Merge pull request #3266 from obophenotype/update-cl-mappings

Use CL-provided mapping set.

docs/bridges.md

@@ -203,23 +203,24 @@ The pipeline may be triggered by invoking the Make target
 `refresh-bridges` (whilst in the in `src/ontology` directory, where the
 Makefile is located). Here is what happens then:
 
-1. Production of a SSSOM mapping set from the Uberon and CL
-   cross-references. The Uberon `-edit` file is merged with the mirrored
-   copy of CL (which is downloaded if not already available) and
-   cross-references from both Uberon and CL are extracted and turned
-   into a SSSOM mapping set. This takes care of all the mappings with
-   the foreign ontologies for which Uberon and CL are the source of
-   truth.
+1. Production of a SSSOM mapping set from the Uberon cross-references.
+   Cross-references are extracted directly from the Uberon `-edit` file
+   and turned into a SSSOM mapping set. This takes care of all the
+   mappings with the foreign ontologies for which Uberon is the source
+   of truth.
 2. Production of a SSSOM mapping sets from ontologies that maintain
    their own mappings as cross-references. The foreign ontologies are
    downloaded and their cross-references are extracted in the same way
-   as the Uberon/CL cross-references are.
+   as the Uberon cross-references are. Note that currently there is no
+   such ontology.
 3. Fetching of externally maintained mapping sets. For ontologies that
    maintain their own mappings and provide a SSSOM mapping set directly,
-   we fetch the mapping set as it is.
+   we fetch the mapping set as it is. This currently concerns FBbt and
+   CL (the CL set brings with it the mappings between CL and all the
+   species-specific ontologies).
 4. Merging of all the mapping sets. We merge the SSSOM mapping set that
-   was derived from the Uberon/CL cross-references (step 1), the sets
-   that were derived from the cross-references of foreign ontologies
+   was derived from the Uberon cross-references (step 1), the sets that
+   were derived from the cross-references of foreign ontologies
    (step 2), and the sets that we obtained directly from foreign
    ontologies (step 3).
 5. Production of the bridges. We apply a large SSSOM/T-OWL ruleset (in

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=                d9dd1f14c02c9157faa08c0c33d811609f31616c2917255ed4dca5559cb438ec
+CONFIG_HASH=                efb88af827f2af6cc513d695dc0dd59380e3e34c4ecf16d3648ebcfbba0aa64f
 
 
 # ----------------------------------------
@@ -65,7 +65,7 @@ PATTERN_RELEASE_FILES=      $(PATTERNDIR)/definitions.owl $(PATTERNDIR)/pattern.
 MAPPINGDIR=                 ../mappings
 MAPPING_TESTER=             sssom validate
 SSSOMPY=                    sssom
-MAPPINGS=                   fbbt cl zfa biomappings uberon-local uberon import-corrections 
+MAPPINGS=                   fbbt cl biomappings uberon-local uberon import-corrections 
 MAPPING_RELEASE_FILES=      $(foreach n,$(MAPPINGS), $(MAPPINGDIR)/$(n).sssom.tsv)
 
 
@@ -202,7 +202,7 @@ all_subsets: $(SUBSET_FILES)
 # ----------------------------------------
 
 
-MAPPINGS =  fbbt cl zfa biomappings uberon-local uberon import-corrections
+MAPPINGS =  fbbt cl biomappings uberon-local uberon import-corrections
 
 MAPPING_FILES = $(patsubst %, $(MAPPINGDIR)/%.sssom.tsv, $(MAPPINGS))
 
@@ -756,10 +756,6 @@ $(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)/zfa.sssom.tsv:
-	test -f $@
-
 # This mappingset is manually curated, so we only check that the file actually exists.
 $(MAPPINGDIR)/biomappings.sssom.tsv:
 	test -f $@

src/ontology/uberon-odk.yaml

@@ -107,8 +107,6 @@ sssom_mappingset_group:
       maintenance: manual
     - id: cl
       maintenance: manual
-    - id: zfa
-      maintenance: manual
     - id: biomappings
       maintenance: manual
     - id: uberon-local
@@ -152,4 +150,4 @@ components:
     - filename: in-subset.owl
     - filename: hra_subset.owl
     - filename: vasculature_class.owl
-    - filename: hra_depiction_3d_images.owl
+    - filename: hra_depiction_3d_images.owl

src/ontology/uberon.Makefile

@@ -1233,55 +1233,41 @@ $(MAPPINGDIR)/uberon-local.sssom.tsv: $(SRC) | all_robot_plugins
 		                    --prefix 'FMA:   http://purl.org/sig/ont/fma/fma' \
 	> $(REPORTDIR)/uberon-xrefs-extraction.txt
 
-# Uberon's "meta" mapping set, made by compiling the "local" set above
-# with the sets obtained from FBbt, CL, and ZFA below.
+# Uberon's "meta" mapping set, containing all mappings between Uberon
+# and foreign ontologies, regardless of where they are maintained. Made
+# by compiling the "local" set above with the FBbt set obtained below.
 $(MAPPINGDIR)/uberon.sssom.tsv: $(MAPPINGDIR)/uberon-local.sssom.tsv \
-				$(MAPPINGDIR)/fbbt.sssom.tsv \
-				$(MAPPINGDIR)/cl.sssom.tsv \
-				$(MAPPINGDIR)/zfa.sssom.tsv
+				$(MAPPINGDIR)/fbbt.sssom.tsv
 	sssom-cli $(foreach src, $^, -i $(src)) \
 		  --prefix-map-from-input \
-		  --rule '(object==UBERON:* || object==CL:*) -> invert()' \
-		  --rule '(subject==UBERON:* || subject==CL:*) -> include()' \
+		  --rule 'object==UBERON:* -> invert()' \
+		  --rule 'subject==UBERON:* -> include()' \
 		  --output $@
 
