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Linked2Safety Architecture

Linked2Safety Architecture. Athos Antoniades, UCY Panagiotis Gouvas, UBITECH. Linked2Safety Main Aspects. Problem Statement Ethical & Legal Aspects Data Cube Definition Linking Data Architecture Overview. 1. Problem Statement. Increasing wealth of primary medical information

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Linked2Safety Architecture

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  1. Linked2Safety Architecture Athos Antoniades, UCY Panagiotis Gouvas, UBITECH

  2. Linked2Safety Main Aspects • Problem Statement • Ethical & Legal Aspects • Data Cube Definition • Linking Data • Architecture Overview

  3. 1. Problem Statement • Increasing wealth of primary medical information • BUT Limited datasets are shared between medical data-providers (fragmentation) • Limited statistical power • Reduced ability to replicate tests • A solution to the above would accelerate clinical research

  4. 2. Ethical & Legal Aspects (1/2) • Respect patients’ anonymity, data’s ownership and privacy • Not possible to transfer or copy patient data from the originating institutions • All machines that hold patient data are need to remain off-line • Computation and analysis will be performed by data providers off-line

  5. 2. Ethical & Legal Aspects (2/2) • Linked2Safety data will not be identifiable and should not lead to the identification of a person’s identity (either directly or indirectly e.g. back-tracing) • We need to strictly adhere to consent form requirements and all ethical and legal issues (European and national) • Legal issues are diverse and different between countries, institutions and studies

  6. Data Cube Generation on Data Provider’s Site • Each data provider generates data cubes from their raw patients’ data • The created data cubes (anonymised data) are then inserted to the Linked2Safety platform Frond-End

  7. Data Cube Approach

  8. 16 year old widow Problem A paper that analyzes data from a specific study reports:

  9. 16 year old widow Problem A paper that analyzes data from a specific study reports:

  10. 16 year old widow Problem A paper that analyzes data from a specific study reports:

  11. Categorization Differences Paper 2 that analyzes data from the same study reports: Paper 1 that analyzes data from a specific study reports:

  12. Perturbation and Cell Suppression Perturbation (+-1) and Cell Suppression (<5) Original Data

  13. 4. Linking Data • Semantic Web is built mainly upon Resource Description Framework models • RDF data model is based upon the idea of making statements about resources • The form of subject-predicate-object expressions is followed (a.k.a. RDF triples) • It is an official W3C specification (2004) • Many serialization/representation formats (XML, JSON etc) • A collection of RDF statements represents a labeled, directed multi-graph

  14. Semantic Interconnection • Interconnection = RDF + Semantic Model + Interfaces function: Carcinogen excretion S2:Cyp1A bioactivity: activation S1:drugX similarTo target: S1: enzY

  15. Semantic Interconnection: Learning New Facts :Protein rdf:type rdf:type stated rdfs: subClassOf inferred :Enzyme rdfs:domain rdfs:domain rdf:type rdf:type Function: Location: Carcinogen excretion :Cyp1A :Cyp2A chr2:123809-123989 In order to achieve such Interconnection, we need to align data to a common format

  16. Semantic Interconnection: Aligning EHR Data

  17. Architectural Overview Semantic Datacube SPARQL

  18. Streamlining the Layers of the Architecture

  19. Data Aggregation Clinical EHR aligned data in CommonEHR (always in Closed-world Room) Data-cube <Patient> <Age>30</Age> <DOB> 1/1/1900</DOB> … </Patient> 0 000 1… 4 8 0 0 5… 0 00 2 0… …… Clinical EHR record A <Patient> <Age>30</Age> <DOB> 1/1/1970</DOB> … </Patient> Clinical EHR record B Data-cube in RDF Format @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>. @prefix sdmx-metadata: <http://purl.org/linked-data/sdmx/2009/metadata#>. <http://linked2safety-project.eu/dataset/data-cube/diabetes/2012-07-20/o1> qb:dataSet <http://linked2safety-project.eu/dataset/data-cube/diabetes/2012-07-20>; sdmx-dimension:Diabetes <http://linked2safety-project.eu/dataset/data-cube/diabetes/diabetes/0>; sdmx-dimension:Weight <http://linked2safety-project.eu/dataset/data-cube/diabetes/weight/1>; sdmx-measure:Cases “0"^^xsd:long; a qb:Observation. <http://linked2safety-project.eu/dataset/data-cube/diabetes/2012-07-20/o2> qb:dataSet <http://linked2safety-project.eu/dataset/data-cube/diabetes/2012-07-20>; sdmx-dimension:Diabetes <http://linked2safety-project.eu/dataset/data-cube/diabetes/diabetes/1>; sdmx-dimension:Weight <http://linked2safety-project.eu/dataset/data-cube/diabetes/weight/1>; sdmx-measure:Cases “8"^^xsd:long; a qb:Observation.

  20. Making Queries

  21. 4. Data Analysis Frond-End

  22. Galaxy Web Portal – Creating DataProcessing Flows

  23. Summary • The most crucial aspects of the project: • Security and Anonymity • Linking Medical Data and Data-cubes • Provide ways of initiating experiments • Integrating securely different partners in different countries • The consortium has come up with innovative solution to address the above

  24. Who to contact • Athos Antoniades Ph.D. - University of Cyprus • Tel: +357 99613238email: athos.antoniades@stremble.com • PanagiotisGouvas - Ph.D. - Ubitech • Tel: +30 211 700 5570email: pgouvas@ubitech.eu

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