Biocurator

GO Database

The GO database is a relational database comprised of the GO ontologies as well as the annotations of genes and gene products to terms in the those ontologies. Housing both the ontologies and the annotations in a single database allows powerful queries of the annotations using the ontology. The GO database is the source of all data available through the legacy AmiGO 1.8 browser and search engine.

Annotation

Annotation is the process of assigning GO terms to gene products. The annotation data in the GO database is contributed by members of the GO Consortium, and the Consortium is continuously encouraging new groups to start contributing their annotations. The list of links below offer details on the GO annotation policies and the annotation process, as well as direct users to other pages of interest on GO annotation conventions, the standard operating procedures used by some consortium members, and the GO annotation file format guide.

Ontology Documentation

The Gene Ontology project provides controlled vocabularies of defined terms representing gene product properties. These cover three domains: Cellular Component, the parts of a cell or its extracellular environment; Molecular Function, the elemental activities of a gene product at the molecular level, such as binding or catalysis; and Biological Process, operations or sets of molecular events with a defined beginning and end, pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms.

GO Annotation File Format 2.0

Annotation data is submitted to the GO Consortium in the form of Gene Association Format, or GAFs. This guide lays out the format specifications for GAF 2.0; for the older GAF 1.0 file syntax, please see the GAF 1.0 file format guide.

Please see the information on the changes in GAF 2.0.

General information about annotation can be found in the GO annotation guide.

The Reference Genome Annotation Project

The GO Consortium coordinated an effort to maximize and optimize GO annotations for a large and representative set of key genomes, known as 'reference genomes'. The Reference Genome Annotation Project aimed to completely annotate twelve reference genomes, producing a resource that may effectively seed automatic annotation efforts of other genomes.

With/From Column Usage

We are aware that there has been some variability in usage of the with/from column. Some groups have used an annotation in combination with the IDs in the with/from field in the same line to indicate specific interactions that occur in pairwise or other specific combinations, while others have used the with/from field to indicate all interactions with that gene that are described in a paper, without any indication as to whether they occur at the same time or not.

Guide to GO Evidence Codes

This document is a guide to the standard usage of the GO evidence codes. Annotators may also find the evidence code decision tree useful in selecting the correct evidence code for an annotation.