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Molecular symmetry and specialization of atomic connectivity by class-based reasoning of chemical structure

chemical structure and function. In the context of the emerging life science semantic web, we have previously investigated multiple strategies for the representation and reasoning of chemical structure, functional groups and chemical attributes using RDF, OWL, SWRL and so-called Description Graphs. Here, we continue our investigation on the representation of molecular structure using class-based approach to infer molecular symmetry and specialization of atomic connectivity. This work provides new design patterns towards representing and reasoning about structured objects.

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Molecular symmetry and specialization of atomic connectivity by class-based reasoning of chemical structure

  1. 1. Molecular symmetry and specialization of atomic connectivity by class-based reasoning of chemical structure Michel Dumontier, Ph.D. Associate Professor of Bioinformatics Department of Biology, School of Computer Science, Institute of Biochemistry, Carleton University Ottawa Institute of Systems Biology Ottawa-Carleton Institute of Biomedical Engineering Professeur Associé, Université Laval1 OWLED2012::Dumontier
  2. 2. chemical structure: molecules consist of atoms connected by bonds Carbon atom single bond Hydrogen atom double bond Nitrogen atom Oxygen atom caffeine2 OWLED2012::Dumontier
  3. 3. First attempt: class-based representation of chemical functional groups HydroxylGroup equivalentTo: CarbonGroup that (hasSingleBondWith some ( OxygenAtom that hasSingleBondWith some HydrogenAtom)) Describing chemical functional groups in OWL-DL for the classification of chemical compounds. Natalia Villanueva-Rosales and Michel Dumontier. OWL: Experiences and Directions (OWLED 2007).3 OWLED2012::Dumontier
  4. 4. automatic classification of chemical functional groups 28 OC4 OWLED2012::Dumontier
  5. 5. Problems 1. Descriptions started at an arbitrary central atom, so all descriptions needed to “specialize these” 2. Not possible to describe a chemical functional groups that are graph-like e.g. contains a cycle5 OWLED2012::Dumontier
  6. 6. OWL representation We really need to represent and reason over structured objects Without structure-based representation, 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 tree6 OWLED2012::Dumontier
  7. 7. Description Graphs • A decidable extension to OWL 2 allowing expression of complex structures as graphs within the ontology • strong separation requirement: atomic properties used as graph edges have to be different to those used in axioms in the main OWL ontology • Rules can be used to enhance OWL with the capacity to express if – then constructions • Using OWL, Description Graphs and Rules we could represent and reason over (classify) chemical structures at the class level. Representing Chemicals using OWL, Description Graphs and Rules. J Hastings, M Dumontier, D Hull, M Horridge, C Steinbeck, U Sattler, R Stevens, T Horne, and K Britz. OWLED 2010.7 OWLED2012::Dumontier
  8. 8. OWL + DG + Rules = Chemical Classification Before After8 OWLED2012::Dumontier
  9. 9. So, what can we do with just OWL? • generate connectivity descriptions for every atom to every other atom – overcome the central atom problem – exponential part list • reason at different levels of granularity – we could describe atoms in terms of 1. the types of atoms they are connected to 2. the exact set of atoms they are connected to 3. the only atoms they are connected to9 OWLED2012::Dumontier
  10. 10. Dataset A) butane, B) pentane, C) iso-butane, D) iso- pentane, E) cyclobutane and F) cyclohexane10 OWLED2012::Dumontier
  11. 11. SDF Method formalization SDF2OWL PHP-based OWLAPI OWL reasoning Protégé 4.2 HermiT Explanation Workbench Inference11 OWLED2012::Dumontier
  12. 12. Formalization separates the chemical graph from the molecule `fully connected atom M` `atom X from molecule A` equivalentTo equivalentTo `atom type` `fully connected atom M` and `has bond with` exactly 1 and `is component part of` `fully connected atom N` some `molecule Y` and ...12 OWLED2012::Dumontier
  13. 13. Symmetry 4 3 1 2 equivalence among 2,3 and 4 as every peripheral atom is connected to the central atom (1)13 OWLED2012::Dumontier
  14. 14. Symmetry 4 5 1 2 3 • For iso-pentane, we get equivalence between atoms 4 & 5 because they are both connected to atoms 1 • we get a different relationship – one of subsumption - between atoms 2 and 4 and atoms 2 and 514 OWLED2012::Dumontier
  15. 15. Atomic specialization 4 5 1 2 3 Basically, atom 2 has a bond to atom 1, as do atoms 4 and 5, but it also has a bond to atom 315 OWLED2012::Dumontier
  16. 16. Symmetry in butane 1 4 2 3 • Equivalence between atoms 1 & 3 as they both share connectivity to atoms 2 & 4, and vice versa. • No equivalence among all atoms, however.16 OWLED2012::Dumontier
  17. 17. But not in cyclohexane • No 2 atoms are connected to the same pair of atoms.17 OWLED2012::Dumontier
  18. 18. Conclusion • We investigated class-based representation where class descriptions consisted of fully qualified cardinality restrictions to other fully- connected atoms. • We found instances of equivalence (symmetry) and specialization (additional bonding), all within a single molecule • Next, we’ll be looking at reasoning across different molecules, but this requires some equivalence between atoms of different molecules.18 OWLED2012::Dumontier
  19. 19. dumontierlab.com michel_dumontier@carleton.ca Website: http://dumontierlab.com Presentations: http://slideshare.com/micheldumontier19 EBI2011::Dumontier