general

General questions about the Gene Ontology.

I want to use GO, but I don't know where to begin

There are a number of possibilities for how researchers can make use the GO.

The Gene Ontology website (http://geneontology.org/) is a very good place to begin learning about our resources, how they are produced, and how we maintain them. It also illustrates how the research community most commonly makes use of these resources and how they can contribute. Exploring the items under the "Documentation" menu will provide you with a very informative overview.

How can I contribute to GO?

We welcome your contributions!

The GO project is constantly evolving, and we welcome feedback from all users. Research groups may contribute to the GOC by either 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.

What is the minimum information to include in a functional analysis paper?

Most journals require authors to submit high-throughput data to public repository as a pre-requisite for publication. As part of this process, the methods used to analyse data need to be reported in detail; this applies to both statistical and functional analysis. For papers describing enrichment analysis using GO, this means that the methods section should include the following information, to ensure the analysis is reproducible (an important criteria for reviewers' approval):
  1. What analysis tool was used and what version

I have a question about gene or protein nomenclature

The GO Consortium is not involved in naming genes at all, in any organism. The GO vocabularies describe attributes of gene products; they are not collections of gene names or protein names.

What are all the possible uses of GO?

It would be impossible to list all the potential applications of GO, but applications for which GO has already been used include the following:

How is the GO used in genome analysis?

Functional annotation of newly sequenced genomes:Genome and full-length cDNA sequence projects often include computational (putative) assignments of molecular function based on sequence similarity to annotated genes or sequences. A common tactic now is to use a computational approach to establish some threshold sequence similarity to a SWISS-PROT sequence. Then the GO associations to the SWISS-PROT sequence can be retrieved and associated with the gene model. Under the GO guidelines, the evidence code for this event would be 'inferred from electronic annotation' (IEA).

Where can I find GO annotations of proteins and ESTs?

Gene objects in model organism databases typically have multiple nucleotide sequences from the public databases associated with them, including expressed sequence tags (ESTs) and one or more protein sequences. There are two ways to obtain sets of sequences with GO annotations:

  • from the model organism databases
  • from the annotation sets for transcripts and proteins contributed to the GO by Compugen and UniProt

How do I cite the GO?

Citation information for the Gene Ontology can be found on the GO Citation Policy page.

What am I allowed to do with the data?

The use and license of all GO data, software, and materials are covered on the Use and license page.