This script updates HMDB for OpenMS
It generates a HMDBMappingFile.tsv and a HMDB2StructMapping.tsv that is used by the AccurateMassSearch
#Steps to do :
- Download "All Metabolites" files as XML from http://www.hmdb.ca/downloads
- extract into folder hmdb_metabolites
- delete hmdb_metabolites.xml
- 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)