Skip to main content
Python Software Foundation 20th Year Anniversary Fundraiser  Donate today!

OMOP CDM utils in Python

Project description


OMOP CDM utils. This repo may be similar to @jbadger3's inspectomop, but this is not a fork.


The OHSDI OMOP Common Data Model allows for the systematic analysis of healthcare observational databases. This is a python library to use the CDM v6 compliant databases using SQLAlchemy as the ORM. pyomop also supports converting query results to a pandas dataframe (see below) for use in machine learning pipelines. See some useful SQL Queries here.


  • Postgres
  • MySQL
  • SqLite
  • More to follow..


pip install pyomop


from pyomop import CdmEngineFactory, CdmVocabulary, CdmVector, Cohort, Vocabulary, metadata
from sqlalchemy.sql import select
import datetime

cdm = CdmEngineFactory()  # Creates SQLite database by default

# Postgres example (db='mysql' also supported)
# cdm = CdmEngineFactory(db='pgsql', host='', port=5432,
#                       user='', pw='',
#                       name='', schema='cdm6')

engine = cdm.engine
# Create Tables if required
# Create vocabulary if required
vocab = CdmVocabulary(cdm)
# vocab.create_vocab('/path/to/csv/files')  # Uncomment to load vocabulary csv files

# SQLAlchemy as ORM
session =  cdm.session
session.add(Cohort(cohort_definition_id=2, subject_id=100,

result = session.query(Cohort).all()
for row in result:

# Convert result to a pandas dataframe
vec = CdmVector()
vec.result = result

# Execute a query and convert it to dataframe
vec.sql_df(cdm, 'TEST') # TEST is defined in
print(vec.df.dtypes) # vec.df is a pandas dataframe
# OR
vec.sql_df(cdm, query='SELECT * from cohort')
print(vec.df.dtypes) # vec.df is a pandas dataframe

command-line usage

pyomop -help


Project details

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for pyomop, version 3.0.0
Filename, size File type Python version Upload date Hashes
Filename, size pyomop-3.0.0-py2.py3-none-any.whl (22.9 kB) File type Wheel Python version py2.py3 Upload date Hashes View

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring DigiCert DigiCert EV certificate Facebook / Instagram Facebook / Instagram PSF Sponsor Fastly Fastly CDN Google Google Object Storage and Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Salesforce Salesforce PSF Sponsor Sentry Sentry Error logging StatusPage StatusPage Status page