Summary: Identifying, amongst millions of publications available in MEDLINE, those that are relevant to specific microRNAs (miRNAs) of interest based on keyword search faces major obstacles. References to miRNA names in the literature often deviate from standard nomenclature for various reasons, since even the official nomenclature evolves. For instance, a single miRNA name may identify two completely different molecules or two different names may refer to the same molecule. mirPub is a database with a powerful and intuitive interface, which facilitates searching for miRNA literature, addressing the aforementioned issues. To provide effective search services, mirPub applies text mining techniques on MEDLINE, integrates data from several curated databases and exploits data from its user community following a crowdsourcing approach. Other key features include an interactive visualization service that illustrates intuitively the evolution of miRNA data, tag clouds summarizing the relevance of publications to particular diseases, cell types or tissues and access to TarBase 6.0 data to oversee genes related to miRNA publications.
Availability And Implementation: mirPub is freely available at http://www.microrna.gr/mirpub/.
Contact: vergoulis@imis.athena-innovation.gr or dalamag@imis.athena-innovation.gr
Supplementary Information: Supplementary data are available at Bioinformatics online.
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| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4410649 | PMC |
| http://dx.doi.org/10.1093/bioinformatics/btu819 | DOI Listing |
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mirPub: a database for searching microRNA publications.
Bioinformatics
May 2015
School of Electrical and Computer Engineering, NTUA, Zografou 15773, IMIS Institute, 'Athena' RC, Marousi 15125, DIANA-Lab, Institute of Molecular Oncology, BSRC 'Alexander Fleming', Vari 16672, Department of Computer & Communication Engineering, University of Thessaly, Volos 38221, Greece and School of Computer Science & Info Tech, RMIT University, Melbourne 3001, Australia.
Summary: Identifying, amongst millions of publications available in MEDLINE, those that are relevant to specific microRNAs (miRNAs) of interest based on keyword search faces major obstacles. References to miRNA names in the literature often deviate from standard nomenclature for various reasons, since even the official nomenclature evolves. For instance, a single miRNA name may identify two completely different molecules or two different names may refer to the same molecule.
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