2022-07-19 Release (#617)

* 2022-07-18 release * remove tmp file * add omo import * new release
oborel · Jul 19, 2022 · a56b953 · a56b953
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commit a56b953
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Showing 40 changed files with 716 additions and 4,572 deletions.
diff --git a/ro-base.json b/ro-base.json
diff --git a/ro-base.obo b/ro-base.obo
@@ -1,5 +1,5 @@
 format-version: 1.2
-data-version: ro/releases/2022-05-23/ro-base.owl
+data-version: ro/releases/2022-07-19/ro-base.owl
 subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension ""
 subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term ""
 subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology ""
@@ -12,6 +12,7 @@ remark: Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo
 remark: Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ro/core.owl>) VersionIRI(<null>))) [Axioms: 310 Logical Axioms: 68]
 remark: Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ro/el-constraints.owl>) VersionIRI(<null>))) [Axioms: 6 Logical Axioms: 2]
 remark: Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ro/generated-axioms.owl>) VersionIRI(<null>))) [Axioms: 18 Logical Axioms: 9]
+remark: Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ro/omo_import.owl>) VersionIRI(<null>))) [Axioms: 3 Logical Axioms: 0]
 remark: Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ro/rohom.owl>) VersionIRI(<null>))) [Axioms: 731 Logical Axioms: 148]
 remark: Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ro/temporal-intervals.owl>) VersionIRI(<null>))) [Axioms: 146 Logical Axioms: 45]
 ontology: ro/ro-base
@@ -1322,6 +1323,7 @@ property_value: RO:0001900 RO:0001901
 property_value: seeAlso FMA:85972 xsd:string
 domain: BFO:0000004 ! independent continuant
 range: BFO:0000004 ! independent continuant
+is_symmetric: true
 is_a: RO:0002323 ! mereotopologically related to
 
 [Typedef]
@@ -4258,6 +4260,7 @@ def: "inverse of branching part of" []
 subset: ro-eco
 subset: RO:0002259
 property_value: IAO:0000117 "Chris Mungall" xsd:string
+is_transitive: true
 is_a: BFO:0000051 ! has part
 is_a: RO:0002375 ! in branching relationship with
 

diff --git a/ro-base.owl b/ro-base.owl
@@ -18,7 +18,7 @@
      xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#"
      xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/ro/ro-base.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/ro/releases/2022-05-23/ro-base.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/ro/releases/2022-07-19/ro-base.owl"/>
         <dc:description xml:lang="en">The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies.</dc:description>
         <dc:title xml:lang="en">OBO Relations Ontology</dc:title>
         <terms:license rdf:resource="https://creativecommons.org/publicdomain/zero/1.0/"/>
@@ -28,6 +28,7 @@
         <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Includes Ontology(OntologyID(OntologyIRI(&lt;http://purl.obolibrary.org/obo/ro/core.owl&gt;) VersionIRI(&lt;null&gt;))) [Axioms: 310 Logical Axioms: 68]</rdfs:comment>
         <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Includes Ontology(OntologyID(OntologyIRI(&lt;http://purl.obolibrary.org/obo/ro/el-constraints.owl&gt;) VersionIRI(&lt;null&gt;))) [Axioms: 6 Logical Axioms: 2]</rdfs:comment>
         <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Includes Ontology(OntologyID(OntologyIRI(&lt;http://purl.obolibrary.org/obo/ro/generated-axioms.owl&gt;) VersionIRI(&lt;null&gt;))) [Axioms: 18 Logical Axioms: 9]</rdfs:comment>
+        <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Includes Ontology(OntologyID(OntologyIRI(&lt;http://purl.obolibrary.org/obo/ro/omo_import.owl&gt;) VersionIRI(&lt;null&gt;))) [Axioms: 3 Logical Axioms: 0]</rdfs:comment>
         <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Includes Ontology(OntologyID(OntologyIRI(&lt;http://purl.obolibrary.org/obo/ro/rohom.owl&gt;) VersionIRI(&lt;null&gt;))) [Axioms: 731 Logical Axioms: 148]</rdfs:comment>
         <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Includes Ontology(OntologyID(OntologyIRI(&lt;http://purl.obolibrary.org/obo/ro/temporal-intervals.owl&gt;) VersionIRI(&lt;null&gt;))) [Axioms: 146 Logical Axioms: 45]</rdfs:comment>
         <foaf:homepage rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI"> https://github.com/oborel/obo-relations/</foaf:homepage>
@@ -141,6 +142,15 @@
 
 
 
+    <!-- http://purl.obolibrary.org/obo/OMO_0002000 -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/OMO_0002000">
+        <obo:IAO_0000115>Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation.</obo:IAO_0000115>
+        <rdfs:label>defined by construct</rdfs:label>
+    </owl:AnnotationProperty>
+
+
+
     <!-- http://purl.obolibrary.org/obo/RO_0001900 -->
 
