Annotation Relations

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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 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


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



Relations Tables (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 directly activating another MF The molecular activity described by an upstream GO MF that directly positively regulates a downstream MF via a direct physical interaction. The two activities act consecutively. GO molecular function directly positively regulates protein kinase activity enabled by PLK1

directly positively regulates histone acetyltransferase activity enabled by KAT7

enables PLK1 enables protein kinase activity directly positively regulates directly positively regulates histone acetyltransferase activity
MF directly inhibiting another MF The molecular activity described by an upstream GO MF that directly negatively regulates a downstream MF via a direct physical interaction. The two activities act consecutively. GO molecular function directly negatively regulates protein kinase activity enabled by PAK1

directly negatively regulates protein kinase activity enabled by ROK

enables PAK1 enables protein kinase activity directly negatively regulates directly negatively regulates protein kinase activity
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

Link to RO documentation

https://github.com/oborel/obo-relations/wiki/ROGuide#interaction-relations