Qualifiers
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 actively encouraging new groups to start contributing annotation. Annotations can be made from published literature where a curator reads and interprets the experiments and results presented in a paper or can be inferred automatically using sequence information or by key word mapping. Details on how to make automatic inferences can be found on the Electronic Annotation page. The GO annotation guide details more about the annotation process; other pages of interest may be the GO annotation conventions, the standard operating procedures used by some consortium members, and the GO annotation file format guide.
Using the Qualifier column
The Qualifier column is used for flags that modify the interpretation of an annotation. Allowable values are NOT, contributes_to, and colocalizes_with.
NOT
NOT may be used with terms from any of the three ontologies.
NOT is used to make an explicit note that the gene product is not associated with the GO term. This is particularly important in cases where associating a GO term with a gene product should be avoided (but might otherwise be made, especially by an automated method). For example, if a protein has sequence similarity to an enzyme (whose activity is GO:nnnnnnn), but has been shown experimentally not to have the enzymatic activity, it can be annotated as NOT GO:nnnnnnn. (Note: in an email exchange from Sept. 2003 this phenomenon was referred to as "sequence dissimilarity.")
NOT can also be used when a cited reference explicitly says (e.g. "our favorite protein is not found in the nucleus"). Prefixing a GO ID with the string NOT allows annotators to state that a particular gene product is NOT associated with a particular GO term. This usage of NOT was introduced to allow curators to document conflicting claims in the literature.
Note that NOT is used when a GO term might otherwise be expected to apply to a gene product, but an experiment, sequence analysis, etc. proves otherwise. (It is not generally used for negative or inconclusive experimental results.)
colocalizes_with
colocalizes_with may be used only with cellular component terms.
Gene products that are transiently or peripherally associated with an organelle or complex may be annotated to the relevant cellular component term, using the colocalizes_with qualifier. This qualifier may also be used in cases where the resolution of an assay is not accurate enough to say that the gene product is a bona fide component member.
Example (from Schizosaccharomyces pombe):
Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p is annotated to spindle pole body ; GO:0005816 and contractile ring ; GO:0005826, using the colocalizes_with qualifier in both cases.
contributes_to
contributes_to may be used only with molecular function terms.
As noted above, an individual gene product that is part of a complex can be annotated to terms that describe the function of the complex. Many such function annotations should use the qualifier contributes_to:
Annotating individual gene products according to attributes of a complex is especially useful for molecular function annotations in cases where a complex has an activity, but not all of the individual subunits do. (For example, there may be a known catalytic subunit and one or more additional subunits, or the activity may only be present when the complex is assembled.) Molecular function annotations of complex subunits that are not known to possess the activity of the complex must include the entry contributes_to in the Qualifier column. The contributes_to qualifier should not be used in biological process annotations. All gene products annotated using contributes_to must also be annotated to a cellular component term representing the complex that possesses the activity.
Annotations using contributes_to will often use the evidence code IC, but other codes may be used as well.
Note that contributes_to is not needed to annotate a catalytic subunit. Furthermore, contributes_to may be used for any non-catalytic subunit, whether the subunit is essential for the activity of the complex or not.
Examples
- Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits are annotated to DNA-dependent RNA polymerase activity (with the contributes_to note), to capture the activity of the complex.
- ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits can be annotated to ATP citrate lyase activity.
- eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three are annotated to ribosome binding, with the contributes_to qualifier. And all three are annotated to the component term for eIF2 complex.
Annotation mailing list
All Consortium annotators should subscribe to the GO discussion mailing list, which provides a forum for the discussion of annotations and specific use questions. Subscription details and archived posts are available on the annotation mailing list information page.
Specific annotation queries can be submitted to the GO annotation tracker at SourceForge. For general queries about annotation not answered by this page, please email the GO helpdesk.
GO Annotation Resources
For more information on annotation, please see the following resources: