guide

Contributing to the Ontology

When you have suggestions for new ontology terms, first make sure the term doesn't exist, either as a primary term or a synonym term. To do this, search the ontology using the AmiGO browser. Requests for new synonyms or clarification of textual definitions are also welcomed.

GOC GitHub Tracker

Contributing to GO

Research groups may contribute to the Gene Ontology Consortium (GOC) by providing suggestions for updating the ontology (e.g. requesting new terms) or by providing GO annotations.

How to contribute to the ontology

ontology-terms-icon.png

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 List

You can follow the activities the activities of the GO consortium by signing up to the go-friends email list. This mailing list sends announcements on major activities of the Gene Ontology Consortium: new services, resource changes and significant advancements are posted.

Subscription information and archived posts to the go-friends list

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.