Scientific Programme Overview

SWAT4LS workshop focused on Semantic Web Applications and Tools for Life Sciences.

The workshop included:

• two invited lectures
• eight oral communications on applications, tools and use cases, selected from submissions
• a poster/demo session (four posters were selected for flash oral presentations)
• a tutorial
• a panel discussion on perspectives of the Semantic Web in life sciences

Invited Lectures

• Semantic web technology in translational cancer research
  Michael Krauthammer, Department of Pathology, Yale University School of Medicine, USA
  Michael Krauthammer received his M.D. degree at the University of Zurich, Switzerland. After board certification (general practitioner), he obtained a Ph.D. in biomedical informatics at Columbia University in New York and joined the Yale Pathology Informatics program in July, 2004. His main research interests are the design of large scale text and image mining systems and research in translational informatics.
  He is the co-director of the bioinformatics core of the Yale SPORE in skin cancer, a large translational research program, and member of the Yale Cancer Center (YCC) informatics steering committee. He is the Yale PI for adopting caBIG's caTISSUE specimen tracking system across the Yale Medical Campus, enabling Yale researcher to manage their tissue banks and share data via the caGRID infrastructure.
  He is involved, on a national level, in enabling the collaboration among existing skin SPORE programs using caBIG technology. The project, termed "melaGRID", that is carried out by using semantic web technologies, will allow for the sharing of clinical, tissue and omics data, and will be instrumental for performing cross-institutional biomarker studies in melanoma.
• Web 2.0 + Web 3.0 = Web 5.0? Using Ontologies to bring Web Services on to the Semantic Web
  Mark Wilkinson, University of British Columbia, Vancouver, Canada
  Mark is an Assistant Professor of Medical Genetics at the University of British Columbia, in Vancouver. He is also PI in Bioinformatics at the Heart & Lung Research Institute at St. Paul's Hospital. His primary research interests relate to the construction and use of Semantic systems in the biomedical domain, and in particular the role of mass-collaboration in the development and maintenance of Semantic Web technologies and frameworks. He is founder and leader of the BioMoby project and founder and leader of the SHARE project.
  He will be discussing the BioMoby project and how it opened his eyes to what the Semantic Web could look like, and what mistakes were made along the way. He will then go on to discuss plans for the next generation of Moby Semantic Web Services, where he attempt to make Web Service access completely transparent, such that the "Deep Web" can be queried just like any other Semantic Web resource.

Tutorial

• Introduction to the W3C for Semantic Web Health Care and Life Sciences Interest Group
  M. Scott Marshall, W3C Semantic Web for Health Care and Life Sciences Interest Group
  The W3C Semantic Web for Health Care and Life Sciences Interest Group (HCLS IG) was recently rechartered for the next three years to continue its mission to develop, advocate for, and support the use of Semantic Web technologies for biological science, translational medicine and health care. Membership in the group has grown to 89 participants, with a wide range of representation from industry and academia. The HCLS tutorial will discuss the challenges and opportunities at hand. An overview of the activities of the each of the current task forces in HCLS will be provided, along with a description of how specific Semantic Web technologies are being applied. Some new developments and the recent Face2Face meeting will also be discussed, as well as how interested parties can participate.

Scientific Programme

Friday November 28, 2008
09.00 - 09.30	Registration and poster hang up
09.30 - 10.00	Keynote lecture Semantic web technology in translational cancer research, M. Krauthammer
10.00 - 11.00	Session on Experiences Semantic Data Integration for Francisella tularensis novicida Proteomic and Genomic Data Nadia Anwar, Ela Hunt, Walter Kolch and Andrew Pitt. Use of shared lexical resources for efficient ontological engineering Antonio Jimeno, Ernesto Jimenez-Ruiz, Rafael Berlanga and Dietrich Rebholz-Schuhmann. KASBi: Knowledge-Based Analysis in Systems Biology Maria del Mar Roldan-Garcia, Ismael Navas-Delgado, Amine Kerzazi, Othmane Chniber, Joaquin Molina and Jose F Aldana Montes.
11.00 - 11.30	Coffee break
11.30 - 12.30	Session on Applications (Tools, Methods, Data) PathExplorer: Service Mining for Biological Pathways on the Web George Zheng and Athman Bouguettaya. GoWeb: A semantic search engine for the life science web Heiko Dietze and Michael Schroeder. Close Integration of ML and NLP Tools in BioAlvis for Semantic Search in Bacteriology Robert Bossy, Alain Kotoujansky, Sophie Aubin and Claire Nedellec.
12.30 - 13.00	Flash poster presentations session (5' each) Supporting Process Development in Bio-jETI by Model Checking and Synthesis Anna-Lena Lamprecht, Tiziana Margaria and Bernhard Steffen. Structuring mined knowledge for the support of hypothesis generation in molecular biology Marco Roos, M. Scott Marshall, Andrew Gibson and Pieter Adriaans. Knowledge management using Wikipedia Dongeun Sun and Seongbin Park. Knowledge Translation: Computing the query potential of bio-ontologies Wee Tiong Ang, Rajaraman Kanagasabai and Christopher Baker.
13.00 - 14.00	Lunch break
14.00 - 14.45	Tutorial Introduction to the W3C for Semantic Web Health Care and Life Sciences Interest Group, M. Scott Marshall
14.45 - 15.30	Poster/Demo Session
15.30 - 16.00	Coffee break
16.00 - 16.45	Session on Perspectives (Tools, Methods, Data) Structuring the life science resourceome for Semantic Systems Biology: lessons from the BioGateway project Erick Antezana, Ward Blondé, Mikel Egaña, Alistair Rutherford, Robert Stevens, Bernard De Baets, Vladimir Mironov and Martin Kuiper. Knowledge Representation for Web Navigation Simon Jupp, Robert Stevens, Sean Bechhofer, Yeliz Yesilada and Patty Kostkova.
16.45 - 17.15	Keynote lecture Using Ontologies to bring Web Services on to the Semantic Web, M. Wilkinson
17.15 - 18.15	Panel discussion If the semantic web is so good, how come most people use OBO for ontologies and perl for data integration? Phil Lord (Chair)

