Vannevar Vision

Published: Exploring PSI-MI XML Collections Using DescribeX October 2, 2007

My first official publication 🙂 Thanks to Reza for putting so much hard work into it as well as his patience for some of the DescribeX bug fixes. Many thanks also go to my professors Mariano and Thodoros who guide and encourage at every opportunity.

Abstract

PSI-MI has been endorsed by the protein informatics community as a standard XML data exchange format for protein-protein interaction datasets. While many public databases support the standard, there is a degree of heterogeneity in the way the proposed XML schema is interpreted and instantiated by different data providers. Analysis of schema instantiation in large collections of XML data is a challenging task that is unsupported by existing tools. In this study we use DescribeX, a novel visualization technique of (semi-)structured XML formats, to quantitatively and qualitatively analyze PSI-MI XML collections at the instance level with the goal of gaining insights about schema usage and to study specific questions such as: adequacy of controlled vocabularies, detection of common instance patterns, and evolution of different data collections. Our analysis shows DescribeX enhances understanding the instance-level structure of PSI-MI data sources and is a useful tool for standards designers, software developers, and PSI-MI data providers.

Reference

Reza Samavi, Mariano Consens, Shahan Khatchadourian, Thodoros Topaloglou. Exploring PSI-MI XML Collections Using DescribeX. Journal of Integrative Bioinformatics, 4(3):70, 2007. Online Journal: link