Automatic classification of protein functions from the literature

Comparative and Functional Genomics

Volumn 4, Issue 1, 2003, Pages 75-79

  Blaschke, Christian ^a   Valencia, Alfonso ^a  

^a CENTRO NACIONAL DE BIOTECNOLOGÍA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; GENE PRODUCT;

ACCESS TO INFORMATION; AUTOMATION; CLASSIFICATION; DNA MICROARRAY; GENE CLUSTER; GENE EXPRESSION PROFILING; GENE FUNCTION; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC DATABASE; GENOMICS; HUMAN; INFORMATION PROCESSING; INFORMATION RETRIEVAL; INFORMATION SYSTEM; MEDICAL LITERATURE; MEDLINE; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FAMILY; PROTEIN FUNCTION; PROTEOMICS; REVIEW;

EID: 0037294256     PISSN: 15316912     EISSN: None     Source Type: Journal    
DOI: 10.1002/cfg.241     Document Type: Review

References (22)

1. Andrade MA, Valencia A. 1998. Automatic extraction of keywords from scientific text: application to the knowledge domain of protein families. Bioinformatics 14: 600-607.
2. Ashburner M, Ball CA, Blake JA, et al. 2000. Gene ontology: tool for the unification of biology. Nature Genet 25: 25-29.
3. Blaschke C. 2002. Applications of Information Extraction Techniques to Molecular Biology. PhD Thesis, University Autónoma de Madrid, Spain.
4. Blaschke C, Oliveros JC, Valencia A. 2001. Mining functional information associated to expression arrays. Funct Integr Genomics 2: 256-268.
5. Blaschke C, Valencia A. 2001. Can bibliographic pointers for known biological data be found automatically? Protein interactions as a case study. Comp Funct Genom 2: 196-206.
6. Blaschke C, Valencia A. 2002. Automatic ontology construction from the literature. Genome Inform Ser Workshop Genome. Universal Academy Press: Tokyo, (in press).
7. Craven M, Kumlien J. 1999. Constructing biological knowledge bases by extracting information from text sources. Proc Int Conf Intell Syst Mol Biol (1999): 77-86.
8. Devos D, Valencia A. 2002. Intrinsic errors in genome annotation. Trends Genet 17: 429-431.
9. Eisen MB, Spellman PT, Brown PO, Botstein D. 1998. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 95: 14863-14868.
10. Franzén K, Eriksson G, Olsson F, Lidén LAP, Cöster J. 2002. Protein names and how to find them. Int J Med Info (in press).
11. Fukuda K, Tsunoda T, Tamura A, Takagi T. 1998. Information extraction: identifying protein names from biological papers. Pac Symp Biocomput (1998): 707-718.
12. Hirschman L. 1998. The evolution of evaluation: lessons from the message understanding conferences. Comput Speech Lang 12: 281-305.
13. Jenssen TK, Lægreid A, Komorowski J, Hovig E. 2001. A literature network of human genes for high-throughput analysis of gene expression. Nature Genet 28: 21-28.
14. Ohta Y, Yamamoto Y, Okazaki T, Uchiyama I, Takagi T. 1997. Automatic construction of knowledge base from biological papers. Proc Int Conf Intell Syst Mol Biol (1997): 218-225.
15. Oliveros JC, Blaschke C, Herrero J, Dopazo J, Valencia A. 2000. Expression profiles and biological function. Genome Inform Ser Workshop Genome Inform (2000): 106-117.
16. Perez-Iratxeta C, Bork P, Andrade MA. 2001. XplorMed: a tool for exploring MEDLINE abstracts. Trends Biochem Sci 26: 573-575.
17. Proux D, Rechenmann F, Julliard L, Pillet V, Jacq B. 1998. Detecting gene symbols and names in biological texts: a first step toward pertinent information extraction. Genome Inform Ser Workshop Genome Inform (1998): 72-80.
18. Raychaudhuri S, Chang JT, Sutphin PD, Altman RB. 2002. Associating genes with gene ontology codes using a maximum entropy analysis of biomedical literature. Genome Res 12: 203-214.
19. Shatkay H, Edwards S, Wilbur WJ, Boguski M. 2000. Genes, themes, and microarrays. Using information retrieval for large-scale gene analysis. Proc Int Conf Intell Syst Mol Biol (2000): 317-328.
20. Tanabe L, Wilbur JW. 2002. Tagging gene and protein names in biomedical text. Bioinformatics 18: 1124-1132.
21. Wilbur WJ, Coffee L. 1994. The effectiveness of document neighboring in search enhancement. Inf Process Manag 30: 253-266.
22. Wilbur WJ, Yang Y. 1996. An analysis of statistical term strength and its use in the indexing and retrieval of molecular biology texts. Comput Biol Med 26: 209.