Merge pull request #32 from obophenotype/ODK-Release-March-22-2022

ODK Release March 22 2022
obophenotype · Mar 22, 2022 · 30d3566 · 30d3566
2 parents ad0ab23 + f3bcf1f
commit 30d3566
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diff --git a/src/ontology/Makefile b/src/ontology/Makefile
diff --git a/src/ontology/imports/ro_import.owl b/src/ontology/imports/ro_import.owl
@@ -16,9 +16,9 @@
      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/wbls/imports/ro_import.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/wbls/releases/2021-12-08/imports/ro_import.owl"/>
-        <dc:source rdf:resource="http://purl.obolibrary.org/obo/ro/releases/2021-12-06/ro.owl"/>
-        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2021-12-08</owl:versionInfo>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/wbls/releases/2022-03-22/imports/ro_import.owl"/>
+        <dc:source rdf:resource="http://purl.obolibrary.org/obo/ro/releases/2022-02-07/ro.owl"/>
+        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-03-22</owl:versionInfo>
     </owl:Ontology>
 
 
@@ -238,6 +238,12 @@
 
 
 
+    <!-- http://purl.org/dc/terms/contributor -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/contributor"/>
+
+
+
     <!-- http://purl.org/dc/terms/creator -->
 
     <owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/creator"/>
@@ -2213,17 +2219,17 @@ For example, A and B may be gene products and binding of B by A positively regul
 
 
 
-    <!-- http://purl.obolibrary.org/obo/ro.owl/RO_0017001 -->
+    <!-- http://purl.obolibrary.org/obo/RO_0017001 -->
 
-    <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/ro.owl/RO_0017001">
+    <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0017001">
         <owl:propertyChainAxiom rdf:parseType="Collection">
             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002215"/>
             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002233"/>
         </owl:propertyChainAxiom>
         <obo:IAO_0000112>A diagnostic testing device utilizes a specimen.</obo:IAO_0000112>
         <obo:IAO_0000115>X utilizes Y means X and Y are material entities, and X is capable of some process P that has input Y.</obo:IAO_0000115>
         <obo:IAO_0000117>Asiyah Lin</obo:IAO_0000117>
-        <obo:IAO_0000117>Bill Duncan (https://orcid.org/0000-0001-9625-1899)</obo:IAO_0000117>
+        <obo:IAO_0000117>https://orcid.org/0000-0001-9625-1899 Bill Duncan</obo:IAO_0000117>
         <obo:IAO_0000232>A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input.</obo:IAO_0000232>
         <obo:IAO_0000232>See github ticket https://github.com/oborel/obo-relations/issues/497</obo:IAO_0000232>
         <oboInOwl:creation_date>2021-11-08</oboInOwl:creation_date>
@@ -2232,6 +2238,57 @@ For example, A and B may be gene products and binding of B by A positively regul
 
 
 
+    <!-- http://purl.obolibrary.org/obo/RO_0019000 -->
+
+    <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0019000">
+        <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002410"/>
+        <rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
+        <rdfs:range rdf:resource="http://purl.obolibrary.org/obo/PATO_0000001"/>
+        <owl:propertyChainAxiom rdf:parseType="Collection">
+            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002211"/>
+            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0019000"/>
+        </owl:propertyChainAxiom>
+        <obo:IAO_0000115>A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C.</obo:IAO_0000115>
+        <terms:contributor rdf:resource="https://orcid.org/0000-0002-8688-6599"/>
+        <rdfs:label>regulates characteristic</rdfs:label>
+    </owl:ObjectProperty>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/RO_0019001 -->
+
+    <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0019001">
+        <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0019000"/>
+        <owl:propertyChainAxiom rdf:parseType="Collection">
+            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002213"/>
+            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0019001"/>
+        </owl:propertyChainAxiom>
+        <obo:IAO_0000115>A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C.</obo:IAO_0000115>
+        <terms:contributor rdf:resource="https://orcid.org/0000-0002-8688-6599"/>
+        <rdfs:label>positively regulates characteristic</rdfs:label>
+    </owl:ObjectProperty>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/RO_0019002 -->
+
+    <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0019002">
+        <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0019000"/>
+        <owl:propertyChainAxiom rdf:parseType="Collection">
+            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002212"/>
+            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0019001"/>
+        </owl:propertyChainAxiom>
+        <owl:propertyChainAxiom rdf:parseType="Collection">
+            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002213"/>
+            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0019002"/>
+        </owl:propertyChainAxiom>
+        <obo:IAO_0000115>A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C.</obo:IAO_0000115>
+        <terms:contributor rdf:resource="https://orcid.org/0000-0002-8688-6599"/>
+        <rdfs:label>negatively regulates characteristic</rdfs:label>
+    </owl:ObjectProperty>
+
+
+
     <!-- 
     ///////////////////////////////////////////////////////////////////////////////////////
     //
@@ -2480,6 +2537,16 @@ For example, A and B may be gene products and binding of B by A positively regul
 
 
 
