Merge pull request #9 from VirtualFlyBrain/release_2022-10-24

release 2022-10-24
VirtualFlyBrain · Oct 24, 2022 · 3e27bc0 · 3e27bc0
2 parents 1606d71 + 619439f
commit 3e27bc0
Show file tree

Hide file tree

Showing 24 changed files with 771 additions and 938 deletions.
diff --git a/imports/caro_import.owl b/imports/caro_import.owl
@@ -12,14 +12,14 @@
      xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"
      xmlns:oboInOwl1="ttp://www.geneontology.org/formats/oboInOwl#">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/vfbext/imports/caro_import.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/vfbext/releases/2022-02-25/imports/caro_import.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/vfbext/releases/2022-10-24/imports/caro_import.owl"/>
         <dc:description>None</dc:description>
         <dc:source rdf:resource="http://purl.obolibrary.org/obo/caro/releases/2022-02-18/caro.owl"/>
         <dc:title>Common Anatomy Reference Ontology</dc:title>
         <terms:license rdf:resource="https://creativecommons.org/licenses/unspecified"/>
         <rdfs:comment>Based on CARO 1.0, with modifications and additions by David Osumi-Sutherland, Chris Mungall, Ramona Walls and Melissa Haendal.</rdfs:comment>
         <owl:versionInfo>2022-02-18</owl:versionInfo>
-        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-02-25</owl:versionInfo>
+        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-10-24</owl:versionInfo>
     </owl:Ontology>
 
 

diff --git a/imports/fbbt_import.owl b/imports/fbbt_import.owl
@@ -18,9 +18,9 @@
      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/vfbext/imports/fbbt_import.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/vfbext/releases/2022-02-25/imports/fbbt_import.owl"/>
-        <dc:source rdf:resource="http://purl.obolibrary.org/obo/fbbt/releases/2022-02-24/fbbt.owl"/>
-        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-02-25</owl:versionInfo>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/vfbext/releases/2022-10-24/imports/fbbt_import.owl"/>
+        <dc:source rdf:resource="http://purl.obolibrary.org/obo/fbbt/releases/2022-10-19/fbbt.owl"/>
+        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-10-24</owl:versionInfo>
     </owl:Ontology>
 
 
@@ -229,14 +229,6 @@
 
 
 
-    <!-- http://purl.obolibrary.org/obo/go#goslim_aspergillus -->
-
-    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/go#goslim_aspergillus">
-        <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/>
-    </owl:AnnotationProperty>
-
-
-
     <!-- http://purl.obolibrary.org/obo/go#goslim_candida -->
 
     <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/go#goslim_candida">
@@ -319,6 +311,12 @@
 
 
 
+    <!-- http://purl.org/dc/terms/date -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/date"/>
+
+
+
     <!-- http://purl.org/dc/terms/source -->
 
     <owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/source"/>
@@ -357,6 +355,12 @@
 
 
 
+    <!-- http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym -->
+
+    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym"/>
+
+
+
     <!-- http://www.geneontology.org/formats/oboInOwl#hasDbXref -->
 
     <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasDbXref">
@@ -945,6 +949,7 @@ A continuant cannot have an occurrent as part: use &apos;participates in&apos;.
 
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002131">
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002323"/>
+        <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#SymmetricProperty"/>
         <owl:propertyChainAxiom rdf:parseType="Collection">
             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000050"/>
             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000050"/>
@@ -2223,13 +2228,14 @@ For example, A and B may be gene products and binding of B by A positively regul
             <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>https://orcid.org/0000-0001-9625-1899 Bill Duncan</obo:IAO_0000117>
+        <obo:IAO_0000115>X device utilizes material 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>https://orcid.org/0000-0001-9625-1899</obo:IAO_0000117>
+        <obo:IAO_0000117>https://orcid.org/0000-0003-2620-0345</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>
-        <rdfs:label xml:lang="en">utilizes</rdfs:label>
+        <oboInOwl:creation_date>2021-11-08T12:00:00Z</oboInOwl:creation_date>
+        <oboInOwl:hasBroadSynonym>utilizes</oboInOwl:hasBroadSynonym>
+        <rdfs:label xml:lang="en">device utilizes material</rdfs:label>
     </owl:ObjectProperty>
 
 
@@ -2544,8 +2550,8 @@ For example, A and B may be gene products and binding of B by A positively regul
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/FBbt_00100313">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/FBbt_00007001"/>
         <obo:IAO_0000115>Anatomical structure that has multiple cells as parts.</obo:IAO_0000115>
-        <oboInOwl:created_by>djs93</oboInOwl:created_by>
-        <oboInOwl:creation_date>2010-11-02T02:25:04Z</oboInOwl:creation_date>
+        <terms:contributor rdf:resource="http://orcid.org/0000-0002-7073-9172"/>
+        <terms:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2010-11-02T02:25:04Z</terms:date>
         <oboInOwl:hasDbXref>UBERON:0010000</oboInOwl:hasDbXref>
         <oboInOwl:hasOBONamespace>fly_anatomy.ontology</oboInOwl:hasOBONamespace>
         <oboInOwl:id>FBbt:00100313</oboInOwl:id>
@@ -2638,7 +2644,6 @@ For example, A and B may be gene products and binding of B by A positively regul
         <oboInOwl:hasRelatedSynonym>single organism process</oboInOwl:hasRelatedSynonym>
         <oboInOwl:hasRelatedSynonym>single-organism process</oboInOwl:hasRelatedSynonym>
         <oboInOwl:id>GO:0008150</oboInOwl:id>
-        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/go#goslim_aspergillus"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/go#goslim_candida"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/go#goslim_chembl"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/go#goslim_metagenomics"/>

