{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T00:13:24Z","timestamp":1773274404766,"version":"3.50.1"},"reference-count":43,"publisher":"Oxford University Press (OUP)","issue":"12","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Protein\u2013protein interaction (PPI) extraction from published biological articles has attracted much attention because of the importance of protein interactions in biological processes. Despite significant progress, mining PPIs from literatures still rely heavily on time- and resource-consuming manual annotations.<\/jats:p>\n               <jats:p>Results: In this study, we developed a novel methodology based on Bayesian networks (BNs) for extracting PPI triplets (a PPI triplet consists of two protein names and the corresponding interaction word) from unstructured text. The method achieved an overall accuracy of 87% on a cross-validation test using manually annotated dataset. We also showed, through extracting PPI triplets from a large number of PubMed abstracts, that our method was able to complement human annotations to extract large number of new PPIs from literature.<\/jats:p>\n               <jats:p>Availability: Programs\/scripts we developed\/used in the study are available at http:\/\/stat.fsu.edu\/~jinfeng\/datasets\/Bio-SI-programs-Bayesian-chowdhary-zhang-liu.zip<\/jats:p>\n               <jats:p>Contact: \u00a0jliu@stat.harvard.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp245","type":"journal-article","created":{"date-parts":[[2009,4,16]],"date-time":"2009-04-16T01:28:58Z","timestamp":1239845338000},"page":"1536-1542","source":"Crossref","is-referenced-by-count":57,"title":["Bayesian inference of protein\u2013protein interactions from biological literature"],"prefix":"10.1093","volume":"25","author":[{"given":"Rajesh","family":"Chowdhary","sequence":"first","affiliation":[{"name":"1 Department of Statistics, Harvard University, Cambridge, MA 02138, 2Marshfield Clinic-Marshfield Center, MCRF-BIRC, 1000 North Oak Avenue, Marshfield, WI 54449 and 3Department of Statistics, Florida State University, Tallahassee, FL 32306, USA"},{"name":"1 Department of Statistics, Harvard University, Cambridge, MA 02138, 2Marshfield Clinic-Marshfield Center, MCRF-BIRC, 1000 North Oak Avenue, Marshfield, WI 54449 and 3Department of Statistics, Florida State University, Tallahassee, FL 32306, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jinfeng","family":"Zhang","sequence":"additional","affiliation":[{"name":"1 Department of Statistics, Harvard University, Cambridge, MA 02138, 2Marshfield Clinic-Marshfield Center, MCRF-BIRC, 1000 North Oak Avenue, Marshfield, WI 54449 and 3Department of Statistics, Florida State University, Tallahassee, FL 32306, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jun S.","family":"Liu","sequence":"additional","affiliation":[{"name":"1 Department of Statistics, Harvard University, Cambridge, MA 02138, 2Marshfield Clinic-Marshfield Center, MCRF-BIRC, 1000 North Oak Avenue, Marshfield, WI 54449 and 3Department of Statistics, Florida State University, Tallahassee, FL 32306, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2009,4,15]]},"reference":[{"key":"2023013111584863100_B1","doi-asserted-by":"crossref","first-page":"D418","DOI":"10.1093\/nar\/gki051","article-title":"The Biomolecular Interaction Network Database and related tools 2005 update","volume":"33","author":"Alfarano","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023013111584863100_B2","doi-asserted-by":"crossref","first-page":"i41","DOI":"10.1093\/bioinformatics\/btm229","article-title":"Manual curation is not sufficient for annotation of genomic databases","volume":"23","author":"Baumgartner","year":"2007","journal-title":"Bioinformatics"},{"key":"2023013111584863100_B3","doi-asserted-by":"crossref","first-page":"827","DOI":"10.1093\/bioinformatics\/bti098","article-title":"PDZBase: a protein-protein interaction database for PDZ-domains","volume":"21","author":"Beuming","year":"2005","journal-title":"Bioinformatics"},{"key":"2023013111584863100_B4","first-page":"60","article-title":"Automatic extraction of biological information from scientific text: protein-protein interactions","author":"Blaschke","year":"1999","journal-title":"Proc. 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