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deleted the 'gatekeeper location' proposal, added the relation of 'al…
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…igned with conserve residue'. define a mutated residue aligned with the conserve residue in a wild type protein.
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@linikujp
linikujp committed Jan 27, 2015
1 parent 9fb0ee0 commit 2c3d2ab
Showing 1 changed file with 77 additions and 125 deletions.
202 changes: 77 additions & 125 deletions gatekeeper/test_gatekeeper.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -11,10 +11,10 @@

<rdf:RDF xmlns="http://purl.obolibrary.org/obo/gatekeepertest.owl#"
xml:base="http://purl.obolibrary.org/obo/gatekeepertest.owl"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/gatekeepertest.owl"/>


Expand Down Expand Up @@ -127,6 +127,15 @@



<!-- http://purl.obolibrary.org/obo/GATEK_0000056 -->

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GATEK_0000056">
<rdfs:label xml:lang="en">aligned with conserve residue</rdfs:label>
<rdfs:comment>a residue in a protein that aligned with the conserve residue in another protein. conserved sequences are similar or identical sequences that occur within nucleic acid sequences (such as RNA and DNA sequences), protein sequences, protein structures or polymeric carbohydrates across species (orthologous sequences) or within different molecules produced by the same organism (paralogous sequences)</rdfs:comment>
</owl:ObjectProperty>



<!--
///////////////////////////////////////////////////////////////////////////////////////
//
Expand Down Expand Up @@ -175,12 +184,6 @@
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000052"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000006"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000005"/>
</owl:Restriction>
</rdfs:subClassOf>
</owl:Class>


Expand All @@ -194,51 +197,6 @@



<!-- http://purl.obolibrary.org/obo/GATEK_0000004 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/GATEK_0000004">
<rdfs:label xml:lang="en">amino acid sequence location</rdfs:label>
<rdfs:comment>a location occpied by a residue in a wild type protein, which is designated by the numerical sequencial position in the case of wild type protein. In the case of subsititue mutation, this location is occupied by a mutated residue. NOTE: The first amino acid in the chain should be considered as having position 1.</rdfs:comment>
<rdfs:comment>is a BFO:three-dimensional spatial region</rdfs:comment>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/GATEK_0000005 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/GATEK_0000005">
<rdfs:label xml:lang="en">gatekeeper location</rdfs:label>
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GATEK_0000004"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000010"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000001"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000004"/>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/GATEK_0000008 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/GATEK_0000008">
<rdfs:label xml:lang="en">135 in ABL1 amino acid sequence</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000004"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000010"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000051"/>
</owl:Restriction>
</rdfs:subClassOf>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/GATEK_0000013 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/GATEK_0000013">
Expand All @@ -255,30 +213,24 @@
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000018"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty>
<rdf:Description>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000045"/>
</rdf:Description>
</owl:onProperty>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000047"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000006"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000008"/>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000014"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000013"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000014"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000013"/>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000056"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000051"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000006"/>
<owl:allValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000008"/>
<owl:onProperty>
<rdf:Description>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000045"/>
</rdf:Description>
</owl:onProperty>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000047"/>
</owl:Restriction>
</rdfs:subClassOf>
<owl:disjointWith rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000051"/>
Expand Down Expand Up @@ -315,8 +267,8 @@
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GATEK_0000050"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000006"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000005"/>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000056"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000001"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
Expand Down Expand Up @@ -363,14 +315,14 @@
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000041"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000045"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000026"/>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000023"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000022"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000023"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000022"/>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000045"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000026"/>
</owl:Restriction>
</rdfs:subClassOf>
</owl:Class>
Expand All @@ -391,12 +343,6 @@
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GATEK_0000022">
<rdfs:label xml:lang="en">Y253 residue in ABL1</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000021"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000006"/>
<owl:allValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000024"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty>
Expand All @@ -411,15 +357,6 @@



<!-- http://purl.obolibrary.org/obo/GATEK_0000024 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/GATEK_0000024">
<rdfs:label xml:lang="en">253 in ABL1 amino acid sequence</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000004"/>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/GATEK_0000025 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/GATEK_0000025">
Expand All @@ -436,8 +373,14 @@
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000025"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000006"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000024"/>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000014"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000013"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000056"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000022"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
Expand All @@ -450,18 +393,6 @@
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000020"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000006"/>
<owl:allValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000024"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000014"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000013"/>
</owl:Restriction>
</rdfs:subClassOf>
</owl:Class>


Expand Down Expand Up @@ -510,13 +441,13 @@
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000045"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000022"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000051"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000045"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000022"/>
</owl:Restriction>
</rdfs:subClassOf>
</owl:Class>
Expand All @@ -528,12 +459,6 @@
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GATEK_0000047">
<rdfs:label xml:lang="en">ABL1_T135I</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000041"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000023"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000051"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000045"/>
Expand All @@ -543,13 +468,19 @@
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GATEK_0000015"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000014"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000013"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000053"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000023"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000051"/>
</owl:Restriction>
</rdfs:subClassOf>
</owl:Class>


Expand Down Expand Up @@ -590,16 +521,6 @@
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GATEK_0000051">
<rdfs:label xml:lang="en">T135 residue in ABL1</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000049"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty>
<rdf:Description>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000045"/>
</rdf:Description>
</owl:onProperty>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000044"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000002"/>
Expand All @@ -608,8 +529,12 @@
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000006"/>
<owl:allValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000008"/>
<owl:onProperty>
<rdf:Description>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000045"/>
</rdf:Description>
</owl:onProperty>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000044"/>
</owl:Restriction>
</rdfs:subClassOf>
</owl:Class>
Expand All @@ -622,6 +547,33 @@
<rdfs:label xml:lang="en">amino acid residue</rdfs:label>
<rdfs:comment>will be replaced by http://purl.obolibrary.org/obo/CHEBI_33708</rdfs:comment>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/GATEK_0000053 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/GATEK_0000053">
<rdfs:label xml:lang="en">substitution mutated quality</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000013"/>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/GATEK_0000054 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/GATEK_0000054">
<rdfs:label xml:lang="en">deletion mutated quality</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000013"/>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/GATEK_0000055 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/GATEK_0000055">
<rdfs:label xml:lang="en">insertion mutated quality</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GATEK_0000013"/>
</owl:Class>
</rdf:RDF>


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