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![Increased expressivity to enable automatic
classification
hydrocarbon equivalentTo
molecule and has_atom only
(carbon atom or hydrogen atom)
peptide cation equivalentTo
peptide and has_charge some double [>, 0.0]
7 22.02.2012 ChEBI ontology](https://image.slidesharecdn.com/hastings-bio-ontologies-120222135253-phpapp01/75/Modularity-requirements-in-bio-ontologies-a-case-study-of-ChEBI-7-2048.jpg)
Uploaded byJanna Hastings
Modularity requirements in bio-ontologies: a case study of ChEBI
The document outlines the Chebi ontology, focusing on its modularity and classification of biologically interesting chemicals. It discusses the challenges of managing large ontologies, emphasizes the need for automated tools for module extraction, and highlights aspects of consistency checking and reasoning within the ontology. The paper also addresses the importance of creating subject-specific modules for better organization and processing efficiency.
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Modularity requirements in bio-ontologies: a case study of ChEBI
- 1. Janna Hastings, Colin Batchelor, Stefan Schulz, Christoph Steinbeck Modularity requirements in bio-ontologies a case study of ChEBI Workshop on Modular Ontologies, ESSLLI, 12 August 2011 EBI is an Outstation of the European Molecular Biology Laboratory.
- 2. ChEBI: an ontology of biologically interesting chemicals ChEBI Ontology chemical entity role chemical substance biological role molecular entity application group chemical role carbonyl compound pharmaceutical solvent carboxy group carboxylic acid antibacterial drug cyclooxygenase has part inhibitor has role cefpodoxime (CHEBI:606443) 2 22.02.2012
- 3. Bio-ontologies are modularby design: domain and granularity Domain Chemistry Granularity Upper level type Material entities Molecular entities Functions and roles of Substances chemical entities 3 22.02.2012 ChEBI ontology
- 4. They are characterisedby large sizes and low expressivity Currently Chemical entities exported (29132) in EL++ Roles (596) Subatomic particles (41) August 2011 29769 classes in total 4 22.02.2012 ChEBI ontology
- 5. Classification practices inchemistry lead to high levels of multiple inheritance 5 22.02.2012 ChEBI ontology
- 6. ChEBI is growing bigger … … and more expressive 6 22.02.2012 ChEBI ontology Image credit: Jonathan J. Dickau
- 7. Increased expressivity toenable automatic classification hydrocarbon equivalentTo molecule and has_atom only (carbon atom or hydrogen atom) peptide cation equivalentTo peptide and has_charge some double [>, 0.0] 7 22.02.2012 ChEBI ontology
- 8. carboxylic acid equivalentTo molecule and has_functional_group some carboxy group tricarboxylic acid equivalentTo molecule and has_functional_group exactly 3 carboxy group 8 22.02.2012 ChEBI ontology
- 9. Size explosion inasserted parts 9 22.02.2012 ChEBI ontology
- 10. Reasoning is requiredfor classification and consistency validation No definitional cycles A part_of B part_of C part_of A Enforcing disjointness Chemical Entity disjoint_from Role … Group disjoint_from Molecule … No disallowed combinations of relations A has_part B ; A conjugate_base_of B 10 22.02.2012 ChEBI ontology
- 11. Reasoning time inseconds Number of fully defined classes 11 22.02.2012 ChEBI ontology
- 12. Modularity and largeontologies smaller modules = faster classification 12 22.02.2012 ChEBI ontology
- 13. A USEFUL modulefor maintenance … is delineated by topic … is comprehensible and easy to work with … is self contained for reasoning tasks 13 22.02.2012 ChEBI ontology
- 14. Subject-specific modules overlap Immunology Drugs Metabolism Carboxylic acids E.g. GO-SLIM approach 14 22.02.2012 ChEBI ontology
- 15. Self-contained modules include all axioms needed for classification and consistency checking upper-level properties constraints (e.g. disjointness) parts hierarchy 15 22.02.2012 ChEBI ontology
- 16. Ontology segmentation tools don’t work very well on ChEBI … yet Topic blind Modules too small Out of memory or too big Long processing times No tool support for recombined viewing/querying 16 22.02.2012 ChEBI ontology
- 17. Interrelating bio-ontologies requires modular imports 17 22.02.2012 ChEBI ontology Image credit: Rameesh Vyas
- 18. The MIREOT mechanismrequires manual selection of module content and manual update of ontology changes Build ontology Choose links terms Extract module 18 22.02.2012 ChEBI ontology
- 19. We need modularontology views Automatic module extraction View V1 based on selection criteria (Topic, Editing) Edit, Validate, write back to source Ontology O 19 22.02.2012 ChEBI ontology
- 20. Views can beimported and are then automatically updated Module extraction View V1 (Topic, Import of views Editing) Ontology O2 Ontology O1 (e.g. biology) (e.g. chemistry) Automatic update 20 22.02.2012 ChEBI ontology
- 21. How do wefacilitate the development of tools for modular ontology engineering? 21 22.02.2012 ChEBI ontology
- 22. 22.02.2012 Thank you Acknowledgements: BBSRC (funding) 22 ChEBI ontology EBI is an Outstation of the European Molecular Biology Laboratory.
Editor's Notes
- #5 29769 classes in latest OWL file release Of these, 28875 are descendents of chemical entity, 596 are roles 41 subatomic particles and 257 are chemical entities not classified as chemical entities, thus, the real count for chems is 29132
- #9 Higher expressivity is not necessarily required for question answering, since the inferred hierarchy can be exported to OWL-EL for question answering.
- #13 I am coming from the software engineering perspective in this talk. Modularity is a tool to design complex systems while focusing on local organisation.
- #20 Tools are needed which are able to perform modularization of existing ontologies for purposes of ease of maintenance, then recombination for query answering.Shared terms between modules (represented only once)good way of thinking about it: Modular VIEWS on the overall ontologyAlso the ability to extract modules for import into other ontologies
- #21 Tools for modularization of existing ontologies for purposes of ease of maintenance, then recombination for query answering Shared terms between modules (represented only once)good way of thinking about it: Modular VIEWS on the overall ontologyAbility to extract modules for import into other ontologies,