Extension and integration of the gene ontology (GO): Combining GO vocabularies with external vocabularies

Genome Research

Volumn 12, Issue 12, 2002, Pages 1982-1991

  Hill, David P ^a   Blake, Judith A ^a   Richardson, Joel E ^a   Ringwald, Martin ^a  

^a JACKSON LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENE PRODUCT;

COMMUNITY; CONTROLLED STUDY; GENE ONTOLOGY; GENETIC DATABASE; GENETIC MANIPULATION; HEART DEVELOPMENT; HYPOTHESIS; INFORMATION PROCESSING; INFORMATION SYSTEM; LINGUISTICS; MAMMAL; MATHEMATICAL COMPUTING; METHODOLOGY; MOLECULAR BIOLOGY; NOMENCLATURE; PRIORITY JOURNAL; REVIEW; SEQUENCE DATABASE; SYSTEM ANALYSIS;

ANIMALS; DATABASES, GENETIC; GENE EXPRESSION; GENES; HEART; HUMANS; INFORMATION MANAGEMENT; MICE; SOFTWARE; TERMINOLOGY;

MAMMALIA;

EID: 0036907158     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.580102     Document Type: Review

References (26)

1. Abdelwahid, E., Pelliniemi, LJ., Nimikoski, H., Simell, O., Tuominen, J., Rahkonen, O., and Jokinen, E. 1999. Apoptosis in the pattern formation of the ventricular wall during mouse heart organogenesis. Anat. Rec. 256: 208-217.
2. Aho, A.V., Hopcroft, J.E., and Ullman, J.D. 1983. Directed graphs. In Data structures and algorithms, pp. 219-221. Addison-Wesley, Reading, MA.
3. Ashburner, M. and Lewis, S. 2002. On ontologies for biologists: The Gene Ontology-Uncoupling the web. In In silico biology. Novartis Symposium (in press).
4. Bard, J.B.L., Kaufman, M.H., Dubreuil, C., Brune, R.M., Burger, A., Baldock, R., and Davidson, D.R. 1998. An internet-accessible database of mouse developmental anatomy based on a systematic nomenclature. Mech. Dev. 74: 111-120.
5. Berman, J.J. and Moore, G.W. 1996. SNOMED-encoded surgical pathology databases: A tool for epidemiologic investigation. Mod. Pathol. 9: 944-950.
6. Biben, C. and Harvey, R.P. 1997. Homeodomain factor Nkx2-5 controls left/right asymmetric expression of bHLH gene eHand during murine heart development. Genes & Dev. 11: 1357-1369.
7. Eferl, R., Sibilia, M., Hilberg, F., Fuchsbichler, A., Kufferath, I., Guertl, B., Zenz, R., Wagner, E.F., and Zatloukal, K. 1999. Functions of c-Jun in liver and heart development. J. Cell Biol. 145: 1049-1061.
8. The Gene Ontology Consortium. 2000. Gene Ontology: Tool for the unification of biology. Nat. Genet. 25: 25-29.
9. The Gene Ontology Consortium. 2001. Creating the gene ontology resource: Design and implementation. Genome Res. 11: 1425-1433.
10. Gimond, C., Baudoin, C., van der Neut, R., Kramer, D., Calafat, J., and Sonnenberg, A. 1998. Cre-loxP-mediated inactivation of the α6A integrin splice variant in vivo: Evidence for a specific functional role of α6A in lymphocyte migration but not in heart development. J. Cell Biol. 143: 253-266.
11. Huang, G.Y., Wessels, A., Smith, B.R., Linask, K.K., Ewart, J.L., and Lo, C.W. 1998. Alteration in connexin 43 gap junction gene dosage impairs conotruncal heart development. Dev. Biol. 198: 32-44.
12. Jaspard, B., Couffinhal, T., Dufourcq, P., Moreau, C., and Duplaa, C. 2000. Expression pattern of mouse sFRP-1 and mWnt-8 gene during heart morphogenesis. Mech. Dev. 90: 263-267.
13. Kaufman, M.H. and Bard, J.B.L. 1999. The heart and its associated vascular system. In The anatomical basis of mouse development, pp. 77-92. Academic Press, London.
14. Kern, M.J., Argao, E.A., and Potter, S.S. 1995. Homeobox genes and heart development. Trends Cardiovasc. Med. 5: 47-54.
15. King, T., Beddington, R.S., and Brown, N.A. 1998. The role of the brachyury gene in heart development and left-right specification in the mouse. Mech. Dev. 79: 29-37.
16. Kirby, M. 1997. The heart. In Embryos, genes and birth defects (ed. Peter Thorogood), pp. 231-250. J. Wiley, Chichester.
17. Lyons, G.E. 1996. Vertebrate heart development. Curr. Opin. Genet. Dev. 6: 454-460.
18. Musen, M.A. 1998. Domain ontologies in software engineering: Use of Protege with the EON architecture. Methods Inf. Med. 37: 540-550.
19. Pereira, F.A., Qiu, Y., Zhou, G., Tsai, M.J., and Tsai, S.Y. 1999. The orphan nuclear receptor COUP-TFII is required for angiogenesis and heart development. Genes & Dev. 13: 1037-1049.
20. Ringwald, M., Eppig, J.T., Begley, D.A., Corradi, J.P., McCright, I.J., Hayamizu, T.F., Hill, D.P., Kadin, J.A., and Richardson, J.E. 2001. The mouse gene expression database. Nucleic Acids Res. 29: 98-101.
21. Rugh, R. 1990. Circulatory system. In The mouse: Its reproduction and development, pp. 268-272. Oxford University Press, New York.
22. Sucov, H.M., Dyson, E., Gumeringer, C.L., Price, J., Chien, K.R., and Evans, R.M. 1994. RXR α mutant mice establish a genetic basis for vitamin A signaling in heart morphogenesis. Genes & Dev. 8: 1007-1018.
23. Swiderski, R.E., Reiter, R.S., Nishimura, D.Y., Alward, W.L., Kalenak, J.W., Searby, C.S., Stone, E.M., Sheffield, V.C., and Lin, J.J. 1999. Expression of the Mf1 gene in developing mouse hearts: Implication in the development of human congenital heart defects. Dev. Dyn. 216: 16-27.
24. Tanaka, M., Chen, Z., Bartunkova, S., Yamasaki, N., and Izumo, S. 1999. The cardiac homeobox gene Csx/Nkx2.5 lies genetically upstream of multiple genes essential for heart development. Development 126: 1269-1280.
25. Tevosian, S.G., Deconinck, A.E., Tanaka, M., Schinke, M., Litovsky, S.H., Izumo, S., Fujiwara, Y., and Orkin, S.H. 2000. FOG-2, a cofactor for GATA transcription factors, is essential for heart morphogenesis and development of coronary vessels from epicardium. Cell 101: 729-739.
26. Woldeyesus, M.T., Britsch, S., Riethmacher, D., Xu, L., Sonnenberg-Riethmacher, E., Abou-Rebyeh, F., Harvey, R., Caroni, P., and Birchmeier. C. 1999. Peripheral nervous system defects in erbB2 mutants following genetic rescue of heart development. Genes & Dev. 13: 2538-2548.