BioNLP 2011 task bacteria biotope – the Alvis system

Proceedings of BioNLP Shared Task 2011 Workshop at the 49th Annual Meeting of the Association for Computational Linguistics: Human Language Technologies, ACL HLT 2011

Volumn , Issue , 2011, Pages 102-111

  Ratkovic, Zorana ^a,b   Golik, Wiktoria ^a   Warnier, Pierre ^a   Veber, Philippe ^a   Nédellec, Claire ^a  

^a INRA Institut National de la Recherche Agronomique   (France)

^b UMR 8094   (France)

Author keywords

[No Author keywords available]

Indexed keywords

NATURAL LANGUAGE PROCESSING SYSTEMS; SEMANTICS;

DOMAIN SPECIFIC; GEOGRAPHICAL LOCATIONS; LEXICAL RESOURCES; ONTOLOGY'S; PARTICIPATING SYSTEMS; PERFORMANCE; RESEARCH GROUPS; SEMANTIC ANALYSIS;

BACTERIA;

EID: 85119285972     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (25)

1. Agrovoc: http://aims.fao.org/website/AGROVOCThesaurus
2. Antti Airola, Sampo Pyysalo, Jari Björne, Tapio Pahnikkala, Filip Ginter, and Tapio Salakoski. 2008. A Graph Kernel for Protein-Protein Interaction Extraction. BioNLP2008: Current Trends in Biomedical Natural Language Processing, pages 1-9.
3. Alan R. Aronson. 2001. Effective mapping of biomedical text to the UMLS Metathesaurus: The MetaMap program. Proceedings of AMIA Symposium 2001, pages 17-21.
4. Emmanuel Desmontils, Christine Jacquin and Laurent Simon. 2003. Ontology enrichment and indexing process. Research report RR-IRIN-03.05, Institut de Recherche en Informatique de Nantes, Nantes, France.
5. Jérôme Euzenat and Pavel Shvaiko. 2007. Ontology matching, Springer Verlag, Heidelberg (DE),page 333.
6. Dawn Field et al. 2008. Towards a richer description of our complete collection of genomes and metagenomes: the Minimum Information about a Genome Sequence (MIGS) specification. Nature Biotechnology 26, pages 541-547.
7. GeoNames: http://www.geonames.org/
8. Gregory Grefenstette. 1994. Explorations in Automatic Thesaurus Discovery. Natural Language Processing and Machine Translation. London: Kluwer Academic Publishers.
9. Barbara J. Grosz, Araving K. Joshi and Scott Weinstein. 1995. Centering: A Framework for Modelling the Local Coherence of Discourse. University of Pennsylvania Institute for Research in Cognitive Science Technical Reports Series.
10. Güneş Erkan, Arzucan Özgür and Dragomir R. Radev. 2007. Semi-Supervised Classification for Extracting Protein Interaction Sentences using Dependency Parsing. Proceedings of the 2007 Joint Conference on Empirical Methods in Natural Language Processing and Computational Natural Language Learning, pages 228-237.
11. Thierry Hamon and Sophie Aubin. 2006. Improving term extraction with terminological resources. In Salakoski, T. et al., editors, Advances in Natural Language Processing 5th International Conference on NLP (Fin-TAL’06), pages 380–387. Springer.
12. Thierry Hamon and Adeline Nazarenko. 2001. Detection of synonymy links between terms: experiment and results, Recent Advances in Computational Terminology. Pages 185-208. John Benjamins.
13. Marti A. Hearst. 1992. Automatic acquisition of hyponyms from large text corpora. In Zampolli, A.(ed.), Proceedings of the 14 th COLING, pages 539–545, Nantes, France.
14. Christian Jacquemin and Evelyne Tzoukermann. 1999. NLP for term variant extraction: A synergy of morphology, lexicon, and syntax. In Strzalkowski, T. (ed.), Natural language information retrieval, volume 7 of Text, speech and language technology, chapter 2, pages 25–74. Dordrecht & Boston: Kluwer Academic Publishers.
15. Matthew A. Jaro. 1989. Advances in record linkage methodology as applied to matching the 1985 census of Tampa, Florida. Journal of the American Statistical Association 84(406), pages 414-20.
16. Jin-Dong Kim, Tomoko Ohta, Sampo Pyysalo, Yoshinobu Kano and Jun’ichi Tsujii. (to appear). Extracting bio-molecular events from literature - the BioNLP’09 shared task. Special issue of the International Journal of Computational Intelligence.
17. Vladimir I. Levenshtein. 1966. Binary codes capable of correcting deletions, insertions and reversals. Doklady akademii nauk SSSR, 163(4):845-848, 1965. In Russian. English translation in Soviet Physics Doklady, 10(8), pages 707-710.
18. Yu-Hsiang Lin and Tyne Liang. 2004. Pronomial and Sortal Anaphora Resolution for Biomedical Literature. In Proceedings of ROCLING XVI: Conference on Computational Linguistics and Speech Processing.
19. Konstantinos Liolios, I-Min A. Chen., Konstantinos Mavromatis, Nektarios Tavernarakis, Philip Hugenholtz, Victor M. Markowitz and Nikos C. Kyrpides. 2009. The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. NAR Epub.
20. Alain-Pierre Manine, Erick Alphonse and Philippe Bessières. 2008. Information extraction as an ontology population task and its application to genic interactions, 20th IEEE Intl. Conf. Tools with Artificial Intelligence, ICTAI'08., vol. II, pp. 74-81.
21. NCBI taxonomy: http://www.ncbi.nlm.nih.gov/Taxonomy/
22. Claire Nédellec, Wiktoria Golik, Sophie Aubin and Robert Bossy. 2010. Building Large Lexicalized Ontologies from Text: a Use Case in Indexing Biotechnology Patents, International Conference on Knowledge Engineering and Knowledge Management (EKAW 2010), Lisbon, Portugal.
23. Isabel Segura-Bedmar, Mario Crespo, César de De Pablo-Sánchez and Paloma Martínez. 2010. Resolving anaphoras for the extraction of drug-drug interactions in pharmacological documents. BMC Bioinformatics 11(Supl 2):S1.
24. Manabu Torii and K. Vijay-Shanker. 2007. Sortal Anaphora Resolution in Medline Abstracts. Computational Intelligence 23, pages 15-27.
25. Zhou GuoDong, Su Jian, Zhang Jie and Zhang Min. 2005. Exploring Various Knowledge in Relation Extraction. In Proceedings of the 43rd Annual Meeting of the ACL, pages 427-434, Ann Arbor. Association for Computational Linguistics.