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
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.
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
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
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
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 ChEBI ontology Image credit: Jonathan J. Dickau
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
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
Size explosion in asserted parts9 22.02.2012 ChEBI ontology
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
Reasoning time in seconds Number of fully defined classes11 22.02.2012 ChEBI ontology
Modularity and large ontologies smaller modules = faster classification12 22.02.2012 ChEBI ontology
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
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
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