Presented at the 2nd ChEBI User Group Workshop. Discusses some of the difficulties encountered in the project which aims to classify chemicals in the ChEBI ontology automatically based on their structures.

1. Automatic classification, logical definitions Janna Hastings, EBI Cheminformatics and Metabolism 2nd ChEBI User Group Workshop, 24 June 2010

3. ChEBI ontology 20.10.10 The ChEBI ontology contains a large asserted is-a hierarchy of chemical classes and compounds Each chemical class is clearly defined in natural language

8. OWL Reasoning ChEBI ontology 20.10.10 neopentane has_atom some ‘carbon atom’ has_atom some ‘hydrogen atom’ neopentane subClassOf (is_a) ‘ hydrocarbon molecular entity’

12. Pre-coordination vs. post-coordination ChEBI ontology 20.10.10

13. Logically defining chemical classes 20.10.10 Goal: transform the textual definitions into logical definitions which are then accessible for automated reasoning ‘ carbonyl compound’ ↔ has_part some ( ‘carbonyl group’ ) ‘ carboxylic acid’ ↔ has_part some ( ‘carboxy group’ ) ‘ monocarboxylic acid’ ↔ has_part exactly 1 ( ‘carboxy group’ ) ‘ hydroxy monocarboxylic acid’ ↔ has_part exactly 1 ( ‘carboxy group’ ) and has_atom only some ( ‘hydrogen atom’ or ‘carbon atom’ or ‘oxygen atom’ ) is_a is_a is_a is_a

14. Foundational classification of molecules ChEBI ontology 20.10.10

17. Classification based on chemical structure ChEBI ontology 20.10.10 Best would be to include the structure in the ontology 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

19. Rules for properties ChEBI ontology 20.10.10 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) cyclobutane tetrahedrane

20. Rules for classes defined by parts ChEBI ontology 20.10.10 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) benzoic acid has this part so: is a carboxylic acid carboxylic acid benzoic acid

23. That’s great, but... ChEBI ontology 20.10.10

25. Substructure search ChEBI ontology 20.10.10 benzoic acid has this part so: is a carboxylic acid carboxylic acid benzoic acid

26. Goal 20.10.10 We extract features from the structural specifications of chemical compounds using standard cheminformatics techniques and use these to automatically classify compounds into defined classes CDK has_part exactly 1 ( ‘carboxy group’ ) has_part some ( ‘cholesterol’ ) 3β-hydroxy-4β-methyl-5α-cholest-7-ene-4α-carboxylic acid has_part only some ( ‘carbon atom’ or ‘oxygen atom’ or ‘hydrogen atom’ ) hydroxy monocarboxylic acid

31. Thank you for your attention