Annotation Relations: Difference between revisions

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= Gene Product to GO Term Relations =
=Purpose of Gene Product to GO Term relations=
Gene Product to GO Term relations serve to specify how directly a gene product is related to the GO term to which it is annotated. Different relations are possible for the different GO aspects, as described below.


== Biological Process ==
[[acts upstream of or within]]


[[acts upstream of or within, positive effect]]
= Gene Product to GO Term relations =


[[acts upstream of or within, negative effect]]  
== Molecular Function ==
* '''if a gene product is directly responsible for a reaction:'''
** [[enables]]
* '''if multiple gene products participate in a reaction:'''
** [[contributes to]]


[[acts upstream of]]
== Biological Process ==


[[acts upstream of, positive effect]]
* '''if a gene product plays a direct role in a process:'''
** [[involved in]]


[[acts upstream of, negative effect]]
* '''if the activity of a gene product is occurs before or is required for a process:'''
**[[acts upstream of]]
**[[acts upstream of, positive effect]]
**[[acts upstream of, negative effect]]


[[involved in]]
* '''if the relation between the activity of a gene product and a process is unknown:'''
**[[acts upstream of or within]]
**[[acts upstream of or within, positive effect]]
**[[acts upstream of or within, negative effect]]


== Molecular Function ==
== Cellular Component ==
[[enables]]
[[is active in]]  


[[contributes to]]
[[located in]]


== Cellular Component ==
[[part of (GP2Term)]]
[[part of (GP2Term)]]
[[is active in]] ?? deprecated ?


[[colocalizes with]]
[[colocalizes with]]
Line 52: Line 59:
[[negatively regulates]]
[[negatively regulates]]


== Biological Process to Cellular Component ==
== Molecular Function or Biological Process to Cellular Component, Cell Type, Anatomical Structure or Organism ==


[[occurs in]]
[[Annotation Extension Relation:occurs_in | occurs_in]]
 
== Biological Process to Cell or Anatomy Term ==
 
[[occurs in]]


== Biological Process to Temporal Phase ==
== Biological Process to Temporal Phase ==
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[[happens during]]
[[happens during]]


== Biological Process to Inputs and Outputs ==
== Molecular Function or Biological Process to Inputs and Outputs ==


[[has input]]
[[Annotation Extension Relation:has input|has input]]


[[has output]]
[[Annotation Extension Relation:has output|has output]]


== Biological Process to Biological Process ==
== Biological Process to Biological Process ==
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*[http://wiki.geneontology.org/index.php/Annotation_usage_examples_for_each_annotation_extension_relation Annotation Extension Relations]
*[http://wiki.geneontology.org/index.php/Annotation_usage_examples_for_each_annotation_extension_relation Annotation Extension Relations]


= Relations Tables (works in progress) =
= Gene Product to GO term Relations =
The valid gp2term relations are in the Relations Ontology under the subset <code>valid_for_go_gp2term</code>.
The valid gp2term relations are in the Relations Ontology under the subset <code>valid_for_go_gp2term</code>.


