Exploring PSI-MI XML Collections Using DescribeX

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 di...

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Published in:Journal of integrative bioinformatics 2007-12, Vol.4 (3), p.123-134
Main Authors: Samavi, Reza, Consens, Mariano, Khatchadourian, Shahan, Topaloglou, Thodoros
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container_title Journal of integrative bioinformatics
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creator Samavi, Reza
Consens, Mariano
Khatchadourian, Shahan
Topaloglou, Thodoros
description 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.
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