Causally upstream of, positive effect

Overview and Scope of Use

• This relation is used in GO-CAMs but not in standard annotation extensions.
• This relation is intended to represent a positive causal effect of on activity on another, where the mechanism is not known.
• The 'causally upstream of, positive effect' relation is used to relate two GO Molecular Functions when:
  • the mechanism that relates the upstream activity to the downstream activity is NOT understood
  • the activities of the gene products in the upstream process occur before events in the downstream process
  • in order for the downstream process to occur normally, the upstream process needs to occur
  • the upstream process has a positive effect on the downstream process

Annotation Usage Guidelines

• Standard Annotation
  • What to capture
    • This relation should not be used for conventional annotations. To capture this information, curators should create a GO_CAM model in the Noctua tool.
  • What not to capture
    • This relation should not be used for conventional annotations. To capture this information, curators should create a GO_CAM model in the Noctua tool.
  • Usage Examples
    • This relation should not be used for conventional annotations. To capture this information, curators should create a GO_CAM model in the Noctua tool.

• GO-CAM Annotation
  • What to capture
    • Relationships between molecular functions when one function has a positive effect on the second function and we know that the first function doesn't directly regulate the second function or provide an input for it.
  • What not to capture
    • Relationships between molecular functions that occur in a sequence in a cell, but the functions are not related causally. They both just happen.
  • Usage Examples
    • A peptidase activity that processes a signaling ligand.
      • http://noctua.geneontology.org/editor/graph/gomodel:632cf60a00000039

Ontology Usage Guidelines

• This relation is not used in the ontology.

Quality Control Checks

• Annotations can be validated using a Shape Expressions (ShEx) representation of allowed relations between ontology terms.

Child Terms

positively regulates

constitutively upstream of

Cross Reference to Relation Ontology (RO)

causally upstream of, positive effect

Review Status

Reviewed on Nov 2, 2022 DavidH

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