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TAMALE Seminar: Evaluating scientific hypotheses using Semantic Web technologies

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This presentation was given as part of the University of Ottawa TAMALE group seminar series: http://tamale.uottawa.ca

This presentation was given as part of the University of Ottawa TAMALE group seminar series: http://tamale.uottawa.ca

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  • .
  • Take home message: HyQue is a project that uses semantic web technologies to represent biological knowledge; and uses those representations to answer questions and do useful work.
  • Transcript

    • 1. Evaluating scientific Hypotheses using semantic web technologies
      Alison Callahan
      TAMALE Seminar
      November 8 2010
    • 2. Why the semantic web?
      PLAIN TEXT
      What you see: “The weather today, November 8, will be cloudy with a high of 7°C”
      What your computer sees: akfalksjdfoaohwoiehroe
      XML
      What you see:
      <weather>
      <date>
      <month>November</month>
      <day>8</day>
      <year>2010</year>
      </date>
      <temperature>
      <value>7</value>
      <unit>Celcius</unit>
      </temperature>
      <conditions>cloudy</conditions>
      </weather>
      What your computer sees:
      <weather>
      <date>
      <month>November</month>
      <day>8</day>
      <year>2010</year>
      </date>
      <temperature>
      <value>5</value>
      <unit>Celcius</unit>
      </temperature>
      <condi>Flurries</condi>
      </weather>
    • 3.
    • 4. Source: http://www.webcitation.org/5u4OJ6rYe
    • 5. RDF
      Resource Description Framework: A W3C standard for representing resources and the relationships between them, and for data exchange on the WWW
      Alison
      reading
      likes
      subject predicate object
      http://people.com#Alisonhttp://feelings.com#likes http://activities.com#reading
      <rdf:RDF>
      <rdf:Descriptionrdf:about="http://people.com#Alison">
      <likesxmlns="http://feelings.com#"
      rdf:resource="http://activities.com#reading"/>
      </rdf:Description>
      </rdf:RDF>
    • 6. educational institution
      foaf:person
      rdf:type
      Carleton University
      rdf:type
      works at
      reading
      Alison
      likes
      has brother
      Chris
      rdf:type
      foaf:person
    • 7. Querying RDF using SPARQL
      SPARQL = SPARQL Protocol and RDF Query Language
      select ?s where {
      ?s rdf:typefoaf:Person .
      }
      http://people.com#Alison
      http://people.com#Christopher
    • 8. OWL: The web ontology language
      OWL allows the representation of ontology concepts in a machine understandable manner
      MotherWomanhasChildPerson
    • 9. Biological SCIENCES and the semantic web
      http://bio2rdf.org http://bioportal.bioontology.org
    • 10. HYQUE
      Hypothesis-based query and evaluation tool
      http://semanticscience.org/projects/hyque
    • 11. Source :http://xkcd.com/242/
    • 12. Source: http://kentsimmons.uwinnipeg.ca/cm1504/introscience.htm
    • 13. Finding evidence to support/refute a hypothesis is becoming increasingly difficult
      Source: http://upload.wikimedia.org/wikipedia/commons/2/26/EnwikipediaArt.PNG
    • 14. HyBrow
      Computationally augmented method for hypothesis evaluation
      • developed by Racunas et al. [1]
      • 15. minimum event-based vocabulary
      • 16. uses consistency checking to evaluate hypotheses
      • 17. constraints
      • 18. rules
      • 19. compares hypotheses using neighborhood functions
      • 20. incremental hypothesis improvement
      [1] Racunas S. A., Shah N. H., Albert I. and Fedoroff N. V. (2004). HyBrow: A prototype system for computer-aided hypothesis evaluation. Bioinformatics 20(S. 1): i1-i8.
    • 21. HyBrow
      • small, manually generated knowledge
      • 22. hard coded Perl rules
      • 23. challenging to apply to a new domain
