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sec2pri / mapping_preprocessing

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Update chemicalAllPrimary.rq #19

Closed tabbassidaloii closed 1 year ago

tabbassidaloii commented 1 year ago

We don't need the compound names

DeniseSl22 commented 1 year ago

Why not @tabbassidaloii ? I thought that was needed for the names2IDs? Wikidata has many more trivial names than ChEBI and HMDB for many compounds...

tabbassidaloii commented 1 year ago

There is a separate query "chemicalPrimarySynonyms.rq" for it, correct?

DeniseSl22 commented 1 year ago

Yes, I need to check if that one also takes out all Primary IDs which do not have a label....

DeniseSl22 commented 1 year ago

I remember again; if I add an "optional" for all the synonyms, the query times out.... So we have to perform two queries, one to get all Primary IDs (and their primary name if available), and one to get the synonyms (if available) for the primaries. @tabbassidaloii