Representing chemicals using OWL, Description Graphs and Rules

OWLED2010:San Francisco:Representing chemicals using OWL, Description Graphs and Rules

Representing chemicalsusing OWL, Description Graphs

and Rules

Janna Hastings, EBI, UKMichel Dumontier, Carleton University, Canada

Duncan Hull, EBI, UKMatthew Horridge, Manchester, UK

Christoph Steinbeck, EBI, UKUlrike Sattler, Manchester, UK

Robert Stevens, Manchester, UKTertia Hӧrne, University of South Africa

Katarina Britz, Meraka Institute, South Africa



Problem

We wish to represent and reason over structured objects

i.e. their representation contains also their parts


Chemical structures

caffeine

Moleculesconsist of atoms

connected by bonds

single bond

double bond

Carbon atom

Hydrogen atom

Nitrogen atom Oxygen atom


Chemical ontology

Chemical ontology consists of chemical classes which can be defined by parts of structures and/or properties of structures

carboxylic acid

cyclic molecule

if molecule has part some carboxy group

if molecule has property cyclic, i.e. a self-connectedcyclic path exists through the molecule’s atoms


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


Description Graphs

A recent, decidable extension to OWL 2, allowing expression of complex structures as graphs within the ontology

A description graph consists of a set of labelled vertices and a set of directed edges

Each description graph has a main class which links the graph to the main OWL ontology


Strong separation

In order to preserve decidability of knowledge bases enriched with description graphs,atomic properties used as graph edges have to be different to those used in axioms in the main OWL ontology

This is known as the strong separation requirement


Rules

Enhance OWL with the capacity to express if – then constructions

Consist of ‘antecedent’ (if conditions) and ‘consequent’ (then result)

Antecedent and consequent are composed of conjunctions of atomic statements


Goal

• 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?


OWL ontology


Chemical description graphs

Generated based on structures converted from a chemical database (ChEBI)


Rules

Generated for properties, e.g. being cyclic

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


Rules

Generated for parthood, e.g. carboxylic acidmolecule(?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

benzoicacid


Testing the reasoning

• Can we use a reasoner to deduce the classification hierarchy based on the graphs and rules?

No asserted hierarchy between test classes and molecules with generated

graphs


Results

Inferred hierarchy shows classified molecules


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?


Results


Experiences

• Difficult to debugTools support needs to be improved

• Difficult to construct rules for properties which depend on all atoms or all bonds in a given molecule

e.g. saturated -> all bonds in molecule are single


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

• Scalability of the reasoning with the rules is a concern


Acknowledgements

• Special thanks to Kirill Degtyarenko, Stefan Schulz, Colin Batchelor, Birte Glimm and the ChEBI team

• Funding: Meraka Institute, South Africa; BBSRC (BB/G022747/1); NSERC Discovery Grant

Technology

Representing chemicals using OWL, Description Graphs and Rules