UMLS scispacy

umls_sample.py

import scispacy
import spacy
from scispacy.abbreviation import AbbreviationDetector
from scispacy.umls_linking import UmlsEntityLinker
nlp = spacy.load("en_core_sci_sm")
#^^^ at this import you area looking at 9 GB RAM consumption 
#even before processing starts


# Add the abbreviation pipe to the spacy pipeline.
abbreviation_pipe = AbbreviationDetector(nlp)
nlp.add_pipe(abbreviation_pipe)
# Adding
# the AbbreviationDetector pipe and setting resolve_abbreviations to True means
# that linking will only be performed on the long form of abbreviations.
linker = UmlsEntityLinker(resolve_abbreviations=True)

nlp.add_pipe(linker)