complete initial assay package? #1153

obi-ontology · Aug 24, 2020 · 099a8c5 · 099a8c5
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diff --git a/src/ontology/OntoFox_inputs/ChEBI_input.txt b/src/ontology/OntoFox_inputs/ChEBI_input.txt
diff --git a/src/ontology/OntoFox_inputs/GO_input.txt b/src/ontology/OntoFox_inputs/GO_input.txt
@@ -157,9 +157,10 @@ http://purl.obolibrary.org/obo/GO_0005739 # mitochondrion
 http://purl.obolibrary.org/obo/GO_0036392 # chemokine (C-C motif) ligand 20 production
 http://purl.obolibrary.org/obo/GO_0001508 # action potential
 http://purl.obolibrary.org/obo/GO_0001172 # transcription, RNA-templated
-http://purl.obolibrary.org/obo/GO_0033130 # acetylcholine receptor binding for TURBO assays
+http://purl.obolibrary.org/obo/GO_0033130 # acetylcholine receptor binding for TURBO assays
 http://purl.obolibrary.org/obo/GO_0071735 # IgG immunoglobulin complex for TURBO assays
 
+
 [Top level source term URIs and target direct superclass URIs]
 http://purl.obolibrary.org/obo/GO_0001047 # core promoter binding
 subClassOf http://purl.obolibrary.org/obo/OBI_0001588 # binding
@@ -449,6 +450,8 @@ http://purl.obolibrary.org/obo/GO_0016570
 subClassOf http://purl.obolibrary.org/obo/GO_0008150
 http://purl.obolibrary.org/obo/GO_0005739
 subClassOf http://purl.obolibrary.org/obo/GO_0043227
+http://purl.obolibrary.org/obo/GO_0071735
+subClassOf http://purl.obolibrary.org/obo/GO_0019814
 
 
 [Source term retrieval setting]

diff --git a/src/ontology/OntoFox_inputs/NCBITaxon_input.txt b/src/ontology/OntoFox_inputs/NCBITaxon_input.txt
@@ -35,7 +35,7 @@ http://purl.obolibrary.org/obo/NCBITaxon_10376
 http://purl.obolibrary.org/obo/NCBITaxon_10358
 http://purl.obolibrary.org/obo/NCBITaxon_160
 # http://purl.obolibrary.org/obo/NCBITaxon_1 # root for TURBO assays
-http://purl.obolibrary.org/obo/NCBITaxon_131567 # cellular organisms for TURBO assays
+# http://purl.obolibrary.org/obo/NCBITaxon_131567 # cellular organisms for TURBO assays
 http://purl.obolibrary.org/obo/NCBITaxon_33317 # Protostomia for TURBO assays
 http://purl.obolibrary.org/obo/NCBITaxon_33340 # Neoptera for TURBO assays
 http://purl.obolibrary.org/obo/NCBITaxon_6656 # Arthropoda for TURBO assays

diff --git a/src/ontology/OntoFox_outputs/ChEBI_imports.owl b/src/ontology/OntoFox_outputs/ChEBI_imports.owl
diff --git a/src/ontology/OntoFox_outputs/GO_imports.owl b/src/ontology/OntoFox_outputs/GO_imports.owl
@@ -90,10 +90,7 @@
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0001047">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0001588"/>
-        <obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">core promoter binding</obo:IAO_0000111>
-        <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for the basal transcription machinery. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.</obo:IAO_0000115>
         <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/go.owl"/>
-        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">core promoter binding</rdfs:label>
     </owl:Class>
 
 
@@ -1239,6 +1236,18 @@
 
 
 
+    <!-- http://purl.obolibrary.org/obo/GO_0033130 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0033130">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0003674"/>
+        <obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">acetylcholine receptor binding</obo:IAO_0000111>
+        <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Interacting selectively and non-covalently with an acetylcholine receptor.</obo:IAO_0000115>
+        <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/go.owl"/>
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">acetylcholine receptor binding</rdfs:label>
+    </owl:Class>
+
+
+
     <!-- http://purl.obolibrary.org/obo/GO_0034061 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0034061">
@@ -1743,6 +1752,18 @@
 
 
 
