CogStack

Repositories

• iCAT

  A docker container for CogStack/MedCAT/HuggingFace development in isolated environments.
  Vim script 0 1 0 0 Updated Oct 30, 2020

• tika-service

  Apache Tika running as a web service
  Java Apache-2.0 4 1 2 1 Updated Oct 30, 2020

• MedCAT

  Medical Concept Annotation Tool

  nlp ner electronic-health-records
  Python 28 103 0 0 Updated Oct 30, 2020

• MedCATtrainer

  A simple interface to inspect, improve and add concepts to biomedical NER+L -> MedCAT.

  nlp machine-learning snomed umls active-learning medcat
  Python Apache-2.0 11 19 1 0 Updated Oct 14, 2020

• medcat-cogstack-workshop
  Jupyter Notebook 1 0 0 0 Updated Sep 10, 2020

• MedCATservice

  Running MedCAT as a RESTful web service

  python nlp docker flask microservices rest spacy
  Python 6 4 1 0 Updated Aug 3, 2020

• CogStack-NiFi

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

  nlp elasticsearch kibana rest data-integration nifi apache-nifi
  Jupyter Notebook Apache-2.0 6 3 3 0 Updated Aug 3, 2020

• nlp2phenome

  using AI model to infer patient phenotypes from identified named entities (instances of biomedical concepts)

  nlp machine-learning ehr-phenotyping
  Python 1 8 0 0 Updated Jul 28, 2020

• gate-nlp-service

  Running GATE NLP applications as RESTful web services

  java nlp docker microservices rest spring snomed
  Java Apache-2.0 2 0 1 0 Updated Jun 30, 2020

• CogStack-SemEHR

  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-2.0 12 48 2 0 Updated Jun 24, 2020

• OAC-NLP
  Python GPL-3.0 1 2 2 0 Updated Mar 27, 2020

• CogStack-Pipeline

  Distributed, fault tolerant batch processing for Natural Language Applications and Search, using remote partitioning

  nlp elasticsearch ocr spring tika alerting tesseract
  Java Apache-2.0 11 24 9 0 Updated Jan 28, 2020

• annotations-ingester

  Send text annotations back to ElasticSearch

  python nlp docker elasticsearch data-pipelines
  Python Apache-2.0 2 0 0 0 Updated Dec 26, 2019

• Neo4J-Loader

  Neo4J-Loader is a service for the NiFi pipeline for loading the UMLS graph (or subsets thereof) together with CogStack Patient-->document-->Annotation-->CUI nodes
  Apache-2.0 0 0 0 0 Updated Jul 31, 2019

• cogstack-jupyter-hub

  Custom Jupyter Hub Docker image with example notebooks
  Jupyter Notebook Apache-2.0 1 0 0 0 Updated Jul 31, 2019

• risk-score-builder

  Map clinical risk score concepts to structured definitions using ontologies, calculate structured risk scores from NLP.
  Python GPL-3.0 1 1 1 0 Updated Jun 24, 2019

• CogStack-Recipes

  Example deployment recipes based on CogStack
  Shell Apache-2.0 2 0 0 0 Updated May 13, 2019

• cogstack-getting-started

  Documentation for Deploying and Configuring CogStack
  Shell 2 4 1 0 Updated Mar 19, 2019

• security

  Forked from opendistro-for-elasticsearch/security
  Java Apache-2.0 142 0 0 0 Updated Mar 11, 2019

• Bio-YODIE

  Forked from GateNLP/Bio-YODIE

  Bio-YODIE is GATE's biomedical named entity linking pipeline.
  Java 9 2 0 0 Updated Nov 8, 2018

• CogStack.github.io

  CogStack Pages Site
  1 0 0 1 Updated Aug 21, 2018

• texscrubber

  Forked from healtex/texscrubber

  Personal information de-identification tool
  Java Apache-2.0 2 0 0 0 Updated Jun 22, 2018

• CogStack-Trial

  Trial Recruitment made easy by using CogStack and SemEHR
  JavaScript 0 3 0 0 Updated Mar 25, 2018

• CogStack-PatientTimeline

  A patient timeline browser build on-top of CogStack
  CSS 0 1 0 0 Updated Oct 5, 2017

• glowing-bear-cogstack-demo

  Forked from thehyve/glowing-bear

  GlowingBear CogStack Demo
  TypeScript GPL-3.0 7 0 0 0 Updated Aug 24, 2017

• bio-yodie-resource-prep

  Forked from GateNLP/bio-yodie-resource-prep

  Scripts to prepare the informational resources required by GATE Bio-YODIE.
  Scala 3 0 0 0 Updated Aug 10, 2017