e-Social Science and Evidence-Based Policy Assessment : Challenges and Solutions

Peer reviewedPreprin

Linking genes to diseases with a SNPedia-Gene Wiki mashup

<p>Abstract</p> <p>Background</p> <p>A variety of topic-focused wikis are used in the biomedical sciences to enable the mass-collaborative synthesis and distribution of diverse bodies of knowledge. To address complex problems such as defining the relationships between genes and disease, it is important to bring the knowledge from many different domains together. Here we show how advances in wiki technology and natural language processing can be used to automatically assemble ‘meta-wikis’ that present integrated views over the data collaboratively created in multiple source wikis.</p> <p>Results</p> <p>We produced a semantic meta-wiki called the Gene Wiki+ that automatically mirrors and integrates data from the Gene Wiki and SNPedia. The Gene Wiki+, available at (<url>http://genewikiplus.org/</url>), captures 8,047 distinct gene-disease relationships. SNPedia accounts for 4,149 of the gene-disease pairs, the Gene Wiki provides 4,377 and only 479 appear independently in both sources. All of this content is available to query and browse and is provided as linked open data.</p> <p>Conclusions</p> <p>Wikis contain increasing amounts of diverse, biological information useful for elucidating the connections between genes and disease. The Gene Wiki+ shows how wiki technology can be used in concert with natural language processing to provide integrated views over diverse underlying data sources.</p

Enriching ontological user profiles with tagging history for multi-domain recommendations

Many advanced recommendation frameworks employ ontologies of various complexities to model individuals and items, providing a mechanism for the expression of user interests and the representation of item attributes. As a result, complex matching techniques can be applied to support individuals in the discovery of items according to explicit and implicit user preferences. Recently, the rapid adoption of Web2.0, and the proliferation of social networking sites, has resulted in more and more users providing an increasing amount of information about themselves that could be exploited for recommendation purposes. However, the unification of personal information with ontologies using the contemporary knowledge representation methods often associated with Web2.0 applications, such as community tagging, is a non-trivial task. In this paper, we propose a method for the unification of tags with ontologies by grounding tags to a shared representation in the form of Wordnet and Wikipedia. We incorporate individuals' tagging history into their ontological profiles by matching tags with ontology concepts. This approach is preliminary evaluated by extending an existing news recommendation system with user tagging histories harvested from popular social networking sites

Highly focused document retrieval in aerospace engineering : user interaction design and evaluation

Purpose – This paper seeks to describe the preliminary studies (on both users and data), the design and evaluation of the K-Search system for searching legacy documents in aerospace engineering. Real-world reports of jet engine maintenance challenge the current indexing practice, while real users’ tasks require retrieving the information in the proper context. K-Search is currently in use in Rolls-Royce plc and has evolved to include other tools for knowledge capture and management. Design/methodology/approach – Semantic Web techniques have been used to automatically extract information from the reports while maintaining the original context, allowing a more focused retrieval than with more traditional techniques. The paper combines semantic search with classical information retrieval to increase search effectiveness. An innovative user interface has been designed to take advantage of this hybrid search technique. The interface is designed to allow a flexible and personal approach to searching legacy data. Findings – The user evaluation showed that the system is effective and well received by users. It also shows that different people look at the same data in different ways and make different use of the same system depending on their individual needs, influenced by their job profile and personal attitude. Research limitations/implications – This study focuses on a specific case of an enterprise working in aerospace engineering. Although the findings are likely to be shared with other engineering domains (e.g. mechanical, electronic), the study does not expand the evaluation to different settings. Originality/value – The study shows how real context of use can provide new and unexpected challenges to researchers and how effective solutions can then be adopted and used in organizations.</p

Connected Information Management

Society is currently inundated with more information than ever, making efficient management a necessity. Alas, most of current information management suffers from several levels of disconnectedness: Applications partition data into segregated islands, small notes don’t fit into traditional application categories, navigating the data is different for each kind of data; data is either available at a certain computer or only online, but rarely both. Connected information management (CoIM) is an approach to information management that avoids these ways of disconnectedness. The core idea of CoIM is to keep all information in a central repository, with generic means for organization such as tagging. The heterogeneity of data is taken into account by offering specialized editors. The central repository eliminates the islands of application-specific data and is formally grounded by a CoIM model. The foundation for structured data is an RDF repository. The RDF editing meta-model (REMM) enables form-based editing of this data, similar to database applications such as MS access. Further kinds of data are supported by extending RDF, as follows. Wiki text is stored as RDF and can both contain structured text and be combined with structured data. Files are also supported by the CoIM model and are kept externally. Notes can be quickly captured and annotated with meta-data. Generic means for organization and navigation apply to all kinds of data. Ubiquitous availability of data is ensured via two CoIM implementations, the web application HYENA/Web and the desktop application HYENA/Eclipse. All data can be synchronized between these applications. The applications were used to validate the CoIM ideas

Chemical information matters: an e-Research perspective on information and data sharing in the chemical sciences

Recently, a number of organisations have called for open access to scientific information and especially to the data obtained from publicly funded research, among which the Royal Society report and the European Commission press release are particularly notable. It has long been accepted that building research on the foundations laid by other scientists is both effective and efficient. Regrettably, some disciplines, chemistry being one, have been slow to recognise the value of sharing and have thus been reluctant to curate their data and information in preparation for exchanging it. The very significant increases in both the volume and the complexity of the datasets produced has encouraged the expansion of e-Research, and stimulated the development of methodologies for managing, organising, and analysing "big data". We review the evolution of cheminformatics, the amalgam of chemistry, computer science, and information technology, and assess the wider e-Science and e-Research perspective. Chemical information does matter, as do matters of communicating data and collaborating with data. For chemistry, unique identifiers, structure representations, and property descriptors are essential to the activities of sharing and exchange. Open science entails the sharing of more than mere facts: for example, the publication of negative outcomes can facilitate better understanding of which synthetic routes to choose, an aspiration of the Dial-a-Molecule Grand Challenge. The protagonists of open notebook science go even further and exchange their thoughts and plans. We consider the concepts of preservation, curation, provenance, discovery, and access in the context of the research lifecycle, and then focus on the role of metadata, particularly the ontologies on which the emerging chemical Semantic Web will depend. Among our conclusions, we present our choice of the "grand challenges" for the preservation and sharing of chemical information

Supporting collaborative improvement of resources in the Khresmoi health information system

Since medical knowledge relies on both scientific knowledge and real-life experience, the importance of user contributions to improve resources in health systems cannot be underestimated. We present work from the Khresmoi project which aims to develop a multilingual multimodal search and access system for biomedical information and documents. Khresmoi targets three distinct user classes with differing levels of medical knowledge and information requirements, namely: general public, general practitioners, and, as an example of an area of clinical expertise, radiologists. The Khresmoi system will provide these users with valuable (whose quality has been evaluated and approved) and enriched (meta information from biomedical knowledge bases is added) medical information, selected to fit their medical knowledge and their preferred language. The system will include novel collaborative components of the system are designed to provide means for users to contribute to the system’s knowledge by adding or correcting annotations to the documents, as well as a collaborative platform where they will be able to share their own files and both annotate and discuss them