Annotation Extension Relation:has input

From GO Public

Contents 1 Definition 2 Synonyms 3 Child terms 4 Scope of use 4.1 Domain 4.2 Range 5 Annotation Extension Usage Examples 5.1 Enhancing Molecular Function and Biological Process Annotations 5.1.1 Response to chemicals 5.1.2 Phosphorylation targets

Definition

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

Synonyms

has_target (EXACT)

localizes (NARROW)

Child terms

• has_direct_input

• has_indirect_input

Scope of use

Domain

BFO:0000007 ! process (Biological Process or Molecular Function)

Range

ENTITY_UNION:0000005 ! chemical, gene product, or complex

Annotation Extension Usage Examples

Enhancing Molecular Function and Biological Process Annotations

Response to chemicals

Here we use the has_input relation - the input to the process is a chemical, the output is some change in state as a result of exposure.

 col5: GO:nnnnnn
 col16: has_input(CHEBI:nnnnn)

Sometimes it is better to request a GO term here

Phosphorylation targets

If protein SGD:A phosphorylates protein SGD:B then annotate A to:

 col5: GO:0004672
 col16: has_input(SGD:B)

GO:0004672 is protein kinase activity

note we would not include a separate annotation line for B, because we only have annotation lines for active participants

strictly speaking, the input is SGD:B in the unphosphorylated state and the output is SGD:B in the phosphorylated state. However, currently we do not have IDs for these separate protein forms. Really B is both an input and an output. We standardize on has_input here.

Note there is no need to say

 col16: has_input(SGD:B),has_input(CHEBI:15422)

or even

 col16: has_input(SGD:B),has_input(CHEBI:15422),has_output(SGD:B),has_output(CHEBI:16761)

These are correct but this is pointless because the additional info is redundant with what we already know about kinase activity (this is actually made computable in MF x CHEBI)

Also there is no need to make a separate col 16 annotation for the phosphorylation process as this can be inferred

If protein SGD:A phosphorylates protein SGD:B and SGD:C then annotate A to:

 col5: GO:0004672 (protein kinase activity)
 col16: has_input(SGD:B),has_input(SGD:C)

There is some redundancy with interaction databases here. Capturing this as GO annotation is more expressive as you can say "A phosphorylates B during pathway C". But if you want to capture this in interaction databases exclusively we have tools for generating GO annotations from these (just as we have tools for capturing GO annotations from pathway databases).

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