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Rat Genome Database RGD

Rat Genome Database RGD

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Rat Genome Database RGD

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  1. Rat Genome DatabaseRGD http://rgd.mcw.edu Dean Pasko Norie de la Cruz RGD Demo ISMB Scotland 8/03/04

  2. RGD Background • Rat Genome Database is a NIH funded project • NHLBI (grant HL64541) • Database went public on June 1, 2000 • RGD’s mission statement: • “RGD curates and integrates all rat genetic • and genomic data and provides access to this data • to support research using the rat as • a genetic model to study human diseases.” RGD Demo ISMB Scotland 8/03/04

  3. RGD Background • RGD’s curation and integration involves many processes: • Manual curation of literature • Informatic curation/validation of both curated and • non-curated data loaded into the database • Leveraging of comparative genomic and functional data • to annotate rat data RGD Demo ISMB Scotland 8/03/04

  4. Comparative Genomics • Rat offers many resources for comparative genomics • Rat is a great model organism for human disease • RGD has tools to relate phenotype and disease • Rat QTL data • Mouse QTL data • Human QTL data • New genome sequence (Nature, April of 2004) • Human and Mouse homolog data and reports • Gene ontology data • Phenotype ontology data • Disease ontology data RGD Demo ISMB Scotland 8/03/04

  5. RGD Tools • RGD’s multi-species and comparative tools • Advance/quick search • Comprehensive for rat data (annotations, ontologies, etc.) • Homologs - searches symbol and name and ontologies (coming soon!) • Virtual Comparative Map (VCMap) – EST/Unigene based • Gene Annotation – query tool for multiple databases for • Rat, Mouse, and Human • RGD’s genome browser • GBrowse (GMOD open source tool) • RGD object specific query tools • Genes, QTLs, Strains, Ontologies, Homologs, etc. RGD Demo ISMB Scotland 8/03/04

  6. RGD Home Page RGD Demo ISMB Scotland 8/03/04

  7. Advanced and QuickSearches RGD Demo ISMB Scotland 8/03/04

  8. Quick & Advanced Search RGD Demo ISMB Scotland 8/03/04

  9. Search for RGD_ID Quick Search & Advanced Search • enter: one RGD_ID or RGD:RGD_ID • returns: report page for the object with that RGD_ID • no other numbers (e.g., Entrez Gene or Ratmap ID) can be searched • only one ID can be searched at a time RGD Demo ISMB Scotland 8/03/04

  10. Quick Search-keyword Results ordered: equals, begins, contains RGD Demo ISMB Scotland 8/03/04

  11. Special CasesQuick Search & Advanced Search RGD Demo ISMB Scotland 8/03/04

  12. Ontology searches • searches term and descendants • if search for “antioxidant”, returns genes annotated to glutathione dehydrogenase (ascorbate) activity, peroxidase activity, etc. RGD Demo ISMB Scotland 8/03/04

  13. Advanced Search • Boolean Logic • AND, OR, NOT • Limit to 1 or more objects RGD Demo ISMB Scotland 8/03/04

  14. Quick Search RGD Demo ISMB Scotland 8/03/04

  15. Advanced Search RGD Demo ISMB Scotland 8/03/04

  16. Results Summary Page RGD Demo ISMB Scotland 8/03/04

  17. Search Results-Genes • Genes • species • symbol • name • gene description • chromosome • location RGD Demo ISMB Scotland 8/03/04

  18. Search Results Report RGD Demo ISMB Scotland 8/03/04

  19. Search Results-QTL • QTL • species • symbol • name • chromosome • trait • subtrait • location RGD Demo ISMB Scotland 8/03/04

  20. Search Results-Strains • Strains • species • symbol • name • location RGD Demo ISMB Scotland 8/03/04

  21. Sort on any column Go back to summary page Show only selected items Select some or all records Download report Search Results RGD Demo ISMB Scotland 8/03/04

  22. Ontology search Object search Alternative search RGD Demo ISMB Scotland 8/03/04

  23. Object Specific Searches RGD Demo ISMB Scotland 8/03/04

  24. QTL Query RGD Demo ISMB Scotland 8/03/04

  25. 10 10: 8 8 QTL Report RGD Demo ISMB Scotland 8/03/04

  26. Gene Query RGD Demo ISMB Scotland 8/03/04

  27. Gene Report RGD Demo ISMB Scotland 8/03/04

  28. Virtual Comparative MapsVCMap RGD Demo ISMB Scotland 8/03/04

  29. VCMap RGD Demo ISMB Scotland 8/03/04

  30. VCMap RGD Demo ISMB Scotland 8/03/04

  31. VCMap RGD Demo ISMB Scotland 8/03/04

  32. VCMap RGD Demo ISMB Scotland 8/03/04

  33. VCMap RGD Demo ISMB Scotland 8/03/04

  34. VCMap RGD Demo ISMB Scotland 8/03/04

  35. VCMap RGD Demo ISMB Scotland 8/03/04

  36. VCMap RGD Demo ISMB Scotland 8/03/04

  37. The Gene Annotation Tool (GATool) RGD Demo ISMB Scotland 8/03/04

  38. Bioinformatics and biological databases • bioinformatics is an oxymoron • biology is complex • informatics wants to abstract to general principles RGD Demo ISMB Scotland 8/03/04

  39. Bioinformatics and biological databases • proliferation reflects complexity of biology • classes of biological databases defined by NAR DB issue • major sequence repositories • gene expression • comparative genomics • gene identification and structure • genetic and physical maps • genomic databases • intermolecular interactions • metabolic pathways and cellular regulation • mutation database • pathology • model organism • uncontrolled: so much data, so little time RGD Demo ISMB Scotland 8/03/04

  40. Bioinformatics and biological databases • the needs of biological research • focus on particular phenomena • disease • organism • toxin • biomolecule • "omics" • data needs to be pulled from various sources RGD Demo ISMB Scotland 8/03/04

  41. Bioinformatics and biological databases • challenges • gather and collate data from various objects • link object data in one coherent package • provide some customizability in output • provide capability for user to do further analyses on output • allow link backs to original sources for more detailed study • uses • hypothesis generation • knowledge base • data mining RGD Demo ISMB Scotland 8/03/04

  42. The Gene Annotation Tool RGD Demo ISMB Scotland 8/03/04

  43. The Gene Annotation Tool • overview • history • llparser • gene annotation tool with locuslink,swissprot,kegg data • gene annotation tool with RGD data and HTML option for linkouts • gene annotation tool with host of new functions and input under development RGD Demo ISMB Scotland 8/03/04

  44. The Gene Annotation Tool • overview • The tool • Receive inputs from user via web form • Packages data and information from several web dbs and returns the output as HTML or a delimited text file RGD Demo ISMB Scotland 8/03/04

  45. The Gene Annotation Tool • inputs • species • rat • mouse • human • data format • comma delimited line • file • interval RGD Demo ISMB Scotland 8/03/04

  46. The Gene Annotation Tool • inputs • data type • gene symbol • gene ids • sequence ids • interval • data field • objects in a given interval • from RGD • from KEGG • from SwissProt • from LocusLink RGD Demo ISMB Scotland 8/03/04

  47. The Gene Annotation Tool • Inputs: species, input data format, data type RGD Demo ISMB Scotland 8/03/04

  48. The Gene Annotation Tool • Inputs: data fields RGD Demo ISMB Scotland 8/03/04

  49. The Gene Annotation Tool • Inputs: data field and output format RGD Demo ISMB Scotland 8/03/04

  50. The Gene Annotation Tool • outputs • HTML • delimited file RGD Demo ISMB Scotland 8/03/04