Bioinformatics related ontologies. Especially for generating RDF content using BioInterchange.

An ontology for describing genomic features and variants; in particular the contents of GFF3, GTF, GVF and VCF files.

• https://raw.github.com/BioInterchange/Ontologies/master/gfvo.xml

Build instructions are intended for collaborators and enthusiasts who would like contributing to the BioInterchange ontologies. The ontologies can be edited using Protege, but a few post-processing steps are necessary to remove additional information that Protege inserts on its own.

Saving an ontology with Protege will introduce explicit class definitions and individuals for external URIs. These have to be removed, so that only BioInterchange URIs are described by the ontologies. A script has been provided that takes care of this, and additionally, increments the patch level version number of the ontologies.

For example, for GFF3O the following commands can be used to create a new cleaned version of the ontology:

<gff3o.xml scripts/cleanse.rb > gff3o.tmp
mv gff3o.tmp gff3o.xml

A regular expression of valid URIs as defined in the Gene Ontology Abbreviation Collection can be automatically generated using the following command:

./scripts/go_xref2xsd_pattern.rb

On Mac OS X, the generated regular expression can be copied into the clipboard for subsequent pasting using the pbcopy command:

./scripts/go_xref2xsd_pattern.rb | pbcopy

The following ontologies were prototypes that eventually merged into the Genomic Feature and Variation Ontology (GFVO).

An ontology for describing GFF3 file contents.

• https://raw.github.com/BioInterchange/Ontologies/master/gff3o.xml

An ontology for describing GVF file contents.

• https://raw.github.com/BioInterchange/Ontologies/master/gvf1o.xml