A system for ontology-based annotation of biomedical data

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 5109 LNBI, Issue , 2008, Pages 144-152

  Jonquet, Clement ^a   Musen, Mark A ^a   Shah, Nigam ^a  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Biomedical data integration; Biomedical ontologies; Concept recognition; Ontology based annotation; Semantic expansion

Indexed keywords

GENE EXPRESSION; HEALTH; INDEXING (OF INFORMATION); INFORMATION THEORY; INTEGRATION; MANAGEMENT; METADATA;

AUTOMATICALLY GENERATED; BIOMEDICAL DATA; BIOMEDICAL DATA INTEGRATION; BIOMEDICAL ONTOLOGIES; BIOMEDICAL RESOURCES; CONCEPT RECOGNITION; DATA INTEGRATIONS; GENE EXPRESSION DATA; LIFE SCIENCES; ONTOLOGY CONCEPTS; ONTOLOGY SEMANTICS; ONTOLOGY-BASED ANNOTATION; PROTOTYPE IMPLEMENTATIONS; SEARCH TOOLS; SEMANTIC EXPANSION; SYSTEM ARCHITECTURES; WORKFLOW PROCESSES;

ONTOLOGY;

EID: 48249140311     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-69828-9_14     Document Type: Conference Paper

References (14)

1. Butte, A.J., Kohane, I.: Creation and implications of a phenome-genome network. Nature Biotechnology 24(1), 55-62 (2006)
2. Butte, A., Chen, R.: Finding disease-related genomic experiments within an international repository: first steps in translational bioinformatics. In: American Medical Informatics Association Annual Symposium, AMIA 2006, Washington DC, USA, p. 106 (2006)
3. Spasic, I., et al.: Text mining and ontologies in biomedicine: making sense of raw text. Brief Bioinformatics 6(3), 239 (2005)
4. Moskovitch, R., Martins, S.B., Behiri, E., Weiss, A., Shahar, Y.: A Comparative Evaluation of Full-text, Concept-based, and Context-sensitive Search. American Medical Informatics Association 14(2), 164-174 (2007)
5. Sneiderman, C.A., et al.: Knowledge-based Methods to Help Clinicians Find Answers in Medline. American Medical Informatics Association 14(6), 772-780 (2007)
6. Shah, N.H., Rubin, D.L., Supekar, K.S., Musen, M.A.: Ontology-based Annotation and Query of Tissue Microarray Data. In: American Medical Informatics Association Annual Symposium, AMIA 2006, Washington DC, USA, pp. 709-713 (2006)
7. Khelif, K., Dieng-Kuntz, R., Barbry, P.: An ontology-based approach to support text mining and information retrieval in the biological domain. Universal Computer Science 13(12), 1881-1907 (2007), Special Issue on Ontologies and their Applications
8. Bhogal, J., Macfarlane, A., Smith, P.: A review of ontology based query expansion. Information Processing and Management 43, 866-886 (2007)
9. Lee, W.J., Raschid, L., Srinivasan, P., Shah, N., Rubin, D., Noy, N.: Using Annotations from Controlled Vocabularies to Find Meaningful Associations. In: Cohen-Boulakia, S., Tannen, V. (eds.) DILS 2007. LNCS (LNBI), vol. 4544, pp. 264-279. Springer, Heidelberg (2007)
10. Caviedesa, J.E., Cimino, J.J.: Towards the development of a conceptual distance metric for the UMLS. Biomedical Informatics 37(2), 77-85 (2004)
11. Ashburner, M., Sim, I., Hute, C.G., Solbrig, H., Storey, M.A., Smith, B., Day-Richter, J., Noy, N.F., Musen, M.A.: National Center for Biomedical Ontology: Advancing Biomedicine through Structured Organization of Scientific Knowledge. OMICS A Journal of Integrative Biology 10(2), 185-198 (2006)
12. Fielding, R.T., Taylor, R.N.: Principled Design of the Modern Web Architecture. ACM Transactions on Internet Technology 2(2), 115-150 (2002)
13. Xuan, W., Dai, M., Mirel, B., Athey, B., Watson, S., Meng, F.: Interactive Medline Search Engine Utilizing Biomedical Concepts and Data Integration. In: BioLINK SIG: Linking Literature, Information and Knowledge for Biology, Vienna, Austria (July 2007)
14. Aronson, A.R.: Effective mapping of biomedical text to the UMLS Metathesaurus: the MetaMap program. In: American Medical Informatics Association Annual Symposium, AMIA 2001, Washington DC, USA, pp. 17-21 (2001)