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Journal of Integrative Bioinformatics

Editor-in-Chief: Schreiber, Falk / Hofestädt, Ralf

Managing Editor: Sommer, Björn

Ed. by Baumbach, Jan / Chen, Ming / Orlov, Yuriy / Allmer, Jens

Editorial Board: Giorgetti, Alejandro / Harrison, Andrew / Kochetov, Aleksey / Krüger, Jens / Ma, Qi / Matsuno, Hiroshi / Mitra, Chanchal K. / Pauling, Josch K. / Rawlings, Chris / Fdez-Riverola, Florentino / Romano, Paolo / Röttger, Richard / Shoshi, Alban / Soares, Siomar de Castro / Taubert, Jan / Tauch, Andreas / Yousef, Malik / Weise, Stephan / Hassani-Pak, Keywan


CiteScore 2017: 0.77

SCImago Journal Rank (SJR) 2017: 0.336

Open Access
Online
ISSN
1613-4516
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Volume 4, Issue 3

Issues

Exploring PSI-MI XML Collections Using DescribeX

Reza Samavi
  • Corresponding author
  • Information Engineering Center, Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, Ontario, M5S 3G8, Canada
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/ Mariano Consens
  • Information Engineering Center, Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, Ontario, M5S 3G8, Canada
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/ Shahan Khatchadourian
  • Information Engineering Center, Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, Ontario, M5S 3G8, Canada
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/ Thodoros Topaloglou
  • Information Engineering Center, Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, Ontario, M5S 3G8, Canada
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Published Online: 2016-10-18 | DOI: https://doi.org/10.1515/jib-2007-70

Summary

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.

About the article

Published Online: 2016-10-18

Published in Print: 2007-12-01


Citation Information: Journal of Integrative Bioinformatics, Volume 4, Issue 3, Pages 123–134, ISSN (Online) 1613-4516, DOI: https://doi.org/10.1515/jib-2007-70.

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© 2007 The Author(s). Published by Journal of Integrative Bioinformatics.. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License. BY-NC-ND 4.0

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