Gff3 to rdf owl converter

Group¶ ↑

• Jerven Bolleman

• Peter Cock

• Toshiaki Katayama

• Rob Buels

• Robert Hoehndorf

• Raoul Bonnal (INGM, BioRuby) Linkedin: it.linkedin.com/in/raoulbonnal

• Michel Dumontier

• Takatomo Fujisawa

• Francesco Strozzi

• Joachim Baran

Code¶ ↑

Code is at code.google.com/p/gff3-to-owl/ and has been updated to use the FALDO ontology.

Example¶ ↑

The line from GFF3

chr01   SGD     chromosome      1       230218  .       .       .       ID=chr01;dbxref=NCBI:NC_001133;Name=chr01

will translate to

<!-- http://phenomebrowser.net/gff3/#chr01 -->

<owl:NamedIndividual rdf:about="http://phenomebrowser.net/gff3/#chr01">
    <rdf:type rdf:resource="http://purl.obolibrary.org/obo/SO_0000340"/>
    <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">chr01</rdfs:label>
    <score rdf:datatype="http://www.w3.org/2001/XMLSchema#string">.</score>
    <phase rdf:datatype="http://www.w3.org/2001/XMLSchema#string">.</phase>
    <strand rdf:datatype="http://www.w3.org/2001/XMLSchema#string">.</strand>
    <dbxref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">NCBI:NC_001133</dbxref>
    <source rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SGD</source>
    <location>
        <rdf:Description>
            <rdf:type rdf:resource="http://phenomebrowser.net/gff3/#Location"/>
            <end>
                <rdf:Description>
                    <rdf:type rdf:resource="http://phenomebrowser.net/gff3/#UnstrandedPosition"/>
                    <position rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">230218</position>
                </rdf:Description>
            </end>
            <start>
                <rdf:Description>
                    <rdf:type rdf:resource="http://phenomebrowser.net/gff3/#UnstrandedPosition"/>
                    <position rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">1</position>
                </rdf:Description>
            </start>
        </rdf:Description>
    </location>
</owl:NamedIndividual>

The URIs will change one it’s decided which URI we will use.