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Bioinformatics Advance Access originally published online on December 20, 2005
Bioinformatics 2006 22(5):597-605; doi:10.1093/bioinformatics/btk016
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
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BioContrasts: extracting and exploiting protein–protein contrastive relations from biomedical literature

Jung-jae Kim 1, Zhuo Zhang 2, Jong C. Park 1 and See-Kiong Ng 2,*

1Computer Science Division & AITrc, Korea Advanced Institute of Science and Technology 373-1 Guseong-dong, Yuseong-gu, Daejeon 305-701 South Korea
2Knowledge Discovery Department, Institute for Infocomm Research 21 Heng Mui Keng Terrace, Singapore 119613, Singapore

*To whom correspondence should be addressed.

Motivation: Contrasts are useful conceptual vehicles for learning processes and exploratory research of the unknown. For example, contrastive information between proteins can reveal what similarities, divergences and relations there are of the two proteins, leading to invaluable insights for better understanding about the proteins. Such contrastive information are found to be reported in the biomedical literature. However, there have been no reported attempts in current biomedical text mining work that systematically extract and present such useful contrastive information from the literature for exploitation.

Results: Our BioContrasts system extracts protein–protein contrastive information from MEDLINE abstracts and presents the information to biologists in a web-application for exploitation. Contrastive information are identified in the text abstracts with contrastive negation patterns such as ‘A but not B’. A total of 799 169 pairs of contrastive expressions were successfully extracted from 2.5 million MEDLINE abstracts. Using grounding of contrastive protein names to Swiss-Prot entries, we were able to produce 41 471 pieces of contrasts between Swiss-Prot protein entries. These contrastive pieces of information are then presented via a user-friendly interactive web portal that can be exploited for applications such as the refinement of biological pathways.

Availability: BioContrasts can be accessed at http://biocontrasts.i2r.a-star.edu.sg. It is also mirrored at http://biocontrasts.biopathway.org

Supplementary information: Supplementary materials are available at Bioinformatics online.

Contact: skng{at}i2r.a-star.edu.sg; park{at}cs.kaist.ac.kr

Received on September 5, 2005; revised on December 15, 2005; accepted on December 16, 2005

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