1. RnaO.owl Colin Batchelor Royal Society of Chemistry, UK 2009-01-05

2. Outline RnaO and OBO RnaO and BFO Simple use cases for the ontology Relations for RnaO How far can we go?

3. RnaO and OBO Commitment to common upper ontology (BFO) Commitment to dividing responsibilities between ontologies: ChEBI for molecular parts (and relations?) SO for sequences GO for RNA function Leaving RnaO to concentrate on RNA…

4. Basic Formal Ontology (1) http://www.ifomis.org/bfo Object: “An independent continuant that is spatially extended, maximally self-connected and self- contained (the parts of a substance are not separated from each other by spatial gaps) and possesses an internal unity. The identity of substantial object entities is independent of that of other entities and can be maintained through time.”

5. Basic Formal Ontology (2) http://www.ifomis.org/bfo Fiat Object Part: “An independent continuant that is part of an object but is not demarcated by any physical discontinuities.”

6. Basic Formal Ontology (3) http://www.ifomis.org/bfo Site: “An independent continuant consisting of a characteristic spatial shape in relation to some arrangement of other continuant entities and of the medium which is enclosed in whole or in part by this characteristic spatial shape. Site entities are entities that can be occupied by other continuant entities.”

7. RNA and BFO http://www.ifomis.org/bfo Objects: RNA molecules Fiat Object Parts: Nucleotides, ribose rings, phosphate groups, nucleobases, nucleosides Sites: Backbone segments and their conformers

8. Simple use cases Classify base pairs according to the Leontis-Westhof scheme (easy) Identify motifs in 3d structures (hard) (Vaguer, but really the most important) Provide bridge between different representations

10. Relations for RnaO (1) Base pairing: pairsWith, pairsWithWW, pairsWithCWW Backbone bonding: fivePrimeTo, threePrimeTo, etc.

11. Relations for RnaO (2) Then: Family1BasePair = hasPart some Nucleobase and (pairsWithCWW some Nucleobase) (this works and classifies base pairings satisfactorily within the LW scheme)

12. Relations for RnaO (3) And: GNRA TetraloopMotif = hasPart some ( Nucleobase and fivePrimeTo some (G and fivePrimeTo some (Nucleobase and fivePrimeTo some (Nucleobase and fivePrimeTo some (A and fivePrimeTo some (Nucleobase and pairsWithCWW some Nucleobase) and pairsWithTHS some G))) and pairsWithTSH some A) and pairsWithCWW some Nucleobase) This is underdetermined and will find false positives. But how many?

13. How far can we go? We have a rudimentary ontology with many of the classes we will need for the full ontology. We have an alignment with BFO. We have a test case where reasoning works. But… we also have an appreciation of the limitations of OWL.