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bridgedb / create-bridgedb-metabolites

Create BridgeDb identity mapping files from HMDB, ChEBI, and Wikidata
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Check retired LIPID MAPS IDs #32

Closed DeniseSl22 closed 3 years ago

DeniseSl22 commented 3 years ago

image

DeniseSl22 commented 3 years ago

More info:

"Removal of classes based on lipid source In keeping with the theme of having a classification scheme dictated by molecular structure and function, the sterol lipid subclasses Phytosterols, Marine sterols and Fungal sterols were retired because these refer to the lipid source (marine) or biological kingdom (plants,fungi). It is possible to identify a particular sterol in more than one of these 3 sources. These subclasses have been replaced by a new set of subclasses based on the carbon skeleton of the sterol core structure (Ergosterols, Gorgosterols, Furostanols,etc.). The details are outlined under the Sterol lipids section below." https://www.lipidmaps.org/data/classification/classification_updates.html

DeniseSl22 commented 3 years ago

The link above also mentions several other IDs which have been removed (do ctrl+f for removed)..... manual work for now, but I think it's worth looking into

egonw commented 3 years ago

That link is about classes. That's a lot harder and we don't have a lot of them in WikiPathways anyway.

egonw commented 3 years ago

Test added.