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Purpose: Biomedical research is being catalyzed by the vast amount of data rapidly collected through the application of information technologies (IT). Despite IT advances, the methods for involving patients and citizens in biomedical research remain static, paper-based and organized around national boundaries and anachronistic legal frameworks. The purpose of this paper is to study the current practices for obtaining consent for biobanking and the legal requirements for reusing the available biomaterial and data in EU and finally to present a novel tool to this direction enabling the secondary use of data and biomaterial.Method: We review existing European legislation for secondary use of patient's biomaterial and data for research, identify types and scopes of consent, formal requirements for consent, and consider their implications for implementing electronic consent tools. To this direction, we proceed further to develop a modular tool, named Donor's Support Tool (DST), designed to connect researchers with participants, and to promote engagement, informed participation and individual decision making.Results: To identify the advantages of our solution we compare our tool with six other relevant approaches. The results show that our tool scores higher than the other tools in functionality, security and intelligence whereas it is the only one free and open-source. In addition, the potential of our solution is shown by a proof of concept deployment in an existing clinical setting, where it was really appreciated, as streamlining the relevant workflow. [ABSTRACT FROM AUTHOR]

Pathway analysis methodologies couple traditional gene expression analysis with knowledge encoded in established molecular pathway networks, offering a promising approach towards the biological interpretation of phenotype differentiating genes. Early pathway analysis methodologies, named as gene set analysis (GSA), view pathways just as plain lists of genes without taking into account either the underlying pathway network topology or the involved gene regulatory relations. These approaches, even if they achieve computational efficiency and simplicity, consider pathways that involve the same genes as equivalent in terms of their gene enrichment characteristics. Most recent pathway analysis approaches take into account the underlying gene regulatory relations by examining their consistency with gene expression profiles and computing a score for each profile. Even with this approach, assessing and scoring single-relations limits the ability to reveal key gene regulation mechanisms hidden in longer pathway sub-paths. We introduce MinePath, a pathway analysis methodology that addresses and overcomes the aforementioned problems. MinePath facilitates the decomposition of pathways into their constituent sub-paths. Decomposition leads to the transformation of single-relations to complex regulation sub-paths. Regulation sub-paths are then matched with gene expression sample profiles in order to evaluate their functional status and to assess phenotype differential power. Assessment of differential power supports the identification of the most discriminant profiles. In addition, MinePath assess the significance of the pathways as a whole, ranking them by their p-values. Comparison results with state-of-the-art pathway analysis systems are indicative for the soundness and reliability of the MinePath approach. In contrast with many pathway analysis tools, MinePath is a web-based system () offering dynamic and rich pathway visualization functionality, with the unique characteristic to color regulatory relations between genes and reveal their phenotype inclination. This unique characteristic makes MinePath a valuable tool for in silico molecular biology experimentation as it serves the biomedical researchers’ exploratory needs to reveal and interpret the regulatory mechanisms that underlie and putatively govern the expression of target phenotypes. [ABSTRACT FROM AUTHOR]

Background: A plethora of publicly available biomedical resources do currently exist and are constantly increasing at a fast rate. In parallel, specialized repositories are been developed, indexing numerous clinical and biomedical tools. The main drawback of such repositories is the difficulty in locating appropriate resources for a clinical or biomedical decision task, especially for non-Information Technology expert users. In parallel, although NLP research in the clinical domain has been active since the 1960s, progress in the development of NLP applications has been slow and lags behind progress in the general NLP domain. The aim of the present study is to investigate the use of semantics for biomedical resources annotation with domain specific ontologies and exploit Natural Language Processing methods in empowering the non-Information Technology expert users to efficiently search for biomedical resources using natural language.Methods: A Natural Language Processing engine which can "translate" free text into targeted queries, automatically transforming a clinical research question into a request description that contains only terms of ontologies, has been implemented. The implementation is based on information extraction techniques for text in natural language, guided by integrated ontologies. Furthermore, knowledge from robust text mining methods has been incorporated to map descriptions into suitable domain ontologies in order to ensure that the biomedical resources descriptions are domain oriented and enhance the accuracy of services discovery. The framework is freely available as a web application at ( http://calchas.ics.forth.gr/ ).Results: For our experiments, a range of clinical questions were established based on descriptions of clinical trials from the ClinicalTrials.gov registry as well as recommendations from clinicians. Domain experts manually identified the available tools in a tools repository which are suitable for addressing the clinical questions at hand, either individually or as a set of tools forming a computational pipeline. The results were compared with those obtained from an automated discovery of candidate biomedical tools. For the evaluation of the results, precision and recall measurements were used. Our results indicate that the proposed framework has a high precision and low recall, implying that the system returns essentially more relevant results than irrelevant.Conclusions: There are adequate biomedical ontologies already available, sufficiency of existing NLP tools and quality of biomedical annotation systems for the implementation of a biomedical resources discovery framework, based on the semantic annotation of resources and the use on NLP techniques. The results of the present study demonstrate the clinical utility of the application of the proposed framework which aims to bridge the gap between clinical question in natural language and efficient dynamic biomedical resources discovery. [ABSTRACT FROM AUTHOR]

