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

[Steffen N. <sne...@ip...>]

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
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                                  +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409