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Create file for PubChem deposition at every release #102

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schymane opened this issue Nov 21, 2019 · 4 comments

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@schymane
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@schymane schymane commented Nov 21, 2019

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.
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@sneumann sneumann commented Nov 21, 2019

Hi, we have started to embed bioschemas information,
e.g. Line 60+ in view-source:https://msbi.ipb-halle.de/MassBank/RecordDisplay2?id=PB006301
and I would prefer if PubChem adopts that. Benefit would be that this way
they can scrape other Bioschemas compatible stuff, I would reckon that Wikipathways
also embeds such information. Otherwise we end up generating and maintaining mappings for PubChem, ChemSpider, CompTox, ... separately. Yours, Steffen
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@schymane schymane commented Nov 21, 2019

Let's discuss with Evan and @egonw at Dagstuhl then ...
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@schymane schymane commented Nov 22, 2019

adding @AlasdairGray in to contribute his Bioschemas wisdom ...
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@egonw egonw commented Nov 22, 2019

@AlasdairGray, I guess a good first step forward is to have that aggregator website you just showed crawl the MassBank website and extract the chemical structures and data record JSON-LD.
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@schymane @sneumann @egonw
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