How to update MB2HMDBmapping.csv?

[jpfeuffer]

@timosachsenberg How was this generated in the first place?

[timosachsenberg]

Didn't try it but was suspecting that https://github.com/OpenMS/MassBankUpdate does

[jpfeuffer]

The issue is for this repository ;) It does not.

[timosachsenberg]

"Note : For updating MB2HMDBmapping.csv you need to update HMDB first : https://github.com/epoyraz/updateHMDB"
is it just a simple linux command maybe? Otherwise I can try to get in contact with the student again.

[jpfeuffer]

I don't fing any script that would do that

[epoyraz]

if i remember correctly, this would generate it:
https://github.com/epoyraz/updateHMDB/blob/master/generateHMDBMappingFile.py

[timosachsenberg]

I think this only generates the HMDBMappingFile but not the map between mass bank and hmdb

[epoyraz]

I vaguely remember that there was not a single .xml file, but thousands of metabocard (?) files.
So the script might needs some update :)

[epoyraz]

I think this only generates the HMDBMappingFile but not the map between mass bank and hmdb

yeah, you are right.

The mapping itself is done via the InChI (if i remember correctly).

This is the first entry. They have the same InChI

• https://massbank.eu/MassBank/RecordDisplay?id=AU107701
• https://hmdb.ca/metabolites/HMDB0001830

Unfortunately, i don't have any more than:

• https://github.com/epoyraz/MassBankUpdate
• https://github.com/epoyraz/updateHMDB

i might have missed to put the script for the MB2HMDBmapping.csv