 # Remote mapping sets
 # -------------------
 
 # The following providers publish their own mapping sets.
-EXTERNAL_SSSOM_PROVIDERS = fbbt cl zfa biomappings
+EXTERNAL_SSSOM_PROVIDERS = fbbt cl biomappings
 
 # All the sets coming from the above ontologies.
 EXTERNAL_SSSOM_SETS = $(foreach provider, $(EXTERNAL_SSSOM_PROVIDERS), $(MAPPINGDIR)/$(provider).sssom.tsv)
 
 # We only refresh external resources under IMP=true
 ifeq ($(strip $(IMP)),true)
 
-# FBbt mapping set. Nominally a simple mirror, but we need a custom rule
-# because the default, ODK-generated rule would ignore the MIR variable.
+# FBbt mapping set. We filter it to only keep UBERON-related mappings
+# (CL-related mappings are already bundled with the CL set).
 $(MAPPINGDIR)/fbbt.sssom.tsv: .FORCE
-	wget "http://purl.obolibrary.org/obo/fbbt/fbbt.sssom.tsv" -O $@
-
-# CL mapping set (extracted from CL cross-references). We need to first
-# merge Uberon with CL, because the treat-xrefs-as-... annotations are
-# only in Uberon; then we need to remove the Uberon terms to avoid
-# extracting the cross-references from them as well.
-$(MAPPINGDIR)/cl.sssom.tsv: $(SRC) $(IMPORTDIR)/local-cl.owl | all_robot_plugins
-	$(ROBOT) merge -i $(SRC) -i $(IMPORTDIR)/local-cl.owl --collapse-import-closure false \
-		 remove --base-iri http://purl.obolibrary.org/obo/CL_ --axioms external \
-		 sssom:xref-extract --mapping-file $@ -v --drop-duplicates \
-		                    --set-id "$(ONTBASE)/mappings/cl-mappings.sssom.tsv" \
-		                    --prefix 'KUPO:  http://purl.obolibrary.org/obo/KUPO_'  \
-		                    --prefix 'SCTID: http://purl.obolibrary.org/obo/SCTID_' \
-		                    --prefix 'FMA:   http://purl.org/sig/ont/fma/fma' \
-	> $(REPORTDIR)/cl-xrefs-extraction.txt
+	wget "http://purl.obolibrary.org/obo/fbbt/fbbt.sssom.tsv" -O - | \
+		sssom-cli --prefix-map-from-input \
+		          --rule 'object==UBERON:* -> include()' \
+		          --output $@
 
-# ZFA mapping set (extracted from ZFA cross-references).
-$(MAPPINGDIR)/zfa.sssom.tsv: $(IMPORTDIR)/local-zfa.owl | all_robot_plugins
-	$(ROBOT) sssom:xref-extract -i $(IMPORTDIR)/local-zfa.owl --mapping-file $@ \
-		                    -v --drop-duplicates \
-		                    --set-id "$(ONTBASE)/mappings/zfa-mappings.sssom.tsv" \
-	> $(REPORTDIR)/zfa-xrefs-extraction.txt
+# CL mapping set. We simply fetch it as it is from CL. It already
+# contains all mappings related to CL (including the FBbt and ZFA ones).
+$(MAPPINGDIR)/cl.sssom.tsv: .FORCE
+	wget "http://purl.obolibrary.org/obo/cl/cl.sssom.tsv" -O $@
 
 # Biomappings mapping set. Nominally a simple mirror, but we need a
 # custom rule for two reasons:
@@ -1321,15 +1307,17 @@ CUSTOM_BRIDGES = $(BRIDGEDIR)/uberon-bridge-to-mba.owl \
 $(TMPDIR)/bridges.rules: $(SCRIPTSDIR)/sssomt.m4 $(BRIDGEDIR)/bridges.rules.m4
 	m4 $^ > $@
 
-# 2. Generate the bridges from the "meta" mapping set.
+# 2. Generate the bridges from the "meta" mapping set and the CL set.
 # Note that merging CL here is not strictly necessary, but doing so
 # allows sssom-inject to filter out any mapping with an inexistent or
 # obsolete Uberon/CL class.
-$(TMPDIR)/bridges: $(SRC) $(IMPORTDIR)/local-cl.owl $(MAPPINGDIR)/uberon.sssom.tsv \
+$(TMPDIR)/bridges: $(SRC) $(IMPORTDIR)/local-cl.owl \
+		   $(MAPPINGDIR)/uberon.sssom.tsv $(MAPPINGDIR)/cl.sssom.tsv \
 		   $(TMPDIR)/bridges.rules $(BRIDGEDIR)/bridges.dispatch \
 		   $(CUSTOM_BRIDGES) | all_robot_plugins
 	$(ROBOT) merge -i $(SRC) -i $(IMPORTDIR)/local-cl.owl \
 		 sssom:inject --sssom $(MAPPINGDIR)/uberon.sssom.tsv \
+		              --sssom $(MAPPINGDIR)/cl.sssom.tsv \
 		              --ruleset $(TMPDIR)/bridges.rules \
 		              --exclude-rule xrefs \
 		              --dispatch-table $(BRIDGEDIR)/bridges.dispatch && \