title: BioTextQuest(+): a knowledge integration platform for literature mining and concept discovery.
abstract: CONCLUSIONS
  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.
  
  
  BACKGROUND
  The service is accessible at http://bioinformatics.med.uoc.gr/biotextquest.
  
  
  BACKGROUND
  g.pavlopoulos@gmail.com or georgios.pavlopoulos@esat.kuleuven.be
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Division of Basic Sciences, University of Crete, Medical School, Heraklion 71110, Greece, Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Greece, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Campus Belval, 7, avenue des Hauts-Fourneaux, L-4362 Esch sur Alzette, Luxembourg, Biological Computation & Process Laboratory (BCPL), Chemical Process & Energy Resources Institute (CPERI), Centre for Research & Technology Hellas (CERTH), PO Box 361, GR-57001 Thessalonica, Greece, Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Ontario, Canada, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, 70013 Heraklion, Crete, Greece and Department of Biological Sciences, Bioinformatics Research Laboratory, University of Cyprus, PO Box 20537, CY 1678, Nicosia, Cyprus.
authors.forename: Nikolas
authors.initials: N
authors.lastname: Papanikolaou
authors.affiliation: Division of Basic Sciences, University of Crete, Medical School, Heraklion 71110, Greece, Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Greece, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Campus Belval, 7, avenue des Hauts-Fourneaux, L-4362 Esch sur Alzette, Luxembourg, Biological Computation & Process Laboratory (BCPL), Chemical Process & Energy Resources Institute (CPERI), Centre for Research & Technology Hellas (CERTH), PO Box 361, GR-57001 Thessalonica, Greece, Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Ontario, Canada, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, 70013 Heraklion, Crete, Greece and Department of Biological Sciences, Bioinformatics Research Laboratory, University of Cyprus, PO Box 20537, CY 1678, Nicosia, Cyprus.
authors.forename: Georgios A
authors.initials: GA
authors.lastname: Pavlopoulos
authors.affiliation: Division of Basic Sciences, University of Crete, Medical School, Heraklion 71110, Greece, Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Greece, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Campus Belval, 7, avenue des Hauts-Fourneaux, L-4362 Esch sur Alzette, Luxembourg, Biological Computation & Process Laboratory (BCPL), Chemical Process & Energy Resources Institute (CPERI), Centre for Research & Technology Hellas (CERTH), PO Box 361, GR-57001 Thessalonica, Greece, Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Ontario, Canada, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, 70013 Heraklion, Crete, Greece and Department of Biological Sciences, Bioinformatics Research Laboratory, University of Cyprus, PO Box 20537, CY 1678, Nicosia, Cyprus.
authors.forename: Evangelos
authors.initials: E
authors.lastname: Pafilis
authors.affiliation: Division of Basic Sciences, University of Crete, Medical School, Heraklion 71110, Greece, Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Greece, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Campus Belval, 7, avenue des Hauts-Fourneaux, L-4362 Esch sur Alzette, Luxembourg, Biological Computation & Process Laboratory (BCPL), Chemical Process & Energy Resources Institute (CPERI), Centre for Research & Technology Hellas (CERTH), PO Box 361, GR-57001 Thessalonica, Greece, Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Ontario, Canada, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, 70013 Heraklion, Crete, Greece and Department of Biological Sciences, Bioinformatics Research Laboratory, University of Cyprus, PO Box 20537, CY 1678, Nicosia, Cyprus.
authors.forename: Theodosios
authors.initials: T
authors.lastname: Theodosiou
authors.affiliation: Division of Basic Sciences, University of Crete, Medical School, Heraklion 71110, Greece, Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Greece, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Campus Belval, 7, avenue des Hauts-Fourneaux, L-4362 Esch sur Alzette, Luxembourg, Biological Computation & Process Laboratory (BCPL), Chemical Process & Energy Resources Institute (CPERI), Centre for Research & Technology Hellas (CERTH), PO Box 361, GR-57001 Thessalonica, Greece, Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Ontario, Canada, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, 70013 Heraklion, Crete, Greece and Department of Biological Sciences, Bioinformatics Research Laboratory, University of Cyprus, PO Box 20537, CY 1678, Nicosia, Cyprus.
authors.forename: Reinhard
authors.initials: R
authors.lastname: Schneider
authors.affiliation: Division of Basic Sciences, University of Crete, Medical School, Heraklion 71110, Greece, Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Greece, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Campus Belval, 7, avenue des Hauts-Fourneaux, L-4362 Esch sur Alzette, Luxembourg, Biological Computation & Process Laboratory (BCPL), Chemical Process & Energy Resources Institute (CPERI), Centre for Research & Technology Hellas (CERTH), PO Box 361, GR-57001 Thessalonica, Greece, Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Ontario, Canada, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, 70013 Heraklion, Crete, Greece and Department of Biological Sciences, Bioinformatics Research Laboratory, University of Cyprus, PO Box 20537, CY 1678, Nicosia, Cyprus.
