anatomy.json: common-anatomy.owl
@@ -932,6 +948,12 @@ composite-vertebrate.owl:
 composite-vertebrate-basic.owl:
 	echo "ERROR: You have configured a custom release artefact ($@); this release artefact needs to be define in uberon.Makefile!" && false
 
+collected-lifestages.owl:
+	echo "ERROR: You have configured a custom release artefact ($@); this release artefact needs to be define in uberon.Makefile!" && false
+
+composite-lifestages.owl:
+	echo "ERROR: You have configured a custom release artefact ($@); this release artefact needs to be define in uberon.Makefile!" && false
+
 common-anatomy.owl:
 	echo "ERROR: You have configured a custom release artefact ($@); this release artefact needs to be define in uberon.Makefile!" && false
 # ----------------------------------------

src/ontology/bridge/bridges.dispatch

@@ -253,3 +253,6 @@ dc-contributor: Melissa Haendel
 
 [zfs-uberon]
 file: uberon-bridge-to-zfs.owl
+
+[sslso-uberon]
+file: uberon-bridge-to-sslso.owl

src/ontology/bridge/bridges.rules

@@ -0,0 +1,125 @@
+# SSSOM is OBO-agnostic and doesn't know about the implicit OBO prefix
+# rule (PFX -> http://purl.obolibrary.org/obo/PFX_); *all* prefixes must
+# be explicitly declared.
+prefix AEO:       <http://purl.obolibrary.org/obo/AEO_>
+prefix BFO:       <http://purl.obolibrary.org/obo/BFO_>
+prefix BSPO:      <http://purl.obolibrary.org/obo/BSPO_>
+prefix CARO:      <http://purl.obolibrary.org/obo/CARO_>
+prefix CL:        <http://purl.obolibrary.org/obo/CL_>
+prefix GO:        <http://purl.obolibrary.org/obo/GO_>
+prefix IAO:       <http://purl.obolibrary.org/obo/IAO_>
+prefix NCBITaxon: <http://purl.obolibrary.org/obo/NCBITaxon_>
+prefix NCIT:      <http://purl.obolibrary.org/obo/NCIT_>
+prefix OG:        <http://purl.obolibrary.org/obo/OG_>
+prefix OGES:      <http://purl.obolibrary.org/obo/OGES_>
+prefix OIO:       <http://www.geneontology.org/formats/oboInOwl#>
+prefix RO:        <http://purl.obolibrary.org/obo/RO_>
+prefix SCTID:     <http://purl.obolibrary.org/obo/SCTID_>
+prefix UBERON:    <http://purl.obolibrary.org/obo/UBERON_>
+%INSERT-TAX-SPECIFIC-PREFIXES
+
+# Uberon may not contain declarations for all the taxa we bridge to, so
+# to be on the safe side we declare all of them preventively.
+%INSERT-TAX-SPECIFIC-DIRECTIVES
+
+# The relation to use in the existential restrictions between Uberon/CL
+# terms and their taxon-specific equivalents: part_of (BFO:0000050) for
+# most cases, except for life stage terms where we use occurs_in
+# (BFO:0000066) instead.
+set_var("TAXREL", BFO:0000050);
+is_a(%{object_id}, UBERON:0000104) -> set_var("TAXREL", BFO:0000066);
+is_a(%{object_id}, UBERON:0000105) -> set_var("TAXREL", BFO:0000066);
+
+# Make sure UBERON and CL classes are on the object side.
+subject==UBERON:* || subject==CL:* -> invert();
+
+# Ignore any mapping to something else than UBERON or CL.
+!(object==UBERON:* || object==CL:*) -> stop();
+
+# Ignore any mapping to an inexistent or obsolete UBERON/CL class.
+!exists(%{object_id}) -> stop();
+
+# Do not allow a same foreign term to be mapped with more than one UBERON/CL class.
+!cardinality==*:1 -> stop();
+
+# Ignore any mapping with a predicate other than those four.
+!(predicate==skos:exactMatch
+  || predicate==skos:narrowMatch
+  || predicate==skos:broadMatch
+  || predicate==semapv:crossSpeciesExactMatch) -> stop();
+
+# Generate cross-reference annotations (for backward compatibility).
+[xrefs] predicate==* -> annotate(%{object_id}, OIO:hasDbXref, "%{subject_id|short}");
+
+# Bridging axiom-generating rules.
