Representing chemicals using OWL, Description Graphs and Rules
-
Upload
michel-dumontier -
Category
Technology
-
view
1.609 -
download
1
description
Transcript of Representing chemicals using OWL, Description Graphs and Rules
![Page 1: Representing chemicals using OWL, Description Graphs and Rules](https://reader036.fdocuments.us/reader036/viewer/2022062703/554e8ed3b4c90573338b4c89/html5/thumbnails/1.jpg)
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
![Page 2: Representing chemicals using OWL, Description Graphs and Rules](https://reader036.fdocuments.us/reader036/viewer/2022062703/554e8ed3b4c90573338b4c89/html5/thumbnails/2.jpg)
OWLED2010:San Francisco:Representing chemicals using OWL, Description Graphs and Rules
![Page 3: Representing chemicals using OWL, Description Graphs and Rules](https://reader036.fdocuments.us/reader036/viewer/2022062703/554e8ed3b4c90573338b4c89/html5/thumbnails/3.jpg)
OWLED2010:San Francisco:Representing chemicals using OWL, Description Graphs and Rules
Problem
We wish to represent and reason over structured objects
i.e. their representation contains also their parts
![Page 4: Representing chemicals using OWL, Description Graphs and Rules](https://reader036.fdocuments.us/reader036/viewer/2022062703/554e8ed3b4c90573338b4c89/html5/thumbnails/4.jpg)
OWLED2010:San Francisco:Representing chemicals using OWL, Description Graphs and Rules
Chemical structures
caffeine
Moleculesconsist of atoms
connected by bonds
single bond
double bond
Carbon atom
Hydrogen atom
Nitrogen atom Oxygen atom
![Page 5: Representing chemicals using OWL, Description Graphs and Rules](https://reader036.fdocuments.us/reader036/viewer/2022062703/554e8ed3b4c90573338b4c89/html5/thumbnails/5.jpg)
OWLED2010:San Francisco:Representing chemicals using OWL, Description Graphs and Rules
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
![Page 6: Representing chemicals using OWL, Description Graphs and Rules](https://reader036.fdocuments.us/reader036/viewer/2022062703/554e8ed3b4c90573338b4c89/html5/thumbnails/6.jpg)
OWLED2010:San Francisco:Representing chemicals using OWL, Description Graphs and Rules
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
![Page 7: Representing chemicals using OWL, Description Graphs and Rules](https://reader036.fdocuments.us/reader036/viewer/2022062703/554e8ed3b4c90573338b4c89/html5/thumbnails/7.jpg)
OWLED2010:San Francisco:Representing chemicals using OWL, Description Graphs and Rules
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
![Page 8: Representing chemicals using OWL, Description Graphs and Rules](https://reader036.fdocuments.us/reader036/viewer/2022062703/554e8ed3b4c90573338b4c89/html5/thumbnails/8.jpg)
OWLED2010:San Francisco:Representing chemicals using OWL, Description Graphs and Rules
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
![Page 9: Representing chemicals using OWL, Description Graphs and Rules](https://reader036.fdocuments.us/reader036/viewer/2022062703/554e8ed3b4c90573338b4c89/html5/thumbnails/9.jpg)
OWLED2010:San Francisco:Representing chemicals using OWL, Description Graphs and Rules
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
![Page 10: Representing chemicals using OWL, Description Graphs and Rules](https://reader036.fdocuments.us/reader036/viewer/2022062703/554e8ed3b4c90573338b4c89/html5/thumbnails/10.jpg)
OWLED2010:San Francisco:Representing chemicals using OWL, Description Graphs and Rules
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?
![Page 11: Representing chemicals using OWL, Description Graphs and Rules](https://reader036.fdocuments.us/reader036/viewer/2022062703/554e8ed3b4c90573338b4c89/html5/thumbnails/11.jpg)
OWLED2010:San Francisco:Representing chemicals using OWL, Description Graphs and Rules
OWL ontology
![Page 12: Representing chemicals using OWL, Description Graphs and Rules](https://reader036.fdocuments.us/reader036/viewer/2022062703/554e8ed3b4c90573338b4c89/html5/thumbnails/12.jpg)
OWLED2010:San Francisco:Representing chemicals using OWL, Description Graphs and Rules
Chemical description graphs
Generated based on structures converted from a chemical database (ChEBI)
![Page 13: Representing chemicals using OWL, Description Graphs and Rules](https://reader036.fdocuments.us/reader036/viewer/2022062703/554e8ed3b4c90573338b4c89/html5/thumbnails/13.jpg)
OWLED2010:San Francisco:Representing chemicals using OWL, Description Graphs and Rules
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
![Page 14: Representing chemicals using OWL, Description Graphs and Rules](https://reader036.fdocuments.us/reader036/viewer/2022062703/554e8ed3b4c90573338b4c89/html5/thumbnails/14.jpg)
OWLED2010:San Francisco:Representing chemicals using OWL, Description Graphs and Rules
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
![Page 15: Representing chemicals using OWL, Description Graphs and Rules](https://reader036.fdocuments.us/reader036/viewer/2022062703/554e8ed3b4c90573338b4c89/html5/thumbnails/15.jpg)
OWLED2010:San Francisco:Representing chemicals using OWL, Description Graphs and Rules
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
![Page 16: Representing chemicals using OWL, Description Graphs and Rules](https://reader036.fdocuments.us/reader036/viewer/2022062703/554e8ed3b4c90573338b4c89/html5/thumbnails/16.jpg)
OWLED2010:San Francisco:Representing chemicals using OWL, Description Graphs and Rules
Results
Inferred hierarchy shows classified molecules
![Page 17: Representing chemicals using OWL, Description Graphs and Rules](https://reader036.fdocuments.us/reader036/viewer/2022062703/554e8ed3b4c90573338b4c89/html5/thumbnails/17.jpg)
OWLED2010:San Francisco:Representing chemicals using OWL, Description Graphs and Rules
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?
![Page 18: Representing chemicals using OWL, Description Graphs and Rules](https://reader036.fdocuments.us/reader036/viewer/2022062703/554e8ed3b4c90573338b4c89/html5/thumbnails/18.jpg)
OWLED2010:San Francisco:Representing chemicals using OWL, Description Graphs and Rules
Results
![Page 19: Representing chemicals using OWL, Description Graphs and Rules](https://reader036.fdocuments.us/reader036/viewer/2022062703/554e8ed3b4c90573338b4c89/html5/thumbnails/19.jpg)
OWLED2010:San Francisco:Representing chemicals using OWL, Description Graphs and Rules
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
![Page 20: Representing chemicals using OWL, Description Graphs and Rules](https://reader036.fdocuments.us/reader036/viewer/2022062703/554e8ed3b4c90573338b4c89/html5/thumbnails/20.jpg)
OWLED2010:San Francisco:Representing chemicals using OWL, Description Graphs and Rules
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
![Page 21: Representing chemicals using OWL, Description Graphs and Rules](https://reader036.fdocuments.us/reader036/viewer/2022062703/554e8ed3b4c90573338b4c89/html5/thumbnails/21.jpg)
OWLED2010:San Francisco:Representing chemicals using OWL, Description Graphs and Rules
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