Topic: "omop-cdm"
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
VectorInstitute/cyclops
A toolkit for evaluating and monitoring AI models in clinical settings
Language: Python - Size: 27.4 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 86 - Forks: 13
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: 4 days ago - Stars: 48 - Forks: 10
Health-Informatics-UoN/carrot-mapper
Streamlined Data Mapping to OMOP
Language: Python - Size: 15.7 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 19 - 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
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
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
fastomop/omcp
Model Context Protocol Server for the Observational Medical Outcomes Partnership (OMOP) Common Data Model
Language: Python - Size: 892 KB - Last synced at: 5 days ago - Pushed at: 6 days ago - Stars: 12 - Forks: 4
dermatologist/omopfhirmap
OMOP <-> FHIR mapper
Language: Java - Size: 1.66 MB - Last synced at: 4 months ago - Pushed at: over 2 years ago - Stars: 12 - Forks: 6
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: 10 days ago - Stars: 9 - 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
databricks-industry-solutions/omop-cdm
Unlocking the Power of Health Data With a Modern Data Lakehouse
Language: Python - Size: 97.7 KB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 8 - Forks: 5
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: 7 days ago - Pushed at: 7 days ago - Stars: 6 - Forks: 2
Health-Informatics-UoN/carrot
Streamlined Data Transformation to OMOP
Language: MDX - Size: 8.13 MB - Last synced at: 8 days ago - Pushed at: 9 days ago - Stars: 6 - Forks: 0
elifdy/omop2survey
The omop2survey Python package transforms standardized response codes from the OMOP CDM survey variables into numeric values and simplifies data preparation by providing functionalities for mapping and converting response codes, as well as handling missing data, facilitating easier and more reliable data analysis
Language: Python - Size: 56.6 KB - Last synced at: 13 days ago - Pushed at: 8 months ago - Stars: 5 - Forks: 0
meerapatelmd/chariot
R Package that supports standardization of clinical data to Athena (athena.ohdsi.org)
Language: R - Size: 35.3 MB - Last synced at: over 2 years ago - Pushed at: over 3 years ago - Stars: 5 - Forks: 0
CNAG-Biomedical-Informatics/convert-pheno-ui
The web UI for Convert-Pheno, a software toolkit for the interconversion of standard data models for phenotypic data
Language: FreeMarker - Size: 251 MB - Last synced at: 24 days ago - Pushed at: 24 days ago - Stars: 4 - Forks: 1
HDRUK/hutch 📦
Former repo for Hutch
Language: C# - Size: 5.85 MB - Last synced at: 6 days ago - Pushed at: over 1 year ago - Stars: 4 - Forks: 4
fabkury/phea
R package for finding patients in SQL databases using formulas and without using SQL joins
Language: R - Size: 22.1 MB - Last synced at: over 2 years ago - Pushed at: over 2 years ago - Stars: 4 - Forks: 0
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
karlopintaric/omop-concept-automapper
An automated system for mapping source medical concepts to OMOP standard concepts using vector similarity search and LLM-based reranking.
Language: Python - Size: 133 KB - Last synced at: 30 days ago - Pushed at: 30 days ago - Stars: 3 - Forks: 0
vemonet/omop-cdm-owl
🦉 An OWL ontology for the OMOP Common Data Model
Language: Python - Size: 161 KB - Last synced at: 6 months ago - Pushed at: over 1 year ago - Stars: 3 - Forks: 0
Health-Informatics-UoN/carrot-transform
Streamlined Data Transformation to OMOP
Language: Python - Size: 1.28 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 2 - Forks: 2
mrueda/omop-csv-validator
The OMOP CSV Validator is a CLI tool that validates CSV files against JSON schemas generated from OMOP Common Data Model (CDM) DDL fiiles
Language: Perl - Size: 38.1 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 2 - Forks: 0
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: 19 days ago - Pushed at: 6 months ago - Stars: 2 - Forks: 1
laminlabs/omop
OMOP Common Data Model.
Language: Python - Size: 113 KB - Last synced at: about 2 months ago - Pushed at: 7 months ago - Stars: 2 - Forks: 0
BIH-MI/ohdsi-compliance
A set of document templates facilitating efficient implementation and operation of an OMOP/OHDSI installation
Size: 230 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 2 - 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
meerapatelmd/polyester2
Create a simulation patient population using Synthea and ETL it into the OMOP Common Data Model
Language: R - Size: 56.9 MB - Last synced at: over 2 years ago - Pushed at: about 4 years ago - Stars: 2 - Forks: 0
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: 3 days ago - Pushed at: about 1 month ago - Stars: 1 - Forks: 0
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
kosuri-indu/PLP-Pipeline
PLP-Pipeline is a patient-level prediction pipeline using Julia and DrWatson. It predicts diabetes onset in hypertension patients by analyzing healthcare data with OMOP CDM. The pipeline includes cohort definition, feature extraction, preprocessing, and model training using L1 Logistic Regression, Random Forest, and XGBoost.
Language: Julia - Size: 137 KB - Last synced at: 1 day ago - Pushed at: 6 months ago - Stars: 1 - Forks: 0
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
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
ngiangre/ROMOPOmics Fork of AndrewC160/ROMOPOmics
R package to parse datasets into SQLite-friendly tables
Language: R - Size: 2.75 MB - Last synced at: 6 days ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 0
BorisDelange/LinkR-content
Public content available for LinkR
Language: R - Size: 25.9 MB - Last synced at: 18 days ago - Pushed at: 18 days ago - Stars: 0 - Forks: 0
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
mi-erasmusmc/PlpBenchmarks
An R package to host RWD benchmark tasks for prediction and assess comparative analyses using the OMOP-CDM.
Language: R - Size: 11.2 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0
evertorres/maternal-health-synthetic-data-omop
Generación de datos sintéticos para salud materna en Colombia
Language: Jupyter Notebook - Size: 18.3 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0
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
tdiprima/Clinical-Chart-Builder
Clinical Chart Builder
Language: Jupyter Notebook - Size: 154 KB - Last synced at: 2 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0
edencehealth/ohdsi-glue
tool to facilitate the setup and ongoing maintenance of OHDSI & EHDEN tool deployments
Language: Python - Size: 160 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 1
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
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
qmarcou/computer_assisted_ICD_coding_paper
Companion code repository to Marcou et al. 2024, Creating a computer assisted ICD coding system: Performance metric choice and use of the ICD hierarchy
Language: Jupyter Notebook - Size: 612 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0
jaygee-on-github/The-APHRC-LSHTM-MUBAS-IDSR-Project
During the pandemic countries in the African region used data systems they built on top of the WHO Integrated Disease Surveillance and Response (IDSR) framework to track COVID-19 and formulate public health responses. Our IDSR project wrangles these data systems into instances of a common data model and conducts network research on top of them.
Size: 19.5 KB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0
