measures characteristic (#717)

* measures characteristic

and inverse 'characteristic measured by'

* fixed 'has characteristic' ref.

* includes obi import file

And domain = planned process
codomain = PATO characteristic

* COB import of planned process

* Adding OBI assay

Note: This should be imported via COB when that is possible.

* revising "measures characteristic" label

and changing range to assay from 'planned process'

* catalogue tweak

* update repo

* remove cob import

* rename process measures characteristic

to "assay measures characteristic" , and similarly for inverse relation.  Superfluous diffs generated though too.

* import characteristic (BFO:0000020) from COB

* update to domain/range 'specifically dependent continuant' / COB characteristic

* terms prefix fix

* tweak inverse defn

* annotation tweaks

* fix typo in characteristic measured by assay definition

---------

Co-authored-by: Anita Caron <[email protected]>
Co-authored-by: Anita Caron <[email protected]>

src/ontology/imports/cob_import.owl

@@ -20,6 +20,7 @@ Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000034>))
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000040>))
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000141>))
 Declaration(Class(<http://purl.obolibrary.org/obo/CL_0000000>))
+Declaration(Class(<http://purl.obolibrary.org/obo/OBI_0000070>))
 Declaration(Class(<http://purl.obolibrary.org/obo/COB_0000121>))
 Declaration(Class(<http://purl.obolibrary.org/obo/COB_0001000>))
 Declaration(Class(<http://purl.obolibrary.org/obo/GO_0003674>))
@@ -180,5 +181,10 @@ AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/GO_0008150> "biol
 SubClassOf(<http://purl.obolibrary.org/obo/GO_0008150> <http://purl.obolibrary.org/obo/BFO_0000015>)
 SubClassOf(<http://purl.obolibrary.org/obo/GO_0008150> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000051> <http://purl.obolibrary.org/obo/GO_0003674>))
 
+# Class: <http://purl.obolibrary.org/obo/OBI_0000070> (assay)
+
+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/BFO_0000015>)
+
 
 )

src/ontology/imports/cob_terms.txt

@@ -1,2 +1,3 @@
+BFO:0000020
 COB:0000121
 COB:0001000

src/ontology/imports/obi_import.owl

@@ -13,6 +13,10 @@ Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/
 Annotation(owl:versionInfo "2023-08-16")
 
 
+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_0000047>))
 Declaration(Class(<http://purl.obolibrary.org/obo/OBI_0000967>))
@@ -33,6 +37,39 @@ Declaration(AnnotationProperty(<http://purl.org/dc/elements/1.1/source>))
 #   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(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_0000047> (processed material)
 
 AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000111> <http://purl.obolibrary.org/obo/OBI_0000047> "processed material"@en)
@@ -96,4 +133,5 @@ 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

@@ -1,4 +1,7 @@
+OBI:0000011
+OBI:0000070
 OBI:0100026
 OBI:0000047
 OBI:0000967
 OBI:0000968
+

src/ontology/ro-edit.owl

@@ -516,6 +516,8 @@ Declaration(ObjectProperty(obo:RO_0009002))
 Declaration(ObjectProperty(obo:RO_0009003))
 Declaration(ObjectProperty(obo:RO_0009004))
 Declaration(ObjectProperty(obo:RO_0009005))
+Declaration(ObjectProperty(obo:RO_0009006))
+Declaration(ObjectProperty(obo:RO_0009007))
 Declaration(ObjectProperty(obo:RO_0009501))
 Declaration(ObjectProperty(obo:RO_0010001))
 Declaration(ObjectProperty(obo:RO_0010002))
@@ -6004,6 +6006,26 @@ AnnotationAssertion(rdfs:label obo:RO_0009005 "has primary substance added"@en)
 SubObjectPropertyOf(obo:RO_0009005 obo:RO_0009001)
 IrreflexiveObjectProperty(obo:RO_0009005)
 
+# Object Property: obo:RO_0009006 (assay measures characteristic)
+
+AnnotationAssertion(obo:IAO_0000112 obo:RO_0009006 "A mass measurement assay measures an material's mass characteristic. A radioactivity detection assay measures the amount of radiation (alpha, beta or gamma ray emmissions) coming from a material."@en)
+AnnotationAssertion(obo:IAO_0000115 obo:RO_0009006 "A relation between an assay and a characteristic, in which the assay generates a data item which is a measure of a characteristic."@en)
+AnnotationAssertion(terms:contributor obo:RO_0009006 <https://orcid.org/0000-0002-8844-9165>)
+AnnotationAssertion(terms:date obo:RO_0009006 "2023-05-23T15:24:15Z"^^xsd:dateTime)
+AnnotationAssertion(rdfs:label obo:RO_0009006 "assay measures characteristic"@en)
+InverseObjectProperties(obo:RO_0009006 obo:RO_0009007)
+ObjectPropertyDomain(obo:RO_0009006 obo:OBI_0000070)
+ObjectPropertyRange(obo:RO_0009006 obo:BFO_0000020)
+
+# Object Property: obo:RO_0009007 (characteristic measured by assay)
+
+AnnotationAssertion(obo:IAO_0000115 obo:RO_0009007 "Inverse of 'assay measures characteristic'"@en)
+AnnotationAssertion(terms:contributor obo:RO_0009007 <https://orcid.org/0000-0002-8844-9165>)
+AnnotationAssertion(terms:date obo:RO_0009007 "2023-05-23T15:29:50Z"^^xsd:dateTime)
+AnnotationAssertion(rdfs:label obo:RO_0009007 "characteristic measured by assay"@en)
+ObjectPropertyDomain(obo:RO_0009007 obo:BFO_0000020)
+ObjectPropertyRange(obo:RO_0009007 obo:OBI_0000070)
+
 # Object Property: obo:RO_0009501 (realized in response to)
 
 AnnotationAssertion(obo:IAO_0000112 obo:RO_0009501 "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions.")
@@ -7242,4 +7264,4 @@ AnnotationAssertion(oboInOwl:inSubset obo:RO_0002086 subsets:ro-eco)
 AnnotationAssertion(oboInOwl:inSubset obo:RO_0002089 subsets:ro-eco)
 AnnotationAssertion(oboInOwl:inSubset obo:RO_0002093 subsets:ro-eco)
 AnnotationAssertion(Annotation(rdfs:comment "This is an experimental annotation") obo:IAO_0000589 rdfs:isDefinedBy "is defined by")
-)
+)