Difference between revisions of "Annotation Extension Relation:has direct input"

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m (Specifying the target molecule of an enzyme activity)
m (Specifying the chemical that was applied and induced a 'response to chemicals')
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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).
 
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).
 
==== Specifying the chemical that was applied and induced a 'response to chemicals' ====
 
 
Here we use the [[has_direct_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_direct_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:
 
 
 
{| class="wikitable" border="1"
 
!DB (Col 2)
 
!Object (Col 3)
 
!GO ID (Col 5)
 
!Reference (Col 6)
 
!Evidence (Col 7)
 
!Extension (Col 16)
 
|-
 
|Q8WY54
 
|PPM1E
 
|GO:0035690 <span style="color:green">cellular response to drug</span>
 
|PMID:20801214
 
|IDA
 
|has_direct_input(CHEBI:6801 <span style="color:green">metformin</span>)
 
|-
 
|}
 
  
 
== Using examples (from above) to demonstrate [[Folding_and_Unfolding]] using the relationship has_direct_input ==
 
== Using examples (from above) to demonstrate [[Folding_and_Unfolding]] using the relationship has_direct_input ==

Revision as of 15:11, 11 June 2014

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Definition

Identifies an entity directly affected (bound, transported, modified, consumed or destroyed) by the gene product's participation in a Molecular Function or Biological Process.

Comment

To use this relationship there must be evidence that the gene product in column 2 is known/predicted to bind the molecular target in column 16.

This can be a co-immunoprecipitation (for example) demonstrated in the paper being annotated, or from evidence available in another paper, or from evidence of protein interactions which have been demonstrated in another paper for orthologous molecules.

Without evidence of a relevant interaction use the relationship has_input

Synonyms

directly_localizes (NARROW)

has_direct_target (EXACT)

has_substrate (NARROW)

Child terms

  • None

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 DNA sequence that was bound by a gene product

Transcription factor binding to potential target sequences in vitro:

Statement from paper:

By performing gel electrophoretic mobility shift assays, we could detect efficient binding of Atf-2 to the elements found in the bec-1 and lgg-1 promoters (Fig. 5C).

(Note that binding to lin-48 is also reported as a positive control).

Gene Name (col 2) GO ID (col 5) Reference (col 6) Evidence (col 7) Annotation Extension (col 16)
WBGene00000220 Atf-2 GO:0001012 RNA polymerase II regulatory region DNA binding PMID:21502138 IDA

has_direct_input(WB:WBGene00000247 bec-1)|has_direct_input(WB:WBGene00002980 lgg-1)|has_direct_input(WB:WBGene00003033 lin-48)

Specifying the target molecule of an enzyme activity

Targets of protein kinase activity:

Example 1 Statement from paper:

A final line of evidence that BAF-1 is a substrate for VRK-1 was obtained with purified recombinant proteins, which demonstrated that BAF-1 was phosphorylated by VRK-1 in vitro (Figure 4H, lower panel). In addition, VRK-1 was autophosphorylated (Figure 4H, upper panel).


Gene Name (col 2) GO ID (col 5) Reference (col 6) Evidence (col 7) Annotation Extension (col 16)
WBGene00017895 Vrk-1 GO:0004672 protein kinase activity PMID:17170708 IDA

has_direct_input(WB:WBGene00000235 baf-1)|has_direct_input(WB:WBGene00017895 vrk-1)

Example 2:

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

Gene Name (col 2) GO ID (col 5) Reference (col 6) Evidence (col 7) Annotation Extension (col 16)
SGD:A A GO:0004672 protein kinase activity PMID:17170708 IDA has_direct_input(SGD:B B)

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:

Gene Name (col 2) GO ID (col 5) Reference (col 6) Evidence (col 7) Annotation Extension (col 16)
SGD:A A GO:0004672 protein kinase activity PMID:17170708 IDA

has_direct_input(SGD:B B)|has_direct_input(CHEBI:15422 ATP)

Or even:

Gene Name (col 2) GO ID (col 5) Reference (col 6) Evidence (col 7) Annotation Extension (col 16)
SGD:A A GO:0004672 protein kinase activity PMID:17170708 IDA

has_direct_input(SGD:B B)|has_direct_input(CHEBI:15422 ATP)|has_output(SGD:B B)|has_output(CHEBI:16761 ADP)

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)

Inclusion of the C16 information in the Molecular Function protein kinase and to the Biological Process phosphorylation can be useful, as these annotation extensions will not be created transitively. However, this information can be inferred computationally.

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

Gene Name (col 2) GO ID (col 5) Reference (col 6) Evidence (col 7) Annotation Extension (col 16)
SGD:A A GO:0004672 protein kinase activity PMID:17170708 IDA

has_direct_input(SGD:B B)|has_direct_input(SGD:C 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).

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

Specifying the DNA sequence that was bound by a gene product

Transcription factor binding to potential target sequences in vitro:

Statement from paper:

By performing gel electrophoretic mobility shift assays, we could detect efficient binding of Atf-2 to the elements found in the bec-1 and lgg-1 promoters (Fig. 5C).

|}

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 WBGene00000220 atf-2 GO:0001012 RNA polymerase II regulatory region DNA binding PMID:21502138 IDA

has_direct_input(WB:WBGene00000247 bec-1)| has_direct_input(WB:WBGene00002980 lgg-1)| has_direct_input(WB:WBGene00003033 lin-48)

Folded WBGene00000220 atf-2 GO:0001012 RNA polymerase II regulatory region DNA binding PMID:21502138 IDA No new GO term created


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