Elements of an annotation: Difference between revisions

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=Elements of an annotation=
=Elements of an annotation=
==Annotation Subject==
==Annotation Subject==
* Annotations subjects consists of valid database identifiers, such as WB:WBGene00003721 or SGD:S000001048.  
* Annotations subjects consists of valid database identifiers, such as WB:WBGene00003721, SGD:S000001048, or UniProt:P99999.  
* Annotations subjects may be genes or gene products (e.g. proteins, including specific isoforms; ncRNAs; and protein complexes)
* Annotations subjects may be genes or gene products (e.g. proteins, including specific isoforms; ncRNAs; and protein complexes)
* The list of valid database prefixes can be found on the [http://amigo.geneontology.org/xrefs GO website].
* The list of valid database prefixes can be found on the [http://amigo.geneontology.org/xrefs GO website].

Revision as of 05:22, 27 September 2021

This page describes the different annotation fields.

Elements of an annotation

Annotation Subject

  • Annotations subjects consists of valid database identifiers, such as WB:WBGene00003721, SGD:S000001048, or UniProt:P99999.
  • Annotations subjects may be genes or gene products (e.g. proteins, including specific isoforms; ncRNAs; and protein complexes)
  • The list of valid database prefixes can be found on the GO website.

Relations

  • Annotation Subjects and GO terms are linked by a Relation from the Relations Ontology.
  • The relations applicable to each aspect of GO as well as usage guidelines can be found in the Annotation_Relations page.

Negation

  • NOT is used to make an annotation statement that the gene product is not associated with the GO term.
  • When combined with an explicit annotation relation, e.g. enables, the NOT qualifier indicates that the gene product does not have that relationship to the GO term.
  • NOT may be used with terms from any of the three ontologies.

In practice, the NOT qualifier is used in two ways:

  1. When a GO term might otherwise be expected to apply to a gene product, but an experiment, sequence analysis, etc. demonstrates otherwise.
  2. When there is conflicting experimental findings in the literature and curators would like to accurately capture all relevant data.

Use of the NOT qualifier 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 represented as Molecular Function GO:nnnnnnn), but has been shown experimentally not to have the enzymatic activity, it can be annotated as NOT GO:nnnnnnn.

In phylogenetic-based annotation, i.e. PAINT, the NOT qualifier is used in conjunction with the IKR (Inferred from Key Residue) evidence code. Here, NOT is used to annotate a gene product when, although homologous to a particular protein family, it has lost essential residues and is very unlikely to be able to carry out an associated function, participate in the expected associated process, or be found in a certain location.

The NOT qualifier is not used to annotate negative or inconclusive experimental results.

GO term

Annotation Extensions

  • Annotation extensions may be added to GO annotations to provide additional contextual information for the assertion.
  • Annotation extensions are structured text that use a relation from the Relations Ontology and an appropriate biological concept or entity to modify the GO annotation, e.g. nucleus 'part of' epithelial cell.
  • Detailed documentation on curation using annotation extensions can be found here: Annotation_Extension

Evidence

Reference

Assigned_by

Every annotation is marked with the name of the group that made the annotation. The group that made the annotation may be different from the database who manages the identifiers and/or the annotation file.

Date

The date the annotation was made or last edited, in YYYYMMDD format.

Review Status

Last reviewed: 2019-04-11