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Evaluating scientific Hypotheses using semantic web technologies,[object Object],Alison Callahan,[object Object],TAMALE Seminar,[object Object],November 8 2010,[object Object]
Why the semantic web?,[object Object],PLAIN TEXT,[object Object],What you see: “The weather today, November 8, will be cloudy with a high of 7°C”,[object Object],What your computer sees: akfalksjdfoaohwoiehroe,[object Object],XML,[object Object],What you see:,[object Object],<weather>,[object Object],   <date>,[object Object],      <month>November</month>,[object Object],      <day>8</day>,[object Object],      <year>2010</year>,[object Object],   </date>,[object Object],   <temperature>,[object Object],      <value>7</value>,[object Object],      <unit>Celcius</unit>,[object Object],    </temperature>,[object Object],    <conditions>cloudy</conditions>,[object Object],</weather>,[object Object],What your computer sees:,[object Object],<weather>,[object Object],   <date>,[object Object],      <month>November</month>,[object Object],      <day>8</day>,[object Object],      <year>2010</year>,[object Object],   </date>,[object Object],   <temperature>,[object Object],      <value>5</value>,[object Object],      <unit>Celcius</unit>,[object Object],    </temperature>,[object Object],    <condi>Flurries</condi>,[object Object],</weather>,[object Object]
TAMALE Seminar: Evaluating scientific hypotheses using Semantic Web technologies
Source: http://www.webcitation.org/5u4OJ6rYe,[object Object]
RDF,[object Object],Resource Description Framework: A W3C standard for representing resources and the relationships between them, and for data exchange on the WWW,[object Object],Alison,[object Object],reading,[object Object],likes,[object Object],	        subject                       predicate                        object,[object Object], http://people.com#Alisonhttp://feelings.com#likes http://activities.com#reading,[object Object],<rdf:RDF>,[object Object],    <rdf:Descriptionrdf:about="http://people.com#Alison">,[object Object],<likesxmlns="http://feelings.com#",[object Object],rdf:resource="http://activities.com#reading"/>,[object Object],    </rdf:Description>,[object Object],</rdf:RDF>,[object Object]
educational institution,[object Object],foaf:person,[object Object],rdf:type,[object Object],Carleton University,[object Object],rdf:type,[object Object],works at,[object Object],reading,[object Object],Alison,[object Object],likes,[object Object],has brother,[object Object],Chris,[object Object],rdf:type,[object Object],foaf:person,[object Object]
Querying RDF using SPARQL,[object Object],SPARQL = SPARQL Protocol and RDF Query Language,[object Object],	select ?s where {,[object Object],		?s rdf:typefoaf:Person .,[object Object],	},[object Object],http://people.com#Alison,[object Object],http://people.com#Christopher,[object Object]
OWL: The web ontology language,[object Object],OWL allows the representation of ontology concepts in a machine understandable manner,[object Object],MotherWomanhasChildPerson,[object Object]
Biological SCIENCES and the semantic web,[object Object],http://bio2rdf.org		 		http://bioportal.bioontology.org,[object Object]
HYQUE,[object Object],Hypothesis-based query and evaluation tool,[object Object],http://semanticscience.org/projects/hyque,[object Object]
Source :http://xkcd.com/242/,[object Object]
Source: http://kentsimmons.uwinnipeg.ca/cm1504/introscience.htm,[object Object]
Finding evidence to support/refute a hypothesis is becoming increasingly difficult,[object Object],Source: http://upload.wikimedia.org/wikipedia/commons/2/26/EnwikipediaArt.PNG,[object Object]
HyBrow,[object Object],Computationally augmented method for hypothesis evaluation,[object Object],[object Object]
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.,[object Object]
HyBrow,[object Object],[object Object]
hard coded Perl rules
challenging to apply to a new domain
needs access to a greater KB,[object Object]
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 producesRDFPaper: Callahan, A., M. Dumontier & N. Shah. 2010. HyQue: Evaluating hypotheses using Semantic Web technologies. Bio-ontologies SIG, ISMB’10, Boston MA.,[object Object],On the web: http://semanticscience.org/projects/hyque,[object Object]
HyQue is composed of …,[object Object],[object Object],Describes generic input hypothesis and output hypothesis evaluation classes,[object Object],Uses upper level classes e.g. ‘proposition’, ‘measurement value’, ‘event’ ,[object Object],[object Object]
SGD data in Bio2RDF
Template event-based SPARQL queries
GO, SO, ChEBI, ECO ontologies,[object Object]
HyQue hypotheses are composed of propositions connected using logical operators (AND, OR…)HyQuehypothesis   ‘proposition’ that ‘has part’ some ‘hypothesis part’,[object Object],Hypothesis part  ‘proposition’ that ‘has component’ some ‘event’,[object Object]
HyQue events,[object Object],Events are composed of conditional assertions on a relation between ‘actor’ and ‘target’ ,[object Object],induces(actor, target, context, location),[object Object],For decidable logic (OWL), an n-ary object is used,[object Object],Event,[object Object],agent_aactor,[object Object],agent_btarget,[object Object],perturbation_contextcontext,[object Object],physical_locationlocation,[object Object]
HyQue Data … but first, a biology primer!,[object Object]
TAMALE Seminar: Evaluating scientific hypotheses using Semantic Web technologies
How are these processes regulated? ,[object Object],Source: http://www.webcitation.org/5u4OelqJO,[object Object]

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TAMALE Seminar: Evaluating scientific hypotheses using Semantic Web technologies

Notas do Editor

  1. .
  2. 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.