GFF3 Validation Tools

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  • An online modENCODE GFF3 validator is available at[[1]] It is limited to files of 3,000,000 lines or less. If you wish to validate larger files, please use the command-line version which can be downloaded from the same site.
  • The Generic Feature Format Version 3 Ontology (GFF3O) is available here: [[2]] and provides a formal description of the GFF3 file format. GFF3O enables the transformation of GFF3 file contents into RDF as demonstrated by the BioInterchange project. Basic GFF3 specification conformance can be verified using imposed restrictions on the ontology's class, object- and data-properties. Genomic coordinates can be either expressed in GFF3O's straightforward representation of GFF3's "start", "end" and "strand" columns, or alternatively, using FALDO instances.
  • FALDO is available here: [[3]] A simple ontology to describe sequence feature positions and regiongs as found in GFF3, DBBJ,EMBL,GenBank files, UniProt, and many other bioinformatics resources.The aim of this mini ontology is to only describe the position of a region or a feature. It does not aim to describe features or regions itself. Instead it depends on resources such as the Sequence Ontology or the UniProt core ontolgy.
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