This subfolder is the home for code related to deposition and annotation of MassBank.EU in PubChem.

The MassBankEU_Export.R script runs on a local copy of MassBank-data and creates files for deposition and annotation.

Deposition

The file MASSBANK_DATA_SUMMARY_MSMS_Unique_Substances.csv is specific to PubChem (has PubChem-specific headers) and has a few SMILES removed (see badlist files). When newly generated, this should be copied to the ECI server \Misc\from_mb_to_pb where it should be detected and sent to the PubChem FTP server ...

Should we need to revoke substances, just expand the delete substances menu item in PubChem Docs to find out how.

Annotation

Updated annotation files should be deposited on the PubChem-MassBank Zenodo record and MassBank_File_Locations.txt should be updated. If any fields change, update the Categories and Display Fields files too, if needed. Let Jeff know when updated files are available (updates are currently manual).

Contacts

• ECI: E. Schymanski, T. Kondic, A. Elapavalore
• PubChem: E. Bolton, B. Shoemaker (deposition), J. Zhang (annotation)