Visual Exploration across Biomedical Databases

TitleVisual Exploration across Biomedical Databases
Publication TypeJournal Articles
Year of Publication2011
AuthorsLieberman MD, Taheri S, Guo H, Mirrashed F, Yahav I, Aris A, Shneiderman B
JournalIEEE/ACM Transactions on Computational Biology and Bioinformatics
Pagination536 - 550
Date Published2011/04//March
ISBN Number1545-5963
KeywordsBioinformatics, Biomedical computing, biomedical databases, cross-database exploration, Data exploration and discovery, Data visualization, database management systems, Databases, Factual, DNA, graph theory, Information Storage and Retrieval, information visualization., Keyword search, medical computing, natural language processing, Proteins, semantic networks, semantics, sequences, text mining, User-Computer Interface, user-defined semantics, visual databases

Though biomedical research often draws on knowledge from a wide variety of fields, few visualization methods for biomedical data incorporate meaningful cross-database exploration. A new approach is offered for visualizing and exploring a query-based subset of multiple heterogeneous biomedical databases. Databases are modeled as an entity-relation graph containing nodes (database records) and links (relationships between records). Users specify a keyword search string to retrieve an initial set of nodes, and then explore intra- and interdatabase links. Results are visualized with user-defined semantic substrates to take advantage of the rich set of attributes usually present in biomedical data. Comments from domain experts indicate that this visualization method is potentially advantageous for biomedical knowledge exploration.