make new release

tibonto · StroemPhi · Jan 11, 2023 · Jan 11, 2023 · 58ca6c746947d10ef741ad4bf5d9f9798a473cde
commit 58ca6c746947d10ef741ad4bf5d9f9798a473cde
diff --git a/aeon-base.owl b/aeon-base.owl
diff --git a/aeon-full.owl b/aeon-full.owl
diff --git a/aeon.owl b/aeon.owl
diff --git a/src/ontology/imports/bfo_import.owl b/src/ontology/imports/bfo_import.owl
@@ -12,8 +12,8 @@
      xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
      xmlns:terms="http://purl.org/dc/terms/">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/aeon/imports/bfo_import.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/aeon/releases/2022-11-25/imports/bfo_import.owl"/>
-        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-11-25</owl:versionInfo>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/aeon/releases/2023-01-11/imports/bfo_import.owl"/>
+        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2023-01-11</owl:versionInfo>
         <prov:wasDerivedFrom rdf:resource="http://purl.obolibrary.org/obo/bfo/2019-08-26/bfo.owl"/>
     </owl:Ontology>
 

diff --git a/src/ontology/imports/envo_import.owl b/src/ontology/imports/envo_import.owl
@@ -11,8 +11,8 @@
      xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
      xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/aeon/imports/envo_import.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/aeon/releases/2022-11-25/imports/envo_import.owl"/>
-        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-11-25</owl:versionInfo>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/aeon/releases/2023-01-11/imports/envo_import.owl"/>
+        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2023-01-11</owl:versionInfo>
         <prov:wasDerivedFrom rdf:resource="http://purl.obolibrary.org/obo/envo/releases/2021-05-14/envo.owl"/>
     </owl:Ontology>
 
@@ -314,7 +314,7 @@
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/ENVO_00000005"/>
         <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
         <owl:annotatedTarget>A primary administrative division of a country, such as a state in the United States.</owl:annotatedTarget>
-        <oboInOwl:hasDbXref>Geonames:http://www.geonames.org/export/codes.html</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Geonames:http://www.geonames.org/export/codes.html</oboInOwl:hasDbXref>
     </owl:Axiom>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/ENVO_00000005"/>

diff --git a/src/ontology/imports/iao_import.owl b/src/ontology/imports/iao_import.owl
@@ -13,8 +13,8 @@
      xmlns:swrlb="http://www.w3.org/2003/11/swrlb#"
      xmlns:terms="http://purl.org/dc/terms/">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/aeon/imports/iao_import.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/aeon/releases/2022-11-25/imports/iao_import.owl"/>
-        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-11-25</owl:versionInfo>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/aeon/releases/2023-01-11/imports/iao_import.owl"/>
+        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2023-01-11</owl:versionInfo>
         <prov:wasDerivedFrom rdf:resource="http://purl.obolibrary.org/obo/iao/2022-11-07/iao.owl"/>
     </owl:Ontology>
 
@@ -625,6 +625,35 @@ every c that is a concretization of g specifically denotes r</obo:IAO_0000116>
 
 
 
+    <!-- http://purl.obolibrary.org/obo/RO_0000058 -->
+
+    <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000058">
+        <owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000059"/>
+        <rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000031"/>
+        <rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
+        <obo:IAO_0000112 xml:lang="en">A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).</obo:IAO_0000112>
+        <obo:IAO_0000112 xml:lang="en">An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).</obo:IAO_0000112>
+        <obo:IAO_0000115 xml:lang="en">A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants.</obo:IAO_0000115>
+        <dc:source rdf:resource="http://purl.obolibrary.org/obo/iao/2022-11-07/iao.owl"/>
+        <rdfs:label xml:lang="en">is concretized as</rdfs:label>
+    </owl:ObjectProperty>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/RO_0000059 -->
+
+    <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000059">
+        <rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
+        <rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000031"/>
+        <obo:IAO_0000112 xml:lang="en">A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).</obo:IAO_0000112>
+        <obo:IAO_0000112 xml:lang="en">An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).</obo:IAO_0000112>
+        <obo:IAO_0000115 xml:lang="en">A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.</obo:IAO_0000115>
+        <dc:source rdf:resource="http://purl.obolibrary.org/obo/iao/2022-11-07/iao.owl"/>
+        <rdfs:label xml:lang="en">concretizes</rdfs:label>
+    </owl:ObjectProperty>
+
+
+
     <!-- http://purl.obolibrary.org/obo/RO_0000079 -->
 
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000079">
@@ -1506,6 +1535,35 @@ every c that is a concretization of g specifically denotes r</obo:IAO_0000116>
 
 
 
