Literature DB >> 24788259

Accessing biomedical literature in the current information landscape.

Ritu Khare1, Robert Leaman, Zhiyong Lu.   

Abstract

Biomedical and life sciences literature is unique because of its exponentially increasing volume and interdisciplinary nature. Biomedical literature access is essential for several types of users including biomedical researchers, clinicians, database curators, and bibliometricians. In the past few decades, several online search tools and literature archives, generic as well as biomedicine specific, have been developed. We present this chapter in the light of three consecutive steps of literature access: searching for citations, retrieving full text, and viewing the article. The first section presents the current state of practice of biomedical literature access, including an analysis of the search tools most frequently used by the users, including PubMed, Google Scholar, Web of Science, Scopus, and Embase, and a study on biomedical literature archives such as PubMed Central. The next section describes current research and the state-of-the-art systems motivated by the challenges a user faces during query formulation and interpretation of search results. The research solutions are classified into five key areas related to text and data mining, text similarity search, semantic search, query support, relevance ranking, and clustering results. Finally, the last section describes some predicted future trends for improving biomedical literature access, such as searching and reading articles on portable devices, and adoption of the open access policy.

Entities:  

Mesh:

Year:  2014        PMID: 24788259      PMCID: PMC4593617          DOI: 10.1007/978-1-4939-0709-0_2

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN: 1064-3745


  59 in total

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Authors:  E C Armstrong
Journal:  WMJ       Date:  1999 Mar-Apr

2.  PubMed Assistant: a biologist-friendly interface for enhanced PubMed search.

Authors:  Jing Ding; Laron M Hughes; Daniel Berleant; Andy W Fulmer; Eve Syrkin Wurtele
Journal:  Bioinformatics       Date:  2005-12-06       Impact factor: 6.937

3.  EBIMed--text crunching to gather facts for proteins from Medline.

Authors:  Dietrich Rebholz-Schuhmann; Harald Kirsch; Miguel Arregui; Sylvain Gaudan; Mark Riethoven; Peter Stoehr
Journal:  Bioinformatics       Date:  2007-01-15       Impact factor: 6.937

4.  Author Name Disambiguation in MEDLINE.

Authors:  Vetle I Torvik; Neil R Smalheiser
Journal:  ACM Trans Knowl Discov Data       Date:  2009-07-01       Impact factor: 2.713

5.  Enabling multi-level relevance feedback on PubMed by integrating rank learning into DBMS.

Authors:  Hwanjo Yu; Taehoon Kim; Jinoh Oh; Ilhwan Ko; Sungchul Kim; Wook-Shin Han
Journal:  BMC Bioinformatics       Date:  2010-04-16       Impact factor: 3.169

6.  Improving links between literature and biological data with text mining: a case study with GEO, PDB and MEDLINE.

Authors:  Aurélie Névéol; W John Wilbur; Zhiyong Lu
Journal:  Database (Oxford)       Date:  2012-06-08       Impact factor: 3.451

7.  PubNet: a flexible system for visualizing literature derived networks.

Authors:  Shawn M Douglas; Gaetano T Montelione; Mark Gerstein
Journal:  Genome Biol       Date:  2005-08-16       Impact factor: 13.583

8.  eTBLAST: a web server to identify expert reviewers, appropriate journals and similar publications.

Authors:  Mounir Errami; Jonathan D Wren; Justin M Hicks; Harold R Garner
Journal:  Nucleic Acids Res       Date:  2007-04-22       Impact factor: 16.971

9.  PubMed related articles: a probabilistic topic-based model for content similarity.

Authors:  Jimmy Lin; W John Wilbur
Journal:  BMC Bioinformatics       Date:  2007-10-30       Impact factor: 3.169

10.  MedlineRanker: flexible ranking of biomedical literature.

Authors:  Jean-Fred Fontaine; Adriano Barbosa-Silva; Martin Schaefer; Matthew R Huska; Enrique M Muro; Miguel A Andrade-Navarro
Journal:  Nucleic Acids Res       Date:  2009-05-08       Impact factor: 16.971

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  11 in total

Review 1.  Community challenges in biomedical text mining over 10 years: success, failure and the future.

Authors:  Chung-Chi Huang; Zhiyong Lu
Journal:  Brief Bioinform       Date:  2015-05-01       Impact factor: 11.622

2.  LitSuggest: a web-based system for literature recommendation and curation using machine learning.

Authors:  Alexis Allot; Kyubum Lee; Qingyu Chen; Ling Luo; Zhiyong Lu
Journal:  Nucleic Acids Res       Date:  2021-07-02       Impact factor: 16.971

Review 3.  Crowdsourcing in biomedicine: challenges and opportunities.

Authors:  Ritu Khare; Benjamin M Good; Robert Leaman; Andrew I Su; Zhiyong Lu
Journal:  Brief Bioinform       Date:  2015-04-17       Impact factor: 11.622

Review 4.  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

Review 5.  The WNT/β-catenin dependent transcription: A tissue-specific business.

Authors:  Simon Söderholm; Claudio Cantù
Journal:  WIREs Mech Dis       Date:  2020-10-21

6.  PubMedPortable: A Framework for Supporting the Development of Text Mining Applications.

Authors:  Kersten Döring; Björn A Grüning; Kiran K Telukunta; Philippe Thomas; Stefan Günther
Journal:  PLoS One       Date:  2016-10-05       Impact factor: 3.240

7.  Abstract Sifter: a comprehensive front-end system to PubMed.

Authors:  Nancy Baker; Thomas Knudsen; Antony Williams
Journal:  F1000Res       Date:  2017-12-21

8.  Analyzing a co-occurrence gene-interaction network to identify disease-gene association.

Authors:  Amira Al-Aamri; Kamal Taha; Yousof Al-Hammadi; Maher Maalouf; Dirar Homouz
Journal:  BMC Bioinformatics       Date:  2019-02-08       Impact factor: 3.169

9.  DrugShot: querying biomedical search terms to retrieve prioritized lists of small molecules.

Authors:  Eryk Kropiwnicki; Alexander Lachmann; Daniel J B Clarke; Zhuorui Xie; Kathleen M Jagodnik; Avi Ma'ayan
Journal:  BMC Bioinformatics       Date:  2022-02-19       Impact factor: 3.307

10.  LitVar: a semantic search engine for linking genomic variant data in PubMed and PMC.

Authors:  Alexis Allot; Yifan Peng; Chih-Hsuan Wei; Kyubum Lee; Lon Phan; Zhiyong Lu
Journal:  Nucleic Acids Res       Date:  2018-07-02       Impact factor: 16.971

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