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Open Access Highly Accessed Software

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

Neil R Smalheiser1*, Wei Zhou2 and Vetle I Torvik1

Author Affiliations

1 Department of Psychiatry and Psychiatric Institute, MC912, University of Illinois at Chicago, Chicago, IL 60612, USA

2 Department of Computer Science, University of Illinois at Chicago, Chicago, IL 60607, USA

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Journal of Biomedical Discovery and Collaboration 2008, 3:2  doi:10.1186/1747-5333-3-2

Published: 15 February 2008

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.