Bootstrapping biomedical ontologies for scientific text using NELL

BioNLP@HLT-NAACL 2012 - Workshop on Biomedical Natural Language Processing, Proceedings

Volumn , Issue , 2012, Pages 11-19

  Movshovitz Attias, Dana ^a   Cohen, William W ^a  

^a CARNEGIE MELLON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; COMPUTATIONAL LINGUISTICS; INFORMATION RETRIEVAL SYSTEMS; ITERATIVE METHODS; NATURAL LANGUAGE PROCESSING SYSTEMS; SEMANTICS;

BIOMEDICAL ONTOLOGIES; BIOMEDICAL TEXT; BOOTSTRAPPING ALGORITHM; INFORMATION EXTRACTION SYSTEMS; LEARN+; ONTOLOGY'S; SCIENTIFIC TEXTS; SEED QUALITY; SEMI-SUPERVISED; WEB TEXTS;

ONTOLOGY;

EID: 85119336856     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (25)

1. M. Ashburner, C.A. Ball, J.A. Blake, D. Botstein, H. Butler, J.M. Cherry, A.P. Davis, K. Dolinski, S.S. Dwight, J.T. Eppig, et al. 2000. Gene ontology: tool for the unification of biology. Nature genetics, 25(1):25.
2. J. Bard, S.Y. Rhee, and M. Ashburner. 2005. An ontology for cell types. Genome Biology, 6(2):R21.
3. R. Bunescu, R. Ge, R.J. Kate, E.M. Marcotte, and R.J. Mooney. 2005. Comparative experiments on learning information extractors for proteins and their interactions. Artificial Intelligence in Medicine, 33(2).
4. J. Callan and M. Hoy. 2009. Clueweb09 data set. http://boston.lti.cs.cmu.edu/Data/clueweb09/.
5. A. Carlson, J. Betteridge, E.R. Hruschka Jr, T.M. Mitchell, and SP Sao Carlos. 2009. Coupling semisupervised learning of categories and relations. Semisupervised Learning for Natural Language Processing, page 1.
6. A. Carlson, J. Betteridge, B. Kisiel, B. Settles, E.R. Hruschka Jr, and T.M. Mitchell. 2010. Toward an architecture for never-ending language learning. In Proceedings of the Twenty-Fourth Conference on Artificial Intelligence (AAAI 2010), volume 2, pages 3-3.
7. J.T. Chang, H. Schütze, and R.B. Altman. 2004. Gapscore: finding gene and protein names one word at a time. Bioinformatics, 20(2):216.
8. K.W. Church and P. Hanks. 1990. Word association norms, mutual information, and lexicography. Computational linguistics, 16(1):22-29.
9. J.R. Curran, T. Murphy, and B. Scholz. 2007. Minimising semantic drift with mutual exclusion bootstrapping. In Proceedings of the 10th Conference of the Pacific Association for Computational Linguistics.
10. K. Degtyarenko, P. De Matos, M. Ennis, J. Hastings, M. Zbinden, A. McNaught, R. Alcántara, M. Darsow, M. Guedj, and M. Ashburner. 2008. Chebi: a database and ontology for chemical entities of biological interest. Nucleic acids research, 36(suppl 1):D344.
11. A. Dolbey, M. Ellsworth, and J. Scheffczyk. 2006. Bioframenet: A domain-specific framenet extension with links to biomedical ontologies. In Proceedings of KR-MED, pages 87-94. Citeseer.
12. K. Eilbeck, S.E. Lewis, C.J. Mungall, M. Yandell, L. Stein, R. Durbin, and M. Ashburner. 2005. The sequence ontology: a tool for the unification of genome annotations. Genome biology, 6(5):R44.
13. Google. 2011. Freebase data dumps. http://download.freebase.com/datadumps/.
14. L. Hirschman, A. Yeh, C. Blaschke, and A. Valencia. 2005. Overview of biocreative: critical assessment of information extraction for biology. BMC bioinformatics, 6(Suppl 1):S1.
15. Z. Kozareva and E. Hovy. 2010. Not all seeds are equal: measuring the quality of text mining seeds. In Human Language Technologies: The 2010 Annual Conference of the North American Chapter of the Association for Computational Linguistics, pages 618-626. Association for Computational Linguistics.
16. J. Krishnamurthy and T.M. Mitchell. 2011. Which noun phrases denote which concepts? In Proceedings of the 49th Annual Meeting of the Association for Computational Linguistics: Human Language Technologies. Association for Computational Linguistics.
17. T. McIntosh and J.R. Curran. 2009. Reducing semantic drift with bagging and distributional similarity. In Proceedings of the Joint Conference of the 47th Annual Meeting of the ACL and the 4th International Joint Conference on Natural Language Processing of the AFNLP: Volume 1-Volume 1, pages 396-404. Association for Computational Linguistics.
18. D. Movshovitz-Attias and W.W. Cohen. 2012. Bootstrapping biomedical ontologies for scientific text using nell. Technical report, Carnegie Mellon University, CMU-ML-12-101.
19. J. Osborne, J. Flatow, M. Holko, S. Lin, W. Kibbe, L. Zhu, M. Danila, G. Feng, and R. Chisholm. 2009. Annotating the human genome with disease ontology. BMC genomics, 10(Suppl 1):S6.
20. P. Pantel, E. Crestan, A. Borkovsky, A.M. Popescu, and V. Vyas. 2009. Web-scale distributional similarity and entity set expansion. In Proceedings of the 2009 Conference on Empirical Methods in Natural Language Processing: Volume 2-Volume 2, pages 938-947. Association for Computational Linguistics.
21. E. Riloff and R. Jones. 1999. Learning dictionaries for information extraction by multi-level bootstrapping. In Proceedings of the National Conference on Artificial Intelligence (AAAI-99), pages 474-479.
22. E. W. Sayers, T. Barrett, D. A. Benson, S. H. Bryant, K. Canese, V. Chetvernin, D. M. Church, M. DiCuccio, R. Edgar, S. Federhen, M. Feolo, L. Y. Geer, W. Helmberg, Y. Kapustin, D. Landsman, D. J. Lipman, T. L. Madden, D. R. Maglott, V. Miller, I. Mizrachi, J. Ostell, K. D. Pruitt, G. D. Schuler, E. Sequeira, S. T. Sherry, M. Shumway, K. Sirotkin, A. Souvorov, G. Starchenko, T. A. Tatusova, L. Wagner, E. Yaschenko, and J. Ye. 2009. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 37:5-15, Jan.
23. V. Vyas, P. Pantel, and E. Crestan. 2009. Helping editors choose better seed sets for entity set expansion. In Proceeding of the 18th ACM conference on Information and knowledge management. ACM.
24. R.C. Wang and W.W. Cohen. 2009. Character-level analysis of semi-structured documents for set expansion. In Proceedings of the 2009 Conference on Empirical Methods in Natural Language Processing: Volume 3- Volume 3, pages 1503-1512. Association for Computational Linguistics.
25. T. Wattarujeekrit, P. Shah, and N. Collier. 2004. Pasbio: predicate-argument structures for event extraction in molecular biology. BMC bioinformatics, 5(1):155.