The RNA Ontology Consortium: An open invitation to the RNA community

RNA

Volumn 12, Issue 4, 2006, Pages 533-541

  Leontis, Neocles B ^a   Altman, Russ B ^b   Berman, Helen M ^c   Brenner, Steven E ^d   Brown, James W ^e   Engelke, David R ^f   Harvey, Stephen C ^g   Holbrook, Stephen R ^h   Jossinet, Fabrice ⁿ   Lewis, Suzanna E ⁱ   Major, François ^j   Mathews, David H ^k   Richardson, Jane S ^l   Williamson, James R ^m   Westhof, Eric ⁿ  

^a BOWLING GREEN STATE UNIVERSITY   (United States)

^b STANFORD UNIVERSITY MEDICAL CENTER   (United States)

^c RUTGERS UNIVERSITY   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e NORTH CAROLINA STATE UNIVERSITY   (United States)

^f UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

^g GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

^h LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

ⁱ UNIVERSITY OF CALIFORNIA   (United States)

^j UNIVERSITÉ DE MONTRÉAL   (Canada)

^k UNIVERSITY OF ROCHESTER MEDICAL CENTER   (United States)

^l DUKE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^m SCRIPPS RESEARCH INSTITUTE   (United States)

ⁿ INST DE BIOL MOLEC ET CELLULAIRE   (France)

more..

Author keywords

3D structure; Biological ontology; RNA; RNA motifs; Sequence alignments

Indexed keywords

RNA;

ARTICLE; COMPUTER ANALYSIS; COMPUTER PROGRAM; DATA BASE; ELECTRONICS; GENETIC LINKAGE; HUMAN; INFORMATION PROCESSING; INTERPERSONAL COMMUNICATION; MEDICAL RESEARCH; MEDICAL SOCIETY; PRIORITY JOURNAL; PROTEIN MOTIF; RNA SEQUENCE; RNA STRUCTURE; SCIENTIST; SEQUENCE ALIGNMENT; TAXONOMY;

DATABASES, GENETIC; INFORMATION DISSEMINATION; INTERNET; RNA; SEQUENCE ALIGNMENT; SOCIETIES;

EID: 33645472732     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.2343206     Document Type: Article

References (51)

