Provides input for: Difference between revisions

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

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

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-== Overview ==
+== Overview and Scope of Use==
-The 'directly provides input for' relation is used to relate two GO Molecular Functions whenever two Molecular Functions succeed one another directly, and the first provides an input for the Molecular Function of the second.  The 'directly provides input for' relation is used to describe a relations, for example, between the Molecular Functions that are part of metabolic pathways.
+*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.
-=== Definition ===
+== Annotation Usage Guidelines==
-P1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c
+*'''What to capture'''
+** Upstream activities that provide a macromolecular input for a downstream activity.
-=== Child Terms ===
+* '''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 of Usage ==
+== Examples ==
-*In GO-CAM models, the 'directly provides input' relation is used for associations between two Molecular Functions.
+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]
-*In glycolysis, triose phosphate isomerase activity 'directly provides input for' glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity.
+[[File:Provides_input.png|500px|Provides input]]
-* Examplar: http://noctua.berkeleybop.org/editor/graph/gomodel:55c3ef4c00000001
-** Inferred GPAD: http://noctua.berkeleybop.org/workbench/annpreview/?model_id=gomodel:5323da1800000002
-== Quality Control Checks ==
+[http://noctua.geneontology.org/workbench/noctua-visual-pathway-editor/?model_id=63d320cd00001536 GO-CAM model]
-== Relations Ontology ==
+==Ontology Usage Guidelines==
-[http://www.ontobee.org/ontology/RO?iri=http://purl.obolibrary.org/obo/RO_0002413 directly provides input for]
+This relation is not used in the ontology.
+== Cross Reference to the Relation Ontology (RO) ==
+[http://www.ontobee.org/ontology/RO?iri=http://purl.obolibrary.org/obo/RO_0002413 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
-Last reviewed: May 11, 2018
 [http://wiki.geneontology.org/index.php/Annotation_Relations Back to: Annotation Relations]
-[[Category: Annotation]]
 [[Category: Relations]]
 [[Category: GO-CAM Relations]]