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Open Access Technical Note

ISDB: Interaction Sentence Database

Michael A Bauer12, Robert E Belford3, Jing Ding4 and Daniel Berleant1*

Author Affiliations

1 Department of Information Science, University of Arkansas at Little Rock, 2801 S. University Ave, Little Rock, AR, 72204, USA

2 University of Arkansas for Medical Sciences, 4301 W. Markham St., Little Rock, AR, 72205, USA

3 Department of Chemistry, University of Arkansas at Little Rock, 2801 S. University Ave, Little Rock, AR, 72204, USA

4 Ohio State University Medical Center, 410 W. 10th Avenue, Columbus, OH, 43210, USA

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BMC Research Notes 2010, 3:122  doi:10.1186/1756-0500-3-122

Published: 3 May 2010

Abstract

Background

Rapid growth in the scientific literature available on-line continues to motivate shifting data analysis from humans to computers. For example, greater knowledge of sentence characteristics indicative of interaction between two biological entities is needed to aid in the creation of better-performing information extraction tools for effectively using this rich body of information.

Findings

The Interaction Sentence Database (ISDB) allows users to retrieve sets of sentences fitting specified characteristics. To support this, a database of sentences from abstracts in MEDLINE was created. The sentences in the database all contain at least two biomolecule terms and one interaction-indicating term. A web interface to the database allows the user to query for sentences containing an interaction-indicating term, a single biomolecule name, or two biomolecule names, as well as for a list of biomolecules co-occurring with a given biomolecule in at least one sentence.

Conclusions

The system supports researchers needing conveniently available sets of sample sentences for corpus-based research on sentence properties. It also illustrates a model architecture for a sentence-based retrieval system which would be useful to people seeking information and knowledge on-line. ISDB can be freely accessed over the Web at http://bioinformatics.ualr.edu/cgi-bin/services/ISDB/isdb.cgi webcite, and the processed database will be provided upon request.