Re: [Psidev-pi-dev] FW: Spec doc

[Eric D. <ede...@sy...>]

I have refreshed the on-line docs at:

http://www.peptideatlas.org/tmp/AnalysisXML_working.html

I notice that several of the xxxx_ref attributes do not have definitions.

Regards,
Eric


> -----Original Message-----
> From: David Creasy [mailto:dc...@ma...]
> Sent: Thursday, December 04, 2008 9:50 AM
> To: Andreas Bertsch
> Cc: psi...@li...
> Subject: Re: [Psidev-pi-dev] FW: Spec doc
> 
> Hi Andreas,
> 
> Andreas Bertsch wrote:
> > Hi David,
> >
> >> Andy suggested:
> >> Andreas can you add: "search tolerance plus value" and "search
> tolerance
> >> minus value" to the CV and mapping file and I'll change the schema,
> does
> >> this seem reasonable to everyone.?
> > Sorry, that is my fault, I have overlooked this structure. I have added
> the cv
> > two terms, 412 and 413, plus and minus value. The Mascot MSMS example
> would
> > look like this using the new terms.
> Thanks. I've updated the Mascot examples, and all seem to validate
> properly now.
> 
> >
> > I have also updated the mapping file accordingly. Now two values
> (exactly two
> > terms) are required, one plus and one minus value. The units are
> directly
> > associated with the two terms. So the "mass units" tree becomes obsolete
> > (absolut(e)ly), and I would suggest to delete it, if there is no good
> reason
> > to keep it.
> Yes, I would think that we can delete these.
> 
>  > I also think that a distinction into absolute and relative is not
>  > necessary as it is clear by specifying the units.
> Agree.
> 
> I've just one remaining validation error:
> 
> Error: CV term used in invalid element: 'PI:00410 - translation start
> codons' at element
> '/AnalysisXML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/Da
> tabaseTranslation/TranslationTable'
> 
> I think that the mapping is wrong - or maybe you need a new parent term
> for this and PI:00025?
> 
> David
> 
> 
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