This Article Full Text Full Text (PDF) Alert me when this article is cited Alert me if a correction is posted Citation Map Services Email this article to a friend Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Kelso, J. Articles by Hide, W. Search for Related Content PubMed PubMed Citation Articles by Kelso, J. Articles by Hide, W. Social Bookmarking                   What's this?

Resources

eVOC: A Controlled Vocabulary for Unifying Gene Expression Data

¹ South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa ² Electric Genetics PTY Ltd. Bellville, South Africa ³ Office of Information Technology, Ludwig Institute for Cancer Research and Swiss Institute of Bioinformatics, Lausanne, Switzerland ⁴ Genetics and Genomics Research Institute, Imperial College Faculty of Medicine, Hammersmith Hospital, London, W12 0NN, UK ⁵ Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX37BN, UK

Expression data contribute significantly to the biological value of the sequenced human genome,providing extensive information about gene structure and the pattern of gene expression. ESTs,together with SAGE libraries and microarray experiment information,provide a broad and rich view of the transcriptome. However, it is difficult to perform large-scale expression mining of the data generated by these diverse experimental approaches. Not only is the data stored in disparate locations,but there is frequent ambiguity in the meaning of terms used to describe the source of the material used in the experiment. Untangling semantic differences between the data provided by different resources is therefore largely reliant on the domain knowledge of a human expert. We present here eVOC,a system which associates labelled target cDNAs for microarray experiments,or cDNA libraries and their associated transcripts with controlled terms in a set of hierarchical vocabularies. eVOC consists of four orthogonal controlled vocabularies suitable for describing the domains of human gene expression data including Anatomical System,Cell Type,Pathology and Developmental Stage. We have curated and annotated 7016 cDNA libraries represented in dbEST,as well as 104 SAGE libraries,with expression information,and provide this as an integrated,public resource that allows the linking of transcripts and libraries with expression terms. Both the vocabularies and the vocabulary-annotated libraries can be retrieved from http://www.sanbi.ac.za/evoc/. Several groups are involved in developing this resource with the aim of unifying transcript expression information.

⁶ Present address: Molecular Genetics/Fugu informatics, Institute of Molecular and Cell Biology, Singapore.

⁷ Corresponding author.
E-MAIL winhide{at}sanbi.ac.za; FAX 27-21-959-2512.

[Supplemental material is available online at www.genome.org.]

CiteULike    Connotea    Del.icio.us    Digg    Reddit    Technorati    What's this?

This article has been cited by other articles:

				T. Castrignano, M. D'Antonio, A. Anselmo, D. Carrabino, A. D'Onorio De Meo, A. M. D'Erchia, F. Licciulli, M. Mangiulli, F. Mignone, G. Pavesi, et al. ASPicDB: A database resource for alternative splicing analysis Bioinformatics, May 15, 2008; 24(10): 1300 - 1304. [Abstract] [Full Text] [PDF]

				A. C. Tzika, R. Helaers, Y. Van de Peer, and M. C. Milinkovitch MANTIS: a phylogenetic framework for multi-species genome comparisons Bioinformatics, January 15, 2008; 24(2): 151 - 157. [Abstract] [Full Text] [PDF]

				I. Scheinin, S. Myllykangas, I. Borze, T. Bohling, S. Knuutila, and J. Saharinen CanGEM: mining gene copy number changes in cancer Nucleic Acids Res., January 11, 2008; 36(suppl_1): D830 - D835. [Abstract] [Full Text] [PDF]

				O. L. Griffith, S. B. Montgomery, B. Bernier, B. Chu, K. Kasaian, S. Aerts, S. Mahony, M. C. Sleumer, M. Bilenky, M. Haeussler, et al. ORegAnno: an open-access community-driven resource for regulatory annotation Nucleic Acids Res., January 11, 2008; 36(suppl_1): D107 - D113. [Abstract] [Full Text] [PDF]

