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TAMALE Seminar: Evaluating scientific hypotheses using Semantic Web technologies
 

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.

TAMALE Seminar: Evaluating scientific hypotheses using Semantic Web technologies TAMALE Seminar: Evaluating scientific hypotheses using Semantic Web technologies Presentation Transcript

  • Evaluating scientific Hypotheses using semantic web technologies
    Alison Callahan
    TAMALE Seminar
    November 8 2010
  • 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>
  • Source: http://www.webcitation.org/5u4OJ6rYe
  • 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>
  • educational institution
    foaf:person
    rdf:type
    Carleton University
    rdf:type
    works at
    reading
    Alison
    likes
    has brother
    Chris
    rdf:type
    foaf:person
  • 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
  • OWL: The web ontology language
    OWL allows the representation of ontology concepts in a machine understandable manner
    MotherWomanhasChildPerson
  • Biological SCIENCES and the semantic web
    http://bio2rdf.org http://bioportal.bioontology.org
  • HYQUE
    Hypothesis-based query and evaluation tool
    http://semanticscience.org/projects/hyque
  • Source :http://xkcd.com/242/
  • Source: http://kentsimmons.uwinnipeg.ca/cm1504/introscience.htm
  • Finding evidence to support/refute a hypothesis is becoming increasingly difficult
    Source: http://upload.wikimedia.org/wikipedia/commons/2/26/EnwikipediaArt.PNG
  • HyBrow
    Computationally augmented method for hypothesis evaluation
    • developed by Racunas et al. [1]
    • minimum event-based vocabulary
    • uses consistency checking to evaluate hypotheses
    • constraints
    • rules
    • compares hypotheses using neighborhood functions
    • 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.
  • HyBrow
    • small, manually generated knowledge
    • hard coded Perl rules
    • challenging to apply to a new domain
    • needs access to a greater KB
  • HyBrow HyQue
    • Hypothesis query and evaluation system
    • Uses RDF/SPARQL/OWL
    • Background knowledge encoded as OWL ontologies
    • Queries Bio2RDF’s dedicated SPARQL endpoints
    • Context-specific rules that consider experimental conditions
    • 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
  • 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
    • SGD data in Bio2RDF
    • Template event-based SPARQL queries
    • GO, SO, ChEBI, ECO ontologies
  • A HyQue hypothesis is a collection of propositions
    • proposition: “a statement expressing something true or false”
    • 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’
  • 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
  • HyQue Data … but first, a biology primer!
  • How are these processes regulated?
    Source: http://www.webcitation.org/5u4OelqJO
  • Where do OUR CELLS get energy?
  • HyQue data: The gal gene network IN YEAST
    • Genes that encode proteins that transport and metabolize galactose
    • permease – gal2p – transports galactose into cells
    • galactokinase – gal1p
    • uridylyltransferase – gal7p
    • epimerase – gal10p
    • phosphoglucomutase –gal5p
    • Regulation – whether the pathway is on or off
    • gal3p
    • gal4p
    • gal80p
    enzymes that use galactose
  • Source: Ostergaardet al. (2000). Nature Biotechnology 18: 1283 - 1286
  • 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)
  • How does HyQue work?
  • 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
  • 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 .

    }
  • 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> .
  • 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
  • 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 .
  • Hypothesis evaluation RDF generated
  • HyQue as a SADI service
    SADI – Semantic Automated Discovery and Integration
    • HyQueSADI ontology to describe input and output of service
    • 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
  • Questions?