Bioinformatician

GO Annotation File (GAF) Format 2.1

Annotation data is submitted to the GO Consortium in the form of gene association files, or GAFs. This guide lays out the format specifications for GAF 2.1; for the previous GAF 2.0 file syntax, please see the GAF 2.0 file format guide.

For the first GAF 1.0 file syntax, please see the GAF 1.0 file format guide.

Please see the information on the changes in GAF 2.1.

TermGenie

TermGenie is a web-based tool for requesting new Gene Ontology classes. TermGenie also allows for an ontology developer to review all generated terms before they are committed to the ontology. The system makes extensive use of OWL axioms (logical definitions), but can be easily used without understanding these axioms.

Download Annotations

Overview

The gene association files submitted by GO Consortium members are shown in the tables below. Files are in the GO annotation file format and are compressed using the UNIX gzip utility. Please see the appropriate README file for further details on the annotation set. Any errors or omissions in annotations should be reported by writing to the GO Helpdesk.

Ontology and annotation data is integrated in the mySQL and XML files. See the GO database guide for more information.

GO Enrichment Analysis

One of the main uses of the GO is to perform enrichment analysis on gene sets. For example, given a set of genes that are up-regulated under certain conditions, an enrichment analysis will find which GO terms are over-represented (or under-represented) using annotations for that gene set.

GO Tools Registry

The GO Tools Registry is no longer supported, we apologized for the inconvenience.

The GOC used to keep a curated listing of GO tools, which was eventually moved to a third party, and then discontinued. This page is maintained as an explanation to users who may be using old links.

External Mapping File Format

Mappings of GO have been made to other many other classification systems; a full list is available on the Mappings to GO page. This page describes the format of these files.

Format Specification

The source of the external file is given in the line beginning !Uses: !Uses:http://www.tigr.org/docs/tigr-scripts/egad_scripts/role_reports.spl, 15 aug 2000.

The line syntax for mappings is:

external database:term identifier (id/name) > GO:GO term name ; GO:id

For example:

SourceForge Links

The GO project pages at the SourceForge site hold information about all of the work currently in progress in the Gene Ontology Consortium.

To submit a request to the Gene Ontology Consortium on any of the subjects shown below, please follow the link corresponding to that subject, and then use the 'Submit New' option.

Trackers for Requests, Suggestions and Comments

GO CVS Repository

Anonymous Access to the GO CVS Repository

Issue the following commands on your machine to create a directory for the GO CVS repository, check out the contents, and update your copy.

user% cd myDirectory

where myDirectory is the directory where you would like to store the GO repository and user% is your command line prompt.

user% mkdir go

Annotation Quality Control

The GO Consortium implements a number of automated checks to check the quality of the annotations submitted to the GO database. These checks are detailed on the annotation quality control checks page.