ISDB: Interaction sentence database

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, and the processed database will be provided upon request. © 2010 Berleant et al; licensee BioMed Central Ltd.