Evaluation of a large-scale biomedical data annotation initiative

BMC Bioinformatics

Volumn 10, Issue SUPPL. 9, 2009, Pages

  Lacson, Ronilda ^a   Pitzer, Erik ^b   Hinske, Christian ^a   Galante, Pedro ^c   Ohno Machado, Lucila ^a  

^a HARVARD MEDICAL SCHOOL   (United States)

^b UNIVERSITY OF APPLIED SCIENCES UPPER AUSTRIA   (Austria)

^c LUDWIG INSTITUTE FOR CANCER RESEARCH   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

GENE EXPRESSION; SEMANTICS;

ANNOTATION STRUCTURES; CRITICAL VARIABLES; INFLAMMATORY BOWEL DISEASE; NATIONAL CANCER INSTITUTE; PARTIAL SIMILARITIES; RHEUMATOID ARTHRITIS; SYSTEMIC LUPUS ERYTHEMATOSUS; TYPE 1 DIABETES MELLITUS;

DISEASES;

BREAST CANCER; CLINICAL DATA REPOSITORY; COLON CANCER; CONFERENCE PAPER; CONTROLLED STUDY; DISEASE CLASSIFICATION; DISEASE COURSE; ENTERITIS; GENE EXPRESSION SYSTEM; HUMAN; INSULIN DEPENDENT DIABETES MELLITUS; MEDICAL INFORMATION SYSTEM; NATIONAL HEALTH ORGANIZATION; RANDOM SAMPLE; RELIABILITY; RHEUMATOID ARTHRITIS; SEMANTICS; SYSTEMIC LUPUS ERYTHEMATOSUS; TISSUE SECTION;

EID: 70349866711     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-S9-S10     Document Type: Conference Paper

References (16)

1. Barrett T, Edgar R. Reannotation of array probes at NCBI's GEO database. Nat Methods 2008, 5(2):117. 10.1038/nmeth0208-117b, 18235428.
2. Ikeo K, Ishi-i J, Tamura T, Gojobori T, Tateno Y. CIBEX: center for information biology gene expression database. C R Biol 2003, 326(10-11):1079-1082. 10.1016/j.crvi.2003.09.034, 14744116.
3. Parkinson H, Sarkans U, Shojatalab M, Abeygunawardena N, Contrino S, Coulson R, Farne A, Lara GG, Holloway E, Kapushesky M, Lilja P, Mukherjee G, Oezcimen A, Rayner T, Rocca-Serra P, Sharma A, Sansone S, Brazma A. ArrayExpress - a public repository for microarray gene expression data at the EBI. Nucleic Acids Res 2005, (33 Database):D553-5. 540010, 15608260.
4. Shah NH, Rubin DL, Supekar KS, Musen MA. Ontology-based annotation and query of tissue microarray data. AMIA Annu Symp Proc 2006, 709-713. 1839511, 17238433.
5. Dudley J, Butte AJ. Enabling integrative genomic analysis of high-impact human diseases through text mining. Pac Symp Biocomput 2008, 580-591.
6. Barrett T, Suzek TO, Troup DB, Wilhite SE, Ngau WC, Ledoux P. NCBI GEO: mining millions of expression profiles - database and tools. Nucleic Acids Res 2005, (33 Database):D562-D566. 539976, 15608262.
7. de Coronado S, Haber MW, Sioutos N, Tuttle MS, Wright LW. NCI Thesaurus: using science-based terminology to integrate cancer research results. Stud Health Technol Inform 2004, 107(Pt 1):33-37.
8. Lee HW, Park YR, Sim J, Park RW, Kim WH, Kim JH. The tissue microarray object model: a data model for storage, analysis, and exchange of tissue microarray experimental data. Arch Pathol Lab Med 2006, 130(7):1004-1013.
9. Lindberg DA, Humphreys BL, McCray AT. The Unified Medical Language System. Methods Inf Med 1993, 32(4):281-291.
10. Pitzer E, Lacson R, Hinske C, Kim J, Galante P, Ohno-Machado L. Large scale sample annotation of GEO. AMIA Summit in Translational Bioinformatics 2009,
11. Fan JW, Friedman C. Semantic classification of biomedical concepts using distributional similarity. J Am Med Inform Assoc 2007, 14(4):467-77. Epub 2007 Apr 25., 2244895, 17460124, 10.1197/jamia.M2314.
12. Wilbur WJ, Rzhetsky A, Shatkay H. New directions in biomedical text annotation: definitions, guidelines and corpus construction. BMC Bioinformatics 2006, 7:356. 1559725, 16867190, 10.1186/1471-2105-7-356.
13. Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, Evangelista C, Kim IF, Soboleva A, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Muertter RN, Edgar R. NCBI GEO: archive for high-throughput functional genomic data. Nucleic Acids Res 2009, (37 Database):D885-90. Epub 2008 Oct 21., 2686538, 18940857, 10.1093/nar/gkn764.
14. Pevner L, Hearst M. A critique and improvement of an evaluation metric for text segmentation. Association for Computational Linguistics 2002, 28(1).
15. Fung KW, Hole WT, Nelson SJ, Srinivasan S, Powell T, Roth L. Integrating SNOMED CT into the UMLS: an exploration of different views of synonymy and quality of editing. J Am Med Inform Assoc 2005, 12(4):486-94. Epub 2005 Mar 31., 1174894, 15802483, 10.1197/jamia.M1767.
16. Camon EB, Barrell DG, Dimmer EC, Lee V, Magrane M, Maslen J. An evaluation of GO annotation retrieval for BioCreAtIvE and GOA. BMC Bioinformatics 2005, 6(Suppl 1):S17. 1869009, 15960829, 10.1186/1471-2105-6-S1-S17.