1. Altman, R.B., Bada, M., Chai, X.J., Carillon, M.W., Chen, R.O., and Abernethy, N.F. 1999. RiboWEB: An ontology-based system for collaborative molecular biology. IEEE Intelligent Systems 14: 68-76.
2. Baader, F., Calvanese, D., McGuinness, D., Nardi, D., and Patel-Schneider, P. 2003. The description logic handbook: Theory, implementation and applications. Cambridge University Press, New York.
3. Bateman, A., Coin, L., Durbin, R., Finn, R.D., Hollich, V., Griffiths-Jones, S., Khanna, A., Marshall, M., Moxon, S., Sonnhammer, E.L., et al. 2004. The Pfam protein families database. Nucleic Acids Res. 32: D138-D141.
4. Berman, H.M. and Westbrook, J. 2003. The need for dictionaries, ontologies, and controlled vocabularies. OMICS 7: 9-10.
5. Berman, H.M., Olson, W.K., Beveridge, D.L., Westbrook, J., Gelbin, A., Demeny, T., Hsieh, S.H., Srinivasan, A.R., and Schneider, B. 1992. The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids. Biophys. J. 63: 751-759.
6. Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., and Bourne, P.E. 2000. The Protein Data Bank. Nucleic Acids Res. 28: 235-242.
7. Branden, C. and Tooze, J. 1999. Introduction to protein structure. Garland, New York.
8. Costa, M. and Michel, F. 1995. Frequent use of the same tertiary motif by self-folding RNAs. EMBO J. 14: 1276-1285.
9. 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.
10. Ferre-D'Amare, A.R. and Doudna, J.A. 1999. RNA folds: Insights from recent crystal structures. Annu. Rev. Biophys. Biomol. Struct. 28: 57-73.
11. Fitzgerald, P.M.D., Westbrook, J.D., Bourne, P.E., McMahon, B., Watenpaugh, K., and Berman, H.M. 2005. Macromolecular Dictionary (mmCIF). In International tables for crystallography (eds. S. Hall and B. McMahon), pp. 295-443. Springer, Dordrecht, The Netherlands.
12. Gautheret, D., Major, F., and Cedergren, R. 1990. Pattern searching/alignment with RNA primary and secondary structures: An effective descriptor for tRNA. Comput. Appl. Biosci. 6: 325-331.
13. _. 1993. Modeling the three-dimensional structure of RNA using discrete nucleotide conformational sets. J. Mol. Biol. 229: 1049-1064.
14. Gendron, P., Lemieux, S., and Major, F. 2001. Quantitative analysis of nucleic acid three-dimensional structures. J. Mol. Biol. 308: 919-936.
15. Griffiths-Jones, S., Moxon, S., Marshall, M., Khanna, A., Eddy, S.R., and Bateman, A. 2005. Rfam: Annotating non-coding RNAs in complete genomes. Nucleic Acids Res. 33: D121-D124.
16. Gruber, T.R. 1993. Ontolingua: A translation approach to portable ontologies. Knowledge Acquisition 5: 199-220.
17. Haarslev, V. and Möller, R. 2003. Racer: An OWL reasoning agent for the semantic web. In Proceedings of the International Workshop on Applications, Products and Services of Web-Based Support Systems, in conjunction with the 2003 IEEE/WIC International Conference on Web Intelligence, pp. 91-95. Halifax, Canada.
18. Hendler, J. 2003. Communication. Science and the semantic web. Science 299: 520-521.
19. Hershkovitz, E., Tannenbaum, E., Howerton, S.B., Sheth, A., Tannenbaum, A., and Williams, L.D. 2003. Automated identification of RNA conformational motifs: Theory and application to the HM LSU 23S rRNA. Nucleic Acids Res. 31: 6249-6257.
20. Hoffmann, B., Mitchell, G.T., Gendron, P., Major, F., Andersen, A.A., Collins, R.A., and Legault, P. 2003. NMR structure of the active conformation of the Varkud satellite ribozyme cleavage site. Proc. Natl. Acad. Sci. 100: 7003-7008.
21. Holbrook, S.R. 2005. RNA structure: The long and the short of it. Curr. Opin. Struct. Biol. 15: 302-308.
22. Horrocks, I. 1998. Using an expressive description logic: FaCT or fiction? In Proceedings of the Sixth International Conference on the Principles of Knowledge Representation and Reasoning. Trento, Italy.
23. Horrocks, I., Patel-Schneider, P.F., and van Harmelen, F. 2003. From SHIQ and RDF to OWL: The making of a web ontology language. J. Web Semantics 1: 7-26.
24. Kumar, A., Smith, B., and Novotny, D. 2005. Biomedical informatics and granularity. Comp. Funct. Genomics 5: 501-508.
25. Lee, J.C. and Gutell, R.R. 2004. Diversity of base-pair conformations and their occurrence in rRNA structure and RNA structural motifs. J. Mol. Biol. 344: 1225-1249.
