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BioTextQuest(+): a knowledge integration platform for literature mining and concept discovery.

TitleBioTextQuest(+): a knowledge integration platform for literature mining and concept discovery.
Publication TypeJournal Article
Year of Publication2014
AuthorsPapanikolaou, Nikolas, Georgios A. Pavlopoulos, Evangelos Pafilis, Theodosios Theodosiou, Reinhard Schneider, Venkata P. Satagopam, Christos A. Ouzounis, Aristides G. Eliopoulos, V. J. Promponas, and Ioannis Iliopoulos
JournalBioinformatics (Oxford, England)
Volume30
Issue22
Pagination3249-56
Date Published2014 Nov 15
ISSN1367-4811
KeywordsAuthorship, Cluster Analysis, Data Mining, Disease, Genes, Humans, Internet, Medical Subject Headings, Proteins, Publications, PubMed, Software
Abstract

SUMMARY: The iterative process of finding relevant information in biomedical literature and performing bioinformatics analyses might result in an endless loop for an inexperienced user, considering the exponential growth of scientific corpora and the plethora of tools designed to mine PubMed(®) and related biological databases. Herein, we describe BioTextQuest(+), a web-based interactive knowledge exploration platform with significant advances to its predecessor (BioTextQuest), aiming to bridge processes such as bioentity recognition, functional annotation, document clustering and data integration towards literature mining and concept discovery. BioTextQuest(+) enables PubMed and OMIM querying, retrieval of abstracts related to a targeted request and optimal detection of genes, proteins, molecular functions, pathways and biological processes within the retrieved documents. The front-end interface facilitates the browsing of document clustering per subject, the analysis of term co-occurrence, the generation of tag clouds containing highly represented terms per cluster and at-a-glance popup windows with information about relevant genes and proteins. Moreover, to support experimental research, BioTextQuest(+) addresses integration of its primary functionality with biological repositories and software tools able to deliver further bioinformatics services. The Google-like interface extends beyond simple use by offering a range of advanced parameterization for expert users. We demonstrate the functionality of BioTextQuest(+) through several exemplary research scenarios including author disambiguation, functional term enrichment, knowledge acquisition and concept discovery linking major human diseases, such as obesity and ageing. AVAILABILITY: The service is accessible at http://bioinformatics.med.uoc.gr/biotextquest. CONTACT: g.pavlopoulos@gmail.com or georgios.pavlopoulos@esat.kuleuven.be SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

DOI10.1093/bioinformatics/btu524
Alternate JournalBioinformatics


by Dr. Radut.