Scientific Programme

Provisional scientific program (all named slots confirmed):

Legenda: Keynotes Tutorials Hands-on sessions

Wednesday – May 2nd

  • 09.00 – 09.30: Opening
  • 09.30 – 10.30: Semantic Interoperability between literature and data resources: from genes to diseases by Dietrich Schuhmann (EBI)
    The biomedical research community stores research results on biological entities in large-scale databases for their experimental data analysis and, in addition, produces semantic resources such as ontologies for the annotation of the entities. For automatic literature analysis, we exploit these resources to improve information retrieval, information extraction, ontology development and the discovery of new knowledge. As a result, the literature research team at the European Bioinformatics Institute has established state of the art solutions for high-throughput analyses of the literature. Current developments lead towards semantic interoperability through standardised data resources, e.g. large-scale annotated corpora, state of the art terminological resources and linked open data.
    The presentation will have a focus on the benefits (and limitations) of the existing ontological resources and will describe several solutions, how the conceptual knowledge can be successfully exploited to filter out relevant information from the scientific literature. The presentation will discuss ongoing efforts to deliver gene-disease associations from different resources exploiting semantic interoperability.
  • 10.30 – 11.00: Coffee-break
  • 11.00 – 12.30: Robust ontology design by Martin Boeker
  • 12.30 – 14.00: Lunch
  • 14.00 – 16.15: User Interaction by Eric Miller
  • The most successful applications marry technical functionality with a high degree of usability, resulting from a thoughtfully designed and intuitive user interface. However, user interaction design (UX) expertise is a distinct skill set, and small development teams working on sophisticated life sciences applications may not always have the available resources to add UX specialists to their project teams.
    This tutorial session (presented by a principal at an application design and development firm with experience building collaborative ontology development tools) is designed to give technical managers and developers an overview of techniques, practices, and tools used to design effective user interfaces. At the end of the session attendees should expect to have acquired knowledge of how user interaction design processes and best practices can be put to use to benefit their own projects.
    We will cover the following:

    • Articulating the challenges of user interaction design, particularly in semantic web-enabled applications
    • Conduct an overview of commonly used staff roles, project processes, and techniques for user interaction design
    • Review available software tools for rapid prototyping, application design, and user testing
    • Discuss best practices as currently articulated in the interaction design community
    • And finally, applying these practices, tools, and techniques to semantic web applications in the life sciences

    Attendees are encouraged to prepare screenshots and descriptions of interaction design challenges for review, discussion, and collaborative editing.

  • 16.15 – 16.45: Coffee-break
  • 16.45 – 18.00: User Interaction by Eric Miller (Cognitive Atlas)
  • 18:00 –     : Breakout sessions (Question and Answers with presenters)

Thursday – May 3rd

  • 09.30 – 10.30: UniProt and RDF: sharing our experiences in moving to the semantic web
    A discussion of many of the issues that we have over come to bring
    UniProt to the semantic web. Current issues that remain and solutions
    that we found. This is an overview of things you should consider when
    moving an existing datasource to the semantic web, building on the
    strengths of previous work. Including on validating data quality.
  • 10.30 – 11.00: Coffee-break
  • 11.00 – 12.30: UniProt and RDF: what is in it for you? by Jerven Bolleman
    Proteins, proteins and more proteins! The Universal protein knowledge
    base is one of the largest data integration points in the life sciences.
    It links more than 160 databases together and provides key annotation
    and information to the biological community. The session shows how you
    can access UniProt information and what you can find inside.
  • 12.30 – 14.00: Lunch
  • 14.00 – 16.15: SPARQLing away at Data Integration using federated queries and SWObjects by Helena Deus
    Life Sciences databases come in many shapes and sizes. A large number of them already exist in the machine readable, interoperable format known as RDF (Resource Description Framework). Many of them, however, still exist in their original relational formats . As popularity of linked life sciences increases, so does the need to support increasingly complex queries and to enable proper linking between datasets. Whereas the single triple store approach was sufficient to support simple use cases that required limited datasets, it is becoming increasingly relevant to enable not only querying and correlating data available through multiple SPARQL endpoint but also data which has not yet been exposed to semantic web technologies.
    SWobjects is a SPARQL 1.1. engine developed by Eric Prud’hommeaux, the W3C contact for the Health Care and Life Sciences Interest Group. Some of its more relevant functionalities include 1) supporting multiple SPARQL service calls in a single query; 2) usage of maps to transform heterogeneous data into a single common representation and 3) serialization of SPARQL queries into SQL
    In this tutorial, we will briefly explain the inner workings of SWobjects, including some the basic features such as the rule templates and SQL serialization. This will be followed by a presentation illustrating of a few successful use cases where query federation enabled discovery and integration of data from multiple biological datasets and subsequent hypothesis building.
  • 16.15 – 16.45: Coffee-break
  • 16.45 – 18.00: Semantic Search for Life Sciences – from drug-target prediction to alternatives for animal experiments by Micheal Schroeder
    GoPubMed is a semantic search engine for the life sciences used by thousands of researchers daily.GoPubMed indexes biomedical literature with life science ontologies and thus facilitates faceted search and browsing. The talk will cover the underlying text-mining technologies and show how they can be used in related applications such as mining of literature for drug side effects and disease-relations to predict drug targets and how to find toxicology literature on alternatives to animal experiments.
  • 18:00 –     : Breakout sessions (Question and Answers with presenters)

Friday – May 4th

  • 09.30 – 10.30: SADI by Luke McCarthy and Mark Wilkinson
    SADI (Semantic Automated Discovery and Integration) is a set of standards-compliant best practices that simplify the discovery and interoperability of Semantic Web Services. This tutorial introduces SADI and what is required of a web service to be SADI-compliant, as well as the options for finding and accessing those services. There will be hands-on exercises in building SADI services and clients.
    More details can be found at the Google code page
  • 10.30 – 11.00: Coffee-break
  • 11.00 – 12.30: SADI by Luke McCarthy/Mark Wilkinson
  • 12.30 – 14.00: Lunch
  • 14.00 – 16.15: SADI by Luke McCarthy/Mark Wilkinson
  • 16.15 – 16.45: Coffee-break
  • 16.45 – 18.00: SADI by Luke McCarthy/Mark Wilkinson
  • 18:00 – : Posters, Social dinner

Saturday – May 5th

  • 09.30 – 10.30: Tentative title: Crowdsourcing Semantic Data by Elena Simperl
    Abstract will be announced shortly
  • 10.30 – 11.00: Coffee-break
  • 11.00 – 12.30: (tentative: emergent areas in Semantic Web Research)

Your feedback is highly appreciated. If you have any speaker suggestions or think your work will fit this workshop, let us know to school at