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Representing the ChEBI ontology in OWL
 

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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    Representing the ChEBI ontology in OWL Representing the ChEBI ontology in OWL Presentation Transcript

    • The ChEBI ontology and OWL Industry Programme Ontology Tutorial European Bioinformatics Institute 13 October 2010 Janna Hastings EBI Chemoinformatics and Metabolism
    • 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
    • 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
    • ChEBI ontology 4/26/2010 A ChEBI entry page
    • ChEBI ontology ChEBI ontology 20.10.10
      • Organised into three sub-ontologies, namely
          • Molecular structure ontology
          • Subatomic particle ontology
          • Role ontology
      ( R ) -adrenaline
    • ChEBI ontology 20.10.10 Molecular structure ontology
    • ChEBI ontology 20.10.10 Role ontology
    • ChEBI internal ontology architecture ChEBI ontology 20.10.10 Oracle database
    • 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
    • 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
    • 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
    • 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
    • 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
    • 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
    • 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
    • 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
    • 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
    • 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’)
    • 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
    • Chemical description graphs + Rules defined to detect cycles and parts Reasoning results: able to perform classification (but scalability a concern)
    • 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
    • Thank you for your attention