Transcript CRAZY SCIENTIST

CRAZY SCIENTIST
CRAZY SCIENTIST
(Mark Wilkinson Posing in his Halloween Costume… he doesn’t usually look like this!)
WILD IDEAS
Grand Unification in Physics
Electromagnetic Force
Weak Nuclear Force
Strong Nuclear Force
Gravity
Are all the same thing…
WILD IDEAS
MY WILD IDEA
Grand Unification
of
Bioinformatics Tools!
MY WILD IDEA
A Query
Is the same as a Workflow
Is the same as an Ontology
Is the same as a Hypothesis
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.
Semantic Automated Discovery and Integration
http://sadiframework.org
Our proposed new Semantic Web Services Framework
Our Wild Research Question
Imagine 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?
WORKFLOW
QUERY:
SELECT images of
mutations from genes in
organism XXX that
share homology to this
gene in organism YYY
Concept:
“Homologous Mutant
Image”
As OWL Axioms
HomologousMutantImage
is owl:equivalentTo {
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”
}
Those axioms
combine to
create an
OWL Class:
homologous
mutant images
QUERY:
Retrieve
owl:homologous
mutant images for
gene XXX
DEMO
Discover members of OWL classes
from distributed data that doesn’t exist…
http://biordf.net/cardioSHARE/
Show me patients whose creatinine level is increasing
over time, along with their latest BUN and creatinine levels.
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX pred: <http://sadiframework.org/ontologies/predicates.owl#>
PREFIX patient: <http://biordf.net/cardioSHARE/>
SELECT ?patient ?bun ?creat
FROM <http://biordf.net/cardioSHARE/ElevatedCreatininePatient>
WHERE {
?patient rdf:type patient:ElevatedCreatininePatient .
?patient pred:latestBUN ?bun .
?patient pred:latestCreatinine ?creat .
}
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
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
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!
MY WILD IDEA
A Query
Is the same as a Workflow
Is the same as an Ontology
Is the same as a Hypothesis
Quod Erat Demonstrandum
:-)
Join us!
SADI and CardioSHARE are Open-Source
projects
Come join us – we’re having a lot of fun!!
http://sadiframework.org
Mark Wilkinson’s Laboratory Website:
http://wilkinsonlab.ca
Fin