+    <!-- http://purl.obolibrary.org/obo/IAO_0000015 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000015">
+        <owl:equivalentClass>
+            <owl:Class>
+                <owl:intersectionOf rdf:parseType="Collection">
+                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000019"/>
+                    <owl:Restriction>
+                        <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000059"/>
+                        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
+                    </owl:Restriction>
+                </owl:intersectionOf>
+            </owl:Class>
+        </owl:equivalentClass>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000019"/>
+        <obo:IAO_0000111 xml:lang="en">information carrier</obo:IAO_0000111>
+        <obo:IAO_0000112 xml:lang="en">In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case.</obo:IAO_0000112>
+        <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
+        <obo:IAO_0000115 xml:lang="en">A quality of an information bearer that imparts the information content</obo:IAO_0000115>
+        <obo:IAO_0000116 xml:lang="en">12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a &apos;delayed wave carrier&apos;.</obo:IAO_0000116>
+        <obo:IAO_0000116>2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it.</obo:IAO_0000116>
+        <obo:IAO_0000117 xml:lang="en">PERSON: Alan Ruttenberg</obo:IAO_0000117>
+        <obo:IAO_0000119 xml:lang="en">Smith, Ceusters, Ruttenberg, 2000 years of philosophy</obo:IAO_0000119>
+        <dc:source rdf:resource="http://purl.obolibrary.org/obo/iao/2022-11-07/iao.owl"/>
+        <rdfs:label xml:lang="en">information carrier</rdfs:label>
+    </owl:Class>
+
+
+
     <!-- http://purl.obolibrary.org/obo/IAO_0000027 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000027">

diff --git a/src/ontology/imports/ico_import.owl b/src/ontology/imports/ico_import.owl
@@ -8,8 +8,8 @@
      xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
      xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/aeon/imports/ico_import.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/aeon/releases/2022-11-25/imports/ico_import.owl"/>
-        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-11-25</owl:versionInfo>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/aeon/releases/2023-01-11/imports/ico_import.owl"/>
+        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2023-01-11</owl:versionInfo>
     </owl:Ontology>
 
 

diff --git a/src/ontology/imports/obi_import.owl b/src/ontology/imports/obi_import.owl
@@ -10,9 +10,9 @@
      xmlns:prov="http://www.w3.org/ns/prov#"
      xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/aeon/imports/obi_import.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/aeon/releases/2022-11-25/imports/obi_import.owl"/>
-        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-11-25</owl:versionInfo>
-        <prov:wasDerivedFrom rdf:resource="http://purl.obolibrary.org/obo/obi/2022-07-11/obi.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/aeon/releases/2023-01-11/imports/obi_import.owl"/>
+        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2023-01-11</owl:versionInfo>
+        <prov:wasDerivedFrom rdf:resource="http://purl.obolibrary.org/obo/obi/2022-12-14/obi.owl"/>
     </owl:Ontology>
 
 
@@ -127,7 +127,7 @@
         <obo:IAO_0000112 xml:lang="en">this investigation realizes this investigator role</obo:IAO_0000112>
         <obo:IAO_0000112 xml:lang="en">this shattering realizes this fragility</obo:IAO_0000112>
         <obo:IAO_0000600 xml:lang="en">to say that b realizes c at t is to assert that there is some material entity d &amp; b is a process which has participant d at t &amp; c is a disposition or role of which d is bearer_of at t&amp; the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])</obo:IAO_0000600>
-        <dc:source rdf:resource="http://purl.obolibrary.org/obo/obi/2022-07-11/obi.owl"/>
+        <dc:source rdf:resource="http://purl.obolibrary.org/obo/obi/2022-12-14/obi.owl"/>
         <rdfs:comment>Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process</rdfs:comment>
         <rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
         <rdfs:label xml:lang="en">realizes</rdfs:label>
@@ -157,7 +157,7 @@
         <obo:IAO_0000119>Person:Alan Ruttenberg</obo:IAO_0000119>
         <obo:IAO_0000119>Person:Helen Parkinson</obo:IAO_0000119>
         <obo:IAO_0000232>2009/09/28 Alan Ruttenberg. Fucoidan-use-case</obo:IAO_0000232>
-        <dc:source rdf:resource="http://purl.obolibrary.org/obo/obi/2022-07-11/obi.owl"/>
+        <dc:source rdf:resource="http://purl.obolibrary.org/obo/obi/2022-12-14/obi.owl"/>
         <rdfs:label>is member of organization</rdfs:label>
     </owl:ObjectProperty>
 
@@ -171,7 +171,7 @@
         <obo:IAO_0000112 xml:lang="en">A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).</obo:IAO_0000112>
         <obo:IAO_0000112 xml:lang="en">An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).</obo:IAO_0000112>
         <obo:IAO_0000115 xml:lang="en">A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.</obo:IAO_0000115>
-        <dc:source rdf:resource="http://purl.obolibrary.org/obo/obi/2022-07-11/obi.owl"/>
+        <dc:source rdf:resource="http://purl.obolibrary.org/obo/obi/2022-12-14/obi.owl"/>
         <rdfs:label xml:lang="en">concretizes</rdfs:label>
     </owl:ObjectProperty>
 
@@ -201,7 +201,7 @@
         <obo:IAO_0000117>Damion Dooley</obo:IAO_0000117>
         <obo:IAO_0000117>Mark Miller</obo:IAO_0000117>
         <dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2019-07-14T07:05:50Z</dc:date>
-        <dc:source rdf:resource="http://purl.obolibrary.org/obo/obi/2022-07-11/obi.owl"/>
+        <dc:source rdf:resource="http://purl.obolibrary.org/obo/obi/2022-12-14/obi.owl"/>
         <rdfs:label xml:lang="en">has representation</rdfs:label>
     </owl:DatatypeProperty>
 
