Biocurator

Preparing GO Annotations for Submission

This page documents the steps required to take when supplying Gene Ontology annotations to the GO Consortium (GOC). For general information on how to conduct GO annotations, please see the GO Annotation Policies Guide.

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

Maintaining complete 'is_a' and 'part_of' trees in cellular component

The cellular component ontology is is_a complete, meaning that every term has a path to the root node which passes solely through is_a relationships. This should be preserved; the following guidelines should help maintain this structure.

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.

Detection and Response To Stimulus

Terms and Structure

The response of a cell or an organism to a stimulus is all the processes that occur as a result of the stimulus occurring within or outside the cell or organism. Detection of the stimulus, the process in which a stimulus is received by a cell and converted into a molecular signal, is thus a class of stimulus response. The general structure of this node is as follows:

  • response to stimulus
    • [i] detection of stimulus
      • [i] detection of [stimulus type] stimulus

Regulation

Regulation

Biological regulation is defined as any process that modulates the frequency, rate or extent of any biological process, quality or function.

The regulates relation