Using Description Logics, Description Graphs and Rules for modelling chemical structures

1. Using Description Logics, Description Graphs and Rules for modelling chemical structures Janna Hastings (Masters student, European Bioinformatics Institute (EBI)) Arina Britz (Meraka) Tertia Hörne (Unisa) MOWS 2010

2. Outline • Complex chemical structures • Description Logics • Description graphs • Introduction of Rules • Research questions • Results • Conclusion MOWS 2010

3. Complex chemical structure Carbon atom single bond Hydrogen atom double bond Nitrogen atom Oxygen atom caffeineMoleculesconsist of atomsconnected by bonds MOWS 2010

4. OWL representation Without structure, all parts must be explicitly asserted(combinatorial explosion for larger molecules) But the structure of complex molecules breaks the OWL Tree Model requirement does not have a model in the shape of a tree MOWS 2010

5. Cyclic chemical structure • Tree model property does not allow for cyclic structures • DL extended with Description Graphs • Main class – link to the main ontology • Classes (concepts) – atoms • Properties (roles)– type of bond between atoms MOWS 2010

6. Knowledge Base • A simple ontology describing classes pertaining to chemical entities • Auto-generated DGs from structures in the CheEBI database • A set of DL-safe rules for structure-base classification MOWS 2010

7. OWL ontology Slim upper ontology developed for experiment MOWS 2010

8. Chemical description graphs Generated based on structures loaded from a chemical database MOWS 2010

9. DL-safe rules • Strong separation requirement: tree roles and graph roles • Rule body may only refer to graph roles (properties of the DG) • Consequent must be a known individual MOWS 2010

10. DL-safe rule (example) Molecule(M)  has_atom(M,A1)  …  has_atom (M,An)  Atom(A1)  …  Atom (An)  Bond(B1)  …  Bond(Bm)  has_bond(Ai1,Bj1)  …  has_bond(Ain,Bjm) → instanceOf(M,Class) MOWS 2010

11. Research questions • Can we represent chemical structures using OWL and Description Graphs? • Can we reason over the information encoded in chemical structures using OWL, Description Graphs and Rules? MOWS 2010

12. Reasoning • HermiT was used • Classification of chemical structures MOWS 2010

13. Testing the performance • How many molecules (description graphs) can we include in our knowledge base? • How does the reasoning task (classification) scale with respect to the number of graphs, both with and without rules in the knowledge base? MOWS 2010

14. Results MOWS 2010

15. Conclusion • Using OWL, Description Graphs and Rules we can represent chemical structures at the class level in our knowledge base and reason over the structural information • Strength: direct encoding of structures using rules • Weaknesses: Property separation requirement Scalability of reasoning with rules is a concern MOWS 2010

16. Acknowledgement – OWLED 2010 • Janna Hastings (use of slides) • Michel Dumontier (Carleton University, Canada) • Duncan Hull (EBI) • Matthew Horridge (University of Manchester) • Christoph Steinbeck (EBI) • Ulrike Sattler (University of Manchester) • Robert Stevens (University of Manchester)  MOWS 2010

17. Thank you! MOWS 2010