Test suite design for ontology concept recognition systems

Proceedings of the 7th International Conference on Language Resources and Evaluation, LREC 2010

Volumn , Issue , 2010, Pages 441-446

  Cohen, K Bretonnel ^a,b   Roeder, Christophe ^a   Baumgartner, William A ^a   Hunter, Lawrence E ^a   Verspoor, Karin ^a  

^a UNIVERSITY OF COLORADO SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF COLORADO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHARACTER RECOGNITION; ONTOLOGY; TESTING;

CANONICAL FORM; FEATURE TYPES; FIELD WORKS; FREE TEXTS; NAMED ENTITY RECOGNITION; ONTOLOGY CONCEPTS; PERFORMANCE ERROR; STRUCTURED TESTS;

SOFTWARE TESTING;

EID: 84985038899     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (32)

1. Boris Beizer. 1990. Software testing techniques, 2nd edition. International Thomson Computer Press.
2. Boris Beizer. 1995. Black-box testing: Techniques for functional testing of software and systems. Wiley.
3. Douglas Biber, Stig Johansson, Geoffrey Leech, Susan Conrad, and Edward Finegan. 1999. Longman grammar of spoken and written English. Pearson.
4. Robert V. Binder. 1999. Testing Object-Oriented Systems: Models, Patterns, and Tools. Addison-Wesley Professional, October.
5. Christian Blaschke, Eduardo A. Leon, Martin Krallinger, and Alfonso Valencia. 2005. Evaluation of BioCreative assessment of task 2. BMC Bioinformatics, 6 Suppl 1.
6. Leonard Bloomfield. 1933. Language. University of Chicago Press.
7. E. B. Camon, D. G. Barrell, E. C. Dimmer, V. Lee, M. Magrane, J. Maslen, D. Binns, and R. Apweiler. 2005. An evaluation of go annotation retrieval for biocreative and goa. BMC Bioinformatics, 6 Suppl 1.
8. Werner Ceusters, Barry Smith, and Louis Goldberg. 2005. A terminological and ontological analysis of the NCI Thesaurus. Methods of Information in Medicine, 44:498-507.
9. K. Bretonnel Cohen, Lorraine Tanabe, Shuhei Kinoshita, and Lawrence Hunter. 2004. A resource for constructing customized test suites for molecular biology entity identification systems. In HLT-NAACL 2004 Workshop: BioLINK 2004, Linking Biological Literature, Ontologies and Databases, pages 1-8. Association for Computational Linguistics.
10. K. Bretonnel Cohen, William A. Baumgartner Jr., and Lawrence Hunter. 2008. Software testing and the naturally occurring data assumption in natural language processing. In Software Engineering, Testing, and Quality Assurance for Natural Language Processing, pages 23-30, Columbus, Ohio, June. Association for Computational Linguistics.
11. Kirill Degtyarenko. 2003. Chemical vocabularies and ontologies for bioinformatics. In Proc 2003 Itnl Chem Info Conf.
12. H.A. Gleason Jr. 1961. An introduction to descriptive linguistics. Holt, Rinehart and Wilson, revised edition.
13. Zellig S. Harris. 1951. Methods in structural linguistics. University of Chicago Press.
14. Lynette Hirschman, Marc Colosimo, Alexander Morgan, and Alexander Yeh. 2005. Overview of BioCreative Task 1B: normalized gene lists. BMC Bioinformatics, 6 Suppl 1.
15. Helen L. Johnson, K. B. Cohen, William A. Baumgartner, Zhiyong Lu, Michael Bada, Todd Kester, Hyunmin Kim, and Lawrence Hunter. 2006. Evaluation of lexical methods for detecting relationships between concepts from multiple ontologies. Pac Symp Biocomput, pages 28-39.
16. Helen L. Johnson, K. Bretonnel Cohen, and Lawrence Hunter. 2007. A fault model for ontology mapping, alignment, and linking systems. In Pacific Symposium on Biocomputing, pages 233-244. World Scientific Publishing Company.
17. Cem Kaner, Hung Quoc Nguyen, and Jack Falk. 1999. Testing computer software, 2nd edition. John Wiley and Sons.
18. Cem Kaner, James Bach, and Bret Pettichord. 2002. Lessons learned in software testing: a context-driven approach. John Wiley and Sons, Inc.
19. S. Kinoshita, K. B. Cohen, P. V. Ogren, and L. Hunter. 2005. BioCreAtIvE Task1A: entity identification with a stochastic tagger. BMC Bioinformatics, 6 Suppl 1.
20. Martin Krallinger, Florian Leitner, Carlos Rodriguez-Penagos, and Alfonso Valencia. 2008. Overview of the protein-protein interaction annotation extraction task of biocreative ii. Genome Biology, 9(Suppl. 2).
21. Brian Marick. 1997. The craft of software testing: subsystem testing including object-based and object-oriented testing. Prentice Hall.
22. Alexander A. Morgan, Benjamin Wellner, Jeffrey B. Colombe, Robert Arens, Marc E. Colosimo, and Lynette Hirschman. 2007. Evaluating human gene and protein mention normalization to unique identifiers. In Pacific Symposium on Biocomputing, pages 281-291.
23. Alexander A. Morgan, 17 other people, K. Bretonnel Cohen, and Lynette Hirschman. 2008. Overview of BioCreative II gene normalization. Genome Biology, 9.
24. Glenford Myers. 1979. The art of software testing. John Wiley and Sons.
25. S. Oepen, K. Netter, and J. Klein. 1998. TSNLP - test suites for natural language processing. In John Nerbonne, editor, Linguistic Databases, chapter 2, pages 13-36. CSLI Publications.
26. Ron Patton. 2005. Software testing. Sams, 2nd edition.
27. Randolph Quirk, Sidney Greenbaum, Geoffrey Leech, and Jan Svartvik. 1985. A comprehensive grammar of the English language. Longman.
28. William J. Samarin. 1967. Field linguistics: A guide to linguistic field work. Irvington.
29. Nigam H. Shah, Nipun Bhatia, Clement Jonquet, Daniel Rubin, Annie P. Chiang, and Mark A. Musen. 2009. Comparison of concept recognizers for building the open biomedical annotator. BMC Bioinformatics, 10.
30. C. Verspoor, C. Joslyn, and G. Papcun. 2003. The Gene Ontology as a source of lexical semantic knowledge for a biological natural language processing application. In Proceedings of the SIGIR'03 Workshop on Text Analysis and Search for Bioinformatics, Toronto, CA, August.
31. Martin Volk. 1998. Markup of a test suite with SGML. In John Nerbonne, editor, Linguistic databases, pages 59-76. CSLI Publications.
32. A. Yeh, A. Morgan, M. Colosimo, and L. Hirschman. 2005. BioCreatve task 1A: gene mention finding evaluation. BMC Bioinformatics, 6(Suppl. 1).