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

# Ensure conda-forge is in your channels
conda config --add channels conda-forge
conda config --set channel_priority strict

# Install the package
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

    # returns a list of the annotations
    annotations = AnnotationParser.parse_annotation_file(annotation_path)

    # returns a dictionary query mapper
    annotations = AnnotationParser.parse_annotation_file_dict(annotation_path)

    # returns a dictionary query mapper from a pandas dataframe
    annotations = AnnotationParser.parse_annotation_pandas(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

    # Resolve the hpo term.
    resolver = QueryResolver(annotations)
    hpo_term = resolver.resolve(query)