txt2hpo 2021.0

HPO concept recognition and phenotype extraction tool

txt2hpo

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.

Installation

Install using pip

pip install txt2hpo

Install from GitHub

git clone https://github.com/GeneDx/txt2hpo.git
cd txt2hpo
python setup.py install

Library usage

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"}]'