Provides input for: Difference between revisions

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== Overview ==
== Overview and Scope of Use==
*The 'directly provides input for' relation is used to relate two GO Molecular Functions when:
*This relation is used in GO-CAMs but not in standard annotation extensions.
**Two Molecular Functions succeed one another directly
* 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.
**The output of the first molecular function is an input of the second Molecular Function.
** 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.


The 'directly provides input for' relation is most commonly used between successive steps of a metabolic pathway.
== Annotation Usage Guidelines==
*'''What to capture'''
** Upstream activities that provide a macromolecular input for a downstream activity.


== Examples of Usage ==
* '''What not to capture'''
'directly provides input' should be reserved to related successive Molecular Functions in GO-CAM models.
** 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].


*In glycolysis, triose phosphate isomerase activity (MF) 'directly provides input for' glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity (MF).
== Examples ==
** triose phosphate isomerase activity converts dihydroxyacetone phosphate (input) to glyceraldehyde-3-phosphate (output) as part of glycolysis. Glyceraldehyde-3-phosphate dehydrogenase converts glyceraldehyde-3-phosphate (input) to 3-phosphonato-D-glyceroyl phosphate(4−) (output).
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]
**http://noctua.geneontology.org/editor/graph/gomodel:632cf60a00000208


*A glucose tansmembrane transporter activity (MF) 'directly provides input for' lactose synthase activity (MF).
[[File:Provides_input.png|500px|Provides input]]
** cytosolic glucose (input) is transported across the Golgi membrane to become Golgi-lumenal glucose (output). In the Golgi lumen the Golgi-lumenal glucose (input) is converted into lactose (output).
**http://noctua.geneontology.org/editor/graph/gomodel:632cf60a00000239?


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


== Quality Control Checks ==
==Ontology Usage Guidelines==
* Shex
This relation is not used in the ontology.
**<MolecularFunction> directly_provides_input_for: ( @<MolecularFunction> OR @<MolecularEvent> )


== Relations Ontology ==
== 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 ==
Last edited September 27, 2022
Last reviewed: February 15, 2023
Last reviewed: May 11, 2018
 
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 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