medcat.linking.context_based_linker

Module Contents

Classes

Linker

Link to a biomedical database.

Attributes

logger

medcat.linking.context_based_linker.logger

class medcat.linking.context_based_linker.Linker(cdb, vocab, config)

Bases: medcat.pipeline.pipe_runner.PipeRunner

Link to a biomedical database.

Parameters:

• cdb (CDB) – The Context Database.

• vocab (Vocab) – The vocabulary.

• config (Config) – The config.

name = 'cat_linker'

__init__(cdb, vocab, config)

Parameters:

• cdb (medcat.cdb.CDB) –

• vocab (medcat.vocab.Vocab) –

• config (medcat.config.Config) –

Return type:

None

_train(cui, entity, doc, add_negative=True)

Parameters:

• cui (str) –

• entity (spacy.tokens.Span) –

• doc (spacy.tokens.Doc) –

• add_negative (bool) –

Return type:

None

__call__(doc)

Parameters:

doc (spacy.tokens.Doc) –

Return type:

spacy.tokens.Doc