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Define spectra table #22

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jorainer opened this issue Jun 27, 2018 · 7 comments
Open
2 tasks

Define spectra table #22

jorainer opened this issue Jun 27, 2018 · 7 comments

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@jorainer
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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
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jorainer commented Jun 27, 2018 •
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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

@stanstrup
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SPLASH?

@jorainer
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jorainer commented Jul 2, 2018

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

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

@jorainer
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jorainer commented Jul 5, 2018

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

@jorainer
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jorainer commented Jul 5, 2018

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 added a commit that referenced this issue Jul 18, 2018
@jorainer
Expand query engine to support multiple database tables
6b9cf36 
- Enable storage of spectrum data in database tables (related to issue #22).
- Expand query engine to support queries starting from specific database tables.
- Add/update relevant documentation and unit tests.
@jorainer
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jorainer commented Nov 8, 2018

Note this picks up issue #17

@jorainer jorainer mentioned this issue Nov 8, 2018
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@stanstrup @jorainer