loinchpo 1.1.2.dev2

Python version of LOINC2HPO

loinchpo

A simple and efficient library for mapping loinc test results to hpo terms.

Requirements

Python 3.5+

Installing with pip

pip install loinchpo

Installing with Conda

conda config --add channels conda-forge
conda config --set channel_priority strict
conda install loinchpo

Usage

Just three steps and you should be able to map your loinc codes to hpo.

1. Parse the annotations using AnnotationParser

A dictionary from file:

annotations = AnnotationParser.parse_annotation_file(annotation_path)

A list from file:

annotations = AnnotationParser.parse_annotation_file(annotation_path, ls=True)

A dictionary from pandas df:

annotations = AnnotationParser.parse_annotation(dataframe)

2. Parse the query files

File path returns a list of queries:

queries = QueryFileParser.parse(query_path)

Single query:

query = Query(loinc_id, outcome)

3. Resolve the hpo term

resolver = QueryResolver(annotations)
hpo_term = resolver.resolve(query)