The gene ontology (GO) project in 2006

Nucleic Acids Research

Volumn 34, Issue , 2006, Pages D322-D326

  Harris, Midori A ^a   Clark, Jennifer I ^a   Ireland, Amelia ^a   Lomax, Jane ^a   Ashburner, Michael ^b   Collins, Russell ^b   Eilbeck, Karen ^c   Lewis, Suzanna ^c   Mungall, Chris ^c   Richter, John ^c   Rubin, Gerald M ^c   Shu, ShengQiang ^c   Blake, Judith A ^d   Bult, Carol J ^d   Diehl, Alexander D ^d   Dolan, Mary E ^d   Drabkin, Harold J ^d   Eppig, Janan T ^d   Hill, David P ^d   Ni, Li ^d   Ringwald, Martin ^d   Balakrishnan, Rama ^e   Binkley, Gail ^e   Michael Cherry, J ^e   Christie, Karen R ^e   Costanzo, Maria C ^e   Dong, Qing ^e   Engel, Stacia R ^e   Fisk, Dianna G ^e   Hirschman, Jodi E ^e   Hitz, Benjamin C ^e   Hong, Eurie L ^e   Lane, Christopher ^e   Miyasato, Stuart ^e   Nash, Robert ^e   Sethuraman, Anand ^e   Skrzypek, Marek ^e   Theesfeld, Chandra L ^e   Weng, Shuai ^e   Botstein, David ^f   Dolinski, Kara ^f   Oughtred, Rose ^f   Berardini, Tanya ^g   Mundodi, Suparna ^g   Rhee, Seung Y ^g   Apweiler, Rolf ^h   Barrell, Daniel ^h   Camon, Evelyn ^h   Dimmer, Emily ^h   Mulder, Nicola ^h   Chisholm, Rex ⁱ   Fey, Petra ⁱ   Gaudet, Pascale ⁱ   Kibbe, Warren ⁱ   Pilcher, Karen ⁱ   Bastiani, Carol A ^j   Kishore, Ranjana ^j   Schwarz, Erich M ^j   Sternberg, Paul ^j   Van Auken, Kimberly ^j   Gwinn, Michelle ^k   Hannick, Linda ^k   Wortman, Jennifer ^k   Aslett, Martin ^l   Berriman, Matthew ^l   Wood, Valerie ^l   Bromberg, Susan ^m   Foote, Cindy ^m   Jacob, Howard ^m   Pasko, Dean ^m   Petri, Victoria ^m   Reilly, Dorothy ^m   Seiler, Kathy ^m   Shimoyama, Mary ^m   Smith, Jennifer ^m   Twigger, Simon ^m   Jaiswal, Pankaj ⁿ   Seigfried, Trent ^o   Collmer, Candace ^p   Howe, Doug ^q   Westerfield, Monte ^q   more..

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d JACKSON LABORATORY   (United States)

^e STANFORD UNIVERSITY   (United States)

^f PRINCETON UNIVERSITY   (United States)

^g GEOPHYSICAL LABORATORY   (United States)

^h EBI   (United Kingdom)

ⁱ NORTHWESTERN UNIVERSITY   (United States)

^j CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

^k Institute for Genome Research   (United States)

^l WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^m MEDICAL COLLEGE OF WISCONSIN   (United States)

ⁿ Cornell University ^*  (United States)

^o IOWA STATE UNIVERSITY   (United States)

^p WELLS COLLEGE   (United States)

^q UNIVERSITY OF OREGON   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOLOGIST; CONTROLLED VOCABULARY; GENE ONTOLOGY; GENOME; HUMAN; COMPUTER INTERFACE; COMPUTER PROGRAM; DATA BASE; GENE; GENE EXPRESSION; GENETIC DATABASE; INTERNET; LINGUISTICS; QUALITY CONTROL; SEQUENCE ANALYSIS; STANDARD;

