Abstract
BackgroundPubMed 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.ResultsIn 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.ConclusionAnne 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.
Highlights
PubMed is designed to provide rapid, comprehensive retrieval of papers that discuss a given topic
We sought to create a tool for carrying out PubMed searches [5] that did not require the user to progressively reformulate the initial query; that would assist the user in finding the most relevant articles quickly and efficiently; and that would summarize the salient features of a given set of articles – e.g., given a set of articles discussing gene X, to give a list of diseases that gene X has been studied in, or given a set of articles on disease Y, to give a list of symptoms that have been described in that disease
2.1 Query interface The PubMed query interface [5] was imported into the Anne O'Tate web page, so that when a user types in a query, it is sent to PubMed using the NCBI E-Utilities (ESearch and EFetch) [6] to obtain the PubMed IDs, and thereby takes advantage of the pre-processing that occurs within PubMed
Summary
3.1 Top ranked important words include important biological concepts It is interesting to notice that the top ranked important words include many abbreviations and gene/protein symbols. The "important words" include specific names such as MMSE (Mini Mental State Examination) and Donepazil (a generic drug name), whereas the cluster-by-topic list includes more general categories, e.g., neuropsychological tests, caregivers, and Parkinson disease (a different but related neurodegenerative disease). They present the user with differing, and to some extent, complementary perspectives
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