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Anne O'Tate: A Tool to Support User-Driven Summarization, Drill-Down and Browsing of PubMed Search Results

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Anne O'Tate: A Tool to Support User-Driven Summarization, Drill-Down and Browsing of PubMed Search Results

Neil R Smalheiser et al. J Biomed Discov Collab.

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.

Figures

Figure 1
Figure 1
The Cluster-by-topic algorithm.
Figure 2
Figure 2
Screenshot of the Anne O'Tate tool returning the PubMed query "dicer."
Figure 3
Figure 3
Screenshot of the Anne O'Tate tool displaying a list of the author names mentioned in the set of articles retrieved by the "dicer" query.
Figure 4
Figure 4
Screenshot of the Anne O'Tate tool displaying a histogram of the publication dates of the set of articles retrieved by the "dicer" query.
Figure 5
Figure 5
Coverage of the cluster-by-topic list across a range of queries. Anonymous queries in the Anne O'Tate query web log were analyzed. For each query, the coverage was computed (i.e., the proportion of MeSH-indexed articles in the PubMed search output that were included in the 15 MeSH-based topical clusters). The results were averaged for retrieved literatures of different size ranges as follows: 0–100 articles, 6 queries; 101–1000 articles, 9 queries; 1001–10000 articles, 9 queries; and >10000 articles, 3 queries.

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References

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