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Re: [Psidev-pi-dev] unimod.obo and XSLT
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From: Henning H. <hen...@go...> - 2008-11-20 11:13:44
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Hi, David Creasy wrote: > Hi Sean, > > Sean L Seymour wrote: >> >> 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. > PSI-MOD doesn't include the MS mod names... and we've not been able to > get these added, so we just can't use it at the moment. I only glance through issues on this list, but I think the above might not be correct. Please check http://psidev.sourceforge.net/mod/data/PSI-MOD.obo and search for "PSI-MS-label". As far as I remember, these have been manually added explicitly for this purpose. -- Best regards, Henning > We intend to just use the MS mod names, but it's easier to validate it > if we have a .obo file. > (btw, I don't think that the .obo file is correct - I don't think that > want new ID's) > >> (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. > Yes, please join us if you can. Still some decisions to be made and it > would really help to have your input... You might like to read: > http://code.google.com/p/psi-pi/issues/detail?id=35 > http://code.google.com/p/psi-pi/issues/detail?id=3 > > > David >> >> Sean >> >> >> >> >> >> >> *"Martin Eisenacher" <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 >> >> >> ------------------------------------------------------------------------- >> This SF.Net email is sponsored by the Moblin Your Move Developer's >> challenge >> Build the coolest Linux based applications with Moblin SDK & win great >> prizes >> Grand prize is a trip for two to an Open Source event anywhere in the >> world >> http://moblin-contest.org/redirect.php?banner_id=100&url=/ >> _______________________________________________ >> Psidev-pi-dev mailing list >> Psi...@li... >> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev >> >> ------------------------------------------------------------------------ >> >> ------------------------------------------------------------------------- >> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge >> Build the coolest Linux based applications with Moblin SDK & win great prizes >> Grand prize is a trip for two to an Open Source event anywhere in the world >> http://moblin-contest.org/redirect.php?banner_id=100&url=/ >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Psidev-pi-dev mailing list >> Psi...@li... >> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev >> > > -- > David Creasy > Matrix Science > 64 Baker Street > London W1U 7GB, UK > Tel: +44 (0)20 7486 1050 > Fax: +44 (0)20 7224 1344 > > dc...@ma... > http://www.matrixscience.com > > Matrix Science Ltd. is registered in England and Wales > Company number 3533898 > > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge > Build the coolest Linux based applications with Moblin SDK & win great prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > > > ------------------------------------------------------------------------ > > _______________________________________________ > Psidev-pi-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev |
