!version: $Revision: 1.2 $
!date: $Date: 2009/02/18 00:07:58 $
go/ontology contents documentation

Gene Ontology - The Ontologies
---------------------------------------------

The current format used by the Gene Ontology Consortium (GOC) is
called OBO v1.2.  The file corresponding to this format is
gene_ontology_edit.obo.  The specification for OBO v1.2 is provided at
the following location:

  http://www.geneontology.org/GO.format.obo-1_2.shtml

This file can be found here:

  ontology/obo_format_1_2/gene_ontology.1_2.obo

We also make available an extended version of the GO. This is
available from:

  ontology/obo_format_1_2/gene_ontology_ext.obo

As of February 2009, the extended version includes inter-ontology
links, and regulation links within the molecular function ontology. If
the software or tools you are using do not handle this appropriately,
it is stronmgly recommended you use the standard version, which has
these links filtered out.

The other files in this directory contain older formats that were
previously used by the GOC.  The specifications of the older formats,
and others used by the GOC, can be found at:

  http://www.geneontology.org/GO.format.shtml

For backwards compatibility reasons, we also provide OBO v1.0 format.
It was used by GOC from February 14, 2004 to October 11, 2006.  This
file is recreated daily from the OBO v1.2 file. The file is present at
two locations:

  ontology/obo_format_1_0/gene_ontology.1_0.obo
  ontology/gene_ontology.obo

It is recommended that you link to the top one.

The other files represent the original so called "flat file" format
used by the GOC between June 16, 1999 and February 14, 2004.  The
ontologies were split into separate files: process.ontology,
function.ontology, and component.ontology.  The term definitions were
also in a separate file named GO.defs.  These files are recreated once
a week from the OBO v1.2 file.

For help please contact the GOC at gohelp@geneontology.org