A marriage of chemistry and biology Aligning the Gene Ontology with CHEBI.
Modularity requirements in bio-ontologies: a case study of ChEBI
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Transcript of Modularity requirements in bio-ontologies: a case study of ChEBI
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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
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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
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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
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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++
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Classification practices in chemistry lead to high levels of multiple inheritance
ChEBI ontology12.04.20235
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ChEBI ontology12.04.20236
ChEBI is growing
bigger …
… and more expressiveImage credit: Jonathan J. Dickau
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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]
ChEBI ontology12.04.20237
Value restriction
Data range restriction
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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
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Size explosion in asserted parts
ChEBI ontology12.04.20239
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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
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ChEBI ontology12.04.202311
Number of fully defined classes
Rea
soni
ng t
ime
in s
econ
dsHermiT classification of ChEBI
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ChEBI ontology12.04.202312
Modularity and large ontologiessmaller modules = faster classification
smaller modules = easier maintenance
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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
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Subject-specific modules overlap
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Drugs
Metabolism
Immunology
Carboxylic acids
E.g. GO-SLIM approach
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Self-contained modules include all axioms needed for
classification and consistency checking
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parts
propertiesupper-level constraints(e.g. disjointness)
hierarchy
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Ontology segmentation tools don’t work very well on ChEBI
… yet
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Modules too small or too big
Out of memoryLong processing times
No tool supportfor recombined
viewing/querying
Topic blind
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ChEBI ontology12.04.202317Image credit: Rameesh Vyas
Interrelating bio-ontologies requires
modular imports
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The MIREOT mechanism requires manual selection of module content
and manual update of ontology changes
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Choose terms
Extract module
Build ontology
links
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We need modular ontology views
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Ontology O
View V1 (Topic, Editing)
Automatic module extractionbased on selection criteria
Edit, Validate,write back to source
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Views can be imported and arethen automatically updated
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Ontology O1 (e.g. chemistry)
View V1 (Topic, Editing)
Module extraction
Ontology O2 (e.g. biology)
Import of views
Automaticupdate
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ChEBI ontology12.04.202321
How do we facilitate
the development of tools
for modular ontology engineering?
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EBI is an Outstation of the European Molecular Biology Laboratory.
Acknowledgements: BBSRC (funding)
Thank you
12.04.2023
ChEBI ontology22