BioMOBY: An open source biological web services proposal
Research Associate of Bioinformatics at the Plant Biotechnology Institute of the National Research Council of Canada. His research interests include database interoperability, user interface design and floral developmental mutants.
Bioinformatician at the University of Saskatchewan. His research interests are focused on the application of Beowulf supercomputers to bioinformatics problems, and the application of wavelet analysis to genome annotation.
Mark D. Wilkinson, BioMOBY Project, Plant Biotechnology Institute, National Research Council Canada, 110 Gymnasium Place, Saskatoon, Saskatchewan, Canada S7N OW9 Tel: +1 306 975 5279 Fax: +1 306 975 4839 E-mail: mwilkinson{at}gene.pbi.nrc.ca
BioMOBY is an Open Source research project which aims to generate an architecture for the discovery and distribution of biological data through web services; data and services are decentralised, but the availability of these resources, and the instructions for interacting with them, are registered in a central location called MOBY Central. BioMOBY adds to the web services paradigm, as exemplified by Universal Data Discovery and Integration (UDDI), by having an object-driven registry query system with object and service ontologies. This allows users to traverse expansive and disparate data sets where each possible next step is presented based on the data object currently in-hand. Moreover, a path from the current data object to a desired final data object could be automatically discovered using the registry. Native BioMOBY objects are lightweight XML, and make up both the query and the response of a simple object access protocol(SOAP) transaction.
Keywords: BioMOBY, web services, interoperability, I3C, UDDI
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|
|
|
|
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|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|