LASIGE: using Conditional Random Fields and ChEBI ontology

*SEM 2013 - 2nd Joint Conference on Lexical and Computational Semantics

Volumn 2, Issue , 2013, Pages 660-666

  Grego, Tiago ^a   Pinto, Francisco ^a   Couto, Francisco M ^a  

^a UNIVERSITY OF LISBON   (Portugal)

Author keywords

[No Author keywords available]

Indexed keywords

CLASSIFICATION (OF INFORMATION); RANDOM PROCESSES; SEMANTICS;

CHEMICAL ENTITY; CONDITIONAL RANDOM FIELD; ENTITY RESOLUTIONS; F MEASURE; LEXICAL SIMILARITY; PARTIAL MATCHING; POST PROCESSING;

ONTOLOGY;

EID: 84947926499     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (18)

1. P. Corbett, C. Batchelor and S. Teufel. 2007. Annotation of chemical named entities. Proceedings of the Workshop on BioNLP 2007: Biological, Translational, and Clinical Language Processing, 57–64.
2. F. M. Couto and M. J. Silva. 2011. Disjunctive shared information between ontology concepts: application to Gene Ontology. Journal of Biomedical Semantics, 2(5).
3. F. M. Couto, P. M. Coutinho and M. J. Silva. 2005. Finding genomic ontology terms in text using evidence content. BMC Bioinformatics, 6 (Suppl 1), S21.
4. K. Degtyarenko, P. Matos, M. Ennis, J. Hastings, M. Zbinden, A. McNaught, R. Alcantara, M. Darsow, M. Guedj and M. Ashburner. 2007. ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Research, 36, D344.
5. D. Faria, C. Pesquita, E. Santos, F. M. Couto, C. Stroe and I. F. Cruz 2012. Testing the AgreementMaker System in the Anatomy Task of OAEI 2012. CoRR, abs/1212.1625, arXiv:1212.1625.
6. J. D. Ferreira and F. M. Couto 2010. Semantic similarity for automatic classification of chemical compounds. PLoS Computational Biology, 6(9).
7. T. Grego, C. Pesquita, H. P. Bastos and F. M. Couto. 2012. Chemical Entity Recognition and Resolution to ChEBI. ISRN Bioinformatics, Article ID 619427.
8. T. Grego, P. Pezik, F. M. Couto and D. Rebholz-Schuhmann. 2009. Identification of Chemical Entities in Patent Documents. Distributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living, volume 5518 of Lecture Notes in Computer Science, 934–941.
9. T. Grego, F. Pinto and F. M. Couto. 2012. Identifying Chemical Entities based on ChEBI. Software Demonstration at the International Conference on Biomedical Ontologies (ICBO).
10. D. M. Jessop, S. E. Adams, E. L. Willighagen, L. Hawizy and P. Murray-Rust 2011. OSCAR4: a flexible architecture for chemical text-mining. Journal of Chemin-formatics, 3(41).
11. J. Lafferty, A. McCallum and F. Pereira. 2001. Conditional random fields: Probabilistic models for segmenting and labeling sequence data. Proceedings of the 18th International Conference on Machine Learning, 282–289.
12. A. K. McCallum. 2002. Mallet: A machine learning for language toolkit. http://mallet.cs.umass.edu.
13. D. Rebholz-Schuhmann, M. Arregui, S. Gaudan, H. Kirsch and A. Jimeno. 2008. Text processing through Web services: calling Whatizit. Bioinformatics, 24(2):296–298.
14. T. Rocktäschel, M. Weidlich and U. Leser. 2012. ChemSpot: A Hybrid System for Chemical Named Entity Recognition. Bioinformatics, 28(12): 1633-1640.
15. I. Segura-Bedmar, P. Martínez and C. de Pablo-Sánchez 2006. Using a shallow linguistic kernel for drug-drug interaction extraction. Journal of Biomedical Informatics, 44(5): 789–804.
16. Y. Wang, J. Xiao, T. O. Suzek, J. Zhang, J. Wang and S. H. Bryant. 2009. PubChem: a public information system for analyzing bioactivities of small molecules. Nucleic Acids Research, 37, W623.
17. D. S. Wishart, C. Knox, A. C. Guo, S. Shrivastava, M. Hassanali, P. Stothard, Z. Chang and J. Woolsey. 2006. DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Research, 34, D668.
18. SemEval 2013. In Proceedings of the 7th International Workshop on Semantic Evaluation