[Psidev-pi-dev] Issue 42 in psi-pi: Issues with the CV

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Comment #43 on issue 42 by dcreasy: Issues with the CV
http://code.google.com/p/psi-pi/issues/detail?id=42

Hi Matt,

Surprised to get any reply from you at all yesterday ;)
You are right, we kind of side stepped the issue of non mzML/mzData input  
formats at
the time, so it's important to hammer it out now. And yes, you are quite  
right, we
should try and support things as generally as possible. Incidentally, my  
proposal for
the CV wasn't quite as narrow as you suggest: MGF->DAT->analysisXML, it  
could be any
engine or format (or no intermediate file) in the middle.

I actually had a slightly different use case in mind - it wasn't for a  
generic
automated pipeline (which as you say is impossible to do reliably), but  
more for
'manual' inspection. So, if someone sees something 'interesting' they stand  
a chance
of finding the original data manually with as few intermediate files as  
possible.
However, you've got me thinking... suppose someone was writing a pipeline.  
They had
MGF files consistently generated by software 'X' and they were using 3  
different
search engines that output analysisXML files. They would surely rather that  
the
identifiers in the analysisXML files were of a consistent format using CV  
rather than
differing format using user params?

I guess I'm not keen on the nativeID idea for the MGF because I couldn't  
see how it
could be implemented retrospectively without the MGF files. Requiring that  
people
re-search their data seems a little harsh. Also, there's bound to be a time  
period
before mzML is widely supported.
For .pkl and concatenated .dta files, there is no option, so I've not  
proposed any
CV. For single dta files, there is no need for CV because it's multiple  
files and we
have the filename. Excuse my ignorance, but what's MS[12]? Is there a  
guaranteed
unique ID for mzXML?

David

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