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 enough to know that the upstream process is not part of the downstream process
* 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
** 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]
*** [http://noctua.geneontology.org/editor/graph/gomodel:635b1e3e00002476 GO-CAM example]


== 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==
[https://ontobee.org/ontology/RO?iri=http://purl.obolibrary.org/obo/RO_0002212 negatively regulates]
 
[https://ontobee.org/ontology/RO?iri=http://purl.obolibrary.org/obo/RO_0012010 removes input for]


== 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

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