software

Sandbox

This is a sandbox page for people wanting to see editing effects on the published site. All changes and edits should be considered temporary.

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

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.

SVN Help

Access to the GO Subversion Repository

Subversion is a version control system; the software can be downloaded from Apache Subversion if it is not installed on your computer.

The GO subversion repository can be also viewed online using the viewvc repository browser.

GO SVN basics

The GO ontology file is stored in the trunk directory of the GO SVN repository:

LEAD Database Schema with Views

GO Database Schema Autodoc

This is the GO LEAD Database Schema documentation, in Autodoc format. Everything on this page was automatically generated from the schema metadata. For more background on the schema, please read GO Database documentation.

note on modules: The tables are partitioned into modules for the purposes of Autodoc. These modules are invisible in the actual instantiations of the database, so the table "go_graph.term" is just simply "term".

LEAD Database Schema

GO Database Schema Autodoc

This is the GO LEAD Database Schema documentation, in Autodoc format. Everything on this page was automatically generated from the schema metadata. For more background on the schema, please read GO Database documentation.

note on modules: The tables are partitioned into modules for the purposes of Autodoc. These modules are invisible in the actual instantiations of the database, so the table "go_graph.term" is just simply "term".