Visualising biological data: a semantic approach to tool and database integration

<p>Abstract</p> <p>Motivation</p> <p>In the biological sciences, the need to analyse vast amounts of information has become commonplace. Such large-scale analyses often involve drawing together data from a variety of different databases, held remotely on the internet or locally on in-house servers. Supporting these tasks are <it>ad hoc </it>collections of data-manipulation tools, scripting languages and visualisation software, which are often combined in arcane ways to create cumbersome systems that have been customised for a particular purpose, and are consequently not readily adaptable to other uses. For many day-to-day bioinformatics tasks, the sizes of current databases, and the scale of the analyses necessary, now demand increasing levels of automation; nevertheless, the unique experience and intuition of human researchers is still required to interpret the end results in any meaningful biological way. Putting humans in the loop requires tools to support real-time interaction with these vast and complex data-sets. Numerous tools do exist for this purpose, but many do not have optimal interfaces, most are effectively isolated from other tools and databases owing to incompatible data formats, and many have limited real-time performance when applied to realistically large data-sets: much of the user's cognitive capacity is therefore focused on controlling the software and manipulating esoteric file formats rather than on performing the research.</p> <p>Methods</p> <p>To confront these issues, harnessing expertise in human-computer interaction (HCI), high-performance rendering and distributed systems, and guided by bioinformaticians and end-user biologists, we are building reusable software components that, together, create a toolkit that is both architecturally sound from a computing point of view, and addresses both user and developer requirements. Key to the system's usability is its direct exploitation of semantics, which, crucially, gives individual components knowledge of their own functionality and allows them to interoperate seamlessly, removing many of the existing barriers and bottlenecks from standard bioinformatics tasks.</p> <p>Results</p> <p>The toolkit, named Utopia, is freely available from <url>http://utopia.cs.man.ac.uk/</url>.</p

CHORUS Deliverable 2.2: Second report - identification of multi-disciplinary key issues for gap analysis toward EU multimedia search engines roadmap

After addressing the state-of-the-art during the first year of Chorus and establishing the existing landscape in multimedia search engines, we have identified and analyzed gaps within European research effort during our second year. In this period we focused on three directions, notably technological issues, user-centred issues and use-cases and socio- economic and legal aspects. These were assessed by two central studies: firstly, a concerted vision of functional breakdown of generic multimedia search engine, and secondly, a representative use-cases descriptions with the related discussion on requirement for technological challenges. Both studies have been carried out in cooperation and consultation with the community at large through EC concertation meetings (multimedia search engines cluster), several meetings with our Think-Tank, presentations in international conferences, and surveys addressed to EU projects coordinators as well as National initiatives coordinators. Based on the obtained feedback we identified two types of gaps, namely core technological gaps that involve research challenges, and “enablers”, which are not necessarily technical research challenges, but have impact on innovation progress. New socio-economic trends are presented as well as emerging legal challenges

BlogForever D2.6: Data Extraction Methodology

This report outlines an inquiry into the area of web data extraction, conducted within the context of blog preservation. The report reviews theoretical advances and practical developments for implementing data extraction. The inquiry is extended through an experiment that demonstrates the effectiveness and feasibility of implementing some of the suggested approaches. More specifically, the report discusses an approach based on unsupervised machine learning that employs the RSS feeds and HTML representations of blogs. It outlines the possibilities of extracting semantics available in blogs and demonstrates the benefits of exploiting available standards such as microformats and microdata. The report proceeds to propose a methodology for extracting and processing blog data to further inform the design and development of the BlogForever platform

A Semantics-based User Interface Model for Content Annotation, Authoring and Exploration

