CRAZY SCIENTIST CRAZY SCIENTIST Mark Wilkinson Posing in

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: 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 Homologous. Mutant. Image is owl: equivalent. To { Gene Q has. Image image P Gene Q has. Sequence Q Gene R has. Sequence R Sequence Q similar. To 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/cardio. SHARE/ Show me patients whose creatinine level is increasing over time, along with their latest BUN and creatinine levels. PREFIX rdf: <http: //www. w 3. org/1999/02/22 -rdf-syntax-ns#> PREFIX pred: <http: //sadiframework. org/ontologies/predicates. owl#> PREFIX patient: <http: //biordf. net/cardio. SHARE/> SELECT ? patient ? bun ? creat FROM <http: //biordf. net/cardio. SHARE/Elevated. Creatinine. Patient> WHERE { ? patient rdf: type patient: Elevated. Creatinine. Patient. ? patient pred: latest. BUN ? bun. ? patient pred: latest. Creatinine ? creat. }

Recap A SPARQL-DL Query is entered into Cardio. SHARE “Elevated. Creatinine. Patient” 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 Elevated. Creatinine. Patient 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 Elevated. Creatinine. Patient 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 Cardio. SHARE 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