An infrastructure for precision medicine through analysis of big data.

BACKGROUND: Nowadays, the increasing availability of omics data, due to both the advancements in the acquisition of molecular biology results and in systems biology simulation technologies, provides the bases for precision medicine. Success in precision medicine depends on the access to healthcare and biomedical data. To this end, the digitization of all clinical exams and medical records is becoming a standard in hospitals. The digitization is essential to collect, share, and aggregate large volumes of heterogeneous data to support the discovery of hidden patterns with the aim to define predictive models for biomedical purposes. Patients' data sharing is a critical process. In fact, it raises ethical, social, legal, and technological issues that must be properly addressed. RESULTS: In this work, we present an infrastructure devised to deal with the integration of large volumes of heterogeneous biological data. The infrastructure was applied to the data collected between 2010-2016 in one of the major diagnostic analysis laboratories in Italy. Data from three different platforms were collected (i.e., laboratory exams, pathological anatomy exams, biopsy exams). The infrastructure has been designed to allow the extraction and aggregation of both unstructured and semi-structured data. Data are properly treated to ensure data security and privacy. Specialized algorithms have also been implemented to process the aggregated information with the aim to obtain a precise historical analysis of the clinical activities of one or more patients. Moreover, three Bayesian classifiers have been developed to analyze examinations reported as free text. Experimental results show that the classifiers exhibit a good accuracy when used to analyze sentences related to the sample location, diseases presence and status of the illnesses. CONCLUSIONS: The infrastructure allows the integration of multiple and heterogeneous sources of anonymized data from the different clinical platforms. Both unstructured and semi-structured data are processed to obtain a precise historical analysis of the clinical activities of one or more patients. Data aggregation allows to perform a series of statistical assessments required to answer complex questions that can be used in a variety of fields, such as predictive and precision medicine. In particular, studying the clinical history of patients that have developed similar pathologies can help to predict or individuate markers able to allow an early diagnosis of possible illnesses.

Improving compliance to guidelines through workflow technology: implementation and results in a stroke unit.

This work describes the results of the implementation of a workflow management system integrated into the electronic clinical chart of a Stroke Unit. The workflow logic is based on the rules provided by the SPREAD guidelines for stroke management. In this way, the already existing clinical chart has been transformed into an evidence-based, real-time decision support system, meanwhile maintaining the same look the users were familiar with. Since the final aim of the work was to improve evidence-based behavior and detect possible organizational bottlenecks, non-compliance to the clinical practice guidelines, before and after the system introduction, have been analyzed, as well as the accuracy of the clinical chart compilation, some care process variables, and system usability. Results show that the system enhances the clinical practice without boring users. Moreover, non-compliance analysis gives rise to ideas for further improvement.

Workflow technology to enrich a computerized clinical chart with decision support facilities.

Literature results and personal experience show that intrusive modalities of presenting suggestions of computerized clinical practice guidelines are detrimental to the routine use of an information system. This paper describes a solution for smoothly integrating a guideline-based decision support system into an existing computerized clinical chart for patients admitted to a Stroke Unit. Since many years, the healthcare personnel were using a commercial product for the ordinary patients' data management, and they were satisfied with it. Thus, the decision support system has been integrated keeping attention to minimize changes and preserve existing human-computer interaction. Our decision support system is based on workflow technology. The paper illustrates the middleware layer developed to allow communication between the workflow management system and the clinical chart. At the same time, the consequent modification of the graphical users' interface is illustrated.