+# The highly repetitive nature of those rules stems from the fact that
+# we need separate rules for each foreign ontology and for both Uberon
+# and CL, if we want to be able to send the corresponding axioms to
+# separate bridge files.
+
+# Taxon-neutral bridges.
+[aeo-uberon] subject==AEO:* object==UBERON:* {
+    predicate==*               -> annotate(%{subject_id}, IAO:0000589, "%{object_label} (AEO)");
+    predicate==skos:exactMatch -> create_axiom("%subject_id EquivalentTo: %object_id");
+}
+[aeo-cl] subject==AEO:* object==CL:* {
+    predicate==*               -> annotate(%{subject_id}, IAO:0000589, "%{object_label} (AEO)");
+    predicate==skos:exactMatch -> create_axiom("%subject_id EquivalentTo: %object_id");
+}
+
+[bfo-uberon] subject==BFO:* object==UBERON:* {
+    predicate==*                -> annotate(%{subject_id}, IAO:0000589, "%{object_label} (BFO)");
+    predicate==skos:narrowMatch -> create_axiom("%object_id SubClassOf: %subject_id");
+}
+[bfo-cl] subject==BFO:* object==CL:* {
+    predicate==*                -> annotate(%{subject_id}, IAO:0000589, "%{object_label} (BFO)");
+    predicate==skos:narrowMatch -> create_axiom("%object_id SubClassOf: %subject_id");
+}
+
+[caro-uberon] subject==CARO:* object==UBERON:* {
+    predicate==*               -> annotate(%{subject_id}, IAO:0000589, "%{object_label} (CARO)");
+    predicate==skos:exactMatch -> create_axiom("%subject_id EquivalentTo: %object_id");
+}
+[caro-cl] subject==CARO:* object==CL:* {
+    predicate==*               -> annotate(%{subject_id}, IAO:0000589, "%{object_label} (CARO)");
+    predicate==skos:exactMatch -> create_axiom("%subject_id EquivalentTo: %object_id");
+}
+
+[go-uberon] subject==GO:* object==UBERON:* {
+    predicate==*               -> annotate(%{subject_id}, IAO:0000589, "%{object_label} (GO)");
+    predicate==skos:exactMatch -> create_axiom("%subject_id EquivalentTo: %object_id");
+}
+[go-cl] subject==GO:* object==CL:* {
+    predicate==*               -> annotate(%{subject_id}, IAO:0000589, "%{object_label} (GO)");
+    predicate==skos:exactMatch -> create_axiom("%subject_id EquivalentTo: %object_id");
+}
+
+[ncit-uberon] subject==NCIT:* object==UBERON:* {
+    predicate==*               -> annotate(%{subject_id}, IAO:0000589, "%{object_label} (NCIT)");
+    predicate==skos:broadMatch -> create_axiom("%subject_id SubClassOf: %object_id");
+}
+[ncit-cl] subject==NCIT:* object==CL:* {
+    predicate==*               -> annotate(%{subject_id}, IAO:0000589, "%{object_label} (NCIT)");
+    predicate==skos:broadMatch -> create_axiom("%subject_id SubClassOf: %object_id");
+}
+
+[oges-uberon] subject==OGES:* object==UBERON:* {
+    predicate==*               -> annotate(%{subject_id}, IAO:0000589, "%{object_label} (OGES)");
+    predicate==skos:broadMatch -> create_axiom("%subject_id SubClassOf: %object_id");
+}
+[ncit-cl] subject==OGES:* object==CL:* {
+    predicate==*               -> annotate(%{subject_id}, IAO:0000589, "%{object_label} (OGES)");
+    predicate==skos:broadMatch -> create_axiom("%subject_id SubClassOf: %object_id");
+}
+
+[sctid-uberon] subject==SCTID:* object==UBERON:* {
+    predicate==*               -> annotate(%{subject_id}, IAO:0000589, "%{object_label} (SCTID)");
+    predicate==skos:broadMatch -> create_axiom("%subject_id SubClassOf: %object_id");
+}
+[sctid-cl] subject==SCTID:* object==CL:* {
+    predicate==*               -> annotate(%{subject_id}, IAO:0000589, "%{object_label} (SCTID)");
+    predicate==skos:broadMatch -> create_axiom("%subject_id SubClassOf: %object_id");
+}
+
+# Taxon-specific bridges.
+%INSERT-TAX-SPECIFIC-BRIDGES