Computer & Information Sciences

Text Mining

Published August 4, 2016 Curated Collections

Across all realms of the sciences, the rapid growth in the number of works published digitally presents new challenges and opportunities for making sense of this wealth of textual information. The maturing field of Text Mining aims to solve problems concerning the retrieval, extraction and analysis of unstructured information in digital text, and revolutionize how scientists access and interpret data that might otherwise remain buried in the literature. PLOS acknowledges the growing body of work in the area of Text Mining by bringing together reviews and research studies to create the PLOS Text Mining Collection. It is no coincidence that research in Text Mining is burgeoning: the widespread uptake of the Open Access publishing model developed by PLOS and other publishers now makes it easier than ever to obtain, mine and redistribute data from published texts.

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Essays and Opinion
Research

Essays and Opinion

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PLOS

PLOS Computational Biology Getting Started in Text Mining
January 25, 2008 K. Bretonnel Cohen, Lawrence Hunter
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10.1371/journal.pcbi.1000411

PLOS Computational Biology Getting Started in Text Mining: Part Two
July 31, 2009 Andrey Rzhetsky, Michael Seringhaus, Mark B. Gerstein
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PLOS

PLOS Computational Biology Open Access: Taking Full Advantage of the Content
March 28, 2008 Philip E. Bourne, J. Lynn Fink, Mark Gerstein
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PLOS

PLOS Computational Biology Biomedical Text Mining and Its Applications
December 24, 2009 Raul Rodriguez-Esteban
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PLOS

PLOS Biology Tough Mining
November 17, 2003 Steven Dickman
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10.1371/journal.pbio.0030065

PLOS Biology Facts from Text—Is Text Mining Ready to Deliver?
February 15, 2005 Dietrich Rebholz-Schuhmann, Harald Kirsch, Francisco Couto

Research

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10.1371/journal.pone.0144717

PLOS ONE Text Mining the History of Medicine
January 6, 2016 Paul Thompson, Riza Theresa Batista-Navarro, Georgios Kontonatsios, Jacob Carter, Elizabeth Toon, John McNaught, Carsten Timmermann, Michael Worboys, Sophia Ananiadou
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10.1371/journal.pone.0156031

PLOS ONE Text Mining of Journal Articles for Sleep Disorder Terminologies
May 20, 2016 Calvin Lam, Fu-Chih Lai, Chia-Hui Wang, Mei-Hsin Lai, Nanly Hsu, Min-Huey Chung
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10.1371/journal.pone.0152725

PLOS ONE DiMeX: A Text Mining System for Mutation-Disease Association Extraction
April 13, 2016 A. S. M. Ashique Mahmood, Tsung-Jung Wu, Raja Mazumder, K. Vijay-Shanker
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10.1371/journal.pone.0134585

PLOS ONE Systematic Analysis of the Molecular Mechanism Underlying Decidualization Using a Text Mining Approach
July 29, 2015 Ji-Long Liu, Tong-Song Wang
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10.1371/journal.pone.0098826

PLOS ONE Discovering Hidden Connections among Diseases, Genes and Drugs Based on Microarray Expression Profiles with Negative-Term Filtering
June 10, 2014 Jain-Shing Wu, E-Fong Kao, Chung-Nan Lee
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10.1371/journal.pone.0079517

PLOS ONE Collective Instance-Level Gene Normalization on the IGN Corpus
November 25, 2013 Hong-Jie Dai, Johnny Chi-Yang Wu, Richard Tzong-Han Tsai
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10.1371/journal.pone.0083147

PLOS ONE Books Average Previous Decade of Economic Misery
January 8, 2014 R. Alexander Bentley, Alberto Acerbi, Paul Ormerod, Vasileios Lampos
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10.1371/journal.pone.0079294

PLOS ONE Cross-Language Opinion Lexicon Extraction Using Mutual-Reinforcement Label Propagation
November 15, 2013 Zheng Lin, Songbo Tan, Yue Liu, Xueqi Cheng, Xueke Xu
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10.1371/journal.pone.0078737

PLOS ONE Biological Diversity in the Patent System
November 12, 2013 Paul Oldham, Stephen Hall, Oscar Forero
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10.1371/journal.pone.0077910

PLOS ONE Experimental Design-Based Functional Mining and Characterization of High-Throughput Sequencing Data in the Sequence Read Archive
October 22, 2013 Takeru Nakazato, Tazro Ohta, Hidemasa Bono
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10.1371/journal.pone.0077868

PLOS ONE Using a Search Engine-Based Mutually Reinforcing Approach to Assess the Semantic Relatedness of Biomedical Terms
November 13, 2013 Yi-Yu Hsu, Hung-Yu Chen, Hung-Yu Kao
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10.1371/journal.pone.0072965

PLOS ONE Learning to Recognize Phenotype Candidates in the Auto-Immune Literature Using SVM Re-Ranking
October 14, 2013 Nigel Collier, Mai-vu Tran, Hoang-quynh Le, Quang-Thuy Ha, Anika Oellrich, Dietrich Rebholz-Schuhmann
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10.1371/journal.pone.0065390

PLOS ONE The SPECIES and ORGANISMS Resources for Fast and Accurate Identification of Taxonomic Names in Text
June 18, 2013 Evangelos Pafilis, Sune P. Frankild, Lucia Fanini, Sarah Faulwetter, Christina Pavloudi, Aikaterini Vasileiadou, Christos Arvanitidis, Lars Juhl Jensen
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10.1371/journal.pone.0064601

