GitHub topics: omop
SevKohler/Eos
ETL engine to transform openEHR into OMOP. Loads OMOCL configuration files.
Language: Java - Size: 857 KB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 12 - Forks: 5
CNAG-Biomedical-Informatics/convert-pheno
A software toolkit for the interconversion of standard data models for phenotypic data
Language: Perl - Size: 124 MB - Last synced at: 2 days ago - Pushed at: about 1 month ago - Stars: 15 - Forks: 1
aphp/Cohort360-FrontEnd
A web application to find patients, build cohorts and visualize health records
Language: TypeScript - Size: 112 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 48 - Forks: 10
OHDSI/Data2Evidence
Data2Evidence is an end-to-end solution for management and analysis of OMOP data - https://data2evidence.org
Language: TypeScript - Size: 173 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 23 - Forks: 5
answerdigital/oxford-omop-data-mapper
A documentation-centric ETL tool, implementing transformations of a number of common clincial datasets into the OMOP CDM.
Language: C# - Size: 24.5 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 9 - Forks: 0
Health-Informatics-UoN/carrot-transform
Streamlined Data Transformation to OMOP
Language: Python - Size: 1.28 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 2 - Forks: 2
Health-Informatics-UoN/carrot-mapper
Streamlined Data Mapping to OMOP
Language: Python - Size: 15.7 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 19 - Forks: 5
Health-Informatics-UoN/carrot
Streamlined Data Transformation to OMOP
Language: MDX - Size: 8.13 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 6 - Forks: 0
BorisDelange/LinkR-content
Public content available for LinkR
Language: R - Size: 25.9 MB - Last synced at: 17 days ago - Pushed at: 17 days ago - Stars: 0 - Forks: 0
OHDSI/BookOfOhdsi-2ndEdition
This repository contains the 2nd edition of the Book
Language: TeX - Size: 9.6 MB - Last synced at: 5 days ago - Pushed at: 23 days ago - Stars: 3 - Forks: 0
miracum/recruit
A Cloud-Native Clinical Trial Recruitment Support System based on HL7 FHIR® and the OMOP CDM
Language: Java - Size: 9.35 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 6 - Forks: 2
AndyRae/omop-list
A curated list of open source OMOP tools and resources
Size: 11.7 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 1 - Forks: 0
thehyve/kotobuki
Update Usagi mappings with kotobuki
Language: Python - Size: 137 KB - Last synced at: 2 days ago - Pushed at: about 1 month ago - Stars: 1 - Forks: 0
SevKohler/OMOCL
Size: 3.1 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 8 - Forks: 2
SAFEHR-data/omopcept
omopcept : an R package to access OMOP conCEPTs (no cons!) and flexible tidyverse compatible R functions for querying and visualising.
Language: R - Size: 17.2 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 13 - Forks: 3
Health-Informatics-UoN/omop-lite
Get an OMOP CDM database running quickly.
Language: Python - Size: 13.1 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 1 - Forks: 2
RADar-AZDelta/Rabbit-in-a-Blender
An ETL pipeline to transform your EMP data to OMOP.
Language: Python - Size: 3.59 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 14 - Forks: 4
National-Clinical-Cohort-Collaborative/guide-to-n3c-v1
Research with the National ClinicalCohort Collaborative (N3C: https://ncats.nih.gov/n3c)
Language: TeX - Size: 252 MB - Last synced at: 2 days ago - Pushed at: 8 months ago - Stars: 13 - Forks: 6
Z0shua/omop-query-assistant-webapp
OMOP CDM query assistant
Language: TypeScript - Size: 514 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0
sidataplus/omop-book
OMOP CDM & OHDSI in Thailand
Language: TeX - Size: 25.9 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 1
BorisDelange/LinkR
A web app for visualization and analysis of healthcare data using OMOP CDM.
Language: R - Size: 33.4 MB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 3 - Forks: 1
edencehealth/sqlalchemy_omopcdm
SQLAlchemy Declarative Mapping Models for OHDSI OMOP CDM
Language: Python - Size: 93.8 KB - Last synced at: 20 days ago - Pushed at: 11 months ago - Stars: 1 - Forks: 0
onefact/healthcare-data
Examples of exploring synthetic healthcare data from the Agency for Healthcare Research and Quality in the United States Department of Health and Human Services, and MITRE Corporation.
Language: Jupyter Notebook - Size: 1.65 MB - Last synced at: about 1 month ago - Pushed at: 11 months ago - Stars: 6 - Forks: 5
callahantiff/OMOP2OBO
OMOP2OBO: A Python Library for mapping OMOP standardized clinical terminologies to Open Biomedical Ontologies
Language: Jupyter Notebook - Size: 92 MB - Last synced at: 3 months ago - Pushed at: almost 2 years ago - Stars: 88 - Forks: 12
miracum/ohdsi-cohort-sync 📦
A tool for backing up OHDSI WebAPI cohorts in a git repository
Language: Python - Size: 110 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0
aphp/eds-scikit
eds-scikit is a Python library providing tools to process and analyse OMOP data
Language: Python - Size: 19.5 MB - Last synced at: 8 days ago - Pushed at: 9 months ago - Stars: 40 - Forks: 5
odikia/omop-support-boilerplate
Boilerplate docs for other OMOP implementers.
