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Create file for PubChem deposition at every release

Open schymane opened this issue 5 years ago • 9 comments

It would be great if we could auto-create a file to deposit in PubChem with every stable release of MassBank-data. To discuss: compound information only (=> relatively easy) or mappings with spectral IDs (slightly more info needed) or actual spectra as well (more work our side). Shall we start with getting a deposit file for compound information only? Then we need e.g.:

PUBCHEM_EXT_DATASOURCE_REGID <= InChIKey, or any unique identifier our side PUBCHEM_EXT_DATASOURCE_SMILES <= SMILES PUBCHEM_EXT_DATASOURCE_CID <= PubChem CID (if available) PUBCHEM_SUBSTANCE_COMMENT <= here we could e.g. provide accession IDs, collapsed PUBCHEM_SUBSTANCE_SYNONYM <= any names our side (can have multiple columns, but maybe e.g. max 3 would be sensible)

@meier-rene @sneumann @tsufz what do you think? If yes, who will look after the file? I would contact PubChem to get us a MassBank login for deposition, so credit goes to MassBank(EU) and we can track our submissions.

schymane avatar Nov 21 '19 16:11 schymane