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

[<cod...@go...>]

Comment #55 on issue 42 by dcreasy: Issues with the CV
http://code.google.com/p/psi-pi/issues/detail?id=42

Um... in discussions with members of the mzML group it's always been agreed  
that this
is what we will be using. Last agreed and documented to use the id at a
teleconference (which Eric also attended) on 2nd October:
http://psidev.info/index.php?q=node/374

As you said above: "Really there's no nativeID for a merged spectrum, so  
anything we
come up with is a workaround." Am I missing something - are you you  
suggesting that
search engines should can not rely on the mzML id value and store this in  
output
files? The mzML schema documentation says, for the id:
<xs:documentation>A unique identifier for this spectrum. It should be  
expected that
external files may use this identifier together with the mzML filename or  
accession
to reference a particular spectrum.</xs:documentation>

Do you think that this is incorrect?

Also, to change the term from spectrumID -> nativeID would, I think be  
confusing. The
term makes perfect sense in the context of an mzML document, but for  
analysisXML it
could easily imply something native to the search engine rather than one of  
its input
files?

btw, the file format of all the input files (spectra, fasta, search engine  
outputs)
are all defined in the analysisXML documents (search on <pf:fileFormat>) so  
I'm not
sure what you mean. (Ah... I see that a couple of the examples seem to be  
missing
these - hopefully they will get corrected soon. Thanks for pointing this  
out.)

David

-- 
You received this message because you are listed in the owner
or CC fields of this issue, or because you starred this issue.
You may adjust your issue notification preferences at:
http://code.google.com/hosting/settings