Semantic Web Service provision: a realistic framework for Bioinformatics programmers

• Published in: Bioinformatics Vol. 23; no. 9; pp. 1178 - 1180
• Main Authors: Gordon, Paul M.K., Trinh, Quang, Sensen, Christoph W.
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 01.05.2007; Oxford Publishing Limited (England)
• Subjects: Bioinformatics; Biological and medical sciences; Computational Biology - methods; Database Management Systems; Databases, Genetic; Fundamental and applied biological sciences. Psychology; General aspects; Information Storage and Retrieval - methods; Internet; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Natural Language Processing; Programming Languages; Semantics; Software; User-Computer Interface; Semantic web; Interpolation; JAVA language; Computer program; Web service; Development; Bioinformatics; Application; Scope note; Framework; Automatic
• ISSN: 1367-4803; 1367-4811; 1460-2059
• DOI: 10.1093/bioinformatics/btm060

Several semantic Web Services clients for Bioinformatics have been released, but to date no support systems for service providers have been described. We have created a framework ('MobyServlet') that very simply allows an existing Java application to conform to the MOBY-S semantic Web Services protocol. Using an existing Java program for codon-pair bias determination as an example, we enumerate the steps required for MOBY-S compliance. With minimal programming effort, such a deployment has the advantages of: (1) wider exposure to the user community by automatic inclusion in all MOBY-S client programs and (2) automatic interoperability with other MOBY-S services for input and output. Complex on-line analysis will become easier for biologists as more developers adopt MOBY-S. Availability: The framework and documentation are freely available from the Java developer's section of http://www.biomoby.org/. Contact: gordonp@ucalgary.ca