Help:Gene Ontology

The Gene Ontology (GO) is a collaborative effort to "standardize the representation of gene and gene product attributes across species and databases."

Overview

The GO can be divided into three main areas:

1. a controlled vocabulary of terms for the products of genes
2. a set of relationships between those terms such as (such as "is a", or "part of")
3. annotations about specific gene products from various species.

The wiki would like to capture as much information as possible in a way that is the most useful to other scientists. GO helps accomplish that task. On each gene product page there is a table for GO annotations. The community encourages the addition of any information you could provide. Even if you are not familiar with GO that is fine, someone else can fill in the missing details later.

GO table

The GO tables on each of the gene-product pages contain all the GO annotations for that particular product. There are nine columns, 99% of the time only 5 of which are used. A quick overview of each of the columns is as such:

Qualifier

This is a term that is used to modify the interpretation of an annotation. For example an annotation that was found to be incorrect can have a "NOT" added as the qualifier.

Some used in EcoliWiki are: NOT, Under_review, and Deprecated

This field is rarely used; some usage rules are vague and currently under debate by the Consortium.

GO ID

The unique number associated with each term. (Prefixed with "GO: ". )

Searching the GONUTS wiki can help you find a suitable GO term.

GO term name

The name of the term. Here are some example terms:

• GO:0000027_!_ribosomal_large_subunit_assembly
• GO:0006530_!_asparagine_catabolic_process
• GO:0003746_!_translation_elongation_factor_activity

GONUTS automatically loads the GO term name when a GO ID is entered in the single-entry annotation table.

Reference(s)

The reference for this annotation.

Typically a Pubmed article id (prefixed with a "PMID: ".), e.g. PMID:1837021

Evidence Code

Probably the most complicated of the fields, the evidence code specifies how the information for this annotation was gained.

• Some examples are "IDA: Inferred from Direct Assay" and "ISS: Inferred from Sequence or Structural Similarity".
• A complete list with explanations can be found at http://www.geneontology.org/GO.evidence.shtml:

with/from

Used when a comparative annotation is used.

For example, when the evidence is "ISS: Inferred from Sequence or Structural Similiarity" is used, you must specify which sequence/structure it is similar to. (Prefixed with a database prefix such as "PDB:" or "UniProt:")

Aspect

A single letter to describe the specific ontology this term is in.

GONUTS automatically loads the Aspect when a GO ID is entered in the single-entry annotation table.

Notes

A free-text place for user notes, big or small.

Status

If this annotation has the required three things: GO ID, reference, and evidence it is complete.

More About the Ontology

The Gene Ontology is comprised of three ontologies:

1. Biological Process (P)
2. Cellular Component (C)
3. Molecular Function (F)

These three are treated in the same fashion and are only conceptually different. The ontology is in the sturcutre of a directed acyclic graph, meaning a hierarchal, non-cyclic tree. Sometimes a term is found to be outside the scope of GO or that could be captured in a better way, that term is then tagged as obsolete.

More Information

• The main Gene Ontology website - http://www.geneontology.org/

The Gene Ontology website contains much helpful information. A few of the pages we find to be most informative are:

• Evidence codes
• Structure of the Ontology
• GO Annotation Policies and Guidelines
• Annotation Conventions