Annotation Extension Relation:has input
From GO Public
Identifies an entity affected (bound, transported, modified, consumed or destroyed) by the gene product's participation in a molecular function or biological process.
Scope of use
BFO:0000007 ! process (Biological Process or Molecular Function)
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
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
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).