petehr

petehr is your Personal Assistant for Creating Research-Ready EHR Data. A Python Toolkit for EHR Processing.

Features

• Text-to-Code Mapping: Convert medical text to standardized medical codes.
• Custom Dictionary Support: Integrate your own medical concept dictionary. For string to medical codes, we recommend using UMLS.
• Lightweight and Efficient: Designed for simplicity and speed in processing EHR data. Note: Negation detection is not available in this version.

Installation

pip install petehr

Usage

from petehr import Text2Code

# Dictionary is a two column CSV file with strings and their corresponding codes.
# Example of a sample String-CUI dictionary:

'''
str,code
Asthma,C0004096
Tuberculosis,C0041296
Tylenol,C0699142
Spinal fusion,C3278509
'''

mapper = Text2Code("sample_dict.csv")

# Convert text to a string of codes
codes = mapper.convert("Patient presents with a history of asthma and reports worsening asthma symptoms over the past.")

print(codes)  # Output: "C0004096,C0041296,C0699142,C3278509"