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>
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
13. Finding evidence to support/refute a hypothesis is becoming increasingly difficult Source: http://upload.wikimedia.org/wikipedia/commons/2/26/EnwikipediaArt.PNG
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.
29. HyQueconsumes and producesRDFPaper: 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
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
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)
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 .
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.