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

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Hi!

I updated the XSLT and unimod.obo in the svn as discussed in the conference.

For an excerpt of the oxidation term (the specificities are property_values) see below.
Of course, the 'property_value: spec_groupX="X"' entries can be dropped.
The names are unique as the UNIMOD ids are.

 Bye
   Martin

[Term]
id: UNIMOD:35
name: Oxidation
def: "Oxidation or Hydroxylation" [FindMod:HYDR RESID:AA0322 PMID:11212008 PMID:11120890 FindMod:DOPA FindMod:CSEA
PMID:14661084 RESID:AA0026 PMID:15569593 RESID:AA0205 RESID:AA0215 RESID:AA0029 RESID:AA0030 PMID:9004526 RESID:AA0028
PMID:11461766 RESID:AA0027 RESID:AA0235 RESID:AA0146 PMID:14661085 PMID:12781462 PMID:2057999 ]
property_value: record_id="35"
property_value: delta_mono_mass="15.994915"
property_value: delta_avge_mass="15.9994"
property_value: delta_composition="O"
property_value: username_of_poster="unimod"
property_value: group_of_poster="admin"
property_value: date_time_posted="2002-08-19 19:17:11"
property_value: date_time_modified="2008-02-15 05:37:07"
property_value: approved="false"
property_value: spec_group1="1"
property_value: spec_hidden_1="true"
property_value: spec_site_1="D"
property_value: spec_position_1="Anywhere"
property_value: spec_classification_1="Post-translational"
property_value: spec_group2="2"
property_value: spec_hidden_2="true"
property_value: spec_site_2="K"
property_value: spec_position_2="Anywhere"
property_value: spec_classification_2="Post-translational"
.

Von: David Creasy [mailto:dc...@ma...] 
Gesendet: Thursday, November 20, 2008 4:36 PM
An: Martin Eisenacher
Cc: 'Sean L Seymour'; psi...@li...
Betreff: Re: AW: [Psidev-pi-dev] unimod.obo and XSLT

Hi Martin, (& Sean)

Yes, you did exactly what we agreed, but maybe we were wrong.... 
I don't think that we need to include the specificity in the CV. So, for the found modifications we have:

   <Peptide id="peptide_2_4" sequenceMass="1614.774567" sequenceLength="13">
      <Modification location="1" residues="M" monoisotopicMassDelta="15.994919">
        <pf:cvParam accession="Oxidation" name="Oxidation" cvRef="PSI-MS-MOD" />
      </Modification>
      <Modification location="9" residues="M" monoisotopicMassDelta="15.994919">
        <pf:cvParam accession="Oxidation" name="Oxidation" cvRef="PSI-MS-MOD" />
      </Modification>
      <peptideSequence>MIKTGESGMTVFR</peptideSequence>
    </Peptide>
Which is fine (and as in the current schema). Having the specificity in the CV is a duplication here.

However, for the search modification we currently have:
        <SearchModification fixedMod="false" >
          <ModName   accession="MOD:TODO" name="Oxidation (M)" cvRef="UNIMOD" />
          <MassDelta value="15.994919" unitAccession="UO:0000221" unitName="Da" />
          <SpecificityRule accession="PI:00188" cvRef="PSI-PI" name="modification specificity variable" />
        </SearchModification>
and we have the following CV:

id: PI:00187, name: modification specificity fixed
id: PI:00188, name: modification specificity variable
id: PI:00189, name: modification specificity N-term
id: PI:00190, name: modification specificity C-term

How about we add a residues attribute to SearchModification and then remove all specificity from the CV? Does this sound
reasonable Sean?
Note that the PSI-MS-MOD names don't include any specificities.
(Also, we seem to now have a duplication of CV and attributes for fixed/variable...). 
Can we discuss further on the call?

David

Martin Eisenacher wrote: 
Hi!

(btw, I don't think that the .obo file is correct - I don't think that want new ID's)

You mean, we want to use the original unimod.xml-record_id?
But we agreed to have one OBO term for each (modification,specificity) pair.

  Bye
   Martin

"Martin Eisenacher"  <mailto:mar...@ru...> <mar...@ru...> 
11/19/2008 08:55 AM 
To
psi...@li... 
cc

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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