Defining Mapping Mashups with BioXMash

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doi doi:10.2390/biecoll-jib-2007-64
submission August 03, 2007
published October 01, 2007

Ela Hunt, Joanna Jakubowska, Caroline Bösinger, and Moira C. Norrie

Correspondence should be addressed to:
Ela Hunt
Department of Computer Science, ETH Zurich, CH-8092 Zurich, Switzerland
hc.zhte.fni@nulltnuh


Abstract

We present a novel approach to XML data integration which allows a biologist to select data from a large XML file repository, add it to a genome map, and produce a mapping mashup showing integrated data in map context. This approach can be used to produce contextual views of arbitrary XML data which relates to objects shown on a map. A biologist using BioXMash searches in XML tags, and is guided by XML path data availability, shown as the number of values reachable via a path, in both global, genome-wide, and local, pergene, context. Then she examines sample values in an area of interest on the map. If required, the resulting data is dumped to files, for subsequent analysis. This is a lightweight integration approach, and differs significantly from other known methods. It assumes that data integration can be performed on a lab computer with limited memory, with no database installation or programming knowledge. It is different from BioMarts which predefine possible data selections, in that arbitrary data sources related to map items can be used. BioXMash offers full textual search in XML paths, shows path statistics, and supports visual verification of data values. Repeated scanning of all XML files at query time is avoided by the use of a high level indexing technique. Our prototype demonstrates this new approach. It efficiently supports data browsing on 2 GB od data from GeneCards with an index size of 40 MB.

Reference

Ela Hunt, Joanna Jakubowska, Caroline Bösinger, and Moira C. Norrie. Defining Mapping Mashups with BioXMash. Journal of Integrative Bioinformatics, 4(3):64, 2007. Online Journal: http://journal.imbio.de/index.php?paper_id=64
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