The Semantic Web and Linked Data movements with the aim of creating, publishing and interconnecting machine readable information have gained traction in the last years. However, the majority of information still is contained in and exchanged using unstructured documents, such as Web pages, text documents, images and videos. This can also not be expected to change, since text, images and videos are the natural way in which humans interact with information. Semantic structuring of content on the other hand provides a wide range of advantages compared to unstructured information. Semantically-enriched documents facilitate information search and retrieval, presentation, integration, reusability, interoperability and personalization. Looking at the life-cycle of semantic content on the Web of Data, we see quite some progress on the backend side in storing structured content or for linking data and schemata. Nevertheless, the currently least developed aspect of the semantic content life-cycle is from our point of view the user-friendly manual and semi-automatic creation of rich semantic content. In this thesis, we propose a semantics-based user interface model, which aims to reduce the complexity of underlying technologies for semantic enrichment of content by Web users. By surveying existing tools and approaches for semantic content authoring, we extracted a set of guidelines for designing efficient and effective semantic authoring user interfaces. We applied these guidelines to devise a semantics-based user interface model called WYSIWYM (What You See Is What You Mean) which enables integrated authoring, visualization and exploration of unstructured and (semi-)structured content. To assess the applicability of our proposed WYSIWYM model, we incorporated the model into four real-world use cases comprising two general and two domain-specific applications. These use cases address four aspects of the WYSIWYM implementation: 1) Its integration into existing user interfaces, 2) Utilizing it for lightweight text analytics to incentivize users, 3) Dealing with crowdsourcing of semi-structured e-learning content, 4) Incorporating it for authoring of semantic medical prescriptions

Large-Scale Pattern-Based Information Extraction from the World Wide Web

Extracting information from text is the task of obtaining structured, machine-processable facts from information that is mentioned in an unstructured manner. It thus allows systems to automatically aggregate information for further analysis, efficient retrieval, automatic validation, or appropriate visualization. This work explores the potential of using textual patterns for Information Extraction from the World Wide Web

A Personal Research Agent for Semantic Knowledge Management of Scientific Literature

The unprecedented rate of scientific publications is a major threat to the productivity of knowledge workers, who rely on scrutinizing the latest scientific discoveries for their daily tasks. Online digital libraries, academic publishing databases and open access repositories grant access to a plethora of information that can overwhelm a researcher, who is looking to obtain fine-grained knowledge relevant for her task at hand. This overload of information has encouraged researchers from various disciplines to look for new approaches in extracting, organizing, and managing knowledge from the immense amount of available literature in ever-growing repositories. In this dissertation, we introduce a Personal Research Agent that can help scientists in discovering, reading and learning from scientific documents, primarily in the computer science domain. We demonstrate how a confluence of techniques from the Natural Language Processing and Semantic Web domains can construct a semantically-rich knowledge base, based on an inter-connected graph of scholarly artifacts – effectively transforming scientific literature from written content in isolation, into a queryable web of knowledge, suitable for machine interpretation. The challenges of creating an intelligent research agent are manifold: The agent's knowledge base, analogous to his 'brain', must contain accurate information about the knowledge `stored' in documents. It also needs to know about its end-users' tasks and background knowledge. In our work, we present a methodology to extract the rhetorical structure (e.g., claims and contributions) of scholarly documents. We enhance our approach with entity linking techniques that allow us to connect the documents with the Linked Open Data (LOD) cloud, in order to enrich them with additional information from the web of open data. Furthermore, we devise a novel approach for automatic profiling of scholarly users, thereby, enabling the agent to personalize its services, based on a user's background knowledge and interests. We demonstrate how we can automatically create a semantic vector-based representation of the documents and user profiles and utilize them to efficiently detect similar entities in the knowledge base. Finally, as part of our contributions, we present a complete architecture providing an end-to-end workflow for the agent to exploit the opportunities of linking a formal model of scholarly users and scientific publications

PERICLES Deliverable 4.3:Content Semantics and Use Context Analysis Techniques

The current deliverable summarises the work conducted within task T4.3 of WP4, focusing on the extraction and the subsequent analysis of semantic information from digital content, which is imperative for its preservability. More specifically, the deliverable defines content semantic information from a visual and textual perspective, explains how this information can be exploited in long-term digital preservation and proposes novel approaches for extracting this information in a scalable manner. Additionally, the deliverable discusses novel techniques for retrieving and analysing the context of use of digital objects. Although this topic has not been extensively studied by existing literature, we believe use context is vital in augmenting the semantic information and maintaining the usability and preservability of the digital objects, as well as their ability to be accurately interpreted as initially intended.PERICLE

Integration and mining of malaria molecular, functional and pharmacological data: how far are we from a chemogenomic knowledge space?

