Merge pull request #3010 from monarch-initiative/release-2021-04-30

release 2021-04-30

src/ontology/imports/chebi_import.obo

@@ -1,5 +1,5 @@
 format-version: 1.2
-data-version: mondo/releases/2021-04-07/imports/chebi_import.owl
+data-version: mondo/releases/2021-04-30/imports/chebi_import.owl
 ontology: mondo/imports/chebi_import
 
 [Term]

src/ontology/imports/chebi_import.owl

@@ -9,7 +9,7 @@
      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/mondo/imports/chebi_import.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/mondo/releases/2021-04-07/imports/chebi_import.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/mondo/releases/2021-04-30/imports/chebi_import.owl"/>
     </owl:Ontology>
 
 

src/ontology/imports/cl_import.obo

@@ -1,5 +1,5 @@
 format-version: 1.2
-data-version: mondo/releases/2021-04-07/imports/cl_import.owl
+data-version: mondo/releases/2021-04-30/imports/cl_import.owl
 subsetdef: added_for_HCA ""
 subsetdef: ubprop:upper_level ""
 ontology: mondo/imports/cl_import

src/ontology/imports/cl_import.owl

@@ -12,7 +12,7 @@
      xmlns:ubprop="http://purl.obolibrary.org/obo/ubprop#"
      xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/mondo/imports/cl_import.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/mondo/releases/2021-04-07/imports/cl_import.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/mondo/releases/2021-04-30/imports/cl_import.owl"/>
     </owl:Ontology>
 
 
@@ -3505,9 +3505,9 @@
         <owl:annotatedTarget>An animal cell that has characteristics of both a fibroblast cell and a smooth muscle cell.</owl:annotatedTarget>
         <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GOC:dsd</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>GOC:tfm</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MESH:D058628</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PMID:19800625</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PMID:20630469</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>MESH:D058628</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>PMID:19800625</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>PMID:20630469</oboInOwl:hasDbXref>
     </owl:Axiom>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/CL_0000186"/>
@@ -3579,10 +3579,10 @@
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/CL_0000192"/>
         <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
         <owl:annotatedTarget>A non-striated, elongated, spindle-shaped cell found lining the digestive tract, uterus, and blood vessels. They develop from specialized myoblasts (smooth muscle myoblast).</owl:annotatedTarget>
-        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MESH:A11.620.520</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>MESH:A11.620.520</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MESH:D032389</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PMID:9315361</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://en.wikipedia.org/wiki/Smooth_muscle_cell</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>http://en.wikipedia.org/wiki/Smooth_muscle_cell</oboInOwl:hasDbXref>
     </owl:Axiom>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/CL_0000192"/>
@@ -4560,7 +4560,7 @@
         <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
         <owl:annotatedTarget>An epithelial cell that lines the peripheral gas exchange region of the lungs of air-breathing vertebrates.</owl:annotatedTarget>
         <oboInOwl:hasDbXref>GOC:tfm</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PMID:20054144</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>PMID:20054144</oboInOwl:hasDbXref>
     </owl:Axiom>
 
 
@@ -11708,7 +11708,7 @@
         <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GOC:msz</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>GOC:tfm</oboInOwl:hasDbXref>
         <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">PMCID:PMC2673126</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>PMCID:PMC2673126</oboInOwl:hasDbXref>
     </owl:Axiom>
 
 
@@ -15378,15 +15378,15 @@
         <obo:IAO_0000115>An epithelial cell derived from ectoderm.</obo:IAO_0000115>
         <oboInOwl:created_by>tmeehan</oboInOwl:created_by>
         <oboInOwl:creation_date>2010-06-29T03:38:22Z</oboInOwl:creation_date>
-        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FMA:69074</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>FMA:69074</oboInOwl:hasDbXref>
         <oboInOwl:hasOBONamespace>cell</oboInOwl:hasOBONamespace>
         <rdfs:label>ecto-epithelial cell</rdfs:label>
     </owl:Class>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/CL_0002077"/>
         <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
         <owl:annotatedTarget>An epithelial cell derived from ectoderm.</owl:annotatedTarget>
-        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FMA:69074</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>FMA:69074</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>GOC:tfm</oboInOwl:hasDbXref>
     </owl:Axiom>
 
@@ -18568,7 +18568,7 @@
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/CL_0002481"/>
         <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
         <owl:annotatedTarget>The flattened smooth myoepithelial cells of mesodermal origin that lie just outside the basal lamina of the seminiferous tubule.</owl:annotatedTarget>
-        <oboInOwl:hasDbXref>GOC:cjm</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GOC:cjm</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>GOC:tfm</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>MP:0006420</oboInOwl:hasDbXref>
     </owl:Axiom>

src/ontology/imports/ecto_import.obo

@@ -1,5 +1,5 @@
 format-version: 1.2
-data-version: mondo/releases/2021-04-07/imports/ecto_import.owl
+data-version: mondo/releases/2021-04-30/imports/ecto_import.owl
 ontology: mondo/imports/ecto_import
 
 [Term]

src/ontology/imports/ecto_import.owl

@@ -11,7 +11,7 @@
      xmlns:swrlb="http://www.w3.org/2003/11/swrlb#"
      xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/mondo/imports/ecto_import.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/mondo/releases/2021-04-07/imports/ecto_import.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/mondo/releases/2021-04-30/imports/ecto_import.owl"/>
     </owl:Ontology>
 
 

src/ontology/imports/ecto_terms.txt

@@ -66,17 +66,23 @@ http://purl.obolibrary.org/obo/ECTO_0002002
 http://purl.obolibrary.org/obo/ECTO_0002032
 http://purl.obolibrary.org/obo/ECTO_0010000
 http://purl.obolibrary.org/obo/ECTO_0010001
+http://purl.obolibrary.org/obo/ECTO_0010002
 http://purl.obolibrary.org/obo/ECTO_0010003
+http://purl.obolibrary.org/obo/ECTO_0400000
 http://purl.obolibrary.org/obo/ECTO_0500000
+http://purl.obolibrary.org/obo/ECTO_0500025
+http://purl.obolibrary.org/obo/ECTO_0600000
 http://purl.obolibrary.org/obo/ECTO_1000000
 http://purl.obolibrary.org/obo/ECTO_1000007
 http://purl.obolibrary.org/obo/ECTO_1000019
 http://purl.obolibrary.org/obo/ECTO_3000000
 http://purl.obolibrary.org/obo/ECTO_3000001
+http://purl.obolibrary.org/obo/ECTO_3000005
 http://purl.obolibrary.org/obo/ECTO_4000000
 http://purl.obolibrary.org/obo/ECTO_4000001
 http://purl.obolibrary.org/obo/ECTO_4000002
 http://purl.obolibrary.org/obo/ECTO_4000003
+http://purl.obolibrary.org/obo/ECTO_4000024
 http://purl.obolibrary.org/obo/ECTO_4000025
 http://purl.obolibrary.org/obo/ECTO_4000026
 http://purl.obolibrary.org/obo/ECTO_4000027
@@ -85,7 +91,12 @@ http://purl.obolibrary.org/obo/ECTO_4000029
 http://purl.obolibrary.org/obo/ECTO_4000030
 http://purl.obolibrary.org/obo/ECTO_4000031
 http://purl.obolibrary.org/obo/ECTO_4000032
+http://purl.obolibrary.org/obo/ECTO_4000033
+http://purl.obolibrary.org/obo/ECTO_4000034
+http://purl.obolibrary.org/obo/ECTO_4000035
+http://purl.obolibrary.org/obo/ECTO_4000036
 http://purl.obolibrary.org/obo/ECTO_5000000
+http://purl.obolibrary.org/obo/ECTO_6000016
 http://purl.obolibrary.org/obo/ECTO_7000008
 http://purl.obolibrary.org/obo/ECTO_7000012
 http://purl.obolibrary.org/obo/ECTO_7000018

src/ontology/imports/envo_import.obo

@@ -1,5 +1,5 @@
 format-version: 1.2
-data-version: mondo/releases/2021-04-07/imports/envo_import.owl
+data-version: mondo/releases/2021-04-30/imports/envo_import.owl
 ontology: mondo/imports/envo_import
 
 [Term]
@@ -39,6 +39,12 @@ def: "An occurrent that has temporal proper parts and for some time t, p s-depen
 def: "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])" []
 is_a: BFO:0000003 ! occurrent
 
+[Term]
+id: BFO:0000016
+name: disposition
+is_a: BFO:0000017 ! realizable entity
+disjoint_from: BFO:0000023 ! role
+
 [Term]
 id: BFO:0000017
 name: realizable entity
@@ -1886,6 +1892,12 @@ id: ENVO:01000435
 name: montane forest
 is_a: ENVO:01001243 ! forest ecosystem
 
+[Term]
+id: ENVO:01000452
+name: environmental disposition
+def: "A disposition which is realised by an environmental system or system parts thereof." []
+is_a: BFO:0000016 ! disposition
+
 [Term]
 id: ENVO:01000543
 name: atmospheric layer
@@ -3818,6 +3830,16 @@ intersection_of: PATO:0000146 ! temperature
 intersection_of: RO:0000052 ENVO:00002005 ! inheres in air
 relationship: RO:0000052 ENVO:00002005 ! inheres in air
 