This work presents a systematic review of long-term risk assessment models for evaluating the probability of developing complications in diabetes patients. Diabetes mellitus can cause many complications if not adequately controlled; risk assessment models can help physicians and patients in identifying the complications most likely to arise and in taking the necessary countermeasures. We identified six large medical studies related to diabetes mellitus upon which current available risk assessment models are built on; all these studies had duration over 5 years and most of them included some common demographic and clinical data strongly related to diabetic complications. The most common predictions for long term diabetes complications are related to cardiovascular diseases and diabetic retinopathy. Our analysis of the literature led us to the conclusion that researchers and medical practitioners should take in account that some limitations undermine the applicability of risk assessment models; for example, it is hard to judge whether results obtained on a specific cohort can be effectively translated to other populations. Nevertheless, all these studies have significantly contributed to identify significant risk factors associated with the major diabetes complications. [ABSTRACT FROM AUTHOR]

PURPOSE: Capitalizing on the promise of patient-reported outcomes (PROs), electronic implementations of PROs (ePROs) are expected to play an important role in the development of novel digital health interventions targeting palliative cancer care. We performed a systematic and mapping review of the scientific literature on the current ePRO-based approaches used for palliative cancer care. METHODS: Following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses statement guidelines, the conducted review answered the research questions: "What are the current ePRO-based approaches for palliative cancer care; what is their contribution/value in the domain of palliative cancer care; and what are the potential gaps, challenges, and opportunities for further research?" After a screening step, the corpus of included articles indexed in PubMed or the Web of Science underwent full text review, which mapped the articles across 15 predefined axes. RESULTS: The corpus of 24 mapped studies includes 9 study protocols, 7 technical tools/solutions, 7 pilot/feasibility/acceptability studies, and 1 evaluation study. The review of the corpus revealed (1) an archetype of ePRO-enabled interventions for palliative cancer care, which most commonly use ePROs as study end point assessment instruments rather than integral intervention components; (2) the fact that the literature has not fully embraced the modern definitions that expand the scope of palliative care; (3) the striking shortage of promising ubiquitous computing devices (eg, smart activity trackers); and (4) emerging evidence about the benefits of narrowing down the target cancer population, especially when combined with modern patient-centered intervention design methodologies. CONCLUSION: Although research on exploiting ePROs for the development of digital palliative cancer care interventions is considerably active and demonstrates several successful cases, there is considerable room for improvement along the directions of the aforementioned findings. [ABSTRACT FROM AUTHOR]

Nowadays, patients have a wealth of information available on the Internet. Despite the potential benefits of Internet health information seeking, several concerns have been raised about the quality of information and about the patient's capability to evaluate medical information and to relate it to their own disease and treatment. As such, novel tools are required to effectively guide patients and provide high-quality medical information in an intelligent and personalised manner. With this aim, this paper presents the Personal Health Information Recommender (PHIR), a system to empower patients by enabling them to search in a high-quality document repository selected by experts, avoiding the information overload of the Internet. In addition, the information provided to the patients is personalised, based on individual preferences, medical conditions and other profiling information. Despite the generality of our approach, we apply the PHIR to a personal health record system constructed for cancer patients and we report on the design, the implementation and a preliminary validation of the platform. To the best of our knowledge, our platform is the only one combining natural language processing, ontologies and personal information to offer a unique user experience. [ABSTRACT FROM AUTHOR]

