Representing the ChEBI ontology in OWL


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Presented at the EBI Industry Programme Ontology tutorial.

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Representing the ChEBI ontology in OWL

  1. 1. The ChEBI ontology and OWL Industry Programme Ontology Tutorial European Bioinformatics Institute 13 October 2010 Janna Hastings EBI Chemoinformatics and Metabolism
  2. 2. Overview <ul><li>Introduction to ChEBI </li></ul><ul><li>Porting ChEBI into OWL format </li></ul><ul><ul><li>Relationship patterns </li></ul></ul><ul><ul><li>Metadata </li></ul></ul><ul><ul><li>Editing and reasoning </li></ul></ul><ul><li>Chemical structures and OWL </li></ul><ul><ul><li>Description graphs and rules </li></ul></ul>ChEBI ontology 20.10.10
  3. 3. Introduction to ChEBI <ul><li>Ch emical E ntities of B iological I nterest </li></ul><ul><li>Focused on ‘small’ chemical entities: no proteins or nucleic acids </li></ul><ul><li>Scope (material entities): mainly molecules, but also salts, polymers, atoms, electrons, groups, residues </li></ul><ul><li>Scope (dependent entities): chemical role, biological role, application </li></ul><ul><li>Access ChEBI at </li></ul>ChEBI ontology 20.10.10
  4. 4. ChEBI ontology 4/26/2010 A ChEBI entry page
  5. 5. ChEBI ontology ChEBI ontology 20.10.10 <ul><li>Organised into three sub-ontologies, namely </li></ul><ul><ul><ul><li>Molecular structure ontology </li></ul></ul></ul><ul><ul><ul><li>Subatomic particle ontology </li></ul></ul></ul><ul><ul><ul><li>Role ontology </li></ul></ul></ul>( R ) -adrenaline
  6. 6. ChEBI ontology 20.10.10 Molecular structure ontology
  7. 7. ChEBI ontology 20.10.10 Role ontology
  8. 8. ChEBI internal ontology architecture ChEBI ontology 20.10.10 Oracle database
  9. 9. A ChEBI entity in OBO format <ul><li>[Term] id: CHEBI:17051 name: fluoride alt_id: CHEBI:49593 alt_id: CHEBI:14271 def: &quot;A monoatomic fluorine that has formula F.&quot; [] synonym: &quot;fluoride(1-)&quot; EXACT IUPAC_NAME [IUPAC:] synonym: &quot;F&quot; RELATED FORMULA [KEGG COMPOUND:] synonym: &quot;[F-]&quot; RELATED SMILES [ChEBI:] synonym: &quot;InChI=1/FH/h1H/p-1/fF/h1h/q-1&quot; RELATED InChI [ChEBI:] xref: Gmelin:14905 &quot;Gmelin Registry Number&quot; xref: NIST Chemistry WebBook:16984-48-8 &quot;CAS Registry Number&quot; xref: KEGG COMPOUND:C00742 &quot;KEGG COMPOUND&quot; is_a: CHEBI:16042 is_a: CHEBI:36895 relationship: is_conjugate_base_of CHEBI:29228 </li></ul>ChEBI ontology 20.10.10
  10. 10. Expressing ChEBI in OWL <ul><li>OWL format version of ChEBI is available via OBO -> OWL translation (provided by the OBO Foundry) </li></ul><ul><li>Motivations for providing ‘primary’ OWL version of ChEBI </li></ul><ul><ul><li>enable the use of modern ontology tools such as Protégé </li></ul></ul><ul><ul><li>provide synonyms in multiple languages (not yet fully supported in OBO format) </li></ul></ul><ul><ul><li>gain control over the logical axiomatization of the ontology </li></ul></ul><ul><ul><li>upgrade to OWL 2 and continue to keep up-to-date </li></ul></ul>ChEBI ontology 20.10.10
  11. 11. ChEBI in OWL: Relationship patterns <ul><li>OBO relationship: X rel Y </li></ul><ul><li>OWL ‘relationships’ expressed as logical axioms, which may have different forms </li></ul><ul><li>e.g. X ⊑  rel.Y (value restriction) (‘only’) or X ⊑  rel.Y (existential quantification) (‘some’) </li></ul><ul><li>Some ChEBI relationships, such as has_part, follow the existential pattern in OWL </li></ul><ul><li>Others, such as has_parent_hydride, might be better expressed with the value restriction pattern </li></ul>ChEBI ontology 20.10.10
