Re: [Psidev-pi-dev] Minutes of Telecon. 11th December

[David C. <dc...@ma...>]

Hi everyone,

 From the minutes:
 > Encoding NCBI translational tables, I'm not sure about the current
 > encoding in the instance doc - id numbers match NCBI accession numbers
 > - just in document references. David to change to make simpler. Add in
 > a translation table source location..

The change isn't so much to make it simpler, but to make it clearer.

<TranslationTable id="1" name="Standard">
  . . .
<PeptideEvidence ... TranslationTable_ref="1">


Will become:
<TranslationTable id="TT_1" name="Standard">
  . . .
<PeptideEvidence ... TranslationTable_ref="TT_1">

The aim is to try and avoid any confusion with the '1' being an NCBI id 
value - it is just an internal reference value.


Now google is back up and running (thought the world would end if google 
went down...), I can check in the changed example file.


 > David to look over and propose a > CV term so it is known where the
 > value has come from.

How about another CV term:

[Term]
id: PI:xxxxx
name: translation table description
def: "A URL that describes the translation table used to translate the 
nucleotides to amino acids." [PSI:PI]
xref_analog: value-type:xsd\:anyURI "The allowed value-type for this CV 
term."
is_a: PI:00011 ! search database details


<pf:cvParam accession="PI:00xxx" name="translation table description" 
cvRef="PSI-PI" 
value="http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes#SG1" 



Does this look reasonable, or can someone think of a better way of doing it?


David

Jennifer Siepen wrote:
> Hi,
> 
> Please find the minutes of todays teleconference here:
> 
> http://www.psidev.info/index.php?q=node/400
> 
> Thanks,
> 
> Jenny
> 

-- 
David Creasy
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dc...@ma...
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