IFMBE Proceedings Vol. 29 Panagiotis D. Bamidis • Nicolas Pallikarakis (Eds.)
XII Mediterranean Conference on Medical and Biological Engineering and Computing 2010 May 27 – 30, 2010 Chalkidiki, Greece
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Editors Panagiotis D. Bamidis Aristotle University of Thessaloniki Lab of Medical Informatics, Medical Scho 541 24 Thessaloniki Greece E-mail:
[email protected] Nicolas Pallikarakis University of Patras Biomedical Technology Unit 265 04 Rio Patras Greece E-mail:
[email protected]
ISSN 1680-0737 ISBN 978-3-642-13038-0
e-ISBN 978-3-642-13039-7
DOI 10.1007/978-3-642-13039-7 Library of Congress Control Number: 2010927933 © International Federation for Medical and Biological Engineering 2010 This work is subject to copyright. All rights are reserved, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilm or in any other way, and storage in data banks. Duplication of this publication or parts thereof is permitted only under the provisions of the German Copyright Law of September 9, 1965, in its current version, and permissions for use must always be obtained from Springer. Violations are liable to prosecution under the German Copyright Law. The use of general descriptive names, registered names, trademarks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. The IFMBE Proceedings is an Official Publication of the International Federation for Medical and Biological Engineering (IFMBE) Typesetting: Scientific Publishing Services Pvt. Ltd., Chennai, India. Cover Design: deblik, Berlin Printed on acid-free paper 987654321 springer.com
SOAP/WSDL-Based Web Services for Biomedicine: Demonstrating the Technique with the CancerResource T. Meinel1,2, M.S. Mueller1, J. Ahmed1, R. Yildiriman2, M. Dunkel1, R. Herwig2, and R. Preissner1 2
1 Charité - University Medicine Berlin/Institute for Physiology/Structural Bioinformatics Group, Berlin, Germany Max Planck Institute for Molecular Genetics/Vertebrate Genomics Department/Bioinformatics Group, Berlin, Germany
Abstract— Web services provide programmatic access to data or tools using internet technology. Several standards have been developed, one sophisticated application is the combination of the Web Service Description Language (WSDL) with the SOAP (originally defined as Simple Object Access Protocol) messaging protocol. We describe the fundamental technology of SOAP/WSDL-based web services and provide concepts to integrate data from independent, distant resources. Several informatics layers are described such as server-client messaging connections, programming languages, libraries, and modularity of web services. We illustrate principles underlying this technology and the types of web services they can be applied to in several functional stages, from simple data retrievals over combined data accesses (workflows) up to dynamically rendered images. As an example that is relevant for biomedicine we highlight the CancerResource as a use case for such diversified applications. The CancerResource is conceptualized to present cancerrelevant drug-target connections to the life sciences, particularly to the field of medical science. In-depth literature data-mining resolved thousands of drug-target connections. CancerResource connects manifold information from different knowledge categories. Targets are genes or proteins, which are well described in public databases like UniProt, Ensembl, and the PDB. Drugs are chemical compounds that specifically act on target genes in cancer tissues; they are collected in databases like DrugBank, SuperDrug, or PubChem. Connectivity Map (C-Map) expression data is an essential source of functional information for CancerResource. A general visualization feature is the organization of genes in pathways; the KEGG database provides cancer-specific pathway maps. For this purpose CancerResource utilizes web service technologies to dynamically combine C-Map expression data with pathways. The CancerResource web interface allows the user to specify problems and helps to understand noticeable behaviors of genes that are implicated in cancer. The ultimate aim of CancerResource is to provide suggestions towards developing specific drug therapies for cancer patients. Keywords— SOAP/WSDL, web service, interoperability, cancer medicine, drug treatment.
I. WEB SERVICES IN BIOMEDICINE The increasing impact of web services is one response of technology to the inflating complexity of data, knowledge,
and information in biomedicine. As recently reviewed [1], the acceptance and the employment of this technology require a broad understanding in basic components of web services. The overall goal of web services is to allow programmatic access to databases and tools that hold data or operate data. Advantages are that own data repositories can be economically used, data multiplication avoided and the problem of updating foreign data is out-sourced to the originators of the data. Such basic ideas imply the interoperability for messages between computers and several initiatives have been established that define and maintain message protocols. The data exchange is enabled by the exhaustive utilization of the internet. Here, the SOAP messaging protocol is based on the eXtended Markup Language XML and is therefore a pervasive standard, which is independent from the type of computer or programming language used. The organization of data and the separation from message transport standards are clear advantages of SOAP. Biomedicine shares a high amount of biological data. Independently from personalized data, which form an important part in biomedicine and require separate solutions for programmatic access, many general issues in bioinformatics or systems biology are oriented toward medical aspects. Such data are molecular items like genes or compounds, organization features like pathway maps or networks, or functional traits of molecular items which are comprised in proteomics or transcriptomics. If data are already publicly available the preferred method of retrieving such data is by programmatic access. The question of discovery of web services and achieving of information about web services is solved in three levels. First, several institutions like the EBI, NCBI, or DDBJ provide large collections of web services and tools. Second, sophisticated methods that utilize semantics to detect appropriate methods according to specific problems are under development. Finally, particularly suitable for single data repositories, initiatives have been founded that invite data providers to announce their web services in registries like the BioCatalogue [2], which is a successor of the EmbraceRegistry [3,4]. Here, the obligate deposition of test clients give programmers detailed insights into methods and constructions of particular web services.
P.D. Bamidis and N. Pallikarakis (Eds.): MEDICON 2010, IFMBE Proceedings 29, pp. 835–838, 2010. www.springerlink.com
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