Gene Ontology^TM Consortium Web Site Map

Section Contents

Gene Ontology - A Bibliography

Publications on GO by members of the GO Consortium
Annotations using GO
Prediction of GO terms
Other publications with substantive discussion of GO
Publications on other OBO ontologies

GO Redistribution and Citation Policy

GO Policy
Cite GO
Submit suggestions
GO Logo

Guide to Addressing a SourceForge Request

Introduction
Claim a request
Editing the GO files using DAG-Edit
DAG-Edit
Add and commit terms
Record your changes
Editing large chunks of an ontology
Saving your edited files
Committing files to the CVS repository
The GO numbers file
Synonyms
Logging out of CVS
What to do when your files won't commit
To close the request in SourceForge

The Beginner's Guide to Modifying the Ontologies

The CVS repository
DAG-Edit
Setting up
Accounts
Mailing lists
Downloading software
Emacs aliases
Accessing the CVS repository
Editing the GO files using DAG-Edit
Assigning your range of GO numbers
Setting your range of numbers within DAG-Edit
Emacs

An introduction to Gene Ontology

What does the Gene Ontology Consortium do?
What GO is NOT
The ontologies
Gene products
Molecular function
Biological process
Cellular component
What do the ontologies look like?
Annotation and tools
File formats
Beyond GO
Cross-products
Mappings to other classification systems
Contributing to GO

File Format Guide

How to use this Guide
Anatomy of a GO Entry
Anatomy of a Flat File
Anatomy of the Definitions File
Syntax for Commonly used Definitions
Syntax for Comments
Obsoletions Merges and Splits
Mappings to Other Classification Systems
XML Version
MySQL Version

Current and Former GO people.

The GO Editorial Office
FlyBase
FlyBase
Saccharomyces Genome Database
Stanford Microarray Database
Mouse Genome Database and Gene Expression Database.
The Arabidopsis Information Resource.
Wormbase
Dictybase
Rat Genome Database
The Pathogen Sequencing Unit
EBI - InterPro - SWISS-PROT - TrEMBL
The Institute for Genomic Research
Gramene
Compugen
AstraZeneca
Incyte Genomics
Former GO People
The GO Consortium Meetings

Submitting suggestions to GO using SourceForge.net

Setting up a SourceForge account
Submitting a suggestion to GO
Keeping track of your requests
Browsing requests

The Guide to Documenting Synonyms

Updating the Synonyms File
Synonym types
The synonyms file
Adding your synonym
Rules For Synonyms

GO Software

Open Source, Free Tools
. . .GO Editors
. . .GO Browsers
. . .Other GO Tools
. . .More General Tools
Closed Source, with License Fee
. . .GO Browsers

GO Editorial Style Guide

How to use this guide
What is a GO term?
General conventions when adding terms
Synonyms
Cross-referencing other databases
Defining terms
Always define new terms
Use of 'standard definitions'
Redefining terms
Adding comments to definitions
Database cross-references
Obsoleting, merging and splitting
Obsolete terms
Merges and splits
Moving terms: understanding relationships
Parent-child relationships
True path rule
Logical
Using sensu for species-specific terms
Ontology-specific guidelines
Biological process guidelines
Molecular function guidelines
Cellular component guidelines

GO Annotation Guide

Description
GO Annotation Conventions
Annotation File Format
Computational Annotation Methods

Current Annotations

Current Annotations by each Database
What are IEA Codes?
View the Terms and Annotations