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Janna Hastings, EBI Cheminformatics and Metabolism




Chemical classification
                                 for the Semantic Web




ACS Skolnik Symposium, Philadelphia,
21 August 2012
                                            EBI is an Outstation of the European Molecular Biology Laboratory.
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

2   21.08.2012
Why classify for the Semantic Web?

                         RDF “triples”:
                 ?subject ?relationship ?object




                          rdf:type

3   21.08.2012
4   21.08.2012
Chemicals, classes and information




                 This is not a molecule

5   21.08.2012
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
6    21.08.2012
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
7    21.08.2012
?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
8   21.08.2012
RDF is a technology for data representation,
OWL is a technology for classification

         Hierarchical
         organisation                                                        Synonyms
           root                                                              Cross-references


     leaves



                                                                          Can be re-used across
    Logical                                                               data sources
    definitions
                                             The Web Ontology Language (OWL)

9    21.08.2012         Hastings et al. Journal of Cheminformatics 2012
                        4:8 doi:10.1186/1758-2946-4-8
ChEBI                                               Chemical entity



     Chemical substance

                                                        Molecular entity
             inorganic molecular entity                                             Group              hydroxy
                                                                                                        group

                                              organic molecular entity
                                                                                            aldehyde
sodium chloride
                             carboxylic acid
                                                                organophosphorous
                                                                    compound




                                                                                              pyridoxal
          acetylsalicylic acid
                                                                                            (vitamin B6)
               (aspirin)
                                                                 chlorfenvinfos

10    21.08.2012                  Hastings et al. Journal of Cheminformatics 2012
                                  4:8 doi:10.1186/1758-2946-4-8
owl:subClassOf




                                                                          rdf:type
     Your data, your favourite identifier
                  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
                  …
                  …

11   21.08.2012
12   21.08.2012
13   21.08.2012
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            Questions?
14   21.08.2012

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Chemical classification for the Semantic Web

  • 1. Janna Hastings, EBI Cheminformatics and Metabolism Chemical classification for the Semantic Web ACS Skolnik Symposium, Philadelphia, 21 August 2012 EBI is an Outstation of the European Molecular Biology Laboratory.
  • 2. 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 2 21.08.2012
  • 3. Why classify for the Semantic Web? RDF “triples”: ?subject ?relationship ?object rdf:type 3 21.08.2012
  • 4. 4 21.08.2012
  • 5. Chemicals, classes and information This is not a molecule 5 21.08.2012
  • 6. 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 6 21.08.2012
  • 7. 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 7 21.08.2012
  • 8. ?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 8 21.08.2012
  • 9. RDF is a technology for data representation, OWL is a technology for classification Hierarchical organisation Synonyms root Cross-references leaves Can be re-used across Logical data sources definitions The Web Ontology Language (OWL) 9 21.08.2012 Hastings et al. Journal of Cheminformatics 2012 4:8 doi:10.1186/1758-2946-4-8
  • 10. ChEBI Chemical entity Chemical substance Molecular entity inorganic molecular entity Group hydroxy group organic molecular entity aldehyde sodium chloride carboxylic acid organophosphorous compound pyridoxal acetylsalicylic acid (vitamin B6) (aspirin) chlorfenvinfos 10 21.08.2012 Hastings et al. Journal of Cheminformatics 2012 4:8 doi:10.1186/1758-2946-4-8
  • 11. owl:subClassOf rdf:type Your data, your favourite identifier 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 … … 11 21.08.2012
  • 12. 12 21.08.2012
  • 13. 13 21.08.2012
  • 14. 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 Questions? 14 21.08.2012