measures characteristic

src/ontology/Makefile

@@ -109,7 +109,7 @@ all_main: $(MAIN_FILES)
 # ----------------------------------------
 
 
-IMPORTS =  omo pato cl envo go other orcidio uberon obi
+IMPORTS =  omo pato cl envo go other orcidio uberon cob obi
 
 IMPORT_ROOTS = $(patsubst %, $(IMPORTDIR)/%_import, $(IMPORTS))
 IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl)
@@ -378,6 +378,16 @@ $(IMPORTDIR)/uberon_import.owl: $(MIRRORDIR)/uberon.owl $(IMPORTDIR)/uberon_term
 		query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \
 		$(ANNOTATE_CONVERT_FILE); fi
 
+## Module for ontology: cob
+
+$(IMPORTDIR)/cob_import.owl: $(MIRRORDIR)/cob.owl $(IMPORTDIR)/cob_terms_combined.txt
+	if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \
+    extract -T $(IMPORTDIR)/cob_terms_combined.txt --copy-ontology-annotations true --force true --method BOT \
+    remove --base-iri $(OBOBASE)/COB --axioms external --preserve-structure false --trim false \
+		remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) -T $(IMPORTDIR)/cob_terms_combined.txt --select complement \
+		query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \
+		$(ANNOTATE_CONVERT_FILE); fi
+
 ## Module for ontology: obi
 
 $(IMPORTDIR)/obi_import.owl: $(MIRRORDIR)/obi.owl $(IMPORTDIR)/obi_terms_combined.txt
@@ -527,6 +537,15 @@ mirror-uberon: | $(TMPDIR)
 		mv [email protected] $(TMPDIR)/[email protected]; fi
 
 
+## ONTOLOGY: cob
+.PHONY: mirror-cob
+.PRECIOUS: $(MIRRORDIR)/cob.owl
+mirror-cob: | $(TMPDIR)
+	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/cob.owl --create-dirs -o $(MIRRORDIR)/cob.owl --retry 4 --max-time 200 &&\
+		$(ROBOT) convert -i $(MIRRORDIR)/cob.owl -o [email protected] &&\
+		mv [email protected] $(TMPDIR)/[email protected]; fi
+
+
 ## ONTOLOGY: obi
 .PHONY: mirror-obi
 .PRECIOUS: $(MIRRORDIR)/obi.owl

src/ontology/catalog-v001.xml

@@ -1,6 +1,7 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <catalog prefer="public" xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog">
     <group id="Folder Repository, directory=, recursive=false, Auto-Update=false, version=2" prefer="public" xml:base="">
+        <uri name="http://purl.obolibrary.org/obo/ro/imports/cob_import.owl" uri="imports/cob_import.owl"/>
         <uri name="http://purl.obolibrary.org/obo/ro/imports/uberon_import.owl" uri="imports/uberon_import.owl"/>
         <uri name="http://purl.obolibrary.org/obo/ro/imports/obi_import.owl" uri="imports/obi_import.owl"/>
         <uri name="http://purl.obolibrary.org/obo/ro/imports/omo_import.owl" uri="imports/omo_import.owl"/>

src/ontology/imports/cob_import.owl

@@ -0,0 +1,20 @@
+Prefix(:=<http://purl.obolibrary.org/obo/ro/imports/cob_import.owl#>)
+Prefix(owl:=<http://www.w3.org/2002/07/owl#>)
+Prefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)
+Prefix(xml:=<http://www.w3.org/XML/1998/namespace>)
+Prefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)
+Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
+
+
+Ontology(<http://purl.obolibrary.org/obo/ro/imports/cob_import.owl>
+<http://purl.obolibrary.org/obo/ro/releases/2023-06-12/imports/cob_import.owl>
+Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/cob/releases/2023-05-12/cob.owl>)
+Annotation(owl:versionInfo "2023-06-12")
+
+Declaration(AnnotationProperty(<http://purl.org/dc/elements/1.1/description>))
+Declaration(AnnotationProperty(<http://purl.org/dc/elements/1.1/source>))
+Declaration(AnnotationProperty(<http://purl.org/dc/elements/1.1/title>))
+Declaration(AnnotationProperty(<http://purl.org/dc/terms/license>))
+
+
+)

src/ontology/imports/obi_import.owl

@@ -11,6 +11,10 @@ Ontology(<http://purl.obolibrary.org/obo/ro/imports/obi_import.owl>
 Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl>)
 Annotation(owl:versionInfo "2023-06-28")
 
+Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000015>))
+Declaration(Class(<http://purl.obolibrary.org/obo/GO_0008150>))
+Declaration(Class(<http://purl.obolibrary.org/obo/OBI_0000011>))
+Declaration(Class(<http://purl.obolibrary.org/obo/OBI_0000070>))
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000040>))
 Declaration(Class(<http://purl.obolibrary.org/obo/OBI_0100026>))
 Declaration(AnnotationProperty(<http://protege.stanford.edu/plugins/owl/protege#defaultLanguage>))
@@ -20,7 +24,9 @@ Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000114>))
 Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000115>))
 Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000116>))
 Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000117>))
+Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000118>))
 Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000119>))
+Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000232>))
 Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000589>))
 Declaration(AnnotationProperty(<http://purl.org/dc/elements/1.1/contributor>))
 Declaration(AnnotationProperty(<http://purl.org/dc/elements/1.1/creator>))
@@ -38,6 +44,42 @@ Declaration(Datatype(xsd:date))
 #   Classes
 ############################
 
+
+# Class: <http://purl.obolibrary.org/obo/GO_0008150> (<http://purl.obolibrary.org/obo/GO_0008150>)
+
+DisjointClasses(<http://purl.obolibrary.org/obo/GO_0008150> <http://purl.obolibrary.org/obo/OBI_0000011>)
+
+# Class: <http://purl.obolibrary.org/obo/OBI_0000011> (planned process)
+
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000111> <http://purl.obolibrary.org/obo/OBI_0000011> "planned process"@en)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000111> <http://purl.obolibrary.org/obo/OBI_0000011> "planned process")
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/OBI_0000011> "Injecting mice with a vaccine in order to test its efficacy")
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000114> <http://purl.obolibrary.org/obo/OBI_0000011> <http://purl.obolibrary.org/obo/IAO_0000122>)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/OBI_0000011> "A process that realizes a plan which is the concretization of a plan specification."@en)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000116> <http://purl.obolibrary.org/obo/OBI_0000011> "'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)")
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000116> <http://purl.obolibrary.org/obo/OBI_0000011> "We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some 
+objectives is a planned process.")
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000117> <http://purl.obolibrary.org/obo/OBI_0000011> "Bjoern Peters")
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000119> <http://purl.obolibrary.org/obo/OBI_0000011> "branch derived")
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000232> <http://purl.obolibrary.org/obo/OBI_0000011> "This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)"@en)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000232> <http://purl.obolibrary.org/obo/OBI_0000011> "6/11/9: Edited at workshop. Used to include: is initiated by an agent")
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OBI_0000011> "planned process"@en)
+SubClassOf(<http://purl.obolibrary.org/obo/OBI_0000011> <http://purl.obolibrary.org/obo/BFO_0000015>)
+
+# Class: <http://purl.obolibrary.org/obo/OBI_0000070> (assay)
+
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000111> <http://purl.obolibrary.org/obo/OBI_0000070> "assay"@en)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/OBI_0000070> "Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.")
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000114> <http://purl.obolibrary.org/obo/OBI_0000070> <http://purl.obolibrary.org/obo/IAO_0000122>)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/OBI_0000070> "A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies."@en)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000116> <http://purl.obolibrary.org/obo/OBI_0000070> "12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation.")
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000117> <http://purl.obolibrary.org/obo/OBI_0000070> "PlanAndPlannedProcess Branch"@en)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000118> <http://purl.obolibrary.org/obo/OBI_0000070> "measuring"@en)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000118> <http://purl.obolibrary.org/obo/OBI_0000070> "scientific observation"@en)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000119> <http://purl.obolibrary.org/obo/OBI_0000070> "OBI branch derived"@en)
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OBI_0000070> "assay"@en)
+SubClassOf(<http://purl.obolibrary.org/obo/OBI_0000070> <http://purl.obolibrary.org/obo/OBI_0000011>)
+
 # Class: <http://purl.obolibrary.org/obo/OBI_0100026> (organism)
 
 AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000111> <http://purl.obolibrary.org/obo/OBI_0100026> "organism"@en)
@@ -57,4 +99,5 @@ AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OBI_0100026> "org
 SubClassOf(<http://purl.obolibrary.org/obo/OBI_0100026> <http://purl.obolibrary.org/obo/BFO_0000040>)
 
 
+
 )

src/ontology/imports/obi_terms.txt

@@ -1 +1,4 @@
-OBI:0100026
+OBI:0000011
+OBI:0000070
+OBI:0100026
+