Re: [Psidev-pi-dev] unimod.obo and XSLT

[Sean L S. <Sey...@ap...>]

Hi All,

I'm rather confused by this decision. (1) Why don't we just use the MS mod 
synonym names that we already worked hard to establish (already have 
accessions as part of PSI-Mod), or is this what you mean by Unimod? If so, 
I don't think they should be called Unimod. (2) Are you really going to 
include the specificity in the accession assigned item? Or is this an 
issue about how modification search setting are indicated, not how 
modifications that have been detected are indicated in the results? I'll 
try to make the meeting tomorrow if it's easier to just set me straight by 
a short discussion than writing it out.

Sean







"Martin Eisenacher" <mar...@ru...> 
11/19/2008 08:55 AM

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Subject
[Psidev-pi-dev] unimod.obo and XSLT






Hi all!

To report modifications of resulting peptides we want to use unimod.

I assembled a XSLT to transform the XML from
http://www.unimod.org/xml/unimod.xml
to a unimod.obo (e.g. with XMLSpy).

For each (modification,specificity) pair an OBO term was created
(technically: a (umod:mod,spec_group) pair was transformed into a term 
with 
a unique accession. For XSLT simplicity the accessions were created as
"PI-UNIMOD:"+record_id+"0"+spec_group, which creates gaps between
accession numbers, but ensures uniqueness).

Only the umod:xref elements PMID, RESID and FindMod are transformed to 
Dbxrefs in 
obo; some of them had an invalid type in the XML, which I corrected
(I will report these to the unimod people).

Other umod:xrefs like "Misc. URL", "Book" or "Other" can be transformed
to property_values later.

I added unimod.obo and unimodXML2OBO.xsl 
to http://code.google.com/p/psi-pi/source/browse/#svn/trunk/cv

Hope that helps...

 Bye
   Martin


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