authors.forename: Venkata P
authors.initials: VP
authors.lastname: Satagopam
authors.affiliation: Division of Basic Sciences, University of Crete, Medical School, Heraklion 71110, Greece, Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Greece, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Campus Belval, 7, avenue des Hauts-Fourneaux, L-4362 Esch sur Alzette, Luxembourg, Biological Computation & Process Laboratory (BCPL), Chemical Process & Energy Resources Institute (CPERI), Centre for Research & Technology Hellas (CERTH), PO Box 361, GR-57001 Thessalonica, Greece, Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Ontario, Canada, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, 70013 Heraklion, Crete, Greece and Department of Biological Sciences, Bioinformatics Research Laboratory, University of Cyprus, PO Box 20537, CY 1678, Nicosia, Cyprus Division of Basic Sciences, University of Crete, Medical School, Heraklion 71110, Greece, Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Greece, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Campus Belval, 7, avenue des Hauts-Fourneaux, L-4362 Esch sur Alzette, Luxembourg, Biological Computation & Process Laboratory (BCPL), Chemical Process & Energy Resources Institute (CPERI), Centre for Research & Technology Hellas (CERTH), PO Box 361, GR-57001 Thessalonica, Greece, Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Ontario, Canada, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, 70013 Heraklion, Crete, Greece and Department of Biological Sciences, Bioinformatics Research Laboratory, University of Cyprus, PO Box 20537, CY 1678, Nicosia, Cyprus.
authors.forename: Christos A
authors.initials: CA
authors.lastname: Ouzounis
authors.affiliation: Division of Basic Sciences, University of Crete, Medical School, Heraklion 71110, Greece, Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Greece, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Campus Belval, 7, avenue des Hauts-Fourneaux, L-4362 Esch sur Alzette, Luxembourg, Biological Computation & Process Laboratory (BCPL), Chemical Process & Energy Resources Institute (CPERI), Centre for Research & Technology Hellas (CERTH), PO Box 361, GR-57001 Thessalonica, Greece, Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Ontario, Canada, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, 70013 Heraklion, Crete, Greece and Department of Biological Sciences, Bioinformatics Research Laboratory, University of Cyprus, PO Box 20537, CY 1678, Nicosia, Cyprus Division of Basic Sciences, University of Crete, Medical School, Heraklion 71110, Greece, Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Greece, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Campus Belval, 7, avenue des Hauts-Fourneaux, L-4362 Esch sur Alzette, Luxembourg, Biological Computation & Process Laboratory (BCPL), Chemical Process & Energy Resources Institute (CPERI), Centre for Research & Technology Hellas (CERTH), PO Box 361, GR-57001 Thessalonica, Greece, Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Ontario, Canada, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, 70013 Heraklion, Crete, Greece and Department of Biological Sciences, Bioinformatics Research Laboratory, University of Cyprus, PO Box 20537, CY 1678, Nicosia, Cyprus.
authors.forename: Aristides G
authors.initials: AG
authors.lastname: Eliopoulos
authors.affiliation: Division of Basic Sciences, University of Crete, Medical School, Heraklion 71110, Greece, Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Greece, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Campus Belval, 7, avenue des Hauts-Fourneaux, L-4362 Esch sur Alzette, Luxembourg, Biological Computation & Process Laboratory (BCPL), Chemical Process & Energy Resources Institute (CPERI), Centre for Research & Technology Hellas (CERTH), PO Box 361, GR-57001 Thessalonica, Greece, Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Ontario, Canada, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, 70013 Heraklion, Crete, Greece and Department of Biological Sciences, Bioinformatics Research Laboratory, University of Cyprus, PO Box 20537, CY 1678, Nicosia, Cyprus.
authors.forename: Vasilis J
authors.initials: VJ
authors.lastname: Promponas
authors.affiliation: Division of Basic Sciences, University of Crete, Medical School, Heraklion 71110, Greece, Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Greece, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Campus Belval, 7, avenue des Hauts-Fourneaux, L-4362 Esch sur Alzette, Luxembourg, Biological Computation & Process Laboratory (BCPL), Chemical Process & Energy Resources Institute (CPERI), Centre for Research & Technology Hellas (CERTH), PO Box 361, GR-57001 Thessalonica, Greece, Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Ontario, Canada, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, 70013 Heraklion, Crete, Greece and Department of Biological Sciences, Bioinformatics Research Laboratory, University of Cyprus, PO Box 20537, CY 1678, Nicosia, Cyprus.
authors.forename: Ioannis
authors.initials: I
authors.lastname: Iliopoulos
mesh_terms: D001319:Authorship; D016000:Cluster Analysis; D057225:Data Mining / Q000379:methods*; D004194:Disease / Q000235:genetics; D005796:Genes; D006801:Humans; D020407:Internet; D046650:Medical Subject Headings; D011506:Proteins; D039781:PubMed; D011642:Publications; D012984:Software
chemical_list: D011506:Proteins