PLOS ONE Phrasal Paraphrase Based Question Reformulation for Archived Question Retrieval
June 21, 2013 Yu Zhang, Wei-Nan Zhang, Ke Lu, Fanglin Wang, Ting Liu, Rongrong Ji
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10.1371/journal.pone.0063184

PLOS ONE Database Citation in Full Text Biomedical Articles
May 29, 2013 Şenay Kafkas, Jee-Hyub Kim, Johanna R. McEntyre
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10.1371/journal.pone.0060954

PLOS ONE Approximate Subgraph Matching-Based Literature Mining for Biomedical Events and Relations
April 17, 2013 Haibin Liu, Lawrence Hunter, Vlado Kešelj, Karin Verspoor
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10.1371/journal.pone.0059030

PLOS ONE The Expression of Emotions in 20th Century Books
March 20, 2013 Alberto Acerbi, Vasileios Lampos, Philip Garnett, R. Alexander Bentley
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10.1371/journal.pone.0058201

PLOS ONE Text Mining Effectively Scores and Ranks the Literature for Improving Chemical-Gene-Disease Curation at the Comparative Toxicogenomics Database
April 17, 2013 Allan Peter Davis, Thomas C. Wiegers, Robin J. Johnson, Jean M. Lay, Kelley Lennon-Hopkins, Cynthia Saraceni-Richards, Daniela Sciaky, Cynthia Grondin Murphy, Carolyn J. Mattingly
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10.1371/journal.pone.0055814

PLOS ONE Large-Scale Event Extraction from Literature with Multi-Level Gene Normalization
April 17, 2013 Sofie Van Landeghem, Jari Björne, Chih-Hsuan Wei, Kai Hakala, Sampo Pyysalo, Sophia Ananiadou, Hung-Yu Kao, Zhiyong Lu, Tapio Salakoski, Yves Van de Peer, Filip Ginter
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10.1371/journal.pone.0055674

PLOS ONE Utilizing Descriptive Statements from the Biodiversity Heritage Library to Expand the Hymenoptera Anatomy Ontology
February 18, 2013 Katja C. Seltmann, Zsolt Pénzes, Matthew J. Yoder, Matthew A. Bertone, Andrew R. Deans
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10.1371/journal.pone.0055656

PLOS ONE Mining Skeletal Phenotype Descriptions from Scientific Literature
February 8, 2013 Tudor Groza, Jane Hunter, Andreas Zankl
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10.1371/journal.pone.0054998

PLOS ONE Automated Authorship Attribution Using Advanced Signal Classification Techniques
February 20, 2013 Maryam Ebrahimpour, Tālis J. Putniņš, Matthew J. Berryman, Andrew Allison, Brian W.-H. Ng, Derek Abbott
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10.1371/journal.pone.0029509

PLOS ONE Connecting the Dots between PubMed Abstracts
January 3, 2012 M. Shahriar Hossain, Joseph Gresock, Yvette Edmonds, Richard Helm, Malcolm Potts, Naren Ramakrishnan
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10.1371/journal.pone.0026556

PLOS ONE Differences among Major Taxa in the Extent of Ecological Knowledge across Four Major Ecosystems
November 2, 2011 Rebecca Fisher, Nancy Knowlton, Russell E. Brainard, M. Julian Caley
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10.1371/journal.pone.0024716

PLOS ONE pubmed2ensembl: A Resource for Mining the Biological Literature on Genes
September 29, 2011 Joachim Baran, Martin Gerner, Maximilian Haeussler, Goran Nenadic, Casey M. Bergman
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10.1371/journal.pone.0020907

PLOS ONE A Network of Genes, Genetic Disorders, and Brain Areas
June 10, 2011 Satoru Hayasaka, Christina E. Hugenschmidt, Paul J. Laurienti
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10.1371/journal.pone.0020181

PLOS ONE Using Workflows to Explore and Optimise Named Entity Recognition for Chemistry
May 25, 2011 BalaKrishna Kolluru, Lezan Hawizy, Peter Murray-Rust, Junichi Tsujii, Sophia Ananiadou
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10.1371/journal.pone.0018029

PLOS ONE Clustering More than Two Million Biomedical Publications: Comparing the Accuracies of Nine Text-Based Similarity Approaches
March 17, 2011 Kevin W. Boyack, David Newman, Russell J. Duhon, Richard Klavans, Michael Patek, Joseph R. Biberstine, Bob Schijvenaars, André Skupin, Nianli Ma, Katy Börner
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10.1371/journal.pone.0015338

PLOS ONE Figure Text Extraction in Biomedical Literature
January 13, 2011 Daehyun Kim, Hong Yu
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10.1371/journal.pcbi.1003117

PLOS Computational Biology ‘HypothesisFinder:’ A Strategy for the Detection of Speculative Statements in Scientific Text
July 25, 2013 Ashutosh Malhotra, Erfan Younesi, Harsha Gurulingappa, Martin Hofmann-Apitius
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10.1371/journal.pcbi.1002199

PLOS Computational Biology Assessing Vaccination Sentiments with Online Social Media: Implications for Infectious Disease Dynamics and Control
October 13, 2011 Marcel Salathé, Shashank Khandelwal
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10.1371/journal.pcbi.1002141

PLOS Computational Biology Using Electronic Patient Records to Discover Disease Correlations and Stratify Patient Cohorts
August 25, 2011 Francisco S. Roque, Peter B. Jensen, Henriette Schmock, Marlene Dalgaard, Massimo Andreatta, Thomas Hansen, Karen Søeby, Søren Bredkjær, Anders Juul, Thomas Werge, Lars J. Jensen, Søren Brunak