Assessment of Software Testing and Quality Assurance in Natural Language Processing Applications and a Linguistically Inspired Approach to Improving It - Trustworthy Eternal Systems via Evolving, Software Data and Knowledge - page 89

Acknowledgements. We would like to thank our co-authors on some of the
work cited in this paper. Lynette Hirschman (The MITRE Corporation) and
Bob Carpenter (Alias-I) have discussed the general issues of software testing
and quality assurance with us extensively. Martin Krallinger's web page at
biocreative.sourceforge.net
listing web-based biomedical NLP services was invaluable in performing the work
reported here. Jonathan M. Cohen (Monterey County Public Defender's Oce)
and John Pestian (Cincinnati Children's Hospital Medical Center) helped us
understand regulatory issues regarding medical software. This work was funded
in part by grants NIH 5 R01 LM009254-06, NIH 5 R01 LM008111-07, NIH 5
R01 GM083649-04, and NIH 5 R01 LM009254-03 to Lawrence E. Hunter.
References
1. Baumgartner Jr., W.A., Lu, Z., Johnson, H.L., Gregory Caporaso, J., Paquette, J.,
Lindemann, A., White, E.K., Medvedeva, O., Bretonnel Cohen, K., Hunter, L.E.:
Concept recognition for extraction protein interaction relations from biomedical
text. Genome Biology 9(suppl. 2), S9 (2008)
2. Beizer, B.: Software testing techniques, 2nd edn. International Thomson Computer
Press (1990)
3. Beizer, B.: Black-box testing: Techniques for functional testing of software and
systems. Wiley (1995)
4. Binder, R.V.: Testing object-oriented systems: models, patterns, and tools.
Addison-Wesley Professional (1999)
5. Chang, G., Roth, C.R., Reyes, C.L., Pornillos, O., Chen, Y.-J., Chen, A.P.: Letters:
Retraction. Science 314, 1875 (2006)
6. Bretonnel Cohen, K., Tanabe, L., Kinoshita, S., Hunter, L.: A resource for con-
structing customized test suites for molecular biology entity identification systems.
In: BioLINK 2004: Linking Biological Literature, Ontologies, and Databases: Tools
for Users, pp. 1-8. Association for Computational Linguistics (2004)
7. Bretonnel Cohen, K., Baumgartner Jr., W.A., Hunter, L.: Software testing and the
naturally occurring data assumption in natural language processing. In: Software
Engineering, Testing, and Quality Assurance for Natural Language Processing, pp.
23-30. Association for Computational Linguistics (2008)
8. Food and Drug Administration, US Department of Health and Human Services,
General principles of software validation: Final guidance for industry and FDA
staff (2002)
9. Hakenberg, J., Leaman, R., Vo, N.H., Jonnalagadda, S., Sullivan, R., Miller, C.,
Tari, L., Baral, C., Gonzalez, G.: Ecient extraction of protein-protein interactions
from full-text articles. IEEE/ACM Transactions on Computational Biology and
Bioinformatics (July 2010)
10. Hirschman, L., Mani, I.: Evaluation. In: Mitkov, R. (ed.) The Oxford Handbook
of Computational Linguistics, ch. 23. Oxford University Press (2003)
11. Hunter, L.E., Lu, Z., Firby, J., Baumgartner Jr., W.A., Johnson, H.L., Ogren, P.V.,
Bretonnel Cohen, K.: OpenDMAP: An open-source, ontology driven concept anal-
ysis engine, with applications to capturing knowledge regarding protein transport,
protein interactions and cell-specific gene expression. BMC Bioinformatics 9(78)
(2008)