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 * #145 Moved some axioms to SWRL ensuring RO is valid DL - @balhoff
 * #134, #135, #136, #137, #138, #142, Added new biotic relations for [GloBI](http://www.globalbioticinteractions.org/) - @diatomsarecool
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@cmungall
cmungall committed Mar 23, 2017
1 parent e9474ca commit 07db785
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62 changes: 60 additions & 2 deletions ro.obo
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252 changes: 248 additions & 4 deletions ro.owl
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Original file line number Diff line number Diff line change
@@ -1,19 +1,21 @@
<?xml version="1.0"?>
<rdf:RDF xmlns="http://purl.obolibrary.org/obo/ro.owl#"
xml:base="http://purl.obolibrary.org/obo/ro.owl"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"
xmlns:xml="http://www.w3.org/XML/1998/namespace"
xmlns:swrlb="http://www.w3.org/2003/11/swrlb#"
xmlns:swrl="http://www.w3.org/2003/11/swrl#"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:cito="http://purl.org/spar/cito/"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:xml="http://www.w3.org/XML/1998/namespace"
xmlns:obo="http://purl.obolibrary.org/obo/"
xmlns:foaf="http://xmlns.com/foaf/0.1/"
xmlns:dc="http://purl.org/dc/elements/1.1/"
xmlns:cito="http://purl.org/spar/cito/"
xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/ro.owl">
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/ro/releases/2016-10-28/ro.owl"/>
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/ro/releases/2017-03-23/ro.owl"/>
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/ro/annotations.owl"/>
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/ro/pato_import.owl"/>
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/ro/temporal-intervals.owl"/>
Expand Down Expand Up @@ -2327,6 +2329,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.</obo:I
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002211"/>
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002305"/>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002335"/>
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002230"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002212"/>
Expand All @@ -2347,6 +2350,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.</obo:I
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002211"/>
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002304"/>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002336"/>
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002212"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002212"/>
Expand Down Expand Up @@ -6930,6 +6934,94 @@ Environments include natural environments or exposures, experimentally applied c



<!-- http://purl.obolibrary.org/obo/RO_0008501 -->

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0008501">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002440"/>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0008502"/>
<obo:IAO_0000115>An interaction relationship wherein a plant or algae is living on the outside surface of another plant.</obo:IAO_0000115>
<obo:IAO_0000119>https://en.wikipedia.org/wiki/Epiphyte</obo:IAO_0000119>
<rdfs:label>epiphyte of</rdfs:label>
</owl:ObjectProperty>



<!-- http://purl.obolibrary.org/obo/RO_0008502 -->

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0008502">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002440"/>
<obo:IAO_0000115>inverse of epiphyte of</obo:IAO_0000115>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/RO_0002259"/>
<rdfs:label>has epiphyte</rdfs:label>
</owl:ObjectProperty>



<!-- http://purl.obolibrary.org/obo/RO_0008503 -->

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0008503">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002444"/>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0008504"/>
<obo:IAO_0000115>A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material</obo:IAO_0000115>
<obo:IAO_0000119>https://en.wikipedia.org/wiki/Kleptoparasitism</obo:IAO_0000119>
<rdfs:label>kleptoparasite of</rdfs:label>
</owl:ObjectProperty>



<!-- http://purl.obolibrary.org/obo/RO_0008504 -->

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0008504">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002445"/>
<obo:IAO_0000115>inverse of kleptoparasite of</obo:IAO_0000115>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/RO_0002259"/>
<rdfs:label>kleptoparasitized by</rdfs:label>
</owl:ObjectProperty>



<!-- http://purl.obolibrary.org/obo/RO_0008505 -->

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0008505">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002321"/>
<obo:IAO_0000115>An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism.</obo:IAO_0000115>
<rdfs:label>creates habitat for</rdfs:label>
</owl:ObjectProperty>



<!-- http://purl.obolibrary.org/obo/RO_0008506 -->

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0008506">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002321"/>
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#SymmetricProperty"/>
<obo:IAO_0000115>An interaction relationship describing organisms that often occur together at the same time and space or in the same environment.</obo:IAO_0000115>
<rdfs:label>co-occurs</rdfs:label>
</owl:ObjectProperty>



