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

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'''THIS RELATION IS DEPRECATED'''
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Curators should use  [http://wiki.geneontology.org/index.php/Annotation_Extension_Relation:has_input has input] to capture inputs/substrates/targets of Molecular Functions
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<pre style="color:#808080">
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==Definition==
 
==Definition==
  
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==Comment==
 
==Comment==
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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.
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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.
  
If the entity is indirectly bound/acted upon by the gene product that is the subject of an annotation, then the relation: has_indirect_input should be considered.
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Without evidence of a relevant interaction use the relationship has_input
  
 
==Synonyms==
 
==Synonyms==
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[[ENTITY_UNION:0000005]] ! chemical, gene product, or complex
 
[[ENTITY_UNION:0000005]] ! chemical, gene product, or complex
  
==Annotation Extension Usage Examples==
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</pre>
 
 
'''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).
 
 
 
{| class="wikitable" border="1"
 
|-
 
! Gene Name (col 2)
 
! GO ID (col 5)
 
! Reference (col 6)
 
! Evidence (col 7)
 
! Annotation Extension (col 16)
 
|-
 
| WBGene00000220
 
|GO:0001012 <span style="color:green">RNA polymerase II regulatory region DNA binding</span>
 
| PMID:21502138
 
| IDA
 
|
 
has_direct_input(WB:WBGene00000247 <span style="color:green">bec-1</span>)|has_direct_input(WB:WBGene00002980 <span style="color:green">lgg-1</span>)|has_direct_input(WB:WBGene00003033 <span style="color:green">lin-48</span>)
 
 
 
|}
 
 
 
 
 
'''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).''
 
 
 
 
 
{| class="wikitable" border="1"
 
|-
 
! Gene Name (col 2)
 
! GO ID (col 5)
 
! Reference (col 6)
 
! Evidence (col 7)
 
! Annotation Extension (col 16)
 
|-
 
| WBGene00017895
 
|GO:0004672 <span style="color:green">protein kinase activity</span>
 
| PMID:17170708
 
| IDA
 
| has_direct_input(WB:WBGene00000235 <span style="color:green">baf-1</span>)|has_direct_input(WB:WBGene00017895  <span style="color:green">vrk-1</span>)
 
|}
 
 
 
Example 2:
 
 
 
''If protein SGD:A phosphorylates protein SGD:B then annotate A to:''
 
 
 
{| class="wikitable" border="1"
 
|-
 
! Gene Name (col 2)
 
! GO ID (col 5)
 
! Reference (col 6)
 
! Evidence (col 7)
 
! Annotation Extension (col 16)
 
|-
 
| SGD:A
 
|GO:0004672 <span style="color:green">protein kinase activity</span>
 
| PMID:17170708
 
| IDA
 
| has_direct_input(SGD:B <span style="color:green">B</span>)
 
|}
 
 
 
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:'''
 
 
 
{| class="wikitable" border="1"
 
|-
 
! Gene Name (col 2)
 
! GO ID (col 5)
 
! Reference (col 6)
 
! Evidence (col 7)
 
! Annotation Extension (col 16)
 
|-
 
| SGD:A
 
|GO:0004672 <span style="color:green">protein kinase activity</span>
 
| PMID:17170708
 
| IDA
 
| has_direct_input(SGD:B <span style="color:green">B</span>)|has_direct_input(CHEBI:15422 <span style="color:green">ATP</span>)
 
|}
 
 
 
'''Or even:'''
 
 
 
{| class="wikitable" border="1"
 
|-
 
! Gene Name (col 2)
 
! GO ID (col 5)
 
! Reference (col 6)
 
! Evidence (col 7)
 
! Annotation Extension (col 16)
 
|-
 
| SGD:A
 
|GO:0004672 <span style="color:green">protein kinase activity</span>
 
| PMID:17170708
 
| IDA
 
| has_direct_input(SGD:B <span style="color:green">B</span>)|has_direct_input(CHEBI:15422 <span style="color:green">ATP</span>)|has_output(SGD:B <span style="color:green">B</span>)|has_output(CHEBI:16761 <span style="color:green">ADP</span>)
 
|}
 
 
 
----
 
  
  

Latest revision as of 13:57, 20 January 2020

THIS RELATION IS DEPRECATED

Curators should use has input to capture inputs/substrates/targets of Molecular Functions

 

==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


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