+    <!-- http://purl.obolibrary.org/obo/PATO_0000001 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/PATO_0000001">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
+        <obo:IAO_0000589>quality (PATO)</obo:IAO_0000589>
+        <rdfs:label>quality</rdfs:label>
+    </owl:Class>
+
+
+
     <!-- 
     ///////////////////////////////////////////////////////////////////////////////////////
     //
@@ -2618,13 +2685,13 @@ For example, A and B may be gene products and binding of B by A positively regul
     <rdf:Description rdf:about="urn:swrl#mf2">
         <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#Variable"/>
     </rdf:Description>
-    <rdf:Description rdf:about="urn:swrl:var#y">
+    <rdf:Description rdf:about="urn:swrl:var#x">
         <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#Variable"/>
     </rdf:Description>
-    <rdf:Description rdf:about="urn:swrl:var#z">
+    <rdf:Description rdf:about="urn:swrl:var#y">
         <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#Variable"/>
     </rdf:Description>
-    <rdf:Description rdf:about="urn:swrl:var#x">
+    <rdf:Description rdf:about="urn:swrl:var#z">
         <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#Variable"/>
     </rdf:Description>
     <rdf:Description>
@@ -3712,6 +3779,50 @@ e.g.  if GP X enables ATPase coupled transporter activity&apos; and &apos;ATPase
             </rdf:Description>
         </swrl:head>
     </rdf:Description>
+    <rdf:Description>
+        <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#Imp"/>
+        <swrl:body>
+            <rdf:Description>
+                <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
+                <rdf:first>
+                    <rdf:Description>
+                        <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
+                        <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0002212"/>
+                        <swrl:argument1 rdf:resource="urn:swrl:var#x"/>
+                        <swrl:argument2 rdf:resource="urn:swrl:var#y"/>
+                    </rdf:Description>
+                </rdf:first>
+                <rdf:rest>
+                    <rdf:Description>
+                        <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
+                        <rdf:first>
+                            <rdf:Description>
+                                <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
+                                <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0019002"/>
+                                <swrl:argument1 rdf:resource="urn:swrl:var#y"/>
+                                <swrl:argument2 rdf:resource="urn:swrl:var#z"/>
+                            </rdf:Description>
+                        </rdf:first>
+                        <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
+                    </rdf:Description>
+                </rdf:rest>
+            </rdf:Description>
+        </swrl:body>
+        <swrl:head>
+            <rdf:Description>
+                <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
+                <rdf:first>
+                    <rdf:Description>
+                        <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
+                        <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0019001"/>
+                        <swrl:argument1 rdf:resource="urn:swrl:var#x"/>
+                        <swrl:argument2 rdf:resource="urn:swrl:var#z"/>
+                    </rdf:Description>
+                </rdf:first>
+                <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
+            </rdf:Description>
+        </swrl:head>
+    </rdf:Description>
     <rdf:Description>
         <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#Imp"/>
         <swrl:body>

diff --git a/src/ontology/non_native_classes.txt b/src/ontology/non_native_classes.txt
@@ -17,4 +17,5 @@ http://purl.obolibrary.org/obo/GO_0008150
 http://purl.obolibrary.org/obo/GO_0016301
 http://purl.obolibrary.org/obo/GO_0016740
 http://purl.obolibrary.org/obo/GO_0016772
+http://purl.obolibrary.org/obo/PATO_0000001
 term
diff --git a/src/ontology/reports/validate_profile_owl2dl_wbls.owl.txt b/src/ontology/reports/validate_profile_owl2dl_wbls.owl.txt
@@ -0,0 +1 @@
+OWL 2 DL Profile Report: [Ontology and imports closure in profile]
diff --git a/src/ontology/reports/wbls-edit.owl-obo-report.tsv b/src/ontology/reports/wbls-edit.owl-obo-report.tsv
@@ -1,4 +1,5 @@
 Level	Rule Name	Subject	Property	Value
+WARN	duplicate_label_synonym	cysticercoid stage	has_exact_synonym	cysticercoid stage
 WARN	missing_definition	part_of	definition	
 WARN	missing_definition	preceded_by	definition	
 WARN	missing_definition	definition	definition	
@@ -12,5 +13,4 @@ WARN	missing_definition	has_obo_format_version	definition
 WARN	missing_definition	has_obo_namespace	definition	
 WARN	missing_definition	has_related_synonym	definition	
 WARN	missing_definition	shorthand	definition	
-WARN	duplicate_label_synonym	cysticercoid stage	has_exact_synonym	cysticercoid stage
 INFO	missing_superclass	worm life stage	rdfs:subClassOf	
diff --git a/src/sparql/iri-range-violation.sparql b/src/sparql/iri-range-violation.sparql
@@ -0,0 +1,19 @@
+PREFIX never_in_taxon: <http://purl.obolibrary.org/obo/RO_0002161>
+PREFIX present_in_taxon: <http://purl.obolibrary.org/obo/RO_0002175>
+PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
+PREFIX dcterms: <http://purl.org/dc/terms/>
+PREFIX foaf: <http://xmlns.com/foaf/0.1/>
+
+SELECT ?term ?property ?value
+WHERE {
+  VALUES ?property {
+    never_in_taxon:
+    present_in_taxon:
+    foaf:depicted_by
+    oboInOwl:inSubset
+    dcterms:contributor  }
+  ?term ?property ?value .
+  FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/WBLS_") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/WBls_")))
+  FILTER (!isIRI(?value))
+}
+
diff --git a/src/sparql/label-with-iri-violation.sparql b/src/sparql/label-with-iri-violation.sparql
@@ -0,0 +1,9 @@
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+
+SELECT ?term ?value
+WHERE {
+  ?term rdfs:label ?value .
+  FILTER (REGEX(?value, "http[s]?[:]"))
+  FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/WBLS_") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/WBls_")))
+}
+
diff --git a/src/sparql/owldef-self-reference-violation.sparql b/src/sparql/owldef-self-reference-violation.sparql
@@ -1,11 +1,12 @@
-prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
-prefix oio: <http://www.geneontology.org/formats/oboInOwl#>
-prefix owl: <http://www.w3.org/2002/07/owl#>
-prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX oio: <http://www.geneontology.org/formats/oboInOwl#>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
 
