Janna Hastings,                                                  Colin Batchelor,                                         ...
ChEBI:             an ontology of biologically interesting chemicals                                           ChEBI Ontol...
Bio-ontologies are modular by design:                        domain and granularity                        Domain         ...
They are characterised by large sizes                         and low expressivity     Currently                          ...
Classification practices in chemistry lead to           high levels of multiple inheritance5   22.02.2012   ChEBI ontology
ChEBI is growing                                   bigger …                        … and more expressive6    22.02.2012   ...
Increased expressivity to enable automatic                      classification           hydrocarbon equivalentTo         ...
carboxylic acid equivalentTo          molecule and has_functional_group some                 carboxy group    tricarboxyli...
Size explosion in asserted parts9   22.02.2012       ChEBI ontology
Reasoning is required for classification and                 consistency validation                  No definitional cycle...
Reasoning time in seconds                                              Number of fully defined classes11                  ...
Modularity and large ontologies                  smaller modules = faster classification12   22.02.2012        ChEBI ontol...
A USEFUL module for maintenance                  … is delineated by topic                  … is comprehensible and        ...
Subject-specific modules overlap                                            Immunology                   Drugs            ...
Self-contained modules                   include all axioms needed for              classification and consistency checkin...
Ontology segmentation tools                  don’t work very well on ChEBI                              … yet             ...
Interrelating bio-ontologies                             requires                        modular imports17   22.02.2012   ...
The MIREOT mechanism requires               manual selection of module content             and manual update of ontology c...
We need modular ontology views                  Automatic module extraction          View V1                  based on sel...
Views can be imported and are                     then automatically updated     Module extraction                    View...
How do we facilitate                  the development of tools                       for modular                  ontology...
22.02.2012                               Thank you                      Acknowledgements: BBSRC (funding)22ChEBI ontology ...
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Modularity requirements in bio-ontologies: a case study of ChEBI

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A wish list for tools for modularity support in bio-ontology engineering based on the ChEBI ontology requirements. Presented at the workshop on modular ontologies, WoMO, 2011, in Ljubljana.

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  • 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
  • Higher expressivity is not necessarily required for question answering, since the inferred hierarchy can be exported to OWL-EL for question answering.
  • I am coming from the software engineering perspective in this talk. Modularity is a tool to design complex systems while focusing on local organisation.
  • 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
  • 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,
  • Modularity requirements in bio-ontologies: a case study of ChEBI

    1. 1. Janna Hastings, Colin Batchelor, Stefan Schulz, Christoph Steinbeck Modularity requirements in bio-ontologies a case study of ChEBIWorkshop on Modular Ontologies, ESSLLI,12 August 2011 EBI is an Outstation of the European Molecular Biology Laboratory.
    2. 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 solventcarboxy group carboxylic acid antibacterial drug cyclooxygenase has part inhibitor has role cefpodoxime (CHEBI:606443)2 22.02.2012
    3. 3. Bio-ontologies are modular by design: domain and granularity Domain Chemistry Granularity Upper level type Material entities Molecular entities Functions and roles of Substances chemical entities3 22.02.2012 ChEBI ontology
    4. 4. They are characterised by large sizes and low expressivity Currently Chemical entities exported (29132) in EL++ Roles (596) Subatomic particles (41) August 2011 29769 classes in total4 22.02.2012 ChEBI ontology
    5. 5. Classification practices in chemistry lead to high levels of multiple inheritance5 22.02.2012 ChEBI ontology
    6. 6. ChEBI is growing bigger … … and more expressive6 22.02.2012 ChEBI ontology Image credit: Jonathan J. Dickau
    7. 7. 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
    8. 8. carboxylic acid equivalentTo molecule and has_functional_group some carboxy group tricarboxylic acid equivalentTo molecule and has_functional_group exactly 3 carboxy group8 22.02.2012 ChEBI ontology
    9. 9. Size explosion in asserted parts9 22.02.2012 ChEBI ontology
    10. 10. Reasoning is required for 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 B10 22.02.2012 ChEBI ontology
    11. 11. Reasoning time in seconds Number of fully defined classes11 22.02.2012 ChEBI ontology
    12. 12. Modularity and large ontologies smaller modules = faster classification12 22.02.2012 ChEBI ontology
    13. 13. A USEFUL module for maintenance … is delineated by topic … is comprehensible and easy to work with … is self contained for reasoning tasks13 22.02.2012 ChEBI ontology
    14. 14. Subject-specific modules overlap Immunology Drugs Metabolism Carboxylic acids E.g. GO-SLIM approach14 22.02.2012 ChEBI ontology
    15. 15. Self-contained modules include all axioms needed for classification and consistency checking upper-level properties constraints (e.g. disjointness) parts hierarchy15 22.02.2012 ChEBI ontology
    16. 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/querying16 22.02.2012 ChEBI ontology
    17. 17. Interrelating bio-ontologies requires modular imports17 22.02.2012 ChEBI ontology Image credit: Rameesh Vyas
    18. 18. The MIREOT mechanism requires manual selection of module content and manual update of ontology changes Build ontology Choose links terms Extract module18 22.02.2012 ChEBI ontology
    19. 19. We need modular ontology views Automatic module extraction View V1 based on selection criteria (Topic, Editing) Edit, Validate, write back to source Ontology O19 22.02.2012 ChEBI ontology
    20. 20. Views can be imported 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 update20 22.02.2012 ChEBI ontology
    21. 21. How do we facilitate the development of tools for modular ontology engineering?21 22.02.2012 ChEBI ontology
    22. 22. 22.02.2012 Thank you Acknowledgements: BBSRC (funding)22ChEBI ontology EBI is an Outstation of the European Molecular Biology Laboratory.

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