chemical ontologies: what are they, what are they for, and what are the challenges
DESCRIPTION
Presented at the 2010 German Conference on Chemoinformatics, in Goslar, Germany, 8 November 2010.TRANSCRIPT
EBI is an Outstation of the European Molecular Biology Laboratory.
Chemical Ontologies
What are they?What are they for?What are the challenges?
Janna Hastings, EBI Chemoinformatics and Metabolism
6th German Conference on Chemoinformatics, Goslar, 8 November 2010
Problem
How do we find the informationwe need?
Data deluge
Multiple databases, heterogeneous data
Ambiguity, multiple synonyms
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Data lost in
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Intelligent systems
The answer is42
I’ll show you why
Logical inference
All men are mortal
Socrates is a man
Therefore, Socrates is mortal
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finding the implications of what you know
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Community terminological standardisation
Dictionary: synonyms, definitions
Hierarchical organisation
Logical model allowing computer inferences beyond what is explicitly encoded
Knowledge-based applications
Ontologies to filter and organise data
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The Web Ontology Language (OWL)
Hierarchicalorganisation
SynonymsCross-references
Logicaldefinitions
Can be re-used inmultiple applications
root
leaves
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ChEBI Ontology
Chemical entity Role
catecholamines
Biological role
Application
hormone
vasodilator agent
(R)-adrenaline
CHEMINF Ontology
DescriptorSoftware library
ACD Labs
logP
-.539-2.369
logD
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Chemical entity
carboxylic acid
acetylsalicylic acid(aspirin)
chlorfenvinfos
organophosphorouscompound
aldehyde
organic molecular entity
inorganic molecular entity
pyridoxal(vitamin B6)
sodium chloride
Molecular entity
Group hydroxy group
Chemical substance
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Role
analgesic
acetylsalicylic acid(aspirin) chlorfenvinfos
insecticide
vitamin
pyridoxal(vitamin B6)
Biological role Application
drug
pesticide
Chemical role
acid
sulfuric acid
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Chemical information entity
DescriptorSoftware library
CDK
logP
OpenBabel
Algorithm
MolecularDescriptor
implements calculates
SubstanceDescriptor
atom count
boiling point
melting pointlargest chain
fused cycles
Hueckel’saromaticity
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Chemical database Bioactivity
databaseBioactivity database Metabolism
databaseMetabolism database
Pathway database
LiteratureLiterature
Chemical entities
Roles
Properties
Unified browsing and querying
Disentangling hierarchies
Disambiguating terminology
Ontology representation in a complex domain
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Sounds great, but...
What are the challenges?
Chemicals and roles
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de Matos, P. et al: Chemical Entities of Biological Interest: an update. NAR Database issue 2010
vitamin
hormone
neurotransmitter
CNS stimulant
carboxylic acid
peptide
trimethylxanthine
polycyclic cage
has role
Chemicals and structures
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J. Hastings, C. Batchelor, C. Steinbeck, S. Schulz: What are chemical structures and their relations? FOIS 2010
chemical entity
molecule
chemical graph
molecular structure
has attribute
What is the structure of Vancomycin?
Representing complex structures
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Chemical classes can be defined by
parts of structures
and/or properties of structures
carboxylic acid
cyclic molecule
if molecule has part some carboxy group
if molecule has property cyclic, i.e. a self-connectedcyclic path exists through the molecule’s atoms
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Pre-compute and assert all parts and properties
Represent atoms and bonds in ontology
Integration of chemoinformatics and ontology toolsIntegration of chemoinformatics and ontology tools
J. Hastings et al.: Representing chemicals using OWL, description graphs and rules. OWLED 2010
Purpose and mode of action
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epinastine
application
antiallergic drug
is a
biological role
histamine antagonist
is a
has rolehas role
C. Batchelor, J. Hastings, C. Steinbeck: Ontological dependence, dispositions and institutional reality in chemistry. FOIS 2010
Single molecule
Independent ofintent
Bulk quantity of molecules
Depends on human intent(e.g. license, prescription)
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Conditions in bioactivity models
Consider aspirin as treatment for a headache
Too few individual molecules will have no effect
Too many tablets will have unpleasant additional effects
Image credit: tell.fll.purdue.edu
J. Hastings, C. Steinbeck, L. Jansen, S. Schulz: Substance concentrations as conditions for the realization of dispositions. ISMB Bio-Ontologies SIG 2010
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Christoph Steinbeck
Paula de Matos
Marcus Ennis
Steve Turner
Adriano Dekker
Kenneth Haug
Rafael Alcántara Martin
Zara Josephs
Pablo Moreno
Kalai Jayaseelan
Mark Rijnbeek
Nico Adams
Colin Batchelor, RSC
Stefan Schulz, Freiburg
Egon Willighagen, Uppsala
Michel Dumontier, Carleton
Leonid Chepelev, Carleton