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Published 20 hours ago • verified publisher icon rformassspectrometry

Define spectra table

Open jorainer opened this issue 7 years ago • 7 comments

Define the spectra database table to hold the spectrum data.

  • [ ] Check what is provided in SDF format (spectra there?).
  • [ ] Check what is provided by different providers (MoNa, HMDB)...

jorainer avatar Jun 27 '18 19:06 jorainer

OK, so we'd need:

  • spectrum_id
  • compound_id
  • polarity
  • collision_energy
  • predicted
  • mz
  • intensity
  • splash

For now I'll keep all in one huge table. we could eventually later split the table into a ms_ms_spectrum and ms_ms_spectrum_metadata table

removed columns (redundant with compound table).

  • precursor
  • name
  • formula
  • inchi
  • inchikey
  • smiles

jorainer avatar Jun 27 '18 20:06 jorainer

SPLASH?

stanstrup avatar Jun 27 '18 20:06 stanstrup

? SPLASH? what do you mean with that @stanstrup ?

jorainer avatar Jul 02 '18 07:07 jorainer

I meant this: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5515539/ It should be in the databases also I think.

stanstrup avatar Jul 02 '18 15:07 stanstrup

Good point. HMDB provides these right away, so I'll import.

jorainer avatar Jul 05 '18 08:07 jorainer

Note: for now I would just add MS/MS spectra and do not import NMR spectra yet... these will have anyway other fields and should then go eventually into another table.

jorainer avatar Jul 05 '18 09:07 jorainer

Note this picks up issue #17

jorainer avatar Nov 08 '18 06:11 jorainer