Literature DB >> 18614002

Seeking a new biology through text mining.

Andrey Rzhetsky1, Michael Seringhaus, Mark Gerstein.   

Abstract

Tens of thousands of biomedical journals exist, and the deluge of new articles in the biomedical sciences is leading to information overload. Hence, there is much interest in text mining, the use of computational tools to enhance the human ability to parse and understand complex text.

Entities:  

Mesh：

Year:  2008        PMID： 18614002      PMCID： PMC2735884          DOI： 10.1016/j.cell.2008.06.029

Source DB:  PubMed          Journal:  Cell        ISSN： 0092-8674            Impact factor:   41.582


  14 in total

1.  Analysis of biomedical text for chemical names: a comparison of three methods.

Authors:  W J Wilbur; G F Hazard; G Divita; J G Mork; A R Aronson; A C Browne
Journal:  Proc AMIA Symp       Date:  1999

2.  Publishing on the semantic web.

Authors:  T Berners-Lee; J Hendler
Journal:  Nature       Date:  2001-04-26       Impact factor: 49.962

3.  Rutabaga by any other name: extracting biological names.

Authors:  Lynette Hirschman; Alexander A Morgan; Alexander S Yeh
Journal:  J Biomed Inform       Date:  2002-08       Impact factor: 6.317

4.  Mapping knowledge domains.

Authors:  Richard M Shiffrin; Katy Börner
Journal:  Proc Natl Acad Sci U S A       Date:  2004-01-23       Impact factor: 11.205

Review 5.  A survey of current work in biomedical text mining.

Authors:  Aaron M Cohen; William R Hersh
Journal:  Brief Bioinform       Date:  2005-03       Impact factor: 11.622

Review 6.  Text mining and its potential applications in systems biology.

Authors:  Sophia Ananiadou; Douglas B Kell; Jun-ichi Tsujii
Journal:  Trends Biotechnol       Date:  2006-10-12       Impact factor: 19.536

7.  SherLoc: high-accuracy prediction of protein subcellular localization by integrating text and protein sequence data.

Authors:  Hagit Shatkay; Annette Höglund; Scott Brady; Torsten Blum; Pierre Dönnes; Oliver Kohlbacher
Journal:  Bioinformatics       Date:  2007-03-28       Impact factor: 6.937

8.  Will a biological database be different from a biological journal?

Authors:  Philip Bourne
Journal:  PLoS Comput Biol       Date:  2005-08       Impact factor: 4.475

9.  Data preparation and interannotator agreement: BioCreAtIvE task 1B.

Authors:  Marc E Colosimo; Alexander A Morgan; Alexander S Yeh; Jeffrey B Colombe; Lynette Hirschman
Journal:  BMC Bioinformatics       Date:  2005-05-24       Impact factor: 3.169

10.  Text-mining and information-retrieval services for molecular biology.

Authors:  Martin Krallinger; Alfonso Valencia
Journal:  Genome Biol       Date:  2005-06-28       Impact factor: 13.583
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  30 in total

1.  Real-time ligand binding pocket database search using local surface descriptors.

Authors:  Rayan Chikhi; Lee Sael; Daisuke Kihara
Journal:  Proteins       Date:  2010-07

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

Review 3.  Novel opportunities for computational biology and sociology in drug discovery.

Authors:  Lixia Yao; James A Evans; Andrey Rzhetsky
Journal:  Trends Biotechnol       Date:  2010-04       Impact factor: 19.536

4.  Identifying overrepresented concepts in gene lists from literature: a statistical approach based on Poisson mixture model.

Authors:  Xin He; Moushumi Sen Sarma; Xu Ling; Brant Chee; Chengxiang Zhai; Bruce Schatz
Journal:  BMC Bioinformatics       Date:  2010-05-20       Impact factor: 3.169

5.  Zsyntax: a formal language for molecular biology with projected applications in text mining and biological prediction.

Authors:  Giovanni Boniolo; Marcello D'Agostino; Pier Paolo Di Fiore
Journal:  PLoS One       Date:  2010-03-03       Impact factor: 3.240

6.  A PubMed-wide associational study of infectious diseases.

Authors:  Vitali Sintchenko; Stephen Anthony; Xuan-Hieu Phan; Frank Lin; Enrico W Coiera
Journal:  PLoS One       Date:  2010-03-10       Impact factor: 3.240

7.  Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions.

Authors:  Soumya Raychaudhuri; Robert M Plenge; Elizabeth J Rossin; Aylwin C Y Ng; Shaun M Purcell; Pamela Sklar; Edward M Scolnick; Ramnik J Xavier; David Altshuler; Mark J Daly
Journal:  PLoS Genet       Date:  2009-06-26       Impact factor: 5.917

8.  Biomedical text mining and its applications.

Authors:  Raul Rodriguez-Esteban
Journal:  PLoS Comput Biol       Date:  2009-12-24       Impact factor: 4.475

9.  Looking at cerebellar malformations through text-mined interactomes of mice and humans.

Authors:  Ivan Iossifov; Raul Rodriguez-Esteban; Ilya Mayzus; Kathleen J Millen; Andrey Rzhetsky
Journal:  PLoS Comput Biol       Date:  2009-11-06       Impact factor: 4.475

10.  Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins.

Authors:  Pingzhao Hu; Sarath Chandra Janga; Mohan Babu; J Javier Díaz-Mejía; Gareth Butland; Wenhong Yang; Oxana Pogoutse; Xinghua Guo; Sadhna Phanse; Peter Wong; Shamanta Chandran; Constantine Christopoulos; Anaies Nazarians-Armavil; Negin Karimi Nasseri; Gabriel Musso; Mehrab Ali; Nazila Nazemof; Veronika Eroukova; Ashkan Golshani; Alberto Paccanaro; Jack F Greenblatt; Gabriel Moreno-Hagelsieb; Andrew Emili
Journal:  PLoS Biol       Date:  2009-04-28       Impact factor: 8.029
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