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i'm using Scispacy (which is awesome!) but when I type 'tau' into the app found here https://scispacy.apps.allenai.org/ the UMLS entity gives me the canonical name of 'MAPT gene' which is what I want. But when I do the exact same thing in my python code based on the app code (see here https://gist.github.com/DeNeutoy/b20860b40b9fa9d33675893c56afde42) the first canonical name on the list is 'uridine triacetate' (the second is 'MAPT gene')

in the app code there is the call 'if show_only_top:break' so I assume somehow their app implementation orders the linked entities differently.

if someone can explain the difference in ordering and how to fix that would be great thanks!!

Charlie Jeynes
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This question was also asked on github (https://github.com/allenai/scispacy/issues/344), and answered there, but I am including the answer below in case anyone ends up here.

The demo app is not currently running the latest version of scispacy, and the inconsistent ordering of the entities was an issue that was fixed in scispacy version 0.4.0.

dking
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