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Noncoding RNAs Databases: Current Status and Trends

  • Vinicius Maracaja-Coutinho
  • Alexandre Rossi Paschoal
  • José Carlos Caris-Maldonado
  • Pedro Vinícius Borges
  • Almir José Ferreira
  • Alan Mitchell Durham
Protocol
Part of the Methods in Molecular Biology book series (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.

Key words

Bioinformatics Databases Noncoding RNAs Biomedicine Biomedical Disease MicroRNA lncRNA Circulating RNAs Review 

Notes

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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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Vinicius Maracaja-Coutinho
    • 1
  • Alexandre Rossi Paschoal
    • 2
  • José Carlos Caris-Maldonado
    • 1
  • Pedro Vinícius Borges
    • 2
  • Almir José Ferreira
    • 3
  • Alan Mitchell Durham
    • 3
  1. 1.Advanced Center for Chronic Diseases—ACCDiS, Facultad de Ciencias Químicas y FarmacéuticasUniversidad de ChileSantiagoChile
  2. 2.Department of Computer Science, Bioinformatics Graduation Program (PPGBIOINFO)Federal University of Technology — ParanáCornélio ProcópioBrazil
  3. 3.Computer Science Department, Instituto de Matemática e EstatísticaUniversidade de São PauloSão PauloBrazil

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