Causally upstream of, positive effect: Difference between revisions

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== Overview ==
== Overview and Scope of Use==
*The 'causally upstream of, positive effect' relation is used to relate two GO Biological Processes or a GO Biological Process to a GO Molecular Function when:
*The 'causally upstream of, positive effect' relation is used to relate GO Biological Processes (BP) and/or GO Molecular Functions (MF) when:
**the mechanism that relates the upstream process to the downstream process or function is known
**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 do not directly regulate (i.e. regulate via a direct physical interaction) the activities of the gene products in the downstream process but are otherwise necessary for the downstream gene product to execute its function
**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
* Domain- Domain refers to the ontology terms that can be further specified with the relation.
** Any biological process
** Any molecular function
* Range- Range describes the ontology terms that can be used to further specify the domain using the relation.
** Any biological process
** Any molecular function


=== Definition ===
== 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.


*Needs formal RO definition and review of placement in hierarchy.
* GO-CAM Annotation
*Proposal: p is causally upstream of, positive effect on q if and only if p precedes q and p and q are linked in a causal chain whereby completion/execution/progression of p increases the frequency, rate or extent of q but not via a direct physical interacction between entities.
** 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


*RO comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y
==Ontology Usage Guidelines==
* This relation is not used in the ontology.


=== Child Terms ===


== Examples of Usage ==
== Quality Control Checks ==
*Regulation of transcription by a DNA-binding transcription factor activity results in increased levels of target mRNA.  Expressed in a GO-CAM model, the transcription process of which the transcription factor activity is a part, has a causally positive effective that acts upstream of the activity of the target. In this case, the transcription factor does not directly regulate the activity of the target, but there is a known, causal process that links the activities of the transcription factor and the product of the transcribed gene.
* Annotations can be validated using a Shape Expressions ([https://github.com/geneontology/go-shapes/blob/master/shapes/go-cam-shapes.shex ShEx]) representation of allowed relations between ontology terms.
**Exemplar GO-CAM model:http://noctua.geneontology.org/editor/graph/gomodel:5a5fc23a00000137
 
== Child Terms ==
[https://ontobee.org/ontology/RO?iri=http://purl.obolibrary.org/obo/RO_0002213 positively regulates]


== Quality Control Checks ==
[https://ontobee.org/ontology/RO?iri=http://purl.obolibrary.org/obo/RO_0012009 constitutively upstream of]


== Relations Ontology ==
== Cross Reference to Relation Ontology (RO) ==
[http://www.ontobee.org/ontology/RO?iri=http://purl.obolibrary.org/obo/RO_0002304 causally upstream of, positive effect]
[http://www.ontobee.org/ontology/RO?iri=http://purl.obolibrary.org/obo/RO_0002304 causally upstream of, positive effect]


== Review Status ==
== Review Status ==
Reviewed on Nov 2, 2022  DavidH


Last reviewed: November 26, 2018


[http://wiki.geneontology.org/index.php/Annotation_Relations Back to: Annotation Relations]
[http://wiki.geneontology.org/index.php/Annotation_Relations Back to: Annotation Relations]


[[Category: Annotation]]
 
[[Category: Relations]]
[[Category: Relations]]
[[Category: GO-CAM Relations]]

Revision as of 10:22, 10 November 2022

Overview and Scope of Use

  • The 'causally upstream of, positive effect' 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
    • in order for the downstream process to occur normally, the upstream process needs to occur
  • Domain- Domain refers to the ontology terms that can be further specified with the relation.
    • Any biological process
    • Any molecular function
  • Range- Range describes the ontology terms that can be used to further specify the domain using the relation.
    • Any biological process
    • Any molecular function

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

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


Back to: Annotation Relations