N. H. Shah, A. P. Chiang, A. J. Butte, R. Chen, and M. A. Musen, Ontology-driven indexing of public datasets for translational bioinformatics, BMC Bioinformatics, vol.10, issue.Suppl 2, 2008.
DOI : 10.1186/1471-2105-10-S2-S1
URL : https://hal.archives-ouvertes.fr/hal-00492025

A. Butte and R. Chen, Finding disease-related genomic experiments within an international repository: first steps in translational bioinformatics, AMIA Annual Symp, p.106, 2006.

O. Bodenreider and R. Stevens, Bio-ontologies: current trends and future directions, Briefings in Bioinformatics, vol.7, issue.3, pp.256-274, 2006.
DOI : 10.1093/bib/bbl027

N. H. Shah, D. L. Rubin, K. S. Supekar, and M. A. Musen, Ontology-based Annotation and Query of Tissue Microarray Data, AMIA Annual Symp, pp.709-713, 2006.

R. Moskovitch, S. B. Martins, E. Behiri, A. Weiss, and Y. Shahar, A Comparative Evaluation of Full-text, Concept-based, and Context-sensitive Search, Journal of the American Medical Informatics Association, vol.14, issue.2, pp.164-174, 2007.
DOI : 10.1197/jamia.M1953

N. H. Shah, Biomedical Data/Content Acquisition, Encyclopedia of Database Systems, 2009.

W. J. Lee, L. Raschid, P. Srinivasan, N. H. Shah, D. Rubin et al., Using Annotations from Controlled Vocabularies to Find Meaningful Associations. 4 th Int, Work. on Data Integration in the Life Sciences, pp.264-279, 2007.

J. E. Caviedesa and J. J. Cimino, Towards the development of a conceptual distance metric for the UMLS, Journal of Biomedical Informatics, vol.37, issue.2, pp.77-85, 2004.
DOI : 10.1016/j.jbi.2004.02.001

C. Jonquet, M. A. Musen, and N. H. Shah, Help will be provided for this task: Ontology-Based Annotator Web Service, Res. Report, pp.2008-1317, 2008.

M. Dai, N. H. Shah, W. Xuan, M. A. Musen, S. J. Watson et al., An Efficient Solution for Mapping Free Text to Ontology Terms, AMIA Summit on Translational Bioinformatics, 2008.

W. Xuan, M. Dai, B. Mirel, B. Athey, S. J. Watson et al., Interactive Medline Search Engine Utilizing Biomedical Concepts and Data Integration, BioLINK SIG: Linking Literature, Information and Knowledge for Biology, pp.55-58, 2007.

N. Bhatia, N. H. Shah, D. L. Rubin, A. P. Chiang, and M. A. Musen, Comparing Concept Recognizers for Ontology-Based Indexing: MGREP vs, MetaMap. AMIA STB, 2009.

A. R. Aronson, Effective mapping of biomedical text to the UMLS Metathesaurus: the MetaMap program, AMIA Annual Symp, pp.17-21, 2001.

C. Jonquet, M. A. Musen, and N. H. Shah, A System for Ontology-Based Annotation of Biomedical Data. 5 th Int, Work. on Data Integration in the Life Sciences, pp.144-152, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00279660

Q. Zou, W. W. Chu, C. Morioka, G. H. Leazer, and H. Kangarloo, IndexFinder: A Method of Extracting Key Concepts from Clinical Texts for Indexing, AMIA Annual Symp, pp.763-767, 2003.

L. H. Reeve and H. Han, CONANN: An Online Biomedical Concept Annotator. 4 th Int, Work. on Data Integration in the Life Sciences, pp.264-279, 2007.
DOI : 10.1007/978-3-540-73255-6_21

N. C. Ide, R. F. Loane, and D. Demner-fushman, Essie: A Concept-based Search Engine for Structured Biomedical Text, Journal of the American Medical Informatics Association, vol.14, issue.3, pp.253-263, 2007.
DOI : 10.1197/jamia.M2233

S. Handschuh and S. Staab, Annotation for the Semantic Web, Frontiers in Artificial Intelligence and Applications, issue.96, 2003.