Add a new inSubset ROBOT template (#2196)

* Add a new inSubset ROBOT template This commit intends to add a new `inSubset` ROBOT template. This commit is related to #2127 (comment) . * Delete example line * Activate template - add OWL file it produces to components - add import statement on uberon-edit.obo - add other related updates - fix superfluous spaces in uberon-odk.yaml file * Activate template - add OWL file it produces to components * Fix incorrect product filename. * Update repo * Update incorrect owl filename * Remove in-taxon references * Re-import in-subset.owl * Replace four spaces with a tab in uberon.Makefile * This syntax error had caused problems.
obophenotype · Mar 17, 2022 · 033b4d7 · 033b4d7
1 parent 0bbaf23
commit 033b4d7
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diff --git a/docs/odk-workflows/RepositoryFileStructure.md b/docs/odk-workflows/RepositoryFileStructure.md
@@ -53,3 +53,4 @@ These are the components in UBERON
 | Filename | URL |
 | -------- | --- |
 | mappings.owl | None |
+| in-subset.owl | None |
diff --git a/src/ontology/Makefile b/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-subset.owl 
 ONTOLOGYTERMS =             $(TMPDIR)/ontologyterms.txt
 PATTERNDIR=                 ../patterns
 PATTERN_TESTER=              dosdp validate -i
@@ -323,6 +323,8 @@ $(COMPONENTSDIR)/%: | $(COMPONENTSDIR)
 
 
 
+
+
 # ----------------------------------------
 # Mirroring upstream ontologies
 # ----------------------------------------

