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Consortium Meeting,Barcelona, 17 November 2004

WP 6.3: Pilot on genomics and chronic inflammation. ACTA Bruno Loos, activity leader Marja Laine Bart Crusius Servaas Morre Arie Jan van Winkelhoff Carol van der Palen Ubele van der Velden Salvador Pena. ISCIII Fernando Martín Sanchez UPM Victor Majo Leicester Anthony Brookes

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Consortium Meeting,Barcelona, 17 November 2004

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  1. WP 6.3: Pilot on genomics and chronic inflammation ACTA Bruno Loos, activity leader Marja Laine Bart Crusius Servaas Morre Arie Jan van Winkelhoff Carol van der Palen Ubele van der Velden Salvador Pena ISCIII Fernando Martín Sanchez UPM Victor Majo Leicester Anthony Brookes AVEIRO Antonio Sousa Pereira Custodix George de Moor Nevi Pasco Consortium Meeting,Barcelona, 17 November 2004

  2. WP 6.3: Pilot on genomics and chronic inflammation challenge Patient - genotype phenotype phenotype how to structure and integrate data streams and use data analysis tools, as is the main goal of INFOBIOMED. how to use the pilot for generic purposes. Consortium Meeting,Barcelona, 17 November 2004

  3. WP 6.3: Pilot on genomics and chronic inflammation WP 6-3 meeting October 11, 2004 Consortium Meeting,Barcelona, 17 November 2004

  4. WP 6.3: Pilot on genomics and chronic inflammation General overview of contents of data warehouse (DWH) DWH (periodontitis) intermediate phenotype disease phenotype genetics infection environment Consortium Meeting,Barcelona, 17 November 2004

  5. WP 6.3: Pilot on genomics and chronic inflammation links External sources Intern Intern { SNPs (SPSS) format format dbSNP Microbiology (paper, excel) Genet lab ….. Locus Micro … Limk arrays Pat Pat Env Env Gene Gene clini clini Micro Micro Direct Direct Interm Interm x x ENSEMBL biol biol pheno pheno pheno pheno { taxon 1 1 Images (X - ray) paper micro 2 2 Life habits data (EMR) paper biol NCBI clinic Smoking data 3 3 ….. 4 4 ICD - io clinic LOINC UMLS n n Environ Data mining ontology smoking Datawarehouse (DWH)/biobank lifestyle Query Clinic Consortium Meeting,Barcelona, 17 November 2004

  6. WP 6.3: Pilot on genomics and chronic inflammation Problems encountered/foreseen: Phenotype Data • Phenotype data handling is poorly developed • Increasingly major hurdle for post-genomics analysis • Standards desperately needed • Teams/components now in place to create a solution Consortium Meeting,Barcelona, 17 November 2004

  7. WP 6.3: Pilot on genomics and chronic inflammation Phenotype representation PHENOTYPE Unique entry ID General Specific Name Category Disease Area Method Sub-Phenotype IDs Free Text Citations Keywords Name Attribute Value Units Qualifiers Consortium Meeting,Barcelona, 17 November 2004

  8. WP 6.3: Pilot on genomics and chronic inflammation Problems encountered/foreseen: Genotype Data • DNA-level description of target SNPs • Lab assays and genotype data handling • Need convenient off-the-shelf solution • Genotype - phenotype relationships Consortium Meeting,Barcelona, 17 November 2004

  9. WP 6.3: Pilot on genomics and chronic inflammation General overview of contents of data warehouse (DWH) DWH (periodontitis) intermediate phenotype disease phenotype genetics infection environment Consortium Meeting,Barcelona, 17 November 2004

  10. WP 6.3: Pilot on genomics and chronic inflammation Demonstrate DMA tool (dental X-ray analyses) developed by AVEIRO with ACTA Consortium Meeting,Barcelona, 17 November 2004

  11. WP 6.3: Pilot on genomics and chronic inflammation Demonstrate DMA tool (dental X-ray analyses) Consortium Meeting,Barcelona, 17 November 2004

  12. WP 6.3: Pilot on genomics and chronic inflammation Demonstrate DMA tool (dental X-ray analyses) Consortium Meeting,Barcelona, 17 November 2004

  13. WP 6.3: Pilot on genomics and chronic inflammation Demonstrate DMA tool (dental X-ray analyses) Consortium Meeting,Barcelona, 17 November 2004

  14. WP 6.3: Pilot on genomics and chronic inflammation • Actions planned/agreed WP 6.3 in 2004 • Define external sources, analyze needs, possibilities, costs, how to feed/download. • Madrid meeting June 2004 (ACTA, ISCIII) • State of the Art Report (ACTA, ISCIII, KI, CUSTODIX, UAVR, UPM) • October meeting (ACTA, ISCIII, KI, CUSTODIX, UAVR, UPM) • State of the Art Report finalizing • Conceptualize data warehouse (DWH) • Convert the SOA report to manuscript for European Dental Journal Consortium Meeting,Barcelona, 17 November 2004

  15. WP 6.3: Pilot on genomics and chronic inflammation STEPS: 1 2 3 4 5 SPSS, Excel, Hard copy, DMA, ……. Data mining (results) DWH (periodontitis) Visualization (ODBC) Consortium Meeting,Barcelona, 17 November 2004

  16. WP 6.3: Pilot on genomics and chronic inflammation STEPS: 1 2 3 4 5 2004 2005 2006 SPSS, Excel, Hard copy, DMA, ……. Data mining (results) DWH (periodontitis) Visualization (ODBC) ACTA, LEIC, UAVR, UPM, ISCIII ACTA, Custodix, LEIC, ISCIII and UPM Consortium Meeting,Barcelona, 17 November 2004

  17. WP 6.3: Pilot on genomics and chronic inflammation Calendar Year 1. Build the periodontitis data warehouse (DWH), employing various tools from partners (ACTA, Leicester, Custodix, Aveiro, ISCIII). Define external sources, analyze needs, possibilities, costs, how to feed/download. Year 2. Feed the DWH (ACTA, UAVR, UPM). Start data-analysis and data-mining, employing various tools from partners (UPM, others…..) Year 3. Continue data-analysis and data-mining, employing various tools from partners (UPM, others…..) Consortium Meeting,Barcelona, 17 November 2004

  18. WP 6.3: Pilot on genomics and chronic inflammation • We are working now on: • Create locally a limited database for immediate use in periodontitis. Think about data input and output (UPM). However, think about creating generic solutions (Leic). • Define ontologies encountered. • Improve the local databases, create ideal solution for genotyping data. • Further development of the tool DMA (Dental Morphology Analyzer) • Convert SOA for publication in a European dental journal. Consortium Meeting,Barcelona, 17 November 2004

  19. WP 6.3: Pilot on genomics and chronic inflammation 0 24 12 36 3 15 1 2 3 1 • DWH definition • Technical specifications • Functional specifications • Assessment of data models • Adaptation of data models • Development of data models • Connecting terminology 2 3 • DWH implementation • filling in data • Analytical trials • interact and testing Consortium Meeting,Barcelona, 17 November 2004

  20. WP 6.3: Pilot on genomics and chronic inflammation Consortium Meeting,Barcelona, 17 November 2004

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