1 / 85

Rat Genome Database RGD

Rat Genome Database RGD. http://rgd.mcw.edu. Dean Pasko Norie de la Cruz. 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

rogersdebra
Download Presentation

Rat Genome Database RGD

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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

More Related