Merge pull request #1627 from EBISPOT/release_3.43.0

EFO release 3.43.0
EBISPOT · Jun 10, 2022 · f328078 · f328078
2 parents 94a1053 + 744e143
commit f328078
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diff --git a/ExFactor Ontology release notes.txt b/ExFactor Ontology release notes.txt
diff --git a/efo-base.owl b/efo-base.owl
diff --git a/src/ontology/components/gwas_import.owl b/src/ontology/components/gwas_import.owl
diff --git a/src/ontology/imports/cl_import.owl b/src/ontology/imports/cl_import.owl
@@ -6177,15 +6177,15 @@ Covers cells actively being cultured or stored in a quiescent state for future u
         <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GO_REF:0000031</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PMID:11532393</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PMID:12457618</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PMID:15032583</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>PMID:15032583</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PMID:15766674</oboInOwl:hasDbXref>
     </owl:Axiom>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/CL_0000825"/>
         <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"/>
         <owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">NKP</owl:annotatedTarget>
         <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PMID:12457618</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PMID:15032583</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>PMID:15032583</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PMID:15766674</oboInOwl:hasDbXref>
     </owl:Axiom>
     <owl:Axiom>

diff --git a/src/ontology/imports/fbbt_import.owl b/src/ontology/imports/fbbt_import.owl
@@ -447,7 +447,7 @@ A continuant cannot be part of an occurrent: use &apos;participates in&apos;. An
         <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBC:DOS</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBC:VH</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FlyBase:FBrf0089570</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FlyBase:FBrf0151275</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>FlyBase:FBrf0151275</oboInOwl:hasDbXref>
     </owl:Axiom>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/FBbt_00000461"/>
@@ -576,7 +576,7 @@ A continuant cannot be part of an occurrent: use &apos;participates in&apos;. An
         <owl:annotatedTarget>Hemocyte of the embryo and larva. Relatively large, irregularly shaped hemocyte (Brehelin, 1982). At the end of the third instar larval stage, plasmatocytes contains numerous inclusions, digitations and pinocytotic vesicles, well developed rough endoplasmic reticulum, Golgi apparatus and small lysosome-like bodies. By the end of the third instar period they also contain numerous phagosomes. Plasmatocytes represent 90-95% of all mature larval hemocytes. They function in the removal of dead cells and microbial pathogens.</owl:annotatedTarget>
         <oboInOwl:hasDbXref>FlyBase:FBrf0037631</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>FlyBase:FBrf0066479</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FlyBase:FBrf0134542</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>FlyBase:FBrf0134542</oboInOwl:hasDbXref>
     </owl:Axiom>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/FBbt_00001685"/>
@@ -646,14 +646,14 @@ A continuant cannot be part of an occurrent: use &apos;participates in&apos;. An
         <oboInOwl:hasDbXref>FlyBase:FBrf0053727</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FlyBase:FBrf0064803</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FlyBase:FBrf0089570</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FlyBase:FBrf0179777</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FlyBase:FBrf0247015</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>FlyBase:FBrf0179777</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>FlyBase:FBrf0247015</oboInOwl:hasDbXref>
     </owl:Axiom>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/FBbt_00001724"/>
         <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"/>
         <owl:annotatedTarget>PTG</owl:annotatedTarget>
-        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FlyBase:FBrf0247015</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>FlyBase:FBrf0247015</oboInOwl:hasDbXref>
     </owl:Axiom>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/FBbt_00001724"/>
@@ -893,7 +893,7 @@ A continuant cannot be part of an occurrent: use &apos;participates in&apos;. An
         <owl:annotatedTarget>Small, bilaterally paired gland that lies caudal to the spermathecae and is connected to the uterus by a duct (McQueen et al., 2022). The gland wall consists of a single layer of secretory cells, each with a large vacuole and a minute acidophilic granule towards the gland lumen (McQueen et al., 2022). It arises from the segment 9 (male genital) primordium in the female genital disc (McQueen et al., 2022).</owl:annotatedTarget>
         <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FlyBase:FBrf0007735</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FlyBase:FBrf0141451</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">doi:10.20944/preprints202201.0223.v1</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FlyBase:FBrf0253444</oboInOwl:hasDbXref>
     </owl:Axiom>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/FBbt_00004914"/>
@@ -905,21 +905,21 @@ A continuant cannot be part of an occurrent: use &apos;participates in&apos;. An
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/FBbt_00004914"/>
         <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"/>
         <owl:annotatedTarget>appendicular gland</owl:annotatedTarget>
-        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">doi:10.20944/preprints202201.0223.v1</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FlyBase:FBrf0253444</oboInOwl:hasDbXref>
     </owl:Axiom>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/FBbt_00004914"/>
         <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"/>
         <owl:annotatedTarget>colleterial gland</owl:annotatedTarget>
         <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FlyBase:FBrf0007735</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">doi:10.20944/preprints202201.0223.v1</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FlyBase:FBrf0253444</oboInOwl:hasDbXref>
     </owl:Axiom>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/FBbt_00004914"/>
         <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"/>
         <owl:annotatedTarget>parovarium</owl:annotatedTarget>
         <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FlyBase:FBrf0031004</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">doi:10.20944/preprints202201.0223.v1</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FlyBase:FBrf0253444</oboInOwl:hasDbXref>
     </owl:Axiom>
 
