Towards an interoperable information infrastructure providing decision support for genomic medicine

Genetic dispositions play a major role in individual disease risk and treatment response. Genomic medicine, in which medical decisions are refined by genetic information of particular patients, is becoming increasingly important. Here we describe our work and future visions around the creation of a distributed infrastructure for pharmacogenetic data and medical decision support, based on industry standards such as the Web Ontology Language (OWL) and the Arden Syntax

Developing a kidney and urinary pathway knowledge base

<p>Abstract</p> <p>Background</p> <p>Chronic renal disease is a global health problem. The identification of suitable biomarkers could facilitate early detection and diagnosis and allow better understanding of the underlying pathology. One of the challenges in meeting this goal is the necessary integration of experimental results from multiple biological levels for further analysis by data mining. Data integration in the life science is still a struggle, and many groups are looking to the benefits promised by the Semantic Web for data integration.</p> <p>Results</p> <p>We present a Semantic Web approach to developing a knowledge base that integrates data from high-throughput experiments on kidney and urine. A specialised KUP ontology is used to tie the various layers together, whilst background knowledge from external databases is incorporated by conversion into RDF. Using SPARQL as a query mechanism, we are able to query for proteins expressed in urine and place these back into the context of genes expressed in regions of the kidney.</p> <p>Conclusions</p> <p>The KUPKB gives KUP biologists the means to ask queries across many resources in order to aggregate knowledge that is necessary for answering biological questions. The Semantic Web technologies we use, together with the background knowledge from the domain’s ontologies, allows both rapid conversion and integration of this knowledge base. The KUPKB is still relatively small, but questions remain about scalability, maintenance and availability of the knowledge itself.</p> <p>Availability</p> <p>The KUPKB may be accessed via <url>http://www.e-lico.eu/kupkb</url>.</p

Provenance Management over Linked Data Streams

Provenance describes how results are produced starting from data sources, curation, recovery, intermediate processing, to the final results. Provenance has been applied to solve many problems and in particular to understand how errors are propagated in large-scale environments such as Internet of Things, Smart Cities. In fact, in such environments operations on data are often performed by multiple uncoordinated parties, each potentially introducing or propagating errors. These errors cause uncertainty of the overall data analytics process that is further amplified when many data sources are combined and errors get propagated across multiple parties. The ability to properly identify how such errors influence the results is crucial to assess the quality of the results. This problem becomes even more challenging in the case of Linked Data Streams, where data is dynamic and often incomplete. In this paper, we introduce methods to compute provenance over Linked Data Streams. More specifically, we propose provenance management techniques to compute provenance of continuous queries executed over complete Linked Data streams. Unlike traditional provenance management techniques, which are applied on static data, we focus strictly on the dynamicity and heterogeneity of Linked Data streams. Specifically, in this paper we describe: i) means to deliver a dynamic provenance trace of the results to the user, ii) a system capable to execute queries over dynamic Linked Data and compute provenance of these queries, and iii) an empirical evaluation of our approach using real-world datasets

Multimodal Wearable Intelligence for Dementia Care in Healthcare 4.0: A Survey

As a new revolution of Ubiquitous Computing and Internet of Things, multimodal wearable intelligence technique is rapidly becoming a new research topic in both academic and industrial fields. Owning to the rapid spread of wearable and mobile devices, this technique is evolving healthcare from traditional hub-based systems to more personalised healthcare systems. This trend is well-aligned with recent Healthcare 4.0 which is a continuous process of transforming the entire healthcare value chain to be preventive, precise, predictive and personalised, with significant benefits to elder care. But empowering the utility of multimodal wearable intelligence technique for elderly care like people with dementia is significantly challenging considering many issues, such as shortage of cost-effective wearable sensors, heterogeneity of wearable devices connected, high demand for interoperability, etc. Focusing on these challenges, this paper gives a systematic review of advanced multimodal wearable intelligence technologies for dementia care in Healthcare 4.0. One framework is proposed for reviewing the current research of wearable intelligence, and key enabling technologies, major applications, and successful case studies in dementia care, and finally points out future research trends and challenges in Healthcare 4.0

TcruziKB: Enabling Complex Queries for Genomic Data Exploration

We developed a novel analytical environment to aid in the examination of the extensive amount of interconnected data available for genome projects. Our focus is to enable flexibility and abstraction from implementation details, while retaining the expressivity required for post-genomic research. To achieve this goal, we associated genomics data to ontologies and implemented a query formulation and execution environment with added visualization capabilities. We use ontology schemas to guide the user through the process of building complex queries in a flexible Web interface. Queries are serialized in SPARQL and sent to servers via Ajax. A component for visualization of the results allows researchers to explore result sets in multiple perspectives to suit different analytical needs. We show a use case of semantic computing with real world data. We demonstrate facilitated access to information through expressive queries in a flexible and friendly user interface. Our system scores 90.54% in a user satisfaction evaluation with 30 subjects. In comparison with traditional genome databases, preliminary evaluation indicates a reduction of the amount of user interaction required to answer the provided sample queries

Biomedical data integration in computational drug design and bioinformatics

[Abstract In recent years, in the post genomic era, more and more data is being generated by biological high throughput technologies, such as proteomics and transcriptomics. This omics data can be very useful, but the real challenge is to analyze all this data, as a whole, after integrating it. Biomedical data integration enables making queries to different, heterogeneous and distributed biomedical data sources. Data integration solutions can be very useful not only in the context of drug design, but also in biomedical information retrieval, clinical diagnosis, system biology, etc. In this review, we analyze the most common approaches to biomedical data integration, such as federated databases, data warehousing, multi-agent systems and semantic technology, as well as the solutions developed using these approaches in the past few years.Red Gallega de Investigación sobre Cáncer Colorrectal; Ref. 2009/58Programa Iberoamericano de Ciencia y Tecnología para el Desarrollo; 209RT- 0366Instituto de Salud Carlos III; PIO52048Instituto de Salud Carlos III; RD07/0067/0005Ministerio de Industria, Turismo y Comercio; TSI-020110-2009-

Linked Data based Health Information Representation, Visualization and Retrieval System on the Semantic Web

Dissertation submitted in partial fulfillment of the requirements for the Degree of Master of Science in Geospatial Technologies.To better facilitate health information dissemination, using flexible ways to represent, query and visualize health data becomes increasingly important. Semantic Web technologies, which provide a common framework by allowing data to be shared and reused between applications, can be applied to the management of health data. Linked open data - a new semantic web standard to publish and link heterogonous data- allows not only human, but also machine to brows data in unlimited way. Through a use case of world health organization HIV data of sub Saharan Africa - which is severely affected by HIV epidemic, this thesis built a linked data based health information representation, querying and visualization system. All the data was represented with RDF, by interlinking it with other related datasets, which are already on the cloud. Over all, the system have more than 21,000 triples with a SPARQL endpoint; where users can download and use the data and – a SPARQL query interface where users can put different type of query and retrieve the result. Additionally, It has also a visualization interface where users can visualize the SPARQL result with a tool of their preference. For users who are not familiar with SPARQL queries, they can use the linked data search engine interface to search and browse the data. From this system we can depict that current linked open data technologies have a big potential to represent heterogonous health data in a flexible and reusable manner and they can serve in intelligent queries, which can support decision-making. However, in order to get the best from these technologies, improvements are needed both at the level of triple stores performance and domain-specific ontological vocabularies