GoPubMed: ontology-based literature search applied to Gene Ontology and PubMed

Lecture Notes in Informatics (LNI), Proceedings - Series of the Gesellschaft fur Informatik (GI)

Volumn P-53, Issue , 2004, Pages 169-178

  Delfs, Ralph ^a   Doms, Andreas ^a   Kozlenkov, Alexander ^b   Schroeder, Michael ^a  

^a DRESDEN UNIVERSITY OF TECHNOLOGY   (Germany)

^b CITY UNIVERSITY   (United Kingdom)

Author keywords

ontologies; term extraction; Text mining

Indexed keywords

GENE ONTOLOGY;

BIOMEDICAL LITERATURE; EXTRACTION ALGORITHMS; GENE ONTOLOGY; LITERATURE SEARCH; ONTOLOGY'S; ONTOLOGY-BASED; PERFORMANCE; SUB-ONTOLOGY; TERM EXTRACTION; TEXT-MINING;

EXTRACTION;

EID: 84924158948     PISSN: 16175468     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (13)

1. C. Blaschke, MA. Andrade, C. Ouzounis, and A. Valencia. Automatic extraction of biological information from scientific text: protein-protein interaction. In Proc. of ISMB, 1999.
2. C. Blaschke, L. Hirschman, and A. Valencia. Information extraction in molecular biology. Briefings in Bioinformatics, 3:154–65, 2002.
3. M.N. Cantor, I.N. Sarakr, R. Gelman, F. Hartel, O. Bodenreider, and Y.A. Lussier. An evaluation of hybrid methods for matching biomedical terminologies: Mapping the GeneOntology to the UMLS. Stud Health Technol Inform., 95:62–7, 2003.
4. C. Friedman, P. Kra, H. Yu, M. Krauthammer, and A. Rzhetsky. Genies: a NLP system for the extraction of molecular pathways from journal articles. In Proc. of ISMB, 2001.
5. K. Fukuda, T. Tsunoda, A. Tamura, and T. Takagi. Toward information extraction: Identifying protein names from biological papers. In Proc. of PSB, 1998.
6. GeneOntologyConsortium. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res., 1(32):D258–61, 2004.
7. Alexa T. McCray, Allen Browne, and Olivier Bodenreider. The lexical properties of the Gene Ontology (GO). In Proc. of AMIA Symp., pages 504–8, 2002.
8. P.V. Ogren, K.B. Cohen, G.K. Acquaah-Mensah, J. Erberlein, and L. Hunter. The compositional structure of Gene Ontology terms. In Proc. of PSB, 2004.
9. C. Perez-Iratxeta, A.J. Perez, P. Bork, and M.A. Andrade. Update on xplormed: A web server for exploring scientific literature. Nucleic Acids Res, 31(13):3866–8, 2003.
10. S. Raychaudhuri, J.T. Chang, P.D. Sutphin, R.B. Altman. Associating genes with GO codes using a maximum entropy analysis of biomedical literature. Gen. Res., 1:203–14, 2002.
11. Tony Smith and John Cleary. Automatically linking medline abstracts to the geneontology. In Proc. of Bio-Ontologies Meeting, Brisbane, Australia, 2003.
12. L. Tanabe, U. Scherf, LH. Smith, JK. Lee, L. Hunter, and JN. Weinstein. Medminer: internettext-mining tool for biomedical information, with application to gene expression profiling. BioTechniques, 27(6):1210–4,1216–7, 1999.
13. James Thomas, David Milward, Christos Ouzounis, Stephen Pulman, and Mark Carroll. Automatic extraction of protein interactions from scientific abstracts. In Proc. of PSB, 2002.