Re: [Psidev-pi-dev] Further work on example instance docs

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

Hi Martin,

Martin Eisenacher wrote:
> Hi,
> 
>> (and agree that Sequence_ref should be
>> mandatory)
Probably anything like this should go in the issues list.

> Agree, too. Shall we add that as a
> comment to remind us?
> At the moment, the psidev.info website
> seems to be down, so I 
> don't know, whether you agreed to use
> the google doc to collect such infos;
> otherwise I would have put that there...
Actually, Julian suggested we just use a Wiki page, so I started one here
http://code.google.com/p/psi-pi/wiki/NotesForFocumentation



> 
>> 1 minor issue:
>> <ProteinDetermination identifier="xxx"
>> ProteinDetectionResultList_ref="result
>> s_from_Mascot" >
>> The name of the _ref attribute should
>> now be: ProteinDetectionList_ref
> Agree, too. Is there a schema-TODO or
> will you, Andy, change that
> by reading this mail? ;-)

Maybe you could this to
http://code.google.com/p/psi-pi/issues/detail?id=27
Or make a separate issue.

> 
>> Question:
>> In ProteinDetermination, there is:
>>        <SpectrumIdentificationList_ref
>> identifier="SIL_1"/>
>> The SpectrumIdentificationList_ref
>> isn't an attribute of
>> ProteinDetermination because there
>> could be more than one
>> SpectrumIdentificationList?
>> Assuming this is the case, then the
>> identifier (SIL_1 in my example) is
>> the reference? So somewhere else there
>> will be:
>> <SpectrumIdentificationList
>> identifier="SIL_1" ...
>>
>> or have I misunderstood?
> No, that is completely what was
> intended.
> That was, because a protein detection
> may use the peptide pool of more
> than one SpectrumIdentification, like:
> 
> <ProteinDetermination
> identifier="ProteinExtractor_analysis"
> ProteinDeterminationProtocol_ref="Protei
> nExtractor_proto"
> ProteinDetectionResultList_ref="ProteinE
> xtractor_results">
> 	<SpectrumIdentificationList_ref
> identifier="SEQUEST_results"/>
> 	<SpectrumIdentificationList_ref
> identifier="Mascot_results"/>
> </ProteinDetermination>
> 
> We could discuss to change it to
> <SpectrumIdentificationList_ref
> ref="SIL1""/>
Yes, I think that would be clearer.

> 
>> And, (losing my memory again), I've
>> forgotten what SpectraData is
>> supposed to be for.
> You mean, in the Input element? It is a
> description (or link) 
> to the spectra data set, i.e. normally a
> mzML file
> or a mgf. It is referenced from the
> SpectrumIdentification element and the
> SpectrumResult elements.
I have added to the wiki

David

> 
>   Bye
>    Martin
> 

-- 
David Creasy
Matrix Science
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dc...@ma...
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