Hi!
Thank you very much for your answer! I tried it but it seems that the new XML from HMDB most likely has some small mistakes concerning the tags:
File “generateHMDB2StructMapping.py”, line 28, in
for event, elem in context:
File “src/lxml/iterparse.pxi”, line 209, in lxml.etree.iterparse.next
File “hmdb_metabolites/hmdb_metabolites.xml”, line 18163858
lxml.etree.XMLSyntaxError: Opening and ending tag mismatch: kiNd line 65535 and kind, line 18163858, column 37
I will download hmdb again and re-try.