  12. 12. ChEBI in OWL: Metadata <ul><li>Metadata in OBO format has a standard, fixed, format: </li></ul><ul><ul><li>name, def </li></ul></ul><ul><ul><li>synonym </li></ul></ul><ul><ul><li>xref </li></ul></ul><ul><li>Metadata in OWL provided for via annotations – a multi-purpose, flexible metadata standard </li></ul><ul><ul><li>name uses rdfs:label </li></ul></ul><ul><ul><li>Synonyms use </li></ul></ul><ul><li> <owl:AnnotationProperty rdf:about=&quot;;/> </li></ul><ul><ul><ul><li>Example of custom ChEBI annotation </li></ul></ul></ul><ul><li> <owl:AnnotationProperty rdf:about=&quot;;/> </li></ul>ChEBI ontology 20.10.10
  13. 13. A ChEBI entity in OWL format <ul><li><owl:Class rdf:about=&quot;;> </li></ul><ul><li>< rdfs:label rdf:datatype=“XMLSchema#string&quot;>vistamycin</rdfs:label> </li></ul><ul><li>< rdfs:subClassOf rdf:resource=&quot;;/> </li></ul><ul><li><rdfs: subClassOf ><owl: Restriction ><owl:onProperty rdf:resource=&quot;;/> </li></ul><ul><li><owl: someValuesFrom rdf:resource=&quot;;/> </owl:Restriction> </rdfs:subClassOf> </li></ul><ul><li>< 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 </li></ul><ul><li>a-D-glucopyranoside</Synonym> </li></ul><ul><li>< Synonym rdf:datatype=“XMLSchema#string&quot;>C17H34N4O10</Synonym> </li></ul><ul><li>< InChIKey rdf:datatype=“XMLSchema#string&quot;>InChIKey=NSKGQURZWSPSBC-VVPCINPTBH</InChIKey> </li></ul><ul><li>< xref rdf:datatype=“XMLSchema#string&quot;>KEGG COMPOUND:25546-65-0</xref> </li></ul><ul><li></owl:Class> </li></ul>ChEBI ontology 20.10.10
  14. 14. ChEBI in OWL: Editing and reasoning <ul><li>Currently the use of a reasoner is not implemented in ChEBI internal processes </li></ul><ul><li>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) </li></ul><ul><li>Adding defined classes makes reasoning potentially slow on an ontology the size of ChEBI </li></ul><ul><li>(but promising results from hypertableau algorithms) </li></ul>ChEBI ontology 20.10.10
  15. 15. Chemical structures and OWL <ul><li>Organic chemical entities are complex structured objects </li></ul>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. 16. Structure-based classification <ul><li>Chemical ontology consists of chemical classes which can be defined by parts of structures and/or properties of structures </li></ul>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. 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. 18. Description Graphs <ul><li>A recent, decidable extension to OWL 2, allowing expression of complex structures as graphs within the ontology </li></ul><ul><li>A description graph consists of a set of labelled vertices and a set of directed edges </li></ul><ul><li>Each description graph has a main class which links the graph to the main OWL ontology </li></ul><ul><li>But, for technical reasons, graph structure cannot be referred to in OWL axioms (‘strong separation’) </li></ul>
  19. 19. Rules <ul><li>Enhance OWL with the capacity to express if – then constructions </li></ul><ul><li>Consist of ‘antecedent’ ( if conditions) and ‘consequent’ ( then result) </li></ul><ul><li>Antecedent and consequent are composed of conjunctions of atomic statements </li></ul><ul><li>Reasoning asserts the consequent if the antecedent is true </li></ul><ul><li> allows reasoning over structure of graphs </li></ul>
  20. 20. Chemical description graphs + Rules defined to detect cycles and parts Reasoning results: able to perform classification (but scalability a concern)
  21. 21. Acknowledgements <ul><li>Funding: BBSRC, EMBL, EU </li></ul><ul><li>Thanks to the ChEBI team led by Christoph Steinbeck </li></ul><ul><li>Thanks also to Colin Batchelor (RSC), Robert Stevens and Uli Sattler (Manchester), </li></ul><ul><li>Michel Dumontier (Carleton, Canada) </li></ul>ChEBI ontology 20.10.10
  22. 22. Thank you for your attention