-SELECT ?c
-WHERE {
-  { ?c owl:equivalentClass [ owl:intersectionOf [ rdf:rest*/rdf:first ?c ] ] }
+SELECT ?term WHERE {
+  { ?term owl:equivalentClass [ owl:intersectionOf [ rdf:rest*/rdf:first ?term ] ] }
     UNION
-  { ?c owl:equivalentClass [ owl:intersectionOf [ rdf:rest*/rdf:first [ owl:someValuesFrom ?c ] ] ] }
+  { ?term owl:equivalentClass [ owl:intersectionOf [ rdf:rest*/rdf:first [ owl:someValuesFrom ?term ] ] ] }
+  FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/WBLS_") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/WBls_")))
 }
+
diff --git a/src/sparql/wbls_terms.sparql b/src/sparql/wbls_terms.sparql
@@ -3,5 +3,5 @@ WHERE {
   { ?s1 ?p1 ?term . }
   UNION
   { ?term ?p2 ?o2 . }
-  FILTER(isIRI(?term) && (regex(str(?term), UCASE("wbls_")) || regex(str(?term), "http://purl.obolibrary.org/obo/WBls_")))
+  FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/WBLS_") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/WBls_")))
 }
diff --git a/wbls-base.json b/wbls-base.json
@@ -10774,11 +10774,11 @@
           },
           {
             "pred": "http://www.w3.org/2002/07/owl#versionInfo",
-            "val": "2021-12-08"
+            "val": "2022-03-22"
           }
         ],
         "subsets": [],
-        "version": "http://purl.obolibrary.org/obo/wbls/releases/2021-12-08/wbls-base.json",
+        "version": "http://purl.obolibrary.org/obo/wbls/releases/2022-03-22/wbls-base.json",
         "xrefs": []
       },
       "nodes": [

diff --git a/wbls-base.obo b/wbls-base.obo
@@ -1,5 +1,5 @@
 format-version: 1.2
-data-version: wbls/releases/2021-12-08/wbls-base.owl
+data-version: wbls/releases/2022-03-22/wbls-base.owl
 date: 15:11:2017 12:24
 saved-by: chris-grove
 auto-generated-by: OBO-Edit 2.2-rc1
@@ -12,7 +12,7 @@ property_value: http://purl.org/dc/elements/1.1/title "C. elegans Development On
 property_value: http://purl.org/dc/elements/1.1/type IAO:8000001
 property_value: http://purl.org/dc/terms/license http://creativecommons.org/licenses/by/4.0/ xsd:string
 property_value: IAO:0000700 WBls:0000075
-property_value: owl:versionInfo "2021-12-08" xsd:string
+property_value: owl:versionInfo "2022-03-22" xsd:string
 
 [Term]
 id: WBls:0000001

diff --git a/wbls-base.owl b/wbls-base.owl
@@ -11,7 +11,7 @@
      xmlns:terms="http://purl.org/dc/terms/"
      xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/wbls/wbls-base.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/wbls/releases/2021-12-08/wbls-base.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/wbls/releases/2022-03-22/wbls-base.owl"/>
         <obo:IAO_0000700 rdf:resource="http://purl.obolibrary.org/obo/WBls_0000075"/>
         <dc:description>Ontology about the development and life stages of the C. elegans</dc:description>
         <dc:title>C. elegans Development Ontology</dc:title>
@@ -24,7 +24,7 @@
         <oboInOwl:saved-by rdf:datatype="http://www.w3.org/2001/XMLSchema#string">chris-grove</oboInOwl:saved-by>
         <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Editors: Wen J. Chen &amp; Daniela Raciti, Raymond Lee, Chris Grove, WormBase, Caltech. Jane Lomax, Wellcome Trust Sanger Institute.</rdfs:comment>
         <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Version: 1.04</rdfs:comment>
-        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2021-12-08</owl:versionInfo>
+        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-03-22</owl:versionInfo>
     </owl:Ontology>
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		OWL 2 DL Profile Report: [Ontology and imports closure in profile]