RECAP-KG: Mining Knowledge Graphs from Raw GP Notes for Remote COVID-19 Assessment in Primary Care

Abstract

Clinical decision-making is a fundamental stage in delivering appropriate care to patients. In recent years several decision-making systems designed to aid the clinician in this process have been developed. However, technical solutions currently in use are based on simple regression models and are only able to take into account simple pre-defined multiple-choice features, such as patient age, pre-existing conditions, smoker status, etc. One particular source of patient data, that available decision-making systems are incapable of processing is the collection of patient consultation GP notes. These contain crucial signs and symptoms - the information used by clinicians in order to make a final decision and direct the patient to the appropriate care. Extracting information from GP notes is a technically challenging problem, as they tend to include abbreviations, typos, and incomplete sentences. This paper addresses this open challenge. We present a framework that performs knowledge graph construction from raw GP medical notes written during or after patient consultations. By relying on support phrases mined from the SNOMED ontology, as well as predefined supported facts from values used in the RECAP (REmote COVID-19 Assessment in Primary Care) patient risk prediction tool, our graph generative framework is able to extract structured knowledge graphs from the highly unstructured and inconsistent format that consultation notes are written in. Our knowledge graphs include information about existing patient symptoms, their duration, and their severity. We apply our framework to consultation notes of COVID-19 patients in the UK COVID-19 Clinical Assesment Servcie (CCAS) patient dataset. We provide a quantitative evaluation of the performance of our framework, demonstrating that our approach has better accuracy than traditional NLP methods when answering questions about patients.