GENIES: A natural-language processing system for the extraction of molecular pathways from journal articles

Bioinformatics

Volumn 17, Issue SUPPL. 1, 2001, Pages

  Friedman, Carol ^a,b   Kra, Pauline ^b   Yu, Hong ^b   Krauthammer, Michael ^b   Rzhetsky, Andrey ^b  

^a CITY UNIVERSITY OF NEW YORK   (United States)

^b Och Spine at New York Presbyterian Hospitals   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; ARTIFICIAL INTELLIGENCE; BIOLOGY; EVALUATION; MOLECULAR BIOLOGY; NATURAL LANGUAGE PROCESSING; PILOT STUDY; PUBLICATION;

ARTIFICIAL INTELLIGENCE; COMPUTATIONAL BIOLOGY; MOLECULAR BIOLOGY; NATURAL LANGUAGE PROCESSING; PERIODICALS; PILOT PROJECTS;

EID: 0035236048     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/17.suppl_1.S74     Document Type: Article

References (36)

1. Ashburner M., Ball C. A., Blake J. A., Botstein D., Butler H., Cherry J. M., Davis A. P., Dolinski K., Dwight S. S., Eppig J. T., Harris M. A., Hill D. P., Issel-Tarver L., Kasarskis A., Lewis S., Matese J. C., Richardson J. E., Ringwald M., Rubin G. M., and Sherlock G. (2000). Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet, 25, 25-9.
2. Bairoch A., and Apweiler R. (2000). The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res., 28, 45-8.
3. Baker P. G., Goble C. A., Bechhofer S., Paton N. W., Stevens R., and Brass A. (1999). An ontology for bioinformatics applications. Bioinformatics, 15, 510-20.
4. Benson D. A., Karsch-Mizrachi I., Lipman D. J., Ostell J., Rapp B. A., and Wheeler D. L. (2000). GenBank. Nucleic Acids Res., 28, 15-8.
5. Blaschke C., Andrade M. A., Ouzounis C., and Valencia A. (1999). Automatic extraction of biological information from scientific text: protein-protein interactions. Ismb, 60-7.
6. Chen R. O., Felciano R., and Altman R. B. (1997). RIBOWEB: linking structural computations to a knowledge base of published experimental data. Ismb, 5, 84-7.
7. Elkins J. S., Friedman C., Boden-Albala B., Sacco R. L., and Hripcsak G. (2000). Coding neuroradiology reports for the Northern Manhattan Stroke Study: a comparison of natural language processing and manual review. Comput. Biomed. Res., 33, 1-10.
8. Friedman C., Alderson P. O., Austin J. H., Cimino J. J., and Johnson S. B. (1994). A general natural-language text processor for clinical radiology. J. Am. Med. Inform. Assoc., 1, 161-74.
9. Friedman C., and Hripcsak G. (1998). Evaluating natural language processors in the clinical domain. Methods Inf. Med., 37, 334-44.
10. Fukuda K., Tamura A., Tsunoda T., and Takagi T. (1998). Toward information extraction: identifying protein names from biological papers. Pac. Symp. Biocomput., 707-18.
11. Hafner C. D., Baclawski K., Futrelle R. P., Fridman N., and Sampath S. (1994). Creating a knowledge base of biological research papers. Ismb, 2, 147-55.
12. Hatzivassiloglou V., Duboue P. A., and Rzhetsky A. (2001). Disambiguating proteins, genes, and RNA in text: a machine learning approach. Ismb, (accepted).
13. Hripcsak G., Friedman C., Alderson P. O., DuMouchel W., Johnson S. B., and Clayton P. D. (1995). Unlocking clinical data from narrative reports: a study of natural language processing. Ann. Intern. Med., 122, 681-8.
14. Hripcsak G., Kuperman G. J., and Friedman C. (1998). Extracting findings from narrative reports: software transferability and sources of physician disagreement. Methods Inf. Med., 37, 1-7.
15. Humphreys B. L., Lindberg D. A., Schoolman H. M., and Barnett G. O. (1998). The Unified Medical Language System: an informatics research collaboration. J. Am. Med. Inform. Assoc., 5, 1-11.
16. Humphreys K., Demetriou G., and Gaizauskas R. (2000). Two applications of information extraction to biological science journal articles: enzyme interactions and protein structures. Pac. Symp. Biocomput., 505-16.
