Bioinformatician

Other File Downloads

References and Evidence Codes

File / Format Download Updated
Database cross-reference list
A list of the abbreviations used by GO in database cross-references.
See also the dbxref Documentation (plain text).
As required

CVS Help

Issue the following commands on your machine to create a directory for the GO CVS repository, check out the contents, and update your copy.

user% cd myDirectory

where myDirectory is the directory where you would like to store the GO repository and user% is your command line prompt.

user% mkdir go

Gene Product Information (GPI) Format

Gene Product Information (GPI) format is used to submit gene and gene product information to the GO Consortium. Please note that the GPI companion file for annotation information uses the GPAD file format.

GPI format version

All annotation files must start with a single line denoting the file format. For GPI it is as follows:

!gpi-version: 1.2

Gene Product Association Data (GPAD) format

The GPAD file is an alternative means of exchanging annotations from the Gene Association File (GAF). The GPAD format is designed to be more normalized than GAF, and is intended to work in conjunction with a separate format for exchanging gene product information.

All annotation files must start with a single line denoting the file format. For GPAD it is as follows:

!gpa-version: 1.1

GO Annotation File Formats

This page documents the file formats used to store gene associations (annotations), data capturing the attributes of gene products using terms from the Gene Ontology. For more general information on annotation, please see the GO annotation guide.

GO Annotation File (GAF) Format 1.0

Annotation data is submitted to the GO Consortium in the form of gene association files, or GAFs. The following document lays out the format specification for GAF 1.0; for the newer GAF 2.0 file syntax, please see the GAF 2.0 file format guide.

More general information on annotation can be found in the GO annotation guide.

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.

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.

Downloads

In these pages you will find the gene association files submitted by members of the Gene Ontology Consortium (Annotations), the various versions of Gene Ontology available for download (Ontology), and mappings from the GO to a number of external vocabularies also built for genome annotation (Mappings).

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.