Annotation Relations
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.
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. | |
Molecular Function to Biological Process | 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. |
Molecular Function to Biological Process
part of - will be covered under context
Biological Process to Molecular Function
causally upstream of, positive effect
causally upstream of negative effect
Molecular Function or Biological Process to Cellular Component, Cell Type, Anatomical Structure or Organism
Biological Process to Temporal Phase
Molecular Function or Biological Process to Inputs and Outputs
Biological Process to Biological Process
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