[CEUR Workshop Proceedings] Vol-559

Copyright © 2009 for the individual papers by the papers' authors. Copying permitted for private and academic purposes. Re-publication of material from this volume requires permission by the copyright owners. This volume is published by its editors.

Semantic Web Applications and Tools for Life Sciences

Proceedings of the Workshop on Semantic Web Applications and Tools for Life Sciences

Amsterdam, The Netherlands, November 20, 2009.

Edited by

M. Scott Marshall 1,2
Albert Burger 3,4
Paolo Romano 5
Adrian Paschke 6,7
Andrea Splendiani 8

1 Adaptive Information Disclosure, Informatics Institute, University of Amsterdam, The Netherlands
2 Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, The Netherlands
3 School of Mathematical and Computer Sciences, Heriot-Watt University
4 MRC Human Genetics Unit, Edinburgh, United Kingdom
5 Bioinformatics, National Cancer Research Institute, Genova, Italy
6 Corporate Semantic Web, Free University Berlin, Berlin
7 Biotechnology Centre, TU Dresden, Dresden, Germany
8 Rothamsted Research, Harpenden, United Kingdom

Table of Contents


  1. TIM: A Semantic Web Application for the Specification of Metadata Items in Clinical Research
    Matthias Löbe, Magnus Knuth, Roland Mücke
  2. Towards the Ontology-based Classification of Lymphoma Patients using Semantic Image Annotations
    Sonja Zillner
  3. Linking Open Drug Data to Cheminformatics and Proteochemometrics
    Egon Willighagen, Jarl Wikberg
  4. Mining Semantic Networks of Bioinformatics e-Resources from the Literature
    Hammad Afzal, James Eales, Robert Stevens, Goran Nenadic
  5. Semantics-Based Composition of EMBOSS Services with Bio-jETI
    Anna-Lena Lamprecht, Stefan Naujokat, Tiziana Margaria, Bernhard Steffen
  6. OBO & OWL: Roundtrip Ontology Transformations
    Syed Hamid Tirmizi, Stuart Aitken, Dilvan A. Moreira, Chris Mungall, Juan Sequeda, Nigam H. Shah, Daniel P. Miranker

Highlight Posters

  1. Weekend Triple Billionaire
    Jerven Bolleman, Thomas Kappler
  2. Towards a Logic-based Assessment of the compatibility of UMLS sources
    Ernesto Jimenez-Ruiz, Bernardo Cuenca Grau, Rafael Berlanga, Ian Horrocks
  3. Using the NCBO Web Services for Concept Recognition and Ontology Annotation of Expression Datasets
    Simon Twigger, Joey Geiger, Jennifer Smith


  1. NeuroLex.org - A semantic wiki for neuroinformatics based on the NIF Standard Ontology
    Stephen Larson, Sarah Maynard, Fahim Imam, Maryann Martone
  2. DC-THERA Directory, a Knowledge Management System for the support of the European Dendritic Cell Immunology Community
    Marco Brandizi, Michaela Gündel, Ciro Scognamiglio, Andrea Splendiani
  3. ContentCVS: A CVS-based Collaborative ONTology ENgineering Tool
    Ernesto Jimenez-Ruiz, Bernardo Cuenca Grau, Ian Horrocks, Rafael Berlanga
  4. A system for repairing missing is-a structure in ontologies
    Patrick Lambrix, Qiang Liu, He Tan
  5. Onto-Frogger: Playing with Semantic Structure
    Amalia Kallergi, Fons J. Verbeek


  1. Semantic access to chemistry data with the ChEBI ontology and web services
    Nico Adams, Paula de Matos, Adriano Dekker, Marcus Ennis, Janna Hastings, Kenneth Haug, Duncan Hull, Zara Josephs, Pablo Moreno, Steve Turner, Christoph Steinbeck
  2. From Ontology for Genetic Interval (OGI) to Sequence Assembly -- Ontology applying to next generation sequencing
    Yu Lin, Hiroshi Tarui, Peter Simons
  3. Ondex: data integration and visualisation for the Semantic Web
    Catherine Canevet, Andrea Splendiani, Shao Chih Kuo, Robert Stevens, Phil Lord, Chris Rawlings
  4. Semantic integration and exploitation of orthology information and genetic disorders
    Jose Antonio Miñarro Giménez, Marisa Madrid, Jesualdo Tomás Fernández-Breis
  5. Towards an Ontology-based Mediation Framework for Integrating Biological Data
    Amine Kerzazi, Ismael Navas-Delgado, Jose F Aldana Montes
  6. Integration of information from different ontologies
    Julia Dmitrieva, Fons J. Verbeek
  7. Observations on Semantic Annotation of Microscope Images for Life Sciences
    Joris Slob, Amalia Kallergi, Fons Verbeek
  8. Semantic Bookmarking for Reference Management
    Alex Logvynovskiy, Mohammad Dastbaz, Chris Imafidon
  9. Using ontologies for querying and analysing protein-protein interaction data
    Pietro Hiram Guzzi, Mario Cannataro

18-Jan-2010: submitted by Andrea Splendiani
19-Jan-2010: published on CEUR-WS.org