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YAMBASE
Alex Ogbonna
YamBase Workshop
Cotonou March 2016
aco46@cornell.edu
YamBase
YamBase
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
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
YamBase
YAMBASE
YamBase
What is new
Account request and login
YamBase
https://github.com/solgenomics
https://yambase.org
https://sweetpotatobase.org
https://musabase.org
https://cassavabase.org
YamBase
Introduction
Central datastore
Provide breeders with tools
Globally accessible resource
Comprehensive information source
YamBase
Why YamBase
Data Archiving
Data Accessibility
Data Integration
Data sharing
Better data analysis
Proper data curation
Data integrity
Good metadata information
YamBase
What you need to use
YamBase
YamBase
Home page
Production: https://yambase.org/
Test: https://yambase-test.sgn.cornell.edu/
YamBase
Responsive Design
YamBase
YamBase Data Structure
Accessions Pedigree
data
Genotyping data
Trait dataPlots
Field data
Trials
YamBase
Account Privileges
Account Type Privileges
none Browse, use tools
“user" User database, forum
“submitter"
create trials, add phenotype
information etc.
YamBase
Create Account
YamBase
Create Account
YamBase
Create Account
After creating your
account, you’ll get
an email
notification from
which you would
activate your
account.
YamBase
Create Account
Create a YamBase account and enter
information to your profile!
YamBase
Yam Trait Ontology
YamBase
Yam Trait Ontology
YamBase
Yam Trait Ontology
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?
YamBase
“Search” menu & Lists
Add list
Combine list
Make public and private
Accessions and plots
Trials
Wizard
Wizard download
YamBase
Accessions and plots
YamBase
Accessions and plots
YamBase
Search accessions
YamBase
Search accessions
YamBase
Trials search
YamBase
Trials search
YamBase
Trials search
YamBase
Wizard search
YamBase
Wizard search
YamBase
Wizard search
YamBase
Wizard search
YamBase
Wizard search
YamBase
Wizard search
YamBase
Wizard search
YamBase
Wizard download
YamBase
Wizard download
YamBase
Using Lists Tool
YamBase
Add New List
View list content
Delete list Download list
Make list public
YamBase
Add New List
YamBase
Add New List
YamBase
Add New List
View list content
YamBase
Add New List
YamBase
Add New List
YamBase
Add New List
YamBase
Combine list
YamBase
Make List Public
Make public
YamBase
View Public List
YamBase
Make List Private
Make private
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
YamBase
“Manage” menu
Crosses
Downloads
Breeding program
Locations
Accessions
YamBase
Manage Breeding Programs
YamBase
Add Breeding Programs
YamBase
Add Breeding Programs
YamBase
Manage Locations
YamBase
Add Locations
YamBase
Add Locations
YamBase
Manage Accessions
YamBase
Add Accessions
YamBase
Accessions Batch Upload
YamBase
Accessions Batch Upload
YamBase
Accessions Batch Upload
YamBase
Pedigree Upload
YamBase
Pedigree Upload
YamBase
Pedigree Upload
YamBase
Manage Crosses
YamBase
Add Crosses
YamBase
Add Crosses
YamBase
Add Crosses
YamBase
Add Crosses
YamBase
Manage Downloads
YamBase
Manage Downloads
YamBase
Manage Downloads
YamBase
Contact us
CONTACT US !
YamBase
Contact us
CONTACT FORM !
Acknowledgements
Lukas
Mueller
Alex
Ogbonna
Bryan
Ellerbrock
Naama
Menda
Isaak
Tecle
Nick
Morales
Guillaume
Bauchet
BMGF
THANK YOU.

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Introduction to YamBase