refresh import modules

tibonto · Aug 22, 2022 · c762628 · c762628
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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/2022-08-15/imports/bfo_import.owl"/>
-        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-08-15</owl:versionInfo>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/aeon/releases/2022-08-22/imports/bfo_import.owl"/>
+        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-08-22</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/cro_import.owl b/src/ontology/imports/cro_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/cro_import.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/aeon/releases/2022-08-15/imports/cro_import.owl"/>
-        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-08-15</owl:versionInfo>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/aeon/releases/2022-08-22/imports/cro_import.owl"/>
+        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-08-22</owl:versionInfo>
         <prov:wasDerivedFrom rdf:resource="http://purl.obolibrary.org/obo/cro/releases/2019-12-11/cro.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/2022-08-15/imports/envo_import.owl"/>
-        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-08-15</owl:versionInfo>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/aeon/releases/2022-08-22/imports/envo_import.owl"/>
+        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-08-22</owl:versionInfo>
         <prov:wasDerivedFrom rdf:resource="http://purl.obolibrary.org/obo/envo/releases/2021-05-14/envo.owl"/>
     </owl:Ontology>
 
@@ -369,7 +369,7 @@
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/ENVO_00000009"/>
         <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
         <owl:annotatedTarget>A political association with effective dominion over a geographic area.</owl:annotatedTarget>
-        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">https://en.wikipedia.org/wiki/State</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>https://en.wikipedia.org/wiki/State</oboInOwl:hasDbXref>
     </owl:Axiom>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/ENVO_00000009"/>

diff --git a/src/ontology/imports/iao_import.owl b/src/ontology/imports/iao_import.owl
@@ -11,8 +11,8 @@
      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/iao_import.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/aeon/releases/2022-08-15/imports/iao_import.owl"/>
-        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-08-15</owl:versionInfo>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/aeon/releases/2022-08-22/imports/iao_import.owl"/>
+        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-08-22</owl:versionInfo>
         <prov:wasDerivedFrom rdf:resource="http://purl.obolibrary.org/obo/iao/2020-12-09/iao.owl"/>
     </owl:Ontology>
 
@@ -1139,67 +1139,6 @@ every c that is a concretization of g specifically denotes r</obo:IAO_0000116>
 
 
 
-    <!-- http://purl.obolibrary.org/obo/BFO_0000027 -->
-
-    <owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000027">
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
-        <obo:BFO_0000179>object-aggregate</obo:BFO_0000179>
-        <obo:BFO_0000180>ObjectAggregate</obo:BFO_0000180>
-        <obo:IAO_0000112 xml:lang="en">a collection of cells in a blood biobank.</obo:IAO_0000112>
-        <obo:IAO_0000112 xml:lang="en">a swarm of bees is an aggregate of members who are linked together through natural bonds</obo:IAO_0000112>
-        <obo:IAO_0000112 xml:lang="en">a symphony orchestra</obo:IAO_0000112>
-        <obo:IAO_0000112 xml:lang="en">an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team)</obo:IAO_0000112>
-        <obo:IAO_0000112 xml:lang="en">defined by fiat: the aggregate of members of an organization</obo:IAO_0000112>
-        <obo:IAO_0000112 xml:lang="en">defined through physical attachment: the aggregate of atoms in a lump of granite</obo:IAO_0000112>
-        <obo:IAO_0000112 xml:lang="en">defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container</obo:IAO_0000112>
-        <obo:IAO_0000112 xml:lang="en">defined via attributive delimitations such as: the patients in this hospital</obo:IAO_0000112>
-        <obo:IAO_0000112 xml:lang="en">the aggregate of bearings in a constant velocity axle joint</obo:IAO_0000112>
-        <obo:IAO_0000112 xml:lang="en">the aggregate of blood cells in your body</obo:IAO_0000112>
-        <obo:IAO_0000112 xml:lang="en">the nitrogen atoms in the atmosphere</obo:IAO_0000112>
-        <obo:IAO_0000112 xml:lang="en">the restaurants in Palo Alto</obo:IAO_0000112>
-        <obo:IAO_0000112 xml:lang="en">your collection of Meissen ceramic plates.</obo:IAO_0000112>
-        <obo:IAO_0000116>An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects </obo:IAO_0000116>
-        <obo:IAO_0000116 xml:lang="en">BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee).</obo:IAO_0000116>
-        <obo:IAO_0000119>ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, &apos;A Theory of Granular Partitions&apos;, in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.</obo:IAO_0000119>
-        <obo:IAO_0000600 xml:lang="en">b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])</obo:IAO_0000600>
-        <obo:IAO_0000602>(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] </obo:IAO_0000602>
-        <dc:source rdf:resource="http://purl.obolibrary.org/obo/iao/2020-12-09/iao.owl"/>
-        <rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
-        <rdfs:label xml:lang="en">object aggregate</rdfs:label>
-    </owl:Class>
-    <owl:Axiom>
-        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000027"/>
-        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000116"/>
-        <owl:annotatedTarget>An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects </owl:annotatedTarget>
-        <obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/0000011"/>
-    </owl:Axiom>
-    <owl:Axiom>
-        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000027"/>
-        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000116"/>
-        <owl:annotatedTarget>An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects </owl:annotatedTarget>
-        <obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/0000301"/>
-    </owl:Axiom>
-    <owl:Axiom>
-        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000027"/>
-        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000119"/>
-        <owl:annotatedTarget>ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, &apos;A Theory of Granular Partitions&apos;, in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.</owl:annotatedTarget>
-        <obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/0000300"/>
-    </owl:Axiom>
-    <owl:Axiom>
-        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000027"/>
-        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000600"/>
-        <owl:annotatedTarget xml:lang="en">b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])</owl:annotatedTarget>
-        <obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/025-004"/>
-    </owl:Axiom>
-    <owl:Axiom>
-        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000027"/>
-        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
-        <owl:annotatedTarget>(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] </owl:annotatedTarget>
-        <obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/025-004"/>
-    </owl:Axiom>
-
-
-
     <!-- http://purl.obolibrary.org/obo/BFO_0000029 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000029">
@@ -1273,78 +1212,6 @@ every c that is a concretization of g specifically denotes r</obo:IAO_0000116>
 
