Spacy 3.0 - specify my own candidate generator to use custom UMLS path

[phil-oxenberg]

I'm in the process of updating my python project from using Spacy 2 to use Spacy 3. My project uses my own versions of Scispacy candidate_generation.py and linking_utils.py in order to use a custom version of concept_aliases.json and other UMLS data files. How do I accomplish this in Spacy 3?

In V2, I simply made copies of candidate_generation.py and linking_utils.py which referenced local copies of the KB data files and instantiated my version of candidate_generation.py and passed the object to the EntitlyLinker constructor like so:

_candidate_generator = CandidateGenerator()
_el = EntityLinker(resolve_abbreviations=True, name="umls",
                                        candidate_generator=_candidate_generator)

My candidate_generation.py, in turn, references my linking_utils.py.

[svlandeg]

Hi! This seems very scispacy-specific, so perhaps it would make more sense to ask advice there?

[phil-oxenberg]

Moved to here