CRAZY SCIENTIST

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CRAZY SCIENTIST
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CRAZY SCIENTIST
(Mark Wilkinson Posing in his Halloween Costume
he doesnt usually look like this!)
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WILD IDEAS
Grand Unification in Physics Electromagnetic
Force Weak Nuclear Force Strong Nuclear
Force Gravity Are all the same thing
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WILD IDEAS
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MY WILD IDEA
Grand Unification of Bioinformatics Tools!
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MY WILD IDEA
A Query Is the same as a Workflow Is the same
as an Ontology Is the same as a Hypothesis
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Wild Idea is enabled by The Semantic Web

• Semantic Web An information system where
  machines can automatically discover information
  from one source, re-interpret it, and correctly
  use it for a purpose that the source had not
  anticipated.

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Semantic Automated Discovery and
Integration http//sadiframework.org Our
proposed new Semantic Web Services Framework
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Our Wild Research QuestionImagine there is a
virtual database containing every result from
every conceivable bioinformatics experiment
(whether or not they have ever been done). How
do we query that database?
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(No Transcript)
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WORKFLOW
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QUERY SELECT images of mutations from genes in
organism XXX that share homology to this gene in
organism YYY
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Concept Homologous Mutant Image
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As OWL AxiomsHomologousMutantImage is
owlequivalentTo Gene Q hasImage image
P Gene Q hasSequence Sequence Q Gene R
hasSequence Sequence R Sequence Q similarTo
Sequence R Gene R my gene of interest
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Those axioms combine to create an OWL
Class homologous mutant images
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QUERY Retrieve owlhomologous mutant images for
gene XXX
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DEMO Discover members of OWL classes from
distributed data that doesnt exist
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http//biordf.net/cardioSHARE/
Show me patients whose creatinine level is
increasing over time, along with their latest
BUN and creatinine levels. PREFIX rdf
lthttp//www.w3.org/1999/02/22-rdf-syntax-nsgt
PREFIX pred lthttp//sadiframework.org/ontologies
/predicates.owlgt PREFIX patient
lthttp//biordf.net/cardioSHARE/gt SELECT ?patient
?bun ?creat FROM lthttp//biordf.net/cardioSHARE/E
levatedCreatininePatientgt WHERE ?patient
rdftype patientElevatedCreatininePatient .
?patient predlatestBUN ?bun . ?patient
predlatestCreatinine ?creat .
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(No Transcript)
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Recap
A SPARQL-DL Query is entered into
CardioSHARE ElevatedCreatininePatient is
defined by an OWL Ontology SHARE Interprets the
OWL Class definition to learn what data needs to
be discovered and/or which analyses need to be
done A workflow is automatically composed and
executed to retrieve and analyse that data
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Recap
A Reasoner is used on the resulting data to find
members of the ElevatedCreatininePatient Ontology
Class Data from those members are returned to
the query. A Workflow is created to execute
the remaining clauses in the query
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Recap
.and The ElevatedCreatininePatient Class is
completely hypothetical!! It came from our
imagination - we believed that those kinds of
patients should exist in the dataset .so it
was a Hypothesis!
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MY WILD IDEA
A Query Is the same as a Workflow Is the same
as an Ontology Is the same as a Hypothesis
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Quod Erat Demonstrandum -)
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Join us!
SADI and CardioSHARE are Open-Source
projects Come join us were having a lot of
fun!! http//sadiframework.org Mark
Wilkinsons Laboratory Website http//wilkinsonla
b.ca
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Fin