17. Iliopoulos I., Enright A. J., and Ouzounis C. (2001). TEXTQUEST: Document Clustering of MEDLINE Abstracts For Concept Discovery In Molecular Biology. Pacif. Symp. Biocomp., 6, 374-383.
18. Jain N. L., and Friedman C. (1997). Identification of findings suspicious for breast cancer based on natural language processing of mammogram reports. Proc. AMIA Annu. Fall Symp., 829-33.
19. Jain N. L., Knirsch C. A., Friedman C., and Hripcsak G. (1996). Identification of suspected tuberculosis patients based on natural language processing of chest radiograph reports. Proc. AMIA Annu. Fall Symp., 542-6.
20. Jenssen T. K., and Vinterbo S. (2000). A set-covering approach to specific search for literature about human genes. Proc. AMIA Symp., 384-8.
21. Kanehisa M., and Goto S. (2000). KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res., 28, 27-30.
22. Karp P. D., Riley M., Paley S. M., Pellegrini-Toole A., and Krummenacker M. (1999). Eco Cyc: Encyclopedia of Escherichia coli genes and metabolism. Nucleic Acids Res., 27, 55-58.
23. Knirsch C. A., Jain N. L., Pablos-Mendez A., Friedman C., and Hripcsak G. (1998). Respiratory isolation of tuberculosis patients using clinical guidelines and an automated clinical decision support system. Infect. Control Hosp. Epidemiol., 19, 94-100.
24. Koike T., and Rzhetsky A. (2000). A graphic editor for analyzing signal-transduction pathways. Gene, 259, 235-244.
25. Krauthammer M., Rzhetsky A., Morozov P., and Friedman C. (2000). Using BLAST for identifying gene and protein names in journal articles. Gene, 259, 245-252.
26. Maroto M., Reshef R., Munsterberg A. E., Koester S., Goulding M., and Lassar A. B. (1997). Ectopic Pax-3 activates MyoD and Myf-5 expression in embryonic mesoderm and neural tissue. Cell, 89, 139-48.
27. McCray A. T., Razi A. M., Bangalore A. K., Browne A. C., and Stavri P. Z. (1996). The UMLS Knowledge Source Server: a versatile Internet-based research tool. Proc. AMIA Annu. Fall Symp., , 164-8.
28. Park J. C., Kim H. S., and Kim J. J. (2001). Bidirectional Incremental Parsing for Automatic Pathway Identification with Combinatory Categorial Grammar. Pacif. Symp. Biocomp., 6, 396-407.
29. Pereira F. C. N., and Warren D. (1980). Definite clause grammars for language analysis - a survey of the formalism and comparison with augmented transition networks. Artificial Intelligence, 13, 231-278.
30. Rindflesch T. C., Hunter L., and Aronson A. R. (1999). Mining molecular binding terminology from biomedical text. Proc. AMIA Symp., 127-31.
31. Rindflesch T. C., Tanabe L., Weinstein J. N., and Hunter L. (2000). EDGAR: extraction of drugs, genes and relations from the biomedical literature. Pac. Symp. Biocomput., 517-28.
32. Rzhetsky A., Koike T., Kalachikov S., Gomez S. M., Krauthammer M., Kaplan S. H., Kra P., Russo J. J., and Friedman C. (2000). A knowledge model for analysis and simulation of regulatory networks. Bioinformatics, 16, 1120-1128.
33. Sekimizu T., Park H. S., and Tsujii J. (1998). Identifying the Interaction between Genes and Gene Products Based on Frequently Seen Verbs in Medline Abstracts. Genome Inform. Ser. Workshop Genome Inform., 9, 62-71.
34. Selkov E., Galimova M., Goryanin I., Gretchkin Y., Ivanova N., Komarov Y., Maltsev N., Mikhailova N., Nenashev V., Overbeek R., Panyushkina E., Pronevitch L., and Selkov E., Jr. (1997). The metabolic pathway collection: an update. Nucleic Acids Res., 25, 37-8.
35. Thomas J., Milward D., Ouzounis C., Pulman S., and Carroll M. (2000). Automatic extraction of protein interactions from scientific abstracts. Pac. Symp. Biocomput., 541-52.
36. Yakushiji A., Tateisi Y., Miyao Y., and Tsujii J. (2001). Event Extraction from Biomedical Papers Using a Full Parser. Pacif. Symp. Biocomp., 6, 408-419.