Anne O'Tate: A tool to support user-driven summarization, drill-down and browsing of PubMed search results

Neil R. Smalheiser, Wei Zhou, Vetle I. Torvik

Research output: Contribution to journalArticle

Abstract

Background: PubMed is designed to provide rapid, comprehensive retrieval of papers that discuss a given topic. However, because PubMed does not organize the search output further, it is difficult for users to grasp an overview of the retrieved literature according to non-topical dimensions, to drill-down to find individual articles relevant to a particular individual's need, or to browse the collection. Results: In this paper, we present Anne O'Tate, a web-based tool that processes articles retrieved from PubMed and displays multiple aspects of the articles to the user, according to pre-defined categories such as the "most important" words found in titles or abstracts; topics; journals; authors; publication years; and affiliations. Clicking on a given item opens a new window that displays all papers that contain that item. One can navigate by drilling down through the categories progressively, e.g., one can first restrict the articles according to author name and then restrict that subset by affiliation. Alternatively, one can expand small sets of articles to display the most closely related articles. We also implemented a novel cluster-by-topic method that generates a concise set of topics covering most of the retrieved articles. Conclusion: Anne O'Tate is an integrated, generic tool for summarization, drill-down and browsing of PubMed search results that accommodates a wide range of biomedical users and needs. It can be accessed at 4. Peer review and editorial matters for this article were handled by Aaron Cohen.

Original languageEnglish (US)
Article number2
JournalJournal of Biomedical Discovery and Collaboration
Volume3
DOIs
StatePublished - Feb 15 2008
Externally publishedYes

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ASJC Scopus subject areas

  • Health Informatics
  • Computer Science Applications
  • History and Philosophy of Science

Cite this

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title = "Anne O'Tate: A tool to support user-driven summarization, drill-down and browsing of PubMed search results",
abstract = "Background: PubMed is designed to provide rapid, comprehensive retrieval of papers that discuss a given topic. However, because PubMed does not organize the search output further, it is difficult for users to grasp an overview of the retrieved literature according to non-topical dimensions, to drill-down to find individual articles relevant to a particular individual's need, or to browse the collection. Results: In this paper, we present Anne O'Tate, a web-based tool that processes articles retrieved from PubMed and displays multiple aspects of the articles to the user, according to pre-defined categories such as the {"}most important{"} words found in titles or abstracts; topics; journals; authors; publication years; and affiliations. Clicking on a given item opens a new window that displays all papers that contain that item. One can navigate by drilling down through the categories progressively, e.g., one can first restrict the articles according to author name and then restrict that subset by affiliation. Alternatively, one can expand small sets of articles to display the most closely related articles. We also implemented a novel cluster-by-topic method that generates a concise set of topics covering most of the retrieved articles. Conclusion: Anne O'Tate is an integrated, generic tool for summarization, drill-down and browsing of PubMed search results that accommodates a wide range of biomedical users and needs. It can be accessed at 4. Peer review and editorial matters for this article were handled by Aaron Cohen.",
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