txt2hpo is a Python library for extracting HPO-encoded phenotypes from text.
txt2hpo recognizes differences in inflection (e.g. hypotonic vs. hypotonia), handles negation and comes with a built-in medical spellchecker.
Install using pip
pip install txt2hpo
Install from GitHub
git clone https://github.com/GeneDx/txt2hpo.git
cd txt2hpo
python setup.py install
from txt2hpo.extract import Extractor
extract = Extractor()
result = extract.hpo("patient with developmental delay and hypotonia")
print(result.hpids)
["HP:0001263", "HP:0001290"]
txt2hpo will attempt to correct spelling errors by default, at the cost of slower processing.
This feature can be turned off by setting the correct_spelling flag to False.
from txt2hpo.extract import Extractor
extract = Extractor(correct_spelling = False)
result = extract.hpo("patient with devlopental delay and hyptonia")
print(result.hpids)
[]
txt2hpo handles negation using negspaCy. To remove negated phenotypes set remove_negated flag to True.
Both the extracted and negated HPO terms can be retrieved.
from txt2hpo.extract import Extractor
extract = Extractor(remove_negated=True)
result = extract.hpo("patient has developmental delay but no hypotonia")
print(result.hpids)
["HP:0001263"]
print(result.negated_hpids)
["HP:0001252"]
txt2hpo picks the longest overlapping phenotype by default. To disable this feature set remove_overlapping flag to False.
from txt2hpo.extract import Extractor
extract = Extractor(remove_overlapping=False)
result = extract.hpo("patient with polycystic kidney disease")
print(result.hpids)
["HP:0000113", "HP:0000112"]
extract = Extractor(remove_overlapping=True)
result = extract.hpo("patient with polycystic kidney disease")
print(result.hpids)
["HP:0000113"]
txt2hpo outputs a valid JSON string, which contains information about extracted HPIDs, their character span and matched string.
from txt2hpo.extract import Extractor
extract = Extractor()
result = extract.hpo("patient with developmental delay and hypotonia")
print(result.json)
'[{"hpid": ["HP:0001290"], "index": [37, 46], "matched": "hypotonia"},
{"hpid": ["HP:0001263"], "index": [13, 32], "matched": "developmental delay"}]'