UCL Institute of Health Informatics


MedCAT/CogStack training course

22 September 2020

MedCAT Training

On 10 and 11 September 2020, University College London and King’s College London jointly ran an introduction to MedCAT and CogStack training course for UK data scientists, supported by funding from Health Data Research UK (HDR UK), the Maudsley Biomedical Research Centre and the Maudsley Charity.  The Medical Concept Annotation Toolkit (MedCAT) can be used to extract information from electronic health records (EHR) and link it to biomedical ontologies like SNOMED-CT and UMLS.  CogStack is an information retrieval and extraction platform that implements open-source enterprise search, natural language processing, analytics, and visualisation technologies to unlock EHR and assist in clinical decision-making and research.  Eighteen people attended the training which covered an introduction on how to use CogStack and MedCAT to organise, structure and analyse EHR, how to set up a CogStack and MedCAT environment, configure pipelines and carry out simple data exploration and presentation, and a number of use cases for MedCAT and Cogtack were demonstrated.  The training will be run again in the Spring 2021 and details will be advertised on the IHI website.