PreBIND and textomy - Mining the biomedical literature for protein-protein interactions using a support vector machine

BMC Bioinformatics

Volumn 4, Issue , 2003, Pages

  Donaldson, Ian ^a   Martin, Joel ^b   de Bruijn, Berry ^b   Wolting, Cheryl ^a   Lay, Vicki ^a   Tuekam, Brigitte ^a   Zhang, Shudong ^c   Baskin, Berivan ^a   Bader, Gary D ^a,d,e   Michalickova, Katerina ^a,d   Pawson, Tony ^a,f   Hogue, Christopher W V ^a,d  

^a MOUNT SINAI HOSPITAL   (Canada)

^b NATIONAL RESEARCH COUNCIL CANADA   (Canada)

^c MDS Proteomics Inc   (Canada)

^d UNIVERSITY OF TORONTO   (Canada)

^e MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

^f UNIVERSITY OF TORONTO   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; COMPUTER; COMPUTER PROGRAM; CONTROLLED STUDY; FACTUAL DATABASE; GENE LOCUS; INFORMATION SYSTEM; MATHEMATICAL COMPUTING; MOLECULAR INTERACTION; NONHUMAN; PROTEIN PROTEIN INTERACTION; REVIEW; SACCHAROMYCES CEREVISIAE; SEQUENCE DATABASE; VALIDATION PROCESS; YEAST;

EID: 2942549190     PISSN: 14712105     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2105-4-11     Document Type: Article

References (32)

