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Discuss the change from pubchemid to chebi URI #59

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Gonza10V opened this issue Nov 7, 2021 · 0 comments

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Gonza10V commented Nov 7, 2021

To transform Flapjack chemicals into SBOL simple chemicals we need to add the ChEBI ontology URI but we collect PubChem CID in Flapjack.

I see two options, look for a mapping from one to the other. PubChem CID items have a Chebi source but I dont know if there is a tool to do it or we need to do it using web scrapping. Example Homoserine lactone (https://pubchem.ncbi.nlm.nih.gov/compound/73509) is related to https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:17289
The second option is just to change the Chemical input on Flapjack.

Gonza10V added the help wanted label

Gonza10V assigned timrudge and gyanezfeliu

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