{| class="wikitable"
{| class="wikitable"
!colspan="3" |Gene Product-to-GO Term Relations | Usage
!colspan="2" |Gene Product-to-GO Term Relations  
! Usage
|-
|-
|rowspan="2"|Molecular Function
|rowspan="2"|Molecular Function
|[[enables]]  
|[[enables]]
|Links a gene product and the Molecular Function that a gene product executes.
|-
|-
|[[contributes to]] (applies to gene products that act as part of complexes)
|[[contributes to]]  
|Links a gene product and the Molecular Function that a gene product executes as part of a complex, in which a Molecular Function cannot be ascribed to an individual subunit or a small set of subunits of a complex. Only the subunits required for the Molecular Function are annotated to the Molecular Function term,  with 'contributes to'.
|-
|-
|rowspan="7"|Biological Process
|rowspan="10"|Biological Process
|[[involved in]]
|[[involved in]]
| Links a gene product and a Biological Process in which the gene product's Molecular Function plays an integral role.
|-
|[[regulates]]
| TO BE CONFIRMED - not in P2GO but in ShEx
|-
|[[positively regulates]]
| TO BE CONFIRMED - not in P2GO but in ShEx
|-
|[[negatively regulates]]
| TO BE CONFIRMED - not in P2GO but in ShEx
|-
|-
|[[acts upstream of or within]]
|[[acts upstream of or within]]
| Links a gene product and a Biological Process for which the evidence is not sufficient to determine the mechanism relating the gene product's activity to a biological process. This is the most general gp2term relation for Biological Process.
|-
|-
|[[acts upstream of or within, positive effect]]
|[[acts upstream of or within, positive effect]]
| Links a gene product and a Biological Process for which the evidence is not sufficient to determine the mechanism relating the gene product's activity to a biological process, but it has been shown that the activity of the gene product has a positive effect on the process.
|-
|-
|[[acts upstream of or within, negative effect]]
|[[acts upstream of or within, negative effect]]
| Links a gene product and a Biological Process for which the evidence is not sufficient to determine the mechanism relating the gene product's activity to a biological process, but it has been shown that the activity of the gene product has a negative effect on the process.
|-
|-
|[[acts upstream of]]
|[[acts upstream of]]
| Links a gene product and a Biological Process for which the evidence is sufficient to determine the mechanism relating a gene product's activity to a biological process and that activity occurs ''before'' that biological process, is not an integral part of the process, nor does it regulate the process.
|-
|-
|[[acts upstream of, positive effect]]
|[[acts upstream of, positive effect]]
| Links a gene product and a Biological Process for which the evidence is sufficient to determine the mechanism relating a gene product's activity to a biological process and that activity occurs ''before'' that biological process, is not an integral part of the process, nor does it regulate the process, and is required for the process to occur.
|-
|-
|[[acts upstream of, negative effect]]
|[[acts upstream of, negative effect]]
| Links a gene product and a Biological Process for which the evidence is sufficient to determine the mechanism relating a gene product's activity to a biological process and that activity occurs ''before'' that biological process, is not an integral part of the process, nor does it regulate the process, and prevents the process from occuring.
|-
|-
|rowspan="4"|Cellular Component
|rowspan="4"|Cellular Component
|[[is active in]]
|[[is active in]]
|Links a gene product and the cellular component in which it is active. Note that this excludes 'protein-containing complex' (GO:0032991) and children; those are linked using 'part of'.
|-
|-
|[[part of]]
|[[part of]]
|For protein complex members, links a gene product and the protein-containing complex (GO:0032991 and children). Non-members should be annotated to 'protein-containing complex binding (GO:0044877)' or a child.
|-
|-
|[[located in]]
|[[located in]]
|Links a gene product and the cellular component in which a gene product has been detected. If there is data about the localization of the activity, this should be captured using 'is active in'. Note that this excludes 'protein-containing complex' (GO:0032991) and children; those are linked using 'part of'.
|-
|-
|[[colocalizes with]]
|[[colocalizes with]]
|Being deprecated. Was used for transient or dynamic localizations.
|}
|}


= Relations Tables (work in progress) =
= Relations Tables - GO-CAM (work in progress) =




