Annotation Extension Relation:causally upstream of

From GO Wiki
Revision as of 09:27, 2 November 2022 by David (talk | contribs) (→‎Annotation Usage Guidelines)
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to navigation Jump to search

Overview and Scope of Use

  • The 'causally upstream of' relation is used to relate GO Biological Processes (BP) and/or GO Molecular Functions (MF) when:
    • the mechanism that relates the upstream process (BP or MF) to the downstream process (BP or MF) is understood
    • the activities of the gene products in the upstream process occur before events in the downstream process and are not part of the process
    • the upstream process is partly responsible for a positive or negative effect on the downstream process, and the downstream process is partly dependent on the upstream process.
  • Domain: Domain refers to the ontology terms that can be further specified with the relation.
    • Biological Process terms
    • Molecular Function terms
  • Range: Range describes the ontology terms that can be used to further specify the domain using the relation.
    • Biological Process terms
    • Molecular Function terms

Annotation Usage Guidelines

  • Standard annotations (Should NOT Be Used)

  • GO-CAM models (Should NOT Be Used)
    • In a GO-CAM model, if a curator wants to indicate that a process (MF or BP) is causally upstream of another process, they should always be able to choose a more specific sub-relation.
  • Examples
    • There are no examples because this relation should not be used directly in models. A more precise child should be used instead.

Ontology Usage Guidelines

This relation should only be used for inference and should not be used in the ontology.

Usage Examples

Quality Control Checks

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

Child Terms

causally upstream of negative effect

causally upstream of, positive effect

constitutively upstream of

removes input for

indirectly causally upstream of


Cross Reference to the Relations Ontology (RO)

causally upstream of

Review Status

Last Reviewed: Nov 2, 2022 DavidH

Back to: Annotation Relations