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

[Jones, A. <And...@li...>]

Hi David,

I think that CV term looks fine to me as long as its use is optional. I guess we
may need to add some other options later in case other translation tables are
used that don't have a URL to identify them,
Cheers
Andy




> -----Original Message-----
> From: David Creasy [mailto:dc...@ma...]
> Sent: 15 December 2008 14:39
> To: psi...@li...
> Subject: Re: [Psidev-pi-dev] Minutes of Telecon. 11th December
> 
> 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?chapt
> er=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
> Matrix Science
> 64 Baker Street
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