Repositories list

• CogStack-NiFi

  Public
  Building data processing pipelines for documents processing with NLP using Apache NiFi and related services

  nlpelasticsearchkibana+ 6restdata-integrationnifiapache-nifidata-pipelineselectronic-health-records

  Python

  •

  Other

  •19•53•0•1•Updated Sep 16, 2025Sep 16, 2025

• cogstack-nlp

  Public
  CogStack NLP, including the Medical Concept Annotation Tool MedCAT

  HTML

  •

  Apache License 2.0

  •2•12•0•6•Updated Sep 15, 2025Sep 15, 2025

• cogstack-platform-toolkit

  Public
  CogStack Platform-wide code, documentation and tooling.

  documentationclouddeployment

  HCL

  •

  Other

  •0•0•0•1•Updated Sep 11, 2025Sep 11, 2025

• cogstack-jupyter-hub

  Public
  Custom Jupyter Hub Docker image with example notebooks

  Jupyter Notebook

  •

  Other

  •1•3•0•0•Updated Sep 8, 2025Sep 8, 2025

• working_with_cogstack

  Public
  Basic setup and easy to follow templates to interact and search CogStack for data analysts

  Python

  •

  Apache License 2.0

  •8•12•0•2•Updated Sep 8, 2025Sep 8, 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.

  nlpmachine-learningsnomed+ 3umlsactive-learningmedcat

  Python

  •

  Apache License 2.0

  •36•85•18•5•Updated Sep 4, 2025Sep 4, 2025

• cogstack-model-gateway

  Public
  A Gateway for accessing Cogstack ModelServe instances

  Python

  •

  Apache License 2.0

  •0•2•0•0•Updated Sep 1, 2025Sep 1, 2025

• CogStack-ModelServe

  Public
  A model serving and governance system for CogStack NLP solutions

  Python

  •

  Apache License 2.0

  •2•1•1•3•Updated Sep 1, 2025Sep 1, 2025

• ocr-service

  Public
  Python

  •

  Other

  •2•4•0•0•Updated Aug 28, 2025Aug 28, 2025

• MedCATv2tutorials

  Public archive
  Tutorials for MedCATv2

  Jupyter Notebook

  •0•2•0•0•Updated Jul 31, 2025Jul 31, 2025

• MedCAT

  Public archive
  Medical Concept Annotation Tool

  healthcarelearnsnomed+ 8nercollaborateumlselectronic-health-recordscovid-19nlpnatural-language-processing+ 1

  Python

  •

  Apache License 2.0

  •112•509•0•1•Updated Jul 25, 2025Jul 25, 2025

• MedCAT2

  Public archive
  MedCATv2

  nlpepr

  Python

  •

  Other

  •1•2•0•1•Updated Jun 25, 2025Jun 25, 2025

• MedCATservice

  Public archive
  Running MedCAT as a RESTful web service

  nlpdockermicroservices+ 6restspacysnomedumlspythonflask

  Python

  •

  Other

  •15•22•0•0•Updated Jun 23, 2025Jun 23, 2025

• MedCATdemowebapp

  Public archive
  Demo web app for MedCAT

  Python

  •0•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

  •11•63•2•0•Updated Jun 17, 2025Jun 17, 2025

• CogStackCohort

  Public
  A MedCAT annotations retrieval tool for cohort identification

  HTML

  •

  Other

  •2•2•0•0•Updated Jun 5, 2025Jun 5, 2025

• MedCATtutorials

  Public
  General tutorials for the setup and use of MedCAT.

  natural-language-processingelectronic-health-recordsclinical-data

  HTML

  •

  MIT License

  •16•40•1•1•Updated May 22, 2025May 22, 2025

• cogstack-rag-search

  Public
  Python

  •0•0•1•0•Updated May 8, 2025May 8, 2025

• text-2-sql

  Public
  Python

  •0•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 handle large datasets.

  Vue

  •

  Apache License 2.0

  •2•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).

  nlpmedicinehealth+ 6healthcarehuggingfaceopengptgpt-4llmchatgpt

  Jupyter Notebook

  •

  Apache License 2.0

  •44•360•3•2•Updated May 30, 2023May 30, 2023

• iCAT

  Public
  A docker container for CogStack/MedCAT/HuggingFace development in isolated environments.

  Vim Script

  •1•3•0•2•Updated May 22, 2023May 22, 2023

• tika-service

  Public
  Apache Tika running as a web service

  Java

  •

  Apache License 2.0

  •5•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)

  nlpmachine-learningehr-phenotyping

  Python

  •2•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-webelectronic-health-recordumls+ 2semantic-querysemantic-annotation

  JavaScript

  •

  Apache License 2.0

  •20•89•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

  •2•5•1•0•Updated Jan 13, 2023Jan 13, 2023

• OAC-NLP

  Public archive
  Python

  •

  GNU General Public License v3.0

  •1•2•2•0•Updated Jan 13, 2023Jan 13, 2023

• CogStack-PatientTimeline

  Public archive
  A patient timeline browser build on-top of CogStack

  SCSS

  •0•3•0•0•Updated Jan 13, 2023Jan 13, 2023

• texscrubber

  Public archive
  Personal information de-identification tool

  Java

  •

  Apache License 2.0

  •2•2•0•0•Updated Jan 13, 2023Jan 13, 2023