Accepted demos

• BioGateway: Query architecture and visualisation of results
  Erick Antezana, Ward Blondé, Mikel Egaña, Alistair Rutherford, Robert Stevens, Bernard De Baets, Vladimir Mironov and Martin Kuiper.

Accepted posters

• The Generation Challenge Programme Model Driven Architecture: Scientific Domain Model and Ontology
  Genevieve Mae Aquino, Jeffrey Detras, Rosemary Shrestha, Martin Senger, Kevin Manansala, Elizabeth Arnaud, Reinhard Simon, Jayashree Balaiji, Thomas Hazekamp, Guy Davenport, Graham McLaren, Theo van Hintum and Richard Bruskiewich.
• The Cell Cycle Ontology: an application ontology supporting the Life Sciences
  Erick Antezana, Mikel Egaña, Ward Blondé, robert Stevens, Bernard De Baets, Vladimir Mironov and Martin Kuiper.
• The ChEBI Ontology: an ontology for chemistry within a biological context
  Janna Hastings, Kirill Degtyarenko, Paula de Matos, Marcus Ennis and Christoph Steinbeck.
• LifeDB: An Autonomous System for Semantic Integration of Life Science Data on Hidden Web
  Anupam Bhattacharjee, Aminul Islam, Mohammad Amin, Shahriyar Hossain, Shazzad Hosain and Hasan Jamil.
• The DC-THERA Directory: A Knowledge Management System to Support Collaboration on Dendritic Cell and Immunology Research
  Michaela Guendel, Ciro Scognamiglio, Marco Brandizi and Andrea Splendiani.
• Goal-Oriented Task Composition for Bioinformatics
  Karen Sutherland and Albert Burger.
• An integrated ontological knowledge base about orthologous genes and proteins
  Jose Antonio Miñarro Gimenez, Marisa Madrid and Jesualdo Tomás Fernández-Breis.
• A Secure Data Repository Integrating Huge Volumes of Digital Contents as a Semantic Web
  Norio Kobayashi, Yuko Makita, Eli Kaminuma, Shuji Kawaguchi, Yuko Yoshida, Yoshiki Mochizuki, Akihiro Matsushima, Manabu Ishii, Ryo Umetsu, Satomi Asano, Naohiko Heida, Tetsuya Sakurai, Takashi Kuromori, Kazuo Shinozaki and Tetsuro Toyoda.
• LifeSKIM: Application for large scale biomedical semantic annotations
  Vassil Momtchev, Georgi Georgiev and Deyan Peychev.
• Penta and Hexa Statements are Suitable for Representing Omics Knowledge on the Semantic Web
  Norio Kobayashi and Tetsuro Toyoda.
• Bio-informatics reactivity features through the Semantic Web
  Tiago Franco, Jose Julio Alferes, Ludwig Krippahl and Ricardo Amador.
• A User-Centred Evaluation Framework for the SeaLife Semantic Web Browsers
  Gayo Diallo, Gemma Madle, Gawesh Jawaheer, Patty Kostkova, Dimitra Alexopoulou, Robert Stevens, Simon Jupp and Khaled Khelif.
• BioGateway: integrated RDF for life science queries
  Erick Antezana, Ward Blondé, Mikel Egaña, Alistair Rutherford, Robert Stevens, Bernard De Baets, Vladimir Mironov and Martin Kuiper.

Presentations

Presentations of oral communications and selected posters are available in the eSI site. Click here.

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