DATABASE MANAGEMENT SYSTEMS; DATABASES, GENETIC; GENE EXPRESSION; GENES; INTERNET; QUALITY CONTROL; SEQUENCE ANALYSIS; SOFTWARE; USER-COMPUTER INTERFACE; VOCABULARY, CONTROLLED;

EID: 33644875286     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkj021     Document Type: Article

References (36)

1. Gruber,T.R. (1993) A translation approach to portable ontology specifications. Knowl. Acq., 5, 199-220.
2. Jones,D.M. and Paton,R. (1999) Toward principles for the representation of hierarchical knowledge in formal ontologies. Data Knowl. Eng., 31, 99-113.
3. Stevens,R., Goble,C.A. and Bechhofer,S. (2000) Ontology-based knowledge representation for bioinformatics. Brief. Bioinform., 1, 398-414.
4. Schulze-Kremer,S. (2002) Ontologies for molecular biology and bioinformatics. In Silico Biol., 2, 179-193.
5. The Gene Ontology Consortium (2000) Gene Ontology: tool for the unification of biology. Nature Genet., 25, 25-29.
6. The Gene Ontology Consortium (2001) Creating the Gene Ontology resource: design and implementation. Genome Res., 11, 1425-1433.
7. Blake,J.A. and Harris,M.A. (2003) The Gene Ontology project: structured vocabularies for molecular biology and their application to genome and expression analysis. In Baxevanis,A.D., Davison,D.B., Page,R.D.M., Petsko,G.A., Stein,L.D. and Stormo,G. (eds), Current Protocols in Bioinformatics. John Wiley & Sons, New York.
8. The Gene Ontology Consortium (2004). The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res., 32, D258-D261.
9. Harris,M.A., Lomax,J., Ireland,A. and Clark,J.I. (2005) The Gene Ontology project. In Subramaniam,S. (ed.), Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. John Wiley & Sons, New York.
10. Lewis,S.E. (2005) Gene Ontology: looking backwards and forwards. Genome Biol., 6, 103.
11. Eilbeck,K. and Lewis,S.E. (2004) Sequence Ontology annotation guide. Comp. Funct. Genomics, 5, 642-647.
12. Dolan,M.E., Ni,L., Camon,E. and Blake,J.A. (2005) A procedure for assessing GO annotation consistency. Bioinformatics, 21 (Suppl. 1), i136-i143.
13. Camon,E.B., Barrell,D.G., Dimmer,E.C., Lee,V., Magrane,M., Maslen,J., Binns,D. and Apweiler,R. (2005) An evaluation of GO annotation retrieval for BioCreAtIvE and GOA. BMC Bioinformatics, 6 (Suppl. 1), S17.
14. Camon,E., Magrane,M., Barrell,D., Lee,V., Dimmer,E., Maslen,J., Binns,D., Harte,N., Lopez,R. and Apweiler,R. (2004) The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology. Nucleic Acids Res., 32, D262-D266.
15. Mungall,C.J. (2005) Obol: integrating language and meaning in bio-ontologies. Comp. Funct. Genomics, 5, 509-520.
16. Khatri,P. and Draghici,S. (2005) Ontological analysis of gene expression data: current tools, limitations, and open problems. Bioinformatics, 21, 3587-3595.
17. King,O.D., Foulger,R.E., Dwight,S.S., White,J.V. and Roth,F.P. (2003) Predicting gene function from patterns of annotation. Genome Res., 13, 896-904.
18. Demir,E., Babur,O., Dogrusoz,U., Gursoy,A., Ayaz,A., Gulesir,G., Nisanci,G. and Cetin-Atalay,R. (2004) An ontology for collaborative construction and analysis of cellular pathways. Bioinformatics, 20, 349-356.
