Merge pull request #202 from Radiobiology-Informatics-Consortium/231117

Merge for release 17-01-2024
Radiobiology-Informatics-Consortium · Jan 17, 2024 · 38adefa · 38adefa
2 parents 2d40fc2 + ec9a728
commit 38adefa
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Showing 10 changed files with 1,630 additions and 1,240 deletions.
diff --git a/rbo-base.owl b/rbo-base.owl
diff --git a/rbo-full.owl b/rbo-full.owl
diff --git a/rbo.owl b/rbo.owl
diff --git a/src/ontology/components/all_templates.owl b/src/ontology/components/all_templates.owl
diff --git a/src/ontology/imports/envo_import.owl b/src/ontology/imports/envo_import.owl
@@ -21288,34 +21288,6 @@ consider revising &apos;pond&apos; semantics</obo:IAO_0000116>
 
 
 
-    <!-- http://purl.obolibrary.org/obo/ENVO_09200002 -->
-
-    <owl:Class rdf:about="http://purl.obolibrary.org/obo/ENVO_09200002">
-        <owl:equivalentClass>
-            <owl:Class>
-                <owl:intersectionOf rdf:parseType="Collection">
-                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/PATO_0001236"/>
-                    <owl:Restriction>
-                        <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
-                        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/ENVO_02500000"/>
-                    </owl:Restriction>
-                </owl:intersectionOf>
-            </owl:Class>
-        </owl:equivalentClass>
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PATO_0001236"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
-                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/ENVO_02500000"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <obo:IAO_0000115>The quality of a environmental system process.</obo:IAO_0000115>
-        <oboInOwl:hasExactSynonym>quality of environmental system process</oboInOwl:hasExactSynonym>
-        <rdfs:label>environmental system process quality</rdfs:label>
-    </owl:Class>
-
-
-
     <!-- http://purl.obolibrary.org/obo/ENVO_09200004 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/ENVO_09200004">

diff --git a/src/ontology/mirror/catalog-v001.xml b/src/ontology/mirror/catalog-v001.xml
diff --git a/src/ontology/rbo-edit.owl b/src/ontology/rbo-edit.owl
@@ -139,7 +139,7 @@ SubClassOf(obo:RBO_00005068 ObjectAllValuesFrom(obo:RO_0002404 obo:ENVO_01001023
 
 # Class: obo:RBO_00015022 (track formation)
 
-EquivalentClasses(obo:RBO_00015022 ObjectSomeValuesFrom(obo:OBI_0000299 obo:RBO_00015023))
+EquivalentClasses(obo:RBO_00015022 ObjectSomeValuesFrom(obo:OBI_0000299 obo:RBO_00015009))
 EquivalentClasses(obo:RBO_00015009 ObjectSomeValuesFrom(obo:RO_0000086 obo:RBO_00015011))
 
 # Class: obo:SO_0000704 (gene)

diff --git a/src/ontology/rbo.Makefile b/src/ontology/rbo.Makefile
@@ -7,7 +7,7 @@
 ##################### CUSTOM IMPORTS#########
 
 imports/chebi_import.owl: mirror/chebi.owl imports/chebi_terms_combined.txt
-	if [ $(IMP) = true ]; then $(ROBOT) extract -i $< -T imports/chebi_terms_combined.txt --force true --method STAR \
+	if [ $(IMP) = true ]; then $(ROBOT) extract -i $< -T imports/chebi_terms_combined.txt --force true --method BOT \
 			annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@; fi
 
 imports/chebi_top_import.owl: mirror/chebi.owl
@@ -48,6 +48,7 @@ imports/envo_import.owl: mirror/envo.owl imports/envo_terms_combined.txt
 		remove -t "PO:0028002" -t BFO:0000001 --trim false --axioms subclass --signature true --preserve-structure false\
 		remove -t "PO:0009012" -t BFO:0000015 --trim false --axioms subclass --signature true --preserve-structure false\
 		remove -t "ENVO:02500000" -t BFO:0000001 --trim false --axioms subclass --signature true --preserve-structure false\
+		remove -t "ENVO:09200002" -t BFO:0000001 --trim false --axioms subclass --signature true --preserve-structure false\
 		remove -t "ENVO:01001174"  --select self --trim true --signature true --preserve-structure false\
 		remove -t "http://purl.obolibrary.org/obo/PATO_0001739" -t "IAO:0000115" --axioms annotation --trim false --signature true \
     query --update ../sparql/inject-subset-declaration.ru \