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|-
|-
| '''MF''' to '''Location'''
| '''MF''' to '''Location'''
|The molecular activity described by the GO MF  ''[[occurs in]]'' a physical location.  
|The molecular activity described by the GO MF  ''[[Annotation Extension Relation:occurs_in | occurs_in]]'' a physical location.  
| GO cellular component, cells, higher anatomical structures (e.g. tissues), organisms
| GO cellular component, cells, higher anatomical structures (e.g. tissues), organisms
|[[occurs in]]
|[[Annotation Extension Relation:occurs_in | occurs_in]]
|protein kinase activity ''[[enabled by]]'' PLK1 ''[[occurs in]]'' cytosol
|protein kinase activity ''[[enabled by]]'' PLK1 ''[[Annotation Extension Relation:occurs_in | occurs_in]]'' cytosol
|[[part of]]
|[[part of]]
| PLK1 ''[[part of]]'' cytosol
| PLK1 ''[[part of]]'' cytosol
| [[occurs in]]
| [[Annotation Extension Relation:occurs_in | occurs_in]]
|PLK1 ''[[enables]]'' protein kinase activity  
|PLK1 ''[[enables]]'' protein kinase activity  
AE: ''[[occurs in]]'' cytosol
AE: ''[[Annotation Extension Relation:occurs_in | occurs_in]]'' cytosol
|-
|-
|'''MF''' to '''Input'''
|'''MF''' to '''Input'''
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|[[happens during]]  
|[[happens during]]  
|''[[happens during]]'' S phase
|''[[happens during]]'' S phase
|-
|'''MF''' directly activating another '''MF'''
|The molecular activity described by an upstream GO MF that ''[[directly positively regulates]]'' a downstream MF via a direct physical interaction. The two activities act consecutively.
|GO molecular function
|[[directly positively regulates]]
|protein kinase activity ''[[enabled by]]'' PLK1
''[[directly positively regulates]]'' histone acetyltransferase activity
''[[enabled by]]'' KAT7
|[[enables]]
|PLK1 ''[[enables]]'' protein kinase activity
|[[directly positively regulates]]
|''[[directly positively regulates]]'' histone acetyltransferase activity
|-
|'''MF''' directly inhibiting another '''MF'''
|The molecular activity described by an upstream GO MF that ''[[directly negatively regulates]]'' a downstream MF via a direct physical interaction. The two activities act consecutively.
|GO molecular function
|[[directly negatively regulates]]
|protein kinase activity ''[[enabled by]]'' PAK1
''[[directly negatively regulates]]'' protein kinase activity
''[[enabled by]]'' ROK
|''[[enables]]''
|PAK1 ''[[enables]]'' protein kinase activity
|[[directly negatively regulates]]
|''[[directly negatively regulates]]'' protein kinase activity
|-
|-
|'''MF''' providing an input for another '''MF'''
|'''MF''' providing an input for another '''MF'''
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|[[colocalizes with]]
|[[colocalizes with]]
|}
|}
==Deprecated relations==
[[Deprecated relations]]


== Link to RO documentation==
== Link to RO documentation==

Revision as of 08:42, 29 June 2022

Purpose of Gene Product to GO Term relations

Gene Product to GO Term relations serve to specify how directly a gene product is related to the GO term to which it is annotated. Different relations are possible for the different GO aspects, as described below.


Gene Product to GO Term relations

Molecular Function

  • if a gene product is directly responsible for a reaction:
  • if multiple gene products participate in a reaction:

Biological Process

  • if a gene product plays a direct role in a process:

Cellular Component

is active in

located in

part of (GP2Term)

colocalizes with

GO-CAM Relations

Molecular Function to Biological Process

part of

causally upstream of or within, positive effect

causally upstream of or within, negative effect

causally upstream of, positive effect

causally upstream of negative effect


Biological Process to Molecular Function

causally upstream of, positive effect

causally upstream of negative effect

positively regulates

negatively regulates

Molecular Function or Biological Process to Cellular Component, Cell Type, Anatomical Structure or Organism

occurs_in

Biological Process to Temporal Phase

happens during

Molecular Function or Biological Process to Inputs and Outputs

has input

has output

Biological Process to Biological Process

Annotation Extension Relations

Gene Product to GO term Relations

The valid gp2term relations are in the Relations Ontology under the subset valid_for_go_gp2term.

