CogStack

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39 repositories

cogstack-nlp
Public
CogStack NLP, including the Medical Concept Annotation Tool MedCAT
HTML
•
Apache License 2.0
•7•41•1•4•Updated Feb 6, 2026Feb 6, 2026
CogStack-ModelServe
Public
A model serving and governance system for CogStack NLP solutions
Python
•
Apache License 2.0
•3•1•2•4•Updated Feb 6, 2026Feb 6, 2026
CogStack-NiFi
Public
Building data processing pipelines for documents processing with NLP using Apache NiFi and related services
nlp elasticsearch kibana rest data-integration nifi apache-nifi data-pipelines electronic-health-records
Python
•
Other
•21•56•0•1•Updated Feb 5, 2026Feb 5, 2026
cogstack-jupyter-hub
Public
Custom Jupyter Hub Docker image with example notebooks
python analytics analysis jupyter-notebook jupyterhub
Python
•
Other
•3•2•0•0•Updated Feb 4, 2026Feb 4, 2026
ocr-service
Public
This is a python fast-api OCR service, attempting to resolve scalability and performance issues. It also relies on tesseract ocr but without the ambiguities of…
ocr scalability tesseract fast-api
Python
•
Other
•3•4•0•0•Updated Jan 30, 2026Jan 30, 2026
dbt_mimic_omop
Public
A resource to convert the MIMIC-IV and MIMIC-IV note datasets into a standard OMOP format.
Python
•0•0•0•0•Updated Jan 28, 2026Jan 28, 2026
cogstack-platform-toolkit
Public
CogStack Platform-wide code, documentation and tooling.
documentation cloud deployment
HCL
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Other
•1•0•0•0•Updated Jan 27, 2026Jan 27, 2026
cogstack-model-gateway
Public
A Gateway for accessing Cogstack ModelServe instances
Python
•
Apache License 2.0
•1•2•6•1•Updated Jan 16, 2026Jan 16, 2026
CogStackCohort
Public
A MedCAT annotations retrieval tool for cohort identification
HTML
•4•2•0•0•Updated Jan 11, 2026Jan 11, 2026
cogstack_dashboards_demo
Public
Demo scripts for CogStack Dashboards
Python
•
Apache License 2.0
•0•0•0•0•Updated Jan 2, 2026Jan 2, 2026
working_with_cogstack
Public
Basic setup and easy to follow templates to interact and search CogStack for data analysts
Python
•
Apache License 2.0
•9•12•0•1•Updated Sep 18, 2025Sep 18, 2025
.github
Public
0•0•0•0•Updated Sep 5, 2025Sep 5, 2025
MedCATtrainer
Public archive
A simple interface to inspect, improve and add concepts to biomedical NER+L -> MedCAT.
nlp machine-learning snomed umls active-learning medcat
Python
•
Apache License 2.0
•36•85•18•5•Updated Sep 4, 2025Sep 4, 2025
MedCATv2tutorials
Public archive
Tutorials for MedCATv2
Jupyter Notebook
•1•2•0•0•Updated Jul 31, 2025Jul 31, 2025
MedCAT
Public archive
Medical Concept Annotation Tool
nlp natural-language-processing information-extraction healthcare learn snomed ner collaborate umls electronic-health-records
Python
•
Apache License 2.0
•117•523•0•1•Updated Jul 25, 2025Jul 25, 2025
MedCAT2
Public archive
MedCATv2
nlp epr
Python
•
Other
•2•4•0•1•Updated Jun 25, 2025Jun 25, 2025
MedCATservice
Public archive
Running MedCAT as a RESTful web service
python nlp docker flask microservices rest spacy snomed umls
Python
•
Other
•16•22•0•0•Updated Jun 23, 2025Jun 23, 2025
MedCATdemowebapp
Public archive
Demo web app for MedCAT
Python
•1•0•0•1•Updated Jun 20, 2025Jun 20, 2025
Foresight
Public
Deep Generative Modelling of Patient Timelines using Electronic Health Records
Jupyter Notebook
•
Apache License 2.0
•14•72•2•0•Updated Jun 17, 2025Jun 17, 2025
MedCATtutorials
Public
General tutorials for the setup and use of MedCAT.
natural-language-processing electronic-health-records clinical-data
HTML
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MIT License
•17•42•1•1•Updated May 22, 2025May 22, 2025
text-2-sql
Public
Python
•1•0•0•0•Updated Apr 7, 2025Apr 7, 2025
AnonCATDemo
Public archive
The Deidentify app uses MedCAT to automatically redact or replace sensitive information in documents. Customisable rules and batch processing make it easy to ha…
Vue
•
Apache License 2.0
•3•2•0•0•Updated Apr 12, 2024Apr 12, 2024
OpenGPT
Public
A framework for creating grounded instruction based datasets and training conversational domain expert Large Language Models (LLMs).
nlp medicine health healthcare huggingface opengpt gpt-4 llm chatgpt
Jupyter Notebook
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Apache License 2.0
•46•361•3•2•Updated May 30, 2023May 30, 2023
iCAT
Public
A docker container for CogStack/MedCAT/HuggingFace development in isolated environments.
Vim Script
•3•3•0•2•Updated May 22, 2023May 22, 2023
tika-service
Public
Apache Tika running as a web service
Java
•
Apache License 2.0
•6•18•1•0•Updated Jan 14, 2023Jan 14, 2023
nlp2phenome
Public archive
using AI model to infer patient phenotypes from identified named entities (instances of biomedical concepts)
nlp machine-learning ehr-phenotyping
Python
•3•10•2•4•Updated Jan 13, 2023Jan 13, 2023
CogStack-SemEHR
Public archive
Surfacing Semantic Data from Clinical Notes in Electronic Health Records for Tailored Care, Trial Recruitment and Clinical Research
semantic-web electronic-health-record umls semantic-query semantic-annotation
JavaScript
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Apache License 2.0
•22•88•3•0•Updated Jan 13, 2023Jan 13, 2023
risk-score-builder
Public archive
Map clinical risk score concepts to structured definitions using ontologies, calculate structured risk scores from NLP.
Python
•
GNU General Public License v3.0
•3•6•1•0•Updated Jan 13, 2023Jan 13, 2023
OAC-NLP
Public archive
Python
•
GNU General Public License v3.0
•2•2•2•0•Updated Jan 13, 2023Jan 13, 2023
CogStack-PatientTimeline
Public archive
A patient timeline browser build on-top of CogStack
SCSS
•1•3•0•0•Updated Jan 13, 2023Jan 13, 2023