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Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W748-52.

botXminer: mining biomedical literature with a new web-based application.

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Science Applications International Corporation-Frederick, Advanced Biomedical Computing Center, SAIC-Frederick Inc., National Cancer Institute-Frederick, Frederick, MD 21702, USA.


This paper outlines botXminer, a publicly available application to search XML-formatted MEDLINE data in a complete, object-relational schema implemented in Oracle XML DB. An advantage offered by botXminer is that it can generate quantitative results with certain queries that are not feasible through the Entrez-PubMed interface. After retrieving citations associated with user-supplied search terms, MEDLINE fields (title, abstract, journal, MeSH and chemical) and terms (MeSH qualifiers and descriptors, keywords, author, gene symbol and chemical), these citations are grouped and displayed as tabulated or graphic results. This work represents an extension of previous research for integrating these citations with relational systems. botXminer has a user-friendly, intuitive interface that can be freely accessed at

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