SOAP/WSDL-based web services for biomedicine: Demonstrating the technique with the cancerresource

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 Cancer- Resource. 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. © 2010 International Federation for Medical and Biological Engineering.