     <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/RO_0001900">
@@ -160,6 +170,29 @@
         <obo:IAO_0000119 rdf:resource="http://www.ncbi.nlm.nih.gov/pubmed/17921072"/>
         <obo:IAO_0000119 rdf:resource="http://www.ncbi.nlm.nih.gov/pubmed/20973947"/>
         <obo:IAO_0000425>Class: ?X DisjointWith: RO_0002162 some ?Y </obo:IAO_0000425>
+        <obo:OMO_0002000 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PREFIX rdfs: &lt;http://www.w3.org/2000/01/rdf-schema#&gt;
+PREFIX owl: &lt;http://www.w3.org/2002/07/owl#&gt;
+PREFIX in_taxon: &lt;http://purl.obolibrary.org/obo/RO_0002162&gt;
+PREFIX never_in_taxon: &lt;http://purl.obolibrary.org/obo/RO_0002161&gt;
+CONSTRUCT {
+  in_taxon: a owl:ObjectProperty .
+  ?x owl:disjointWith [
+    a owl:Restriction ;
+    owl:onProperty in_taxon: ;
+    owl:someValuesFrom ?taxon
+  ] .
+  ?x rdfs:subClassOf [
+    a owl:Restriction ;
+    owl:onProperty in_taxon: ;
+    owl:someValuesFrom [
+      a owl:Class ;
+      owl:complementOf ?taxon
+    ]
+  ] .
+}
+WHERE {
+  ?x never_in_taxon: ?taxon .
+}</obo:OMO_0002000>
         <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">never in taxon</rdfs:label>
         <rdfs:seeAlso rdf:resource="https://github.com/obophenotype/uberon/wiki/Taxon-constraints"/>
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002172"/>
@@ -175,6 +208,25 @@
         <obo:IAO_0000118>shares no parts with</obo:IAO_0000118>
         <obo:IAO_0000119 rdf:resource="http://www.ncbi.nlm.nih.gov/pubmed/22293552"/>
         <obo:IAO_0000425>Class: &lt;http://www.w3.org/2002/07/owl#Nothing&gt; EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y)</obo:IAO_0000425>
+        <obo:OMO_0002000 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PREFIX owl: &lt;http://www.w3.org/2002/07/owl#&gt;
+PREFIX part_of: &lt;http://purl.obolibrary.org/obo/BFO_0000050&gt;
+PREFIX mutually_spatially_disjoint_with: &lt;http://purl.obolibrary.org/obo/RO_0002171&gt;
+CONSTRUCT {
+  part_of: a owl:ObjectProperty .
+  [
+    a owl:Restriction ;
+    owl:onProperty part_of: ;
+    owl:someValuesFrom ?x ;
+    owl:disjointWith [
+      a owl:Restriction ;
+      owl:onProperty part_of: ;
+      owl:someValuesFrom ?y
+    ]
+  ]
+}
+WHERE {
+  ?x mutually_spatially_disjoint_with: ?y .
+}</obo:OMO_0002000>
         <rdfs:label xml:lang="en">mutually spatially disjoint with</rdfs:label>
         <rdfs:seeAlso rdf:resource="http://purl.obolibrary.org/obo/RO_0002163"/>
         <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern</rdfs:seeAlso>
@@ -225,6 +277,31 @@
         <obo:IAO_0000115>S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S</obo:IAO_0000115>
         <obo:IAO_0000117>https://orcid.org/0000-0002-6601-2165</obo:IAO_0000117>
         <obo:IAO_0000119 rdf:resource="http://www.ncbi.nlm.nih.gov/pubmed/22293552"/>
+        <obo:OMO_0002000 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PREFIX rdfs: &lt;http://www.w3.org/2000/01/rdf-schema#&gt;
+PREFIX owl: &lt;http://www.w3.org/2002/07/owl#&gt;
+PREFIX in_taxon: &lt;http://purl.obolibrary.org/obo/RO_0002162&gt;
+PREFIX present_in_taxon: &lt;http://purl.obolibrary.org/obo/RO_0002175&gt;
+CONSTRUCT {
+  in_taxon: a owl:ObjectProperty .
+  ?witness rdfs:label ?label .
+  ?witness rdfs:subClassOf ?x .
+  ?witness rdfs:subClassOf [
+    a owl:Restriction ;
+    owl:onProperty in_taxon: ;
+    owl:someValuesFrom ?taxon
+  ] .
+}
+WHERE {
+  ?x present_in_taxon: ?taxon .
+  BIND(IRI(CONCAT(
+    &quot;http://purl.obolibrary.org/obo/RO_0002175#&quot;,
+    MD5(STR(?x)),
+    &quot;-&quot;,
+    MD5(STR(?taxon))
+  )) as ?witness)
+  BIND(CONCAT(STR(?x), &quot; in taxon &quot;, STR(?taxon)) AS ?label)
+}</obo:OMO_0002000>
+        <rdfs:comment>The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology.</rdfs:comment>
         <rdfs:label xml:lang="en">present in taxon</rdfs:label>
         <rdfs:seeAlso rdf:resource="https://github.com/obophenotype/uberon/wiki/Taxon-constraints"/>
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002172"/>
@@ -2933,6 +3010,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.</obo:I
 
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002150">
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002323"/>
+        <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#SymmetricProperty"/>
         <rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000004"/>
         <rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000004"/>
         <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
@@ -7623,6 +7701,7 @@ the a supports either the existence of b, or the truth value of b.</obo:IAO_0000
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002569">
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002375"/>
+        <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
         <obo:IAO_0000115>inverse of branching part of</obo:IAO_0000115>
         <obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/RO_0002259"/>