Add a new inSubset ROBOT template

docs/odk-workflows/RepositoryFileStructure.md

@@ -53,3 +53,4 @@ These are the components in UBERON
 | Filename | URL |
 | -------- | --- |
 | mappings.owl | None |
+| in-taxon.owl | None |

src/ontology/Makefile

@@ -47,7 +47,7 @@ TODAY ?=                    $(shell date +%Y-%m-%d)
 OBODATE ?=                  $(shell date +'%d:%m:%Y %H:%M')
 VERSION=                    $(TODAY)
 ANNOTATE_ONTOLOGY_VERSION = annotate -V $(ONTBASE)/releases/$(VERSION)/$@ --annotation owl:versionInfo $(VERSION)
-OTHER_SRC =                 $(PATTERNDIR)/definitions.owl $(COMPONENTSDIR)/mappings.owl 
+OTHER_SRC =                 $(PATTERNDIR)/definitions.owl $(COMPONENTSDIR)/mappings.owl $(COMPONENTSDIR)/in-taxon.owl 
 ONTOLOGYTERMS =             $(TMPDIR)/ontologyterms.txt
 PATTERNDIR=                 ../patterns
 PATTERN_TESTER=              dosdp validate -i
@@ -323,6 +323,8 @@ $(COMPONENTSDIR)/%: | $(COMPONENTSDIR)
 
 
 
+
+
 # ----------------------------------------
 # Mirroring upstream ontologies
 # ----------------------------------------

src/ontology/components/in-taxon.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/uberon/components/in-taxon.owl"/>
+
+    <!-- This is a placeholder, it will be regenerated when makefile is first executed -->
+</rdf:RDF>

src/ontology/uberon-edit.obo

@@ -54,6 +54,7 @@ treat-xrefs-as-equivalent: OG
 treat-xrefs-as-equivalent: VSAO
 treat-xrefs-as-is_a: VHOG
 remark: Aurelie Comte, Bill Bug, Catherine Leroy, Duncan Davidson and Trish Whetzel are also contributors. However their ORCIDs were not found.
+import: http://purl.obolibrary.org/obo/uberon/components/in-taxon.owl
 import: http://purl.obolibrary.org/obo/uberon/components/mappings.owl
 import: http://purl.obolibrary.org/obo/uberon/components/vasculature_class.owl
 import: http://purl.obolibrary.org/obo/uberon/imports/bfo_import.owl
@@ -147141,8 +147142,8 @@ id: UBERON:0011390
 name: pudendal nerve
 def: "The pudendal nerve is a somatic nerve in the pelvic region that innervates the external genitalia of both sexes, as well as sphincters for the bladder and the rectum. It originates in Onuf's nucleus in the sacral region of the spinal cord." [Wikipedia:Pudendal_nerve]
 synonym: "internal pudendal nerve" RELATED [Wikipedia:Pudendal_nerve]
-synonym: "nervus pudendae" EXACT LATIN [doi:10.1002/ca.23705]
 synonym: "nervus pudendae" EXACT DEPRECATED [doi:10.1002/ca.23705]
+synonym: "nervus pudendae" EXACT LATIN [doi:10.1002/ca.23705]
 synonym: "nervus pudendales" EXACT LATIN [doi:10.1002/ca.23705]
 synonym: "pudenal nerve" RELATED [Wikipedia:Pudendal_nerve]
 synonym: "pudendal" BROAD [Wikipedia:Pudendal_nerve]

src/ontology/uberon-odk.yaml

@@ -10,11 +10,11 @@ export_formats:
   - owl
   - obo
   - json
-namespaces: 
+namespaces:
   - http://purl.obolibrary.org/obo/UBERON_
   - http://purl.obolibrary.org/obo/uberon#
   - http://purl.obolibrary.org/obo/UBPROP_
-release_artefacts: 
+release_artefacts:
   - base
   - full
   - simple
@@ -33,7 +33,7 @@ import_group:
       mirror_from: https://raw.githubusercontent.com/obophenotype/pro_obo_slim/master/pr_slim.owl
     - id: cl
     - id: go
-    - id: envo 
+    - id: envo
     - id: ro
     - id: bspo
     - id: chebi
@@ -87,23 +87,24 @@ subset_group:
 robot_java_args: '-Xmx20G'
 robot_report:
   release_reports: False
-  fail_on : ERROR
-  use_labels : False
-  custom_profile : True
-  report_on :
+  fail_on: ERROR
+  use_labels: False
+  custom_profile: True
+  report_on:
     - edit
-  custom_sparql_checks :
-    - equivalent-classes 
+  custom_sparql_checks:
+    - equivalent-classes
     - owldef-self-reference
     - illegal-annotation-property
     - taxon-range
     - orcid-contributor
-  custom_sparql_exports : 
+  custom_sparql_exports:
     - basic-report
 owltools_memory: '20G'
 create_obo_metadata: FALSE
 documentation:
   documentation_system: mkdocs
 components:
   products:
-    - filename: mappings.owl
+    - filename: mappings.owl
+    - filename: in-taxon.owl

src/ontology/uberon.Makefile

@@ -1675,6 +1675,14 @@ uberon-nif-merged.obo:  uberon-nif-merged.owl
 %-names.txt: %.obo
 	grep ^name: $< | grep -v obsolete | perl -npe 's@name: @@' > $@.tmp && sort -u $@.tmp > $@
 
+# ----------------------------------------
+# ROBOT PATTERNS AND TEMPLATES
+# ----------------------------------------
+
+$(COMPONENTSDIR)/in-subset.owl: $(SRC) $(TEMPLATEDIR)/in-subset.template.tsv 
+    $(ROBOT) template --template $(TEMPLATEDIR)/in-subset.template.tsv \
+  annotate --ontology-iri $(ONTBASE)/$@ --output $(COMPONENTSDIR)/in-subset.owl
+
 # ----------------------------------------
 # DEAD SIMPLE DESIGN PATTERNS
 # ----------------------------------------

src/templates/in-subset.template.tsv

@@ -0,0 +1,2 @@
+Class ID	Subset tag	PROVENANCE
+ID	AI oboInOwl:inSubset	>AI oboInOwl:source