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Re: [Psidev-ms-dev] TraML: Proposing to use EDAM ontology for <Compound>
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From: Jon I. <ji...@eb...> - 2012-01-31 13:49:19
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Dear chaps I guess using ontology definitions is a good thing if you have the resources to do it and the ontologies you want are up to scratch. Anyhow, to reiterate what Matus said, if you decide on that route, then we'll very gladly add whatever new identifiers, formats or anything else that you might need. The idea in any case is that EDAM will provide a comprehensive catalogue of all common data identifiers and formats. So, please feel free to keep in touch! Cheers Jon > Hi Steffen, > > Oliver explained the way we tried to solve it in the case of mzTab. > > There have been several e-mails and conversations in the past about the general problem here and > this is the adaptation of proteomics data format (such as traML or mzML) to work with metabolomics > data. For instance, our colleagues here at the EBI (the group headed by C. Steinbeck) are going to > use mzML and also mzTab for the MS derived data because there is not much well established in the > metabolomics field. > > So the general problem is should we really try to move this really forward? This of course would > mean a lot of extra work like, you say, working with new ontologies. But in my opinion is > something that will need to get done sooner or later. > > I would like to know your opinion on this. Anyone else's opinion is of course also welcome. Maybe, > a lot of things have already been done and I am not aware of them. > > Thanks, > > Juan > > > On 25 Jan 2012, at 15:06, Oliver Kohlbacher wrote: > >> Steffen, >> >> you might want to have a look at the mzTab specification, more precisely >> at the 'small molecule table' therein. >> The approach chosen there is rather pragmatic: a database ID and a chemical >> formula. Chemical formula is of course well specified and for most practical >> purposes database IDs like PubChem or HMDB are entirely sufficient imho. >> >> http://code.google.com/p/mztab/wiki/FileFormat#Format_Specification >> >> CHeers, >> Oliver >> >> >> On Jan 25, 2012, at 3:12 PM, Steffen Neumann wrote: >> >>> Hi, >>> >>> I am currently preparing a set of MRM Transitions >>> as showcase for TraML in Metabolomics. >>> >>> I'll need to specify for which <Compound> a transition >>> was obtained. Currently, we only have cvParams >>> for "predicted isoelectric point", "theoretical mass" >>> and children of "chemical compound formula": >>> http://www.peptideatlas.org/schemas/TraML/1.0.0/TraML1.0.0.html#Compound >>> >>> This is a) far from complete, and b) underspecified, >>> because MS:1000867 "structural formula" does not specify >>> whether the value shall be SMILES, InChI or whatever. >>> >>> Is there a way to embrace (pun intended :-) >>> the EDAM (EMBRACE Data and Methods) ontology of [...] identifiers >>> for <Compound> ? Then we'd have something like this: >>> >>> <TraML> >>> <cv URI="http://edamontology.org/ontology?format=obo" >>> fullName="EDAM (EMBRACE Data And Methods)" id="EDAM" version="unknown" /> >>> ... >>> <Compound> >>> <cvParam accession="EDAM_data:1172" cvRef="EDAM" name="PubChem CID" value="932" /> >>> </Compound> >>> >>> EDAM has entries for a gazillion different compound identifiers: >>> http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=EDAM&termId=EDAM_data:1086&termName=Compound%20identifier >>> >>> and InChI, SMILES, molecular formula: >>> http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=EDAM&termId=EDAM_format%3A2035&termName=Chemical%20formula%20format >>> >>> The only downside I can see is that the converters and validators >>> need to slurp in another ontology of respectable size. >>> >>> Thoughts ? >>> >>> Yours, >>> Steffen >>> >>> >>> -- >>> IPB Halle AG Massenspektrometrie & Bioinformatik >>> Dr. Steffen Neumann http://www.IPB-Halle.DE >>> Weinberg 3 http://msbi.bic-gh.de >>> 06120 Halle Tel. +49 (0) 345 5582 - 1470 >>> +49 (0) 345 5582 - 0 >>> sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> Keep Your Developer Skills Current with LearnDevNow! >>> The most comprehensive online learning library for Microsoft developers >>> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, >>> Metro Style Apps, more. Free future releases when you subscribe now! >>> http://p.sf.net/sfu/learndevnow-d2d >>> _______________________________________________ >>> Psidev-ms-dev mailing list >>> Psi...@li... >>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev >> >> --- >> Oliver Kohlbacher (oli...@un...) >> Professor, Applied Bioinformatics, Center for Bioinformatics Tuebingen >> Dept. of Computer Science, University of Tuebingen >> phone: +49-7071-29-70457 http://abi.inf.uni-tuebingen.de >> >> vCard at: http://abi.inf.uni-tuebingen.de/People/kohlbach/vCard >> >> >> >> >> >> >> >> >> >> >> >> ------------------------------------------------------------------------------ >> Keep Your Developer Skills Current with LearnDevNow! >> The most comprehensive online learning library for Microsoft developers >> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, >> Metro Style Apps, more. Free future releases when you subscribe now! >> http://p.sf.net/sfu/learndevnow-d2d >> _______________________________________________ >> Psidev-ms-dev mailing list >> Psi...@li... >> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev > > |
