Annotation Relations: Difference between revisions
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|'''MF''' to '''Input''' | |'''MF''' to '''Input''' | ||
| | |The molecular activity described by the GO MF ''[[has input]]'' one or more entities whose state is modified (bound, transported, consumed, or destroyed) by the activity. | ||
| ChEBI molecule (includes information biomacromolecule) | | ChEBI molecule (includes information biomacromolecule) | ||
|[[has input]] | |[[has input]] |
Revision as of 12:18, 7 February 2020
Gene Product to GO Term Relations
Biological Process
acts upstream of or within, positive effect
acts upstream of or within, negative effect
acts upstream of, positive effect
acts upstream of, negative effect
Molecular Function
Cellular Component
is active in ?? deprecated ?
GO-CAM Relations
Molecular Function to Gene Product
Molecular Function to Cellular Component
Molecular Function to Molecular Function
Molecular Function to Biological Process
causally upstream of or within, positive effect
causally upstream of or within, negative effect
causally upstream of, positive effect
causally upstream of negative effect
Molecular Function to Inputs and Outputs
Molecular Function to Temporal Phase
Biological Process to Molecular Function
causally upstream of, positive effect
causally upstream of negative effect
Biological Process to Cellular Component
Biological Process to Cell or Anatomy Term
Biological Process to Temporal Phase
Biological Process to Inputs and Outputs
Biological Process to Biological Process
Annotation Extension Relations
Relations Tables (works in progress)
Gene Product-to-GO Term Relations | |
---|---|
Molecular Function | enables |
contributes to (applies to gene products that act as part of complexes) | |
Biological Process | involved in |
acts upstream of or within | |
acts upstream of or within, positive effect | |
acts upstream of or within, negative effect | |
acts upstream of | |
acts upstream of, positive effect | |
acts upstream of, negative effect | |
Cellular Component | is active in |
part of | |
located in | |
colocalizes with |
GO-CAM Relations | ||
---|---|---|
Molecular Function | ||
Molecular Function - Gene Product | enabled by | protein kinase activity enabled by PLK1 |
Molecular Function - Location | occurs in | protein kinase activity occurs in cytosol |
Molecular Function - Input | has input | protein kinase activity has input MCM3 |
Molecular Function - Output | has output | protein kinase activity has output MCM3-2P |
Molecular Function - Temporal Phase | happens during | protein kinase activity happens during G1 phase |
Molecular Function - Molecular Function | directly positively regulates | protein kinase activity directly positively regulates ion transmembrane transporter activity |
Molecular Function - Molecular Function | directly negatively regulates | protein kinase activity directly negatively regulates peroxidase activity |
Molecular Function - Molecular Function | directly provides input for | peptidase activity directly provides input for receptor activity |
Relations Tables (Pascale - work in progress)
In Google doc for now: https://docs.google.com/spreadsheets/d/1vkBVTyUg1tjipUtYGan5Ob0vE14H_j6O-PuTH9619eg/edit#gid=0
Linking Molecular Functions | ||||||||
---|---|---|---|---|---|---|---|---|
Link | Curation Statement | Allowed values | GO-CAM | GPAD Output | ||||
GO-CAM relation | GO-CAM Example | GPAD relation (gene product-to-term) | GPAD example (gene product-to-term) | GPAD annotation extension (see note below) | GPAD annotation extension example | |||
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 modified (bound, transported, consumed, or destroyed) by the activity. | ChEBI molecule (includes information biomacromolecule) | has input | protein kinase activity has input MCM3 | AE: has input | PLK1 enables protein kinase activity AE:has input MCM3 | ||
MF to Temporal Phase | Identify the temporal phase during which a Molecular Function is executed or developmental stages in life stage ontologies | GO:0044848 biological phase and children or terms from developmental stages in life stage ontologies. | happens during | protein kinase activity happens during G1 phase | AE: happens during | PLK1 enables protein kinase activity AE: happens during G1 phase | ||
MF activating a Molecular Function | Indicate two consecutive GO Molecular Functions, in which the first Molecular Function has a positive effect on the second one. | GO Molecular Function | directly positively regulates | protein kinase activity directly positively regulates ion transmembrane transporter activity | AE: directly positively regulates | PLK1 enables protein kinase activity AE: directly positively regulates ion transmembrane transporter activity | ||
MF inhibiting a Molecular Function | Indicate two consecutive GO Molecular Functions, in which the first Molecular Function has a negative effect on the second one. | GO Molecular Function | directly negatively regulates | protein kinase activity directly negatively regulates peroxidase activity | AE: directly negatively regulates | PLK1 enables protein kinase activity AE: directly negatively regulates peroxidase activity | ||
MF to Molecular Function | Relate two GO Molecular Functions that succeed one another directly, and the first provides an input for the Molecular Function of the second. Main use is to connect consecutive metabolic reactions. | GO Molecular Function | directly provides input for | peptidase activity directly provides input for receptor activity Example wrong - provide metabolic example | AE: directly provides input for |
- 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 |
Link to RO documentation
https://github.com/oborel/obo-relations/wiki/ROGuide#interaction-relations