Wnt pathway curation using automated natural language processing: Combining statistical methods with partial and full parse for knowledge extraction

Bioinformatics

Volumn 21, Issue 8, 2005, Pages 1653-1658

  Santos, Carlos ^a   Eggle, Daniela ^a   States, David J ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

WNT PROTEIN;

ACCURACY; ARTICLE; AUTOMATION; BIOINFORMATICS; CALCULATION; CHI SQUARE TEST; CONTROLLED STUDY; INFORMATION PROCESSING; INFORMATION RETRIEVAL; INTERNET; LANGUAGE; PRIORITY JOURNAL; PROTEIN DATABASE; SIGNAL TRANSDUCTION; STANDARDIZATION; STATISTICAL ANALYSIS;

EID: 17444417880     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti165     Document Type: Article

References (24)

1. Abney,S. (1996a) Partial parsing via finite-state cascades. J. Natural Language Eng., 2, 337-344.
2. Abney,S. (1996b) Statistical Methods and Linguistics. The MIT Press, Cambridge, MA.
3. Andrade,M.A. and Valencia,A. (1997) Automatic annotation for biological sequences by extraction of keywords from MEDLINE abstracts. Development of a prototype system. Proc. Int. Conf. Intell. Syst. Mol. Biol., 5, 25-32.
4. Bader,G.D. and Hogue,C.W. (2002) Analyzing yeast protein-protein interaction data obtained from different sources. Nat. Biotechnol., 20, 991-997.
5. Blaschke,C. et al (1999) Automatic extraction of biological information from scientific text: protein-protein interactions. Proceedings of the AAAI Conference on Intelligent Systems for Molecular Biology (ISMB), AAAI Press, pp. 60-67.
6. Braun,M.M., Etheridge,A., Bernard,A., Robertson,C.P. and Roelink,H. (2003) Wnt signaling is required at distinct stages of development for the induction of the posterior forebrain. Development 130, 5579-5587.
7. Chen,S., Guttridge,D.C., You,Z., Zhang,Z., Fribley,A., Mayo,M.W., Kitajewski,J. and Wang,C.Y. (2001) Wnt-1 signaling inhibits apoptosis by activating beta-catenin/T cell factor-mediated transcription. J. Cell Biol., 152, 87-96.
8. Daraselia,N., Yuryev,A., Egorov,S., Novichkova,S., Nikitin,A. and Mazo,I. (2004) Extracting human protein interactions from MEDLINE using a full-sentence parser. Bioinformatics, 20, 604-611.
9. Iliopoulos,I., Enright,A.J. and Ouzounis,C.A. (2001) Textquest: document clustering of Medline abstracts for concept discovery in molecular biology. Pac. Symp. Biocomput., 384-395.
10. Kishida,M., Hino,S., Michiue,T., Yamamoto,H., Kishida,S., Fukui,A., Asashima,M. and Kikuchi,A. (2001) Synergistic activation of the Wnt signaling pathway by Dvl and casein kinase Iepsilon. J. Biol. Chem., 276, 33147-33155.
11. Koike,A., Kobayashi,Y. and Takagi,T. (2003) Kinase pathway database: an integrated protein-kinase and NLP-based protein-interaction resource. Genome Res., 13, 1231-1243.
12. Lagutin,O.V., Zhu,C.C., Kobayashi,D., Topczewski,J., Shimamura,K., Puelles,L., Russell,H.R., McKinnon,P.J., Solnica-Krezel,L. and Oliver,G. (2003) Six3 repression of Wnt signaling in the anterior neuroectoderm is essential for vertebrate forebrain development. Genes Dev., 17, 368-379.
13. Liu,C., Nakamura,E., Knezevic,V., Hunter,S., Thompson,K. and Mackem,S. (2003) A role for the mesenchymal T-box gene Brachyury in AER formation during limb development. Development, 130, 1327-1337.
14. Marcotte,E.M., Xenarios,I. and Eisenberg,D. (2001) Mining literature for protein-protein interactions. Bioinformatics, 17 359-363.
15. National Center for Biotechnoly Information - Entrez Programming Utilities (2004) (NCBI).
16. Nusse,R. (2004) The Wnt gene Homepage (Howard Hughes Medical Insitiute).
17. Raychaudhuri,S., Schutze,H. and Altman,R.B. (2002) Using text analysis to identify functionally coherent gene groups. Genome Res. 12, 1582-1590.
18. Rosner,A., Miyoshi,K., Landesman-Bollag,E., Xu,X., Seldin,D.C., Moser,A.R., MacLeod,C.L., Shyamala,G., Gillgrass,A.E. and Cardiff,R.D. (2002) Pathway pathology: histological differences between ErbR/Ras and Wnt pathway transgenic mammary tumors. Am. J. Pathol., 161, 1087-1097.
19. Sleator,D. and Temperlyl,D. (1991) Parsing English with a Link Grammar. Carnegie Mellon University, Computer Science Technical Report CMU-CS-91-916.
20. Song,D.H., Dominguez,I., Mizuno,J., Kaut,M., Mohr,S.C. and Seldin,D.C. (2003) CK2 phosphorylation of the armadillo repeat region of beta-catenin potentiates Wnt signaling. J. Biol. Chem., 278, 24018-24025.
21. Stapley,B.J. and Benoit,G. (2000) Biobibliometrics: information retrieval and visualization from co-occurrences of gene names in Medline abstracts. Pac. Symp. Biocomput., 529-540.
22. Stephens,M., Palakal,M., Mukhopadhyay,S., Raje,R. and Mostafa,J. (2001) Detecting gene relations from Medline abstracts. Pac. Symp. Biocomput., pp. 483-495.
23. Temkin,J.M. and Gilder,M.R. (2003) Extraction of protein interaction information from unstructured text using a context-free grammar. Bioinformatics, 19, 2046-2053.
24. Wilbur,W.J. and 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, 209-222.