Category: FHIR

Using Python to Parse HL7 and CCD Documents in Healthcare

By Stephen Fitzmeyer, MD

Python is a powerful programming language that can be used to parse and manipulate healthcare data in the HL7 and CCD formats. In this article, we will explore how to use Python to extract and process data from HL7 and CCD documents.

First, let’s start by understanding the structure of HL7 and CCD documents. HL7 messages are comprised of segments, which contain fields and subfields that represent different types of data. CCD documents, on the other hand, are based on the HL7 Clinical Document Architecture (CDA) standard and use XML to represent the data.

To parse HL7 messages in Python, we can use the hl7apy library, which is an open-source Python library for working with HL7 messages. Here’s an example of how to use hl7apy to extract patient demographic information from an HL7 message:

from hl7apy.parser import parse_message

# Parse the HL7 message

msg = parse_message(‘MSH|^~\&|HIS|BLG|LIS|BLG|20200528163415||ADT^A04|MSG0001|P|2.3||||||UNICODE’)

# Get the patient name

patient_name = msg.pid[5][0].value

# Get the patient date of birth

dob = msg.pid[7].value

# Get the patient sex

sex = msg.pid[8].value

# Print the patient information

print(“Patient Name: ” + patient_name)

print(“Date of Birth: ” + dob)

print(“Sex: ” + sex)

##########

In this example, we’re using the parse_message() method from the hl7apy library to parse the HL7 message. We then use the message object to extract the patient name, date of birth, and sex from the PID segment.

To parse CCD documents in Python, we can use the ElementTree library, which is included in the Python standard library. Here’s an example of how to use ElementTree to extract medication information from a CCD document:

import xml.etree.ElementTree as ET

# Parse the CCD document

tree = ET.parse(‘ccd.xml’)

# Get the medication section

medications = tree.findall(‘.//{urn:hl7-org:v3}section[@code=”10160-0″]/{urn:hl7-org:v3}entry/{urn:hl7-org:v3}substanceAdministration’)

# Print the medication information

for med in medications:

    drug_name = med.find(‘{urn:hl7-org:v3}consumable/{urn:hl7-org:v3}manufacturedProduct/{urn:hl7-org:v3}manufacturedMaterial/{urn:hl7-org:v3}name/{urn:hl7-org:v3}part’).text

    dosage = med.find(‘{urn:hl7-org:v3}doseQuantity/{urn:hl7-org:v3}value’).text

    start_date = med.find(‘{urn:hl7-org:v3}effectiveTime/{urn:hl7-org:v3}low’).attrib[‘value’]

    end_date = med.find(‘{urn:hl7-org:v3}effectiveTime/{urn:hl7-org:v3}high’).attrib[‘value’]

    print(“Drug Name: ” + drug_name)

    print(“Dosage: ” + dosage)

    print(“Start Date: ” + start_date)

    print(“End Date: ” + end_date)

   ##########

In this example, we’re using the findall() method from the ElementTree library to find all the medication sections in the CCD document. We then use the find() method to extract the drug name, dosage, start and end date for each medication and print out the results.

Using Python to parse HL7 and CCD documents can be very useful in healthcare applications. For example, we can use these techniques to extract and analyze data from electronic health records (EHRs) to identify patterns and trends in patient care and outcomes. This can help healthcare providers to improve the quality of care, reduce costs, and enhance patient safety.

In conclusion, Python is a powerful tool for parsing and manipulating healthcare data in the HL7 and CCD formats. By using Python to extract and process data from these documents, we can gain valuable insights into patient care and outcomes, which can help to improve healthcare delivery and patient outcomes.

Author: Stephen Fitzmeyer, M.D.
Physician Informaticist
Founder of Patient Keto
Founder of Warp Core Health
Founder of Jax Code Academy, jaxcode.com

Connect with Dr. Stephen Fitzmeyer:
Twitter: @PatientKeto
LinkedIn: linkedin.com/in/sfitzmeyer/

HL7: The Technicalities and Use Cases in Healthcare

By Stephen Fitzmeyer, MD

HL7 (Health Level Seven) is a widely adopted standard in healthcare for exchanging information between various healthcare applications, such as electronic health record systems, laboratory information systems, and radiology information systems. The standard defines a set of rules and formats for the exchange of clinical and administrative data. In this article, we will explore the technicalities of HL7 and provide examples of how it can be used in healthcare.

HL7 is composed of several messages, each containing one or more segments. Segments are made up of fields, and fields can contain subfields. Each segment contains information about a specific aspect of a patient’s clinical or administrative data. The most common message types in HL7 are the ADT (Admit, Discharge, Transfer), ORM (Order), and ORU (Observation Result) messages.

For example, an ADT message might contain information about a patient’s admission to the hospital, including their demographic information, admission date and time, and the admitting physician’s name. An ORM message might contain information about a laboratory test order, including the test name, patient’s name, and date and time the test was ordered. An ORU message might contain information about the results of a laboratory test, including the test name, patient’s name, and the actual test results.

HL7 can be used in a variety of ways to exchange data between healthcare applications. For example, a laboratory information system might send an ORU message to an electronic health record system when the results of a laboratory test are ready. The electronic health record system can then display the results to the provider, allowing them to make informed decisions about the patient’s care.

Another example is the use of HL7 in medical billing. A hospital’s billing system might receive ADT messages from an electronic health record system when a patient is admitted, transferred, or discharged. The billing system can then use this information to generate a claim for payment from the patient’s insurance company.

In addition to facilitating data exchange between healthcare applications, HL7 can also be used to integrate clinical decision support systems (CDSS) into electronic health record systems. CDSS systems can analyze patient data and provide recommendations to providers, such as suggesting alternative medications or highlighting potential drug interactions. By integrating CDSS systems with electronic health record systems using HL7, providers can make more informed decisions and improve patient outcomes.

In conclusion, HL7 is a widely adopted standard in healthcare for exchanging clinical and administrative data between various healthcare applications. HL7 messages contain segments and fields that contain patient data, and there are several message types used for different purposes. HL7 can be used to exchange data between applications, integrate CDSS systems into electronic health record systems, and facilitate medical billing. By adopting HL7, healthcare providers can improve patient outcomes and streamline administrative processes.

Author: Stephen Fitzmeyer, M.D.
Physician Informaticist
Founder of Patient Keto
Founder of Warp Core Health
Founder of Jax Code Academy, jaxcode.com

Connect with Dr. Stephen Fitzmeyer:
Twitter: @PatientKeto
LinkedIn: linkedin.com/in/sfitzmeyer/

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