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Introduction to YamBase

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Introduction to YamBase database.

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Introduction to YamBase

  1. 1. YAMBASE Alex Ogbonna YamBase Workshop Cotonou March 2016 aco46@cornell.edu
  2. 2. YamBase
  3. 3. YamBase
  4. 4. YamBase Outline 9:00 YamBase overview 9:30 Accounts and Logins 10:00 Searching YamBase 10:30 Working with list 11:00 The search Wizard 11:30 Introduction to Managing data using YamBase 12:00 Adding accessions, images and pedigree 12:30 Lunch 1:00 Adding Crosses 1:30 Trial creation and upload 2:00 Generating files for the Android field book 2:30 Upload phenotypic data from the fieldbook 3:00 Uploading field trial coordinates (field map) 3:30 Uploading historic data 4:00 session ends
  5. 5. YamBase Workshop Hands-on You are expected to use your laptop and the YamBase test server We would love to learn about your processes as a way of feedback to further improve the database
  6. 6. YamBase YAMBASE YamBase What is new Account request and login
  7. 7. YamBase https://github.com/solgenomics https://yambase.org https://sweetpotatobase.org https://musabase.org https://cassavabase.org
  8. 8. YamBase Introduction Central datastore Provide breeders with tools Globally accessible resource Comprehensive information source
  9. 9. YamBase Why YamBase Data Archiving Data Accessibility Data Integration Data sharing Better data analysis Proper data curation Data integrity Good metadata information
  10. 10. YamBase What you need to use YamBase
  11. 11. YamBase Home page Production: https://yambase.org/ Test: https://yambase-test.sgn.cornell.edu/
  12. 12. YamBase Responsive Design
  13. 13. YamBase YamBase Data Structure Accessions Pedigree data Genotyping data Trait dataPlots Field data Trials
  14. 14. YamBase Account Privileges Account Type Privileges none Browse, use tools “user" User database, forum “submitter" create trials, add phenotype information etc.
  15. 15. YamBase Create Account
  16. 16. YamBase Create Account
  17. 17. YamBase Create Account After creating your account, you’ll get an email notification from which you would activate your account.
  18. 18. YamBase Create Account Create a YamBase account and enter information to your profile!
  19. 19. YamBase Yam Trait Ontology
  20. 20. YamBase Yam Trait Ontology
  21. 21. YamBase Yam Trait Ontology
  22. 22. YamBase Exercise Go to Yam test site Yambase-test.sgn.cornell.edu Go to ontology browser Browser the Yam Ontology Find the term “no. of setts planted” How is it defined?
  23. 23. YamBase “Search” menu & Lists Add list Combine list Make public and private Accessions and plots Trials Wizard Wizard download
  24. 24. YamBase Accessions and plots
  25. 25. YamBase Accessions and plots
  26. 26. YamBase Search accessions
  27. 27. YamBase Search accessions
  28. 28. YamBase Trials search
  29. 29. YamBase Trials search
  30. 30. YamBase Trials search
  31. 31. YamBase Wizard search
  32. 32. YamBase Wizard search
  33. 33. YamBase Wizard search
  34. 34. YamBase Wizard search
  35. 35. YamBase Wizard search
  36. 36. YamBase Wizard search
  37. 37. YamBase Wizard search
  38. 38. YamBase Wizard download
  39. 39. YamBase Wizard download
  40. 40. YamBase Using Lists Tool
  41. 41. YamBase Add New List View list content Delete list Download list Make list public
  42. 42. YamBase Add New List
  43. 43. YamBase Add New List
  44. 44. YamBase Add New List View list content
  45. 45. YamBase Add New List
  46. 46. YamBase Add New List
  47. 47. YamBase Add New List
  48. 48. YamBase Combine list
  49. 49. YamBase Make List Public Make public
  50. 50. YamBase View Public List
  51. 51. YamBase Make List Private Make private
  52. 52. YamBase Exercise Go to wizard Select “breeding program “ on the first select box and select “IITA” Select “trials” in the second select box and select any two trials Make list of common accessions in both trials. List name should be “yourname_commonAccession” Make list of accessions that are found in both trials. List name should be “yourname_Accession” Create an accession list with name “yourname_list” Open to verify that the list type is set correctly Edit the list Set list to public Combine yourname_list and yourname_commonAccessions
  53. 53. YamBase “Manage” menu Crosses Downloads Breeding program Locations Accessions
  54. 54. YamBase Manage Breeding Programs
  55. 55. YamBase Add Breeding Programs
  56. 56. YamBase Add Breeding Programs
  57. 57. YamBase Manage Locations
  58. 58. YamBase Add Locations
  59. 59. YamBase Add Locations
  60. 60. YamBase Manage Accessions
  61. 61. YamBase Add Accessions
  62. 62. YamBase Accessions Batch Upload
  63. 63. YamBase Accessions Batch Upload
  64. 64. YamBase Accessions Batch Upload
  65. 65. YamBase Pedigree Upload
  66. 66. YamBase Pedigree Upload
  67. 67. YamBase Pedigree Upload
  68. 68. YamBase Manage Crosses
  69. 69. YamBase Add Crosses
  70. 70. YamBase Add Crosses
  71. 71. YamBase Add Crosses
  72. 72. YamBase Add Crosses
  73. 73. YamBase Manage Downloads
  74. 74. YamBase Manage Downloads
  75. 75. YamBase Manage Downloads
  76. 76. YamBase Contact us CONTACT US !
  77. 77. YamBase Contact us CONTACT FORM !
  78. 78. Acknowledgements Lukas Mueller Alex Ogbonna Bryan Ellerbrock Naama Menda Isaak Tecle Nick Morales Guillaume Bauchet BMGF
  79. 79. THANK YOU.

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