Extraction of Clinical Information from Clinical Reports: an Application to the Study of Medication Overuse Headaches in Italy.

International audienceA i2b2-Pavia pilot project has been recently activated at the Headache Centre of the C. Mondino Institute of Neurology, in Pavia, with the aim of investigating Medical Overuse Headaches. The software infrastructure so far implemented automatically extracts and integrates data coming from different sources into a repository purposely designed for multidimensional inspection. A great effort has been devoted to train a Natural Language Processing system able to extract medical concepts from Italian clinical reports

BigQ: A NoSQL based framework to handle genomic variants in i2b2

Background: Precision medicine requires the tight integration of clinical and molecular data. To this end, it is mandatory to define proper technological solutions able to manage the overwhelming amount of high throughput genomic data needed to test associations between genomic signatures and human phenotypes. The i2b2 Center (Informatics for Integrating Biology and the Bedside) has developed a widely internationally adopted framework to use existing clinical data for discovery research that can help the definition of precision medicine interventions when coupled with genetic data. i2b2 can be significantly advanced by designing efficient management solutions of Next Generation Sequencing data. Results: We developed BigQ, an extension of the i2b2 framework, which integrates patient clinical phenotypes with genomic variant profiles generated by Next Generation Sequencing. A visual programming i2b2 plugin allows retrieving variants belonging to the patients in a cohort by applying filters on genomic variant annotations. We report an evaluation of the query performance of our system on more than 11 million variants, showing that the implemented solution scales linearly in terms of query time and disk space with the number of variants. Conclusions: In this paper we describe a new i2b2 web service composed of an efficient and scalable document-based database that manages annotations of genomic variants and of a visual programming plug-in designed to dynamically perform queries on clinical and genetic data. The system therefore allows managing the fast growing volume of genomic variants and can be used to integrate heterogeneous genomic annotations

Beyond Cohort Selection: An Analytics-Enabled i2b2

The i2b2 software is a widely adopted solution for secondary use of clinical data for clinical research, specifically designed for cohort identification. i2b2 is still lacking functionalities for data analysis. The aim of this work is to empower the i2b2 framework enabling clinical researchers to perform statistical analyses for accelerating the process of hypothesis testing. To this aim we have developed a flexible extension of i2b2 able to exploit different statistical engines. We have implemented some first applications for basic statistics and survival analyses, exploiting this extension and accessible through suitable user interfaces designed with a special consideration for usability