26. Lemieux, S. and Major, F. 2002. RNA canonical and non-canonical base pairing types: A recognition method and complete repertoire. Nucleic Acids Res. 30: 4250-4263.
27. Leontis, N.B. and Westhof, E. 2001. Geometric nomenclature and classification of RNA base pairs. RNA 7: 499-512.
28. _. 2003. Analysis of RNA motifs. Curr. Opin. Struct. Biol. 13: 300-308.
29. Leontis, N.B., Stombaugh, J., and Westhof, E. 2002. The non-Watson-Crick base pairs and their associated isostericity matrices. Nucleic Acids Res. 30: 3497-3531.
30. Lewis, S.E. 2005. Gene Ontology: Looking backwards and forwards. Genome Biol. 6: 103.
31. Luciano, J.S. 2005. PAX of mind for pathway researchers. Drug Discov. Today 10: 937-942.
32. Major, F. and Thibault, P. 2005. Computer modeling of RNA 3D structure. In Encyclopedia of molecular biology and molecular medicine (ed. R.A. Meyers), pp. 605-636. VCH Publishers, Inc., New York.
33. Major, F., Turcotte, M., Gautheret, D., Lapalme, G., Fillion, E., and Cedergren, R. 1991. The combination of symbolic and numerical computation for three-dimensional modeling of RNA. Science 253: 1255-1260.
34. Major, F., Lemieux, S., Larose, M., and Thibault, P. 2005. Modelling RNA three-dimensional structure by combining short nucleotide interaction cycles. Eur. Biophys. J. 34: 560.
35. Moore, P.B. 1999. Structural motifs in RNA. Annu. Rev. Biochem. 68: 287-300.
36. Murray, L.J., Arendall III, W.B., Richardson, D.C., and Richardson, J.S. 2003. RNA backbone is rotameric. Proc. Natl. Acad. Sci. 100: 13904-13909.
37. Musen, M.A. 1992. Dimensions of knowledge sharing and reuse. Comput. Biomed. Res. 25: 435-467.
38. Neumann, E. 2005. A life science Semantic Web: Are we there yet? Sci. STKE http://stke.sciencemag.stke.com.
39. Noller, H.F. 2005. RNA structure: Reading the ribosome. Science 309: 1508-1514.
40. Noy, N.F. and McGuinness, D.L. 2001. "Ontology development 101: A guide to creating your first ontology." Stanford Knowledge Systems Laboratory Technical Report KSL-01-05/Stanford Medical Informatics Technical Report SMI-2001-0880, Stanford University, Stanford, CA.
41. Noy, N.F., Crubezy, M., Fergerson, R.W., Knublauch, H., Tu, S.W., Vendetti, J., and Musen, M.A. 2003. Protege-2000: An open-source ontology-development and knowledge-acquisition environment. AMIA Annu. Symp. Proc. 2003: 953.
42. Schneider, B., Zdenek, M., and Berman, H.M. 2004. RNA conformational classes. Nucleic Acids Res. 32: 1666-1677.
43. Smith, B. 2004a. Beyond concepts: Ontology as reality representation. In Proceedings of FOIS 2004 International Conference on Formal Ontology and Information Systems (eds. A. Varzi and L. Vieu). IOS Press, Amsterdam.
44. _. 2004b. The logic of biological classification and the foundations of biomedical ontology. In Invited papers from the 10th International Conference in Logic Methodology and Philosophy of Science (ed. D. Westerstahl). Elsevier, North-Holland.
45. Smith, B., Ceusters, W., Klagges, B., Kohler, J., Kumar, A., Lomax, J., Mungall, C., Neuhaus, F., Rector, A.L., and Rosse, C. 2005. Relations in biomedical ontologies. Genome Biol. 6: R46.
46. Stevens, R., Goble, C.A., and Bechhofer, S. 2000. Ontology-based knowledge representation for bioinformatics. Brief. Bioinform. 1: 398-414.
47. Thompson, J.D., Holbrook, S.R., Katoh, K., Koehl, P., Moras, D., Westhof, E., and Poch, O. 2005. MAO: A Multiple Alignment Ontology for nucleic acid and protein sequences. Nucleic Acids Res. 33: 4164-4171.
48. Wadley, L.M. and Pyle, A.M. 2004. The identification of novel RNA structural motifs using COMPADRES: An automated approach to structural discovery. Nucleic Acids Res. 32: 6650-6659.
49. Waugh, A., Gendron, P., Altman, R., Brown, J.W., Case, D., Gautheret, D., Harvey, S.C., Leontis, N., Westbrook, J., Westhof, E., et al. 2002. RNAML: A standard syntax for exchanging RNA information. RNA 8: 707-717.
50. Westbrook, J., Ito, N., Nakamura, H., Henrick, K., and Berman, H.M. 2005. PDBML: The representation of archival macromolecular structure data in XML. Bioinformatics 21: 988-992.
51. Whirl-Carrillo, M., Gabashvili, I.S., Bada, M., Banatao, D.R., and Altman, R.B. 2002. Mining biochemical information: Lessons taught by the ribosome. RNA 8: 279-289.