Introduction to YamBase

1. YAMBASE Alex Ogbonna YamBase Workshop Cotonou March 2016 aco46@cornell.edu

2. YamBase

3. YamBase

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. 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. YamBase YAMBASE YamBase What is new Account request and login

7. YamBase https://github.com/solgenomics https://yambase.org https://sweetpotatobase.org https://musabase.org https://cassavabase.org

8. YamBase Introduction Central datastore Provide breeders with tools Globally accessible resource Comprehensive information source

9. YamBase Why YamBase Data Archiving Data Accessibility Data Integration Data sharing Better data analysis Proper data curation Data integrity Good metadata information

10. YamBase What you need to use YamBase

11. YamBase Home page Production: https://yambase.org/ Test: https://yambase-test.sgn.cornell.edu/

12. YamBase Responsive Design

13. YamBase YamBase Data Structure Accessions Pedigree data Genotyping data Trait dataPlots Field data Trials

14. YamBase Account Privileges Account Type Privileges none Browse, use tools “user" User database, forum “submitter" create trials, add phenotype information etc.

15. YamBase Create Account

16. YamBase Create Account

17. YamBase Create Account After creating your account, you’ll get an email notification from which you would activate your account.

18. YamBase Create Account Create a YamBase account and enter information to your profile!

19. YamBase Yam Trait Ontology

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. YamBase “Search” menu & Lists Add list Combine list Make public and private Accessions and plots Trials Wizard Wizard download

24. YamBase Accessions and plots

25. YamBase Accessions and plots

26. YamBase Search accessions

27. YamBase Search accessions

28. YamBase Trials search

31. YamBase Wizard search

38. YamBase Wizard download

39. YamBase Wizard download

40. YamBase Using Lists Tool

41. YamBase Add New List View list content Delete list Download list Make list public

42. YamBase Add New List

44. YamBase Add New List View list content

48. YamBase Combine list

49. YamBase Make List Public Make public

50. YamBase View Public List

51. YamBase Make List Private Make private

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. YamBase “Manage” menu Crosses Downloads Breeding program Locations Accessions

54. YamBase Manage Breeding Programs

55. YamBase Add Breeding Programs

56. YamBase Add Breeding Programs

57. YamBase Manage Locations

58. YamBase Add Locations

59. YamBase Add Locations

60. YamBase Manage Accessions

61. YamBase Add Accessions

62. YamBase Accessions Batch Upload

65. YamBase Pedigree Upload

68. YamBase Manage Crosses

69. YamBase Add Crosses

73. YamBase Manage Downloads

76. YamBase Contact us CONTACT US !

77. YamBase Contact us CONTACT FORM !

78. Acknowledgements Lukas Mueller Alex Ogbonna Bryan Ellerbrock Naama Menda Isaak Tecle Nick Morales Guillaume Bauchet BMGF

79. THANK YOU.