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CRAZY SCIENTIST

Explore the grand unification of bioinformatics with a Semantic Web framework. Query a virtual bioinformatics database, create homologous mutant image axioms, and execute complex SPARQL-DL queries with CardioSHARE. Join the fun at SADI and CardioSHARE projects!

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CRAZY SCIENTIST

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  1. CRAZY SCIENTIST

  2. CRAZY SCIENTIST (Mark Wilkinson Posing in his Halloween Costume… he doesn’t usually look like this!)

  3. WILD IDEAS Grand Unification in Physics Electromagnetic Force Weak Nuclear Force Strong Nuclear Force Gravity Are all the same thing…

  4. WILD IDEAS

  5. MY WILD IDEA Grand Unification of Bioinformatics Tools!

  6. MY WILD IDEA A Query Is the same as a Workflow Is the same as an Ontology Is the same as a Hypothesis

  7. 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 itfor a purpose that the source had not anticipated.

  8. Semantic Automated Discovery and Integration http://sadiframework.org Our proposed new Semantic Web Services Framework

  9. 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?

  10. WORKFLOW

  11. QUERY: SELECT images of mutations from genes in organism XXX that share homology to this gene in organism YYY

  12. Concept: “Homologous Mutant Image”

  13. As OWL AxiomsHomologousMutantImage 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” }

  14. Those axioms combine to create an OWL Class: homologous mutant images

  15. QUERY: Retrieve owl:homologous mutant images for gene XXX

  16. DEMO Discover members of OWL classes from distributed data that doesn’t exist…

  17. 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 . • }

  18. Recap A SPARQL-DL Query is entered into CardioSHARE “ElevatedCreatininePatient” is defined by an OWL Ontology SHAREInterprets 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

  19. 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

  20. 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!

  21. MY WILD IDEA A Query Is the same as a Workflow Is the same as an Ontology Is the same as a Hypothesis

  22. Quod Erat Demonstrandum:-)

  23. 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

  24. Credits Benjamin VanderValk (SADI & CardioSHARE) Luke McCarthy (SADI & CardioSHARE) SoroushSamadian (CardioSHARE) IO Informatics (Knowledge Explorer API) microsoftResearch Fin

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