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 GO Biological Processes (BP) and/or GO Molecular Functions (MF) 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 (BP or MF) to the downstream process (BP or MF) is understood
**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
**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
**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==
== Annotation Usage Guidelines==
* Standard Annotation
* 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
** 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.
***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
* 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
**Usage Examples
***A peptidase activity that processes a signaling ligand.  
***A peptidase activity that processes a signaling ligand.  
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* This relation is not used in the ontology.
* This relation is not used in the ontology.


==Scope of Use==
* 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


== Quality Control Checks ==
== Quality Control Checks ==
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== Child Terms ==
== Child Terms ==
[https://ontobee.org/ontology/RO?iri=http://purl.obolibrary.org/obo/RO_0002213 positively regulates]
[https://ontobee.org/ontology/RO?iri=http://purl.obolibrary.org/obo/RO_0012009 constitutively upstream of]


== Cross Reference to Relation Ontology (RO) ==
== Cross Reference to Relation Ontology (RO) ==
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== Review Status ==
== Review Status ==
Reviewed on Sept 26, 2022  DavidH
Reviewed on Nov 2, 2022  DavidH


Reviewed on Oct 26, 2022 DavidH


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

Retrieved from "https://wiki.geneontology.org/index.php?title=Causally_upstream_of,_positive_effect&oldid=83610"