GO Annotation Standard Operating Procedures

This page documents some of the standard operating procedures used by members of the GO Consortium during the process of annotation. Please note that these do not represent the best, or only ways to carry out annotation, but are simply a guide to how some groups currently annotate.

GO Annotation Conventions

Annotation Conventions

This page contains guidelines which apply to all annotation methods and are particularly useful for manual literature-based annotation. More information on annotation can be found in the introduction to GO Annotation Policies and Guidelines and the GO Annotation Standard Operating Procedures.

Cellular Component Ontology Guidelines

The cellular component ontology describes locations, at the levels of subcellular structures and macromolecular complexes. Examples of cellular components include 'nuclear inner membrane', with the synonym 'inner envelope', and the 'ubiquitin ligase complex', with several subtypes of these complexes represented.

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.


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GO File Format Guide

GO Formats

The GO File Format Guide documents the structure and syntax of the files available on the GO website, to assist users who need to read, write parsers for, or create these files. The following file formats are documented separately:


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.


The Gene Ontology Project