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Noncoding RNAs Databases: Current Status and Trends

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Book cover Computational Biology of Non-Coding RNA

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1912))

Abstract

One of the most important resources for researchers of noncoding RNAs is the information available in public databases spread over the internet. However, the effective exploration of this data can represent a daunting task, given the large amount of databases available and the variety of stored data. This chapter describes a classification of databases based on information source, type of RNA, source organisms, data formats, and the mechanisms for information retrieval, detailing the relevance of each of these classifications and its usability by researchers. This classification is used to update a 2012 review, indexing now more than 229 public databases. This review will include an assessment of the new trends for ncRNA research based on the information that is being offered by the databases. Additionally, we will expand the previous analysis focusing on the usability and application of these databases in pathogen and disease research. Finally, this chapter will analyze how currently available database schemas can help the development of new and improved web resources.

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Acknowledgments

VMC was funded by grants from Comisión Nacional de Investigación Científica y Tecnológica (CONICYT): grants FONDECYT (11161020), PAI (PAI79170021), and FONDAP (15130011), Chile. ARP was funded by Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), grant 00454505/2014-0, Brazil. AMD was funded by CNPq (309566/2015­0) and Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) (25/2013), Brazil.

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Authors and Affiliations

  1. Advanced Center for Chronic Diseases—ACCDiS, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile

    Vinicius Maracaja-Coutinho & José Carlos Caris-Maldonado

  2. Department of Computer Science, Bioinformatics Graduation Program (PPGBIOINFO), Federal University of Technology — Paraná, Cornélio Procópio, Brazil

    Alexandre Rossi Paschoal & Pedro Vinícius Borges

  3. Computer Science Department, Instituto de Matemática e Estatística, Universidade de São Paulo, São Paulo, Brazil

    Almir José Ferreira & Alan Mitchell Durham

Authors
  1. Vinicius Maracaja-Coutinho
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  2. Alexandre Rossi Paschoal
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  3. José Carlos Caris-Maldonado
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  4. Pedro Vinícius Borges
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  5. Almir José Ferreira
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  6. Alan Mitchell Durham
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Corresponding author

Correspondence to Alan Mitchell Durham .

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Editors and Affiliations

  1. Department of Dermatology, Erlangen University Hospital, Erlangen, Germany

    Xin Lai

  2. Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany

    Shailendra K. Gupta

  3. Department of Dermatology, Erlangen University Hospital, Erlangen, Germany

    Julio Vera

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Maracaja-Coutinho, V., Paschoal, A.R., Caris-Maldonado, J.C., Borges, P.V., Ferreira, A.J., Durham, A.M. (2019). Noncoding RNAs Databases: Current Status and Trends. In: Lai, X., Gupta, S., Vera, J. (eds) Computational Biology of Non-Coding RNA. Methods in Molecular Biology, vol 1912. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8982-9_10

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  • DOI: https://doi.org/10.1007/978-1-4939-8982-9_10

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  • Online ISBN: 978-1-4939-8982-9

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