Refresh imports in preparation of CL release (#2498)

* Refresh imports in preparation of CL release Refresh imports in preparation of CL release * update HRA subsets
obophenotype · Aug 16, 2024 · 30ea87b · 30ea87b
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diff --git a/src/mappings/fbbt.sssom.tsv b/src/mappings/fbbt.sssom.tsv
@@ -6,11 +6,12 @@
 #mapping_set_id: "http://purl.obolibrary.org/obo/fbbt/fbbt-mappings.sssom.tsv"
 #mapping_set_description: "Mappings between the Drosophila Anatomy Ontology and foreign ontologies."
 #creator_id:
+#  - "ORCID:0000-0002-1373-1705"
 #  - "ORCID:0000-0002-6095-8718"
 #license: "https://creativecommons.org/licenses/by/4.0/"
 #subject_source: "obo:fbbt.owl"
 #object_source: "obo:cl.owl"
-#mapping_date: "2024-05-31"
+#mapping_date: "2024-07-12"
 subject_id	subject_label	predicate_id	object_id	mapping_justification
 FBbt:00000092	primordial germ cell	semapv:crossSpeciesExactMatch	CL:0000301	semapv:ManualMappingCuration
 FBbt:00000124	epithelial cell	semapv:crossSpeciesExactMatch	CL:0000066	semapv:ManualMappingCuration

diff --git a/src/ontology/components/hra_subset.owl b/src/ontology/components/hra_subset.owl
@@ -2197,6 +2197,15 @@
 
 
 
+    <!-- http://purl.obolibrary.org/obo/CL_0002483 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/CL_0002483">
+        <obo:RO_0002175 rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_9606"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas"/>
+    </owl:Class>
+
+
+
     <!-- http://purl.obolibrary.org/obo/CL_0002521 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/CL_0002521">
@@ -2242,6 +2251,15 @@
 
 
 
+    <!-- http://purl.obolibrary.org/obo/CL_0002562 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/CL_0002562">
+        <obo:RO_0002175 rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_9606"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas"/>
+    </owl:Class>
+
+
+
     <!-- http://purl.obolibrary.org/obo/CL_0002565 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/CL_0002565">
@@ -2917,15 +2935,6 @@
 
 
 
-    <!-- http://purl.obolibrary.org/obo/CL_0017011 -->
-
-    <owl:Class rdf:about="http://purl.obolibrary.org/obo/CL_0017011">
-        <obo:RO_0002175 rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_9606"/>
-        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas"/>
-    </owl:Class>
-
-
-
     <!-- http://purl.obolibrary.org/obo/CL_0019002 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/CL_0019002">
@@ -4132,15 +4141,6 @@
 
 
 
-    <!-- http://purl.obolibrary.org/obo/CL_4032000 -->
-
-    <owl:Class rdf:about="http://purl.obolibrary.org/obo/CL_4032000">
-        <obo:RO_0002175 rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_9606"/>
-        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas"/>
-    </owl:Class>
-
-
-
     <!-- http://purl.obolibrary.org/obo/CL_4033003 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/CL_4033003">

diff --git a/src/ontology/imports/merged_import.owl b/src/ontology/imports/merged_import.owl
@@ -7,8 +7,8 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/cl/imports/merged_import.owl>
-<http://purl.obolibrary.org/obo/cl/releases/2024-08-07/imports/merged_import.owl>
-Annotation(owl:versionInfo "2024-08-07")
+<http://purl.obolibrary.org/obo/cl/releases/2024-08-16/imports/merged_import.owl>
+Annotation(owl:versionInfo "2024-08-16")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000002>))
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000003>))
@@ -3443,6 +3443,7 @@ Declaration(Class(<http://purl.obolibrary.org/obo/GO_0035993>))
 Declaration(Class(<http://purl.obolibrary.org/obo/GO_0036022>))
 Declaration(Class(<http://purl.obolibrary.org/obo/GO_0036035>))
 Declaration(Class(<http://purl.obolibrary.org/obo/GO_0036037>))
+Declaration(Class(<http://purl.obolibrary.org/obo/GO_0036053>))
 Declaration(Class(<http://purl.obolibrary.org/obo/GO_0036072>))
 Declaration(Class(<http://purl.obolibrary.org/obo/GO_0036075>))
 Declaration(Class(<http://purl.obolibrary.org/obo/GO_0036093>))
@@ -4262,6 +4263,8 @@ Declaration(Class(<http://purl.obolibrary.org/obo/GO_0046903>))
 Declaration(Class(<http://purl.obolibrary.org/obo/GO_0046907>))
 Declaration(Class(<http://purl.obolibrary.org/obo/GO_0046928>))
 Declaration(Class(<http://purl.obolibrary.org/obo/GO_0046929>))
+Declaration(Class(<http://purl.obolibrary.org/obo/GO_0046930>))
+Declaration(Class(<http://purl.obolibrary.org/obo/GO_0046931>))
 Declaration(Class(<http://purl.obolibrary.org/obo/GO_0046942>))
 Declaration(Class(<http://purl.obolibrary.org/obo/GO_0046943>))
 Declaration(Class(<http://purl.obolibrary.org/obo/GO_0047496>))
@@ -51792,6 +51795,18 @@ AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/GO_0036037> "CD8-
 EquivalentClasses(<http://purl.obolibrary.org/obo/GO_0036037> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/GO_0001775> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0004009> <http://purl.obolibrary.org/obo/CL_0000625>)))
 SubClassOf(<http://purl.obolibrary.org/obo/GO_0036037> <http://purl.obolibrary.org/obo/GO_0046631>)
 
