Infrastructure release - no content changes

EBISPOT · Oct 13, 2023 · 9b70c7e · 9b70c7e
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diff --git a/.github/workflows/qc.yml b/.github/workflows/qc.yml
@@ -19,7 +19,7 @@ jobs:
   ontology_qc:
     # The type of runner that the job will run on
     runs-on: ubuntu-latest
-    container: obolibrary/odkfull:v1.4
+    container: obolibrary/odkfull:latest
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:

diff --git a/docs/odk-workflows/RepositoryFileStructure.md b/docs/odk-workflows/RepositoryFileStructure.md
@@ -17,7 +17,7 @@ These are the current imports in HANCESTRO
 | Import | URL | Type |
 | ------ | --- | ---- |
 | obi | http://purl.obolibrary.org/obo/obi.owl | custom |
-| geo | http://purl.obolibrary.org/obo/geo.owl | slme |
+| geo | http://purl.obolibrary.org/obo/geo.owl | custom |
 | bfo | http://purl.obolibrary.org/obo/bfo.owl | slme |
 | ro | http://purl.obolibrary.org/obo/ro.owl | None |
 

diff --git a/hancestro-base.json b/hancestro-base.json
@@ -22,12 +22,9 @@
         "val" : "http://creativecommons.org/licenses/by/4.0/"
       }, {
         "pred" : "http://www.w3.org/2002/07/owl#versionInfo",
-        "val" : "2023-07-31"
-      }, {
-        "pred" : "http://www.w3.org/2002/07/owl#versionInfo",
-        "val" : "3.0"
+        "val" : "2023-10-13"
       } ],
-      "version" : "http://purl.obolibrary.org/obo/hancestro/releases/2023-07-31/hancestro-base.json"
+      "version" : "http://purl.obolibrary.org/obo/hancestro/releases/2023-10-13/hancestro-base.json"
     },
     "nodes" : [ {
       "id" : "http://dbpedia.org/resource/Afghanistan",

diff --git a/hancestro-base.obo b/hancestro-base.obo
@@ -1,14 +1,13 @@
 format-version: 1.2
-data-version: hancestro/releases/2023-07-31/hancestro-base.owl
+data-version: hancestro/releases/2023-10-13/hancestro-base.owl
 ontology: hancestro/hancestro-base
 property_value: http://purl.org/dc/elements/1.1/description "Human ancestry ontology for the NHGRI GWAS Catalog" xsd:string
 property_value: http://purl.org/dc/elements/1.1/title "Human Ancestry Ontology" xsd:string
 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/
 property_value: IAO:0000700 HANCESTRO:0004
 property_value: IAO:0000700 HANCESTRO:0304
-property_value: owl:versionInfo "2023-07-31" xsd:string
-property_value: owl:versionInfo "3.0" xsd:decimal
+property_value: owl:versionInfo "2023-10-13" xsd:string
 
 [Term]
 id: American:Samoa

diff --git a/hancestro-base.owl b/hancestro-base.owl
@@ -11,15 +11,14 @@
      xmlns:terms="http://purl.org/dc/terms/"
      xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/hancestro/hancestro-base.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/hancestro/releases/2023-07-31/hancestro-base.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/hancestro/releases/2023-10-13/hancestro-base.owl"/>
         <obo:IAO_0000700 rdf:resource="http://purl.obolibrary.org/obo/HANCESTRO_0004"/>
         <obo:IAO_0000700 rdf:resource="http://purl.obolibrary.org/obo/HANCESTRO_0304"/>
         <dc:description>Human ancestry ontology for the NHGRI GWAS Catalog</dc:description>
         <dc:title>Human Ancestry Ontology</dc:title>
         <dc:type rdf:resource="http://purl.obolibrary.org/obo/IAO_8000001"/>
         <terms:license rdf:resource="http://creativecommons.org/licenses/by/4.0/"/>
-        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#decimal">3.0</owl:versionInfo>
-        <owl:versionInfo>2023-07-31</owl:versionInfo>
+        <owl:versionInfo>2023-10-13</owl:versionInfo>
     </owl:Ontology>
 
 
@@ -13940,5 +13939,5 @@ category does not include all native populations within the Arctic circle for ex
 
 
 
-<!-- Generated by the OWL API (version 4.5.25) https://github.com/owlcs/owlapi -->
+<!-- Generated by the OWL API (version 4.5.26) https://github.com/owlcs/owlapi -->
 
