Install METLIN locally

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Install METLIN locally

October 21, 2011, 03:15:41 AM

Hello,

I was wondering if there is a version of METLIN (even a limited one) that can be downloaded and installed on a local server (using SQL dumps or other flat files), similar to the ChEBI database. As I am trying to build an analysis/annotation pipeline for the lab I work, it would be really useful. Otherwise, is there a programmatic access to METLIN outside the web interface? Thanks in advance!

Panos

Re: Install METLIN locally

Reply #1 – October 21, 2011, 03:26:06 AM

Dear Panos,

First of all, thank you for using METLIN as one of your metabolomic data search. Unfortunately, we do not offer any downloadable database nor local installation. However, we offer a batch search that allows you to search many distinct masses at the same time with multiple adducts as targets. Hopefully, this resolves your issues. Please do not hesitate to contact me if you have any questions.

Re: Install METLIN locally

Reply #2 – October 21, 2011, 04:15:21 AM

Thanks for the quick reply. Unfortunately, the batch search from the website is not very helpful as long as there isn't any programmatic access to it (e.g. in the form of a PHP query), since I would like to incorporate the search in a pipeline. Or is there some kind of programmatic access? Thanks again!

Re: Install METLIN locally

Reply #3 – October 21, 2011, 12:44:36 PM

Hi,

Quote from: "panos"

Unfortunately, the batch search from the website is not very helpful as long as there isn't any programmatic access to it

Look out for the SOAP interface,
http://metlin.scripps.edu/soap/

Yours,
Steffen

Re: Install METLIN locally

Reply #4 – October 21, 2011, 07:53:01 PM

We are currently updating and improving the database. The recent modifications are not reflected in the SOAP interface yet. We are hoping to bring it back online once the update process is complete.

Re: Install METLIN locally

Reply #5 – October 24, 2011, 03:44:30 AM

Hi,

Thanks for the replies. I have looked in the past a little bit on the SOAP interface. It should get part of my job done but it would be nice if you could post at some time an example of how it can be used from R (if it is possible) using e.g. RSOAP. I believe that there are many people out there who would benefit from a more complete programmatic access to METLIN as it represents a great data source... Thanks again.

Panos

Re: Install METLIN locally

Reply #6 – November 15, 2011, 04:25:06 PM

I am also wanting to access the database programmatically. Is the SOAP interface back online?

Cheers,
Chris

Re: Install METLIN locally

Reply #7 – November 15, 2011, 05:02:07 PM

Hi Chris,

SOAP Interface is not available at the moment, we will announce the service when it will be available. Please check the website occasionally.

Thank you,
Kevin

Re: Install METLIN locally

Reply #8 – November 15, 2011, 08:24:14 PM

Cheers Kevin, thanks for your reply.

Re: Install METLIN locally

Reply #9 – September 20, 2012, 07:36:53 PM

Hi

First of all, thanks for a great tool!

Is there a chance that you would add the option for advanced batch search? I have an extensive list of compounds (KEGG id), and I would like to know if they are in the Metlin database (result=1) or not (result=0). I can do the advanced search for KEGG ids but only one at a time and with 3k+ compounds that is going to take a long time.

I think this extension can be useful in order to verify that the mass spectrometry results do not contain a certain compound because it is not there and not only because it is not in the Metlin database.

Thanks in advance.