Introduction to YamBase
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This document provides an outline for a YamBase workshop held in Cotonou, Benin in March 2016. The workshop agenda covers an overview of YamBase, account creation and login, searching YamBase, working with lists, the search wizard, managing data, and uploading various types of data including accessions, images, pedigrees, crosses, and field trial data. The document explains what YamBase is, its benefits, and how to access and use the YamBase test site. It also covers the YamBase data structure and account privileges, and includes exercises for participants to complete hands-on with the YamBase test server during the workshop.
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
- 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/
- 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.
- 17. YamBase Create Account After creating your account, youll 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!
- 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
- 41. YamBase Add New List View list content Delete list Download list Make list public
- 44. YamBase Add New List View list content
- 49. YamBase Make List Public Make public
- 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
- 79. THANK YOU.