Language: HTML - Size: 57.6 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0
spe-uob/2020-HealthcareLakeETL
FHIR to OMOP using PySpark on AWS Glue
Language: Python - Size: 1.65 MB - Last synced at: 7 days ago - Pushed at: over 4 years ago - Stars: 14 - Forks: 4
DZD-eV-Diabetes-Research/dzd-omop-cdm-python-models
A Python data class representation of the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM)
Language: Python - Size: 2.98 MB - Last synced at: 18 days ago - Pushed at: 6 months ago - Stars: 2 - Forks: 1
MIT-LCP/mimic-omop
Mapping the MIMIC-III database to the OMOP schema
Language: PLpgSQL - Size: 24.7 MB - Last synced at: 5 months ago - Pushed at: over 1 year ago - Stars: 132 - Forks: 49
USM-CHU-FGuyon/BlendedICU
OMOP standardization pipeline for ICU databases
Language: Python - Size: 9.81 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 38 - Forks: 14
SAFEHR-data/starter-guide
Starter guide for working with SAFEHR-data
Language: Jupyter Notebook - Size: 1.54 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0
RADar-AZDelta/lib_airflow
Custom Airflow operators and hooks, that help to upload our raw hospital data to Google Cloud.
Language: Python - Size: 188 KB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 0 - Forks: 0
SAFEHR-data/omopcat
Summary of OMOP data and display in a public data catalogue
Language: R - Size: 1.12 MB - Last synced at: 27 days ago - Pushed at: 7 months ago - Stars: 1 - Forks: 0
elementechemlyn/yet-another-omop-loader
Yet Another OMOP Loader is a tool designed to load data into an OMOP Common Data Model Postgres database. It includes functionality to check the state of the database and handle various command line arguments to support pipeline operations.
Language: Python - Size: 15.6 KB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 0 - Forks: 1
centre-for-health-informatics/Django-OMOP 📦
The OMOP Common Data Model(v6) implemented in Django (v3)
Language: Python - Size: 4.68 MB - Last synced at: 6 days ago - Pushed at: over 4 years ago - Stars: 7 - Forks: 4
JuliaHealth/OMOPCommonDataModel.jl
Pure Julia implementation of the OMOP Common Data Model (CDM)
Language: Julia - Size: 33.8 MB - Last synced at: 19 days ago - Pushed at: 3 months ago - Stars: 6 - Forks: 2
UK-IPOP/omop-nlp
Script to convert OMOP NOTE table to NOTE_NLP table
Language: Python - Size: 22.5 KB - Last synced at: 3 months ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0
sween/ohdsi-intersystems-omop-platform Fork of chgl/charts
Helm Chart for Connecting Atlas to Intersystems OMOP Platform
Language: Smarty - Size: 1020 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0
kclhi/ohdsi
:whale2: OHDSI stack Docker configuration
Language: Shell - Size: 37.1 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 4 - Forks: 0
elifdy/omopsurvey
omopsurvey python package
Language: Python - Size: 165 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0
lifebit-ai/gel-data-queries-resources
Notebooks and scripts for querying programmatically source and OMOP data
Language: Jupyter Notebook - Size: 26.4 KB - Last synced at: over 1 year ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0
lifebit-ai/cynapse-data-queries-resources
Notebooks and scripts for querying programmatically source and OMOP data
Language: Jupyter Notebook - Size: 4.88 KB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0
NCBI-Codeathons/OMOPOmics
Patient 'omics data in OMOP format
Language: HTML - Size: 35.5 MB - Last synced at: 5 days ago - Pushed at: over 5 years ago - Stars: 9 - Forks: 2
oa-ri-algo-platform/cohort-love-Achilles Fork of OHDSI/Achilles
We identified some bugs/limitations in Achilles (https://github.com/OHDSI/Achilles). We fixed the code in this repository. We are searching for authorization to push these fixes to the community. In the mean time, this repository will be the one used for the cohort-love project.
Size: 7.47 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0
NajiaAhmadi/Benchmarking-Analysis-of-PLP-vs-MLR3
This repo contains analysis performed for paper "A comparative patient-level prediction study in OMOP CDM – insights from study on synthetic data".
