Textpresso: An ontology-based information retrieval and extraction system for biological literature

PLoS Biology

Volumn 2, Issue 11, 2004, Pages

  Müller, Hans Michael ^a   Kenny, Eimear E ^a   Sternberg, Paul W ^a  

^a CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCELERATION; ACCURACY; ALLELE; ARTICLE; AUTOMATION; CAENORHABDITIS ELEGANS; CELL POPULATION; CORRELATION ANALYSIS; DATA ANALYSIS; DATA BASE; EXTRACTION; GENE; GENE CONTROL; INFORMATION PROCESSING; INFORMATION RETRIEVAL; MEDICAL LITERATURE; MEDICAL RESEARCH; MOLECULAR BIOLOGY; MOLECULAR INTERACTION; PHENOTYPE; PUBLISHING; SEMANTICS; STATISTICAL SIGNIFICANCE; SYSTEM ANALYSIS; ALGORITHM; ANIMAL; BIBLIOGRAPHIC DATABASE; BIOLOGY; CHEMISTRY; COMPUTER INTERFACE; COMPUTER PROGRAM; DOCUMENTATION; GENETIC DATABASE; INFORMATION SERVICE; INTERNET; LITERATURE; MEDICAL INFORMATICS; MEDICAL INFORMATION SYSTEM; MEDLINE; METHODOLOGY; NATURAL LANGUAGE PROCESSING;

CAENORHABDITIS ELEGANS;

CAENORHABDITIS ELEGANS PROTEIN;

ABSTRACTING AND INDEXING; ALGORITHMS; ANIMALS; BIOLOGY; CAENORHABDITIS ELEGANS; CAENORHABDITIS ELEGANS PROTEINS; COMPUTATIONAL BIOLOGY; DATABASES, BIBLIOGRAPHIC; DATABASES, GENETIC; INFORMATION SERVICES; INFORMATION STORAGE AND RETRIEVAL; INTERNET; LITERATURE; MEDICAL INFORMATICS; MEDLINE; NATURAL LANGUAGE PROCESSING; PUBMED; SOFTWARE; UNIFIED MEDICAL LANGUAGE SYSTEM; USER-COMPUTER INTERFACE;

EID: 14044254746     PISSN: 15449173     EISSN: None     Source Type: Journal    
DOI: 10.1371/journal.pbio.0020309     Document Type: Article

References (30)

