W748–W752 Nucleic Acids Research, 2006, Vol. 34, Web Server issue doi:10.1093/nar/gkl194 botXminer: mining biomedical literature with a new web-based application Uma Mudunuri, Robert Stephens, David Bruining, David Liu and Frank J. Lebeda1,* Science Applications International Corporation-Frederick, Advanced Biomedical Computing Center, SAIC-Frederick Inc., National Cancer Institute-Frederick, Frederick, MD 21702, USA and 1US Army Medical Research Institute for Infectious Diseases, Integrated Toxicology Division, Fort Detrick, MD 21702-5011, USA Received February 21, 2006; Revised and Accepted March 21, 2006 ABSTRACT This paper outlines botXminer, a publicly available application to search XML-formatted MEDLINE data in a complete, object-relational schema imple- mented in Oracle XML DB. An advantage offered by botXminer is that it can generate quantitative res- ults with certain queries that are not feasible through the Entrez-PubMed interface. After retrieving cita- tions associated with user-supplied search terms, MEDLINE fields (title, abstract, journal, MeSH and chemical) and terms (MeSH qualifiers and descrip- tors, keywords, author, gene symbol and chemical), these citations are grouped and displayed as tabu- lated 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 http://botdb.abcc.ncifcrf.gov. INTRODUCTION The National Library of Medicine’s (NLM) MEDLINE/ PubMed biomedical literature database (http://www.nlm.nih. gov/bsd/licensee/2006_baseline_doc.html) is rapidly expand- ing and as of the 2006 edition, the baseline database contains more than 15 million citations. A number of papers have introduced tools to perform searches more advanced than those available with the current Entrez-PubMed user interface to mine the abstracts (1–4). To have more control in conduct- ing searches, investigators have also started to reorganize the MEDLINE data into structured relational systems (5) or to exploit different data formats and create new databases (http:// www.ebi.ac.uk/~lcwang/medline/index.htm). These NLM citations are available in several formats (e.g. MEDLINE, ASN.1, and so on). Importing these citation data into a traditional, relational database limits the query capability to SQL (Structured Query Language) techniques. The eXtensible Markup Language (XML) format, however, is emerging as a de facto standard for the hierarchical organiza- tion of data in a highly granular structure, and provides a much richer query capability beyond what is available through tradi- tional SQL. Oracle XML DB, available in Oracle 9i and 10g, recognizes this new format. It supports both the necessary massive storage requirements and the extensions to traditional SQL that enable a different kind of query which is hierarchical and highly granular. An early study using Oracle XML DB involved the evaluation of data-form standards and database technologies for medical informatics systems (6) (http://dcb. cit.nih.gov/publications/download/cims_performance.pdf). As described by Wang et al. (6), the set of utilities associated with XML DB permits data to be represented both as XML elements from XML documents and as cells within relational tables. A recently developed website that includes a specialized, Oracle-based resource for the clostridial neurotoxins, BotDB (7) (http://botdb.abcc.ncifcrf.gov), has been extended to conduct literature searches of MEDLINE/PubMed using botXminer. The application of XML DB for botXminer was based, in large measure, on the documentation and thorough analysis of an original implementation using XML-formatted MEDLINE citations (http://www.ebi.ac.uk/~lcwang/medline/ index.htm). An advantage offered by botXminer over PubMed is that it can make certain queries possible that cannot be performed using the Entrez-PubMed interface. The practical example herein illustrates how citations, containing user- supplied search terms, selected MEDLINE search ﬁelds and terms, are grouped and displayed as hyperlinked tabulated or graphic results. A more detailed technical description of the architecture associated with botXminer and other applications will appear elsewhere. METHODS Of the more than 15 million MEDLINE XML records created through the 2005 production year that were loaded into Oracle XML DB, a limited reference subset was generated *To whom correspondence should be addressed: Tel: +1 301 619 4279; Fax: +1 301 619 2348; Email: frank.lebeda@amedd.army.mil The Author 2006. Published by Oxford University Press. All rights reserved. The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. 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