Similar to this previous question on databases capturing chemical compound interactions with other biological structures, but extending from that to tissue- or sample-specific data, I would like to know which databases you recommend for human metabolomics data. In other words, while MetaCyc, KEGG and others are useful, I wish to learn which compounds have been detected in, for example, human plasma, urine or saliva, or from a specific tissue.
HMDB, the human metabolite database is an excellent resource on human metabolites. Each metabolite has a metabocard, which also lists the biofluids that it occurs in.
For some metabolites it also lists physiological concentrations. For example: Urea
HMDB is a good one of course
These also might help,there's PathCase: http://nashua.case.edu/PathwaysMAW/Web/ which allows a user to browse and search by metabolites, view in pathways, etc.
Polysearch isn't particularly a metabolomics database, but you can search several databases by metabolite of interest: http://wishart.biology.ualberta.ca/polysearch/index.htm
Unfortunately, neither seems to have a way to find which metabolites are in a particular sample or tissue. I'm not sure of any others.
I've written up an integrated metabolomics database that facilitates inference through a simple to use REST API:
There are also Python packages available for faster querying:
If you already have pip installed, you can install it quickly using the following command:
pip install dimedbpy