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4th International SWAT4LS Workshop

Semantic Web Applications and Tools for Life Sciences

December 9th, 2011
London, UK

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Scientific Programme


Wednesday 7th December 2011 (Hackathon day)

Location: Venue in Central London (to be finalized)
Co-roganized with the Open Knowledge Fundation Open Science Working Group and JISC
The hackathon, co-organized by JISC, SWAT4LS and OKF will focus on the integration and elaboration of disease specific information. It will focus on a small number of cases, and it will include gathering information from several sources (including open literature), its annotation and its mashup and visualizatio
More details to be posted later

Thursday 8th December 2011 (Tutorial day)

Location: Venue in Central London (to be finalized)
Confirmed tutorials
  • The Semantic Web: A Deep Dive Tutorial, J Phil Brooks, Lilly Research Laboratories, Lilly Systems Biology
    This tutorial will combine instructor-led training with a hands-on lab to provide a deep dive into many of the key fundamentals of the Semantic Web. Concepts covered in the session will include RDF, OWL, inferencing, the use of ontologies to synchronize vocabularies, relational to semantic mapping, semantic integration, and others. Attendees will perform hands-on lab exercises using the TopBraid Composer tool to reinforce their learning.
  • NCBO Web Services and Development of Semantic Applications,Trish Wehtzel, NCBO
    Ontologies provide domain knowledge to drive data integration and information retrieval. The National Center for Biomedical Ontology provides a suite of ontology-based Web services for the development of semantically aware software applications. This presentation will provide an overview of these Web services and their use within software applications.
More tutorials to be announced soon

Friday 9th December 2011 (Workshop day)

Location: Welcome Trust Collection Conference Center
9.00-18.30SWAT4LS Workshop
The Workshop will include:
  • Keynotes
  • Paper presentations
  • Poster session
  • Demo session
  • Industry session
  • Panel discussion
The program will be integrated by an optional social dinner and possibly a visit to the Welcome Collection.


More keynotes to be confirmed

Tetsuro Toyoda: Future Biology is Semantic Information Science
Global cloud frameworks for bioinformatics research databases become huge and heterogeneous; solutions face various diametric challenges comprising cross integration, retrieval, security and openness. To address this, as of March 2011 organizations including RIKEN published 192 mammalian, plant and protein life sciences databases having 7.5 million data records, integrated as Linked Open or Private Data (LOD/LPD) using, the Scientists' Networking System or a “Virtual Laboratory Centre,” providing numerous virtual labs for semantic-web-based data management and collaboration of various purposes. is thus designed to discover novel relationships between data, because automatic intelligent agent generates for each data item a summary content displaying the linked information via Semantic Web. We demonstrate we successfully used the SciNetS interface across 26 million semantic relationships for biological applications including genome design, sequence processing, inference over phenotype databases, full-text search indexing and human-readable contents like ontology and LOD tree viewers.
Tetsuro Toyoda was born in Tokyo, Japan, in 1968. He graduated from the Faculty of Pharmaceutical Sciences at the University of Tokyo in 1992, and obtained his PhD in 1997 from the same university. He started as a researcher at the Institute of Medical Molecular Design in 1997, and joined RIKEN as team leader in the Genomic Sciences Center in 2001. He became director of the RIKEN Bioinformatics and Systems Engineering Division when it was established in 2008. His expertise is in bioinformatics and computer-aided rational design of biomolecules, including rational database-supported drug design based on protein structural information and rational genome design in synthetic biology for biomass engineering. He promotes Japan’s database integration projects as a member of several national database committees.

Douglas Kell: Semantic approaches in Biotechnology and Biological Sciences
The rise of ‘big data’ and their attendant metadata in biology requires new methods for their optimal exploitation, for which semantic approaches offer both potential and real benefits. I illustrate this with a number of examples, including the principled description of biochemical networks [1] and a semantic approach to linking the biochemical literature and its underpinning data [2-4].
[1] Herrgård MJ, 31 others and Kell DB: A consensus yeast metabolic network obtained from a community approach to systems biology. Nature Biotechnol 2008; 26:1155-1160.
[2] Attwood TK, Kell DB, McDermott P, Marsh J, Pettifer S, Thorne D: Utopia Documents: linking scholarly literature with research data. Bioinformatics 2010; 26:i568-574.
[3] Attwood TK, Kell DB, McDermott P, Marsh J, Pettifer SR, Thorne D: Calling International Rescue: knowledge lost in literature and data landslide! Biochem J 2009; 424:317-333.
[4] Pettifer SR, Thorne D, McDermott P, Marsh J, Villéger A, Kell DB, Attwood TK: Visualising biological data: a semantic approach to tool and database integration. BMC Bioinformatics 2009; 10:S19.

Before taking up the post of BBSRC Chief Executive in October 2008, Douglas Kell was the Director of the Manchester Centre for Integrative Systems Biology based in the Manchester Interdisciplinary Biocentre (MIB). His research covers a broad range of topics from analytical chemistry to systems biology, usually coupled to biochemical and data modelling. He continues to work at the MIB one day a week. He joined UMIST in 2002, which merged with the Victoria University of Manchester to form The University of Manchester in 2004.
He was, from 1997 until 2002, Director of Research of the Institute of Biological Sciences at the University of Aberystwyth.  He held a personal Chair with the University of Aberystwyth for 10 years until 2002. He is a Director of Aber Instruments, which won the Queen’s Award for Export Achievement in 1998.
Prof Kell was a member of BBSRC Council 2001-2006, member of Strategy Board 2005-2006, member of the Bioscience for Industry Strategy Panel 2007-present and chaired the review of BBSRC's Bioenergy research in 2006. Prof Kell was born in London in 1953. He is married with three children. Prof K

Wendy Hall: To be announced

Accepted papers, posters and demos

To be announced

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Sponsorship opportunities

We are corrently open for sponsorship oppurtunities. We offer sponsorship packages for corporate industries and special packages for small and medium enterprises active in the Semantic Web market.
Please visit the sponsorship section for more information.

SWAT4LS 2011 is endorsed by :

  National Center for Biomedical Ontologies


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