get_scispacy_entity_linker

get_scispacy_entity_linker(prefix, *, ontology_kwargs=None, candidate_generator_kwargs=None, **entity_linker_kwargs)

Get an entity linker for usage with scispacy.

Parameters:

• prefix (str) – The ontology’s prefix, such as go` for Gene Ontology, ``doid for the Disease Ontology, or more.

• ontology_kwargs (GetOntologyKwargs | None) – keyword arguments to pass to pyobo.get_ontology(), such as version.

• candidate_generator_kwargs (dict[str, Any] | None) – keyword arguments to pass to scispacy.candidate_generation.CandidateGenerator, such as ef_search

• entity_linker_kwargs (Any) – keyword arguments to pass to scispacy.linking.EntityLinker, such as ef_search

Returns:

An object that can be applied in a spacy natural language processing workflow, namely to apply grounding/named entity normalization to recognized named entities.

Return type:

EntityLinker