1. Alper S, Kenyon C (2002) The zinc finger protein REF-2 functions with the Hox genes to inhibit cell fusion in the ventral epidermis of C. elegans. Development 129: 3335-3348.
2. Andrade MA, Bork P (2000) Automated extraction of information in molecular biology. FEBS Lett 476: 12-17.
3. Bei Y, Hogan J, Berkowitz LA, Soto M, Rocheleau CE, et al. (2002) SRC-1 and Wnt signaling act together to specify endoderm and to control cleavage orientation in early C. elegans embryos. Dev Cell 3: 113-125.
4. Blaschke C, Valencia A (2001) Can bibliographic pointers for known biological data be found automatically? Protein interactions as a case study. Comp Funct Genomics 2: 196-206.
5. Blaschke C, Valencia A (2002) Molecular biology nomenclature thwarts information-extraction progress. IEEE Intell Syst 17: 73-76.
6. Boxem M, van den Heuvel S (2002) C. elegans class B synthetic multivulva genes act in G(1) regulation. Curr Biol 12: 906-911.
7. Brill E (1992) A simple rule-based part of speech tagger. In: Proceedings of the third conference on applied natural processing. Trento (Italy): ACL. pp 152-155.
8. de Bruijn B, Martin J (2002) Getting to the (c)ore of knowledge: Mining biomedical literature. Int J Med Inf 67: 7-18.
9. Donaldson I, Martin J, de Bruijn B, Wolting C, Lay V, et al. (2003) PreBIND and Textomy - mining the biomedical literature for protein-protein interactions using a support vector machine. BMC Bioinformatics 4: 11.
10. Francis R, McGrath G, Zhang J, Ruddy DA, Sym M, et al. (2002) aph-1 and pen-2 are required for Notch pathway signaling, gamma-secretase cleavage of beta-APP, and presenilin protein accumulation. Dev Cell 3: 85-97.
11. Friedman C, Kra P, Hong Y, Krauthammer M, Rzhetsky A (2001) GENIES: A natural-language processing system for the extraction of molecular pathways from journal articles. Bioinformatics 17: S74-S82.
12. Fukuda K, Tsunoda T, Tamura A, Takagi T (1998) Towards information extraction: Identifying protein names from biological papers. Pac Symp Biocomput 1998: 707-718.
13. The Gene Ontology Consortium (2000) Gene Ontology: Tool for the unification of biology. Nat Genet 25: 25-29.
14. Gupta BP, Sternberg PW (2002) Tissue-specific regulation of the LIM homeobox gene lin-11 during development of the Caenorhabditis elegans egg-laying system. Dev Biol 247: 102-115.
15. Hanisch D, Fluck J, Mevissen HT, Zimmer R (2003) Playing biology's name game: Identifying protein names in scientific text. Pac Symp Biocomput 2003: 403-414.
16. Huang NN, Mootz DE, Vidal M, Hunter CP, Walhout AJ (2002) MEX3 interacting proteins link cell polarity to asymmetric gene expression in Caenorhabditis elegans. Development 129: 747-759.
17. Jenssen TK, Lægreid A, Komorowski J, Hovig E (2001) A literature network of human genes for high-throughput analysis of gene expression. Nat Genet 28: 21-28.
18. Maduzia LL, Gumienny TL, Zimmerman CM, Wang H, Shetgiri P, et al. (2002) lon-1 regulates Caenorhabditis elegans body size downstream of the dbl-1 TGF beta signaling pathway. Dev Biol 246: 418-428.
19. Marcotte EM, Xenarios I, Eisenberg D (2001) Mining literature for protein-protein interactions. Bioinformatics 17: (Suppl 1) 359-363.
20. Norman KR, Moerman DG (2002) Alpha spectrin is essential for morphogenesis and body wall muscle formation in Caenorhabditis elegans. J Cell Biol 157: 665-677.
21. Ono T, Hishigaki H, Tanigami A, Takagi T (2001) Automated extraction of information on protein-protein interactions from the biological literature. Bioinformatics 17: 155-161.
22. Piekny AJ, Mains PE (2002) Rho-binding kinase (LET-502) and myosin phosphatase (MEL-11) regulate cytokinesis in the early Caenorhabditis elegans embryo. J Cell Sci 115: 2271-2282.
23. 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 9: 72-80.
24. Rindflesch TC, Tanabe L, Weinstein JN, Hunter L (2000) EDGAR: Extraction of drugs, genes and relations from the biomedical literature. Pac Symp Biocomput 2000: 515-524.
25. Scott BA, Avidan MS, Crowder CM (2002) Regulation of hypoxic death in C. elegans by the insulin/IGF receptor homolog DAF-2. Science 296: 2388-2391.
26. Sekimizu T, Park HS, Jun'ichi T (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.
27. Staab S editor (2002) Mining information for functional genomics. IEEE Intell Syst 17: 66.
28. Stapley BJ, Benoit G (2000) Biobibliometrics: Information retrieval and visualization from co-occurrences of gene names in Medline abstracts. Pac Symp Biocomput 2000: 529-540.
29. Stein L, Sternberg P, Durbin R, Thierry-Mieg J, Spieth J (2001) WormBase: Network access to the genome and biology of Caenorhabditis elegans. Nucleic Acids Res 29: 82-86.
30. Thomas J, Milward D, Ouzounis C, Pulman S, Carroll M (2000) Automatic extraction of protein interactions from scientific abstracts. Pac Symp Biocomput 2000: 502-513