Has input: Difference between revisions

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==== Specifying the chemical that was applied and induced a 'response to chemicals' ====
==== Specifying the chemical that was applied and induced a 'response to chemicals' ====
<span style="color:blue">I think that has_direct_input might be a better relationship choice, so I have added this example to the has_direct_input page but left the example her for confirmation (Ruth)</span>
<span style="color:blue">I think that has_direct_input might be a better relationship choice, so I have added this example to the has_direct_input page but left the example here for confirmation (Ruth)</span>


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.
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.

Revision as of 10:58, 11 June 2014

Back to Annotation usage examples for each annotation extension relation

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

If you know that the target is bound by the annotated gene product then consider using this child relationship

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

Specifying the chemical that was applied and induced a 'response to chemicals'

I think that has_direct_input might be a better relationship choice, so I have added this example to the has_direct_input page but left the example here for confirmation (Ruth)

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


Cellular response to drug

Statement from paper: incubation of cells with low concentrations of phenformin and depletion of Ppm1E increased AMPK phosphorylation

So one of the annotations would be:


DB (Col 2) Object (Col 3) GO ID (Col 5) Reference (Col 6) Evidence (Col 7) Extension (Col 16)
Q8WY54 PPM1E GO:0035690 cellular response to drug PMID:20801214 IDA has_input(CHEBI:6801 metformin)

Specifying the protein which is a target of a Biological Process

Proteolysis targets

Statement from paper: MICA shedding by tumor cells was inhibited by silencing of the related ADAM10 and ADAM17 proteases

So one of the annotations would be:

DB (Col 2) Object (Col 3) GO ID (Col 5) Reference (Col 6) Evidence (Col 7) Extension (Col 16)
O14672 ADAM10 GO:0006509 membrane protein ectodomain proteolysis PMID:18676862 IMP has_input(UNIPROT:Q29983 MICA)

Using examples (from above) to demonstrate Folding_and_Unfolding using the relationship has_input

Specifying the protein which is a target of a Biological Process

Proteolysis targets

Statement from paper: MICA shedding by tumor cells was inhibited by silencing of the related ADAM10 and ADAM17 proteases

Folded/unfolded Gene Name (col 2) GO ID (col 5) Reference (col 6) Evidence (col 7) Annotation Extension (col 16) Parent terms of new folded GO term
Unfolded O14672 ADAM10 GO:0006509 membrane protein ectodomain proteolysis PMID:18676862 IMP has_input(UNIPROT:Q29983 MICA)
Folded O14672 ADAM10 GO:0006509 membrane protein ectodomain proteolysis PMID:18676862 IMP No new GO term created



Back to Annotation usage examples for each annotation extension relation