+# Class: <http://purl.obolibrary.org/obo/GO_0036053> (glomerular endothelium fenestra)
+
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "GOC:cjm") Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "MP:0011454") Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "PMID:19129259") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/GO_0036053> "A large plasma membrane-lined circular pore that perforates the flattened glomerular endothelium and, unlike those of other fenestrated capillaries, is not spanned by diaphragms; the density and size of glomerular fenestrae account, at least in part, for the high permeability of the glomerular capillary wall to water and small solutes.")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#created_by> <http://purl.obolibrary.org/obo/GO_0036053> "bf")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#creation_date> <http://purl.obolibrary.org/obo/GO_0036053> "2011-12-12T10:53:24Z")
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "PMID:19129259") <http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/GO_0036053> "GEnC fenestration")
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "PMID:19129259") <http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/GO_0036053> "glomerular endothelial cell fenestration")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/GO_0036053> "cellular_component")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/GO_0036053> "GO:0036053")
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/GO_0036053> "glomerular endothelium fenestra")
+SubClassOf(<http://purl.obolibrary.org/obo/GO_0036053> <http://purl.obolibrary.org/obo/GO_0046930>)
+
 # Class: <http://purl.obolibrary.org/obo/GO_0036072> (direct ossification)
 
 AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "GO_REF:0000034") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/GO_0036072> "The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance, that does not require the replacement of preexisting tissues.")
@@ -62426,6 +62441,32 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://pu
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/GO_0046929> "negative regulation of neurotransmitter secretion")
 EquivalentClasses(<http://purl.obolibrary.org/obo/GO_0046929> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/GO_0065007> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002212> <http://purl.obolibrary.org/obo/GO_0007269>)))
 
+# Class: <http://purl.obolibrary.org/obo/GO_0046930> (pore complex)
+
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "ISBN:0198506732") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/GO_0046930> "A protein complex providing a discrete opening in a membrane that allows the passage of gases and/or liquids.")
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000233> <http://purl.obolibrary.org/obo/GO_0046930> "https://github.com/geneontology/go-ontology/issues/20452"^^xsd:anyURI)
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/GO_0046930> "pore")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/GO_0046930> "cellular_component")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/GO_0046930> "channel-forming toxin activity")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/GO_0046930> "pore-forming toxin activity")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/GO_0046930> "GO:0046930")
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/GO_0046930> "pore complex")
+SubClassOf(<http://purl.obolibrary.org/obo/GO_0046930> <http://purl.obolibrary.org/obo/GO_0032991>)
+SubClassOf(<http://purl.obolibrary.org/obo/GO_0046930> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/GO_0016020>))
+
+# Class: <http://purl.obolibrary.org/obo/GO_0046931> (pore complex assembly)
+
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "GOC:jl") Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "GOC:mah") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/GO_0046931> "The aggregation, arrangement and bonding together of a set of components to form a pore complex. A pore complex is a small opening in a membrane that allows the passage of liquids and/or gases.")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/GO_0046931> "pore biosynthesis")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/GO_0046931> "pore formation")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/GO_0046931> "biological_process")
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "GOC:mah") <http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/GO_0046931> "pore complex biogenesis")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/GO_0046931> "pore-forming toxin activity")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/GO_0046931> "GO:0046931")
+AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/GO_0046931> "See also the cellular component term 'pore complex ; GO:0046930'.")
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/GO_0046931> "pore complex assembly")
+EquivalentClasses(<http://purl.obolibrary.org/obo/GO_0046931> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/GO_0022607> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002588> <http://purl.obolibrary.org/obo/GO_0046930>)))
+
 # Class: <http://purl.obolibrary.org/obo/GO_0046942> (carboxylic acid transport)
 
 AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "GOC:ai") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/GO_0046942> "The directed movement of carboxylic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carboxylic acids are organic acids containing one or more carboxyl (COOH) groups or anions (COO-).")

diff --git a/src/patterns/definitions.owl b/src/patterns/definitions.owl
@@ -6,8 +6,9 @@ Prefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)
 Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
-Ontology(<http://purl.obolibrary.org/obo/cl/releases/2024-08-09/patterns/definitions.owl>
-Annotation(owl:versionInfo "2024-08-09")
+Ontology(<http://purl.obolibrary.org/obo/cl/patterns/definitions.owl>
+<http://purl.obolibrary.org/obo/cl/releases/2024-08-16/patterns/definitions.owl>
+Annotation(owl:versionInfo "2024-08-16")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/CL_0000031>))
 Declaration(Class(<http://purl.obolibrary.org/obo/CL_0000084>))