diff --git a/imports/obi_import.owl b/imports/obi_import.owl
@@ -1,15 +1,85 @@
 <?xml version="1.0"?>
 <rdf:RDF xmlns="http://purl.obolibrary.org/obo/vfbext/imports/obi_import.owl#"
      xml:base="http://purl.obolibrary.org/obo/vfbext/imports/obi_import.owl"
+     xmlns:dc="http://purl.org/dc/elements/1.1/"
      xmlns:obo="http://purl.obolibrary.org/obo/"
      xmlns:owl="http://www.w3.org/2002/07/owl#"
      xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
      xmlns:xml="http://www.w3.org/XML/1998/namespace"
      xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
-     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
+     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
+     xmlns:terms="http://purl.org/dc/terms/"
+     xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/vfbext/imports/obi_import.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/vfbext/releases/2022-02-25/imports/obi_import.owl"/>
-        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-02-25</owl:versionInfo>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/vfbext/releases/2022-10-24/imports/obi_import.owl"/>
+        <protege:defaultLanguage rdf:datatype="http://www.w3.org/2001/XMLSchema#string">en</protege:defaultLanguage>
+        <obo:IAO_0000589 xml:lang="en">Ontology for Biomedical Investigations</obo:IAO_0000589>
+        <dc:contributor xml:lang="en">Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester</dc:contributor>
+        <dc:creator xml:lang="en">Alan Ruttenberg</dc:creator>
+        <dc:creator xml:lang="en">Allyson Lister</dc:creator>
+        <dc:creator xml:lang="en">Barry Smith</dc:creator>
+        <dc:creator xml:lang="en">Bill Bug</dc:creator>
+        <dc:creator xml:lang="en">Bjoern Peters</dc:creator>
+        <dc:creator xml:lang="en">Carlo Torniai</dc:creator>
+        <dc:creator xml:lang="en">Chris Mungall</dc:creator>
+        <dc:creator xml:lang="en">Chris Stoeckert</dc:creator>
+        <dc:creator xml:lang="en">Chris Taylor</dc:creator>
+        <dc:creator xml:lang="en">Christian Bolling</dc:creator>
+        <dc:creator xml:lang="en">Cristian Cocos</dc:creator>
+        <dc:creator xml:lang="en">Daniel Rubin</dc:creator>
+        <dc:creator xml:lang="en">Daniel Schober</dc:creator>
+        <dc:creator xml:lang="en">Dawn Field</dc:creator>
+        <dc:creator xml:lang="en">Dirk Derom</dc:creator>
+        <dc:creator xml:lang="en">Elisabetta Manduchi</dc:creator>
+        <dc:creator xml:lang="en">Eric Deutsch</dc:creator>
+        <dc:creator xml:lang="en">Frank Gibson</dc:creator>
+        <dc:creator xml:lang="en">Gilberto Fragoso</dc:creator>
+        <dc:creator xml:lang="en">Helen C. Causton</dc:creator>
+        <dc:creator xml:lang="en">Helen Parkinson</dc:creator>
+        <dc:creator xml:lang="en">Holger Stenzhorn</dc:creator>
+        <dc:creator xml:lang="en">James A. Overton</dc:creator>
+        <dc:creator xml:lang="en">James Malone</dc:creator>
+        <dc:creator xml:lang="en">Jay Greenbaum</dc:creator>
+        <dc:creator xml:lang="en">Jeffrey Grethe</dc:creator>
+        <dc:creator xml:lang="en">Jennifer Fostel</dc:creator>
+        <dc:creator xml:lang="en">Jessica Turner</dc:creator>
+        <dc:creator xml:lang="en">Jie Zheng</dc:creator>
+        <dc:creator xml:lang="en">Joe White</dc:creator>
+        <dc:creator xml:lang="en">John Westbrook</dc:creator>
+        <dc:creator xml:lang="en">Kevin Clancy</dc:creator>
+        <dc:creator xml:lang="en">Larisa Soldatova</dc:creator>
+        <dc:creator xml:lang="en">Lawrence Hunter</dc:creator>
+        <dc:creator xml:lang="en">Liju Fan</dc:creator>
+        <dc:creator xml:lang="en">Luisa Montecchi</dc:creator>
+        <dc:creator xml:lang="en">Matthew Brush</dc:creator>
+        <dc:creator xml:lang="en">Matthew Pocock</dc:creator>
+        <dc:creator xml:lang="en">Melanie Courtot</dc:creator>
+        <dc:creator xml:lang="en">Melissa Haendel</dc:creator>
+        <dc:creator xml:lang="en">Mervi Heiskanen</dc:creator>
+        <dc:creator xml:lang="en">Monnie McGee</dc:creator>
+        <dc:creator xml:lang="en">Norman Morrison</dc:creator>
+        <dc:creator xml:lang="en">Philippe Rocca-Serra</dc:creator>
+        <dc:creator xml:lang="en">Phillip Lord</dc:creator>
+        <dc:creator xml:lang="en">Pierre Grenon</dc:creator>
+        <dc:creator xml:lang="en">Richard Bruskiewich</dc:creator>
+        <dc:creator xml:lang="en">Richard Scheuermann</dc:creator>
+        <dc:creator xml:lang="en">Robert Stevens</dc:creator>
+        <dc:creator xml:lang="en">Ryan R. Brinkman</dc:creator>
+        <dc:creator xml:lang="en">Stefan Wiemann</dc:creator>
+        <dc:creator xml:lang="en">Susanna-Assunta Sansone</dc:creator>
+        <dc:creator xml:lang="en">Tanya Gray</dc:creator>
+        <dc:creator xml:lang="en">Tina Hernandez-Boussard</dc:creator>
+        <dc:creator xml:lang="en">Trish Whetzel</dc:creator>
+        <dc:creator xml:lang="en">Yongqun He</dc:creator>
+        <dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2009-07-31</dc:date>
+        <dc:description xml:lang="en">The Ontology for Biomedical Investigations (OBI) is build in a collaborative, international effort and will serve as a resource for annotating biomedical investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. This ontology arose from the Functional Genomics Investigation Ontology (FuGO) and will contain both terms that are common to all biomedical investigations, including functional genomics investigations and those that are more domain specific.</dc:description>
+        <dc:format xml:lang="en">OWL-DL</dc:format>
+        <dc:subject xml:lang="en">An ontology for the annotation of biomedical and functional genomics experiments.</dc:subject>
+        <terms:license>http://creativecommons.org/licenses/by/4.0/</terms:license>
+        <terms:title>Ontology for Biomedical Investigations</terms:title>
+        <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them.</rdfs:comment>
+        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-07-11</owl:versionInfo>
+        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-10-24</owl:versionInfo>
     </owl:Ontology>
 
