BRC Bioinformatics Seminar: Semantic Annotation of Patient Records for Search and Visualisation

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Date(s) - 19/04/2016
1:00 pm - 2:00 pm

Social, Genetic and Developmental Psychiatry Centre (MRC), Seminar Room A & B


Title: Semantic Annotation of Patient Records for Search and Visualisation

Dr Angus Roberts, Senior Research Fellow, Natural Language Processing, Department of Computer Science, University of Sheffield

Dr Honghan Wu, Post Doctoral Data Scientist, SGDP Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London

Abstract: The digitization of patient records creates new possibilities for technology-aided research and clinical support. NLP technologies such as those provided by GATE, which has been in use at SLAM for extraction of clinical facts for some years, is now being used to enable a rich semantic augmentation of free text patient data, facilitating a deeper exploration and understanding. We have used Bio-YODIE, an biomedical named entity normalization system developed in the context of the KConnect project, to link mentions such as drugs, diseases and symptoms in over a million CRIS records to their entry in biomedical knowledge bases. We demonstrate how this enables semantic search and visualization using GATE Mimir and GATE Prospector.

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