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



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

The regulates relation

Protein Complexes

Definition of a Protein Complex

A cellular component should include more than one gene product; complexes of one gene product with a cofactor, e.g. heme and chlorophyll, should not be included. Homomultimeric proteins, e.g. the homodimeric alcohol dehydrogenase, may be included as cellular component terms, as should heteromultimeric proteins, e.g. hemoglobin with alpha and beta chains.

Membrane Proteins

As GO cellular component terms describe locations where a gene product may act, rather than physical features of proteins or RNAs, the terms integral membrane protein and peripheral membrane protein are present only as non-exact synonyms. GO distinguishes classes of membrane-related location:

extrinsic component of membrane ; GO:0019898 refers to gene products that are associated with membranes, but are neither directly embedded in the membrane nor anchored by covalent bonds to any moiety embedded in the membrane.


The set of standard terms below can be applied to each developing structure in each species covered in the ontology. However it is generally not practical to implement every term for every structure, since this would lead to a massive proliferation of terms. Where one term e.g. x development, is present, the rest of the terms for the development of x are considered to be implied, without having actually been implemented. Further terms are generally only implemented when they are required for annotation.