Biocurator

Reviewing GO annotations for a gene or protein

Open a Gene Ontology browser (e.g.AmiGO, QuickGO) and search for the gene or gene protein record of interest by entering it in the 'Search' field, then browse associated annotations and follow links to see the full list of annotations:

Reviewing GO annotations associated with a scientific article

Open a Gene Ontology browser, (e.g.AmiGO, QuickGO) and enter a PubMed identifier (PMID) for the paper of interest in the 'Search' field.

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.

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:

GO Editor Guides

These guides explain how to add to or alter the gene ontologies. They are intended for those members of the consortium whose job it is to make such modifications to the GO. However we make them available here for anyone who is interested to know how this work is carried out.

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

Evidence Code Decision Tree

The following flow chart illustrates the steps that a curator typically takes when deciding what evidence code should be applied to an annotation. Please see the evidence code guide for more information on each of the codes.

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.

Other File Downloads

References and Evidence Codes

File / Format Download Updated
Database cross-reference list
A list of the abbreviations used by GO in database cross-references.
See also the dbxref Documentation (plain text).
As required