<!-- http://purl.obolibrary.org/obo/RO_0008507 -->

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0008507">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002618"/>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0008508"/>
<obo:IAO_0000115>An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation.</obo:IAO_0000115>
<rdfs:label>lays eggs on</rdfs:label>
</owl:ObjectProperty>



<!-- http://purl.obolibrary.org/obo/RO_0008508 -->

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0008508">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002619"/>
<obo:IAO_0000115>An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation.</obo:IAO_0000115>
<rdfs:label>has eggs laid on by</rdfs:label>
</owl:ObjectProperty>



<!-- http://purl.obolibrary.org/obo/RO_HOM0000001 -->

<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_HOM0000001">
Expand Down Expand Up @@ -7527,6 +7619,158 @@ Environments include natural environments or exposures, experimentally applied c
</owl:Class>
</rdfs:subClassOf>
</owl:Restriction>



<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Rules
//
///////////////////////////////////////////////////////////////////////////////////////
-->

<rdf:Description rdf:about="urn:swrl#x">
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#Variable"/>
</rdf:Description>
<rdf:Description rdf:about="urn:swrl#y">
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#Variable"/>
</rdf:Description>
<rdf:Description rdf:about="urn:swrl#z">
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#Variable"/>
</rdf:Description>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#Imp"/>
<swrl:body>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
<rdf:first>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
<swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0002327"/>
<swrl:argument1 rdf:resource="urn:swrl#x"/>
<swrl:argument2 rdf:resource="urn:swrl#y"/>
</rdf:Description>
</rdf:first>
<rdf:rest>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
<rdf:first>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
<swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/BFO_0000066"/>
<swrl:argument1 rdf:resource="urn:swrl#y"/>
<swrl:argument2 rdf:resource="urn:swrl#z"/>
</rdf:Description>
</rdf:first>
<rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
</rdf:Description>
</rdf:rest>
</rdf:Description>
</swrl:body>
<swrl:head>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
<rdf:first>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
<swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<swrl:argument1 rdf:resource="urn:swrl#x"/>
<swrl:argument2 rdf:resource="urn:swrl#z"/>
</rdf:Description>
</rdf:first>
<rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
</rdf:Description>
</swrl:head>
</rdf:Description>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#Imp"/>
<swrl:body>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
<rdf:first>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
<swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0002212"/>
<swrl:argument1 rdf:resource="urn:swrl#x"/>
<swrl:argument2 rdf:resource="urn:swrl#y"/>
</rdf:Description>
</rdf:first>
<rdf:rest>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
<rdf:first>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
<swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0002213"/>
<swrl:argument1 rdf:resource="urn:swrl#y"/>
<swrl:argument2 rdf:resource="urn:swrl#z"/>
</rdf:Description>
</rdf:first>
<rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
</rdf:Description>
</rdf:rest>
</rdf:Description>
</swrl:body>
<swrl:head>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
<rdf:first>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
<swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0002212"/>
<swrl:argument1 rdf:resource="urn:swrl#x"/>
<swrl:argument2 rdf:resource="urn:swrl#z"/>
</rdf:Description>
</rdf:first>
<rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
</rdf:Description>
</swrl:head>
</rdf:Description>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#Imp"/>
<swrl:body>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
<rdf:first>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
<swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0002213"/>
<swrl:argument1 rdf:resource="urn:swrl#x"/>
<swrl:argument2 rdf:resource="urn:swrl#y"/>
</rdf:Description>
</rdf:first>
<rdf:rest>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
<rdf:first>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
<swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0002212"/>
<swrl:argument1 rdf:resource="urn:swrl#y"/>
<swrl:argument2 rdf:resource="urn:swrl#z"/>
</rdf:Description>
</rdf:first>
<rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
</rdf:Description>
</rdf:rest>
</rdf:Description>
</swrl:body>
<swrl:head>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
<rdf:first>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
<swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0002212"/>
<swrl:argument1 rdf:resource="urn:swrl#x"/>
<swrl:argument2 rdf:resource="urn:swrl#z"/>
</rdf:Description>
</rdf:first>
<rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
</rdf:Description>
</swrl:head>
</rdf:Description>
</rdf:RDF>


Expand Down
62 changes: 60 additions & 2 deletions src/ontology/ro.obo
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