Annotation Relations: Difference between revisions

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|[[indirectly positively regulates]]
|[[indirectly positively regulates]]
|This relation is intended to represent a positive regulatory effect via a larger process (module) that is reused in many contexts, and the curator does not want to reproduce that module in this GO-CAM. The mechanism is known (e.g. transcription and translation) but the process is not specific to this context, and would not be included in the model.
|This relation is intended to represent a positive regulatory effect via a larger process (module) that is reused in many contexts, and the curator does not want to reproduce that module in this GO-CAM. The mechanism is known (e.g. transcription and translation) but the process is not specific to this context, and would not be included in the model.
|-
|rowspan="6"|Molecular Function to Biological Process
|[[causally upstream of or within]]
|Links an activity and a Biological Process when the mechanism relating the activity to the Biological Process is not known. This is the most general Molecular Function to Biological Process relations.  ''Curators should always strive to use one of the more specific child relations that capture the directionality of the effect, either positive or negative.''
|-
|[[causally upstream of or within, negative effect]]
|Links an activity and a Biological Process when the mechanism relating the activity to the Biological Process is not known, but the activity has a positive effect on the process.
|-
|[[causally upstream of or within, positive effect]]
|Links an activity and a Biological Process when the mechanism relating the activity to the Biological Process is not known, but the activity has a negative effect on the process.
|-
|[[causally upstream of]]
|Links an activity and a Biological Process when the mechanism relating the activity to a Biological Process is known and the activity occurs before the Biological Process but does not regulate it. ''Curators should always strive to use one of the more specific child relations that capture the directionality of the effect, either positive or negative.''
|-
|[[causally upstream of, negative effect]]
|Links an activity and a Biological Process when the mechanism relating an activity to a Biological Process is known and the activity occurs before the Biological Process, reduces or prevents the process from occurring, but does not regulate it.
|-
|[[causally upstream of, positive effect]]
|Links an activity and a Biological Process when the mechanism relating an activity to a Biological Process is known and the activity occurs before the Biological Process, is required for the process to occur, but does not regulate it.
|-
|-
|rowspan="2"|Small Molecule to Molecular Function
|rowspan="2"|Small Molecule to Molecular Function
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== Contextual Relations ==
== Other Noctua Relations - UNDER REVIEW ==
In GO-CAMs, contextual relations are used to provide information that qualifies where, e.g. cellular components, anatomical entities, and when, e.g. biological phases, activities occur.  Contextual relations can also provide information on specific targets of activities, e.g. small molecules and gene products.


{| class="wikitable"
{| class="wikitable"
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!Usage
!Usage
|-
|-
|rowspan="1"|Molecular Function to Gene Product
|rowspan="6"|Molecular Function to Biological Process
|[[enabled by]]
|[[causally upstream of or within]]
|Links a Molecular Function to a gene or gene product that executes the activity.
|Links an activity and a Biological Process when the mechanism relating the activity to the Biological Process is not known. This is the most general Molecular Function to Biological Process relations.  ''Curators should always strive to use one of the more specific child relations that capture the directionality of the effect, either positive or negative.''
|-
|-
|rowspan="1"|Molecular Function to Biological Process
|[[causally upstream of or within, negative effect]]
|[[part of]]
|Links an activity and a Biological Process when the mechanism relating the activity to the Biological Process is not known, but the activity has a positive effect on the process.
|Links a Molecular Function to a Biological Process when the Molecular Function is an integral part of the Biological Process.
|-
|-
|rowspan="1"|Molecular Function or Biological Process to Anatomical Entity
|[[causally upstream of or within, positive effect]]
|[[occurs in]]
|Links an activity and a Biological Process when the mechanism relating the activity to the Biological Process is not known, but the activity has a negative effect on the process.
|Links a Molecular Function or a Biological Process to the anatomical entity, e.g. a GO cellular component or a cell or tissue type, ''where'' it occurs.
|-
|-
|rowspan="1"|Anatomical Entity to Anatomical Entity
|[[causally upstream of]]
|[[part of]]
|Links an activity and a Biological Process when the mechanism relating the activity to a Biological Process is known and the activity occurs before the Biological Process but does not regulate it. ''Curators should always strive to use one of the more specific child relations that capture the directionality of the effect, either positive or negative.''
|Links anatomical entities to one another to refine the location of the entity, e.g. a [http://amigo.geneontology.org/amigo/term/GO:0005634 nucleus] may be part of an [https://ontobee.org/ontology/UBERON?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0002563 intestinal epithelial cell].  
|-
|-
|rowspan="1"|Molecular Function or Biological Process to Temporal Phase
|[[causally upstream of, negative effect]]
|[[happens during]]
|Links an activity and a Biological Process when the mechanism relating an activity to a Biological Process is known and the activity occurs before the Biological Process, reduces or prevents the process from occurring, but does not regulate it.
|Links a Molecular Function or Biological Process to a biological phase or stage, e.g. [http://amigo.geneontology.org/amigo/term/GO:0000279 M phase] or [https://ontobee.org/ontology/WBls?iri=http://purl.obolibrary.org/obo/WBls_0000106 L1 larval stage] ''when'' it occurs.
|-
|-
|rowspan="2"|Molecular Function or Biological Process to Inputs and Outputs
|[[causally upstream of, positive effect]]
|[[has input]]
|Links an activity and a Biological Process when the mechanism relating an activity to a Biological Process is known and the activity occurs before the Biological Process, is required for the process to occur, but does not regulate it.
|Links a Molecular Function or Biological Process to a specific molecular target acted upon.
|-
|[[has output]]
|Links a Molecular Function or Biological Process to the specific molecular output produced by the reaction or process.
|-
|-
|}
|}