diff --git a/src/ontology/catalog-v001.xml b/src/ontology/catalog-v001.xml
diff --git a/src/ontology/components/in-subset.owl b/src/ontology/components/in-subset.owl
@@ -0,0 +1,15 @@
+<?xml version="1.0"?>
+<rdf:RDF xmlns="http://purl.obolibrary.org/obo/uberon/components/in-subset.owl#"
+     xml:base="http://purl.obolibrary.org/obo/uberon/components/in-subset.owl"
+     xmlns:owl="http://www.w3.org/2002/07/owl#"
+     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+     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#">
+    <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/uberon/components/in-subset.owl"/>
+</rdf:RDF>
+
+
+
+<!-- Generated by the OWL API (version 4.5.6) https://github.com/owlcs/owlapi -->
+
diff --git a/src/ontology/components/mappings.owl b/src/ontology/components/mappings.owl
@@ -196,7 +196,7 @@
   <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_6001056">
     <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBbt:00001056</oboInOwl:hasDbXref>
   </Class>
-  <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_6001057">
+  <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0002346">
     <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBbt:00001057</oboInOwl:hasDbXref>
   </Class>
   <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_6001059">
@@ -205,12 +205,6 @@
   <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_6001060">
     <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBbt:00001060</oboInOwl:hasDbXref>
   </Class>
-  <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0002346">
-    <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBbt:00001061</oboInOwl:hasDbXref>
-  </Class>
-  <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000934">
-    <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBbt:00001102</oboInOwl:hasDbXref>
-  </Class>
   <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_6001135">
     <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBbt:00001135</oboInOwl:hasDbXref>
   </Class>
@@ -457,21 +451,15 @@
   <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_6003024">
     <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBbt:00003024</oboInOwl:hasDbXref>
   </Class>
+  <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_6003039">
+    <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBbt:00003039</oboInOwl:hasDbXref>
+  </Class>
   <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0001555">
     <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBbt:00003125</oboInOwl:hasDbXref>
   </Class>
   <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000165">
     <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBbt:00003126</oboInOwl:hasDbXref>
   </Class>
-  <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0001245">
-    <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBbt:00003148</oboInOwl:hasDbXref>
-  </Class>
-  <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0015231">
-    <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBbt:00003152</oboInOwl:hasDbXref>
-  </Class>
-  <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0007100">
-    <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBbt:00003154</oboInOwl:hasDbXref>
-  </Class>
   <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0015230">
     <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBbt:00003154</oboInOwl:hasDbXref>
   </Class>
@@ -481,9 +469,6 @@
   <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_6003259">
     <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBbt:00003259</oboInOwl:hasDbXref>
   </Class>
-  <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0001135">
-    <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBbt:00003525</oboInOwl:hasDbXref>
-  </Class>
   <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_6003559">
     <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBbt:00003559</oboInOwl:hasDbXref>
   </Class>
@@ -652,9 +637,6 @@
   <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000991">
     <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBbt:00004858</oboInOwl:hasDbXref>
   </Class>
-  <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0004909">
-    <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBbt:00004859</oboInOwl:hasDbXref>
-  </Class>
   <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000474">
     <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBbt:00004864</oboInOwl:hasDbXref>
   </Class>
@@ -664,9 +646,6 @@
   <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0003199">
     <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBbt:00004894</oboInOwl:hasDbXref>
   </Class>
-  <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0004911">
-    <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBbt:00004896</oboInOwl:hasDbXref>
-  </Class>
   <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000994">
     <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBbt:00004921</oboInOwl:hasDbXref>
   </Class>
@@ -679,9 +658,6 @@
   <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000473">
     <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBbt:00004928</oboInOwl:hasDbXref>
   </Class>
-  <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0004910">
-    <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBbt:00004955</oboInOwl:hasDbXref>
-  </Class>
   <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0006868">
     <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBbt:00004958</oboInOwl:hasDbXref>
   </Class>
@@ -724,7 +700,7 @@
   <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_6005037">
     <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBbt:00005037</oboInOwl:hasDbXref>
   </Class>
-  <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0003127">
+  <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_6005043">
     <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBbt:00005043</oboInOwl:hasDbXref>
   </Class>
   <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_6005054">
@@ -736,7 +712,7 @@
   <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0001008">
     <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBbt:00005056</oboInOwl:hasDbXref>
   </Class>
-  <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0001009">
+  <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0009054">
     <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBbt:00005057</oboInOwl:hasDbXref>
   </Class>
   <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0002323">
@@ -754,12 +730,6 @@
   <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000383">
     <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBbt:00005069</oboInOwl:hasDbXref>
   </Class>
-  <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0005090">
-    <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBbt:00005073</oboInOwl:hasDbXref>
-  </Class>
-  <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0014895">
-    <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBbt:00005073</oboInOwl:hasDbXref>
-  </Class>
   <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0001016">
     <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBbt:00005093</oboInOwl:hasDbXref>
   </Class>
@@ -772,6 +742,9 @@
   <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_6005096">
     <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBbt:00005096</oboInOwl:hasDbXref>
   </Class>
+  <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000934">
+    <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBbt:00005097</oboInOwl:hasDbXref>
+  </Class>
   <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000010">
     <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBbt:00005098</oboInOwl:hasDbXref>
   </Class>
@@ -781,24 +754,15 @@
   <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0001018">
     <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBbt:00005100</oboInOwl:hasDbXref>
   </Class>
-  <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0001020">
-    <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBbt:00005103</oboInOwl:hasDbXref>
-  </Class>
   <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0001021">
     <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBbt:00005105</oboInOwl:hasDbXref>
   </Class>
   <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0001027">
     <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBbt:00005136</oboInOwl:hasDbXref>
   </Class>
-  <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000045">
-    <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBbt:00005137</oboInOwl:hasDbXref>
-  </Class>
   <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0002606">
     <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBbt:00005139</oboInOwl:hasDbXref>
   </Class>
-  <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0004732">
-    <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBbt:00005140</oboInOwl:hasDbXref>
-  </Class>
   <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000020">
     <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBbt:00005155</oboInOwl:hasDbXref>
   </Class>
@@ -1066,7 +1030,7 @@
   <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_6007248">
     <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBbt:00007248</oboInOwl:hasDbXref>
   </Class>
-  <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000480">
+  <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0034923">
     <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBbt:00007276</oboInOwl:hasDbXref>
   </Class>
   <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000477">
@@ -1147,9 +1111,15 @@
   <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_6041000">
     <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBbt:00041000</oboInOwl:hasDbXref>
   </Class>
+  <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0001245">
+    <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBbt:00047153</oboInOwl:hasDbXref>
+  </Class>
   <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_6057001">
     <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBbt:00057001</oboInOwl:hasDbXref>
   </Class>
+  <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0015231">
+    <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBbt:00058291</oboInOwl:hasDbXref>
+  </Class>
   <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0034926">
     <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBbt:00100152</oboInOwl:hasDbXref>
   </Class>