Provides input for: Difference between revisions
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== 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 | * 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: | ||
** | **The upstream and downstream activities succeed one another directly | ||
**The output of the first | **The output of the first activity is an input of the second activity. | ||
**The output of the first | **The output of the first activity is not available in ChEBI. | ||
== Annotation Usage Guidelines== | == Annotation Usage Guidelines== | ||
*'''What to capture''' | *'''What to capture''' | ||
** Upstream activities that provide | ** Upstream activities that provide a macromolecular input for a downstream activity. | ||
* '''What not to capture''' | * '''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]] | [[File:Provides_input.png|500px|Provides input]] | ||
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==Ontology Usage Guidelines== | ==Ontology Usage Guidelines== | ||
This relation is not used in the ontology. | |||
== Cross Reference to the Relation Ontology (RO) == | == Cross Reference to the Relation Ontology (RO) == | ||
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== Review Status == | == Review Status == | ||
Last reviewed: February | Last reviewed: February 15, 2023 | ||
Reviewed by: Cristina Casals, Marc Feuermann, Pascale Gaudet, David Hill, Patrick Masson, Paul Thomas, Kimberly Van Auken | 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
Ontology Usage Guidelines
This relation is not used in the ontology.
Cross Reference to the Relation Ontology (RO)
Review Status
Last reviewed: February 15, 2023
Reviewed by: Cristina Casals, Marc Feuermann, Pascale Gaudet, David Hill, Patrick Masson, Paul Thomas, Kimberly Van Auken