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Exploring PSI-MI XML Collections Using DescribeX

Samavi, Reza ; Consens, Mariano ; Khatchadourian, Shahan ; Topaloglou, Thodoros

Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516)


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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.


Institution: Faculty of Technology, Research Groups in Informatics
DDC classification: Data processing, computer science, computer systems

Suggested Citation:
Samavi, Reza ; Consens, Mariano ; Khatchadourian, Shahan ; Topaloglou, Thodoros  (2007)  Exploring PSI-MI XML Collections Using DescribeX. Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516), 4(3), 2007. Special Issue: 4th Integrative Bioinformatics Workshop, Gent, Belgium

Online-Journal: http://journal.imbio.de/index.php?paper_id=70
URL: http://biecoll.ub.uni-bielefeld.de/volltexte/2007/251



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