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Briefings in Bioinformatics Advance Access originally published online on December 6, 2008
Briefings in Bioinformatics 2009 10(2):139-152; doi:10.1093/bib/bbn044
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© The Author 2008. Published by Oxford University Press. For Permissions, please email: journals.permissions@oxfordjournals.org

This article appears in the following Briefings in Bioinformatics issue: Special Issue: Semantic Web for Health Care and Life Sciences: A Review of the State of the Art [View the issue table of contents]

Linked data and provenance in biological data webs

Jun Zhao, Alistair Miles, Graham Klyne and David Shotton

Corresponding author. Jun Zhao, Image Bioinformatics Research Group, Department of Zoology, University of Oxford, The Tinbergen Building, South Parks Road, Oxford, OX1 3PS, UK. Tel: 0044-(0)1865 281 094; Fax: 0044-(0)1865 271 211; E-mail: jun.zhao{at}zoo.ox.ac.uk

The Web is now being used as a platform for publishing and linking life science data. The Web's linking architecture can be exploited to join heterogeneous data from multiple sources. However, as data are frequently being updated in a decentralized environment, provenance information becomes critical to providing reliable and trustworthy services to scientists. This article presents design patterns for representing and querying provenance information relating to mapping links between heterogeneous data from sources in the domain of functional genomics. We illustrate the use of named resource description framework (RDF) graphs at different levels of granularity to make provenance assertions about linked data, and demonstrate that these assertions are sufficient to support requirements including data currency, integrity, evidential support and historical queries.

Keywords: linked data, provenance, trust, named graphs, semantic web

Submitted: July 31, 2008. Received (in revised form): September 24, 2008.


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