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Representing the ChEBI ontology in OWL

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Presented at the EBI Industry Programme Ontology tutorial.

Presented at the EBI Industry Programme Ontology tutorial.

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  • 1. The ChEBI ontology and OWL Industry Programme Ontology Tutorial European Bioinformatics Institute 13 October 2010 Janna Hastings EBI Chemoinformatics and Metabolism
  • 2. Overview
    • Introduction to ChEBI
    • Porting ChEBI into OWL format
      • Relationship patterns
      • Metadata
      • Editing and reasoning
    • Chemical structures and OWL
      • Description graphs and rules
    ChEBI ontology 20.10.10
  • 3. Introduction to ChEBI
    • Ch emical E ntities of B iological I nterest
    • Focused on ‘small’ chemical entities: no proteins or nucleic acids
    • Scope (material entities): mainly molecules, but also salts, polymers, atoms, electrons, groups, residues
    • Scope (dependent entities): chemical role, biological role, application
    • Access ChEBI at http://www.ebi.ac.uk/chebi/
    ChEBI ontology 20.10.10
  • 4. ChEBI ontology 4/26/2010 A ChEBI entry page
  • 5. ChEBI ontology ChEBI ontology 20.10.10
    • Organised into three sub-ontologies, namely
        • Molecular structure ontology
        • Subatomic particle ontology
        • Role ontology
    ( R ) -adrenaline
  • 6. ChEBI ontology 20.10.10 Molecular structure ontology
  • 7. ChEBI ontology 20.10.10 Role ontology
  • 8. ChEBI internal ontology architecture ChEBI ontology 20.10.10 Oracle database
  • 9. A ChEBI entity in OBO format
    • [Term] id: CHEBI:17051 name: fluoride alt_id: CHEBI:49593 alt_id: CHEBI:14271 def: "A monoatomic fluorine that has formula F." [] synonym: "fluoride(1-)" EXACT IUPAC_NAME [IUPAC:] synonym: "F" RELATED FORMULA [KEGG COMPOUND:] synonym: "[F-]" RELATED SMILES [ChEBI:] synonym: "InChI=1/FH/h1H/p-1/fF/h1h/q-1" RELATED InChI [ChEBI:] xref: Gmelin:14905 "Gmelin Registry Number" xref: NIST Chemistry WebBook:16984-48-8 "CAS Registry Number" xref: KEGG COMPOUND:C00742 "KEGG COMPOUND" is_a: CHEBI:16042 is_a: CHEBI:36895 relationship: is_conjugate_base_of CHEBI:29228
    ChEBI ontology 20.10.10
  • 10. Expressing ChEBI in OWL
    • OWL format version of ChEBI is available via OBO -> OWL translation (provided by the OBO Foundry)
    • Motivations for providing ‘primary’ OWL version of ChEBI
      • enable the use of modern ontology tools such as Protégé
      • provide synonyms in multiple languages (not yet fully supported in OBO format)
      • gain control over the logical axiomatization of the ontology
      • upgrade to OWL 2 and continue to keep up-to-date
    ChEBI ontology 20.10.10
  • 11. ChEBI in OWL: Relationship patterns
    • OBO relationship: X rel Y
    • OWL ‘relationships’ expressed as logical axioms, which may have different forms
    • e.g. X ⊑  rel.Y (value restriction) (‘only’) or X ⊑  rel.Y (existential quantification) (‘some’)
    • Some ChEBI relationships, such as has_part, follow the existential pattern in OWL
    • Others, such as has_parent_hydride, might be better expressed with the value restriction pattern
    ChEBI ontology 20.10.10
  • 12. ChEBI in OWL: Metadata
    • Metadata in OBO format has a standard, fixed, format:
      • name, def
      • synonym
      • xref
    • Metadata in OWL provided for via annotations – a multi-purpose, flexible metadata standard
      • name uses rdfs:label
      • Synonyms use
    • <owl:AnnotationProperty rdf:about=&quot;http://purl.obolibrary.org/obo#Synonym&quot;/>
        • Example of custom ChEBI annotation
