Include XAO life stage terms in collected-lifestages.

Ensure that collected/composite-lifestages contains the life stage terms
from the Xenopus Anatomy Ontology.

This requires a custom step in which we extract all XAO life-stage terms
(all terms under XAO:1000000, including XAO:1000000 itself) and create
bridging axioms between those terms and the corresponding Uberon terms.

src/ontology/bridge/bridge-xao-ls.rules

@@ -0,0 +1,16 @@
+# This ruleset creates a special bridge for just the life stage terms
+# of XAO.
+prefix BFO:       <http://purl.obolibrary.org/obo/BFO_>
+prefix NCBITaxon: <http://purl.obolibrary.org/obo/NCBITaxon_>
+prefix UBERON:    <http://purl.obolibrary.org/obo/UBERON_>
+prefix XAO:       <http://purl.obolibrary.org/obo/XAO_>
+
+declare(NCBITaxon:8353);
+declare(BFO:0000066, /type="object_property");
+
+# Looking for any exact cross-species mapping between a Uberon term and
+# a XAO term below "Xenopus developmental stage" (XAO:1000000).
+subject==UBERON:* predicate==semapv:crossSpeciesExactMatch is_a(%{object_id}, XAO:1000000) -> {
+    annotate(%{object_id}, IAO:0000589, "%{subject_label} (xenopus)");
+    create_axiom("%object_id EquivalentTo: %subject_id and (BFO:0000066 some NCBITaxon:8353)");
+}

src/ontology/uberon.Makefile

@@ -1113,7 +1113,8 @@ COLLECTED_lifestages_SOURCES =       $(SUBSETDIR)/life-stages-minimal.owl \
 				     $(BRIDGEDIR)/uberon-bridge-to-wbls.owl \
 				     $(BRIDGEDIR)/uberon-bridge-to-mmusdv.owl \
 				     $(BRIDGEDIR)/uberon-bridge-to-hsapdv.owl \
-				     $(BRIDGEDIR)/uberon-bridge-to-sslso.owl
+				     $(BRIDGEDIR)/uberon-bridge-to-sslso.owl \
+				     $(TMPDIR)/xao-ls-bridged.owl
 
 
 # Composite pipeline proper
@@ -1188,6 +1189,18 @@ composite-vertebrate.owl: $(TMPDIR)/composite-vertebrate.owl
 composite-lifestages.owl: $(TMPDIR)/composite-lifestages.owl
 	$(ROBOT) annotate -i $< --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) -o $@
 
+# XAO contains both anatomical terms and life stage terms. To build
+# collected-lifestages (step 1c above), we need to extract the life stage
+# terms only (all descendants of XAO:1000000, "Xenopus developmental stage"),
+# and bridge them with corresponding Uberon terms.
+$(TMPDIR)/xao-ls-bridged.owl: $(IMPORTDIR)/local-xao.owl \
+				       $(MAPPINGDIR)/uberon-local.sssom.tsv \
+				       | all_robot_plugins
+	$(ROBOT) extract -i $< --method MIREOT --branch-from-term XAO:1000000 \
+		 sssom:inject --sssom $(MAPPINGDIR)/uberon-local.sssom.tsv \
+		              --ruleset $(BRIDGEDIR)/bridge-xao-ls.rules \
+		              -o $@
+
 
 # Some special products derived from the products generated above
 # ----------------------------------------