Elements of an annotation: Difference between revisions

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==Negation==
==Negation==


*NOT is used to make an annotation statement that the gene product is not associated with the GO term.
* The NOT statement indicates that the gene product does not enable a Molecular Function, is not part of a Biological Process or is not located in a specific Cellular Component.
*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 statements are only used when a user might expect that the gene product would have a specific biological property (MF, BP or CC).  
*NOT may be used with terms from any of the three ontologies.
* Contrary to positive annotations, NOT statements propagate ''down'' the ontology. For instance, <code> gene product NOT enables protein kinase activity</code> means that the gene product does not enable serine/tyrosine protein kinase activity or threonine protein kinase activity either.
* Both positive AND NOT statements can be used in cases where there is conflicting experimental findings in the literature.
* NOT annotations can be supported by experiments that show the lack of activity (or BP, CC), or based on sequence data that it has lost essential residues and is unlikely to be able to carry out a function, participate in a process, or be found in a certain location. In this case the evidence code is [http://wiki.geneontology.org/index.php/Inferred_from_Key_Residues_(IKR) IKR (Inferred from Key Residue)] evidence code.


In practice, the NOT qualifier is used in two ways:
'''When NOT to use negation'''
 
* The NOT qualifier should be not used to annotate negative or inconclusive experimental results.
#When a GO term might otherwise be expected to apply to a gene product, but an experiment, sequence analysis, etc. demonstrates otherwise.
* The NOT qualifier should be not used to describe specific contexts in which the gene product is not active (i.e, should not be used in combination with an extension).
#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 [http://wiki.geneontology.org/index.php/Inferred_from_Key_Residues_(IKR) 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==
==GO term==

Revision as of 07:24, 19 April 2022

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 UniProtKB: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

  • The NOT statement indicates that the gene product does not enable a Molecular Function, is not part of a Biological Process or is not located in a specific Cellular Component.
  • NOT statements are only used when a user might expect that the gene product would have a specific biological property (MF, BP or CC).
  • Contrary to positive annotations, NOT statements propagate down the ontology. For instance, gene product NOT enables protein kinase activity means that the gene product does not enable serine/tyrosine protein kinase activity or threonine protein kinase activity either.
  • Both positive AND NOT statements can be used in cases where there is conflicting experimental findings in the literature.
  • NOT annotations can be supported by experiments that show the lack of activity (or BP, CC), or based on sequence data that it has lost essential residues and is unlikely to be able to carry out a function, participate in a process, or be found in a certain location. In this case the evidence code is IKR (Inferred from Key Residue) evidence code.

When NOT to use negation

  • The NOT qualifier should be not used to annotate negative or inconclusive experimental results.
  • The NOT qualifier should be not used to describe specific contexts in which the gene product is not active (i.e, should not be used in combination with an extension).

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