diff --git a/hancestro-full.json b/hancestro-full.json
@@ -19,12 +19,9 @@
         "val" : "http://creativecommons.org/licenses/by/4.0/"
       }, {
         "pred" : "http://www.w3.org/2002/07/owl#versionInfo",
-        "val" : "2023-07-31"
-      }, {
-        "pred" : "http://www.w3.org/2002/07/owl#versionInfo",
-        "val" : "3.0"
+        "val" : "2023-10-13"
       } ],
-      "version" : "http://purl.obolibrary.org/obo/hancestro/releases/2023-07-31/hancestro-full.json"
+      "version" : "http://purl.obolibrary.org/obo/hancestro/releases/2023-10-13/hancestro-full.json"
     },
     "nodes" : [ {
       "id" : "http://dbpedia.org/resource/Afghanistan",
@@ -3100,7 +3097,7 @@
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
           "val" : "preceded_by"
         }, {
-          "pred" : "http://purl.org/dc/elements/1.1/source",
+          "pred" : "http://purl.org/dc/terms/source",
           "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by"
         } ]
       }
@@ -5314,7 +5311,7 @@
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
           "val" : "has_participant"
         }, {
-          "pred" : "http://purl.org/dc/elements/1.1/source",
+          "pred" : "http://purl.org/dc/terms/source",
           "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant"
         } ]
       }
@@ -5492,46 +5489,6 @@
           "val" : "http://purl.obolibrary.org/obo/RO_0001901"
         } ]
       }
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/RO_0001018",
-      "lbl" : "contained in",
-      "type" : "PROPERTY",
-      "meta" : {
-        "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000111",
-          "val" : "contained in"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
-          "val" : "Containment is location not involving parthood, and arises only where some immaterial continuant is involved."
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
-          "val" : "Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation.    If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows:    c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
-          "val" : "Intended meaning:\ndomain: material entity\nrange: spatial region or site (immaterial continuant)\n        "
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
-          "val" : "contained_in"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0001900",
-          "val" : "http://purl.obolibrary.org/obo/RO_0001901"
-        } ]
-      }
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/RO_0001019",
-      "lbl" : "contains",
-      "type" : "PROPERTY",
-      "meta" : {
-        "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000111",
-          "val" : "contains"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0001900",
-          "val" : "http://purl.obolibrary.org/obo/RO_0001901"
-        } ]
-      }
     }, {
       "id" : "http://purl.obolibrary.org/obo/RO_0001025",
       "lbl" : "located_in",
@@ -5563,7 +5520,7 @@
           "pred" : "http://purl.obolibrary.org/obo/RO_0001900",
           "val" : "http://purl.obolibrary.org/obo/RO_0001901"
         }, {
-          "pred" : "http://purl.org/dc/elements/1.1/source",
+          "pred" : "http://purl.org/dc/terms/source",
           "val" : "http://www.obofoundry.org/ro/#OBO_REL:located_in"
         }, {
           "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
@@ -6956,19 +6913,6 @@
           "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations"
         } ]
       }
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/RO_0002610",
-      "lbl" : "correlated with",
-      "type" : "PROPERTY",
-      "meta" : {
-        "definition" : {
-          "val" : "A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes."
-        },
-        "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000232",
-          "val" : "Groups both positive and negative correlation"
-        } ]
-      }
     }, {
       "id" : "http://purl.obolibrary.org/obo/RO_0002629",
       "lbl" : "directly positively regulates",
@@ -7232,22 +7176,6 @@
           "val" : "2021-11-08T12:00:00Z"
         } ]
       }
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/RO_0017003",
-      "lbl" : "positively correlated with",
-      "type" : "PROPERTY",
-      "meta" : {
-        "definition" : {
-          "val" : "A relation between entities in which one increases or decreases as the other does the same."
-        },
-        "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
-          "val" : "directly correlated with"
-        }, {
-          "pred" : "http://purl.org/dc/terms/contributor",
-          "val" : "https://orcid.org/0000-0003-1909-9269"
-        } ]
-      }
     }, {
       "id" : "http://purl.obolibrary.org/obo/RO_0019000",
       "lbl" : "regulates characteristic",
@@ -14926,10 +14854,6 @@
       "sub" : "http://purl.obolibrary.org/obo/RO_0012012",
       "pred" : "subPropertyOf",
       "obj" : "http://purl.obolibrary.org/obo/RO_0012011"
-    }, {
-      "sub" : "http://purl.obolibrary.org/obo/RO_0017003",
-      "pred" : "subPropertyOf",
-      "obj" : "http://purl.obolibrary.org/obo/RO_0002610"
     }, {
       "sub" : "http://purl.obolibrary.org/obo/RO_0019000",
       "pred" : "subPropertyOf",
@@ -14982,10 +14906,6 @@
       "sub" : "http://purl.obolibrary.org/obo/RO_0001015",
       "pred" : "inverseOf",
       "obj" : "http://purl.obolibrary.org/obo/RO_0001025"
-    }, {
-      "sub" : "http://purl.obolibrary.org/obo/RO_0001018",
-      "pred" : "inverseOf",
-      "obj" : "http://purl.obolibrary.org/obo/RO_0001019"
     }, {
       "sub" : "http://purl.obolibrary.org/obo/RO_0002022",
       "pred" : "inverseOf",
@@ -17798,10 +17718,6 @@
       "predicateId" : "http://purl.obolibrary.org/obo/RO_0000091",
       "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ],
       "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000016" ]
-    }, {
-      "predicateId" : "http://purl.obolibrary.org/obo/RO_0001018",
-      "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ],
-      "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ]
     }, {
       "predicateId" : "http://purl.obolibrary.org/obo/RO_0002018",
       "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ],
@@ -17899,9 +17815,6 @@
     }, {
       "predicateId" : "http://purl.obolibrary.org/obo/RO_0002314",
       "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0000052", "http://purl.obolibrary.org/obo/BFO_0000050" ]
-    }, {
-      "predicateId" : "http://purl.obolibrary.org/obo/RO_0001018",
-      "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0001025", "http://purl.obolibrary.org/obo/BFO_0000050" ]
     }, {
       "predicateId" : "http://purl.obolibrary.org/obo/RO_0001025",
       "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0001025", "http://purl.obolibrary.org/obo/BFO_0000050" ]