 
@@ -1221,7 +1221,7 @@ A continuant cannot be part of an occurrent: use &apos;participates in&apos;. An
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/FBbt_00005508"/>
         <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
         <owl:annotatedTarget>Embryonic structure from which the mushroom body is derived. The development of the mushroom body proceeds as follows: axonogenesis of embryonic Kenyon cells starts late in embryonic stage 14. The axons from these cells extend towards the lateral protocerebral tract (LTP). During stage 16, a second set of Kenyon cell fibers form a second tract, closely apposed to the first. By late stage 16, both tracts extend anteriorly beyond the LTP to form the distal part of the peduncle. These tracts make a sharp medial turn close to the boundary with the deutocerebrum to form the medial lobe. By late stage 17 the vertical lobe has emerged as a collateral outgrowth from the point where these tracts bend. Finally, the calyx forms near to the end of embryogenesis.</owl:annotatedTarget>
-        <oboInOwl:hasDbXref>FlyBase:FBrf0144836</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FlyBase:FBrf0144836</oboInOwl:hasDbXref>
     </owl:Axiom>
 
 
@@ -2159,7 +2159,7 @@ A continuant cannot be part of an occurrent: use &apos;participates in&apos;. An
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/FBbt_00005669"/>
         <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
         <owl:annotatedTarget>Small ganglion of the embryonic stomatogastric nervous system. By stage 16 it is located on the left hand side of the embryo, between the two brain hemispheres and behind the supraesophageal commissure. It is more compact than the paraesophageal ganglion and occupies a more dorsal position. It contains approximately 10-12 neurons.</owl:annotatedTarget>
-        <oboInOwl:hasDbXref>FlyBase:FBrf0078614</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FlyBase:FBrf0078614</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FlyBase:FBrf0089570</oboInOwl:hasDbXref>
     </owl:Axiom>
 
@@ -2328,7 +2328,7 @@ A continuant cannot be part of an occurrent: use &apos;participates in&apos;. An
         <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBC:DOS</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBC:VH</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FlyBase:FBrf0089570</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FlyBase:FBrf0151275</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>FlyBase:FBrf0151275</oboInOwl:hasDbXref>
     </owl:Axiom>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/FBbt_00005822"/>
@@ -2493,7 +2493,7 @@ A continuant cannot be part of an occurrent: use &apos;participates in&apos;. An
         <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
         <owl:annotatedTarget>Unpaired neuron with its cell body found along the midline of the embryonic/larval ventral nerve cord (Fontana and Crews, 2012). There are around 18 of these per segment in the late embryo, which are derived from midline precursors (MP1-6) or the median neuroblast (MNB) (Fontana and Crews, 2012). Two sets of neurons can be distinguished; ventral neurons (including MP3 and VUM neurons) and medial neurons (including MP1 and MNB descendants) (Kearney et al., 2004).</owl:annotatedTarget>
         <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FlyBase:FBrf0180108</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FlyBase:FBrf0219766</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>FlyBase:FBrf0219766</oboInOwl:hasDbXref>
     </owl:Axiom>
 
 
@@ -2758,7 +2758,7 @@ A continuant cannot be part of an occurrent: use &apos;participates in&apos;. An
         <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
         <owl:annotatedTarget>Primordium of the embryo that will give rise to the adult eye. It corresponds to the most anterior region that develops from the visual primordium.</owl:annotatedTarget>
         <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FlyBase:FBrf0089570</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FlyBase:FBrf0151275</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>FlyBase:FBrf0151275</oboInOwl:hasDbXref>
     </owl:Axiom>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/FBbt_10005249"/>