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Re: [Psidev-pi-dev] unimod.obo and XSLT
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From: David C. <dc...@ma...> - 2008-11-20 15:35:37
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Hi Martin, (& Sean)<br>
<br>
Yes, you did exactly what we agreed, but maybe we were wrong.... <br>
I don't think that we need to include the specificity in the CV. So,
for the found modifications we have:<br>
<br>
<tt> <Peptide id="peptide_2_4" sequenceMass="1614.774567"
sequenceLength="13"><br>
<Modification location="1" residues="M"
monoisotopicMassDelta="15.994919"><br>
<pf:cvParam accession="Oxidation" name="Oxidation"
cvRef="PSI-MS-MOD" /><br>
</Modification><br>
<Modification location="9" residues="M"
monoisotopicMassDelta="15.994919"><br>
</tt><tt> <pf:cvParam accession="Oxidation" name="Oxidation"
cvRef="PSI-MS-MOD" /><br>
</tt><tt> </Modification><br>
<peptideSequence>MIKTGESGMTVFR</peptideSequence><br>
</Peptide><br>
</tt>Which is fine (and as in the current schema). Having the
specificity in the CV is a duplication here.<br>
<br>
However, for the search modification we currently have:<br>
<tt> <SearchModification fixedMod="false" ><br>
<ModName accession="MOD:TODO" name="Oxidation (M)"
cvRef="UNIMOD" /><br>
<MassDelta value="15.994919" unitAccession="UO:0000221"
unitName="Da" /><br>
<SpecificityRule accession="PI:00188" cvRef="PSI-PI"
name="modification specificity variable" /><br>
</SearchModification><br>
</tt>and we have the following CV:<br>
<br>
id: PI:00187, name: modification specificity fixed<br>
id: PI:00188, name: modification specificity variable<br>
id: PI:00189, name: modification specificity N-term<br>
id: PI:00190, name: modification specificity C-term<br>
<br>
How about we add a residues attribute to SearchModification and then
remove all specificity from the CV? Does this sound reasonable Sean?<br>
Note that the PSI-MS-MOD names don't include any specificities.<br>
(Also, we seem to now have a duplication of CV and attributes for
fixed/variable...). <br>
Can we discuss further on the call?<br>
<br>
David<br>
<br>
Martin Eisenacher wrote:
<blockquote
cite="mid:002b01c94b1b$d9f4f780$8ddee680$@eis...@ru..."
type="cite">
<pre wrap="">Hi!
</pre>
<blockquote type="cite">
<pre wrap="">(btw, I don't think that the .obo file is correct - I don't think that want new ID's)
</pre>
</blockquote>
<pre wrap=""><!---->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" <a class="moz-txt-link-rfc2396E" href="mailto:mar...@ru..."><mar...@ru...></a>
11/19/2008 08:55 AM
To
<a class="moz-txt-link-abbreviated" href="mailto:psi...@li...">psi...@li...</a>
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
<a class="moz-txt-link-freetext" href="http://www.unimod.org/xml/unimod.xml">http://www.unimod.org/xml/unimod.xml</a>
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 <a class="moz-txt-link-freetext" href="http://code.google.com/p/psi-pi/source/browse/#svn/trunk/cv">http://code.google.com/p/psi-pi/source/browse/#svn/trunk/cv</a>
Hope that helps...
Bye
Martin
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</pre>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
David Creasy
Matrix Science
64 Baker Street
London W1U 7GB, UK
Tel: +44 (0)20 7486 1050
Fax: +44 (0)20 7224 1344
<a class="moz-txt-link-abbreviated" href="mailto:dc...@ma...">dc...@ma...</a>
<a class="moz-txt-link-freetext" href="http://www.matrixscience.com">http://www.matrixscience.com</a>
Matrix Science Ltd. is registered in England and Wales
Company number 3533898</pre>
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