Overview of the Bacteria Biotope Task at BioNLP Shared Task 2016

Proceedings of the Annual Meeting of the Association for Computational Linguistics

Volumn , Issue , 2016, Pages 12-22

  Deĺeger, Louise ^a   Bossy, Robert ^a   Chaix, Estelle ^a   Ba, Mouhamadou ^a   Ferŕe, Arnaud ^a,b   Bessìeres, Philippe ^a   Ńedellec, Claire ^a  

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

^b UFR 919 Laboratoire d'Informatique Pour la Mécanique et les Sciences de l'Ingénieur   (France)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL LINGUISTICS; ECOSYSTEMS;

EVALUATION METRICS; FUNDAMENTAL RESEARCH; KNOWLEDGE SOURCES; ONTOLOGY'S; RESEARCH AND APPLICATION; SUBTASK;

BACTERIA;

EID: 85101058862     PISSN: 0736587X     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (22)

1. Mouhamadou Ba and Robert Bossy. 2016. Interoperability of corpus processing work-flow engines: the case of alvisnlp/ml in openminted. In Richard Eckart de Castilho, Sophia Ananiadou, Thomas Margoni, Wim Peters, and Stelios Piperidis, editors, Proceedings of the Workshop on Cross- Platform Text Mining and Natural Language Processing Interoperability (INTEROP 2016) at LREC 2016, pages 15-18, Portoroz, Slovenia, May. European Language Resources Association (ELRA).
2. Robert Bossy, Julien Jourde, Alain-Pierre Manine, Philippe Veber, Erick Alphonse, Maarten Van De Guchte, Philippe Bessìeres, and Claire Ńedellec. 2012. Bionlp shared task-the bacteria track. BMC bioinformatics, 13(11):1.
3. Robert Bossy, Wiktoria Golik, Zorana Ratkovic, Philippe Bessìeres, and Claire Ńedellec. 2013. Bionlp shared task 2013-an overview of the bacteria biotope task. In Proceedings of the BioNLP Shared Task 2013 Workshop, pages 161-169.
4. Robert Bossy, Wiktoria Golik, Zorana Ratkovic, Dialekti Valsamou, Philippe Bessìeres, and Claire Ńedellec. 2015. Overview of the gene regulation network and the bacteria biotope tasks in bionlp'13 shared task. BMC bioinformatics, 16(10):1.
5. Pier Luigi Buttigieg, Norman Morrison, Barry Smith, Christopher J Mungall, and Suzanna E Lewis. 2013. The environment ontology: contextualising biological and biomedical entities. Journal of biomedical semantics, 4(1):1.
6. Estelle Chaix, Bertrand Dubreucq, Abdelhak Fatihi, Dialekti Valsamou, Robert Bossy, Mouhamadou Ba, Louise Deĺeger, Pierre Zweigenbaum, Philippe Bessìeres, Loic Lepiniec, and Claire Ńedellec. 2016. Overview of the regulatory network of plant seed development (seedev) task at the bionlp shared task 2016. In Proceedings of the 4th BioNLP Shared Task workshop, Berlin, Germany, August. Association for Computational Linguistics.
7. Scott Federhen. 2012. The ncbi taxonomy database. Nucleic acids research, 40(D1):D136-D143.
8. C Fellbaum. 1998. Wordnet: An on-line lexical database and some of its applications.
9. Jenny Rose Finkel, Trond Grenager, and Christopher Manning. 2005. Incorporating non-local information into information extraction systems by gibbs sampling. In Proceedings of the 43rd Annual Meeting on Association for Computational Linguistics, pages 363-370. Association for Computational Linguistics.
10. Melissa Merrill Floyd, Jane Tang, Matthew Kane, and David Emerson. 2005. Captured diversity in a culture collection: case study of the geographic and habitat distributions of environmental isolates held at the american type culture collection. Applied and Environmental Microbiology, 71(6):2813-2823.
11. Wiktoria Golik, Pierre Warnier, and Claire Ńedellec. 2011. Corpus-based extension of termino-ontology by linguistic analysis: a use case in biomedical event extraction. In WS 2 Workshop Extended Abstracts, 9th International Conference on Terminology and Artificial Intelligence, pages 37-39.
12. Marion Gremse, Antje Chang, Ida Schomburg, Andreas Grote, Maurice Scheer, Christian Ebeling, and Dietmar Schomburg. 2011. The brenda tissue ontology (bto): the first all-integrating ontology of all organisms for enzyme sources. Nucleic acids research, 39(suppl 1):D507-D513.
13. George Hripcsak and Adam S Rothschild. 2005. Agreement, the f-measure, and reliability in information retrieval. Journal of the American Medical Informatics Association, 12(3):296-298.
14. Natalia Ivanova, Susannah G Tringe, Konstantinos Liolios, Wen-Tso Liu, Norman Morrison, Philip Hugenholtz, and Nikos C Kyrpides. 2010. A call for standardized classification of metagenome projects. Environmental microbiology, 12(7):1803-1805.
15. Jin-Dong Kim, Tomoko Ohta, Sampo Pyysalo, Yoshinobu Kano, and Jun'ichi Tsujii. 2009. Overview of bionlp'09 shared task on event extraction. In Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing: Shared Task, pages 1-9. Association for Computational Linguistics.
16. Jin-Dong Kim, Sampo Pyysalo, Tomoko Ohta, Robert Bossy, Ngan Nguyen, and Jun'ichi Tsujii. 2011. Overview of bionlp shared task 2011. In Proceedings of the BioNLP Shared Task 2011 Workshop, pages 1-6. Association for Computational Linguistics.
17. Claire Ńedellec, Robert Bossy, Jin-Dong Kim, Jung- Jae Kim, Tomoko Ohta, Sampo Pyysalo, and Pierre Zweigenbaum. 2013. Overview of bionlp shared task 2013. In Proceedings of the BioNLP Shared Task 2013 Workshop, pages 1-7.
18. Fŕederic Papazian, Robert Bossy, and Claire Ńedellec. 2012. Alvisae: a collaborative web text annotation editor for knowledge acquisition. In Proceedings of the Sixth Linguistic Annotation Workshop, pages 149-152. Association for Computational Linguistics.
19. Aidan C Parte. 2013. Lpsnlist of prokaryotic names with standing in nomenclature. Nucleic acids research, page gkt1111.
20. Miguel Pignatelli, Andŕes Moya, and Javier Tamames. 2009. Envdb, a database for describing the environmental distribution of prokaryotic taxa. Environmental Microbiology Reports, 1(3):191-197.
21. Zorana Ratkovic, Wiktoria Golik, and Pierre Warnier. 2012. Event extraction of bacteria biotopes: a knowledge-intensive nlp-based approach. BMC bioinformatics, 13(11):1.
22. James Z Wang, Zhidian Du, Rapeeporn Payattakool, S Yu Philip, and Chin-Fu Chen. 2007. A new method to measure the semantic similarity of go terms. Bioinformatics, 23(10):1274-1281.