Ecosyste.ms: Repos

An open API service providing repository metadata for many open source software ecosystems.

GitHub topics: omop

Repositories

CNAG-Biomedical-Informatics/convert-pheno

A software toolkit for the interconversion of standard data models for phenotypic data

Language: Perl - Size: 79.7 MB - Last synced: about 7 hours ago - Pushed: about 8 hours ago - Stars: 9 - Forks: 1

miracum/ohdsi-cohort-sync

A tool for backing up OHDSI WebAPI cohorts in a git repository

Language: Python - Size: 74.2 KB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 0 - Forks: 0

andysouth/omopcept

omopcept : an R package to access OMOP conCEPTs (all pros, no cons!) and flexible tidyverse compatible R functions for querying.

Language: R - Size: 17 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 5 - Forks: 1

RADar-AZDelta/Rabbit-in-a-Blender

An ETL pipeline to transform your EMP data to OMOP.

Language: Python - Size: 3.64 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 9 - Forks: 2

elifdy/omopsurvey

omopsurvey python package

Language: Python - Size: 165 KB - Last synced: 5 days ago - Pushed: 8 days ago - Stars: 1 - Forks: 0

National-COVID-Cohort-Collaborative/guide-to-n3c-v1

Research with the National COVID Cohort Collaborative (N3C: https://ncats.nih.gov/n3c)

Language: TeX - Size: 244 MB - Last synced: 5 days ago - Pushed: 6 days ago - Stars: 10 - Forks: 4

Health-Informatics-UoN/CaRROT-Mapper

Carrot: Convenient And Reusable Rapid Omop Transformer.

Language: Python - Size: 3.86 MB - Last synced: 17 days ago - Pushed: 17 days ago - Stars: 9 - Forks: 3

USM-CHU-FGuyon/BlendedICU

OMOP standardization pipeline for ICU databases

Language: Python - Size: 10.1 MB - Last synced: 19 days ago - Pushed: 20 days ago - Stars: 23 - Forks: 6

RADar-AZDelta/lib_airflow

Custom Airflow operators and hooks, that help to upload our raw hospital data to Google Cloud.

Language: Python - Size: 145 KB - Last synced: 20 days ago - Pushed: 20 days ago - Stars: 0 - Forks: 0

JuliaHealth/OMOPCommonDataModel.jl

Pure Julia implementation of the OMOP Common Data Model (CDM)

Language: Julia - Size: 261 KB - Last synced: 21 days ago - Pushed: almost 4 years ago - Stars: 5 - Forks: 1

onefact/synthetic-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: 1.64 MB - Last synced: 22 days ago - Pushed: 23 days ago - Stars: 4 - Forks: 4

callahantiff/OMOP2OBO

OMOP2OBO: A Python Library for mapping OMOP standardized clinical terminologies to Open Biomedical Ontologies

Language: Jupyter Notebook - Size: 92 MB - Last synced: 23 days ago - Pushed: 8 months ago - Stars: 78 - Forks: 12

SevKohler/Eos

ETL engine to transform openEHR into OMOP. Loads OMOCL configuration files.

Language: Java - Size: 417 KB - Last synced: 30 days ago - Pushed: 30 days ago - Stars: 6 - Forks: 1

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: about 1 month ago - Pushed: 8 months 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: about 1 month ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

miracum/recruit

A Cloud-Native Clinical Trial Recruitment Support System based on HL7 FHIR and the OMOP CDM

Language: Java - Size: 7.84 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 3 - Forks: 1

aphp/Cohort360

A web application to find patients, build cohorts and visualize health records

Language: TypeScript - Size: 97.1 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 37 - Forks: 9

aphp/eds-scikit

eds-scikit is a Python library providing tools to process and analyse OMOP data

Language: Python - Size: 13.8 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 31 - Forks: 5

BorisDelange/LinkR

A web app for visualization and analysis of healthcare data using OMOP CDM.

Language: R - Size: 13.1 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0

SevKohler/OMOCL

Size: 20.5 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 4 - Forks: 2

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: 21.3 MB - Last synced: 24 days ago - Pushed: 24 days ago - Stars: 3 - Forks: 0

UK-IPOP/omop-nlp

Script to convert OMOP NOTE table to NOTE_NLP table

Language: Python - Size: 19.5 KB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 0 - Forks: 0

MIT-LCP/mimic-omop

Mapping the MIMIC-III database to the OMOP schema

Language: PLpgSQL - Size: 24.7 MB - Last synced: about 2 months ago - Pushed: 2 months ago - Stars: 118 - Forks: 46

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: 3 months ago - Pushed: 3 months 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: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

BorisDelange/LinkR-content

Public content available for LinkR

Language: R - Size: 14.1 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0

edencehealth/sqlalchemy_omopcdm

SQLAlchemy Declarative Mapping Models for OHDSI OMOP CDM

Language: Python - Size: 97.7 KB - Last synced: 17 days ago - Pushed: 17 days 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: 25 days ago - Pushed: about 1 year ago - Stars: 19 - Forks: 4

centre-for-health-informatics/Django-OMOP 📦

The OMOP Common Data Model(v6) implemented in Django (v3)

Language: Python - Size: 4.68 MB - Last synced: 6 months ago - Pushed: over 3 years ago - Stars: 6 - Forks: 3

sidataplus/omop-book

OMOP CDM & OHDSI in Thailand

Language: TeX - Size: 25.9 MB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 0 - Forks: 0

haydenbspence/Polyphemus

Polyphemus is a framework for coordinating specialty trained NLP models, with a focus on LLMs for use in applications to support observational medical research.

Language: Python - Size: 726 KB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 2 - Forks: 0

PEDSnet/Data-Quality-Analysis

The PEDSnet Data Quality Assessment Toolkit (OMOP CDM)

Language: R - Size: 1.11 MB - Last synced: about 1 month ago - Pushed: about 3 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: 7 months ago - Pushed: about 3 years ago - Stars: 2 - Forks: 3

equipe22/pymedext_core

core of pymedext source

Language: Python - Size: 12.3 MB - Last synced: 7 months ago - Pushed: almost 3 years ago - Stars: 2 - Forks: 0

NCBI-Codeathons/OMOPOmics

Patient 'omics data in OMOP format

Language: HTML - Size: 35.5 MB - Last synced: 7 months ago - Pushed: almost 4 years ago - Stars: 8 - Forks: 2

sidataplus/omop-core

Part of OMOP NHSO TCELS project

Language: Dockerfile - Size: 134 KB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 0 - Forks: 0

sidataplus/omop_linkage_dbt

Facilitate the linkage of OMOP CDM databases from different sources

Size: 338 KB - Last synced: 8 months ago - Pushed: 8 months 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: 4 months ago - Pushed: 4 months 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: about 2 months ago - Pushed: 9 months ago - Stars: 2 - Forks: 1

thehyve/ohdsi-etl-prias

Transformation from PRIAS to the OMOP CDM

Language: R - Size: 3.63 MB - Last synced: about 1 month ago - Pushed: about 1 year ago - Stars: 2 - Forks: 1

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: about 1 month ago - Pushed: over 1 year 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: about 1 month ago - Pushed: about 1 year 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: 8 months ago - Pushed: 8 months 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: 4 months ago - Pushed: almost 3 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: about 1 year ago - Pushed: about 1 year ago - Stars: 2 - Forks: 0

Related Keywords

omop 60 omop-cdm 17 ohdsi 14 cdm 11 etl 6 fhir 4 python 4 julia 3 mimic-iii 3 cohort-studies 3 data-visualization 3 health 3 etl-pipeline 3 rstats 3 data-science 3 r 3 omop-cdm-database 3 machine-learning 3 health-data 3 ehr-data 3 nlp 3 sqlalchemy 2 cohort-analysis 2 healthcare 2 cohorts 2 django 2 medical 2 emr 2 openehr-content 2 covid-19 2 phenopacket 2 shiny 2 healthcare-data 2 data-analysis 2 health-informatics 2 ohdsi-webapi 2 ehr-phenotyping 2 ehr 2 data-transformation 2 open-biomedical-ontologies 2 openehr 2 statistics 1 federated-learning 1 summary 1 vantage6 1 bi 1 algorithm 1 python3 1 precision-medicine 1 elm 1 omics 1 infrastructure 1 database 1 data-wrangling 1 brat 1 bioc 1 elasticsearch 1 annotation 1 pedsnet 1 data-quality-checks 1 data-quality 1 llm 1 informatics 1 sklearn 1 pytorch 1 c19 1 cda-parser 1 clinical 1 hack 1 hl7 1 jailbreak 1 patient 1 rpa 1 security 1 coursera 1 docker 1 sql 1 sqlite3 1 abra-collaboratory 1 computational-phenotyping 1 phenotyping 1 api 1 gin 1 golang 1 gorm 1 model 1 phenotypes 1 annotation-tool 1 clinical-notes 1 drug-discovery 1 medical-text 1 medical-text-mining 1 hematology 1 research 1 sickle-cell 1 preprocessing 1 i2b2 1 ontology 1 aws-glue 1 etl-jobs 1