modularity requirements in bio-ontologies: a case study of chebi
DESCRIPTION
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.TRANSCRIPT
EBI is an Outstation of the European Molecular Biology Laboratory.
Modularity requirements in bio-ontologiesa case study of ChEBI
Janna Hastings, Colin Batchelor,
Stefan Schulz, Christoph Steinbeck
Workshop on Modular Ontologies, ESSLLI,12 August 2011
ChEBI: an ontology of biologically interesting chemicals
12.04.20232
ChEBI Ontology
chemical entity role
carboxylic acid
application
antibacterial drug
cefpodoxime (CHEBI:606443)
pharmaceutical
biological role
chemical role
chemical substance
molecular entitygroup
carbonyl compoundsolvent
has role
cyclooxygenaseinhibitor
carboxy group
has part
Bio-ontologies are modular by design:domain and granularity
ChEBI ontology12.04.20233
Chemistry
Molecular entities
Substances
Functions and roles of
chemical entities
Domain
Granularity Upper level type
Material entities
They are characterised by large sizes and low expressivity
ChEBI ontology12.04.20234
Chemical entities (29132)Roles (596)Subatomic par-ticles (41)
August 2011 29769 classes in total
Currentlyexportedin EL++
Classification practices in chemistry lead to high levels of multiple inheritance
ChEBI ontology12.04.20235
ChEBI ontology12.04.20236
ChEBI is growing
bigger …
… and more expressiveImage 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]
ChEBI ontology12.04.20237
Value restriction
Data range restriction
ChEBI ontology12.04.20238
carboxylic acid equivalentTo
molecule and has_functional_group some carboxy group
tricarboxylic acid equivalentTo
molecule and has_functional_group exactly 3 carboxy group
Cardinality restriction
Size explosion in asserted parts
ChEBI ontology12.04.20239
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 B
ChEBI ontology12.04.202310
ChEBI ontology12.04.202311
Number of fully defined classes
Rea
soni
ng t
ime
in s
econ
dsHermiT classification of ChEBI
ChEBI ontology12.04.202312
Modularity and large ontologiessmaller modules = faster classification
smaller modules = easier maintenance
ChEBI ontology12.04.202313
A USEFUL module for maintenance
… is delineated by topic
… is comprehensible and easy to work with
… is self contained for reasoning tasks
Subject-specific modules overlap
ChEBI ontology12.04.202314
Drugs
Metabolism
Immunology
Carboxylic acids
E.g. GO-SLIM approach
Self-contained modules include all axioms needed for
classification and consistency checking
ChEBI ontology12.04.202315
parts
propertiesupper-level constraints(e.g. disjointness)
hierarchy
Ontology segmentation tools don’t work very well on ChEBI
… yet
ChEBI ontology12.04.202316
Modules too small or too big
Out of memoryLong processing times
No tool supportfor recombined
viewing/querying
Topic blind
ChEBI ontology12.04.202317Image credit: Rameesh Vyas
Interrelating bio-ontologies requires
modular imports
The MIREOT mechanism requires manual selection of module content
and manual update of ontology changes
ChEBI ontology12.04.202318
Choose terms
Extract module
Build ontology
links
We need modular ontology views
ChEBI ontology12.04.202319
Ontology O
View V1 (Topic, Editing)
Automatic module extractionbased on selection criteria
Edit, Validate,write back to source
Views can be imported and arethen automatically updated
ChEBI ontology12.04.202320
Ontology O1 (e.g. chemistry)
View V1 (Topic, Editing)
Module extraction
Ontology O2 (e.g. biology)
Import of views
Automaticupdate
ChEBI ontology12.04.202321
How do we facilitate
the development of tools
for modular ontology engineering?
EBI is an Outstation of the European Molecular Biology Laboratory.
Acknowledgements: BBSRC (funding)
Thank you
12.04.2023
ChEBI ontology22