Fix almost all unsatisfiability issues

obi-ontology · Aug 27, 2024 · ec60b63 · ec60b63
1 parent 96ba715
commit ec60b63
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Showing 6 changed files with 66 additions and 61 deletions.
diff --git a/src/ontology/OntoFox_inputs/GO_input.txt b/src/ontology/OntoFox_inputs/GO_input.txt
@@ -41,6 +41,7 @@ http://purl.obolibrary.org/obo/GO_0004448 # isocitrate dehydrogenase [NAD(P)+] a
 http://purl.obolibrary.org/obo/GO_0004457 # lactate dehydrogenase activity
 http://purl.obolibrary.org/obo/GO_0004540 # ribonuclease activity
 http://purl.obolibrary.org/obo/GO_0005216
+http://purl.obolibrary.org/obo/GO_0005488 # binding
 http://purl.obolibrary.org/obo/GO_0005575
 http://purl.obolibrary.org/obo/GO_0005577 # fibrinogen complex
 http://purl.obolibrary.org/obo/GO_0005694
@@ -179,8 +180,6 @@ http://purl.obolibrary.org/obo/GO_0140730 # amphiregulin production
 http://purl.obolibrary.org/obo/GO_0140779 # XCL1 production
 
 [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
 http://purl.obolibrary.org/obo/GO_0001788
 subClassOf http://purl.obolibrary.org/obo/GO_0008150
 http://purl.obolibrary.org/obo/GO_0001806 
@@ -264,7 +263,7 @@ subClassOf http://purl.obolibrary.org/obo/GO_0032991
 http://purl.obolibrary.org/obo/GO_0019882 
 subClassOf http://purl.obolibrary.org/obo/GO_0008150
 http://purl.obolibrary.org/obo/GO_0019904 
-subClassOf http://purl.obolibrary.org/obo/OBI_0001588
+subClassOf http://purl.obolibrary.org/obo/GO_0005488
 http://purl.obolibrary.org/obo/GO_0030041 
 subClassOf http://purl.obolibrary.org/obo/GO_0008150
 http://purl.obolibrary.org/obo/GO_0030097 
@@ -394,7 +393,7 @@ subClassOf http://purl.obolibrary.org/obo/BFO_0000040
 http://purl.obolibrary.org/obo/GO_0043316 
 subClassOf http://purl.obolibrary.org/obo/GO_0001906
 http://purl.obolibrary.org/obo/GO_0043565 
-subClassOf http://purl.obolibrary.org/obo/OBI_0001588
+subClassOf http://purl.obolibrary.org/obo/GO_0005488
 http://purl.obolibrary.org/obo/GO_0048869 
 subClassOf http://purl.obolibrary.org/obo/GO_0008150
 http://purl.obolibrary.org/obo/GO_0050896 

diff --git a/src/ontology/OntoFox_outputs/GO_imports.owl b/src/ontology/OntoFox_outputs/GO_imports.owl
@@ -89,7 +89,7 @@
     <!-- http://purl.obolibrary.org/obo/GO_0001046 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0001046">
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0003674"/>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0005488"/>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0043565"/>
         <obo:IAO_0000111>core promoter sequence-specific DNA binding</obo:IAO_0000111>
         <obo:IAO_0000115>Binding to a sequence of DNA that is part of a core promoter region. The core promoter is composed of the transcription start site and binding sites for the RNA polymerase and the basal transcription machinery. The transcribed region might be described as a gene, cistron, or operon.</obo:IAO_0000115>
@@ -99,15 +99,6 @@
 
 
 
-    <!-- http://purl.obolibrary.org/obo/GO_0001047 -->
-
-    <owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0001047">
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0001588"/>
-        <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/go.owl"/>
-    </owl:Class>
-
-
-
     <!-- http://purl.obolibrary.org/obo/GO_0001172 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0001172">
@@ -313,7 +304,7 @@
     <!-- http://purl.obolibrary.org/obo/GO_0003823 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0003823">
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0003674"/>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0005488"/>
         <obo:IAO_0000111>antigen binding</obo:IAO_0000111>
         <obo:IAO_0000115>Binding to an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen. Antigen binding by an MHC protein complex allows the antigen to be displayed to a T cell or NK cell.</obo:IAO_0000115>
         <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/go.owl"/>
@@ -514,6 +505,18 @@
 
 
 
