Causally upstream of, negative effect: Difference between revisions

From GO Wiki
Jump to navigation Jump to search
 
(8 intermediate revisions by 3 users not shown)
Line 1: Line 1:
== Overview and Scope of Use==
== Overview and Scope of Use==
*This relation is used in GO-CAMs but not in standard annotation extensions.
*This relation is used in GO-CAMs but not in standard annotation extensions.
* This relation is intended to represent a negative causal effect of on activity on another, where the mechanism is not known.
* This relation is intended to represent a negative causal effect of one activity on another, where the mechanism is not known.
*The 'causally upstream of, negative effect' relation is used to relate two GO Molecular Functions when:
*The 'causally upstream of, negative effect' relation is used to relate two GO Molecular Functions when:
**the mechanism that relates the upstream molecular function to the downstream molecular function is not understood
**the mechanism that relates the upstream activity to the downstream activity is not understood
**the upstream molecular function occurs before the downstream molecular function
**the upstream activity occurs before the downstream activity
**the upstream molecular function has a negativ3 effect on the downstream molecular function
**the upstream activity has a negative effect on the downstream activity


== Annotation Usage Guidelines==
== Annotation Usage Guidelines==
Line 11: Line 11:
** Relationships between molecular functions when a negative effect has been demonstrated but the mechanism is not known.
** Relationships between molecular functions when a negative effect has been demonstrated but the mechanism is not known.
* '''What not to capture'''
* '''What not to capture'''
** Relationships where the mechanism is known. These should be represented by other relationships.
** Relationships where the mechanism is known. These should be represented by [https://wiki.geneontology.org/Annotation_Relations#Causal_Relations other relationships].


== Annotation Usage Guidelines ==
*'''What to capture'''
*'''What not to capture'''
== Examples ==
== Examples ==
* mRNA decapping enzymes generally act on messages that repress translation and target them to P bodies for degradation. This is part of normal mRNA turnover in the cell and is not specific to individual RNAs. This process would be causally upstream and have a negative effect on the functions of the proteins encoded by the RNAs. [https://pubmed.ncbi.nlm.nih.gov/16179257/ reference link]
* There are currently no examples of when this relation would be used between two Molecular Functions, as for causal models, the curator should be able to choose a more specific relation.
** [http://noctua.geneontology.org/editor/graph/gomodel:635b1e3e00002476 GO-CAM example]
* If you have an example of when you'd like to use this relation, please bring the example to a GO Annotation conference call.


== Ontology Usage Guidelines ==
== Ontology Usage Guidelines ==
Line 28: Line 24:


== Review Status ==
== Review Status ==
Last reviewed: October 31, 2022 David
Last reviewed: February 8, 2023
 
Reviewed by: Cristina Casals, Marc Feuermann, Pascale Gaudet, David Hill, Patrick Masson, Paul Thomas, Kimberly Van Auken
 


[http://wiki.geneontology.org/index.php/Annotation_Relations Back to: Annotation Relations]
[http://wiki.geneontology.org/index.php/Annotation_Relations Back to: Annotation Relations]

Latest revision as of 08:54, 23 March 2023

Overview and Scope of Use

  • This relation is used in GO-CAMs but not in standard annotation extensions.
  • This relation is intended to represent a negative causal effect of one activity on another, where the mechanism is not known.
  • The 'causally upstream of, negative effect' relation is used to relate two GO Molecular Functions when:
    • the mechanism that relates the upstream activity to the downstream activity is not understood
    • the upstream activity occurs before the downstream activity
    • the upstream activity has a negative effect on the downstream activity

Annotation Usage Guidelines

  • What to capture
    • Relationships between molecular functions when a negative effect has been demonstrated but the mechanism is not known.
  • What not to capture
    • Relationships where the mechanism is known. These should be represented by other relationships.

Examples

  • There are currently no examples of when this relation would be used between two Molecular Functions, as for causal models, the curator should be able to choose a more specific relation.
  • If you have an example of when you'd like to use this relation, please bring the example to a GO Annotation conference call.

Ontology Usage Guidelines

This relation is not used in the ontology.

Relations Ontology

causally upstream of, negative effect

Review Status

Last reviewed: February 8, 2023

Reviewed by: Cristina Casals, Marc Feuermann, Pascale Gaudet, David Hill, Patrick Masson, Paul Thomas, Kimberly Van Auken


Back to: Annotation Relations