Bioinformatics Vol. 17 no. 90001 2001
Pages S74-S82
© 2001 Oxford University Press
GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles
1 Computer Science Dept, Queens College
CUNY, Flushing, NY, 11367, USA
2 Department of Medical Informatics,
Columbia University, New York, 10032, USA
3 Genome Center, Columbia University, New
York, 10032, USA
Received on January 31, 2001
; revised on March 30, 2001
; accepted on March 30, 2001
Systems that extract structured information from natural language passages have been highly successful in specialized domains. The time is opportune for developing analogous applications for molecular biology and genomics. We present a system, GENIES, that extracts and structures information about cellular pathways from the biological literature in accordance with a knowledge model that we developed earlier. We implemented GENIES by modifying an existing medical natural language processing system, MedLEE, and performed a preliminary evaluation study. Our results demonstrate the value of the underlying techniques for the purpose of acquiring valuable knowledge from biological journals.
Contact: friedman.carol{at}dmi.columbia.edu
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  J.-W. Fan and C. Friedman Semantic Classification of Biomedical Concepts Using Distributional Similarity J. Am. Med. Inform. Assoc., July 1, 2007; 14(4): 467 - 477. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. Rebholz-Schuhmann, H. Kirsch, M. Arregui, S. Gaudan, M. Riethoven, and P. Stoehr EBIMed--text crunching to gather facts for proteins from Medline Bioinformatics, January 15, 2007; 23(2): e237 - e244. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Y. A. Lussier and Y. Liu Computational Approaches to Phenotyping: High-Throughput Phenomics Proceedings of the ATS, January 1, 2007; 4(1): 18 - 25. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Rzhetsky, I. Iossifov, J. M. Loh, and K. P. White Microparadigms: Chains of collective reasoning in publications about molecular interactions PNAS, March 28, 2006; 103(13): 4940 - 4945. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Saric, L. J. Jensen, R. Ouzounova, I. Rojas, and P. Bork Extraction of regulatory gene/protein networks from Medline Bioinformatics, March 15, 2006; 22(6): 645 - 650. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 X. Wu, L. Zhu, J. Guo, D.-Y. Zhang, and K. Lin Prediction of yeast protein-protein interaction network: insights from the Gene Ontology and annotations. Nucleic Acids Res., January 1, 2006; 34(7): 2137 - 2150. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Hao, X. Zhu, M. Huang, and M. Li Discovering patterns to extract protein-protein interactions from the literature: Part II Bioinformatics, August 1, 2005; 21(15): 3294 - 3300. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. Hoffmann, M. Krallinger, E. Andres, J. Tamames, C. Blaschke, and A. Valencia Text Mining for Metabolic Pathways, Signaling Cascades, and Protein Networks Sci. Signal., May 10, 2005; 2005(283): pe21 - pe21. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Jelier, G. Jenster, L. C. J. Dorssers, C. C. van der Eijk, E. M. van Mulligen, B. Mons, and J. A. Kors Co-occurrence based meta-analysis of scientific texts: retrieving biological relationships between genes Bioinformatics, May 1, 2005; 21(9): 2049 - 2058. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Divoli and T. K. Attwood BioIE: extracting informative sentences from the biomedical literature Bioinformatics, May 1, 2005; 21(9): 2138 - 2139. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Tao, C. Friedman, and Y. A. Lussier Visualizing information across multidimensional post-genomic structured and textual databases Bioinformatics, April 15, 2005; 21(8): 1659 - 1667. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Droit, G. G Poirier, and J. M Hunter Experimental and bioinformatic approaches for interrogating protein-protein interactions to determine protein function J. Mol. Endocrinol., April 1, 2005; 34(2): 263 - 280. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Koike, Y. Niwa, and T. Takagi Automatic extraction of gene/protein biological functions from biomedical text Bioinformatics, April 1, 2005; 21(7): 1227 - 1236. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Chen, H. Liu, and C. Friedman Gene name ambiguity of eukaryotic nomenclatures Bioinformatics, January 15, 2005; 21(2): 248 - 256. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. M. Wilkinson and B. A. Huberman A method for finding communities of related genes PNAS, April 6, 2004; 101(suppl_1): 5241 - 5248. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Yu, X. Zhu, D. Greenbaum, J. Karro, and M. Gerstein TopNet: a tool for comparing biological sub-networks, correlating protein properties with topological statistics Nucleic Acids Res., January 14, 2004; 32(1): 328 - 337. [Abstract] [Full Text] [PDF]
|
|