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      Abstract Sifter: a comprehensive front-end system to PubMed

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          Abstract

          The Abstract Sifter is a Microsoft Excel based application that enhances existing search capabilities of PubMed. The Abstract Sifter assists researchers to search effectively, triage results, and keep track of articles of interest. The tool implements an innovative “sifter” functionality for relevance ranking, giving the researcher a way to find articles of interest quickly. The tool also gives researchers a view of the literature landscape for a set of entities such as chemicals or genes. The Abstract Sifter is available as a Microsoft Excel macro-enabled workbook application.

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          Most cited references 2

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          Accessing biomedical literature in the current information landscape.

          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.
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            nancycolebaker/LitInfo: PubMed Abstract Sifter public release v.1.

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              Author and article information

              Contributors
              Role: ConceptualizationRole: MethodologyRole: SoftwareRole: Writing – Original Draft Preparation
              Role: Project AdministrationRole: Writing – Review & Editing
              Role: ConceptualizationRole: Writing – Original Draft PreparationRole: Writing – Review & Editing
              Journal
              F1000Res
              F1000Res
              F1000Research
              F1000Research
              F1000 Research Limited (London, UK )
              2046-1402
              21 December 2017
              2017
              : 6
              Affiliations
              [1 ]Leidos, Research Triangle Park, NC, USA
              [2 ]National Center for Computational Toxicology, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
              [1 ]National Institutes of Health, Bethesda, MD, USA
              [1 ]Unit of Toxicological Sciences, Swetox, Karolinska Institutet, Södertälje, Sweden
              Author notes

              No competing interests were disclosed.

              Competing interests: No competing interests were disclosed.

              Competing interests: No competing interests were disclosed.

              Article
              10.12688/f1000research.12865.1
              5801564
              29479422
              Copyright: © 2017 Baker N et al.

              This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

              Product
              Funding
              Funded by: U.S. Environmental Protection Agency
              Research in this publication was supported by the U.S. Environmental Protection Agency.
              The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
              Categories
              Software Tool Article
              Articles
              Bioinformatics

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