Detection of protein catalytic sites in the biomedical literature

Pacific Symposium on Biocomputing

Volumn , Issue , 2013, Pages 433-444

  Verspoor, Karin ^a   Mackinlay, Andrew ^a   Cohn, Judith D ^b   Wall, Michael E ^b  

^a CSIRO   (Australia)

^b LOS ALAMOS NATIONAL LABORATORY   (United States)

Author keywords

Biomedical literature; Biomedical natural language processing; Catalytic site; Information extraction; Machine learning; Protein functional sites; Text mining

Indexed keywords

ARTIFICIAL INTELLIGENCE; CLASSIFICATION (OF INFORMATION); INFORMATION RETRIEVAL; LEARNING ALGORITHMS; LEARNING SYSTEMS; LINGUISTICS; NATURAL LANGUAGE PROCESSING SYSTEMS; PROTEINS; TELLURIUM COMPOUNDS; TEXT PROCESSING;

AMBIGUITY OF INFORMATION; BIOMEDICAL LITERATURE; CATALYTIC SITES; COMPUTATIONAL PREDICTIONS; PROTEIN FUNCTION ANNOTATION; PROTEIN FUNCTIONAL SITES; TEXT MINING; TEXT MINING TECHNIQUES;

DATA MINING;

AMINO ACID; LIGAND; PROTEIN;

ARTICLE; ARTIFICIAL INTELLIGENCE; BINDING SITE; BIOLOGY; CHEMISTRY; CLASSIFICATION; DATA MINING; ENZYME ACTIVE SITE; METABOLISM; NATURAL LANGUAGE PROCESSING; PROTEIN DATABASE; STATISTICS; STATISTICS AND NUMERICAL DATA;

AMINO ACIDS; ARTIFICIAL INTELLIGENCE; BINDING SITES; CATALYTIC DOMAIN; COMPUTATIONAL BIOLOGY; DATA MINING; DATABASES, PROTEIN; LIGANDS; NATURAL LANGUAGE PROCESSING; PROTEINS;

EID: 84891420537     PISSN: 23356928     EISSN: 23356936     Source Type: Journal    
DOI: None     Document Type: Conference Paper

References (17)

1. S.-A. Marashi, EXCLI Journal 4, 87 (2005).
2. Y. Ofran, M. Punta, R. Schneider and B. Rost, Drug Discov Today 10, 1475 (2005).
3. K. M. Verspoor, J. D. Cohn, K. Ravikumar and M. E. Wall, PLoS One 7, e32171 (2012).
4. C. T. Porter, G. J. Bartlett and J. M. Thornton, Nucleic Acids Research 32, D129 (2004).
5. M. L. Benson and et al, New Mathematics and Natural Computation 06, 49 (2010).
6. H. Cunningham, D. Maynard, K. Bontcheva and et al, Text Processing with GATE (V. 6) 2011.
7. M. L. Benson, R. D. Smith, N. A. Khazanov, B. Dimcheff, J. Beaver, P. Dresslar, J. Nerothin and H. A. Carlson, Nucleic Acids Research 36, D674 (2008).
8. N. Naderi and R. Witte, BMC Genomics 13, S20 (2012).
9. The Gene Ontology Consortium, Nat Genet 25, 25 (2000).
10. K. Nagel, A. Jimeno-Yepes and D. Rebholz-Schuhmann, BMC Bioinf 10 Suppl 8, S4 (2009).
11. K. Ravikumar, H. Liu, J. D. Cohn, M. E. Wall and K. M. Verspoor, J Biomed Sem 3, S2 (2012).
12. H. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. Bhat, H. Weissig, I. Shindyalov and P. Bourne, Nucleic Acids Research 28, 235 (2000).
13. K. Tomanek, J. Wermter and U. Hahn, A reappraisal of sentence and token splitting for life science documents, in POT 12th MEDINFO, (IOS Press, 2007).
14. Y. Tsuruoka, Y. Tateishi, J. D. Kim, T. Ohta, J. Mcnaught, S. Ananiadou and J. Tsujii, Developing a robust part-of-speech tagger for biomedical text, in POT 10th Panhellenic Conf on Informatics, 2005.
15. H. Liu, T. Christiansen, W. Baumgartner and K. Verspoor, J Biomed Sem 3, 3 (2012).
16. K. B. Cohen, H. L. Johnson, K. Verspoor, C. Roeder and L. Hunter, BMC Bioinf 11, 1 (2010).
17. W. Baumgartner, K. Cohen, L. Fox, G. Acquaah-Mensah and L. Hunter, Bioinf 23, i41 (2007).