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

2. RGD Demo ISMB Scotland 8/03/04 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 Background

3. RGD Demo ISMB Scotland 8/03/04 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 Background

4. RGD Demo ISMB Scotland 8/03/04 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 Comparative Genomics

5. RGD Demo ISMB Scotland 8/03/04 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 Tools

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

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

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

9. RGD Demo ISMB Scotland 8/03/04 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

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

11. RGD Demo ISMB Scotland 8/03/04 Special Cases Quick Search & Advanced Search EnterSearch keyword1 keyword2“keyword1 keyword2” a; the; as; etc.will not perform search (returns not found) amperforms search NM_, A1-NM; A1

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

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

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

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

16. RGD Demo ISMB Scotland 8/03/04 Results Summary Page FoundReturns more than one objectintermediate page: list of objects and # of each found > 10 of a single object found intermediate page: # of the object found < 10 of a single object found results page

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

39. RGD Demo ISMB Scotland 8/03/04 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

40. RGD Demo ISMB Scotland 8/03/04 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

41. RGD Demo ISMB Scotland 8/03/04 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

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

43. RGD Demo ISMB Scotland 8/03/04 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

44. RGD Demo ISMB Scotland 8/03/04 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

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

46. RGD Demo ISMB Scotland 8/03/04 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

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

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

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

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

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

52. RGD Demo ISMB Scotland 8/03/04 The Gene Annotation Tool Outputs: with chromosomal region as input

53. RGD Demo ISMB Scotland 8/03/04 The Gene Annotation Tool Outputs: with TIGR ids as input

54. RGD Demo ISMB Scotland 8/03/04 The Gene Annotation Tool Outputs: with Affy ids as input

55. RGD Demo ISMB Scotland 8/03/04 The Gene Annotation Tool internals –identifiers –data processing –scripts

56. RGD Demo ISMB Scotland 8/03/04 The Gene Annotation Tool –identifiers GA id RGD id Ll id SP id KEGG id Unigene id GB est id GB mRNA id TIGR id Affy id

57. RGD Demo ISMB Scotland 8/03/04 The Gene Annotation Tool integration –predefined queries ontology browser genome browser reports –linkouts Other tools Rgd reports Data from other web dbs

58. RGD Demo ISMB Scotland 8/03/04 The Gene Annotation Tool integration –predefined queries: ontology browser

59. RGD Demo ISMB Scotland 8/03/04 The Gene Annotation Tool integration –predefined queries: genome browser

60. RGD Demo ISMB Scotland 8/03/04 The Gene Annotation Tool upcoming developments –saved queries –notebook –advanced data mining (?)

61. RGD Demo ISMB Scotland 8/03/04 GBrowse Genome Browser

62. RGD Demo ISMB Scotland 8/03/04 Genome Browser

63. RGD Demo ISMB Scotland 8/03/04 Search for QTL names Genome Browser Displays matching QTLs on each chromosome

64. RGD Demo ISMB Scotland 8/03/04 Genome Browser

65. RGD Demo ISMB Scotland 8/03/04 Genome Browser

66. RGD Demo ISMB Scotland 8/03/04 Genome browser -- ontology tracks annotated objects best evidence high level aggregators

67. RGD Demo ISMB Scotland 8/03/04 Genome browser -- annotated object tracks

68. RGD Demo ISMB Scotland 8/03/04 Genome browser -- best evidence tracks

69. RGD Demo ISMB Scotland 8/03/04 Genome browser -- higher level aggregators

70. RGD Demo ISMB Scotland 8/03/04 Genome browser -- Integration -- visual inspection

71. RGD Demo ISMB Scotland 8/03/04 Genome browser -- Integration -- linkouts

72. RGD Demo ISMB Scotland 8/03/04 Ontologies

73. RGD Demo ISMB Scotland 8/03/04 Implementation of Multiple Ontologies at the Rat Genome Database Ontologies are controlled vocabularies that order concepts in a hierarchical fashion Currently three ontologies are being used to annotate genes, QTLs, strains and homologs  Gene Ontology (GO) Component Function Process  Phenotype Ontology (PO)  Disease Ontology (DO)

74. RGD Demo ISMB Scotland 8/03/04 Implementation of Multiple Ontologies at the Rat Genome Database

75. RGD Demo ISMB Scotland 8/03/04 Implementation of Multiple Ontologies at the Rat Genome Database Multiple object type reports – genes, QTLs and strains – can be retrieved using terms for any of the ontologies used for annotations Multiple ontology reports can be accessed from the annotations associated with any particular object type Program for Genetic Application PhysGen - Physiogenomics of Stressors in Derived Consomic Rats 

76. RGD Demo ISMB Scotland 8/03/04 Information integration – navigating through ontologies and objects

77. RGD Demo ISMB Scotland 8/03/04 Information integration – navigating through ontologies and objects

78. RGD Demo ISMB Scotland 8/03/04 Information integration – navigating through ontologies and objects

79. RGD Demo ISMB Scotland 8/03/04 Information integration – navigating through ontologies and objects

80. RGD Demo ISMB Scotland 8/03/04 Information integration – navigating through ontologies and objects

81. RGD Demo ISMB Scotland 8/03/04 Information integration – navigating through ontologies and objects

82. RGD Demo ISMB Scotland 8/03/04 Information integration – navigating through ontologies and objects

83. RGD Demo ISMB Scotland 8/03/04

84. Rat Genome Database Howard Jacob, Principal Investigator Simon Twigger, Co-Principal Investigator Anne Kwitek, Advisor Weihong Jin, Webmaster Peter Tonellato, Advisor Collaborators: MGI, RGSC, NCBI, UniProt, Ensembl, RatMap, BIND Data Integration and Comparative Analysis Susan Bromberg, Team Leader Cindy Foote, Offsite Curator Glenn Harris, Curator Rajni Nigam, Curator Dorothy Reilly, Offsite Curator Angela Zuniga-Meyer, Curation Assistant Data Exploration and Discovery Mary Shimoyama, Team leader Nataliya Nenasheva, Curation Assistant Victoria Petri, GO Curator Charles Wang, Curator Database and Tool Management Dean Pasko, Team Leader Jiali Chen, Analyst/Project Programmer Henry Fan, Analyst/Project Programmer Wenhua Wu, Bioinformatics Specialist Lan Zhao, Analyst/Project Programmer Data Mining and Advanced Tool Development Norie de la Cruz, Team Leader Hang Liu, Analyst/Project Programmer Jed Mathis, Data Analyst/Programmer

85. RGD Demo ISMB Scotland 8/03/04