Data Integration in the Life Sciences: 7th International Conference, DILS 2010, Gothenburg, Sweden, August 25-27, 2010. Proceedings / Edition 1

by Patrick Lambrix, Graham Kemp

Overview

The development and increasingly widespread deployment of high-throughput experimental methods in the life sciences is giving rise to numerous large, c- plex and valuable data resources. This foundation of experimental data und- pins the systematic study of organismsand diseases, which increasinglydepends on the development of models of biological systems. The development of these models often requires integration of diverse experimental data resources; once constructed, the models themselves become data and present new integration challenges for tasks such as interpretation, validation and comparison. The Data Integration in the Life Sciences (DILS) Conference series brings together data and knowledge management researchers from the computer s- ence research community with bioinformaticians and computational biologists, to improve the understanding of how emerging data integration techniques can address requirements identified in the life sciences. DILS 2010 was the seventh event in the series and was held in Goth- burg, Sweden during August 25–27, 2010. The associated proceedings contain 14 peer-reviewed papers and 2 invited papers. The sessions addressed ontology engineering, and in particular, evolution, matching and debugging of ontologies, akeycomponentforsemanticintegration;Web servicesasanimportanttechn- ogy for data integration in the life sciences; data and text mining techniques for discovering and recognizing biomedical entities and relationships between these entities; and information management, introducing data integration solutions for different types of applications related to cancer, systems biology and - croarray experimental data, and an approach for integrating ranked data in the life sciences.

Product Details

ISBN-13:	9783642151194
Publisher:	Springer Berlin Heidelberg
Publication date:	10/14/2010
Series:	Lecture Notes in Computer Science , #6254
Edition description:	2010
Pages:	215
Product dimensions:	6.20(w) x 9.20(h) x 0.50(d)

Table of Contents

Invited Talks

Provenance Management for Data Exploration Juliana Freire 1

High-Performance Systems for in Silico Microscopy Imaging Studies Fusheng Wang Tahsin Kurc Patrick Widener Tony Pan Jun Kong Lee Cooper David Gutman Ashish Sharma Sharath Cholleti Vijay Kumar Joel Saltz 3

Ontology Engineering

Discovering Evolving Regions in Life Science Ontologies Michael Hartung Anika Gross Toralf Kirsten Erhard Rahm 19

On Matching Large Life Science Ontologies in Parallel Anika Gross Michael Hartung Toralf Kirsten Erhard Rahm 35

A System for Debugging Missing Is-a Structure in Networked Ontologies Qiang Liu Patrick Lambrix 50

Web Services

On the Secure Sharing and Aggregation of Data to Support Systems Biology Research Andrew Simpson Mark Slaymaker David Gavaghan 58

Helping Biologists Effectively Build Workflows, without Programming Paul M.K. Gordon Ken Barker Christoph W. Sensen 74

A Data Warehouse Approach to Semantic Integration of Pseudomonas Data Kamar Marrakchi Abdelaali Briache Amine Kerzazi Ismael Navas-Delgado José Francisco Aldana-Montes Mohamed Ettayebi Khalid Lairini Badr Din Rossi Hassani 90

Data Mining and Text Mining

The Cinderella of Biological Data Integration: Addressing Some of the Challenges of Entity and Relationship Mining from Patent Sources Ithipol Suriyawongkul Christopher Southan Sorel Muresan 106

Algorithm for Grounding Mutation Mentions from Text to Protein Sequences Jonas Bergman Laurila Rajaraman Kanagasabai Christopher J.O. Baker 122

Handling Missing Features with Boosting Algorithms for Protein-Protein Interaction Prediction Fabrizio Smeraldi Michael Defoin-Platel Mansoor Saqi 132

Instance Discovery and Schema Matching with Applications to Biological Deep Web Data Integration Tantan Liu Fan Wang Gagan Agrawal 148

Information Management

Integrative Information Management for Systems Biology Neil Swainston Daniel Jameson Peter Li Irena Spasic Pedro Mendes Norman W. Paton 164

An Integration Architecture Designed to Deal with the Issues of Biological Scope, Scale and Complexity Hector Rovira Sarah Killcoyne Ilya Shmulevich John Boyle 179

Quality Assessment of MAGE-ML Genomic Datasets Using DescribeX Lorena Etcheverry Shahan Khatchadourian Mariano Consens 192

Search Computing: Integrating Ranked Data in the Life Sciences Marco Masseroli Norman W. Paton Giorgio Ghisalberti 207

Author Index 215