    • <owl:AnnotationProperty rdf:about=&quot;http://purl.obolibrary.org/obo#SMILES&quot;/>
    ChEBI ontology 20.10.10
  • 13. A ChEBI entity in OWL format
    • <owl:Class rdf:about=&quot;http://purl.obolibrary.org/obo/CHEBI_10003&quot;>
    • < rdfs:label rdf:datatype=“XMLSchema#string&quot;>vistamycin</rdfs:label>
    • < rdfs:subClassOf rdf:resource=&quot;http://purl.obolibrary.org/obo/CHEBI_22479&quot;/>
    • <rdfs: subClassOf ><owl: Restriction ><owl:onProperty rdf:resource=&quot;http://purl.obolibrary.org/obo#has_parent_hydride&quot;/>
    • <owl: someValuesFrom rdf:resource=&quot;http://purl.obolibrary.org/obo/CHEBI_36372&quot;/> </owl:Restriction> </rdfs:subClassOf>
    • < Synonym rdf:datatype=“XMLSchema#string&quot;>(1R,2R,3S,4R,6S)-4,6-diamino-3-hydroxy-2-(beta-D-ribofuranosyloxy)cyclohexyl 2,6-diamino-2,6-dideoxy-alph
    • a-D-glucopyranoside</Synonym>
    • < Synonym rdf:datatype=“XMLSchema#string&quot;>C17H34N4O10</Synonym>
    • < InChIKey rdf:datatype=“XMLSchema#string&quot;>InChIKey=NSKGQURZWSPSBC-VVPCINPTBH</InChIKey>
    • < xref rdf:datatype=“XMLSchema#string&quot;>KEGG COMPOUND:25546-65-0</xref>
    • </owl:Class>
    ChEBI ontology 20.10.10
  • 14. ChEBI in OWL: Editing and reasoning
    • Currently the use of a reasoner is not implemented in ChEBI internal processes
    • Our database architecture does not yet support OWL ‘defined classes’ (complex logical expressions are hard to squeeze into an entity-relationship ontology-as-graph model)
    • Adding defined classes makes reasoning potentially slow on an ontology the size of ChEBI
    • (but promising results from hypertableau algorithms)
    ChEBI ontology 20.10.10
  • 15. Chemical structures and OWL
    • Organic chemical entities are complex structured objects
    ChEBI ontology 20.10.10 caffeine Molecules consist of atoms connected by bonds single bond double bond Carbon atom Hydrogen atom Nitrogen atom Oxygen atom
  • 16. Structure-based classification
    • Chemical ontology consists of chemical classes which 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
  • 17. OWL representation Without internal structure, all parts must be explicitly asserted (which leads to a combinatorial explosion for larger molecules) But the internal structure of complex molecules cannot be encoded in OWL ontology axioms due to their cycles does not have a model in the shape of a tree
  • 18. Description Graphs
    • A recent, decidable extension to OWL 2, allowing expression of complex structures as graphs within the ontology
    • A description graph consists of a set of labelled vertices and a set of directed edges
    • Each description graph has a main class which links the graph to the main OWL ontology
    • But, for technical reasons, graph structure cannot be referred to in OWL axioms (‘strong separation’)
  • 19. Rules
    • Enhance OWL with the capacity to express if – then constructions
    • Consist of ‘antecedent’ ( if conditions) and ‘consequent’ ( then result)
    • Antecedent and consequent are composed of conjunctions of atomic statements
    • Reasoning asserts the consequent if the antecedent is true
    •  allows reasoning over structure of graphs
  • 20. Chemical description graphs + Rules defined to detect cycles and parts Reasoning results: able to perform classification (but scalability a concern)
  • 21. Acknowledgements
    • Funding: BBSRC, EMBL, EU
    • Thanks to the ChEBI team led by Christoph Steinbeck
    • Thanks also to Colin Batchelor (RSC), Robert Stevens and Uli Sattler (Manchester),
    • Michel Dumontier (Carleton, Canada)
    ChEBI ontology 20.10.10
  • 22. Thank you for your attention

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