Everybody

Connecting annotations: LEGO Models

The Gene Ontology Consortium is moving towards a more expressive way of describing the function of gene products that allows annotations to be connected together to give a complete function of what each gene does in the context of a larger biological process. The new model is called LEGO, for "Logical Extension of the Gene Ontology".

Background

For example, with the current datamodel and Gene Association Files, it's possible to make two statements:
  • TEM1 enables GTPase activity
  • BFA1 enables GTPase inhibitor activity

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.

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.

Thank You for Contacting GO

Thank you, your submission has been submitted to the GO JIRA system.

Representing "phases" in GO biological process

The GOC has recently introduced a new term biological phase (GO:0044848), as a direct subclass of biological process. This class represents a distinct period or stage during which biological processes can occur. Biological phases do not share any is_a parent terms with other biological processes (i.e. they are is_a disjoint). They can be related to other biological processes with happens_during relationships e.g. DNA replication happens_during S-phase. They can also be regulated by other biological processes.

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

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.