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CDAPubMed: a browser extension to retrieve EHR-based biomedical literature

DOI: 10.1186/1472-6947-12-29

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We have developed CDAPubMed, an open-source web browser extension to integrate EHR features in biomedical literature retrieval approaches. Clinical users can use CDAPubMed to: (i) load patient clinical documents, i.e., EHRs based on the Health Level 7-Clinical Document Architecture Standard (HL7-CDA), (ii) identify relevant terms for scientific literature search in these documents, i.e., Medical Subject Headings (MeSH), automatically driven by the CDAPubMed configuration, which advanced users can optimize to adapt to each specific situation, and (iii) generate and launch literature search queries to a major search engine, i.e., PubMed, to retrieve citations related to the EHR under examination.CDAPubMed is a platform-independent tool designed to facilitate literature searching using keywords contained in specific EHRs. CDAPubMed is visually integrated, as an extension of a widespread web browser, within the standard PubMed interface. It has been tested on a public dataset of HL7-CDA documents, returning significantly fewer citations since queries are focused on characteristics identified within the EHR. For instance, compared with more than 200,000 citations retrieved by breast neoplasm, fewer than ten citations were retrieved when ten patient features were added using CDAPubMed. This is an open source tool that can be freely used for non-profit purposes and integrated with other existing systems.More than 700,000 biomedical articles were published in 2009 and indexed in MEDLINE [1]. At this rate, an internist like other medical specialists, in fact would have to read at least 20 scientific papers every day to keep up-to-date with this overwhelming number of yearly citations [2]. To address this information explosion, different kinds of search engines, such as PubMed [3] or HubMed [4], for instance, supplement biomedical literature databases. These engines provide instant access to the biomedical literature. However, the large volume of available citations often lea


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