BackgroundNext Generation Sequencing (NGS) is playing a key role in therapeutic decision making for the cancer prognosis and treatment. The NGS technologies are producing a massive amount of sequencing datasets. Often, these datasets are published from the isolated and different sequencing facilities. Consequently, the process of sharing and aggregating multisite sequencing datasets are thwarted by issues such as the need to discover relevant data from different sources, built scalable repositories, the automation of data linkage, the volume of the data, efficient querying mechanism, and information rich intuitive visualisation.ResultsWe present an approach to link and query different sequencing datasets (TCGA, COSMIC, REACTOME, KEGG and GO) to indicate risks for four cancer types – Ovarian Serous Cystadenocarcinoma (OV), Uterine Corpus Endometrial Carcinoma (UCEC), Uterine Carcinosarcoma (UCS), Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (CESC) – covering the 16 healthy tissue-specific genes from Illumina Human Body Map 2.0. The differentially expressed genes from Illumina Human Body Map 2.0 are analysed together with the gene expressions reported in COSMIC and TCGA repositories leading to the discover of potential biomarkers for a tissue-specific cancer.ConclusionWe analyse the tissue expression of genes, copy number variation (CNV), somatic mutation, and promoter methylation to identify associated pathways and find novel biomarkers. We discovered twenty (20) mutated genes and three (3) potential pathways causing promoter changes in different gynaecological cancer types. We propose a data-interlinked platform called BIOOPENER that glues together heterogeneous cancer and biomedical repositories. The key approach is to find correspondences (or data links) among genetic, cellular and molecular features across isolated cancer datasets giving insight into cancer progression from normal to diseased tissues. The proposed BIOOPENER platform enriches mutations by filling in missing links from TCGA, COSMIC, REACTOME, KEGG and GO datasets and provides an interlinking mechanism to understand cancer progression from normal to diseased tissues with pathway components, which in turn helped to map mutations, associated phenotypes, pathways, and mechanism.

Background Modern smartphones contain sophisticated high-end hardware features, offering high computational capabilities at extremely manageable costs and have undoubtedly become an integral part in users' daily life. Additionally, smartphones offer a well-established ecosystem that is easily discoverable and accessible via the marketplaces of differing mobile platforms, thus encouraging the development of many smartphone apps. Such apps are not exclusively used for entertainment purposes but are also commonplace in health care and medical use. A variety of those health and medical apps exist within the context of tinnitus, a phantom sound perception in the absence of any physical external source. Objective In this paper, we shed light on existing smartphone apps addressing tinnitus by providing an up-to-date overview. Methods Based on PRISMA guidelines, we systematically searched and identified existing smartphone apps on the most prominent app markets, namely Google Play Store and Apple App Store. In addition, we applied the Mobile App Rating Scale (MARS) to evaluate and assess the apps in terms of their general quality and in-depth user experience. Results Our systematic search and screening of smartphone apps yielded a total of 34 apps (34 Android apps, 26 iOS apps). The mean MARS scores (out of 5) ranged between 2.65-4.60. The Tinnitus Peace smartphone app had the lowest score (mean 2.65, SD 0.20), and Sanvello—Stress and Anxiety Help had the highest MARS score (mean 4.60, SD 0.10). The interrater agreement was substantial (Fleiss κ=0.74), the internal consistency was excellent (Cronbach α=.95), and the interrater reliability was found to be both high and excellent—Guttman λ6=0.94 and intraclass correlation, ICC(2,k) 0.94 (95% CI 0.91-0.97), respectively. Conclusions This work demonstrated that there exists a plethora of smartphone apps for tinnitus. All of the apps received MARS scores higher than 2, suggesting that they all have some technical functional value. However, nearly all identified apps were lacking in terms of scientific evidence, suggesting the need for stringent clinical validation of smartphone apps in future. To the best of our knowledge, this work is the first to systematically identify and evaluate smartphone apps within the context of tinnitus.