				G. Spudich, X. M. Fernandez-Suarez, and E. Birney Genome browsing with Ensembl: a practical overview Brief Funct Genomic Proteomic, October 29, 2007; (2007) elm025v1. [Abstract] [Full Text] [PDF]

				K. J. Gaulton, K. L. Mohlke, and T. J. Vision A computational system to select candidate genes for complex human traits Bioinformatics, May 1, 2007; 23(9): 1132 - 1140. [Abstract] [Full Text] [PDF]

				M. L. Tress, P. L. Martelli, A. Frankish, G. A. Reeves, J. J. Wesselink, C. Yeats, P. l. Olason, M. Albrecht, H. Hegyi, A. Giorgetti, et al. The implications of alternative splicing in the ENCODE protein complement PNAS, March 27, 2007; 104(13): 5495 - 5500. [Abstract] [Full Text] [PDF]

				S. Tang, Z. Zhang, S. L. Tan, M.-H. E. Tang, A. P. Kumar, S. K. Ramadoss, and V. B. Bajic KBERG: KnowledgeBase for Estrogen Responsive Genes Nucleic Acids Res., January 12, 2007; 35(suppl_1): D732 - D736. [Abstract] [Full Text] [PDF]

				C. Seoighe, V. Nembaware, and K. Scheffler Maximum likelihood inference of imprinting and allele-specific expression from EST data Bioinformatics, December 15, 2006; 22(24): 3032 - 3039. [Abstract] [Full Text] [PDF]

				R. A. George, J. Y. Liu, L. L. Feng, R. J. Bryson-Richardson, D. Fatkin, and M. A. Wouters Analysis of protein sequence and interaction data for candidate disease gene prediction Nucleic Acids Res., November 14, 2006; 34(19): e130 - e130. [Abstract] [Full Text] [PDF]

				P. Khatri, V. Desai, A. L. Tarca, S. Sellamuthu, D. E. Wildman, R. Romero, and S. Draghici New Onto-Tools: Promoter-Express, nsSNPCounter and Onto-Translate. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W626 - W631. [Abstract] [Full Text] [PDF]

				S. B. Montgomery, O. L. Griffith, M. C. Sleumer, C. M. Bergman, M. Bilenky, E. D. Pleasance, Y. Prychyna, X. Zhang, and S. J. M. Jones ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation Bioinformatics, March 1, 2006; 22(5): 637 - 640. [Abstract] [Full Text] [PDF]

				N. Vinckenbosch, I. Dupanloup, and H. Kaessmann Evolutionary fate of retroposed gene copies in the human genome PNAS, February 28, 2006; 103(9): 3220 - 3225. [Abstract] [Full Text] [PDF]

				S. Stamm, J.-J. Riethoven, V. Le Texier, C. Gopalakrishnan, V. Kumanduri, Y. Tang, N. L. Barbosa-Morais, and T. A. Thanaraj ASD: a bioinformatics resource on alternative splicing Nucleic Acids Res., January 1, 2006; 34(suppl_1): D46 - D55. [Abstract] [Full Text] [PDF]

				A. Mehrle, H. Rosenfelder, I. Schupp, C. del Val, D. Arlt, F. Hahne, S. Bechtel, J. Simpson, O. Hofmann, W. Hide, et al. The LIFEdb database in 2006 Nucleic Acids Res., January 1, 2006; 34(suppl_1): D415 - D418. [Abstract] [Full Text] [PDF]

				O. Ogasawara, M. Otsuji, K. Watanabe, T. Iizuka, T. Tamura, T. Hishiki, S. Kawamoto, and K. Okubo BodyMap-Xs: anatomical breakdown of 17 million animal ESTs for cross-species comparison of gene expression Nucleic Acids Res., January 1, 2006; 34(suppl_1): D628 - D631. [Abstract] [Full Text] [PDF]

