timosachsenberg / updateHMDB

update script for HMDB in OpenMS

This script updates HMDB for OpenMS

It generates a HMDBMappingFile.tsv and a HMDB2StructMapping.tsv that is used by the AccurateMassSearch

#Steps to do :

1. Download "All Metabolites" files as XML from http://www.hmdb.ca/downloads
   
2. extract into folder hmdb_metabolites
3. delete hmdb_metabolites.xml
4. execute python scripts:

python generateHMDB2StructMapping.py 
python generateHMDBMappingFile.py

Note : currently, there is one line that contains a UTF-8 Character, you have to edit it manually ( in the HMDB2StructMapping.tsv file)