Knowledge graphs are becoming more and more prevalent on the web, ranging from small taxonomies, to large knowledge bases containing a vast amount of information. To construct such knowledge graphs either automatically or manually, tools are necessary for their quick exploration and understanding. Semantic summaries have been proposed as a key technology enabling the quick understanding and exploration of large knowledge graphs. Among the methods proposed for generating summaries, structural methods exploit primarily the structure of the graph in order to generate the result summaries. Approaches in the area focus on identifying the most important nodes and usually employ a single centrality measure, capturing a specific perspective on the notion of a node's importance. Moving from one centrality measure to many however, has the potential to generate a more objective view on nodes' importance, leading to better summaries. In this paper, we present SumMER, the first structural summarization technique exploiting machine learning techniques for RDF/S KGs. SumMER explores eight centrality measures and then exploits machine learning techniques for optimally selecting the most important nodes. Then those nodes are linked formulating a subgraph out of the original graph. We experimentally show that combining centrality measures with machine learning effectively increases the quality of the generated summaries. [ABSTRACT FROM AUTHOR]

Personal health record (PHR) systems are a rapidly expanding area in the field of health information technology which motivates an ongoing research towards their evaluation in several different aspects. In this direction, we present a systematic review of the currently available PHR systems. Initially, we define a clear and concise set of requirements for efficient PHR systems which is based on real-world implementation experiences of several European research projects and also on established and widely used formal standards. Subsequently, these requirements are used to perform a systematic evaluation of existing PHR system implementations. Our evaluation study provides a thorough requirement analysis and an insight on the current status of personal health record systems. The results of the present work can therefore be used as a basis for future evaluation studies which should be conducted periodically as technology evolves and requirements are revised. [ABSTRACT FROM AUTHOR]

In an epoch where shared decision making is gaining importance, a patient's commitment to and knowledge about his/her health condition is becoming more and more relevant. Health literacy is one of the most important factors in enhancing the involvement of patients in their care. Nevertheless, other factors can impair patient processing and understanding of health information: psychological aspects and cognitive style may affect the way patients approach, select, and retain information. This paper describes the development and validation of a short and easy to fill-out questionnaire that measures and collects psycho-cognitive information about patients, named ALGA-C. ALGA-C is a multilingual, multidevice instrument, and its validation was carried out in healthy people and breast cancer patients. In addition to the aforementioned questionnaire, a patient profiling mechanism has also been developed. The ALGA-C Profiler enables physicians to rapidly inspect each patient's individual cognitive profile and see at a glance the areas of concern. With this tool, doctors can modulate the language, vocabulary, and content of subsequent discussions with the patient, thus enabling easier understanding by the patient. This, in turn, helps the patient formulate questions and participate on an equal footing in the decision-making processes. Finally, a preview is given on the techniques under consideration for exploiting the constructed patient profile by a personal health record (PHR). Predefined rules will use a patient's profile to personalise the contents of the information presented and to customise ways in which users complete their tasks in a PHR system. This optimises information delivery to patients and makes it easier for the patient to decide what is of interest to him/her at the moment. [ABSTRACT FROM AUTHOR]

Developments in information and communication technology have changed the way healthcare processes are experienced by both patients and healthcare professionals: more and more services are now available through computers and mobile devices. Smartphones are becoming useful tools for managing one's health, and today, there are many available apps meant to increase self-management, empowerment and quality of life. However, there are concerns about the implications of using mHealth and apps: data protection issues, concerns about sharing information online, and the patients' capacity for discerning effective and valid apps from useless ones. The new General Data Protection Regulation has been introduced in order to give uniformity to data protection regulations among European countries but shared guidelines for mHealth are yet to develop. A unified perspective across Europe would increase the control over mHealth exploitation, making it possible to think of mHealth as effective and standard tools for future medical practice. [ABSTRACT FROM AUTHOR]

