guide

Contributing to GO

Research groups may contribute to the Gene Ontology Consortium (GOC) by providing suggestions for updating the ontology (e.g. requests for new terms) or by providing annotations, that is, associations between genes or gene products and ontology terms. Suggested edits are reviewed by the ontology editors and implemented where appropriate.

The following pages explain how you can contribute to the project. Please begin by choosing whether you wish to contribute annotations or terms to the Gene Ontology.

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.

GO Mailing Lists

Contact GO

The Gene Ontology project very much encourages input from the community into both the content of the GO and annotation using GO. We are very happy to work with others to ensure that the GO is both complete and accurate, and we also very much encourage communities to submit GO annotations for inclusion in the GO database. Please contact us.

GO Consortium Photo Album

  • GO Consortium Meeting, Hôtel Mont Gabriel, Sainte-Adèle, Québec, Canada, October 21–23, 2008
  • GO Consortium Meeting, Jesus College, Cambridge University, Cambridge, UK, January 8–10, 2007
  • Annotation Camp, Stanford University, Palo Alto, California, USA, July 12–14, 2006
  • Annotation Workshop, Stanford University, Palo Alto, California, USA, July 10–11, 2006
  • GO Consortium Meeting, St. Croix, US Virgin Islands, March 31–April 2, 2006

Authoritative Database Groups

Authoritative Database Groups Where two or more databases are submitting data on the same species the GO Consortium encourages the model whereby one database group collects all annotation data for that species, removes the redundant (duplicate) annotations, and then submits the total dataset to the central repository. This ensures that no redundant annotations will appear in the master dataset. The table below documents those species for which a single database group is responsible for collating and submitting annotations.

Authoritative Database Groups

Authoritative Database Groups Where two or more databases are submitting data on the same species the GO Consortium encourages the model whereby one database group collects all annotation data for that species, removes the redundant (duplicate) annotations, and then submits the total dataset to the central repository. This ensures that no redundant annotations will appear in the master dataset. The table below documents those species for which a single database group is responsible for collating and submitting annotations.

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:

Temporal information in Annotation Extensions

Adding temporal information

Using biological process terms to enhance cellular component annotations

Cellular component annotations can be enhanced by specifying that localization is observed during a specific biological process, e.g. a cell cycle phase. These annotations are constructed by putting the exists_during relationship and the identifier from the biological process ontology in the annotation extension column.

Use cases

1. A gene product is localized to the nuclear periphery in S phase, G2, and mitosis (S. pombe Ulp1; PMID:11884512)

Spatial information in Annotation Extensions

Adding spatial information

Usefulness of capturing cell type or tissue type specific location of action

Investigative methods that work solely with a specific tissue or cell type (such as laser capture microdissection) are becoming more commonplace and allow for downstream genetic or proteomic analyses that are not contaminated by surrounding tissue. In addition the separation of subcelluar particles via cell fractionation techniques enables the study of the constituents of a particular cell part/organelle.

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.