 

diff --git a/imports/ro_import.owl b/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/vfbext/imports/ro_import.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/vfbext/releases/2022-02-25/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">2022-02-25</owl:versionInfo>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/vfbext/releases/2022-10-24/imports/ro_import.owl"/>
+        <dc:source rdf:resource="http://purl.obolibrary.org/obo/ro/releases/2022-09-07/ro.owl"/>
+        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-10-24</owl:versionInfo>
     </owl:Ontology>
 
 
@@ -279,6 +279,12 @@
 
 
 
+    <!-- http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym -->
+
+    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym"/>
+
+
+
     <!-- http://www.geneontology.org/formats/oboInOwl#hasDbXref -->
 
     <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasDbXref">
@@ -857,6 +863,7 @@ Examples include: the relationship between two channels collected simultaneously
 
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002131">
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002323"/>
+        <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#SymmetricProperty"/>
         <owl:propertyChainAxiom rdf:parseType="Collection">
             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000050"/>
             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000050"/>
@@ -2129,13 +2136,14 @@ For example, A and B may be gene products and binding of B by A positively regul
             <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>https://orcid.org/0000-0001-9625-1899 Bill Duncan</obo:IAO_0000117>
+        <obo:IAO_0000115>X device utilizes material 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>https://orcid.org/0000-0001-9625-1899</obo:IAO_0000117>
+        <obo:IAO_0000117>https://orcid.org/0000-0003-2620-0345</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>
-        <rdfs:label xml:lang="en">utilizes</rdfs:label>
+        <oboInOwl:creation_date>2021-11-08T12:00:00Z</oboInOwl:creation_date>
+        <oboInOwl:hasBroadSynonym>utilizes</oboInOwl:hasBroadSynonym>
+        <rdfs:label xml:lang="en">device utilizes material</rdfs:label>
     </owl:ObjectProperty>
 
 

diff --git a/src/ontology/imports/caro_import.owl b/src/ontology/imports/caro_import.owl
@@ -12,14 +12,14 @@
      xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"
      xmlns:oboInOwl1="ttp://www.geneontology.org/formats/oboInOwl#">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/vfbext/imports/caro_import.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/vfbext/releases/2022-02-25/imports/caro_import.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/vfbext/releases/2022-10-24/imports/caro_import.owl"/>
         <dc:description>None</dc:description>
         <dc:source rdf:resource="http://purl.obolibrary.org/obo/caro/releases/2022-02-18/caro.owl"/>
         <dc:title>Common Anatomy Reference Ontology</dc:title>
         <terms:license rdf:resource="https://creativecommons.org/licenses/unspecified"/>
         <rdfs:comment>Based on CARO 1.0, with modifications and additions by David Osumi-Sutherland, Chris Mungall, Ramona Walls and Melissa Haendal.</rdfs:comment>
         <owl:versionInfo>2022-02-18</owl:versionInfo>
-        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-02-25</owl:versionInfo>
+        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-10-24</owl:versionInfo>
     </owl:Ontology>