+[Term]
+id: ENVO:09200002
+name: environmental system process quality
+def: "The quality of a environmental system process." []
+synonym: "quality of environmental system process" EXACT []
+is_a: PATO:0001236 ! process quality
+intersection_of: PATO:0001236 ! process quality
+intersection_of: RO:0000052 ENVO:02500000 ! inheres in environmental system process
+relationship: RO:0000052 ENVO:02500000 ! inheres in environmental system process
+
 [Term]
 id: ENVO:09200004
 name: porosity of soil
@@ -4401,6 +4423,17 @@ name: elongated
 def: "A quality inhering in a bearer by virtue of the bearer's length being notably higher than its width." []
 is_a: PATO:0000052 ! shape
 
+[Term]
+id: PATO:0001236
+name: process quality
+def: "A quality which inheres in an process." []
+synonym: "quality of a process" EXACT []
+synonym: "quality of occurrent" EXACT []
+synonym: "quality of process" EXACT []
+synonym: "relational quality of occurrent" EXACT []
+is_a: PATO:0000001 ! quality
+disjoint_from: PATO:0001241 ! physical object quality
+
 [Term]
 id: PATO:0001241
 name: physical object quality

src/ontology/imports/envo_import.owl

@@ -9,7 +9,7 @@
      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/mondo/imports/envo_import.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/mondo/releases/2021-04-07/imports/envo_import.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/mondo/releases/2021-04-30/imports/envo_import.owl"/>
     </owl:Ontology>
 
 
@@ -653,6 +653,16 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000</obo:IAO_0000115>
 
 
 
+    <!-- http://purl.obolibrary.org/obo/BFO_0000016 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000016">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000017"/>
+        <owl:disjointWith rdf:resource="http://purl.obolibrary.org/obo/BFO_0000023"/>
+        <rdfs:label xml:lang="en">disposition</rdfs:label>
+    </owl:Class>
+
+
+
     <!-- http://purl.obolibrary.org/obo/BFO_0000017 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000017">
@@ -5103,6 +5113,16 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000</obo:IAO_0000115>
 
 
 
+    <!-- http://purl.obolibrary.org/obo/ENVO_01000452 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/ENVO_01000452">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000016"/>
+        <obo:IAO_0000115>A disposition which is realised by an environmental system or system parts thereof.</obo:IAO_0000115>
+        <rdfs:label>environmental disposition</rdfs:label>
+    </owl:Class>
+
+
+
     <!-- http://purl.obolibrary.org/obo/ENVO_01000543 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/ENVO_01000543">
@@ -12241,6 +12261,34 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000</obo:IAO_0000115>
 
 
 
+    <!-- http://purl.obolibrary.org/obo/ENVO_09200002 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/ENVO_09200002">
+        <owl:equivalentClass>
+            <owl:Class>
+                <owl:intersectionOf rdf:parseType="Collection">
+                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/PATO_0001236"/>
+                    <owl:Restriction>
+                        <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
+                        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/ENVO_02500000"/>
+                    </owl:Restriction>
+                </owl:intersectionOf>
+            </owl:Class>
+        </owl:equivalentClass>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PATO_0001236"/>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
+                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/ENVO_02500000"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
+        <obo:IAO_0000115>The quality of a environmental system process.</obo:IAO_0000115>
+        <oboInOwl:hasExactSynonym>quality of environmental system process</oboInOwl:hasExactSynonym>
+        <rdfs:label>environmental system process quality</rdfs:label>
+    </owl:Class>
+
+
+
     <!-- http://purl.obolibrary.org/obo/ENVO_09200004 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/ENVO_09200004">
@@ -13338,6 +13386,21 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000</obo:IAO_0000115>
 
 
 
+    <!-- http://purl.obolibrary.org/obo/PATO_0001236 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/PATO_0001236">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PATO_0000001"/>
+        <owl:disjointWith rdf:resource="http://purl.obolibrary.org/obo/PATO_0001241"/>
+        <obo:IAO_0000115>A quality which inheres in an process.</obo:IAO_0000115>
+        <oboInOwl:hasExactSynonym>quality of a process</oboInOwl:hasExactSynonym>
+        <oboInOwl:hasExactSynonym>quality of occurrent</oboInOwl:hasExactSynonym>
+        <oboInOwl:hasExactSynonym>quality of process</oboInOwl:hasExactSynonym>
+        <oboInOwl:hasExactSynonym>relational quality of occurrent</oboInOwl:hasExactSynonym>
+        <rdfs:label>process quality</rdfs:label>
+    </owl:Class>
+
+
+
     <!-- http://purl.obolibrary.org/obo/PATO_0001241 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/PATO_0001241">