Question: Know Of Any Human Metabolomics Databases?
5
gravatar for Larry_Parnell
7.7 years ago by
Larry_Parnell16k
Boston, MA USA
Larry_Parnell16k wrote:

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.

database • 2.9k views
ADD COMMENTlink modified 3 months ago by Keiron O'Shea10 • written 7.7 years ago by Larry_Parnell16k
4
gravatar for Martijn Van Iersel
7.7 years ago by
Netherlands
Martijn Van Iersel560 wrote:

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

ADD COMMENTlink written 7.7 years ago by Martijn Van Iersel560

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

ADD REPLYlink written 7.7 years ago by Larry_Parnell16k

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.

ADD REPLYlink written 7.7 years ago by Larry_Parnell16k
3
gravatar for Treylathe
7.7 years ago by
Treylathe940
San Francisco
Treylathe940 wrote:

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.

ADD COMMENTlink written 7.7 years ago by Treylathe940

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.

ADD REPLYlink written 7.7 years ago by Larry_Parnell16k
2
gravatar for Chris Evelo
7.7 years ago by
Chris Evelo10.0k
Maastricht, The Netherlands
Chris Evelo10.0k wrote:

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.

ADD COMMENTlink written 7.7 years ago by Chris Evelo10.0k

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

ADD REPLYlink written 7.4 years ago by Egon Willighagen5.2k

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.

ADD REPLYlink written 7.4 years ago by Chris Evelo10.0k

This wiki no longer exists.

ADD REPLYlink written 3.3 years ago by Egon Willighagen5.2k
0
gravatar for Egon Willighagen
3.0 years ago by
Maastricht
Egon Willighagen5.2k wrote:

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

ADD COMMENTlink written 3.0 years ago by Egon Willighagen5.2k
0
gravatar for Keiron O'Shea
3 months ago by
Aberystwyth University
Keiron O'Shea10 wrote:

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
ADD COMMENTlink modified 3 months ago • written 3 months ago by Keiron O'Shea10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1669 users visited in the last hour