Gene Product-to-GO Term Relations Usage
Molecular Function enables Links a gene product and the Molecular Function that a gene product executes.
contributes to Links a gene product and the Molecular Function that a gene product executes as part of a complex, in which a Molecular Function cannot be ascribed to an individual subunit or a small set of subunits of a complex. Only the subunits required for the Molecular Function are annotated to the Molecular Function term, with 'contributes to'.
Biological Process involved in  Links a gene product and a Biological Process in which the gene product's Molecular Function plays an integral role.
regulates  TO BE CONFIRMED - not in P2GO but in ShEx
positively regulates TO BE CONFIRMED - not in P2GO but in ShEx
negatively regulates TO BE CONFIRMED - not in P2GO but in ShEx
acts upstream of or within Links a gene product and a Biological Process for which the evidence is not sufficient to determine the mechanism relating the gene product's activity to a biological process. This is the most general gp2term relation for Biological Process.
acts upstream of or within, positive effect Links a gene product and a Biological Process for which the evidence is not sufficient to determine the mechanism relating the gene product's activity to a biological process, but it has been shown that the activity of the gene product has a positive effect on the process.
acts upstream of or within, negative effect Links a gene product and a Biological Process for which the evidence is not sufficient to determine the mechanism relating the gene product's activity to a biological process, but it has been shown that the activity of the gene product has a negative effect on the process.
acts upstream of Links a gene product and a Biological Process for which the evidence is sufficient to determine the mechanism relating a gene product's activity to a biological process and that activity occurs before that biological process, is not an integral part of the process, nor does it regulate the process.
acts upstream of, positive effect Links a gene product and a Biological Process for which the evidence is sufficient to determine the mechanism relating a gene product's activity to a biological process and that activity occurs before that biological process, is not an integral part of the process, nor does it regulate the process, and is required for the process to occur.
acts upstream of, negative effect Links a gene product and a Biological Process for which the evidence is sufficient to determine the mechanism relating a gene product's activity to a biological process and that activity occurs before that biological process, is not an integral part of the process, nor does it regulate the process, and prevents the process from occuring.
Cellular Component is active in Links a gene product and the cellular component in which it is active. Note that this excludes 'protein-containing complex' (GO:0032991) and children; those are linked using 'part of'.
part of For protein complex members, links a gene product and the protein-containing complex (GO:0032991 and children). Non-members should be annotated to 'protein-containing complex binding (GO:0044877)' or a child.
located in Links a gene product and the cellular component in which a gene product has been detected. If there is data about the localization of the activity, this should be captured using 'is active in'. Note that this excludes 'protein-containing complex' (GO:0032991) and children; those are linked using 'part of'.
colocalizes with Being deprecated. Was used for transient or dynamic localizations.

Relations Tables - GO-CAM (work in progress)

In Google doc for now: https://docs.google.com/spreadsheets/d/1vkBVTyUg1tjipUtYGan5Ob0vE14H_j6O-PuTH9619eg/edit#gid=0


Molecular Function
 Link  Curation Statement Allowed values (range)  GO-CAM GPAD Output
GO-CAM relation GO-CAM statement GPAD relation (gene product-to-term) GPAD example (gene product-to-term) GPAD annotation extension relation (see note below) GPAD example (annotation extension)
MF to Annotated Entity The molecular activity described by the GO MF is enabled by the annotated entity. genes, gene products, protein-containing complexes enabled by protein kinase activity enabled by PLK1 enables PLK1 enables protein kinase activity n/a n/a
MF to Location The molecular activity described by the GO MF occurs_in a physical location. GO cellular component, cells, higher anatomical structures (e.g. tissues), organisms occurs_in protein kinase activity enabled by PLK1 occurs_in cytosol part of PLK1 part of cytosol occurs_in PLK1 enables protein kinase activity

AE: occurs_in cytosol

MF to Input The molecular activity described by the GO MF has input one or more entities whose state is changed (bound, transported, modified, consumed, or destroyed) by the activity. genes, gene products, protein-containing complexes, chemicals has input protein kinase activity enabled by PLK1 has input KAT7 enables PLK1 enables protein kinase activity has input has input KAT7
MF to Output The molecular activity described by the GO MF has output one or more entities whose state was changed (bound, transported, modified, consumed, or destroyed) by the activity. genes, gene products, protein-containing complexes, chemicals has output protein kinase activity enabled by PLK1 has output phosphorylated KAT7 enables PLK1 enables protein kinase activity has output has output phosphorylated KAT7
MF to Temporal Phase The molecular activity described by the GO MF happens during a specific temporal or developmental stage. biological phases (e.g. cell cycle phases), developmental stages (e.g. larval stage) happens during protein kinase activity enabled by PLK1 happens during S phase enables PLK1 enables protein kinase activity happens during happens during S phase
MF providing an input for another MF The molecular activity described by an upstream GO MF that directly provides input for for a downstream MF. The two activities act consecutively. The intended use is to connect catalytic activities that are part of a metabolic pathway. GO molecular function directly provides input for 6-phosphofructokinase activity enabled by PFK

directly provides input for fructose bisphosphate aldolase activity enabled by ALDOA

enables PFK enables 6-phosphofructose kinase activity directly provides input for directly provides input for fructose bisphosphate aldolase activity
MF part of a BP The molecular activity enabled by a gene product is an integral part of the BP. GO molecular function part of 6-phosphofructokinase activity enabled by PFK part of glycolytic process through fructose-6-phosphate involved in PFK involved in glycolytic process through fructose-6-phosphate
  • Annotation Extensions are only output in the GPAD file if the evidence for the primary annotation and the annotation extension is the same.
Biological Process
Linked entities Usage Types of objects (range) GO-CAM / GP2Term relation in GPAD output
BP to Gene Product Indicate that a gene product's activity (MF) plays an inherent role in some Biological Process. ChEBI information biomacromolecule (genes and gene products) part of was missing from other table
BP to Gene Product Indicate that a gene product's activity (MF) directly regulates the rate or occurrence of some Biological Process. ChEBI information biomacromolecule (genes and gene products) regulates was missing from other table
Legacy Biological Process
Relations to capture annotations derived from weak evidence. We aim to replace these annotations as more knowledge is accumulated.
BP to Gene Product Indicate that the mechanism relating a gene product's activity to a biological process is unknown, and the gene product's activity has an unknown effect on the process. ChEBI information biomacromolecule (genes and gene products) acts upstream of or within
BP to Gene Product Indicate that the mechanism relating a gene product's activity to a biological process is unknown, but the gene product's activity has a positive or activating effect on the process. ChEBI information biomacromolecule (genes and gene products) acts upstream of or within, positive effect
BP to Gene Product Indicate that the mechanism relating a gene product's activity to a biological process is unknown, but the gene product's activity has a negative or inhibitory effect on the process. ChEBI information biomacromolecule (genes and gene products) acts upstream of or within, negative effect
BP to Gene Product Indicate that the experimental evidence is sufficient to determine the mechanism relating a gene product's activity (MF) to a biological process and that activity occurs before that biological process, is not an integral part of the process, nor does it regulate the process. ChEBI information biomacromolecule (genes and gene products) acts upstream of
BP to Gene Product Indicate that a gene product's activity (MF) is: 1) executed before the beginning of the process, 2) is not part of the process, and 3) is required for the process to occur. ChEBI information biomacromolecule (genes and gene products) acts upstream of, positive effect
BP to Gene Product Indicate that a gene product's activity (MF) is: 1) executed before the beginning of the process, 2) is not part of the process, and 3) does not directly negatively regulate the process. ChEBI information biomacromolecule (genes and gene products) acts upstream of, negative effect
Cellular component
GO-CAM relations Usage Example Corresponding Gene Product to GO Term relation in GPAD output
is active in The Cellular Component in which the gene or gene product enables its Molecular Function. PLK1 is active in nucleus is active in
part of (a) Relates a cellular component to some cellular component, cell or anatomical structure that it is part of. (b) It may also be used to relate a molecular function or biological process to a biological process or developmental stage of which it is a part. Represented as an AE: TLR4 is active perinuclear region of cytoplasm part of CL:0000451 (dendritic cell) Annotation Extension:part of
located in Gene product detected in a cellular location, but not shown to be active there. PLK1 located in in nucleus located in
colocalizes with Represents transient or peripheral associations. PLK1 colocalizes with in nucleus colocalizes with

Deprecated relations

Deprecated relations

Link to RO documentation

https://github.com/oborel/obo-relations/wiki/ROGuide#interaction-relations