DES-ncRNA: A knowledgebase for exploring information about human micro and long noncoding RNAs based on literature-mining

Adil Salhi, Magbubah Essack, Tanvir Alam, Vladan P. Bajic, Lina Ma, Aleksandar Radovanovic, Benoit Marchand, Sebastian Schmeier, Zhang Zhang, Vladimir B. Bajic

Research output: Contribution to journalArticle

Abstract

Noncoding RNAs (ncRNAs), particularly microRNAs (miRNAs) and long ncRNAs (lncRNAs), are important players in diseases and emerge as novel drug targets. Thus, unraveling the relationships between ncRNAs and other biomedical entities in cells are critical for better understanding ncRNA roles that may eventually help develop their use in medicine. To support ncRNA research and facilitate retrieval of relevant information regarding miRNAs and lncRNAs from the plethora of published ncRNA-related research, we developed DES-ncRNA (www.cbrc.kaust.edu.sa/des_ncrna). DES-ncRNA is a knowledgebase containing text- and data-mined information from public scientific literature and other public resources. Exploration of mined information is enabled through terms and pairs of terms from 19 topic-specific dictionaries including, for example, antibiotics, toxins, drugs, enzymes, mutations, pathways, human genes and proteins, drug indications and side effects, mutations, diseases, etc. DES-ncRNA contains approximately 878,000 associations of terms from these dictionaries of which 36,222 (5,373) are with regards to miRNAs (lncRNAs). We provide several ways to explore information regarding ncRNAs to users including controlled generation of association networks as well as hypotheses generation. We show an example how DES-ncRNA can aid research on Alzheimer disease and suggest potential therapeutic role for Fasudil. DES-ncRNA is a powerful tool that can be used on its own or as a complement to the existing resources, to support research in human ncRNA. To our knowledge, this is the only knowledgebase dedicated to human miRNAs and lncRNAs derived primarily through literature-mining enabling exploration of a broad spectrum of associated biomedical entities, not paralleled by any other resource.

Original languageEnglish (US)
Pages (from-to)963-971
Number of pages9
JournalRNA Biology
Volume14
Issue number7
DOIs
StatePublished - Jul 3 2017

Keywords

  • Alzheimer disease
  • Noncoding RNA
  • bioinformatics
  • data-mining
  • information integration
  • knowledgebase
  • literature-mining
  • long noncoding RNA
  • microRNA
  • text-mining

ASJC Scopus subject areas

  • Molecular Biology
  • Cell Biology

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  • Cite this

    Salhi, A., Essack, M., Alam, T., Bajic, V. P., Ma, L., Radovanovic, A., Marchand, B., Schmeier, S., Zhang, Z., & Bajic, V. B. (2017). DES-ncRNA: A knowledgebase for exploring information about human micro and long noncoding RNAs based on literature-mining. RNA Biology, 14(7), 963-971. https://doi.org/10.1080/15476286.2017.1312243