introduction to yambase

YAMBASEAlex Ogbonna

YamBase Workshop

Cotonou March 2016

[email protected]

YamBase

YamBase

Outline9:00 YamBase overview9:30 Accounts and Logins10:00 Searching YamBase10:30 Working with list11:00 The search Wizard11:30 Introduction to Managing data using YamBase12:00 Adding accessions, images and pedigree 12:30 Lunch 1:00 Adding Crosses1:30 Trial creation and upload2:00 Generating files for the Android field book2:30 Upload phenotypic data from the fieldbook3:00 Uploading field trial coordinates (field map)3:30 Uploading historic data

4:00 session ends

YamBase

Workshop

Hands-onYou 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

YAMBASEYamBase

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 toolsGlobally 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 Pedigreedata

Genotyping data

Trait dataPlots

Field data

Trials

YamBase

Account PrivilegesAccount Type Privileges

none Browse, use tools

“user" User database, forum

“submitter" create trials, add phenotype information etc.

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

ExerciseGo 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 & ListsAdd list

Combine list

Make public and private

Accessions and plots

Trials

WizardWizard download

YamBase

Accessions and plots

YamBase

Search accessions

YamBase

Trials search

YamBase

Wizard search

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

View list content

YamBase

Add New List

YamBase

Combine list

YamBase

Make List Public

Make public

YamBase

View Public List

YamBase

Make List Private

Make private

YamBase

ExerciseGo to wizard

Select “breeding program “ on the first select box and select “IITA”Select “trials” in the second select box and select any two trialsMake 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 correctlyEdit the listSet list to publicCombine yourname_list and yourname_commonAccessions

YamBase

“Manage” menuCrosses

Downloads

Breeding programLocations

Accessions

YamBase

Manage Breeding Programs

YamBase

Add Breeding Programs

YamBase

Manage Locations

YamBase

Add Locations

YamBase

Manage Accessions

YamBase

Add Accessions

YamBase

Accessions Batch Upload

YamBase

Pedigree Upload

YamBase

Manage Crosses

YamBase

Add Crosses

YamBase

Manage Downloads

YamBase

Contact us

CONTACT US !

YamBase

Contact us

CONTACT FORM !

Acknowledgements

Lukas Mueller

AlexOgbonna

BryanEllerbrock

NaamaMenda

IsaakTecle

NickMorales

Guillaume Bauchet

BMGF

THANK YOU.

introduction to yambase

Presentations & Public Speaking