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The Website of RAD (RNA Abundance Database) Part II

The Website of RAD (RNA Abundance Database) Part II. Junmin Liu. (presentation 10/09/03). “Raddies”. Greg Grant Hongxian He Junmin Liu Matt Mailman Elisabetta Manduchi Shannon McWeeney (now at OHSU) Angel Pizarro Chris Stoeckert Trish Whetzel. Outline. The goal of the RAD website

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The Website of RAD (RNA Abundance Database) Part II

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  1. The Website of RAD (RNA Abundance Database)Part II Junmin Liu (presentation 10/09/03)

  2. “Raddies” Greg Grant Hongxian He Junmin Liu Matt Mailman Elisabetta Manduchi Shannon McWeeney (now at OHSU) Angel Pizarro Chris Stoeckert Trish Whetzel

  3. Outline • The goal of the RAD website • Overview of RAD3 schema • RAD3: Ontology emphasis • What’s new on the RAD website • Conclusion • Future direction • Question

  4. Goal of RAD website • Provide the fully annotated information for each deposited microarray study. • Cover every aspect of microarray study, e.g. experimental design, sample preparation, hybridization, data collection, data processing and analysis, in variety of formats such as text, graphics and MAGE-ML. • Provide limited web-based data analysis tools, just for demonstration purpose • Provide instruction for public to download RAD-StudyAnnotation and RAD-Querier packages

  5. RAD3 schema • Tables can be divided into nine parts: • Platform tables • Assay to Quantification tables • Study Design tables • BioMaterials tables • Quantification Result tables • Processing tables • Analysis Result tables • Misc tables: Protocol, Contact, Ontologies • Integrity Checks tables • Suite of Biomaterial tables to cover sample treatment in great detail. • More structured Study Design tables to facilitate the cross-study microarray data comparison • Flexible data process or analysis tables to fit any process or analysis type • OntologyEntry----better suit the MGED efforts (MIAME, Ontology)

  6. BioMaterialMeasurement OntologyEntry BioMaterialCharacteristic Treatment BioMaterialImp LabelMethod BioSource BioSample LabeledExtract AssayLEX AssayBioMaterial Assay BioMaterials Grayfilling indicates a view of a generic table Limefilling indicates a linking table Orangefilling indicates a table showing the connection to another table group Purplefilling indicates the OntologyEntry table

  7. OntologyEntry • Purpose • Provide common terms and details necessary to create instances of a microarray experiment • Benefits • Known terms with a defined meaning • Minimize free text in database • Web queries can be generated using CV terms

  8. RAD WebsiteGeneral structure • Menu based • Home --- Query --- Tools --- Download --- Data Submission --- Get RAD --- Publication • Web interface written in html, php and perl cgi scripts • BioMatGraph package generates sample preparation information using AT&T Lab’sGraphViz. • Expression profile querier package has C, Perl, Java Applet compoments

  9. What’s new • Enhanced query interface --- search for study, array and protocol • Automatically generate graphic display of the biomaterials used in a study or assay • Expression profile querier applet • Provide information about how to install RAD

  10. Analysis • Xcluster: only provide three datasets, the tree display script doesn’t work for a cluster of over 1000 genes • PaGE: provide four replication studys, one pancreatic developmental time series and three stem cell molecular signature study datasets • MvA plot: works on all 2-channel microarray datasets • Expression profile querier: currently being applied to two Novartis datasets

  11. CLICK ! CLICK ! CLICK!......

  12. UML Diagram of Expression Profile Querier Invoke ReportMaker

  13. Conclusions The RAD web reflects the new RAD schema as well as the well developed ontology concepts. The RAD website emphasizes on providing microarray data and covering every aspect of microarray study in variety of formats such as text, graphics. Provide limited ways to analyze the microarray data online.

  14. Future Direction • Provide useful and meaningful to display the analysis result • Provide more sophisticated query interface to answer some gene-orientated question like “give a gene, find its and its transcription factors’ expression level cross different tissues in different studys”. • Provide this RAD-Querier for public download along with the RAD-StudyAnnotator • Integrate the effort of displaying expression data on our three websites: Allgene, PlasmoDB, EPConDB, RAD. • Integrate all the common effort on all cbil websites.

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