Skip to content

Commit

Permalink
Added definitions for inverses, fixes #51
Browse files Browse the repository at this point in the history 
Also added SPARQL CONSTRUCT that populates these based on subset property
  • Loading branch information
@cmungall
cmungall committed Aug 24, 2016
1 parent c5c0142 commit 4afcf47
Show file tree
Hide file tree
Showing 2 changed files with 49 additions and 0 deletions.
27 changes: 27 additions & 0 deletions src/ontology/ro-edit.owl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,7 @@
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/ro/el-constraints.owl"/>
<dc:description xml:lang="en">The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies.</dc:description>
<foaf:homepage rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI"> https://github.com/oborel/obo-relations/</foaf:homepage>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 26 Logical Axioms: 0]</rdfs:comment>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 32 Logical Axioms: 0]</rdfs:comment>
<dc:source rdf:resource="http://obofoundry.org/ro"/>
<dc:title xml:lang="en">OBO Relations Ontology</dc:title>
Expand Down Expand Up @@ -1854,6 +1855,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.</obo:I
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002320"/>
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115>inverse of derived by descent from</obo:IAO_0000115>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/RO_0002259"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">has derived by descendant</rdfs:label>
</owl:ObjectProperty>
Expand Down Expand Up @@ -2129,6 +2131,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.</obo:I
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2002/07/owl#topObjectProperty"/>
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#FunctionalProperty"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115>inverse of has phenotype</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Chris Mungall</obo:IAO_0000117>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/RO_0002259"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
Expand Down Expand Up @@ -2165,6 +2168,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.</obo:I
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002388"/>
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115>inverse of develops from</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Chris Mungall</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">David Osumi-Sutherland</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Terry Meehan</obo:IAO_0000117>
Expand Down Expand Up @@ -2290,6 +2294,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.</obo:I

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002209">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002445"/>
<obo:IAO_0000115>inverse of parasitoid of</obo:IAO_0000115>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/RO_0002259"/>
<rdfs:label>has parasitoid</rdfs:label>
</owl:ObjectProperty>
Expand All @@ -2301,6 +2306,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.</obo:I
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002210">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002203"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115>inverse of directly develops from</obo:IAO_0000115>
<obo:IAO_0000118>developmental precursor of</obo:IAO_0000118>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/RO_0002259"/>
<rdfs:label xml:lang="en">directly develops into</rdfs:label>
Expand Down Expand Up @@ -2525,6 +2531,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.</obo:I
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002221">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002220"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115>inverse of surrounded by</obo:IAO_0000115>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<obo:RO_0001900 rdf:resource="http://purl.obolibrary.org/obo/RO_0001901"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/RO_0002259"/>
Expand Down Expand Up @@ -2874,6 +2881,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.</obo:I

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002249">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<obo:IAO_0000115>inverse of has active ingredient</obo:IAO_0000115>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/RO_0002259"/>
<rdfs:label>active ingredient in&apos;</rdfs:label>
</owl:ObjectProperty>
Expand All @@ -2895,6 +2903,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.</obo:I

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002253">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002375"/>
<obo:IAO_0000115>inverse of connecting branch of</obo:IAO_0000115>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/RO_0002259"/>
<rdfs:label>has connecting branch</rdfs:label>
</owl:ObjectProperty>
Expand Down Expand Up @@ -2931,6 +2940,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.</obo:I
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000050"/>
</owl:propertyChainAxiom>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115>inverse of has developmental contribution from</obo:IAO_0000115>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/RO_0002259"/>
<rdfs:label xml:lang="en">developmentally contributes to</rdfs:label>
Expand Down Expand Up @@ -3523,6 +3533,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002335">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002334"/>
<obo:IAO_0000115>inverse of negatively regulates</obo:IAO_0000115>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/RO_0002259"/>
<rdfs:label xml:lang="en">negatively regulated by</rdfs:label>
Expand All @@ -3534,6 +3545,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002336">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002334"/>
<obo:IAO_0000115>inverse of positively regulates</obo:IAO_0000115>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/RO_0002259"/>
<rdfs:label xml:lang="en">positively regulated by</rdfs:label>
Expand Down Expand Up @@ -3689,6 +3701,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002352">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000056"/>
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002328"/>
<obo:IAO_0000115>inverse of has input</obo:IAO_0000115>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/RO_0002259"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
Expand All @@ -3702,6 +3715,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002353">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000056"/>
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002328"/>
<obo:IAO_0000115>inverse of has output</obo:IAO_0000115>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/RO_0002259"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
Expand Down Expand Up @@ -4404,6 +4418,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002427">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002501"/>
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
<obo:IAO_0000115>inverse of causally upstream of or within</obo:IAO_0000115>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<obo:IAO_0000119 rdf:resource="http://purl.obolibrary.org/obo/ro/docs/causal-relations"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/RO_0002259"/>
Expand Down Expand Up @@ -4932,6 +4947,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002458">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002438"/>
<obo:IAO_0000115>inverse of preys on</obo:IAO_0000115>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<obo:IAO_0000118>has predator</obo:IAO_0000118>
<obo:IAO_0000118>is target of predation interaction with</obo:IAO_0000118>
Expand Down Expand Up @@ -5565,6 +5581,7 @@ the a supports either the existence of b, or the truth value of b.</obo:IAO_0000