= Annotation Extension Relations =
= Annotation Extension Relations =

Revision as of 09:56, 15 February 2023

Gene Product to GO term Relations

Gene product to GO term relations serve to specify how a gene product is related to a GO term to which it is annotated. Different relations are possible for the different GO aspects, as described in the table below. When using a standard GO annotation tool, such as Protein2GO, curators choose the relations directly in the tool. In Noctua, most of the gene product to term relations are derived from the underlying data model; curators do not choose the gene product to term relations directly. For more details and specific examples of usage, click on the link to the relations page.

GO Aspect Gene Product-to-GO Term Relation Usage
Molecular Function enables Links a gene product to a Molecular Function it executes.
contributes to Links a gene product to a Molecular Function that it executes as part of a macromolecular complex, in which the 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.
acts upstream of or within Links a gene product and a Biological Process when the mechanism relating the gene product's activity to the Biological Process is not known. This is the most general gene product to GO term relation for Biological Process. Curators should always strive to use one of the more specific child relations that capture the directionality of the effect, either positive or negative.
acts upstream of or within, positive effect Links a gene product and a Biological Process when the mechanism relating the gene product's activity to the Biological Process is not known, but 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 when the mechanism relating the gene product's activity to the Biological Process is not known, but the activity of the gene product has a negative effect on the process.
acts upstream of Links a gene product and a Biological Process when the mechanism relating a gene product's activity to a Biological Process is known and the activity occurs before the Biological Process but does not regulate it. Curators should always strive to use one of the more specific child relations that capture the directionality of the effect, either positive or negative.
acts upstream of, positive effect Links a gene product and a Biological Process when the mechanism relating a gene product's activity to a Biological Process is known and the activity occurs before the Biological Process, is required for the process to occur, but does not regulate it.
acts upstream of, negative effect Links a gene product and a Biological Process when the mechanism relating a gene product's activity to a Biological Process is known and the activity occurs before the Biological Process, prevents or reduces the process, but does not regulate the process.
Cellular Component is active in Links a gene product and a Cellular Component, specifically a cellular anatomical anatomy or virion component, in which it enables its Molecular Function. Note that 'is active in' is not used for relating gene products to a protein-containing complex; those associations use 'part of'.
located in Links a gene product and the Cellular Component, specifically a cellular anatomical anatomy or virion component, in which a gene product has been detected. Note that 'is active in' is not used for relating gene products to a protein-containing complex; those associations use 'part of'.
part of Links a gene product and a protein-containing complex.
colocalizes with Being deprecated. Was used for transient or dynamic localizations.

GO-CAM Relations

GO-CAM models can use causal (e.g. directly positively regulates) and contextual (e.g. occurs in) relations. For more details and specific examples of usage, click on the link to the relations page.

Contextual Relations

In GO-CAMs, contextual relations are used to provide information that qualifies where, e.g. cellular components, anatomical entities, and when, e.g. biological phases, activities occur. Contextual relations can also provide information on specific targets of activities, e.g. small molecules and gene products.

