allenai / allenai/scispacy

Entity linking future directions

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enhancement
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I was wondering if you all had any thoughts on developments in the python ecosystem for entity linking since the original 2019 ScispaCy paper. I see a number of comparisons in it to MetaMap, some of the early code on adding native entity linking (https://github.com/allenai/scispacy/pull/72, https://github.com/allenai/scispacy/pull/88), and then lots of more recent requests for extensions to linking like https://github.com/allenai/scispacy/issues/428, https://github.com/allenai/scispacy/issues/346, and https://github.com/allenai/scispacy/issues/331 which all got me curious as to whether or not you all are aware of or have potentially considered other methods/libraries for NEN. [Gilda](https://github.com/indralab/gilda) ([paper](https://www.biorxiv.org/content/10.1101/2021.09.10.459803v1)) is one we've been experimenting with since its dependencies are relatively light and its offline execution time is definitely good enough for high-throughput NER + NEN pipelines. The sources/ontologies covered by it include a number that make a useful complement to what's supported in ScispaCy:

Screen Shot 2022-04-14 at 7 23 03 PM

I'm not really advocating for it, and I can't speak to the validity of the methodological differences between it and what you all have done, but I am curious if you all are watching other projects like this and considering either integrating them or pointing users at them if they are looking for support over more nomenclatures/ontologies.

Thanks in advance for any insight here and for all the work you've done on this library!

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