@@ -324,7 +324,7 @@
         <obo:IAO_0000117 xml:lang="en">Alan Ruttenberg</obo:IAO_0000117>
         <obo:IAO_0000119 xml:lang="en">OBI Plan and Planned Process branch</obo:IAO_0000119>
         <obo:IAO_0000119 xml:lang="en">OBI_0000344</obo:IAO_0000119>
-        <dc:source rdf:resource="http://purl.obolibrary.org/obo/obi/2022-07-11/obi.owl"/>
+        <dc:source rdf:resource="http://purl.obolibrary.org/obo/obi/2022-12-14/obi.owl"/>
         <rdfs:comment xml:lang="en">2/3/2009 Comment from OBI review.
 
 Action specification not well enough specified.
@@ -385,10 +385,18 @@ Request that IAO either clarify these or change definitions not to use them</rdf
 
 
 
+    <!-- http://purl.obolibrary.org/obo/NCBITaxon_33208 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_33208">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_33154"/>
+    </owl:Class>
+
+
+
     <!-- http://purl.obolibrary.org/obo/NCBITaxon_33213 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_33213">
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_33154"/>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_33208"/>
     </owl:Class>
 
 
@@ -417,9 +425,8 @@ Request that IAO either clarify these or change definitions not to use them</rdf
         <obo:IAO_0000111>Homo sapiens</obo:IAO_0000111>
         <obo:IAO_0000118>human</obo:IAO_0000118>
         <obo:IAO_0000118>human being</obo:IAO_0000118>
-        <obo:IAO_0000118>man</obo:IAO_0000118>
         <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ncbitaxon.owl"/>
-        <dc:source rdf:resource="http://purl.obolibrary.org/obo/obi/2022-07-11/obi.owl"/>
+        <dc:source rdf:resource="http://purl.obolibrary.org/obo/obi/2022-12-14/obi.owl"/>
         <rdfs:label>Homo sapiens</rdfs:label>
     </owl:Class>
 
@@ -453,7 +460,7 @@ objectives is a planned process.</obo:IAO_0000116>
         <obo:IAO_0000232>6/11/9: Edited at workshop. Used to include: is initiated by an agent</obo:IAO_0000232>
         <obo:IAO_0000232 xml:lang="en">This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)</obo:IAO_0000232>
         <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
-        <dc:source rdf:resource="http://purl.obolibrary.org/obo/obi/2022-07-11/obi.owl"/>
+        <dc:source rdf:resource="http://purl.obolibrary.org/obo/obi/2022-12-14/obi.owl"/>
         <rdfs:label xml:lang="en">planned process</rdfs:label>
     </owl:Class>
 
@@ -499,7 +506,7 @@ for now.</obo:IAO_0000116>
         <obo:IAO_0000117>PERSON: Philippe Rocca-Serra</obo:IAO_0000117>
         <obo:IAO_0000117>PERSON: Susanna Sansone</obo:IAO_0000117>
         <obo:IAO_0000119>GROUP: OBI</obo:IAO_0000119>
-        <dc:source rdf:resource="http://purl.obolibrary.org/obo/obi/2022-07-11/obi.owl"/>
+        <dc:source rdf:resource="http://purl.obolibrary.org/obo/obi/2022-12-14/obi.owl"/>
         <rdfs:label xml:lang="en">organization</rdfs:label>
     </owl:Class>
 
@@ -522,7 +529,7 @@ OBI doesn&apos;t take position as to  when an organism starts or ends being an o
 This issue is outside the scope of OBI.</obo:IAO_0000116>
         <obo:IAO_0000117>GROUP: OBI Biomaterial Branch</obo:IAO_0000117>
         <obo:IAO_0000119 xml:lang="en">WEB: http://en.wikipedia.org/wiki/Organism</obo:IAO_0000119>
-        <dc:source rdf:resource="http://purl.obolibrary.org/obo/obi/2022-07-11/obi.owl"/>
+        <dc:source rdf:resource="http://purl.obolibrary.org/obo/obi/2022-12-14/obi.owl"/>
         <rdfs:label xml:lang="en">organism</rdfs:label>
     </owl:Class>
 

diff --git a/src/ontology/imports/obib_import.owl b/src/ontology/imports/obib_import.owl
@@ -10,8 +10,8 @@
      xmlns:prov="http://www.w3.org/ns/prov#"
      xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/aeon/imports/obib_import.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/aeon/releases/2022-11-25/imports/obib_import.owl"/>
-        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-11-25</owl:versionInfo>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/aeon/releases/2023-01-11/imports/obib_import.owl"/>
+        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2023-01-11</owl:versionInfo>
         <prov:wasDerivedFrom rdf:resource="http://purl.obolibrary.org/obo/obib/2021-11-12/obib.owl"/>
     </owl:Ontology>