Annotation Relations: Difference between revisions

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|rowspan="1"|Molecular Function to Biological Process
|rowspan="1"|Molecular Function to Biological Process
|[[part of]]
|[https://wiki.geneontology.org/Part_of_relation part of]
|Links a Molecular Function to a Biological Process when the Molecular Function is an integral part of the Biological Process.
|Links a Molecular Function to a Biological Process when the Molecular Function is an integral part of the Biological Process.
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|rowspan="1"|Anatomical Entity to Anatomical Entity
|rowspan="1"|Anatomical Entity to Anatomical Entity
|[[part of]]
|[https://wiki.geneontology.org/Part_of_relation part of]
|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].  
|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].  
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|rowspan="9"|Molecular Function to Molecular Function
|rowspan="9"|Molecular Function to Molecular Function
|[[causally upstream of, negative effect]]
|[[causally upstream of, negative effect]]
|Links two activities when the upstream activity has a negative causal effect on the downstream activity but the mechanism is not known.
|Links two activities when the upstream activity has a negative causal effect (decreasing or inhibiting) on the downstream activity but the mechanism is not known.
|-
|-
|[[causally upstream of, positive effect]]
|[[causally upstream of, positive effect]]
|Links two activities when the upstream activity has a positive causal effect on the downstream activity but the mechanism is not known.
|Links two activities when the upstream activity has a positive causal effect (increasing or activating) on the downstream activity but the mechanism is not known.
|-
|-
|[[provides input for]]   
|[[provides input for]]   
|Links two successive activities where the product (output) of the upstream activity is the substrate (input) for the downstream activity, and the product is a macromolecule (i.e. DNA, RNA, protein).
|Links two successive activities when the product (output) of the upstream activity is the substrate (input) for the downstream activity, and the product is a macromolecule (i.e. DNA, RNA, protein).
|-
|-
|[[removes input for]]
|[[removes input for]]
|Links two activities where the upstream activity has a negative causal effect on the downstream activity when the two activities act on or modify the same molecular target at the same site(s).  
|Links two activities when the upstream activity has a negative causal effect (decreasing or inhibiting) on the downstream activity and the two activities act on or modify the same molecular target at the same site(s).  
|-
|-
|[[constitutively upstream of]]
|[[constitutively upstream of]]
|Links two activities when the upstream activity is REQUIRED FOR the downstream activity, but does not regulate the downstream activity.
|Links two activities when the upstream activity is required for the downstream activity, but does not regulate the downstream activity.
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|[[directly negatively regulates]]
|[[directly negatively regulates]]
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|[[indirectly negatively regulates]]
|[[indirectly negatively regulates]]
|Links two activities when the upstream activity has a negative regulatory effect on the downstream activity via a larger process (e.g. proteasome-mediated protein degradation) that is reused in many contexts and the curator does not want to reproduce that process in the GO-CAM. The mechanism by which the upstream activity controls the downstream activity must be known.
|Links two activities when the upstream activity has a negative regulatory effect (decreasing or inhibiting) on the downstream activity via a larger process (e.g. proteasome-mediated protein degradation) that is reused in many contexts and the curator does not want to reproduce that process in the GO-CAM. The mechanism by which the upstream activity controls the downstream activity must be known.
|-
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|[[indirectly positively regulates]]
|[[indirectly positively regulates]]
|Links two activities when the upstream activity has a positive regulatory effect on the downstream activity via a larger process (e.g. transcription) that is reused in many contexts and the curator does not want to reproduce that process in the GO-CAM. The mechanism by which the upstream activity controls the downstream activity must be known.
|Links two activities when the upstream activity has a positive regulatory effect (increasing or activating) on the downstream activity via a larger process (e.g. transcription) that is reused in many contexts and the curator does not want to reproduce that process in the GO-CAM. The mechanism by which the upstream activity controls the downstream activity must be known.
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|rowspan="2"|Small Molecule to Molecular Function
|rowspan="2"|Small Molecule to Molecular Function
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== Other Noctua Relations - UNDER REVIEW ==
== Other Contextual Relations ==
These additional Molecular Function to Biological Process relations can be used to relate MFs to BPs when either the exact causal relationship is not known, or it is known that an MF is causally upstream of a BP and not part of that BP.


{| class="wikitable"
{| class="wikitable"
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|rowspan="6"|Molecular Function to Biological Process
|rowspan="6"|Molecular Function to Biological Process
|[[causally upstream of or within]]
|[[causally upstream of or within | <span style="color:grey">causally upstream of or within</span>]]
|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.''
|<span style="color:grey">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.  ''Although this relation is used in the MOD imports into Noctua for new annotation, curators should always strive to use one of the more specific child relations that capture the directionality of the effect, either positive or negative.''</span>
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|[[causally upstream of or within, negative effect]]
|[[causally upstream of or within, negative effect]]
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|[[causally upstream of or within, positive effect]]
|[[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.
|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.''
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|[[causally upstream of, negative effect]]
|[[causally upstream of, negative effect]]
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= Gene Product to GO term Relations =
= Gene Product to GO term Relations ("qualifiers") =


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.
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.
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|Links a gene product and the Cellular Component, specifically a [http://amigo.geneontology.org/amigo/term/GO:0110165 cellular anatomical anatomy] or [http://amigo.geneontology.org/amigo/term/GO:0044423 virion component], in which a gene product has been detected.  Note that 'is active in' is not used for relating gene products to a [http://amigo.geneontology.org/amigo/term/GO:0032991 protein-containing complex]; those associations use 'part of'.
|Links a gene product and the Cellular Component, specifically a [http://amigo.geneontology.org/amigo/term/GO:0110165 cellular anatomical anatomy] or [http://amigo.geneontology.org/amigo/term/GO:0044423 virion component], in which a gene product has been detected.  Note that 'is active in' is not used for relating gene products to a [http://amigo.geneontology.org/amigo/term/GO:0032991 protein-containing complex]; those associations use 'part of'.
|-
|-
|[[part of]]
|[https://wiki.geneontology.org/Part_of_relation part of]
|Links a gene product and a [http://amigo.geneontology.org/amigo/term/GO:0032991 protein-containing complex].
|Links a gene product and a [http://amigo.geneontology.org/amigo/term/GO:0032991 protein-containing complex].
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Revision as of 08:54, 16 March 2023

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 Links two activities when the upstream activity has a negative causal effect (decreasing or inhibiting) on the downstream activity but the mechanism is not known.
causally upstream of, positive effect Links two activities when the upstream activity has a positive causal effect (increasing or activating) on the downstream activity but the mechanism is not known.
provides input for Links two successive activities when the product (output) of the upstream activity is the substrate (input) for the downstream activity, and the product is a macromolecule (i.e. DNA, RNA, protein).
removes input for Links two activities when the upstream activity has a negative causal effect (decreasing or inhibiting) on the downstream activity and the two activities act on or modify the same molecular target at the same site(s).
constitutively upstream of Links two activities when the upstream activity is required for the downstream activity, but does not regulate the downstream activity.
directly negatively regulates Links two activities when the upstream activity has a negative causal effect (decreasing or inhibiting) on an immediately downstream activity. Immediately means there is no intervening activity. The mechanism by which the upstream activity controls the downstream activity must be known.
directly positively regulates Links two activities when the upstream activity has a positive causal effect (increasing or activating) on an immediately downstream activity. Immediately means there is no intervening activity. The mechanism by which the upstream activity controls the downstream activity must be known.
indirectly negatively regulates Links two activities when the upstream activity has a negative regulatory effect (decreasing or inhibiting) on the downstream activity via a larger process (e.g. proteasome-mediated protein degradation) that is reused in many contexts and the curator does not want to reproduce that process in the GO-CAM. The mechanism by which the upstream activity controls the downstream activity must be known.
indirectly positively regulates Links two activities when the upstream activity has a positive regulatory effect (increasing or activating) on the downstream activity via a larger process (e.g. transcription) that is reused in many contexts and the curator does not want to reproduce that process in the GO-CAM. The mechanism by which the upstream activity controls the downstream activity must be known.
Small Molecule to Molecular Function is small molecule activator of Links a small molecule and an activity, when the small molecule activates the activity.
is small molecule inhibitor of Links a small molecule and an activity, when the small molecule inhibits the activity.

Other Contextual Relations

These additional Molecular Function to Biological Process relations can be used to relate MFs to BPs when either the exact causal relationship is not known, or it is known that an MF is causally upstream of a BP and not part of that BP.

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. Although this relation is used in the MOD imports into Noctua for new annotation, 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, 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.

Gene Product to GO term Relations ("qualifiers")

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.

Annotation Extension Relations


Noctua to Standard Annotation Conversion Table (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.