Distributed modules for text annotation and IE applied to the biomedical domain

International Journal of Medical Informatics

Volumn 75, Issue 6, 2006, Pages 496-500

  Kirsch, Harald ^a   Gaudan, Sylvain ^a   Rebholz Schuhmann, Dietrich ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

Gene ontology; Information extraction; Online tool; Protein protein interaction; Text mining; UniProt

Indexed keywords

COMPUTER SOFTWARE; DATA MINING; INFORMATION RETRIEVAL; PROTEINS; SERVERS; XML;

GENE ONTOLOGY; INFORMATION EXTRACTION; ONLINE TOOL; PROTEIN-PROTEIN INTERACTION; TEXT MINING; UNIPROT;

COMPUTER AIDED DIAGNOSIS;

ARTICLE; BIOINFORMATICS; COMPUTER PROGRAM; DATA BASE; INFORMATION PROCESSING; INFORMATION RETRIEVAL; MEDICAL LITERATURE; NOMENCLATURE; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION;

ABSTRACTING AND INDEXING; ARTIFICIAL INTELLIGENCE; BIOLOGY; DATABASE MANAGEMENT SYSTEMS; DOCUMENTATION; INFORMATION STORAGE AND RETRIEVAL; MEDICINE; NATURAL LANGUAGE PROCESSING; PERIODICALS; SEMANTICS; SOFTWARE; TERMINOLOGY; USER-COMPUTER INTERFACE; VOCABULARY, CONTROLLED;

EID: 33646475127     PISSN: 13865056     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ijmedinf.2005.06.011     Document Type: Article

References (13)

1. Albert S., Gaudan S., Knigge H., Raetsch A., Delgado A., Huhse B., Kirsch H., Albers M., Rebholz-Schuhmann D., and Koegl M. Computer-assisted generation of a protein-interaction database for nuclear receptors. Mol. Endocrinol. 17 8 (2003) 1555-1567
2. Chang J., Schutze H., and Altman R. Creating an online dictionary of abbreviations from medline. J. Am. Med. Assoc. 9 6 (2002) 612-620
3. Gaizauskas R., Demetriou G., Artymiuk P., and Willett P. Protein structures and information extraction from biological texts: the pasta system. Bioinformatics 19 1 (2003) 135-143
4. Hanisch D., Fluck J., Mevissen H.-T., and Zimmer R. Playing biology's name game: identifying protein names in scientific text. Proceedings of the Pacific Symposium on Biocomputing (2003)
5. Hopcroft J., and Ullman J. Introduction to Automata Theory Languages and Computation (1979), Addison Wesley
6. Huang M., Zhu X., Hao Y., Payan D., Qu K., and Li M. Discovering patterns to extract protein-protein interactions from full texts. Bioinformatics 20 18 (2004) 3604-3612
7. Muller H., Kenny E., and Sternberg M. Textpresso: an ontology-based information retrieval and extraction system for biological literature. Publ. Library Sci. 2 11 (2004) e309
8. Rebholz-Schuhmann D., Marcel S., Albert S., Tolle R., Casari G., and Kirsch H. Automatic extraction of mutations from medline and cross-validation with omim. Nucl. Acids Res. 32 1 (2004) 135-142
9. Rzhetsky A., Iossifov I., Koike T., Krauthammer M., Kra P., Morris M., Yu H., Weng P.D., Wilbur W., Hatzivas-siloglou V., and Friedman C. Geneways: a system for extracting, analyzing, visualizing, and integrating molecular pathway data. J. Biomed. Informat. 37 1 (2004) 43-53
10. Schwartz S., and Hearst M. A simple algorithm for identifying abbreviation definitions in biomedical text. Proceedings of the Pacific Symposium on Bio-computing (2003)
11. Shah P., Perez-Iratxeta C., and Andrade M. Information extraction from full text scientific articles: where are the keywords?. Bioinformatics 4 20 (2003)
12. Temkin J., and Gilder M. Extraction of protein interaction information from unstructured text using a context-free grammar. Bioinformatics 19 16 (2003) 2046-2053
13. Yeh A., Hirschman L., and Morgan A. Evaluation of text data mining for database curation: lessons learned from the kdd challenge cup. Bioinformatics 19 (2003) i331-i339