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

Uma Mudunuri | Zendy; R. Scott Stephens | Zendy; David H. Bruining | Zendy; Derong Liu | Zendy; Frank J. Lebeda | Zendy

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

Author(s) -

Uma Mudunuri,

R. Scott Stephens,

David H. Bruining,

Derong Liu,

Frank J. Lebeda

Publication year - 2006

Publication title -

nucleic acids research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.008

H-Index - 537

eISSN - 1362-4954

pISSN - 0305-1048

DOI - 10.1093/nar/gkl194

Subject(s) - information retrieval , computer science , oracle , schema (genetic algorithms) , xml , medline , world wide web , interface (matter) , bioinformatics , biology , programming language , biochemistry , bubble , maximum bubble pressure method , parallel computing

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 http://botdb.abcc.ncifcrf.gov.

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