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.

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 Laval
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2. chemical structure:
molecules consist of atoms connected by bonds
Carbon atom single bond
Hydrogen atom double bond
Nitrogen atom Oxygen atom
caffeine
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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).
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4. automatic classification of chemical
functional groups
28 OC
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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 cycle
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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 tree
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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.
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8. OWL + DG + Rules = Chemical
Classification
Before After
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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 to
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10. Dataset
A) butane, B) pentane, C) iso-butane, D) iso-
pentane, E) cyclobutane and F) cyclohexane
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11. SDF Method
formalization SDF2OWL
PHP-based
OWLAPI
OWL
reasoning Protégé 4.2
HermiT
Explanation
Workbench
Inference
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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 ...
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13. Symmetry
4 3
1
2
equivalence among 2,3 and 4 as
every peripheral atom is connected to the central atom (1)
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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 5
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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 3
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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.
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17. But not in cyclohexane
• No 2 atoms are connected to the same
pair of atoms.
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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.
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19. dumontierlab.com
michel_dumontier@carleton.ca
Website: http://dumontierlab.com
Presentations: http://slideshare.com/micheldumontier
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