Representing chemicals using OWL, Description Graphs and Rules

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Objects can be said to be structured when their representation also contains their parts. While OWL in general can describe structured objects, description graphs are a recent, decidable extension to OWL which support the description of classes of structured objects whose parts are related in complex ways. Classes of chemical entities
such as molecules, ions and groups (parts of molecules) are often characterized by the way in which the constituent atoms of their instances are connected via chemical bonds. For chemoinformatics tools and applications, this internal structure is represented using chemical graphs. We here present a chemical knowledge base based on the standard chemical graph model using description graphs, OWL and rules. We include in our ontology chemical classes, groups, and molecules, together with their
structures encoded as description graphs. We show how role-safe rules can be used to determine parthood between groups and molecules based on the graph structures and to determine basic chemical properties. Finally, we investigate the scalability of the technology used through the development of an automatic utility to convert standard chemical graphs into description graphs, and converting a large number of diverse graphs obtained from a publicly available chemical database

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Representing chemicals using OWL, Description Graphs and Rules

  1. 1. Representing chemicalsusing OWL, Description Graphsand Rules<br />Janna Hastings, EBI, UKMichel Dumontier, Carleton University, CanadaDuncan Hull, EBI, UKMatthew Horridge, Manchester, UKChristoph Steinbeck, EBI, UKUlrike Sattler, Manchester, UKRobert Stevens, Manchester, UKTertia Hӧrne, University of South AfricaKatarina Britz, Meraka Institute, South Africa<br />OWLED2010:San Francisco:Representing chemicals using OWL, Description Graphs and Rules<br />
  2. 2. OWLED2010:San Francisco:Representing chemicals using OWL, Description Graphs and Rules<br />
  3. 3. Problem<br />We wish to represent and reason over structured objects<br /> i.e. their representation contains also their parts<br />OWLED2010:San Francisco:Representing chemicals using OWL, Description Graphs and Rules<br />
  4. 4. Chemical structures<br />single bond<br />Carbon atom<br />Hydrogen atom<br />double bond<br />Nitrogen atom<br />Oxygen atom<br />caffeineMoleculesconsist of atomsconnected by bonds<br />OWLED2010:San Francisco:Representing chemicals using OWL, Description Graphs and Rules<br />
  5. 5. Chemical ontology<br />Chemical ontology consists of chemical classes which can be defined by parts of structuresand/or properties of structures<br />carboxylic acid<br />if molecule has part<br />some carboxy group<br />cyclic molecule<br />if molecule has property cyclic, i.e. a self-connectedcyclic path exists through the molecule’s atoms<br />OWLED2010:San Francisco:Representing chemicals using OWL, Description Graphs and Rules<br />
  6. 6. OWL representation<br />Without structure, all parts must be explicitly asserted(combinatorial explosion for larger molecules)<br />But the structure of complex molecules breaks the OWL Tree Model requirement<br />does not have a model in the shape of a tree<br />OWLED2010:San Francisco:Representing chemicals using OWL, Description Graphs and Rules<br />
  7. 7. Description Graphs<br />A recent, decidable extension to OWL 2, allowing expression of complex structures as graphs within the ontology<br />A description graph consists of a set of labelled vertices and a set of directed edges<br />Each description graph has a main class which links the graph to the main OWL ontology<br />OWLED2010:San Francisco:Representing chemicals using OWL, Description Graphs and Rules<br />
  8. 8. Strong separation<br />In order to preserve decidability of knowledge bases enriched with description graphs,<br /> atomic properties used as graph edges have to be different to those used in axioms in the main OWL ontology<br />This is known as the strong separation requirement<br />OWLED2010:San Francisco:Representing chemicals using OWL, Description Graphs and Rules<br />