+    <!-- http://purl.obolibrary.org/obo/GO_0005488 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0005488">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0003674"/>
+        <obo:IAO_0000111>binding</obo:IAO_0000111>
+        <obo:IAO_0000115>The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule.</obo:IAO_0000115>
+        <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/go.owl"/>
+        <rdfs:label>binding</rdfs:label>
+    </owl:Class>
+
+
+
     <!-- http://purl.obolibrary.org/obo/GO_0005575 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0005575">
@@ -853,7 +856,7 @@
     <!-- http://purl.obolibrary.org/obo/GO_0019904 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0019904">
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0001588"/>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0005488"/>
         <obo:IAO_0000111>protein domain specific binding</obo:IAO_0000111>
         <obo:IAO_0000115>Binding to a specific domain of a protein.</obo:IAO_0000115>
         <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/go.owl"/>
@@ -1657,7 +1660,7 @@
     <!-- http://purl.obolibrary.org/obo/GO_0043565 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0043565">
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0001588"/>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0005488"/>
         <obo:IAO_0000111>sequence-specific DNA binding</obo:IAO_0000111>
         <obo:IAO_0000115>Binding to DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.</obo:IAO_0000115>
         <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/go.owl"/>
@@ -2143,12 +2146,6 @@
         <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/go.owl"/>
         <rdfs:label>XCL1 production</rdfs:label>
     </owl:Class>
-
-
-
-    <!-- http://purl.obolibrary.org/obo/OBI_0001588 -->
-
-    <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0001588"/>
 </rdf:RDF>
 
 

diff --git a/src/ontology/modules/assays.owl b/src/ontology/modules/assays.owl
@@ -1040,6 +1040,12 @@
 
 
 
+    <!-- http://purl.obolibrary.org/obo/GO_0005488 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0005488"/>
+
+
+
     <!-- http://purl.obolibrary.org/obo/GO_0005577 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0005577"/>
@@ -5443,7 +5449,7 @@
                         <owl:someValuesFrom>
                             <owl:Restriction>
                                 <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
-                                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0001588"/>
+                                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GO_0005488"/>
                             </owl:Restriction>
                         </owl:someValuesFrom>
                     </owl:Restriction>
@@ -7055,7 +7061,7 @@
                 <owl:someValuesFrom>
                     <owl:Restriction>
                         <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
-                        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0001588"/>
+                        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GO_0005488"/>
                     </owl:Restriction>
                 </owl:someValuesFrom>
             </owl:Restriction>
@@ -8445,12 +8451,6 @@
 
 
 
-    <!-- http://purl.obolibrary.org/obo/OBI_0001588 -->
-
-    <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0001588"/>
-
-
-
     <!-- http://purl.obolibrary.org/obo/OBI_0001591 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0001591">
@@ -8765,7 +8765,7 @@
                 <owl:someValuesFrom>
                     <owl:Restriction>
                         <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
-                        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0001588"/>
+                        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GO_0005488"/>
                     </owl:Restriction>
                 </owl:someValuesFrom>
             </owl:Restriction>

diff --git a/src/ontology/modules/obsolete.owl b/src/ontology/modules/obsolete.owl
@@ -40,6 +40,12 @@
 
 
 
+    <!-- http://purl.obolibrary.org/obo/IAO_0000116 -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000116"/>
+
+
+
     <!-- http://purl.obolibrary.org/obo/IAO_0000117 -->
 
     <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000117"/>
@@ -834,6 +840,24 @@
 
 
 
+    <!-- http://purl.obolibrary.org/obo/OBI_0001588 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0001588">
+        <rdfs:subClassOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
+        <obo:IAO_0000112>A peptide binding to an MHC molecule to form a complex.</obo:IAO_0000112>
+        <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
+        <obo:IAO_0000115 xml:lang="en">The process of material entities forming complexes.</obo:IAO_0000115>
+        <obo:IAO_0000116>9/28/11 BP: The disposition referenced is the one of the ligand to bind the molecule. This along with binding as a function / process needs to be figured out with GO which is inconsistent at this point.</obo:IAO_0000116>
+        <obo:IAO_0000117>PERSON: Bjoern Peters, Randi Vita</obo:IAO_0000117>
+        <obo:IAO_0000119>IEDB</obo:IAO_0000119>
+        <obo:IAO_0000231 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000228"/>
+        <obo:IAO_0100001 rdf:resource="http://purl.obolibrary.org/obo/GO_0005488"/>
+        <rdfs:label>obsolete_binding</rdfs:label>
+        <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
+    </owl:Class>
+
+
+
     <!-- http://purl.obolibrary.org/obo/OBI_0001611 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0001611">

