Application Ontology for INSDC

The INSDC and DDBJ databases standardisation effort

How to create owl

ruby ftdoc2ttl.rb  --full > nucleotide.ttl.raw
rapper -i turtle -o turtle nucleotide.ttl.raw http://ddbj.nig.ac.jp/ontologies/nucleotide/ > nucleotide.ttl

How to update owl

TODO

sample querying sparql

get all featues

select ?feature, ?label, ?comment where 
{
?feature rdfs:subClassOf <http://insdc.org/owl/Feature>.
?feature rdfs:label ?label.
?feature rdfs:comment ?comment.
}

get all qualifiers

select ?qualifier, ?qualifier_label, ?qualifier_comment where 
{
?qualifier rdfs:label ?qualifier_label.
?qualifier rdfs:comment ?qualifier_comment.
?qualifier rdfs:domain ?feature.
?feature rdfs:label ?feature_label.
} order by ?qualifier

get qualifiers of source featuers

select ?feature_label, ?qualifier_label, ?qualifier_type,?qualifier_comment where {
?s owl:annotatedSource ?feature;
   owl:annotatedTarget [
        a owl:Restriction ;
        owl:onProperty ?qualifier
    ] .
?s <http://www.w3.org/2000/01/rdf-schema#isDefinedBy> ?o.
?qualifier rdfs:label ?qualifier_label.
?o rdfs:label ?qualifier_type.
?qualifier rdfs:comment ?qualifier_comment.
?qualifier rdfs:domain ?feature.
?feature rdfs:label ?feature_label.
FILTER(?feature_label = "source")
} order by ?qualifier_type