LLL'05 challenge: Genic interaction extraction - identification of language patterns based on alignment and finite state automata

Learning Language in Logic - Challenge Task: Extracting Relations from Bio-Medical Texts, LLL 2005 - ICML 2005 Workshop

Volumn , Issue , 2005, Pages 31-37

  Hakenberg, Jorg ^a   Plake, Conrad ^a   Leser, Ulf ^a   Kirsch, Harald ^b   Rebholz Schuhmann, Dietrich ^b  

^a HUMBOLDT UNIVERSITY   (Germany)

^b EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

INTERACTION EXTRACTION; LANGUAGE PATTERNS; PART OF SPEECH; SCIENTIFIC TEXTS; SEQUENCE ALIGNMENTS; SYSTEM USE; TEXTUAL REPRESENTATION;

GENETIC ALGORITHMS; OPTIMIZATION;

ALIGNMENT;

EID: 84873423575     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (19)

1. Brants, T. (2000). TnT - a statistical part-of-speech tagger. Proc 6th Applied NLP Conference. Seattle, USA.
2. Chen, H., & Sharp, B. M. (2004). Content-rich biological network constructed by mining PubMed abstracts. BMC Bioinformatics, 5, 147.
3. Daraselia, N., Yuryev, A., Egorov, S., Novichkova, S., Nikitin, A., & Mazo, I. (2004). Extracting human protein interactions from medline using a fullsentence parser. Bioinformatics, 20, 604-611.
4. Ding, J., Berleant, D., Nettleton, D., & Wurtele, E. (2002). Mining MEDLINE: Abstracts, Sentences, or Phrases? Pacific Symposium on Biocomputing (pp. 326-337). Kaua'i, Hawaii, USA.
5. Genic Interaction Extraction Challenge (2005). Learning Language in Logic Workshop (LLL). http://genome.jouy.inra.fr/texte/LLLchallenge/.
6. Hakenberg, J., Bickel, S., Plake, C., Brefeld, U., Zahn, H., Faulstich, L., Leser, U., & Scheffer, T. (2005). Systematic Feature Evaluation for Gene Name Recognition. BMC Bioinformatics, 6, S9.
7. Hirschman, L., Yeh, A., Blaschke, C., & Valencia, A. (2005). Overview of BioCreAtIvE: critical assessment of information extraction for biology. BMC Bioinformatics, 6, 1.
8. Huang, M., Zhu, X., Hao, Y., Payan, D. G., Qu, K., & Li, M. (2004). Discovering patterns to extract protein-protein interactions from full texts. Bioinformatics, 20, 3604-3612.
9. Needleman, S., & Wunsch, C. (1970). A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol., 48, 443-53.
10. Plake, C., Hakenberg, J., & Leser, U. (2005a). Learning Patterns for Information Extraction from Free Text. Proc Workshop des Arbeitskreises Knowledge Discovery. Karlruhe, Germany.
11. Plake, C., Hakenberg, J., & Leser, U. (2005b). Optimizing Syntax Patterns for Discovering Protein- Protein Interactions. Proc ACM Symposium for Applied Computing, Bioinformatics track. Santa Fe, USA.
12. Porter, M. (1980). An algorithm for suffix stripping. Program, 130-137.
13. Rosario, B., & Hearst, M. (2004). Classifying semantic relations in bioscience texts. Proceedings of the 42nd Annual Meeting of the Association for Computational Linguistics, ACL. Barcelona, Spain.
14. Santorini, B. (1990). Part-of-speech tagging guidelines for the Penn Treebank Project (Technical Report). MS-CIS-90-47, University of Pennsylvania.
15. Saric, J., Jensen, L., Ouzounova, R., Rojas, I., & Bork, P. (2005). Large-scale Extraction of Protein/Gene Relations for Model Organisms. Proc Symp on Semantic Mining in Biomedicine (p. 50). Hinxton, UK.
16. Smith, T., & Waterman, M. (1981). Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
17. Stapley, B., Kelley, L., & Sternberg, M. (2002). Predicting the sub-cellular location of proteins from text using support vector machines. Proceedings of the Pacific Symposium on Biocomputing (pp. 374- 385).
18. Temkin, J. M., & Gilder, M. R. (2003). Extraction of protein interaction information from unstructured text using a context-free grammar. Bioinformatics, 19, 2046-2053.
19. Xiao, J., Su, J., Zhou, G., & Tan, C. (2005). Protein-Protein Interaction Extraction: A Supervised Learning Approach. Proc Symp on Semantic Mining in Biomedicine (pp. 51-59). Hinxton, UK.