Causally upstream of, negative effect: Difference between revisions

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== Overview and Scope of Use ==
== Overview and Scope of Use==
*The 'causally upstream of, negative effect' relation is used to relate GO Biological Processes (BP) and/or GO Molecular Functions (MF) when:
*This relation is used in GO-CAMs but not in standard annotation extensions.
**the mechanism that relates the upstream process (BP or MF) to the downstream process (BP or MF) is understood
* This relation is intended to represent a negative causal effect of one activity on another, where the mechanism is not known.
**the activities of the gene products in the upstream process occur before some event in the downstream process
*The 'causally upstream of, negative effect' relation is used to relate two GO Molecular Functions when:
**the execution of the upstream event impinges on the downstream event by decreasing its execution
**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 ==
== Annotation Usage Guidelines==
* Standard Annotation (This relation should not be used for standard annotations.)
* '''What to capture'''
** Guidelines
** Relationships between molecular functions when a negative effect has been demonstrated but the mechanism is not known.
*** What to capture
* '''What not to capture'''
*** What not to capture
** Relationships where the mechanism is known. These should be represented by [https://wiki.geneontology.org/Annotation_Relations#Causal_Relations other relationships].
* Examples


* GO-CAM Annotation
== Examples ==
** Guidelines
* 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.
*** What to capture
* If you have an example of when you'd like to use this relation, please bring the example to a GO Annotation conference call.
*** What not to capture
* Examples


== Ontology Usage Guidelines ==
== Ontology Usage Guidelines ==
 
This relation is not used in the ontology.
== Quality Control Checks ==
* Annotations can be validated using a Shape Expressions ([https://github.com/geneontology/go-shapes/blob/master/shapes/go-cam-shapes.shex ShEx]) representation of allowed relations between ontology terms.'''(STILL NEEDS TO BE ENTERED)'''
 
== Child Terms==


== Relations Ontology ==
== Relations Ontology ==
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== 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