      • 24. needs access to a greater KB
    • HyBrow HyQue
      • Hypothesis query and evaluation system
      • 25. Uses RDF/SPARQL/OWL
      • 26. Background knowledge encoded as OWL ontologies
      • 27. Queries Bio2RDF’s dedicated SPARQL endpoints
      • 28. Context-specific rules that consider experimental conditions
      • 29. HyQueconsumes and producesRDF
      Paper: Callahan, A., M. Dumontier & N. Shah. 2010. HyQue: Evaluating hypotheses using Semantic Web technologies. Bio-ontologies SIG, ISMB’10, Boston MA.
      On the web: http://semanticscience.org/projects/hyque
    • 30. HyQue is composed of …
      • HyQue hypothesis ontology
      Describes generic input hypothesis and output hypothesis evaluation classes
      Uses upper level classes e.g. ‘proposition’, ‘measurement value’, ‘event’
      • HyBrow SPARQL endpoint
      • 31. SGD data in Bio2RDF
      • 32. Template event-based SPARQL queries
      • 33. GO, SO, ChEBI, ECO ontologies
    • A HyQue hypothesis is a collection of propositions
      • proposition: “a statement expressing something true or false”
      • 34. HyQue hypotheses are composed of propositions connected using logical operators (AND, OR…)
      HyQuehypothesis ‘proposition’ that ‘has part’ some ‘hypothesis part’
      Hypothesis part ‘proposition’ that ‘has component’ some ‘event’
    • 35. HyQue events
      Events are composed of conditional assertions on a relation between ‘actor’ and ‘target’
      induces(actor, target, context, location)
      For decidable logic (OWL), an n-ary object is used
      Event
      agent_aactor
      agent_btarget
      perturbation_contextcontext
      physical_locationlocation
    • 36. HyQue Data … but first, a biology primer!
    • 37.
    • 38. How are these processes regulated?
      Source: http://www.webcitation.org/5u4OelqJO
    • 39. Where do OUR CELLS get energy?
    • 40. HyQue data: The gal gene network IN YEAST
      • Genes that encode proteins that transport and metabolize galactose
      • 41. permease – gal2p – transports galactose into cells
      • 42. galactokinase – gal1p
      • 43. uridylyltransferase – gal7p
      • 44. epimerase – gal10p
      • 45. phosphoglucomutase –gal5p
      • 46. Regulation – whether the pathway is on or off
      • 47. gal3p
      • 48. gal4p
      • 49. gal80p
      enzymes that use galactose
    • 50. Source: Ostergaardet al. (2000). Nature Biotechnology 18: 1283 - 1286
    • 51. HyQue data
      Experimentally determined interactions between the GAL proteins
      Properties of the genes that encode these proteins (SGD)
      Literature-based evidence (citations)
      Knowledge about cellular locations and events (GO)
      Types of evidence supporting these interactions (ECO)
    • 52. How does HyQue work?
    • 53. Individual events parsed from input hypothesis RDF
      hypothesis
      :h a hyque:Hypothesis ;
      a hyque:AND ;
      hyque:hasPart :p1 ;
      hyque:hasPart :p2 ;
      hyque:hasPart :p3 .
      :p1 a hyque:AND ;
      hyque:hasComponent :e1 ;
      hyque:hasComponent :e2 .
      :e1 a <http://bio2rdf.org/go:0006810> ;
      hybrow:is_negated “0”^^xsd:boolean ;
      hybrow:agent_a <http://bio2rdf.org/sgd:Gal2p> ;
      hybrow:agent_b <http://bio2rdf.org/chebi:28260> .
      :e2 a <http://bio2rdf.org/go:0005488> ;
      hybrow:is_negated “0”^^xsd:boolean ;
      hybrow:agent_a <http://bio2rdf.org/sgd:Gal3p> ;
      hybrow:agent_b <http://bio2rdf.org/sgd:Gal80p> .
      has part
      hypothesis part 1
      has component
      gal2p transports galactose
      gal3p binds to gal80p
    • 54. Template SPARQL queries completed based on event properties
      :e1 a go:0006810 ;
      hybrow:is_negated "0" ;
      hybrow:agent_asgd:Gal2p ;
      hybrow:agent_bchebi:28260 .
      construct { … } where {

      ?event hybrow:is_negated ?negated .
      ?event hybrow:physical_operator ?physical_operator .
      ?event hybrow:agent_a <http://bio2rdf.org/sgd:Gal2p> .

