Know Of Any Human Metabolomics Databases?

Question

[Larry_Parnell]

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.

Answer 1

[Martijn Van Iersel]

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

[Larry_Parnell]

Martijn, thank you for your suggestion. I know of HMDB and in fact it is the only such database I know. It is especially useful as most if not all values are for serum. +1

[Larry_Parnell]

With only 420 metabolites in its database, I find PathCase something to keep in mind, but not so useful for my intentions as HMDB. Now, on to the download to collect the protein:metabolite links.

Answer 2

[Treylathe]

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.

[Larry_Parnell]

Trey, thank you as well for your response. I have heard of Wishart's group, but knew nothing of PathCase. As I am thinking of clinical samples analyzed as part of phenotype measuring for our GWAS work, knowing the sample is important.

Answer 3

[Chris Evelo]

The [?]NuGOwiki[?] is an interesting initiative where they try to combine chemicai information (taken from HMDB) with biological information and make it available as a wiki.

[Egon Willighagen]

That looks like a very interesting resource? Who's behind the wiki? Email address? The wiki is devoid of information of copyright/licensing info...

[Chris Evelo]

NuGOwiki is an initiative from NuGO, the Nutrigenomics Organisation (see nugo.org). I think Jildau Bouwman at TNO Zeist leads the that. The licensing thing is probably just an omission.

[Egon Willighagen]

This wiki no longer exists.

Answer 4

[Egon Willighagen]

MetaboLights is a database for experimental metabolomics data. It's indexed by observed metabolites.

Answer 5

[Keiron O'Shea]

I've written up an integrated metabolomics database that facilitates inference through a simple to use REST API:

https://dimedb.ibers.aber.ac.uk/

There are also Python packages available for faster querying:

https://github.com/AberystwythSystemsBiology/dimedbpy

If you already have pip installed, you can install it quickly using the following command:

pip install dimedbpy