19. Perez-Iratxeta,C., Bork,P. and Andrade,M.A. (2002) Association of genes to genetically inherited diseases using data mining. Nature Genet., 31, 316-319.
20. Bodenreider,O. (2004) The Unified Medical Language System (UMLS): integrating biomedical terminology. Nucleic Acids Res., 32, D267-D270.
21. Lomax,J. and McCray,A.T. (2004) Mapping the Gene Ontology into the unified medical language system. Comp. Funct. Genomics, 4, 345-361.
22. Stevens,R., Wroe,C., Bechhofer,S., Lord,P., Rector,A. and Goble,C. (2003) Building ontologies in DAML + OIL. Comp. Funct. Genomics, 4, 133-141.
23. Lord,P., Stevens,R.D., Goble,C.A. and Horrocks,I. (2005) Description logics: OWL and DAML + OIL. In Subramaniam,S. (ed.), Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. John Wiley & Sons.
24. Wroe,C.J., Stevens,R., Goble,C.A. and Ashburner,M. (2003) A methodology to migrate the Gene Ontology to a description logic environment using DAML+OIL. Pac. Symp. Biocomput., 2003, 624-635.
25. Williams,J. and Andersen,W. (2003) Bringing ontology to the Gene Ontology. Comp. Funct. Genomics, 4, 90-93.
26. Yeh,I., Karp,P.D., Noy,N.F. and Altman,R.B. (2003) Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO). Bioinformatics, 19, 241-248.
27. Hirschman,L., Yeh,A., Blaschke,C. and Valencia,A. (2005) Overview of BioCreAtIvE: critical assessment of information extraction for biology. BMC Bioinformatics, 6 (Suppl. 1), S1.
28. Müller,H.-M., Kenny,E.E. and Sternberg,P.W. (2004) Textpresso: an ontology-based information retrieval and extraction system for biological literature. PLoS Biol., 2, e309.
29. Zeeberg,B.R., Feng,W., Wang,G., Wang,M.D., Fojo,A.T., Sunshine,M., Narasimhan,S., Kane,D.W., Reinhold,W.C., Lababidi,S. et al. (2003) GoMiner: a resource for biological interpretation of genomic and proteomic data. Genome Biol., 4, R28.
30. Zeeberg,B., Qin,H., Narasimhan,S., Sunshine,M., Cao,H., Kane,D., Reimers,M., Stephens,R., Bryant,D., Burt,S. et al. (2005) High-Throughput GoMiner, an 'industrial-strength' integrative Gene Ontology tool for interpretation of multiple-microarray experiments, with application to studies of Common Variable Immune deficiency (CVID). BMC Bioinformatics, 6, 168.
31. Gentleman,R.C., Carey,V.J., Bates,D.M., Bolstad,B., Dettling,M., Dudoit,S., Ellis,B., Gautier,L., Ge,Y., Gentry,J. et al. (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol., 5, R80.
32. Joshi-Tope,G., Gillespie,M., Vastrik,I., D'Eustachio,P., Schmidt,E., de Bono,B., Jassal,B., Gopinath,G.R., Wu,G.R., Matthews,L. et al. (2005) Reactome: a knowledgebase of biological pathways. Nucleic Acids Res., 33, D428-D432.
33. Smith,B., Ceusters,W., Klagges,B., Khler,J., Kumar,A., Lomax,J., Mungall,C., Neuhaus,F., Rector,A.L. and Rosse,C. (2005) Relations in biomedical ontologies. Genome Biol., 6, R46.
34. Eilbeck,K., Lewis,S.E., Mungall,C.J., Yandell,M., Stein,L., Durbin,R. and Ashburner,M. (2005) The Sequence Ontology: a tool for the unification of genome annotations. Genome Biol., 6, R44.
35. Stoeckert,C.J. and Parkinson,H. (2003) The MGED ontology: a framework for describing functional genomics experiments. Comp. Funct. Genomics, 4, 127-132.
36. Benson,D.A., Karsch-Mizrachi,I., Lipman,D.J., Ostell,J. and Wheeler,D.L. (2005) GenBank. Nucleic Acids Res., 33, D34-D38.