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Rat Genome Database RGD

Rat Genome Database RGD. http://rgd.mcw.edu. Glenn Harris – The Basics Victoria Petri - Ontologies Dean Pasko – Tools. RGD Background. Rat Genome Database is a NIH funded project NHLBI (grant HL64541) Database went public on June 1, 2000 RGD’s mission statement:

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Rat Genome Database RGD

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  1. Rat Genome DatabaseRGD http://rgd.mcw.edu Glenn Harris – The Basics Victoria Petri - Ontologies Dean Pasko – Tools RGD Demo Neuroscience 2004 10/22/04

  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.” RGD Demo Neuroscience 2004 10/22/04

  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 Neuroscience 2004 10/22/04

  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 • Pathway ontology data RGD Demo Neuroscience 2004 10/22/04

  5. RGD Tools • RGD’s multi-species and comparative tools • Advance/quick search • Comprehensive for rat data (annotations, ontologies, etc.) • 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) • GViewer • RGD object specific query tools • Genes, QTLs, Strains, Ontologies, Homologs, etc. RGD Demo Neuroscience 2004 10/22/04

  6. RGD Home Page RGD Demo Neuroscience 2004 10/22/04

  7. Quick and AdvancedSearches RGD Demo Neuroscience 2004 10/22/04

  8. Quick & Advanced Search RGD Demo Neuroscience 2004 10/22/04

  9. Quick Search RGD Demo Neuroscience 2004 10/22/04

  10. Advanced Search RGD Demo Neuroscience 2004 10/22/04

  11. Sort on any column Select some or all records Download report Go back to summary page Show only selected items Search Results RGD Demo Neuroscience 2004 10/22/04

  12. Search Results Report RGD Demo Neuroscience 2004 10/22/04

  13. Object Specific Searches RGD Demo Neuroscience 2004 10/22/04

  14. QTL Query RGD Demo Neuroscience 2004 10/22/04

  15. QTL Report RGD Demo Neuroscience 2004 10/22/04

  16. Gene Query RGD Demo Neuroscience 2004 10/22/04

  17. Gene Report RGD Demo Neuroscience 2004 10/22/04

  18. Strain Query RGD Demo Neuroscience 2004 10/22/04

  19. Strain Report RGD Demo Neuroscience 2004 10/22/04

  20. Ontologies RGD Demo Neuroscience 2004 10/22/04

  21. Implementation of Multiple Ontologies at the Rat Genome Database Ontologies are controlled vocabularies that order concepts in a hierarchical fashion Currently four ontologies are being used to annotate genes, QTL, strains and homologues  Gene Ontology (GO) Component Function Process •  Phenotype Ontology (MP) • Disease Ontology (DO) • Pathway Ontology (PW) RGD Demo Neuroscience 2004 10/22/04

  22. Implementation of Multiple Ontologies at the Rat Genome Database Information integration – navigating through ontologies and objects Various object type reports – genes, QTLs, strains, homologues – can be retrieved by selecting terms belonging to any of the four ontologies used Various ontology reports - GO, DO, MP and PW- can be retrieved from the annotations associated with a particular object type in that object report All ontology reports incorporate a genome-wide view of the chromosomal distribution of genes or QTL associated with the ontology term used in the search via GViewer tool RGD Demo Neuroscience 2004 10/22/04

  23. Information integration – navigating through ontologies and objects RGD Demo Neuroscience 2004 10/22/04

  24. Information integration – navigating through ontologies and objects RGD Demo Neuroscience 2004 10/22/04

  25. Information integration – navigating through ontologies and objects RGD Demo Neuroscience 2004 10/22/04

  26. Information integration – navigating through ontologies and objects RGD Demo Neuroscience 2004 10/22/04

  27. Information integration – navigating through ontologies and objects RGD Demo Neuroscience 2004 10/22/04

  28. Information integration – navigating through ontologies and objects RGD Demo Neuroscience 2004 10/22/04

  29. Information integration – navigating through ontologies and objects RGD Demo Neuroscience 2004 10/22/04

  30. Information integration – navigating through ontologies and objects RGD Demo Neuroscience 2004 10/22/04

  31. Information integration – navigating through ontologies and objects RGD Demo Neuroscience 2004 10/22/04

  32. Information integration – navigating through ontologies and objects RGD Demo Neuroscience 2004 10/22/04

  33. Information integration – navigating through ontologies and objects SNP density track Genes Annotations Evidence Codes Tracks RGD Demo Neuroscience 2004 10/22/04

  34. Information integration – navigating through ontologies and objects RGD Demo Neuroscience 2004 10/22/04

  35. Information integration – navigating through ontologies and objects RGD Demo Neuroscience 2004 10/22/04

  36. Information integration – navigating through ontologies and objects RGD Demo Neuroscience 2004 10/22/04

  37. Information integration – navigating through ontologies and objects RGD Demo Neuroscience 2004 10/22/04

  38. Information integration – navigating through ontologies and objects RGD Demo Neuroscience 2004 10/22/04

  39. Implementation of Multiple Ontologies at the Rat Genome Database Information integration – navigating through ontologies and objects Various object type reports – genes, QTLs, strains, homologues – can be retrieved by selecting terms belonging to any of the four ontologies used Various ontology reports - GO, DO, MP and PW - can be retrieved from the annotations associated with a particular object type in that object report RGD Demo Neuroscience 2004 10/22/04

  40. Tools Submit Data VCMap GBrowse Gene Annotation RGD Demo Neuroscience 2004 10/22/04

  41. QTL Registration Strain Registration Strain Registration Gene Registration Data Registration RGD Demo Neuroscience 2004 10/22/04

  42. Nomenclature Rules RGD Demo Neuroscience 2004 10/22/04

  43. VCMap RGD Demo Neuroscience 2004 10/22/04

  44. VCMap RGD Demo Neuroscience 2004 10/22/04

  45. VCMap RGD Demo Neuroscience 2004 10/22/04

  46. The Gene Annotation Tool • Overview • Receive inputs from user via web form • Packages data and information from several web databases and returns the output as HTML or a delimited text file • Utility for users: • Micro-array • Comparative studies (Syntenic regions) RGD Demo Neuroscience 2004 10/22/04

  47. The Gene Annotation Tool RGD Demo Neuroscience 2004 10/22/04

  48. The Gene Annotation Tool RGD Demo Neuroscience 2004 10/22/04

  49. The Gene Annotation Tool • Outputs • HTML format hyperlinks to database reports • delimited file RGD Demo Neuroscience 2004 10/22/04

  50. The Gene Annotation Tool • Outputs: with chromosomal region as input RGD Demo Neuroscience 2004 10/22/04

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