Provides input for: Difference between revisions

From GO Wiki
Jump to navigation Jump to search
 
(21 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 connect successive enzymatic reactions in a pathway, i.e. where the product (output) of the upstream activity is the substrate (input) for the downstream activity.
* This relation links two successive activities, i.e. where the product (output) of the upstream activity is the substrate (input) for the downstream activity, and the product is a macromolecule.
** When the output molecule of the upstream activity is available in ChEBI, curators should not use this relation, and should instead connect the successive activities via the output molecule: [upstream] has_output [ChEBI] is_input [downstream].
** When the output molecule of the upstream activity is available in ChEBI, curators should not use this relation, and should instead connect the successive activities via the output molecule: [upstream activity] has_output [ChEBI] is_input [downstream activity].
** When the output molecule is not available (usually a modified protein or RNA), use: [upstream] provides_input_for [downstream].
** When the output molecule is not available (usually a modified protein or RNA), use: [upstream activity] provides_input_for [downstream activity].
*The 'provides input for' relation is used to relate two GO Molecular Functions when:
*The 'provides input for' relation is used to relate two GO Molecular Functions when:
**Two Molecular Functions succeed one another directly
**The upstream and downstream activities succeed one another directly
**The output of the first molecular function is an input of the second Molecular Function.  
**The output of the first activity is an input of the second activity.  
**The output of the first molecular function is not available in ChEBI.
**The output of the first activity is not available in ChEBI.


== Annotation Usage Guidelines==
== Annotation Usage Guidelines==
*'provides input for' should be reserved to related successive Molecular Functions in GO-CAM models.
*'''What to capture'''
** Upstream activities that provide a macromolecular input for a downstream activity.
 
* '''What not to capture'''
** Causal connections between molecular activities in which all inputs and outputs are described in ChEBI; instead, connect the successive activities via the output molecule: [upstream activity] has_output [ChEBI] is_input [downstream activity].  For an example, see [http://noctua.geneontology.org/workbench/noctua-visual-pathway-editor/?model_id=61f34dd300001044 GO-CAM model with inputs and outputs].
 
== Examples ==
== Examples ==
AKT1 phosphorylates RAC1, creating phosphorylated RAC1 (which is not in ChEBI); phosphorylated RAC1 is then the input (target) for FBXL19, the substrate adaptor for ubiquitination and degradation of RAC1. [https://pubmed.ncbi.nlm.nih.gov/23512198/ PMID:23512198]
[[File:Provides_input.png|500px|Provides input]]


[http://noctua.geneontology.org/workbench/noctua-visual-pathway-editor/?model_id=63d320cd00001536]
[http://noctua.geneontology.org/workbench/noctua-visual-pathway-editor/?model_id=63d320cd00001536 GO-CAM model]


==Ontology Usage Guidelines==
==Ontology Usage Guidelines==
* This relation is not used in the ontology.
This relation is not used in the ontology.


== Cross Reference to the Relation Ontology (RO) ==
== Cross Reference to the Relation Ontology (RO) ==
[http://www.ontobee.org/ontology/RO?iri=http://purl.obolibrary.org/obo/RO_0002413 directly provides input for]
[http://www.ontobee.org/ontology/RO?iri=http://purl.obolibrary.org/obo/RO_0002413 provides input for]


== Review Status ==
== Review Status ==
Reviewed: Nov 2, 2022 DavidH
Last reviewed: February 15, 2023
 
Reviewed by: Cristina Casals, Marc Feuermann, Pascale Gaudet, David Hill, Patrick Masson, Paul Thomas, Kimberly Van Auken





Latest revision as of 10:26, 16 March 2023

Overview and Scope of Use

  • This relation is used in GO-CAMs but not in standard annotation extensions.
  • This relation links two successive activities, i.e. where the product (output) of the upstream activity is the substrate (input) for the downstream activity, and the product is a macromolecule.
    • When the output molecule of the upstream activity is available in ChEBI, curators should not use this relation, and should instead connect the successive activities via the output molecule: [upstream activity] has_output [ChEBI] is_input [downstream activity].
    • When the output molecule is not available (usually a modified protein or RNA), use: [upstream activity] provides_input_for [downstream activity].
  • The 'provides input for' relation is used to relate two GO Molecular Functions when:
    • The upstream and downstream activities succeed one another directly
    • The output of the first activity is an input of the second activity.
    • The output of the first activity is not available in ChEBI.

Annotation Usage Guidelines

  • What to capture
    • Upstream activities that provide a macromolecular input for a downstream activity.
  • What not to capture
    • Causal connections between molecular activities in which all inputs and outputs are described in ChEBI; instead, connect the successive activities via the output molecule: [upstream activity] has_output [ChEBI] is_input [downstream activity]. For an example, see GO-CAM model with inputs and outputs.

Examples

AKT1 phosphorylates RAC1, creating phosphorylated RAC1 (which is not in ChEBI); phosphorylated RAC1 is then the input (target) for FBXL19, the substrate adaptor for ubiquitination and degradation of RAC1. PMID:23512198

Provides input

GO-CAM model

Ontology Usage Guidelines

This relation is not used in the ontology.

Cross Reference to the Relation Ontology (RO)

provides input for

Review Status

Last reviewed: February 15, 2023

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


Back to: Annotation Relations