Re: [Psidev-ms-dev] TraML: Proposing to use EDAM ontology for <Compound>

[Oliver K. <koh...@in...>]

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
> 
> 
> 
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---
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