CogStack

All

30 repositories

MedCAT
Public
Medical Concept Annotation Tool
healthcare learn snomed ner collaborate umls electronic-health-records covid-19 nlp natural-language-processing
Python
•
Other
•103•447•3•3•Updated Oct 28, 2024Oct 28, 2024
MedCATtrainer
Public
A simple interface to inspect, improve and add concepts to biomedical NER+L -> MedCAT.
nlp machine-learning snomed umls active-learning medcat
Python
•
Other
•34•71•16•6•Updated Oct 25, 2024Oct 25, 2024
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
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Other
•19•37•0•1•Updated Oct 9, 2024Oct 9, 2024
working_with_cogstack
Public
Basic setup and easy to follow templates to interact and search CogStack for data analysts
Jupyter Notebook
•
Apache License 2.0
•6•9•0•0•Updated Oct 8, 2024Oct 8, 2024
MedCATservice
Public
Running MedCAT as a RESTful web service
nlp docker microservices rest spacy snomed umls python flask
Python
•14•17•0•0•Updated Oct 7, 2024Oct 7, 2024
MedCATtutorials
Public
General tutorials for the setup and use of MedCAT.
natural-language-processing electronic-health-records clinical-data
HTML
•
MIT License
•15•31•2•1•Updated Sep 30, 2024Sep 30, 2024
CogStack-ModelServe
Public
A model serving and governance system for CogStack NLP solutions
Python
•
Other
•1•0•0•0•Updated Sep 27, 2024Sep 27, 2024
MedCATdemowebapp
Public
Demo web app for MedCAT
Python
•0•0•0•0•Updated May 22, 2024May 22, 2024
AnonCATDemo
Public
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
CogStackCohort
Public
A MedCAT annotations retrieval tool for cohort identification
HTML
•
Other
•1•2•0•0•Updated Feb 23, 2024Feb 23, 2024
Foresight
Public
Deep Generative Modelling of Patient Timelines using Electronic Health Records
Jupyter Notebook
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Apache License 2.0
•6•50•2•0•Updated Jan 8, 2024Jan 8, 2024
ocr-service
Public
Python
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Other
•2•4•0•0•Updated Oct 19, 2023Oct 19, 2023
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
•
Apache License 2.0
•39•336•3•2•Updated May 30, 2023May 30, 2023
iCAT
Public
A docker container for CogStack/MedCAT/HuggingFace development in isolated environments.
Vim Script
•1•2•0•2•Updated May 22, 2023May 22, 2023
tika-service
Public
Apache Tika running as a web service
Java
•
Apache License 2.0
•4•15•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
•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-web electronic-health-record umls semantic-query semantic-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
glowing-bear-cogstack-demo
Public archive
GlowingBear CogStack Demo
TypeScript
•
GNU General Public License v3.0
•12•0•0•0•Updated Jan 13, 2023Jan 13, 2023
CogStack-Trial
Public archive
Trial Recruitment made easy by using CogStack and SemEHR
JavaScript
•1•5•0•0•Updated Jan 13, 2023Jan 13, 2023
CogStack-Recipes
Public archive
Example deployment recipes based on CogStack
Shell
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Apache License 2.0
•1•1•0•0•Updated Jan 13, 2023Jan 13, 2023
medcat-cogstack-workshop
Public archive
Jupyter Notebook
•4•2•0•0•Updated Jan 13, 2023Jan 13, 2023
cogstack-jupyter-hub
Public archive
Custom Jupyter Hub Docker image with example notebooks
Jupyter Notebook
•
Apache License 2.0
•1•2•0•0•Updated Jan 13, 2023Jan 13, 2023
CogStack-Pipeline
Public archive
Distributed, fault tolerant batch processing for Natural Language Applications and Search, using remote partitioning
nlp ocr tika alerting tesseract semantic-search elasticsearch spring batch-processing cogstack
Java
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Other
•13•41•0•0•Updated Jan 13, 2023Jan 13, 2023
gate-nlp-service
Public archive
Running GATE NLP applications as RESTful web services
java nlp docker microservices rest spring snomed gate umls
Java
•
Apache License 2.0
•3•2•1•0•Updated Dec 22, 2022Dec 22, 2022
annotations-ingester
Public
Send text annotations back to ElasticSearch
python nlp docker elasticsearch data-pipelines
Python
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Apache License 2.0
•2•2•0•0•Updated Sep 6, 2022Sep 6, 2022
cogstack-getting-started
Public archive
Documentation for Deploying and Configuring CogStack
Shell
•2•5•1•0•Updated Mar 19, 2019Mar 19, 2019