      ?event hybrow:agent_b <http://bio2rdf.org/chebi:28260> .
      ?actor semsci:isLocatedIn ?actor_gp_id_location .
      ?actor_gp_id_locationrdf:type ?actor_location_type .
      ?actor semsci:hasFunction ?actor_gp_id_function .
      ?actor_gp_id_functionrdf:type ?actor_function .

      }
    • 55. SPARQL query results retrieved
      hybrow_data:2c1789a3019fd2fe9843d507824fc591
      rdf:type <http://bio2rdf.org/go:0044092> .
      hybrow:is_negated "0" .
      hybrow:agent_a sgd:Gal3p ;
      hybrow:agent_b sgd:Gal80p ;
      hybrow:actor_type <http://bio2rdf.org/chebi:36080> ;
      hybrow:target_type <http://bio2rdf.org/chebi:36080> ;
      hybrow:physical_context <http://bio2rdf.org/go:0005634> ;
      hybrow:physical_operator <http://bio2rdf.org/go:0005488> .
      hybrow_data:b09f7cc043201b47610c874499448a23
      rdf:type <http://bio2rdf.org/go:0005488> ;
      hybrow:is_negated "0" ;
      hybrow:agent_a sgd:Gal3p ;
      hybrow:agent_b sgd:Gal80p ;
      hybrow:actor_type <http://bio2rdf.org/chebi:36080> ;
      hybrow:target_type <http://bio2rdf.org/chebi:36080> ;
      hybrow:physical_context <http://bio2rdf.org/go:0005634> ;
      hybrow:physical_operator <http://bio2rdf.org/go:0005488> .
    • 56. Query results evaluated based on rule sets
      ‘binding’ rule:
      Is event negated?
      If yes, subtract 2
      Is physical operator ‘binding’?
      If yes, add 1; if no, subtract 1
      Is actor of type ‘protein’ or ‘small molecule’?
      If yes, add 1; if of type ‘gene’, subtract 1
      Is target of type ‘protein’ or ‘small molecule’?
      If yes, add 1; if of type ‘gene’, subtract 1
      Does actor have known ‘binding’ function?
      If yes, add 1
      GO:0005488
      CHEBI:36080
      SO:0000236
    • 57. Result scores based on operators between events
      Final score = e1 score + e2 score + e3 score + e4 score
      Final score = maximum of e5, e6 or e7 scores
      :p1 a hyque:AND ;
      hyque:hasComponent :e1 ;
      hyque:hasComponent :e2 ; hyque:hasComponent :e3 ;
      hyque:hasComponent :e4 .
      :p2 a hyque:OR ;
      hyque:hasComponent :e5 ;
      hyque:hasComponent :e6 ;
      hyque:hasComponent :e7 .
    • 58. Hypothesis evaluation RDF generated
    • 59.
    • 60.
    • 61. HyQue as a SADI service
      SADI – Semantic Automated Discovery and Integration
      • HyQueSADI ontology to describe input and output of service
      • 62. Users can post a hypothesis in RDF and receive the hypothesis evaluation in RDF
    • ACKNOWLEDGEMENTS
      My supervisor: Dr. Michel Dumontier
      Project collaborator: Dr. Nigam Shah http://stanford.edu/~nigam
      The Dumontier Lab: http://dumontierlab.com
      Funding: NSERC to MD
    • 63. Questions?

    ×