+    <!-- http://purl.obolibrary.org/obo/GO_0071735 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0071735">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0019814"/>
+        <obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">IgG immunoglobulin complex</obo:IAO_0000111>
+        <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A protein complex composed of two identical immunoglobulin heavy chains of an IgG isotype and two identical immunoglobulin light chains, held together by disulfide bonds. An IgG immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph.</obo:IAO_0000115>
+        <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/go.owl"/>
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">IgG immunoglobulin complex</rdfs:label>
+    </owl:Class>
+
+
+
     <!-- http://purl.obolibrary.org/obo/GO_0071924 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0071924">

diff --git a/src/ontology/OntoFox_outputs/NCBITaxon_imports.owl b/src/ontology/OntoFox_outputs/NCBITaxon_imports.owl
@@ -197,7 +197,7 @@
     <!-- http://purl.obolibrary.org/obo/NCBITaxon_1206794 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_1206794">
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_33213"/>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_33317"/>
         <obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ecdysozoa</obo:IAO_0000111>
         <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ncbitaxon.owl"/>
         <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ecdysozoa</rdfs:label>
@@ -219,7 +219,7 @@
     <!-- http://purl.obolibrary.org/obo/NCBITaxon_197562 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_197562">
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_1206794"/>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_6656"/>
         <obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pancrustacea</obo:IAO_0000111>
         <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ncbitaxon.owl"/>
         <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pancrustacea</rdfs:label>
@@ -320,6 +320,39 @@
 
 
 
+    <!-- http://purl.obolibrary.org/obo/NCBITaxon_33317 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_33317">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_33213"/>
+        <obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Protostomia</obo:IAO_0000111>
+        <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ncbitaxon.owl"/>
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Protostomia</rdfs:label>
+    </owl:Class>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/NCBITaxon_33340 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_33340">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_197562"/>
+        <obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Neoptera</obo:IAO_0000111>
+        <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ncbitaxon.owl"/>
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Neoptera</rdfs:label>
+    </owl:Class>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/NCBITaxon_33392 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_33392">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_33340"/>
+        <obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Holometabola</obo:IAO_0000111>
+        <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ncbitaxon.owl"/>
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Holometabola</rdfs:label>
+    </owl:Class>
+
+
+
     <!-- http://purl.obolibrary.org/obo/NCBITaxon_3702 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_3702">
@@ -441,6 +474,18 @@
 
 
 
+    <!-- http://purl.obolibrary.org/obo/NCBITaxon_6656 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_6656">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_1206794"/>
+        <obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Arthropoda</obo:IAO_0000111>
+        <obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">arthropods</obo:IAO_0000118>
+        <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ncbitaxon.owl"/>
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Arthropoda</rdfs:label>
+    </owl:Class>
+
+
+
     <!-- http://purl.obolibrary.org/obo/NCBITaxon_6668 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_6668">
@@ -467,7 +512,7 @@
     <!-- http://purl.obolibrary.org/obo/NCBITaxon_7227 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_7227">
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_197562"/>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_33392"/>
         <obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Drosophila melanogaster</obo:IAO_0000111>
         <obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">fruit fly</obo:IAO_0000118>
         <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ncbitaxon.owl"/>
@@ -476,6 +521,89 @@
 
 
 
+    <!-- http://purl.obolibrary.org/obo/NCBITaxon_7434 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_7434">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_33392"/>
+        <obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Aculeata &lt;wasps, ants, and bees&gt;</obo:IAO_0000111>
+        <obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Aculeata</obo:IAO_0000118>
+        <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ncbitaxon.owl"/>
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Aculeata &lt;wasps, ants, and bees&gt;</rdfs:label>
+    </owl:Class>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/NCBITaxon_7438 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_7438">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_7434"/>
+        <obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Vespidae</obo:IAO_0000111>
+        <obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">wasps</obo:IAO_0000118>
+        <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ncbitaxon.owl"/>
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Vespidae</rdfs:label>
+    </owl:Class>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/NCBITaxon_7439 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_7439">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_7438"/>
+        <obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Vespinae</obo:IAO_0000111>
+        <obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">hornets and yellowjackets</obo:IAO_0000118>
+        <obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">true wasps</obo:IAO_0000118>
+        <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ncbitaxon.owl"/>
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Vespinae</rdfs:label>
+    </owl:Class>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/NCBITaxon_7440 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_7440">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_7439"/>
+        <obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Dolichovespula</obo:IAO_0000111>
+        <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ncbitaxon.owl"/>
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Dolichovespula</rdfs:label>
+    </owl:Class>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/NCBITaxon_7441 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_7441">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_7440"/>
+        <obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Dolichovespula maculata</obo:IAO_0000111>
+        <obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">bald-faced hornet</obo:IAO_0000118>
+        <obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">white-face hornet</obo:IAO_0000118>
+        <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ncbitaxon.owl"/>
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Dolichovespula maculata</rdfs:label>
+    </owl:Class>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/NCBITaxon_7442 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_7442">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_7440"/>
+        <obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Dolichovespula arenaria</obo:IAO_0000111>
+        <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ncbitaxon.owl"/>
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Dolichovespula arenaria</rdfs:label>
+    </owl:Class>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/NCBITaxon_7456 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_7456">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_7438"/>
+        <obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Polistes</obo:IAO_0000111>
+        <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ncbitaxon.owl"/>
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Polistes</rdfs:label>
+    </owl:Class>
+
+
+
     <!-- http://purl.obolibrary.org/obo/NCBITaxon_7742 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_7742">