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EBI is an Outstation of the European Molecular Biology Laboratory.
Chemical Ontologies
What are they?
What are they for?
W...
Problem
How do we find
the information
we need?
Data deluge
Multiple databases, heterogeneous data
Ambiguity, multiple syn...
J. Hastings Chemical Ontology30.01.153
Intelligent systems
The answer
is
42
I’ll show you
why
Logical inference
All men are mortal
Socrates is a man
Therefore, Socrates is mortal
J. Hastings Chemical Ontology30.01.15...
J. Hastings Chemical Ontology30.01.155
Community terminological standardisation
Dictionary: synonyms, definitions
Hierarch...
Ontologies to filter and organise data
J. Hastings Chemical Ontology30.01.156
The Web Ontology Language (OWL)
Hierarchical...
J. Hastings Chemical Ontology30.01.157
ChEBI Ontology
Chemical entity Role
catecholamines
Biological role
Application
horm...
J. Hastings Chemical Ontology30.01.158
Chemical entity
carboxylic acid
acetylsalicylic acid
(aspirin)
chlorfenvinfos
organ...
J. Hastings Chemical Ontology30.01.159
Role
analgesic
acetylsalicylic acid
(aspirin) chlorfenvinfos
insecticide
vitamin
py...
J. Hastings Chemical Ontology30.01.1510
Chemical information entity
DescriptorSoftware library
CDK
logP
OpenBabel
Algorith...
J. Hastings Chemical Ontology30.01.1511
Chemical
database Bioactivity
database
Bioactivity
database Metabolism
database
Me...
Disentangling hierarchies
Disambiguating terminology
Ontology representation in a complex domain
J. Hastings Chemical Onto...
Chemicals and roles
J. Hastings Chemical Ontology30.01.1513
de Matos, P. et al: Chemical Entities of Biological Interest: ...
Chemicals and structures
J. Hastings Chemical Ontology30.01.1514
J. Hastings, C. Batchelor, C. Steinbeck, S. Schulz: What ...
Representing complex structures
J. Hastings Chemical Ontology30.01.1515
Chemical classes can be defined by
parts of struct...
J. Hastings Chemical Ontology30.01.1516
Pre-compute
and assert
all parts and
properties
Represent
atoms and
bonds in
ontol...
Purpose and mode of action
J. Hastings Chemical Ontology30.01.1517
epinastine
application
antiallergic drug
is a
biologica...
J. Hastings Chemical Ontology30.01.1518
Conditions in bioactivity models
Consider aspirin as treatment for a headache
Too ...
J. Hastings Chemical Ontology30.01.1519
Christoph Steinbeck
Paula de Matos
Marcus Ennis
Steve Turner
Adriano Dekker
Kennet...
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Chemical ontologies: what are they, what are they for, and what are the challenges

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Presented at the 2010 German Conference on Chemoinformatics, in Goslar, Germany, 8 November 2010.

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Chemical ontologies: what are they, what are they for, and what are the challenges

  1. 1. 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
  2. 2. Problem How do we find the information we need? Data deluge Multiple databases, heterogeneous data Ambiguity, multiple synonyms J. Hastings Chemical Ontology30.01.152 Data lost in
  3. 3. J. Hastings Chemical Ontology30.01.153 Intelligent systems The answer is 42 I’ll show you why
  4. 4. Logical inference All men are mortal Socrates is a man Therefore, Socrates is mortal J. Hastings Chemical Ontology30.01.154 finding the implications of what you know
  5. 5. J. Hastings Chemical Ontology30.01.155 Community terminological standardisation Dictionary: synonyms, definitions Hierarchical organisation Logical model allowing computer inferences beyond what is explicitly encoded Knowledge-based applications
  6. 6. Ontologies to filter and organise data J. Hastings Chemical Ontology30.01.156 The Web Ontology Language (OWL) Hierarchical organisation Synonyms Cross-references Logical definitions Can be re-used in multiple applications root leaves
  7. 7. J. Hastings Chemical Ontology30.01.157 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
  8. 8. J. Hastings Chemical Ontology30.01.158 Chemical entity carboxylic acid acetylsalicylic acid (aspirin) chlorfenvinfos organophosphorous compound aldehyde organic molecular entity inorganic molecular entity pyridoxal (vitamin B6) sodium chloride Molecular entity Group hydroxy group Chemical substance
  9. 9. J. Hastings Chemical Ontology30.01.159 Role analgesic acetylsalicylic acid (aspirin) chlorfenvinfos insecticide vitamin pyridoxal (vitamin B6) Biological role Application drug pesticide Chemical role acid sulfuric acid
  10. 10. J. Hastings Chemical Ontology30.01.1510 Chemical information entity DescriptorSoftware library CDK logP OpenBabel Algorithm Molecular Descriptor implements calculates Substance Descriptor atom count boiling point melting point largest chain fused cycles Hueckel’s aromaticity
  11. 11. J. Hastings Chemical Ontology30.01.1511 Chemical database Bioactivity database Bioactivity database Metabolism database Metabolism database Pathway database LiteratureLiterature Chemical entities Roles Properties Unified browsing and querying
  12. 12. Disentangling hierarchies Disambiguating terminology Ontology representation in a complex domain J. Hastings Chemical Ontology30.01.1512 Sounds great, but... What are the challenges?
  13. 13. Chemicals and roles J. Hastings Chemical Ontology30.01.1513 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
  14. 14. Chemicals and structures J. Hastings Chemical Ontology30.01.1514 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?
  15. 15. Representing complex structures J. Hastings Chemical Ontology30.01.1515 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-connected cyclic path exists through the molecule’s atoms
  16. 16. J. Hastings Chemical Ontology30.01.1516 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
  17. 17. Purpose and mode of action J. Hastings Chemical Ontology30.01.1517 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 of intent Bulk quantity of molecules Depends on human intent (e.g. license, prescription)
  18. 18. J. Hastings Chemical Ontology30.01.1518 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
  19. 19. J. Hastings Chemical Ontology30.01.1519 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

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