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002508">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002566"/>
<obo:IAO_0000115>inverse of determined by</obo:IAO_0000115>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<obo:IAO_0000589>determines (material entity to system)</obo:IAO_0000589>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/RO_0002259"/>
Expand Down Expand Up @@ -5619,6 +5636,7 @@ the a supports either the existence of b, or the truth value of b.</obo:IAO_0000

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002511">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002330"/>
<obo:IAO_0000115>inverse of transcribed from</obo:IAO_0000115>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://www.ncbi.nlm.nih.gov/pubmed/20226267</obo:IAO_0000119>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/RO_0002259"/>
Expand Down Expand Up @@ -5986,6 +6004,7 @@ the a supports either the existence of b, or the truth value of b.</obo:IAO_0000
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002445"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002445"/>
</owl:propertyChainAxiom>
<obo:IAO_0000115>inverse of hyperparasite of</obo:IAO_0000115>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<oboInOwl:hasRelatedSynonym>has epiparasite</oboInOwl:hasRelatedSynonym>
<oboInOwl:hasRelatedSynonym>has hyperparasite</oboInOwl:hasRelatedSynonym>
Expand Down Expand Up @@ -6038,6 +6057,7 @@ the a supports either the existence of b, or the truth value of b.</obo:IAO_0000

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002558">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002616"/>
<obo:IAO_0000115>inverse of is evidence for</obo:IAO_0000115>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<obo:IAO_0000119 rdf:resource="http://www.ncbi.nlm.nih.gov/pubmed/25052702"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/RO_0002259"/>
Expand Down Expand Up @@ -6153,6 +6173,7 @@ the a supports either the existence of b, or the truth value of b.</obo:IAO_0000

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002569">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002375"/>
<obo:IAO_0000115>inverse of branching part of</obo:IAO_0000115>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/RO_0002259"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
Expand Down Expand Up @@ -6236,6 +6257,7 @@ the a supports either the existence of b, or the truth value of b.</obo:IAO_0000
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/CARO_0000003"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/CARO_0000003"/>
<obo:IAO_0000115>inverse of has skeleton</obo:IAO_0000115>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/RO_0002259"/>
<rdfs:label>skeleton of</rdfs:label>
Expand Down Expand Up @@ -6678,6 +6700,7 @@ the a supports either the existence of b, or the truth value of b.</obo:IAO_0000

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002633">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002445"/>
<obo:IAO_0000115>inverse of ectoparasite of</obo:IAO_0000115>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/RO_0002259"/>
<rdfs:label>has ectoparasite</rdfs:label>
</owl:ObjectProperty>
Expand Down Expand Up @@ -6721,6 +6744,7 @@ the a supports either the existence of b, or the truth value of b.</obo:IAO_0000

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002637">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002445"/>
<obo:IAO_0000115>inverse of mesoparasite of</obo:IAO_0000115>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/RO_0002259"/>
<rdfs:label>has mesoparasite</rdfs:label>
</owl:ObjectProperty>
Expand All @@ -6743,6 +6767,7 @@ the a supports either the existence of b, or the truth value of b.</obo:IAO_0000

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002639">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002635"/>
<obo:IAO_0000115>inverse of intercellular endoparasite of</obo:IAO_0000115>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/RO_0002259"/>
<rdfs:label>has intercellular endoparasite</rdfs:label>
</owl:ObjectProperty>
Expand All @@ -6765,6 +6790,7 @@ the a supports either the existence of b, or the truth value of b.</obo:IAO_0000

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002641">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002635"/>
<obo:IAO_0000115>inverse of intracellular endoparasite of</obo:IAO_0000115>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/RO_0002259"/>
<rdfs:label>has intracellular endoparasite</rdfs:label>
</owl:ObjectProperty>
Expand Down Expand Up @@ -7436,6 +7462,7 @@ Environments include natural environments or exposures, experimentally applied c
<rdfs:label xml:lang="en">term replaced by</rdfs:label>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0000092">
<obo:IAO_0000115>inverse of has disposition</obo:IAO_0000115>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/RO_0002259"/>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0001000">
Expand Down
22 changes: 22 additions & 0 deletions src/ontology/sparql/addMetadataForInverse.sparql
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,22 @@
prefix oio: <http://www.geneontology.org/formats/oboInOwl#>
prefix def: <http://purl.obolibrary.org/obo/IAO_0000115>
prefix owl: <http://www.w3.org/2002/07/owl#>
prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
prefix in_subset: <http://www.geneontology.org/formats/oboInOwl#inSubset>
prefix dbi: <http://purl.obolibrary.org/obo/RO_0002259>
prefix RO: <http://purl.obolibrary.org/obo/RO_>

CONSTRUCT {
?q def: ?gendef
}
WHERE
{
?p a owl:ObjectProperty .
?p rdfs:label ?pLabel .
?p owl:inverseOf ?q .
?q in_subset: dbi: .
FILTER( NOT EXISTS {?q def: ?qdef } )
BIND(CONCAT("inverse of ", str(?pLabel)) AS ?gendef)

}

0 comments on commit 4afcf47

Please sign in to comment.