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Update of the BAFG spectral data#392

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olessmn wants to merge 2 commits into
MassBank:devfrom
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Open

Update of the BAFG spectral data#392
olessmn wants to merge 2 commits into
MassBank:devfrom
olessmn:dev

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@olessmn

@olessmn olessmn commented May 29, 2026

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Dear MassBank Team,

I would like to update the BAFG spectral data on MassBank.
This pull request includes:

Additional information:
Since August 2025, we regularly publish our spectral database on Zenodo (https://zenodo.org/records/20426911). This database (Collective Spectral Library; CSL) is a collaborative effort involving currently five laboratories in Germany.

I developed a package (https://github.com/bafg-bund/csl-tools) to export the spectral data of our database in the MassBank-format.

The version of the database and the package is written into the file, for example: MS$DATA_PROCESSING: COMMENT Export with csl-tools 1.1.0 and CSL_v26.2.

As we are constantly curating and correcting our records, it is easiest to regenerate all TXT files when exporting our records for MassBank. Therefore, the content of the TXT files may change; however, the file name (and accession ID) will remain unchanged.

Validator
This time I used your validator to correct issues before my pull request ;) (It helped a lot).
Only the following issue is left:

08:58:33 ERROR massbank.cli.Validator - Formula generated from InChI string in "CH$IUPAC" field does not match formula in "CH$FORMULA".
Formula from CH$IUPAC:   C18H19BrN6O5
Formula from CH$FORMULA: [C18H19BrN6O5]-
08:58:33 ERROR massbank.cli.Validator - ACCESSION: MSBNK-BAFG-CSL25011734712
08:58:33 ERROR massbank.cli.Validator - ^
08:58:33 ERROR massbank.cli.Validator - Error in file C:\Users\lessmann\Data\csl-tools\user\export\massbank\2026\BAFG\MSBNK-BAFG-CSL25011734712.txt at line 1.

In this case, we think that [C18H19BrN6O5]- is correct, as the compound was indeed measured at [M]-.

Questions

  • The validator did not allow CC BY 4.0 for the field LICENSE:, therefore we used CC BY. We would prefer adding the version (if possible). Or is there a reason for that?
  • After our last update, MassBank added this ChemOnt information to all records (e.g.: CH$LINK: ChemOnt CHEMONTID:0000331; Organic compounds; [...]
    I couldn't find that ChemOnt database, and didn't know how to integrate this information into our export tool. It is totally ok, if you can add it to the records, but then you may have to do it for every update (as our txt-files are regenerated).

Please let me know if the contribution requires further adjustments.
Thank you!
Best regards,
Ole

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