1. The ChEBI ontology Modelling chemical entities: current challenges
OBML Workshop, Universitat Leipzig
26 November 2009
Janna Hastings, EBI Chemoinformatics and Metabolism

2. Overview Introduction to ChEBI Role ontology
Chemical dispositions: acid/base, proton donor
Function: enzyme inhibitor, pesticide
Complex involvement of social reality: drug roles.
Natural products, metabolites
Chemical entities and realism
Chemical graphs, ‘derivation’ and realism
ChEBI ontology

3. Introduction to ChEBI Chemical Entities of Biological Interest
Focused on ‘small’ chemical entities (no proteins or nucleic acids)
Scope (material entities): mainly molecules, but also salts, polymers, atoms, electrons, groups, …
Scope (dependent entities): chemical role, biological role, application
Access ChEBI at
ChEBI ontology

4. ChEBI ontology Organised into three sub-ontologies, namely
Molecular structure ontology
Subatomic particle ontology
Role ontology
(R)-adrenaline
ChEBI ontology

5. Molecular structure ontology
ChEBI ontology

6. Role ontology
ChEBI ontology

7. Modelling chemical activities
ChEBI ontology

8. Chemical dispositions
Currently classified as ‘chemical role’ in ChEBI: acid/base, proton donor/acceptor, solvent, buffer, antioxidant
We say that these are dispositions because
- mind/institution independent
- depend on the structure of the chemical entity
- realization results in fundamental change in structure
Note that acid/base and proton acceptor/donor are examples of mutually ontologically dependent dispositions
ChEBI ontology

9. Chemical Functions Biological function Artefactual function
Co-evolution of small molecules and protein receptors: enzyme inhibitor, activator
Ascription of function by natural selection, evolution
Artefactual function
Design or selection of chemical entity for purpose e.g. fluorochrome, pesticide.
Ascription of function by design
ChEBI ontology

10. Chemical roles
Complex interplay of social reality and biological function: modelling drug roles
A chemical acts as a drug when it is prescribed by a professional with the relevant institutional status (doctor, pharmacist) in the course of a particular treatment course.
A drug role can be grounded in a biological function (analgesic – COX inhibitor) or it may not (placebo)
ChEBI ontology

11. Roles which are not roles
Natural products, metabolites
A chemical entity is a metabolite by virtue of being the output of some biological process
A chemical entity is a natural product by virtue of being the output of some biological process and not occurring spontaneously in nature
Currently in ChEBI, natural product classes are scattered throughout the structure ontology while metabolite and secondary metabolite are in the role ontology
ChEBI ontology

12. Chemical entities and realism
ChEBI ontology

13. Chemical graphs
hydrogens may be implicit
ChEBI ontology

14. Formal derivation ‘Formal derivation’ (IUPAC)
parent hydride
functional parent
Used for naming chemical entities
has parent hydride
ChEBI ontology

15. Molecules which don’t exist
Computational chemistry focuses on the design and computational assessment of molecules which may or may not be synthesised, depending on the outcome of computational calculations of their properties
These ‘candidate’ chemicals can be fully described in terms of their constituent parts and the connectivity between them in the form of a chemical graph
But, all molecules in ChEBI are represented by their respective chemical graph; so
… is the existence criterion important?
ChEBI ontology

16. Thank you for your attention