Chemical classification for the Semantic Web

EBI is an Outstation of the European Molecular Biology Laboratory.

Chemical classification for the Semantic Web

Janna Hastings, EBI Cheminformatics and Metabolism

ACS Skolnik Symposium, Philadelphia,

21 August 2012

Classification conveys the type for data

The Semantic Web makes data of all types

available, open and interlinked

Classification using OWL ontologies

dramatically enhances the potential of the

chemical Semantic Web

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Why classify for the Semantic Web?

RDF “triples”:

?subject ?relationship ?object

rdf:type

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Chemicals, classes and information

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This is not a molecule

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Molecules are small

They are three-dimensional

Their structures can vary according to their environment

We say they have the same type

when they share important properties

All caffeine molecules have type caffeine

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There are many different ways to

represent molecules

InChI=1S/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3

SMILES=Cn1cnc2n(C)c(=O)n(C)c(=O)c12

Name=caffeine

Name=1,3,7-trimethyl-3,7-dihydro-1H-purine-2,6-dione

Identifier=KEGG COMPOUND:C07481

None of these are (themselves) molecules

They describe and approximate

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?subject ?relationship ?object

Science aims to make discoveries of general rules

about the things that that data are about

Classification puts the scientific

knowledge into the data

RDF is a technology for data representation,

OWL is a technology for classification

Hastings et al. Journal of Cheminformatics 2012

4:8 doi:10.1186/1758-2946-4-8

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The Web Ontology Language (OWL)

Hierarchical

organisation Synonyms

Cross-references

Logical

definitions

Can be re-used across

data sources

root

leaves

Hastings et al. Journal of Cheminformatics 2012

4:8 doi:10.1186/1758-2946-4-8

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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

ChEBI

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InChI=1S/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3

SMILES=Cn1cnc2n(C)c(=O)n(C)c(=O)c12

Name=caffeine

Name=1,3,7-trimethyl-3,7-dihydro-1H-purine-2,6-dione

Identifier=KEGG COMPOUND:C07481

…

…

rdf:type

owl:subClassOf

Your data, your favourite identifier

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Thanks

Christoph Steinbeck

Marcus Ennis, Gareth Owen, Steve Turner, Adriano Dekker,

Venkatesh Muthukrishnan, ChEBI users

Leonid Chepelev, Michel Dumontier, Colin Batchelor, Evan

Bolton, Nico Adams, Egon Willighagen, Despoina Magka,

Robert Stevens, Andrew Dalke

Funding: BBSRC, EU

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Questions?