GFF3 is a tab-delimited, ontology-aware format of genomic features. It should be beneficial to represent such genomic features in RDF so that we can exchange data and make queries with SW technologies.


  • Erick Antezana
  • Alberto Labarga
  • Yu Lin
  • Hideya KAWAJI
  • Venkata Satagopam
  • Jerven Bolleman
  • Mitsuteru Nakao
  • ...



Mapping GFF2RDF (proposal)

The following table is in a very inmature state...

GFF Element RDF (XML) Description
Column 1: "seqid" <gff:seqid rdf:about="#ctg123"> ?
Column 2: "source" <gff:source>1000</gff:source> ?
Column 3: "type" <gff:type rdf:about="#SO:0000704"> | <rdfs:SubClassOf rdf:resource="#SO:0000704" /> This is constrained to be either: (a) a term from the "lite" sequence ontology, SOFA; or (b) a SOFA accession number. It must map to a rdfs:subclassof (lin's proposal)
Column 4: "start" <gff:start>1000</gff:start> ?
Column 5: "end" <gff:stop>9000</gff:stop> ?
Column 6: "score" <gff:score>5.8e-42</gff:score> ?
Column 7: "strand" <gff:strand>+</gff:strand> ?
Column 8: "phase" <gff:phase>.</gff:phase> ?
Column 9: "attributes" <gff:attributes><rdf:Description>...</rdf:Description></gff:attributes> ?

Attribute Mapping (proposal)

A list of feature attributes in the format tag=value. Multiple tag=value pairs are separated by semicolons. URL escaping rules are used for tags or values containing the following characters: ",=;". Spaces are allowed in this field, but tabs must be replaced with the ? URL escape.

Attribute tags RDF (XML) Description
Column 1: "ID"
Column 2: "Name"
Column 3: "Alias"
Column 4: "Parent"
Column 5: "Target"
Column 6: "Gap"
Column 7: "Derives_from"
Column 8: "Note"
Column 9: "Dbxref"
Column 10: "Ontology_term"



  • application to general genomic features (BED, etc)?
  • Genomic coordinate system (0-based / 1-based)
  • Dasty?
  • Attributes is more important for describing an object.

Expected milestones

  • Mapping GGF2RDF (by Q1?)
  • Tools (in PERL, Python and Ruby) implementing such translation
  • Sample RDF data into a triple store (e.g. OpenVirtuoso?)
  • Sample SPARQL queries
  • Divulgation (poster? or article?)