Towards interoperable bioinformatics web services for integrated applications

The generation of unprecedented amounts of genomic-scale data on a daily basis has created an awareness of the need for more effective interaction between biological researchers and the bioinformatics tools they use. A comprehensive report from the 2nd Database Center for Lifescience (DCBLS) BioHackathon, held in March 2009, was published last month in Journal of Biomedical Semantics. At this meeting, software developers and genome biologists were brought together to discuss issues regarding incomplete interoperability between individual data and analytical tools. The ultimate goal of the meeting was to collaboratively evaluate the feasibility of addressing real-world biological problems by utilizing web services to create data “mashups” with existing tools in the hope of developing stable and usable research platforms.

Although solving real-world challenges proved to be difficult because of interoperability problems identified with existing web services, it was noted that semantic technologies, which was a common thread throughout the 2nd BioHackathon, could be the answer. As the themes of the hackathons continuously evolve year by year, it was agreed that the scope and focus of the 3rd BioHackathon, in 2010, would be on the interpretation of biological knowledge with semantic web technologies.

The 3rd BioHackathon explored targeted queries which could potentially be resolved by Semantic Web technologies. Data providers and tool developers surveyed existing extensible storage systems and sought to develop supporting text mining and visualisation systems for end-user applications. This year’s upcoming 4th BioHackathon will focus on developing technologies to handle Linked Data in life science. Several members of the Editorial Board of Journal of Biomedical Semantics will be contributing to the discussions on the development of semantic web series, triple stores, ontologies, visualization and Open Bio tools for Resource Description Framework (RDF) data as well as SPARQL Protocol and RDF Query Language endpoints.

The importance of consolidating the vast amount and variety of biomedical data, to facilitate efficient interpretation of biological knowledge, continues to gain recognition, and the BioHackathons have proven to be very effective for the intensive development of interoperability projects.

Adeline Siew – Assistant Editor

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