Literature DB >> 23150036

Text-mining solutions for biomedical research: enabling integrative biology.

Dietrich Rebholz-Schuhmann1, Anika Oellrich, Robert Hoehndorf.   

Abstract

In response to the unbridled growth of information in literature and biomedical databases, researchers require efficient means of handling and extracting information. As well as providing background information for research, scientific publications can be processed to transform textual information into database content or complex networks and can be integrated with existing knowledge resources to suggest novel hypotheses. Information extraction and text data analysis can be particularly relevant and helpful in genetics and biomedical research, in which up-to-date information about complex processes involving genes, proteins and phenotypes is crucial. Here we explore the latest advancements in automated literature analysis and its contribution to innovative research approaches.

Mesh:

Year:  2012        PMID: 23150036     DOI: 10.1038/nrg3337

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN: 1471-0056            Impact factor:   53.242


  96 in total

1.  Association of genes to genetically inherited diseases using data mining.

Authors:  Carolina Perez-Iratxeta; Peer Bork; Miguel A Andrade
Journal:  Nat Genet       Date:  2002-05-13       Impact factor: 38.330

2.  OBO-Edit--an ontology editor for biologists.

Authors:  John Day-Richter; Midori A Harris; Melissa Haendel; Suzanna Lewis
Journal:  Bioinformatics       Date:  2007-06-01       Impact factor: 6.937

3.  The human disease network.

Authors:  Kwang-Il Goh; Michael E Cusick; David Valle; Barton Childs; Marc Vidal; Albert-László Barabási
Journal:  Proc Natl Acad Sci U S A       Date:  2007-05-14       Impact factor: 11.205

4.  High-performance gene name normalization with GeNo.

Authors:  Joachim Wermter; Katrin Tomanek; Udo Hahn
Journal:  Bioinformatics       Date:  2009-02-02       Impact factor: 6.937

5.  Individualizing therapies in type 2 diabetes mellitus based on patient characteristics: what we know and what we need to know.

Authors:  Robert J Smith; David M Nathan; Silva A Arslanian; Leif Groop; Robert A Rizza; Jerome I Rotter
Journal:  J Clin Endocrinol Metab       Date:  2010-03-01       Impact factor: 5.958

6.  Establishing a distributed system for the simple representation and integration of diverse scientific assertions.

Authors:  Matthias Samwald; Holger Stenzhorn
Journal:  J Biomed Semantics       Date:  2010-06-22

7.  Automatic recognition of conceptualization zones in scientific articles and two life science applications.

Authors:  Maria Liakata; Shyamasree Saha; Simon Dobnik; Colin Batchelor; Dietrich Rebholz-Schuhmann
Journal:  Bioinformatics       Date:  2012-02-08       Impact factor: 6.937

8.  How to link ontologies and protein-protein interactions to literature: text-mining approaches and the BioCreative experience.

Authors:  Martin Krallinger; Florian Leitner; Miguel Vazquez; David Salgado; Christophe Marcelle; Mike Tyers; Alfonso Valencia; Andrew Chatr-aryamontri
Journal:  Database (Oxford)       Date:  2012-03-21       Impact factor: 3.451

9.  Integrating protein-protein interactions and text mining for protein function prediction.

Authors:  Samira Jaeger; Sylvain Gaudan; Ulf Leser; Dietrich Rebholz-Schuhmann
Journal:  BMC Bioinformatics       Date:  2008-07-22       Impact factor: 3.169

10.  Comparison of concept recognizers for building the Open Biomedical Annotator.

Authors:  Nigam H Shah; Nipun Bhatia; Clement Jonquet; Daniel Rubin; Annie P Chiang; Mark A Musen
Journal:  BMC Bioinformatics       Date:  2009-09-17       Impact factor: 3.169

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  85 in total

1.  A literature search tool for intelligent extraction of disease-associated genes.

Authors:  Jae-Yoon Jung; Todd F DeLuca; Tristan H Nelson; Dennis P Wall
Journal:  J Am Med Inform Assoc       Date:  2013-09-02       Impact factor: 4.497

2.  Finding potentially new multimorbidity patterns of psychiatric and somatic diseases: exploring the use of literature-based discovery in primary care research.

Authors:  Rein Vos; Sil Aarts; Erik van Mulligen; Job Metsemakers; Martin P van Boxtel; Frans Verhey; Marjan van den Akker
Journal:  J Am Med Inform Assoc       Date:  2013-06-17       Impact factor: 4.497

3.  Use of ontology structure and Bayesian models to aid the crowdsourcing of ICD-11 sanctioning rules.

Authors:  Yun Lou; Samson W Tu; Csongor Nyulas; Tania Tudorache; Robert J G Chalmers; Mark A Musen
Journal:  J Biomed Inform       Date:  2017-02-10       Impact factor: 6.317

4.  A new version of the ANDSystem tool for automatic extraction of knowledge from scientific publications with expanded functionality for reconstruction of associative gene networks by considering tissue-specific gene expression.

Authors:  Vladimir A Ivanisenko; Pavel S Demenkov; Timofey V Ivanisenko; Elena L Mishchenko; Olga V Saik
Journal:  BMC Bioinformatics       Date:  2019-02-05       Impact factor: 3.169

5.  Learning predictive models of drug side-effect relationships from distributed representations of literature-derived semantic predications.

Authors:  Justin Mower; Devika Subramanian; Trevor Cohen
Journal:  J Am Med Inform Assoc       Date:  2018-10-01       Impact factor: 4.497

Review 6.  Big data in medicine is driving big changes.

Authors:  F Martin-Sanchez; K Verspoor
Journal:  Yearb Med Inform       Date:  2014-08-15

Review 7.  Informatics Support for Basic Research in Biomedicine.

Authors:  Thomas C Rindflesch; Catherine L Blake; Marcelo Fiszman; Halil Kilicoglu; Graciela Rosemblat; Jodi Schneider; Caroline J Zeiss
Journal:  ILAR J       Date:  2017-07-01

8.  A comprehensive and quantitative comparison of text-mining in 15 million full-text articles versus their corresponding abstracts.

Authors:  David Westergaard; Hans-Henrik Stærfeldt; Christian Tønsberg; Lars Juhl Jensen; Søren Brunak
Journal:  PLoS Comput Biol       Date:  2018-02-15       Impact factor: 4.475

9.  A knowledge base of vasopressin actions in the kidney.

Authors:  Akshay Sanghi; Matthew Zaringhalam; Callan C Corcoran; Fahad Saeed; Jason D Hoffert; Pablo Sandoval; Trairak Pisitkun; Mark A Knepper
Journal:  Am J Physiol Renal Physiol       Date:  2014-07-23

Review 10.  Integrating bioinformatics approaches for a comprehensive interpretation of metabolomics datasets.

Authors:  Dinesh Kumar Barupal; Sili Fan; Oliver Fiehn
Journal:  Curr Opin Biotechnol       Date:  2018-02-06       Impact factor: 9.740

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