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Bioinformatics Advance Access published online on October 17, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm495
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Mining experimental evidence of molecular function claims from the literature

Crangle, Colleen E. 1,*, J. Michael Cherry 2, Eurie L. Hong 2 and Alex Zbyslaw 1

1Converspeech LLC, 60 Kirby Place, Palo Alto, CA 94301, USA.
2Department of Genomics, Stanford University, Stanford, CA 94025, USA.

*To whom correspondence should be addressed. Dr. Colleen Crangle, E-mail: crangle{at}converspeech.com


  Abstract

Motivation: The rate at which gene-related findings appear in the scientific literature makes it difficult if not impossible for biomedical scientists to keep fully informed and up to date. The importance of these findings argues for the development of automated methods that can find, extract, and summarize this information. This paper reports on methods for determining the molecular function claims that are being made in a scientific article, specifically those that are backed by experimental evidence.

Results: The most significant result is that for molecular function claims based on direct assays, our methods achieved recall of 70.7% and precision of 65.7%. Furthermore, our methods correctly identified in the text 44.6% of the specific molecular function claims backed up by direct assays, but with a precision of only 0.92%, a disappointing outcome that led to an examination of the different kinds of errors. These results were based on an analysis of 1,823 articles from the literature of S. cerevisiae (budding yeast).

Availability: The annotation files for S. cerevisiae are available from ftp:/genome-ftp.stanford.edu/pub/yeast/data_download/literature_curation/gene_association.sgd.gz. The draft protocol vocabulary is available by request from the first author.

Contact: crangle{at}converspeech.com

Associate Editor: Dr. Limsoon Wong

Received on March 16, 2007; revised on September 27, 2007; accepted on September 28, 2007

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