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. 2015 May 1;31(9):1502-4.
doi: 10.1093/bioinformatics/btu819. Epub 2014 Dec 20.

mirPub: a database for searching microRNA publications

Thanasis Vergoulis  1 , Ilias Kanellos  1 , Nikos Kostoulas  2 , Georgios Georgakilas  1 , Timos Sellis  2 , Artemis Hatzigeorgiou  1 , Theodore Dalamagas  2
Affiliations

mirPub: a database for searching microRNA publications

Thanasis Vergoulis et al. Bioinformatics. .

Abstract

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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Figures

Fig. 1.
Fig. 1.
mirPub's text mining method. miRBase Parser produces the set of ‘official names’ consisting of all miRNA and family names recorded in miRBase. Term Extractor expands this set to produce the set of ‘miRNA terms’, which also contains variants of the official names based on predefined modification rules (see Section 2). Publication Indexer builds an inverted index on MEDLINE texts and association extractor utilizes this index to retrieve efficiently all appearances of miRNA terms in literature. The aforementioned appearances indicate miRNA publication associations
See this image and copyright information in PMC

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Publication types