 
 
-    <!-- http://purl.obolibrary.org/obo/BFO_0000040 -->
-
-    <owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000040">
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000004"/>
-        <owl:disjointWith rdf:resource="http://purl.obolibrary.org/obo/BFO_0000141"/>
-        <obo:BFO_0000179>material</obo:BFO_0000179>
-        <obo:BFO_0000180>MaterialEntity</obo:BFO_0000180>
-        <obo:IAO_0000112 xml:lang="en">a flame</obo:IAO_0000112>
-        <obo:IAO_0000112 xml:lang="en">a forest fire</obo:IAO_0000112>
-        <obo:IAO_0000112 xml:lang="en">a human being</obo:IAO_0000112>
-        <obo:IAO_0000112 xml:lang="en">a hurricane</obo:IAO_0000112>
-        <obo:IAO_0000112 xml:lang="en">a photon</obo:IAO_0000112>
-        <obo:IAO_0000112 xml:lang="en">a puff of smoke</obo:IAO_0000112>
-        <obo:IAO_0000112 xml:lang="en">a sea wave</obo:IAO_0000112>
-        <obo:IAO_0000112 xml:lang="en">a tornado</obo:IAO_0000112>
-        <obo:IAO_0000112 xml:lang="en">an aggregate of human beings.</obo:IAO_0000112>
-        <obo:IAO_0000112 xml:lang="en">an energy wave</obo:IAO_0000112>
-        <obo:IAO_0000112 xml:lang="en">an epidemic</obo:IAO_0000112>
-        <obo:IAO_0000112 xml:lang="en">the undetached arm of a human being</obo:IAO_0000112>
-        <obo:IAO_0000115 xml:lang="en">An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.</obo:IAO_0000115>
-        <obo:IAO_0000116 xml:lang="en">BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60</obo:IAO_0000116>
-        <obo:IAO_0000116 xml:lang="en">BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.</obo:IAO_0000116>
-        <obo:IAO_0000116 xml:lang="en">BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.</obo:IAO_0000116>
-        <obo:IAO_0000600 xml:lang="en">A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])</obo:IAO_0000600>
-        <obo:IAO_0000601 xml:lang="en">Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])</obo:IAO_0000601>
-        <obo:IAO_0000601 xml:lang="en">every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])</obo:IAO_0000601>
-        <obo:IAO_0000602>(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] </obo:IAO_0000602>
-        <obo:IAO_0000602>(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] </obo:IAO_0000602>
-        <obo:IAO_0000602>(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] </obo:IAO_0000602>
-        <dc:source rdf:resource="http://purl.obolibrary.org/obo/iao/2020-12-09/iao.owl"/>
-        <rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
-        <rdfs:label xml:lang="en">material entity</rdfs:label>
-    </owl:Class>
-    <owl:Axiom>
-        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
-        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000600"/>
-        <owl:annotatedTarget xml:lang="en">A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])</owl:annotatedTarget>
-        <obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/019-002"/>
-    </owl:Axiom>
-    <owl:Axiom>
-        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
-        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000601"/>
-        <owl:annotatedTarget xml:lang="en">Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])</owl:annotatedTarget>
-        <obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/020-002"/>
-    </owl:Axiom>
-    <owl:Axiom>
-        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
-        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000601"/>
-        <owl:annotatedTarget xml:lang="en">every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])</owl:annotatedTarget>
-        <obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/021-002"/>
-    </owl:Axiom>
-    <owl:Axiom>
-        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
-        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
-        <owl:annotatedTarget>(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] </owl:annotatedTarget>
-        <obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/019-002"/>
-    </owl:Axiom>
-    <owl:Axiom>
-        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
-        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
-        <owl:annotatedTarget>(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] </owl:annotatedTarget>
-        <obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/021-002"/>
-    </owl:Axiom>
-    <owl:Axiom>
-        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
-        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
-        <owl:annotatedTarget>(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] </owl:annotatedTarget>
-        <obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/020-002"/>
-    </owl:Axiom>
-
-
-
     <!-- http://purl.obolibrary.org/obo/BFO_0000141 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000141">

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/2022-08-15/imports/ico_import.owl"/>
-        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-08-15</owl:versionInfo>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/aeon/releases/2022-08-22/imports/ico_import.owl"/>
+        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-08-22</owl:versionInfo>
     </owl:Ontology>
 
 

diff --git a/src/ontology/imports/obi_import.owl b/src/ontology/imports/obi_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/obi_import.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/aeon/releases/2022-08-15/imports/obi_import.owl"/>
-        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-08-15</owl:versionInfo>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/aeon/releases/2022-08-22/imports/obi_import.owl"/>
+        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-08-22</owl:versionInfo>
         <prov:wasDerivedFrom rdf:resource="http://purl.obolibrary.org/obo/obi/2022-07-11/obi.owl"/>
     </owl:Ontology>