Deprecated formats

Ontology formats

GO currently provides the Gene Ontology in the OBO 1.2 format (as produced by the OWL API) and other formats; see the ontology download page for more information about current ontology file formats.

  • The GO Consortium no longer uses or supports the flat file format, which was deprecated in 2009.
  • OBO-XML and FASTA files were retired in 2018. OBO-XML was a direct XML serialization of the OBO 1.2 format specification. The schema is specified using RELAX-NG compact syntax: obo-xml.rnc.
  • RDF-XML and OWL (old mapping) formats of the ontology were retired in early 2021. For users of the GO-RDF/XML version of the ontology, we recommend the OWL RDF/XML version. For OWL users, we continue to support the legacy obo2owl translation, but users are strongly encouraged to switch to the new translation.
  • OBO 1.0 file format was the previous iteration of the OBO format and was retired in 2018.

Annotation formats

GO currently provides annotations in GPAD 1.1/GPI 1.2 as well as GAF 2.2, and encourages anyone consuming or producing GAF 2.1 or older to adopt the newest format. See the annotation download page for more information about current annotation file formats.

Please contact the GO Helpdesk if you have any questions.