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cui: Concept uniqe ID
source_val: Source value in the text
text: the text of a document where source_val was found
"""
# First add the name, get bac all cuis that link to this name
all_cuis = self._add_name(cui, source_val, is_pref_name, only_new=only_new, desc=desc, tui=tui)
# Now add context if text is present
if (text is not None and (source_val in text or text_inds)) or \
(spacy_doc is not None and (text_inds or tkn_inds)):
if spacy_doc is None:
spacy_doc = self(text)
if tkn_inds is None:
tkn_inds = tkn_inds_from_doc(spacy_doc=spacy_doc, text_inds=text_inds,
source_val=source_val)
if tkn_inds is not None and len(tkn_inds) > 0:
self.add_concept_cntx(cui, text, tkn_inds, spacy_doc=spacy_doc, lr=lr, anneal=anneal,
negative=negative)
if manually_created:
all_cuis.remove(cui)
for _cui in all_cuis:
self.add_concept_cntx(_cui, text, tkn_inds, spacy_doc=spacy_doc, lr=lr, anneal=anneal,
negative=True)
in the current CDB.
Examples:
Do not use.
'''
# First add the name, get bac all cuis that link to this name
all_cuis = self._add_name(cui, source_val, is_pref_name, only_new=only_new, desc=desc, tui=tui)
# Now add context if text is present
if (text is not None and (source_val in text or text_inds)) or \
(spacy_doc is not None and (text_inds or tkn_inds)):
if spacy_doc is None:
spacy_doc = self(text)
if tkn_inds is None:
tkn_inds = tkn_inds_from_doc(spacy_doc=spacy_doc, text_inds=text_inds,
source_val=source_val)
if tkn_inds is not None and len(tkn_inds) > 0:
self.add_concept_cntx(cui, text, tkn_inds, spacy_doc=spacy_doc, lr=lr, anneal=anneal,
negative=negative)
if manually_created:
all_cuis.remove(cui)
for _cui in all_cuis:
self.add_concept_cntx(_cui, text, tkn_inds, spacy_doc=spacy_doc, lr=lr, anneal=anneal,
negative=True)