Directly positively regulates

WIP

Overview and Scope of Use

• The 'directly provides input for' relation is used to relate two GO Molecular Functions when:
  • Two Molecular Functions succeed one another directly
  • The output of the first molecular function is an input of the second Molecular Function.
• Domain: Domain refers to the ontology terms that can be further specified with the relation.
  • GO Molecular Functions
• Range: Range describes the ontology terms that can be used to further specify the domain using the relation.
  • GO Molecular Functions

The 'directly provides input for' relation is most commonly used between successive steps of a metabolic pathway.

Annotation Usage Guidelines

• Standard Annotation
  • 'directly provides input for' should not be used for conventional annotations. Instead its use should be reserved for GO-CAM models.

• GO-CAM Annotation
  • 'directly provides input' should be reserved to related successive Molecular Functions in GO-CAM models.
  • Usage Examples
    • In glycolysis, triose phosphate isomerase activity (MF) 'directly provides input for' glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity (MF).
      • 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).
      • http://noctua.geneontology.org/editor/graph/gomodel:632cf60a00000208
    • A glucose tansmembrane transporter activity (MF) 'directly provides input for' lactose synthase activity (MF).
      • • 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?

Ontology Usage Guidelines

• This relation is not used in the ontology.

Quality Control Checks

• Shex
  • https://github.com/geneontology/go-shapes/blob/master/shapes/go-cam-shapes.shex
  • Search this file for 'directly_provides_input_for'.

Child Terms

None

Cross Reference to the Relation Ontology (RO)

directly provides input for

Review Status

Reviewed: Nov 22, 2022 Kimberly

Back to: Annotation Relations

USAGE OF THIS RELATION HAS BEEN DEPRECATED

 
== Overview ==
The 'directly positively regulates' relation is used to relate two GO Molecular Functions whenever two Molecular Functions succeed one another directly, and the first regulates the activity of the second via a direct physical interactions.  The 'directly positively regulates' relation is used to describe a relation, for example, between a ligand and the receptor that it activates.
=== Definition ===
Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2.

=== Child Terms ===

== Examples of Usage ==
*In GO-CAM models, the 'directly positively regulates' relation is used for associations between two Molecular Functions.

*In canonical Wnt signaling, a Wnt ligand 'directly positively regulates' the activity of a Frizzled receptor.
* Examplar: http://noctua.berkeleybop.org/editor/graph/gomodel:56d1143000003025

== Quality Control Checks ==

== Relations Ontology ==

Review Status

Last reviewed: August 8, 2019