1. Satellite Workshop on RNA Ontology RNA 2005 Tenth Annual Meeting of the RNA Society Banff, May 23st and May 24rth

2. Is there a danger, in molecular biology, that the accumulation of data will get so far ahead of its assimilation into a conceptual framework that the data will eventually prove an encumbrance ? John MADDOX, 1988.

3. All science is either physics or stamp collecting. Rutherford.

4. The bacterial ribosome : 270 000 atoms (C,N, O, P) 55 proteins 3 RNA (4600 nucleotides)

5. Even with the knowledge of the quantum physics of water molecules, it would be impossible to deduce the laws of formation of waves in the sea. Ken WILSON.

6. How can we go beyond organizing data banks of Sequences,Structures,Motifs, Genomes ?

7. Are our concepts relevant ?

8. Towards a RNA ontology ?

9. Why do we bother about classification ? What are our aims ?

10. 2) Extract information about 3D folding; 1) Derive accurate & meaningful alignments; 3) Derive rules for RNA evolution; 4) Search genomes for non-coding RNAs.

12. Physical entity : base or base pair Attributes: three edges (W_C, H, S_E) Attribute: glycosidic angle (syn or anti) Non-physical entity : base pair relationship Attribute: interacting edges (ordered pair of edges) Attribute: orientations of glycosidic bonds (cis or trans)

13. Many other molecular attributes… Where to stop ?

14. Granularity within the Consortium 1.Tools for crystallographers -NDB tools -Jane Richardson (backbone) - Base pair families 2. Tools for the analysis, classification, and search of crystal structures - Backbone (Eli, Jane, …), SCOR - Annotate (Major), RNAview (NDB) - s2s (Jossinet), FR3D (Leontis)

15. Granularity within the Consortium 3.Tools for alignments -RFAM -s2s 4. Tools for 1D to 2D - Mfold, … - D. Mathews 5. Tools for 1D/2D to 3D - McSYM - Manip/Fragment

16. Comparisons of 3D structures Comparisons of sequences

17. The K-turn The C-motif

18. K-Turn

19. Sugar-edge Hoogsteen ACGU U A C G I1 I2 I1 I2 I1 I2 trans A CG U U A C G I1 (I2) I2 trans Sugar-edge I6 A CG U U A C G i2 I3 I4 i2 I1 I5 I2 cis I3 I2 I5I6 Watson-Crick 92 82 100 77 The K-turn motif

20. Watson-Crick I6 A CG U U A C G i2 I3 I4 i2 I1 I5 I2 cis I3 I2 I5I6 Watson-Crick Cis Watson-Crick/Watson-crick G85 C97 ACGU U A C G 7 (0) trans 0 (7) - - 0 (6) 801 (786) 0 (7) 0 (3) 6 (0) 11 (17) 0 (3) 3 (0) 92 82 100 77

21. Sugar-edge Hoogsteen ACGU U A C G I1 I2 I1 I2 I1 I2 trans G97 A80 ACGU U A C G 675 (673) 4 (4) 145 (145) trans - - 0 (2) A98 ACGU U A C G 583 (580) 126 (125) 113 (112) trans 0 (1) - 0 (3) 1 (1) 0 (1) 1 (0) 0 (3) 0 (1) 3 (0) G79 - Trans Hoogsteen/Sugar-edge 92 82 100 77 2 (0) 0 (2)

22. A CG U U A C G I1 (I2) I2 trans Sugar-edge A98 G81 ACGU U A C G 6 (6) trans - - 810 (807) 1 (1) 1 (4) 7 (7) 0 (3) 3 (0) 640 (641) 3 (2) A80 G94 ACGU U A C G 38 (38) trans - - 15 (15) 130 (130) 1 (1) Cis Sugar-edge/Sugar-edge 92 82 100 77

23. 375 390 372

24. Hoogsteen Watson-Crick ACGU U A C G I1 I4 I5 I4 I1I2 I3 trans A CG U U A C G I1 (I2) I2 trans Sugar-edge Watson-Crick I6 A CG U U A C G i2 I3 I4 i2 I1 I5 I2 cis I3 I2 I5I6 Watson-Crick The C motif (I3)I3 I5 I4(I4)I4(I4) I4 I2

25. I6 A CG U U A C G i2 I3 I4 i2 I1 I5 I2 cis I3 I2 I5I6 Watson-Crick The C motif 0 (1) A CG U A C G 0 (2) 0 (16) 328 (134) 2 (0) 445 (246) 0 (182) cis 0 (12) 0 (181) 0 (1) 0 (16) U 29 (1) 0 (12) - - 1 (1) G371 C390 ACG U A C G cis 0 (1) U 804 (801) - - 1 (0) U375 A389 0 (1) 0 (2) 0 (2) 0 (2)

26. The C motif A CG U A C G 29 (29) 328 (327) 2 (0) cis 3 (3) 0 (1) U 444 (444) 1 (1) - - C390 A374 A CG U U A C G I1 (I2) I2 trans Sugar-edge Watson-Crick (I3)I3 I5 I4(I4)I4(I4) 0 (1) 0 (2)

27. The C motif A CG U A C G 804 (803) 1 (0) cis 0 (1) U 1 (1) - - A389 C372 0 (1) Hoogsteen Watson-Crick ACGU U A C G I1 I4 I5 I4 I1I2 I3 trans I4 I2