In the last decade, clinicians have started to shift from an individualistic perspective of the patient towards family-centred models of care, due to the increasing evidence from research and clinical practice of the crucial role of significant others in determining the patient's adjustment to cancer disease and management. eHealth tools can be considered a means to compensate the services gap and support outpatient care flows. Within the works of the European H2020 iManageCancer project, a review of the literature in the field of family resilience was conducted, in order to determine how to monitor the patient and his/her family's resilience through an eHealth platform. An analysis of existing family resilience questionnaires suggested that no measure was appropriate for cancer patients and their families. For this reason, a new family resilience questionnaire (named FaRe) was developed to screen the patient's and caregiver's psycho-emotional resources. Composed of 24 items, it is divided into four subscales: Communication and Cohesion, Perceived Family Coping, Religiousness and Spirituality, and Perceived Social Support. Embedded in the iManageCancer eHealth platform, it allows users and clinicians to monitor the patient's and the caregivers' resilience throughout the cancer trajectory. [ABSTRACT FROM AUTHOR]

Clinical decision support systems can play a crucial role in healthcare delivery as they promise to improve health outcomes and patient safety, reduce medical errors and costs and contribute to patient satisfaction. Used in an optimal way, they increase the quality of healthcare by proposing the right information and intervention to the right person at the right time in the healthcare delivery process. This paper reports on a specific approach to integrated clinical decision support and patient guidance in the cancer domain as proposed by the H2020 iManageCancer project. This project aims at facilitating efficient self-management and management of cancer according to the latest available clinical knowledge and the local healthcare delivery model, supporting patients and their healthcare providers in making informed decisions on treatment choices and in managing the side effects of their therapy. The iManageCancer platform is a comprehensive platform of interconnected mobile tools to empower cancer patients and to support them in the management of their disease in collaboration with their doctors. The backbone of the iManageCancer platform comprises a personal health record and the central decision support unit (CDSU). The latter offers dedicated services to the end users in combination with the apps iManageMy-Health and iSupportMyPatients. The CDSU itself is composed of the so-called Care Flow Engine (CFE) and the model repository framework (MRF). The CFE executes personalised and workflow oriented formal disease management diagrams (Care Flows). In decision points of such a Care Flow, rules that operate on actual health information of the patient decide on the treatment path that the system follows. Alternatively, the system can also invoke a predictive model of the MRF to proceed with the best treatment path in the diagram. Care Flow diagrams are designed by clinical experts with a specific graphical tool that also deploys these diagrams as executable workflows in the CFE following the Business Process Model and Notation (BPMN) standard. They are exposed as services that patients or their doctors can use in their apps in order to manage certain aspects of the cancer disease like pain, fatigue or the monitoring of chemotherapies at home. The mHealth platform for cancer patients is currently being assessed in clinical pilots in Italy and Germany and in several end-user workshops. [ABSTRACT FROM AUTHOR]

Background: The adoption in oncology of Clinical Decision Support (CDS) may help clinical users to efficiently deal with the high complexity of the domain, lead to improved patient outcomes, and reduce the current knowledge gap between clinical research and practice. While significant effort has been invested in the implementation of CDS, the uptake in the clinic has been limited. The barriers to adoption have been extensively discussed in the literature. In oncology, current CDS solutions are not able to support the complex decisions required for stratification and personalized treatment of patients and to keep up with the high rate of change in therapeutic options and knowledge.Results: To address these challenges, we propose a framework enabling efficient implementation of meaningful CDS that incorporates a large variety of clinical knowledge models to bring to the clinic comprehensive solutions leveraging the latest domain knowledge. We use both literature-based models and models built within the p-medicine project using the rich datasets from clinical trials and care provided by the clinical partners. The framework is open to the biomedical community, enabling reuse of deployed models by third-party CDS implementations and supporting collaboration among modelers, CDS implementers, biomedical researchers and clinicians. To increase adoption and cope with the complexity of patient management in oncology, we also support and leverage the clinical processes adhered to by healthcare organizations. We design an architecture that extends the CDS framework with workflow functionality. The clinical models are embedded in the workflow models and executed at the right time, when and where the recommendations are needed in the clinical process.Conclusions: In this paper we present our CDS framework developed in p-medicine and the CDS implementation leveraging the framework. To support complex decisions, the framework relies on clinical models that encapsulate relevant clinical knowledge. Next to assisting the decisions, this solution supports by default (through modeling and implementation of workflows) the decision processes as well and exploits the knowledge embedded in those processes. [ABSTRACT FROM AUTHOR]