The organization and mining of malaria genomic and post-genomic data is highly motivated by the necessity to predict and characterize new biological targets and new drugs. Biological targets are sought in a biological space designed from the genomic data from Plasmodium falciparum, but using also the millions of genomic data from other species. Drug candidates are sought in a chemical space containing the millions of small molecules stored in public and private chemolibraries. Data management should therefore be as reliable and versatile as possible. In this context, we examined five aspects of the organization and mining of malaria genomic and post-genomic data: 1) the comparison of protein sequences including compositionally atypical malaria sequences, 2) the high throughput reconstruction of molecular phylogenies, 3) the representation of biological processes particularly metabolic pathways, 4) the versatile methods to integrate genomic data, biological representations and functional profiling obtained from X-omic experiments after drug treatments and 5) the determination and prediction of protein structures and their molecular docking with drug candidate structures. Progresses toward a grid-enabled chemogenomic knowledge space are discussed.Comment: 43 pages, 4 figures, to appear in Malaria Journa

Final FLaReNet deliverable: Language Resources for the Future - The Future of Language Resources

Language Technologies (LT), together with their backbone, Language Resources (LR), provide an essential support to the challenge of Multilingualism and ICT of the future. The main task of language technologies is to bridge language barriers and to help creating a new environment where information flows smoothly across frontiers and languages, no matter the country, and the language, of origin. To achieve this goal, all players involved need to act as a community able to join forces on a set of shared priorities. However, until now the field of Language Resources and Technology has long suffered from an excess of individuality and fragmentation, with a lack of coherence concerning the priorities for the field, the direction to move, not to mention a common timeframe. The context encountered by the FLaReNet project was thus represented by an active field needing a coherence that can only be given by sharing common priorities and endeavours. FLaReNet has contributed to the creation of this coherence by gathering a wide community of experts and making them participate in the definition of an exhaustive set of recommendations

Context-based multimedia semantics modelling and representation

The evolution of the World Wide Web, increase in processing power, and more network bandwidth have contributed to the proliferation of digital multimedia data. Since multimedia data has become a critical resource in many organisations, there is an increasing need to gain efficient access to data, in order to share, extract knowledge, and ultimately use the knowledge to inform business decisions. Existing methods for multimedia semantic understanding are limited to the computable low-level features; which raises the question of how to identify and represent the high-level semantic knowledge in multimedia resources.In order to bridge the semantic gap between multimedia low-level features and high-level human perception, this thesis seeks to identify the possible contextual dimensions in multimedia resources to help in semantic understanding and organisation. This thesis investigates the use of contextual knowledge to organise and represent the semantics of multimedia data aimed at efficient and effective multimedia content-based semantic retrieval.A mixed methods research approach incorporating both Design Science Research and Formal Methods for investigation and evaluation was adopted. A critical review of current approaches for multimedia semantic retrieval was undertaken and various shortcomings identified. The objectives for a solution were defined which led to the design, development, and formalisation of a context-based model for multimedia semantic understanding and organisation. The model relies on the identification of different contextual dimensions in multimedia resources to aggregate meaning and facilitate semantic representation, knowledge sharing and reuse. A prototype system for multimedia annotation, CONMAN was built to demonstrate aspects of the model and validate the research hypothesis, H₁.Towards providing richer and clearer semantic representation of multimedia content, the original contributions of this thesis to Information Science include: (a) a novel framework and formalised model for organising and representing the semantics of heterogeneous visual data; and (b) a novel S-Space model that is aimed at visual information semantic organisation and discovery, and forms the foundations for automatic video semantic understanding