Minutes from May 13th 2010 call

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Response to Conference Call Thursday May 13th 2010

Present: Varsha, Becky, Pascale, Karen, Yasmin, Ruth, Li, Rama, Michele G.

Pascale took us through the results of the response to survey:

Overview: There's ALOT of inconsistency with whether the response to terms are being used in annotation AND the evidence codes being used for the annotation.


Example 1 : Cellular response to gamma irradiation

Background: The kinase of activity of a protein is upregulated in response to gamma irradiation. Outcome: Most people said YES they would annotate to 'response to irradiation' with IDA.

One point that came out is that we need to tweak the definition of GO:0006975:

  • DNA damage induced protein phosphorylation ; GO:0006975
    • The widespread phosphorylation of various molecules, triggering many downstream processes, that occurs in response to the detection of DNA damage.

to:

  • protein phosphorylation in response to DNA damage ; GO:0006975
    • synonym: DNA damage induced protein phosphorylation [EXACT]
    • Phosphorylation of a molecule that occurs in response to the detection of DNA damage.


Example 2 : response to cadmium ion

Background: gene expression is upregulated in response to cadmium Outcome: There's still ALOT of inconsistency between databases about whether you can annotate a gene that is being upregulated with 'response to'

  • Rama, Karen and Li would NOT use response to in this situation.
  • Pascale pointed out that it may be useful if there is no other information available, but SGD would still not use it even then because it's so unreliable and isn't a useful assay of whether a GP is involved in a process or not.



OVERALL POINTS (also added to the general wiki)

RESPONSE VS CELLULAR RESPONSE

  • Most annotators use 'response to' terms rather than 'cellular response to' terms. We need a way to direct people to the more specific cellular terms.
    • Could add a comment to all the 'response to' terms: If the response is at the cellular level, consider instead annotating to 'cellular response to x'.
    • Add guidelines to the web pages
    • Add a checking script


EVIDENCE CODES

  • There's confusion over IMP vs IDA. We need to expand on the specific examples of when to use each. Is it an in-vivo vs in-vitro distinction?
  • In some cases it's ok to use IDA and 'response to' but do we want a script to bring them up as warning: are you sure you want to use this evidence code type thing?


DEFINITION OF 'RESPONSE TO'

  • We need to distinguish what is DOING the change, and what is BEING changed. Proposed change to the definition:
  • cellular response to stimulus ; GO:0051716
    • A change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus.

>

    • Any process that results in a change in state or activity of a cell (......) as a result of a stimulus.