Merge pull request #181 from Radiobiology-Informatics-Consortium/new_…

…changes New changes
Radiobiology-Informatics-Consortium · Sep 14, 2023 · 2d40fc2 · 2d40fc2
2 parents d42e099 + f678fcd
commit 2d40fc2
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Showing 16 changed files with 64,127 additions and 6,721 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/catalog-v001.xml b/src/ontology/catalog-v001.xml
@@ -30,6 +30,9 @@
   <uri name="http://purl.obolibrary.org/obo/rbo/imports/chebi_import.owl" uri="imports/chebi_import.owl"/>
   <uri name="http://purl.obolibrary.org/obo/rbo/imports/chebi_import.obo" uri="imports/chebi_import.obo"/>
 
+  <uri name="http://purl.obolibrary.org/obo/rbo/imports/chebi_top_import.owl" uri="imports/chebi_top_import.owl"/>
+  <uri name="http://purl.obolibrary.org/obo/rbo/imports/chebi_top_import.obo" uri="imports/chebi_top_import.obo"/>
+
   <uri name="http://purl.obolibrary.org/obo/rbo/imports/go_import.owl" uri="imports/go_import.owl"/>
   <uri name="http://purl.obolibrary.org/obo/rbo/imports/go_import.obo" uri="imports/go_import.obo"/>
 

diff --git a/src/ontology/components/all_templates.owl b/src/ontology/components/all_templates.owl
diff --git a/src/ontology/imports/chebi_import.owl b/src/ontology/imports/chebi_import.owl
diff --git a/src/ontology/imports/chebi_terms.txt b/src/ontology/imports/chebi_terms.txt
@@ -1,5 +1,4 @@
-CHEBI:24432
-CHEBI:33250
+CHEBI:24432 # exact
 obo:CHEBI_30216 # alpha particle
 CHEBI:30222 # neutron
 CHEBI:24636 # proton
@@ -8,3 +7,4 @@ CHEBI:36348  # pi meson
 CHEBI:36347  # nuclear particle
 CHEBI:36080
 CHEBI:33695
+CHEBI:33314
diff --git a/src/ontology/imports/chebi_terms_top.txt b/src/ontology/imports/chebi_terms_top.txt
@@ -0,0 +1,2 @@
+CHEBI:33250
+CHEBI:22313
diff --git a/src/ontology/imports/chebi_top_import.owl b/src/ontology/imports/chebi_top_import.owl
diff --git a/src/ontology/imports/obi_import.owl b/src/ontology/imports/obi_import.owl
@@ -11,9 +11,9 @@
      xmlns:terms="http://purl.org/dc/terms/"
      xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/rbo/imports/obi_import.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/rbo/releases/2022-10-05/imports/obi_import.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/rbo/releases/2023-07-06/imports/obi_import.owl"/>
         <dc:source rdf:resource="http://purl.obolibrary.org/obo/obi/2022-07-11/obi.owl"/>
-        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-10-05</owl:versionInfo>
+        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2023-07-06</owl:versionInfo>
     </owl:Ontology>
 
 

diff --git a/src/ontology/imports/obi_terms.txt b/src/ontology/imports/obi_terms.txt
@@ -9,4 +9,4 @@ obo:OBI_0000272 # protocol
 obo:OBI_0002983 # altitude measurement datum
 obo:OBI_0001138 # x-ray machine
 http://purl.obolibrary.org/obo/OBI_0302889 # irradiation
-
+http://purl.obolibrary.org/obo/OBI_0000299 # has specified output
diff --git a/src/ontology/rbo-edit.owl b/src/ontology/rbo-edit.owl
@@ -18,6 +18,7 @@ Import(<http://purl.obolibrary.org/obo/doid/subsets/DO_RAD_slim.owl>)
 Import(<http://purl.obolibrary.org/obo/rbo/components/all_templates.owl>)
 Import(<http://purl.obolibrary.org/obo/rbo/imports/bfo_import.owl>)
 Import(<http://purl.obolibrary.org/obo/rbo/imports/chebi_import.owl>)
+Import(<http://purl.obolibrary.org/obo/rbo/imports/chebi_top_import.owl>)
 Import(<http://purl.obolibrary.org/obo/rbo/imports/chmo_import.owl>)
 Import(<http://purl.obolibrary.org/obo/rbo/imports/cob_import.owl>)
 Import(<http://purl.obolibrary.org/obo/rbo/imports/efo_import.owl>)
@@ -79,6 +80,10 @@ SubClassOf(obo:BFO_0000023 obo:BFO_0000017)
 
