Biocurator

The Cell Cycle

The representation of the cell cycle in GO is split into two sections: the physical processes that occur and the temporal stages—prophase, anaphase and so on—used to describe sets of events. This method of representation is used to prevent true path problems when organisms differ from the "canonical" (usually S. cerevisiae) cell cycle.

Terms and Structure

The cell cycle node sits under cellular process ; GO:0007049 and is split into types of cell cycle (meiotic or mitotic) and stages (M phase, S phase, etc.), plus a regulation term.

  • cell cycle

    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

    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 defines the universe of concepts relating to gene functions (‘GO terms’), and how these functions are related to each other (‘relations’). It is constantly revised and expanded as biological knowledge accumulates.

    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

    A GO annotation consists of a GO term associated with a specific reference that describes the work or analysis upon which the association between a specific GO term and gene product is based. Each annotation must also include an evidence code to indicate how the annotation to a particular term is supported. Although evidence codes do reflect the type of work or analysis described in the cited reference which supports the GO term to gene product association, they are not necessarily a classification of types of experiments/analyses.