A network approach for managing and processing big cancer data in clouds

Translational cancer research requires integrative analysis of multiple levels of big cancer data to identify and treat cancer. In order to address the issues that data is decentralised, growing and continually being updated, and the content living or archiving on different information sources partially overlaps creating redundancies as well as contradictions and inconsistencies, we develop a data network model and technology for constructing and managing big cancer data. To support our data network approach for data process and analysis, we employ a semantic content network approach and adopt the CELAR cloud platform. The prototype implementation shows that the CELAR cloud can satisfy the on-demanding needs of various data resources for management and process of big cancer data

A Semantic-Based Information Management System to Support Innovative Product Design

International competition and the rapidly global economy, unified by improved communication and transportation, offer to the consumers an enormous choice of goods and services. The result is that companies now require quality, value, time to market and innovation to be successful in order to win the increasing competition. In the engineering sector this is traduced in need of optimization of the design process and in maximization of re-use of data and knowledge already existing in the company. The “SIMI-Pro” (Semantic Information Management system for Innovative Product design) system addresses specific deficiencies in the conceptual phase of product design when knowledge management, if applied, is often sectorial. Its main contribution is in allowing easy, fast and centralized collection of data from multiple sources and in supporting the retrieval and re-use of a wide range of data that will help stylists and engineers shortening the production cycle. SIMI-Pro will be one of the first prototypes to base its information management and its knowledge sharing system on process ontology and it will demonstrate how the use of centralized network systems, coupled with Semantic Web technologies, can improve inter-working activities and interdisciplinary knowledge sharing

Ontology-assisted database integration to support natural language processing and biomedical data-mining

Successful biomedical data mining and information extraction require a complete picture of biological phenomena such as genes, biological processes, and diseases; as these exist on different levels of granularity. To realize this goal, several freely available heterogeneous databases as well as proprietary structured datasets have to be integrated into a single global customizable scheme. We will present a tool to integrate different biological data sources by mapping them to a proprietary biomedical ontology that has been developed for the purposes of making computers understand medical natural language

Tailored information dashboards: A systematic mapping of the literature

Information dashboards are extremely useful tools to exploit knowledge. Dashboards enable users to reach insights and to identify patterns within data at-a-glance. However, dashboards present a series of characteristics and configurations that could not be optimal for every user, thus requiring the modification or variation of its features to fulfill specific user requirements. This variation process is usually referred to as customization, personalization or adaptation, depending on how this variation process is achieved. Given the great number of users and the exponential growth of data sources, tailoring an information dashboard is not a trivial task, as several solutions and configurations could arise. To analyze and understand the current state-of-the-art regarding tailored information dashboards, a systematic mapping has been performed. This mapping focus on answering questions regarding how existing dashboard solutions in the literature manage the customization, personalization and/or adaptation of its elements to produce tailored displays

WikiPathways: building research communities on biological pathways.

Here, we describe the development of WikiPathways (http://www.wikipathways.org), a public wiki for pathway curation, since it was first published in 2008. New features are discussed, as well as developments in the community of contributors. New features include a zoomable pathway viewer, support for pathway ontology annotations, the ability to mark pathways as private for a limited time and the availability of stable hyperlinks to pathways and the elements therein. WikiPathways content is freely available in a variety of formats such as the BioPAX standard, and the content is increasingly adopted by external databases and tools, including Wikipedia. A recent development is the use of WikiPathways as a staging ground for centrally curated databases such as Reactome. WikiPathways is seeing steady growth in the number of users, page views and edits for each pathway. To assess whether the community curation experiment can be considered successful, here we analyze the relation between use and contribution, which gives results in line with other wiki projects. The novel use of pathway pages as supplementary material to publications, as well as the addition of tailored content for research domains, is expected to stimulate growth further