BackgroundSeveral query federation engines have been proposed for accessing public Linked Open Data sources. However, in many domains, resources are sensitive and access to these resources is tightly controlled by stakeholders; consequently, privacy is a major concern when federating queries over such datasets. In the Healthcare and Life Sciences (HCLS) domain real-world datasets contain sensitive statistical information: strict ownership is granted to individuals working in hospitals, research labs, clinical trial organisers, etc. Therefore, the legal and ethical concerns on (i) preserving the anonymity of patients (or clinical subjects); and (ii) respecting data ownership through access control; are key challenges faced by the data analytics community working within the HCLS domain. Likewise statistical data play a key role in the domain, where the RDF Data Cube Vocabulary has been proposed as a standard format to enable the exchange of such data. However, to the best of our knowledge, no existing approach has looked to optimise federated queries over such statistical data.ResultsWe present SAFE: a query federation engine that enables policy-aware access to sensitive statistical datasets represented as RDF data cubes. SAFE is designed specifically to query statistical RDF data cubes in a distributed setting, where access control is coupled with source selection, user profiles and their access rights. SAFE proposes a join-aware source selection method that avoids wasteful requests to irrelevant and unauthorised data sources. In order to preserve anonymity and enforce stricter access control, SAFE’s indexing system does not hold any data instances—it stores only predicates and endpoints. The resulting data summary has a significantly lower index generation time and size compared to existing engines, which allows for faster updates when sources change.ConclusionsWe validate the performance of the system with experiments over real-world datasets provided by three clinical organisations as well as legacy linked datasets. We show that SAFE enables granular graph-level access control over distributed clinical RDF data cubes and efficiently reduces the source selection and overall query execution time when compared with general-purpose SPARQL query federation engines in the targeted setting.

Smartphones containing sophisticated high-end hardware and offering high computational capabilities at extremely manageable costs have become mainstream and an integral part of users’ lives. Widespread adoption of smartphone devices has encouraged the development of many smartphone applications, resulting in a well-established ecosystem, which is easily discoverable and accessible via respective marketplaces of differing mobile platforms. These smartphone applications are no longer exclusively limited to entertainment purposes but are increasingly established in the scientific and medical field. In the context of tinnitus, the ringing in the ear, these smartphone apps range from relief, management, self-help, all the way to interfacing external sensors to better understand the phenomenon. In this paper, we aim to bring forth the smartphone applications in and around tinnitus. Based on the PRISMA guidelines, we systematically analyze and investigate the current state of smartphone apps, that are directly applied in the context of tinnitus. In particular, we explore Google Scholar, CiteSeerX, Microsoft Academics, Semantic Scholar for the identification of scientific contributions. Additionally, we search and explore Google’s Play and Apple’s App Stores to identify relevant smartphone apps and their respective properties. This review work gives (1) an up-to-date overview of existing apps, and (2) lists and discusses scientific literature pertaining to the smartphone apps used within the context of tinnitus.

Abstract. The increase in the volume and heterogeneity of biomedical data sources has motivated researchers to embrace Linked Data (LD) technologies to solve the ensuing integration challenges and enhance information discovery. As an integral part of the EU GRANATUM project, a Linked Biomedical Dataspace (LBDS) was developed to semantically interlink data from multiple sources and augment the design of in silico experiments for cancer chemoprevention drug discovery. The different components of the LBDS facilitate both the bioinformaticians and the biomedical researchers to publish, link, query and visually explore the heterogeneous datasets. We have extensively evaluated the usability of the entire platform. In this paper, we showcase three different workflows depicting real-world scenarios on the use of LBDS by the domain users to intuitively retrieve meaningful information from the integrated sources. We report the important lessons that we learned through the challenges encountered and our accumulated experience during the collaborative processes which would make it easier for LD practitioners to create such dataspaces in other domains. We also provide a concise set of generic recommendations to develop LD platforms useful for drug discovery.