Language: R - Size: 143 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0
BiomedSciAI/DPM360
Repository for Disease Progression Modeling workbench 360 - An end-to-end deep learning model training framework in python on OMOP data
Language: JavaScript - Size: 9.56 MB - Last synced at: about 2 months ago - Pushed at: over 2 years ago - Stars: 19 - Forks: 4
E-Health/gocdm
GORM models and APIs for CDM v 6.0
Language: Go - Size: 146 KB - Last synced at: 10 months ago - Pushed at: over 2 years ago - Stars: 3 - Forks: 2
PEDSnet/Data-Quality-Analysis
The PEDSnet Data Quality Assessment Toolkit (OMOP CDM)
Language: R - Size: 1.11 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 24 - Forks: 6
ABMI/SOCRATex
SOCRATex: Staged Optimization of Curation, Regularization, and Annotation of clinical Text
Language: R - Size: 86.9 KB - Last synced at: almost 2 years ago - Pushed at: over 4 years ago - Stars: 2 - Forks: 3
sidataplus/omop-core
Part of OMOP NHSO TCELS project
Language: Dockerfile - Size: 134 KB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0
sidataplus/omop_linkage_dbt
Facilitate the linkage of OMOP CDM databases from different sources
Size: 338 KB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0
sidataplus/omop-vocab-loader
Load OHDSI Vocab from Athena into PostgreSQL DB
Language: Python - Size: 10.7 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0
pedro-cmat/v6-summary-omop-py
Federated summary algorithm for a RDB following the OMOP CDM and using Vantage6
Language: Python - Size: 29.3 KB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 2 - Forks: 1
thehyve/ohdsi-etl-prias
Transformation from PRIAS to the OMOP CDM
Language: R - Size: 3.63 MB - Last synced at: 2 months ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 2
lifebit-ai/bi-data-queries-resources
Notebooks and scripts for querying programmatically source and OMOP data
Language: Jupyter Notebook - Size: 3.91 KB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 0
PheMA/cql-on-omop
Runs CQL phenotype definitions against an OMOP repository
Language: Java - Size: 2.14 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 12 - Forks: 2
RADar-AZDelta/AZDelta-OMOP-CDM
Holds the OMOP CDM folder structure containing the queries, Usagi CSV's and custom concept CSV's (used by Rabbit-in-a-Blender)
Language: Jinja - Size: 37 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 1 - Forks: 0
ieeta-pt/DrAC
Extracting Patients' information from clinical notes and export them to an OMOP CDM database.
Language: Python - Size: 572 KB - Last synced at: over 1 year ago - Pushed at: about 4 years ago - Stars: 27 - Forks: 7
stjude-biohackathon/KIDS23-Team3
SCCRIP (Sickle Cell Clinical Research and Intervention Program) established a longitudinal cohort at multiple sites with Sickle Cell Disease (SCD) in 2014 managed by St. Jude Clinical Hematology. A new collaborator for SCCRIP has longitudinal data for 600 SCD patients in OMOP CDM format and this effort is to convert OMOP CDM to SCCRIP format.
Language: R - Size: 6.21 MB - Last synced at: over 2 years ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 0
bcbi/OMOPDataSciencePipelines.jl
Language: Julia - Size: 96.7 KB - Last synced at: 5 months ago - Pushed at: about 2 years ago - Stars: 2 - Forks: 1
bcbi/PreprocessMD.jl
Medically-informed data preprocessing for machine learning
Language: Julia - Size: 444 KB - Last synced at: 20 days ago - Pushed at: about 2 years ago - Stars: 6 - Forks: 3
i2b2-omop/i2o-transform
PCORnet Ontology to OMOP - beta!
Language: TSQL - Size: 30.5 MB - Last synced at: 16 days ago - Pushed at: over 1 year ago - Stars: 11 - Forks: 5
dermatologist/omopcdm-dot-net
:notebook: .Net library for OMOP CDM management
Language: C# - Size: 104 KB - Last synced at: 16 days ago - Pushed at: over 4 years ago - Stars: 5 - Forks: 0
equipe22/pymedext_core
core of pymedext source
Language: Python - Size: 12.3 MB - Last synced at: 2 months ago - Pushed at: about 4 years ago - Stars: 2 - Forks: 0
phenopackets/omop-exporter
Export Phenopackets from OMOP
Language: Java - Size: 692 KB - Last synced at: over 2 years ago - Pushed at: almost 4 years ago - Stars: 2 - Forks: 0
jerrodanzalone/Rural-Urban-Mapping-Protocol-for-Linking-External-Sources
This pilot project deploys a supplemental OMOP table to map external measures of rurality (RUCC and RUCA).
Language: Python - Size: 20.2 MB - Last synced at: almost 2 years ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 0
omic/jailbreak
We jailbreak your medical records and genomics data. For free.
Language: JavaScript - Size: 11.3 MB - Last synced at: over 2 years ago - Pushed at: over 2 years ago - Stars: 17 - Forks: 1
c85/mimic-omop-etl
A short exercise mapping MIMIC.DIAGNOSES_ICD table to the OMOP.CONDITION_OCCURRENCE table.
Size: 1.78 MB - Last synced at: 10 days ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0
krashr-ds/healthcare-sql
OMOP cohort creation SQL
Size: 84 KB - Last synced at: over 2 years ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 1
MaastrichtU-BISS/IMI_SOPHIA_DMS_OMOP
OMOP conversion pipeline for IMI SOPHIA project at Maastricht University
Language: R - Size: 6.84 KB - Last synced at: over 2 years ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0
callahantiff/PheKnowVec
Translational Computational Phenotyping
Language: Python - Size: 17.7 MB - Last synced at: 3 months ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 0
kant2002/cdm
The SQL Server project for OHDSI database CDM format
Language: C# - Size: 26.4 KB - Last synced at: 3 months ago - Pushed at: about 7 years ago - Stars: 0 - Forks: 0
