Elements of an annotation: Difference between revisions

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The group that made the annotation may be different from the database who manages the identifiers and/or the annotation file.  
The group that made the annotation may be different from the database who manages the identifiers and/or the annotation file.  


= Avoiding redundancy=
Where two or more databases are submitting data on the same species we encourage the model whereby one database group collects all annotation data for that species, removes the redundant (duplicate) annotations, and then submits the total dataset to the central repository. This ensures that no redundant annotations will appear in the master dataset. Please see the list of species and relevant database groups for more details. We understand that annotating groups will also wish to make their full dataset available to the public. For this purpose, the GO Consortium makes all of the individual datasets available from the GO website, via the GO web CVS interface, or from the directory go/gene-associations/ in the GO CVS repository. All of the individual datasets are also listed in the annotation downloads table, and all individual groups will clearly be given credit for the work that they have done. The non-redundant set is only used as the master copy that appears in AmiGO and similar tools.





Revision as of 09:19, 14 March 2019

  TO BE COMPLETED: Add something about annotation extensions + isoforms 


Elements of an annotation

Annotation Subject

  • Annotations subjects consists of valid database identifiers, such as WB:WBGene00003721 or SGD:S000001048.
  • 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

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

A gene product can be annotated to zero or more terms from each ontology.

AnnotationExtensions

Annotation_Extensions

  TO REVIEW

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.



Old wiki pages to review