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Re: [Psidev-pi-dev] unimod.obo and XSLT
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From: Martin E. <mar...@ru...> - 2008-11-20 14:25:37
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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" <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 |