1. Bader GD and Hogue CW BIND - a data specification for storing and describing biomolecular interactions, molecular complexes and pathways Bioinformatics 2000, 16:465-477
2. Bader GD, Donaldson I, Wolting C, Ouellette BF, Pawson T and Hogue CW BIND - The Biomolecular Interaction Network Database Nucleic Acids Res 2001, 29:242-245
3. Sekimizu T, Park HS and Tsujii J Identifying the Interaction between Genes and Gene Products Based on Frequently Seen Verbs in Medline Abstracts Genome Inform Ser Workshop Genome Inform 1998, 9:62-71
4. Rindflesch TC, Tanabe L, Weinstein JN and Hunter L EDGAR: extraction of drugs, genes and relations from the biomedical literature Pac Symp Biocomput 2000, 517-528
5. Humphreys K, Demetriou G and Gaizauskas R Two applications of information extraction to biological science journal articles: enzyme interactions and protein structures Pac Symp Biocomput 2000, 505-516
6. Proux D, Rechenmann F and Julliard L A pragmatic information extraction strategy for gathering data on genetic interactions Proc Int Conf Intell Syst Mol Biol 2000, 8:279-285
7. Stapley BJ and Benoit G Biobibliometrics: information retrieval and visualization from co- occurrences of gene names in Medline abstracts Pac Symp Biocomput 2000, 529-540
8. Thomas J, Milward D, Ouzounis C, Pulman S and Carroll M Automatic extraction of protein interactions from scientific abstracts Pac Symp Biocomput 2000, 541-552
9. Blaschke C and Valencia A The potential use of SUISEKI as a protein interaction discovery tool Genome Inform Ser Workshop Genome Inform 2001, 12:123-134
10. Friedman C, Kra P, Yu H, Krauthammer M and Rzhetsky A GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles Bioinformatics 2001, 17:S74-NaN
11. Jenssen TK, Laegreid A, Komorowski J and Hovig E A literature network of human genes for high-throughput analysis of gene expression Nat Genet 2001, 28:21-28
12. Ono T, Hishigaki H, Tanigami A and Takagi T Automated extraction of information on protein-protein interactions from the biological literature Bioinformatics 2001, 17:155-161
13. Marcotte EM, Xenarios I and Eisenberg D Mining literature for protein-protein interactions Bioinformatics 2001, 17:359-363
14. Wong L PIES, a protein interaction extraction system Pac Symp Biocomput 2001, 520-531
15. Pruitt KD and Maglott DR RefSeq and LocusLink: NCBI genecentered resources Nucleic Acids Res 2001, 29:137-140
16. Dwight SS, Harris MA, Dolinski K, Ball CA, Binkley G, Christie KR, Fisk DG, Issel-Tarver L, Schroeder M, Sherlock G, Sethuraman A, Weng S, Botstein D and Cherry JM Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO) Nucleic Acids Res 2002, 30:69-72
17. Ostell JM, Wheelan SJ and Kans JA The NCBI data model Bioinformatics (Edited by: Baxevanis AD and Ouellette B F) New York, John Wiley and Sons, Inc. 2001, 43:19-43
18. Wheeler DL, Church DM, Lash AE, Leipe DD, Madden TL, Pontius JU, Schuler GD, Schriml LM, Tatusova TA, Wagner L and Rapp BA Database resources of the National Center for Biotechnology Information: 2002 update Nucleic Acids Res 2002, 30:13-16
19. Cortes C and Vapnik V Support-Vector Networks Machine Learning 1995, 20:273-297
20. Joachims T Text categorization with Support Vector Machines: Learning with many relevant features. Machine Learning: ECML-98, Tenth European Conference on Machine Learning. 1998, 137-142
21. Dumais S, Platt J, Heckerman D and Sahami M Inductive learning algorithms and representations for text categorization. Proceedings of the International Conference on Information and Knowledge Management. 1998, 148-155
22. de Bruijn B, Martin J, Wolting C and Donaldson I Extracting sentences to justify categorization. Proceedings of the American Society for Information Science and Technology Annual Meeting. ASIST. 2001, 450-457
23. Boeckmann B, Bairoch A, Apweiler R, Blatter MC, Estreicher A, Gasteiger E, Martin MJ, Michoud K, O'Donovan C, Phan I, Pilbout S and Schneider M The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003 Nucleic Acids Res 2003, 31:365-370
24. Fukuda K, Tamura A, Tsunoda T and Takagi T Toward information extraction: identifying protein names from biological papers Pac Symp Biocomput 1998, 707-718
25. Michalickova K, Bader GD, Dumontier M, Lieu HC, Betel D, Isserlin R and Hogue CW SeqHound: biological sequence and structure database as a platform for bioinformatics research BMC Bioinformatics 2002, 3:32
26. Salton G The SMART Retrieval System. Englewood Cliffs, NJ, Prentice Hall 1971,
27. Mitchell T Machine Learning McGraw-Hill 1997, 414
28. Mewes HW, Frishman D, Guldener U, Mannhaupt G, Mayer K, Mokrejs M, Morgenstern B, Munsterkotter M, Rudd S and Weil B MIPS: a database for genomes and protein sequences Nucleic Acids Res 2002, 30:31-34
29. Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, Adams SL, Millar A, Taylor P, Bennett K, Boutilier K, Yang L, Wolting C, Donaldson I, Schandorff S, Shewnarane J, Vo M, Taggart J, Goudreault M, Muskat B, Alfarano C, Dewar D, Lin Z, Michalickova K, Willems AR, Sassi H, Nielsen PA, Rasmussen KJ, Andersen JR, Johansen LE, Hansen LH, Jespersen H, Podtelejnikov A, Nielsen E, Crawford J, Poulsen V, Sorensen BD, Matthiesen J, Hendrickson RC, Gleeson F, Pawson T, Moran MF, Durocher D, Mann M, Hogue CW, Figeys D and Tyers M Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry Nature 2002, 415:180-183
30. Bader GD and Hogue CW Analyzing yeast protein-protein interaction data obtained from different sources Nat Biotechnol 2002, 20:991-997
31. Ostell JM, Wheelan SJ and Kans JA The NCBI data model Methods Biochem Anal 2001, 43:19-43
32. McCallum Andrew Kachites Bow: A toolkit for statistical language modeling, text retrieval, classification and clustering http://www.cs.cmu.edu/~mccallum/bow 1996.