 SubClassOf(obo:CHEBI_33252 ObjectSomeValuesFrom(obo:RO_0002493 obo:RBO_00002118))
 
+# Class: obo:CHEBI_36080 (protein)
+
+SubClassOf(obo:CHEBI_36080 obo:CHEBI_33695)
+
 # Class: obo:CHEBI_50906 (role)
 
 SubClassOf(obo:CHEBI_50906 obo:BFO_0000017)
@@ -87,6 +92,18 @@ SubClassOf(obo:CHEBI_50906 obo:BFO_0000017)
 
 SubClassOf(obo:CL_0000000 obo:BFO_0000040)
 
+# Class: obo:CL_0017502 (acidophilic cytoplasm)
+
+SubClassOf(obo:CL_0017502 obo:GO_0005737)
+
+# Class: obo:CL_0017503 (basophilic cytoplasm)
+
+SubClassOf(obo:CL_0017503 obo:GO_0005737)
+
+# Class: obo:CL_0017504 (polychromatophilic cytoplasm)
+
+SubClassOf(obo:CL_0017504 obo:GO_0005737)
+
 # Class: obo:DOID_4 (disease)
 
 SubClassOf(obo:DOID_4 obo:BFO_0000016)
@@ -109,7 +126,6 @@ SubClassOf(obo:PO_0009012 obo:BFO_0000015)
 
 # Class: obo:RBO_00002118 (Radioactive decay)
 
-# change to the 115 radiation new thing concept
 SubClassOf(obo:RBO_00002118 ObjectSomeValuesFrom(obo:OBI_0000299 obo:RBO_00015000))
 SubClassOf(obo:RBO_00002118 ObjectMinCardinality(1 obo:OBI_0000293 obo:CHEBI_33252))
 
@@ -121,16 +137,18 @@ SubClassOf(obo:RBO_00002122 ObjectSomeValuesFrom(obo:RO_0002234 obo:RBO_010016))
 
 SubClassOf(obo:RBO_00005068 ObjectAllValuesFrom(obo:RO_0002404 obo:ENVO_01001023))
 
-# Class: obo:UBERON_0000000 (processual entity)
+# Class: obo:RBO_00015022 (track formation)
 
-SubClassOf(obo:UBERON_0000000 obo:BFO_0000003)
+EquivalentClasses(obo:RBO_00015022 ObjectSomeValuesFrom(obo:OBI_0000299 obo:RBO_00015023))
+EquivalentClasses(obo:RBO_00015009 ObjectSomeValuesFrom(obo:RO_0000086 obo:RBO_00015011))
 
-SubClassOf(obo:CL_0017502 obo:GO_0005737)
-SubClassOf(obo:CL_0017503 obo:GO_0005737)
-SubClassOf(obo:CL_0017504 obo:GO_0005737)
+# Class: obo:SO_0000704 (gene)
 
 SubClassOf(obo:SO_0000704 obo:BFO_0000040)
-SubClassOf(obo:CHEBI_36080 obo:CHEBI_33695)
+
+# Class: obo:UBERON_0000000 (processual entity)
+
+SubClassOf(obo:UBERON_0000000 obo:BFO_0000003)
 
 
 AnnotationAssertion(oboInOwl:hasExactSynonym obo:UO_0000160 "micromole per square meter per second")

diff --git a/src/ontology/rbo.Makefile b/src/ontology/rbo.Makefile
@@ -7,7 +7,11 @@
 ##################### 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 BOT \
+	if [ $(IMP) = true ]; then $(ROBOT) extract -i $< -T imports/chebi_terms_combined.txt --force true --method STAR \
+			annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@; fi
+
+imports/chebi_top_import.owl: mirror/chebi.owl
+	if [ $(IMP) = true ]; then $(ROBOT) extract -i $< --branch-from-terms imports/chebi_terms_top.txt --force true --method MIREOT \
 			annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@; fi
 
 imports/chmo_import.owl: mirror/chmo.owl imports/chmo_terms_combined.txt