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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 2018: 0.90

SCImago Journal Rank (SJR) 2018: 0.315

Open Access
Online
ISSN
1613-4516
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Volume 13, Issue 4

Issues

DaTo: an atlas of biological databases and tools

Qilin Li
  • Department of Bioinformatics, College of Life Sciences, Zhejiang University, 310058 Hangzhou, China
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/ Yincong Zhou
  • Department of Bioinformatics, College of Life Sciences, Zhejiang University, 310058 Hangzhou, China
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/ Yingmin Jiao
  • Department of Bioinformatics, College of Life Sciences, Zhejiang University, 310058 Hangzhou, China
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/ Zhao Zhang
  • Department of Bioinformatics, College of Life Sciences, Zhejiang University, 310058 Hangzhou, China
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/ Lin Bai
  • Department of Bioinformatics, College of Life Sciences, Zhejiang University, 310058 Hangzhou, China
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/ Li Tong
  • Department of Bioinformatics, College of Life Sciences, Zhejiang University, 310058 Hangzhou, China
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/ Xiong Yang
  • Department of Bioinformatics, College of Life Sciences, Zhejiang University, 310058 Hangzhou, China
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/ Björn Sommer
  • Computational Life Sciences, Department of Computer and Information Science, University of Konstanz, 78457 Konstanz, Germany
  • Faculty of Information Technology, Monash University, 3800 Melbourne, Australia
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/ Ralf Hofestädt
  • Department of Bioinformatics and Medical Informatics, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany
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/ Ming Chen
  • Corresponding author
  • Department of Bioinformatics, College of Life Sciences, Zhejiang University, 310058 Hangzhou, China
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Published Online: 2017-04-20 | DOI: https://doi.org/10.1515/jib-2016-297

Summary

This work presents DaTo, a semi-automatically generated world atlas of biological databases and tools. It extracts raw information from all PubMed articles which contain exact URLs in their abstract section, followed by a manual curation of the abstract and the URL accessibility. DaTo features a user-friendly query interface, providing extensible URL-related annotations, such as the status, the location and the country of the URL. A graphical interaction network browser has also been integrated into the DaTo web interface to facilitate exploration of the relationship between different tools and databases with respect to their ontology-based semantic similarity. Using DaTo, the geographical locations, the health statuses, as well as the journal associations were evaluated with respect to the historical development of bioinformatics tools and databases over the last 20 years. We hope it will inspire the biological community to gain a systematic insight into bioinformatics resources. DaTo is accessible via http://bis.zju.edu.cn/DaTo/.

About the article

Published Online: 2017-04-20

Published in Print: 2016-06-01


Citation Information: Journal of Integrative Bioinformatics, Volume 13, Issue 4, Pages 30–38, ISSN (Online) 1613-4516, DOI: https://doi.org/10.1515/jib-2016-297.

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© 2016 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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