Annotation Relations: Difference between revisions

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|[[part of]]
|[[part of]]
| PLK1 ''[[part of]]'' cytosol
| PLK1 ''[[part of]]'' cytosol
| PLK1 ''[[enables]]'' protein kinase activity AE: ''[[occurs in]]'' cytosol
| [[occurs in]]
|
|PLK1 ''[[enables]]'' protein kinase activity AE: ''[[occurs in]]'' cytosol
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|'''MF''' to '''Input'''
|'''MF''' to '''Input'''

Revision as of 12:07, 7 February 2020

Gene Product to GO Term Relations

Biological Process

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

involved in

Molecular Function

enables

contributes to

Cellular Component

part of (GP2Term)

is active in ?? deprecated ?

colocalizes with

GO-CAM Relations

Molecular Function to Gene Product

enabled by

Molecular Function to Cellular Component

occurs in

Molecular Function to Molecular Function

directly provides input for

directly positively regulates

directly negatively regulates

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

Molecular Function to Inputs and Outputs

has input

has output

Molecular Function to Temporal Phase

happens during

Biological Process to Molecular Function

causally upstream of, positive effect

causally upstream of negative effect

positively regulates

negatively regulates

Biological Process to Cellular Component

occurs in

Biological Process to Cell or Anatomy Term

occurs in

Biological Process to Temporal Phase

happens during

Biological Process to Inputs and Outputs

has input

has output

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 term 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 term 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 Identify an entity affected targeted? (bound, transported, modified, consumed or destroyed) by the gene product's participation in a molecular function (or biological process). 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