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bridgedb / create-bridgedb-metabolites

Create BridgeDb identity mapping files from HMDB, ChEBI, and Wikidata
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HMDB secondary IDS #8

Closed DeniseSl22 closed 6 years ago

DeniseSl22 commented 6 years ago

In order to remove the secondary IDs from HMDB, I wrote a script in Python to obtain the secondary IDs from the XML file. The output (CSV) with in the first column Secondary ID and in the second column Primary ID, can now be run with a similar Jenkins test as the one for ChEBI.

The CSV should be updated with new HMDB updates (latest on was run on the end of march release of 2018).

DeniseSl22 commented 6 years ago

This issue is already mentioned in another repository (https://github.com/BiGCAT-UM/WikiPathwaysCurator/issues/1). I will close this issue, and keep on working in the other one.