Wishart bank downloader (version 1.1.2)

What is the specific bank you want to download? :

All banks are extracted from downloads section on Whishart web portals.

Which output format do you need? :

Proposed formats are lighter than downloaded raw files and adapted to annotation tools.

Level of script verbose :

Information about script running.

Authors Charlotte Joly, Delphine Centeno, Lain Pavot, Yann Guitton and Franck Giacomoni

Please cite If you use this tool, please add the following reference: Wishart DS, Guo AC, Oler E, et al., HMDB 5.0: the Human Metabolome Database for 2022. Nucleic Acids Res. 2022. Jan 7;50(D1):D622–31.

HMDB bank downloader

Description

Download a bank containing information (like : HMDB id, Name, mz, inchikey)

from HMDB online web portal and convert it into W4M annotation tool input formats.

Workflow position

/repository/static/images/d0b8faa0bc3e3a01/.%2Fstatic%2Fimages%2Fmetabolomics%2Fhmdb.png

Parameters

What is the specific bank you want to download: Choose whether specific metabolite banks:

Urine

Serum

cerebrospinal fluid

...
Which output format do you need: tabular : for W4M BiH annotation tool as example

json : still in construction

Output files

Two types of files: REF_HMDB_BANKNAME.tabular: for W4M BiH annotation tool as example

Working example

Refer to the corresponding W4M HowTo section: http://workflow4metabolomics.org/howto: Format Data For Postprocessing

Perform LCMS Annotations

And their "W4M courses 2020":: Using Galaxy4Metabolomics - W4M table format for Galaxy

Annotation Banks - Annotation