  9. 9. Rules<br />Enhance OWL with the capacity to express if – then constructions<br />Consist of ‘antecedent’ (if conditions) and ‘consequent’ (then result)<br />Antecedent and consequent are composed of conjunctions of atomic statements<br />OWLED2010:San Francisco:Representing chemicals using OWL, Description Graphs and Rules<br />
  10. 10. Goal<br />Can we represent chemical structures using OWL and Description Graphs?<br />Can we reason over the information encoded in chemical structures using OWL, Description Graphs and Rules?<br />OWLED2010:San Francisco:Representing chemicals using OWL, Description Graphs and Rules<br />
  11. 11. OWL ontology<br />OWLED2010:San Francisco:Representing chemicals using OWL, Description Graphs and Rules<br />
  12. 12. Chemical description graphs<br />Generated based on structures converted from a chemical database (ChEBI)<br />OWLED2010:San Francisco:Representing chemicals using OWL, Description Graphs and Rules<br />
  13. 13. Rules<br />Generated for properties, e.g. being cyclic<br />molecule(?x), atom(?a1), atom (?a2), atom(?a3), atom(?a4), bond(?b1), bond (?b2), bond(?b3), bond (?b4), has_atom(?x, ?a1), has_atom(?x, ?a2), has_atom(?x, ?a3), has_atom(?x, ?a4),has_bond(?a1, ?b1), has_bond(?a1, ?b4), has_bond(?a2, ?b1), has_bond(?a2, ?b2),has_bond(?a3, ?b2), has_bond(?a3, ?b3), has_bond(?a4, ?b3), has_bond(?a4, ?b4)-> cyclic_entity(?x)<br />cyclobutane<br />tetrahedrane<br />OWLED2010:San Francisco:Representing chemicals using OWL, Description Graphs and Rules<br />
  14. 14. Rules<br />Generated for parthood, e.g. carboxylic acid<br />molecule(?y), atom(?a0), oxygen_atom(?a1), carbon_atom(?a2), oxygen_atom (?a3), has_atom(?y, ?a0), has_atom (?y, ?a1), has_atom (?y, ?a2), has_atom (?y, ?a3), double_bond(?b0), single_bond (?b1), single_bond (?b2), has_bond(?a0, ?b2), has_bond(?a1, ?b1), has_bond(?a2, ?b0), has_bond(?a2, ?b1), has_bond(?a2, ?b2), has_bond(?a3, ?b0) -> carboxylic_acid(?y)<br />carboxylic acid<br />benzoicacid<br />benzoic acid has this part so: is a carboxylic acid<br />OWLED2010:San Francisco:Representing chemicals using OWL, Description Graphs and Rules<br />
  15. 15. Testing the reasoning<br />Can we use a reasoner to deduce the classification hierarchy based on the graphs and rules? <br />No asserted hierarchy between test classes and molecules with generated graphs<br />OWLED2010:San Francisco:Representing chemicals using OWL, Description Graphs and Rules<br />
  16. 16. Results<br />Inferred hierarchy shows classified molecules<br />OWLED2010:San Francisco:Representing chemicals using OWL, Description Graphs and Rules<br />
  17. 17. Testing the performance<br />How many molecules (description graphs) can we include in our knowledge base?<br />How does the reasoning task (classification) scale with respect to the number of graphs, both with and without rules in the knowledge base?<br />OWLED2010:San Francisco:Representing chemicals using OWL, Description Graphs and Rules<br />
  18. 18. Results<br />OWLED2010:San Francisco:Representing chemicals using OWL, Description Graphs and Rules<br />
  19. 19. Experiences<br />Difficult to debug<br />Tools support needs to be improved<br />Difficult to construct rules for properties which depend on all atoms or all bonds in a given molecule<br /> e.g. saturated -> all bonds in molecule are single<br />OWLED2010:San Francisco:Representing chemicals using OWL, Description Graphs and Rules<br />
  20. 20. Conclusion<br />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<br />Scalability of the reasoning with the rules is a concern<br />OWLED2010:San Francisco:Representing chemicals using OWL, Description Graphs and Rules<br />
  21. 21. Acknowledgements<br />Special thanks to KirillDegtyarenko, Stefan Schulz, Colin Batchelor, BirteGlimm and the ChEBI team<br />Funding: Meraka Institute, South Africa; BBSRC (BB/G022747/1); NSERC Discovery Grant<br />OWLED2010:San Francisco:Representing chemicals using OWL, Description Graphs and Rules<br />

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