ReasoningWithSequenceOntology

Motivation

For any owl:Class in a OWL+RDF/XML ontology , print all parent. Then we can run a ~reasoner with a SPARQL query.

Example with Sequence Ontology:

• go to bioportal http://bioportal.bioontology.org/ontologies/SO?p=summary and download SO as RDF
• transform with

 xsltproc owl/reasoner.xsl so.xml  > flat.rdf

output:

<?xml version="1.0"?>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:obo="http://purl.obolibrary.org/obo/" xmlns:obo2="http://data.bioontology.org/metadata/obo/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:owl="http://www.w3.org/2002/07/owl#" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:metadata="http://data.bioontology.org/metadata/">
  <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_subsetdef">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_subsetdef"/>
  </owl:Class>
  <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_synonymtypedef">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_synonymtypedef"/>
  </owl:Class>
  <owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0000001">
    <rdfs:label>region</rdfs:label>
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0000001"/>
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0000110"/>
  </owl:Class>
  <owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0000002">
    <rdfs:label>sequence_secondary_structure</rdfs:label>
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0000002"/>
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0001411"/>
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0000001"/>
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0000110"/>
  </owl:Class>
  <owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0000003">
    <rdfs:label>G_quartet</rdfs:label>
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0000003"/>
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0000002"/>
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0001411"/>
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0000001"/>
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0000110"/>
  </owl:Class>
(...)
  <owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_1001288">
    <rdfs:label>stop_codon_signal</rdfs:label>
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_1001288"/>
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_1001268"/>
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0000836"/>
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0000834"/>
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0000833"/>
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0001411"/>
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0000001"/>
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0000110"/>
  </owl:Class>
  <owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_2000061">
    <rdfs:label>databank_entry</rdfs:label>
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_2000061"/>
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0000695"/>
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0001409"/>
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0000001"/>
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0000110"/>
  </owl:Class>
  <owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_3000000">
    <rdfs:label>gene_segment</rdfs:label>
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_3000000"/>
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0000842"/>
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0001411"/>
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0000001"/>
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0000110"/>
  </owl:Class>
</rdf:RDF>