Metabolomics challenge: Shared metabolites, or those coming from different pathways, or used by multiple biosynthetic pathways are understandably difficult to put in there. But with unique metabolites and for those which have 1-2 isoforms why a tool is not yet developed to map them directly to chromosomal locations (and genes) in models (say, A. thaliana or Humans) ? Would not it provide more insights into co-regulation of groups/ clustered appearance/ depletion of metabolites ? Just like KEGG-mapping or Paintomics ? Please advice if any such tools exist already (and am unaware of!) !
I am venturing this one, but perhaps it's because there isn't a one to one correspondence between genes and metabolites. Some metabolites could be generated by more than one enzyme depending on the activated pathway. Having said this a catalog with redundant entries still would not be a bad idea and I think you can find something like that in MSIGDB.
I havent tried doing this earlier, but when I have to convert or map identifiers for proteins or genes, I use Uniprot mapping tool.
Chromosome maps are custom made CGI tools basically using some already available perl tools and a CGI or PHP interface to run command from server.
If you are sure there is a relation table existing for A. thaliana and KEGG we can make custom tools for direct integration for KEGG to arabidopsis map.
Meanwhile try TAIR seqviewer
http://tairvm09.tacc.utexas.edu/servlets/sv
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