Ontology Pair Allowed Relation Usage
Molecular Function to Gene Product enabled by Links a Molecular Function to a gene or gene product that executes the activity.
Molecular Function to Biological Process part of Links a Molecular Function to a Biological Process when the Molecular Function is an integral part of the Biological Process.
Molecular Function or Biological Process to Anatomical Entity occurs in Links a Molecular Function or a Biological Process to the anatomical entity, e.g. a GO cellular component or a cell or tissue type, where it occurs.
Anatomical Entity to Anatomical Entity part of Links anatomical entities to one another to refine the location of the entity, e.g. a nucleus may be part of an intestinal epithelial cell.
Molecular Function or Biological Process to Temporal Phase happens during Links a Molecular Function or Biological Process to a biological phase or stage, e.g. M phase or L1 larval stage when it occurs.
Molecular Function or Biological Process to Inputs and Outputs has input Links a Molecular Function or Biological Process to a specific molecular target acted upon.
has output Links a Molecular Function or Biological Process to the specific molecular output produced by the reaction or process.

Causal Relations

Ontology Pair Allowed Relation Usage
Molecular Function to Molecular Function causally upstream of, negative effect This relation is intended to represent a negative causal effect of one activity on another, where the mechanism is not known.
causally upstream of, positive effect This relation is intended to represent a positive causal effect of on activity on another, where the mechanism is not known.
provides input for This relation is intended to connect successive activities, i.e. where the product (output) of the upstream activity is the substrate (input) for the downstream activity, and the product is a macromolecule.
removes input for This relation is intended to represent a negative causal effect of an upstream activity on a downstream activity, in which the two activities act on or modify the same molecular target at the same site(s). As a result, the execution of the upstream activity prevents the downstream activity from occurring (or reduces its rate).
constitutively upstream of This relation is intended to represent that an upstream activity can be REQUIRED FOR a downstream activity, but does not regulate the downstream activity.
directly negatively regulates This relation is intended to represent a causal effect in which an upstream activity has a negative (decreasing or inhibiting) effect on an immediately downstream activity. Immediately means there is no intervening activity. The mechanism by which the upstream activity controls the downstream activity should be known.
directly positively regulates This relation is intended to represent a causal effect in which an upstream activity has a positive (increasing or activating) effect on an immediately downstream activity. Immediately means there is no intervening activity. The mechanism by which the upstream activity controls the downstream activity should be known.
indirectly negatively regulates This relation is intended to represent a negative regulatory effect via a larger process (module) that is reused in many contexts, and the curator does not want to reproduce that module in this GO-CAM. The mechanism is known (e.g. proteasome-mediated protein degradation) but the process is not specific to this context, and would not be included in the model.
indirectly positively regulates This relation is intended to represent a positive regulatory effect via a larger process (module) that is reused in many contexts, and the curator does not want to reproduce that module in this GO-CAM. The mechanism is known (e.g. transcription and translation) but the process is not specific to this context, and would not be included in the model.
Small Molecule to Molecular Function is small molecule activator of Links a small molecule and a Molecular Function, when the small molecule activates the Molecular Function.
is small molecule inhibitor of Links a small molecule and a Molecular Function, when the small molecule inhibits the Molecular Function.

Other Noctua Relations - UNDER REVIEW

Ontology Pair Allowed Relation Usage
Molecular Function to Biological Process causally upstream of or within Links an activity and a Biological Process when the mechanism relating the activity to the Biological Process is not known. This is the most general Molecular Function to Biological Process relations. Curators should always strive to use one of the more specific child relations that capture the directionality of the effect, either positive or negative.
causally upstream of or within, negative effect Links an activity and a Biological Process when the mechanism relating the activity to the Biological Process is not known, but the activity has a positive effect on the process.
causally upstream of or within, positive effect Links an activity and a Biological Process when the mechanism relating the activity to the Biological Process is not known, but the activity has a negative effect on the process.
causally upstream of Links an activity and a Biological Process when the mechanism relating the activity to a Biological Process is known and the activity occurs before the Biological Process but does not regulate it. Curators should always strive to use one of the more specific child relations that capture the directionality of the effect, either positive or negative.
causally upstream of, negative effect Links an activity and a Biological Process when the mechanism relating an activity to a Biological Process is known and the activity occurs before the Biological Process, reduces or prevents the process from occurring, but does not regulate it.
causally upstream of, positive effect Links an activity and a Biological Process when the mechanism relating an activity to a Biological Process is known and the activity occurs before the Biological Process, is required for the process to occur, but does not regulate it.


Annotation Extension Relations


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

RO-relevant documentation

The valid gp2term relations are in the Relations Ontology under the subset valid_for_go_gp2term. https://github.com/oborel/obo-relations/wiki/ROGuide#interaction-relations