diff --git a/src/ontology/obi-edit.owl b/src/ontology/obi-edit.owl
@@ -12581,7 +12581,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29</obo:IAO_0000119>
                     <rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000027"/>
                     <owl:Restriction>
                         <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
-                        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0001588"/>
+                        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GO_0005488"/>
                     </owl:Restriction>
                 </owl:intersectionOf>
             </owl:Class>
@@ -14118,11 +14118,11 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html</obo:IAO_0000119>
     <!-- http://purl.obolibrary.org/obo/OBI_0001503 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0001503">
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0001588"/>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0005488"/>
         <rdfs:subClassOf>
             <owl:Class>
                 <owl:intersectionOf rdf:parseType="Collection">
-                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0001588"/>
+                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/GO_0005488"/>
                     <owl:Restriction>
                         <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/COB_0000087"/>
                         <owl:someValuesFrom>
@@ -14840,7 +14840,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&amp;compression=N
                             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0001191"/>
                             <owl:Restriction>
                                 <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
-                                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0001588"/>
+                                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GO_0005488"/>
                             </owl:Restriction>
                         </owl:intersectionOf>
                     </owl:Class>
@@ -14932,7 +14932,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&amp;compression=N
                             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0001180"/>
                             <owl:Restriction>
                                 <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
-                                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0001588"/>
+                                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GO_0005488"/>
                             </owl:Restriction>
                         </owl:intersectionOf>
                     </owl:Class>
@@ -14961,7 +14961,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&amp;compression=N
                             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0001171"/>
                             <owl:Restriction>
                                 <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
-                                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0001588"/>
+                                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GO_0005488"/>
                             </owl:Restriction>
                         </owl:intersectionOf>
                     </owl:Class>
@@ -14979,22 +14979,6 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&amp;compression=N
 
 
 
-    <!-- http://purl.obolibrary.org/obo/OBI_0001588 -->
-
-    <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0001588">
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0008150"/>
-        <obo:IAO_0000111>binding</obo:IAO_0000111>
-        <obo:IAO_0000112>A peptide binding to an MHC molecule to form a complex.</obo:IAO_0000112>
-        <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
-        <obo:IAO_0000115 xml:lang="en">The process of material entities forming complexes.</obo:IAO_0000115>
-        <obo:IAO_0000116>9/28/11 BP: The disposition referenced is the one of the ligand to bind the molecule. This along with binding as a function / process needs to be figured out with GO which is inconsistent at this point.</obo:IAO_0000116>
-        <obo:IAO_0000117>PERSON: Bjoern Peters, Randi Vita</obo:IAO_0000117>
-        <obo:IAO_0000119>IEDB</obo:IAO_0000119>
-        <rdfs:label>binding</rdfs:label>
-    </owl:Class>
-
-
-
     <!-- http://purl.obolibrary.org/obo/OBI_0001596 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0001596">
@@ -15044,7 +15028,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&amp;compression=N
                             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0001554"/>
                             <owl:Restriction>
                                 <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
-                                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0001588"/>
+                                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GO_0005488"/>
                             </owl:Restriction>
                         </owl:intersectionOf>
                     </owl:Class>
@@ -15073,7 +15057,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&amp;compression=N
                             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0001554"/>
                             <owl:Restriction>
                                 <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
-                                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0001588"/>
+                                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GO_0005488"/>
                             </owl:Restriction>
                         </owl:intersectionOf>
                     </owl:Class>
@@ -15582,7 +15566,7 @@ https://sourceforge.net/tracker/?func=detail&amp;aid=3512891&amp;group_id=177891
     <!-- http://purl.obolibrary.org/obo/OBI_0001702 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0001702">
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0001588"/>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0005488"/>
         <rdfs:subClassOf>
             <owl:Restriction>
                 <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/COB_0000087"/>
@@ -21100,7 +21084,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre
                             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0001180"/>
                             <owl:Restriction>
                                 <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
-                                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0001588"/>
+                                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GO_0005488"/>
                             </owl:Restriction>
                         </owl:intersectionOf>
                     </owl:Class>
@@ -21128,7 +21112,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre
                             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0001191"/>
                             <owl:Restriction>
                                 <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
-                                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0001588"/>
+                                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GO_0005488"/>
                             </owl:Restriction>
                         </owl:intersectionOf>
                     </owl:Class>
@@ -29844,7 +29828,7 @@ Possible ecological risks of transgenic organism release when transgenes affect
                 </owl:someValuesFrom>
             </owl:Restriction>
         </owl:equivalentClass>
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0008150"/>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0005488"/>
         <obo:IAO_0000111>epitope binding by adaptive immune receptor</obo:IAO_0000111>
         <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
         <obo:IAO_0000115 xml:lang="en">is the process in which an adaptive immune receptor binds to a material entity (realizing its disposition). The binding affinity is significant enough to trigger an immune response. Specifically, transient non-specific binding of adaptive immune receptors occurring during immune surveillance is not considered significant binding.</obo:IAO_0000115>
@@ -30716,7 +30700,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it
     <!-- http://purl.obolibrary.org/obo/OBI_1110057 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_1110057">
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0001588"/>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0005488"/>
         <rdfs:subClassOf>
             <owl:Restriction>
                 <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/COB_0000087"/>