				X. Mao, T. Cai, J. G. Olyarchuk, and L. Wei Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary Bioinformatics, October 1, 2005; 21(19): 3787 - 3793. [Abstract] [Full Text] [PDF]

				Z. Kan, P. W. Garrett-Engele, J. M. Johnson, and J. C. Castle Evolutionarily conserved and diverged alternative splicing events show different expression and functional profiles Nucleic Acids Res., September 29, 2005; 33(17): 5659 - 5666. [Abstract] [Full Text] [PDF]

				The FANTOM Consortium, P. Carninci, T. Kasukawa, S. Katayama, J. Gough, M. C. Frith, N. Maeda, R. Oyama, T. Ravasi, B. Lenhard, et al. The Transcriptional Landscape of the Mammalian Genome Science, September 2, 2005; 309(5740): 1559 - 1563. [Abstract] [Full Text] [PDF]

				V. B. Bajic, M. Veronika, P. S. Veladandi, A. Meka, M.-W. Heng, K. Rajaraman, H. Pan, and S. Swarup Dragon Plant Biology Explorer. A Text-Mining Tool for Integrating Associations between Genetic and Biochemical Entities with Genome Annotation and Biochemical Terms Lists Plant Physiology, August 1, 2005; 138(4): 1914 - 1925. [Abstract] [Full Text] [PDF]

				P. Khatri, S. Sellamuthu, P. Malhotra, K. Amin, A. Done, and S. Draghici Recent additions and improvements to the Onto-Tools Nucleic Acids Res., July 1, 2005; 33(suppl_2): W762 - W765. [Abstract] [Full Text] [PDF]

				N. Kirschbaum-Slager, R. B. Parmigiani, A. A. Camargo, and S. J. de Souza Identification of human exons overexpressed in tumors through the use of genome and expressed sequence data Physiol Genomics, May 11, 2005; 21(3): 423 - 432. [Abstract] [Full Text] [PDF]

				T.-H. Kim, Y.-J. Jeon, W.-Y. Kim, and H.-S. Kim HESAS: HERVs Expression and Structure Analysis System Bioinformatics, April 15, 2005; 21(8): 1699 - 1700. [Abstract] [Full Text] [PDF]

				S. Orchard, H. Hermjakob, and R. Apweiler Annotating the Human Proteome Mol. Cell. Proteomics, April 1, 2005; 4(4): 435 - 440. [Abstract] [Full Text] [PDF]

				N. Tiffin, J. F. Kelso, A. R. Powell, H. Pan, V. B. Bajic, and W. A. Hide Integration of text- and data-mining using ontologies successfully selects disease gene candidates Nucleic Acids Res., March 14, 2005; 33(5): 1544 - 1552. [Abstract] [Full Text] [PDF]

				V. Curwen, E. Eyras, T. D. Andrews, L. Clarke, E. Mongin, S. M.J. Searle, and M. Clamp The Ensembl Automatic Gene Annotation System Genome Res., May 1, 2004; 14(5): 942 - 950. [Abstract] [Full Text] [PDF]

				E. Eyras, M. Caccamo, V. Curwen, and M. Clamp ESTGenes: Alternative Splicing From ESTs in Ensembl Genome Res., May 1, 2004; 14(5): 976 - 987. [Abstract] [Full Text] [PDF]

				A. Kasprzyk, D. Keefe, D. Smedley, D. London, W. Spooner, C. Melsopp, M. Hammond, P. Rocca-Serra, T. Cox, and E. Birney EnsMart: A Generic System for Fast and Flexible Access to Biological Data Genome Res., January 1, 2004; 14(1): 160 - 169. [Abstract] [Full Text] [PDF]

				T. A. Thanaraj, S. Stamm, F. Clark, J.-J. Riethoven, V. Le Texier, and J. Muilu ASD: the Alternative Splicing Database Nucleic Acids Res., January 1, 2004; 32(90001): D64 - 69. [Abstract] [Full Text] [PDF]