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

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

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/DatabaseTranslation/TranslationTable'

I think that the mapping is wrong - or maybe you need a new parent term 
for this and PI:00025?

David