Introduction to GO annotations
A GO annotation is a statement about the function of a particular gene. GO annotations are created by associating a gene or gene product with a GO term. Together, these statements comprise a “snapshot” of current biological knowledge. Hence, GO annotations capture statements about how a gene functions at the molecular level, where in the cell it functions, and what biological processes (pathways, programs) it helps to carry out.
There are four pieces of information that uniquely identify a GO annotation. Although there are additional components a curator can use to indicate more information, including qualifiers and annotation extensions, at the very minimum an annotation consists of:
- Gene product (may be a protein, RNA, etc.)
- GO term
Different pieces of knowledge regarding gene function may be established to different degrees, which is why each GO annotation always refers to the evidence upon which it is based. All GO annotations are ultimately supported by the scientific literature, either directly or indirectly. In GO, the supporting evidence is presented in the form of a GO Evidence Codes and either a published reference or description of the methodology used to create the annotation. The GO evidence codes describe the type of evidence and reflect how far removed the annotated assertion is from direct experimental evidence, and whether this evidence was reviewed by an expert biocurator.
Semantics of a GO annotation
Associations of gene products to GO terms are statements that describe
- Molecular Function: the molecular activities of individual gene products
- Cellular Component: where the gene products are active
- Biological Process: the pathways and larger processes to which that gene product’s activity contributes
General principles of GO annotations
- Annotations represent the normal functions of gene products.
- A gene product can be annotated to zero or more terms from each ontology.
- Each annotation is supported by an GO Evidence Codes from the Evidence and Conclusions Ontology and a reference.
- Gene products are annotated to the most granular term in the ontology that is supported by the available evidence.
- By the transitivity principle, an annotation to a GO term implies annotation to all its parents.
- GO annotations are meant to reflect the most up-to-date view of a gene product’s role in biology.
- Because biological knowledge changes, annotations for a given gene product may change to reflect changes in knowledge and/or changes in the ontology.
- There is an open-world assumption, that is, if a gene product is unannotated then its role is still unknown.
Some annotations are modified by qualifiers, which have specific usage rules and meanings within GO. The NOT, contributes_to, and colocalizes_with qualifiers are used in the GAF format.
The NOT qualifier
NOT is used to make an explicit note that a gene product has been experimentally demonstrated not to be able to carry out a particular activity or it has been shown to have had a loss of function (e.g. loss of an active site or rapid divergence after a duplication event) over the course of evolution. 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 is annotated as NOT GO:nnnnnnn. NOT is also used when a cited reference explicitly says (e.g. “our favorite protein is not found in the nucleus”). Qualifying an annotation with the qualifier NOT allows annotators to state that a particular gene product is not associated with a particular GO term. It 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.)
The contributes_to qualifier
A gene product is associated with a GO Molecular Function term using the qualifier ‘contributes_to’ when it is a member of a complex that is defined as an “irreducible molecular machine” - where a particular Molecular Function cannot be ascribed to an individual subunit or small set of subunits of a complex. Note that the ‘contributes_to’ qualifier is specific to Molecular Functions.
The colocalizes_with qualifier
Colocalizes_with indicates a transient or peripheral association of the protein with an organelle or complex. For example, human microtubule depolymerase KIF2A is dynamically localized to spindle poles, regulating the degradation of microtubule during mitotic progression. Therefore KIF2A ia annotated to GO:0000922: spindle pole using the colocalizes_with qualifier, based on PMID:18411309.
Annotation extensions provide additional information about a GO annotation that cannot be captured in a single GO term. Please see publications describing annotation extensions: Huntley & Lovering 2017 and Huntley et al. 2014. Annotation extensions are available in both the GAF File Format and the GPAD File Format.
Annotation quality control
The GO Consortium implements a number of automated queries to check the quality of the annotations submitted to the GO database.
GO-Causal Activity Models
GO-Causal Activity Models (GO-CAMs) use a defined “grammar” for linking multiple standard GO annotations into larger models of biological function (such as “pathways”) in a semantically structured manner. Minimally, a GO-CAM model must connect at least two standard GO annotations (GO-CAM example).
The primary unit of biological modeling in GO-CAM is a molecular activity, e.g. protein kinase activity, of a specific gene product or complex. A molecular activity is an activity carried out at the molecular level by a gene product; this is specified by a term from the GO MF ontology. GO-CAM models are thus connections of GO MF annotations enriched by providing the appropriate context in which that function occurs. All connections in a GO-CAM model, e.g. between a gene product and activity, two activities, or an activity and additional contextual information, are made using clearly defined semantic relations from the Relations Ontology.
GO-CAMs can be browsed and visualized at http://geneontology.org/go-cam
Types of GO annotation files
GO as a dynamic source of biological annotations
GO aims to represent the current state of knowledge in biology, hence it is constantly revised and expanded as biological knowledge accumulates.
With the ever-increasing number of published articles, experiments and methods, covering all biology with the latest annotations is always challenging. We therefore invite researchers and computational scientists to submit requests for missing, erroneous or out-of-date annotations to improve the GO database.
GO statistics are available both for the current release and over time.