GRIN global pilot data migration for in vitro cassava collection at CIAT

1. Diego Gonzalez
d.f.gonzalez@cgiar.org
Angela Hernández
a.hernandez@cgiar.org
GRIN-Global Pilot Data Migration for in vitro
Cassava Collection
Joint National Plant
Germplasm System Meeting
June 14-16, 2016
Fort Collins, Colorado-USA

2. Rationale behind
Over the last 15 years CIAT has developed an "in house" genetic resources information system, which
makes data about the collections available on the web, and supports the genebank workflows.
 Software (data entries, reports) technology is becoming outdated
 Poor scalability and problems with the new versions of operating systems and web
applications.
Evaluate an alternative for adoption: GRIN-Global
• Pilot data migration for in vitro Cassava collection
• To capitalize on possible community of practice

3. GRIN-Global Pilot Data Migration for in vitro Cassava Collection
Duration: 1 Year (2015)
The objective of this Project is to develop a plan of data migration from the CIAT-GRP
information system to GRIN-Global and integrate one of our mobile applications with
this system in view of the possible adoption
Work team:
• in vitro Cassava Genebank Staff (2): Coordinator, Assistance
• documentation & databases Genebank Staff (2): Coordinator, Systems Analyst

4. Ericson Aranzales
Coordinator of the in vitro Cassava
Collection
Monica Velez
Research Assistance of the
in vitro Cassava Laboratory
Diego Gonzalez
IT Engineer of the Genebank
documentationDr. Daniel Debouck
Leader of the Genetic Resources Program

5. May 2015, GG Training
By Marty and Juan Carlos

6. Data Migration Process
Data migrated and
validated
Genebank processes
Introduction/Acquisition Indexation Conservation Regeneration Safety duplication Characterization / EvaluationsDistribution
Data Mapping /
Migration requirements
CIAT GRP
Database
GRIN-
Global data
dictionary
Genebank
documentation
needs
Source DB
Staging
tables GG DB
Transform
LoadExtract
Cleansing
Tool developed
with the rules of migration Curation data
• Disaggregate
tables
• Duplicate data
• Data with special
characters,
misspelled
• Data consistency
• Integrity

7. Ericson Aranzales, Coordinator of the in vitro Cassava Collection

8. • Definition of Inventory Maintenance Policies for in vitro Cassava Collection
• Changes in the names of the dataviews according with the genebank handling
• Inventory definitions
• Definition of code values (actions names)
• Translation to Spanish the field names
• Added trigger to GG Database to enable automatic indexation availability
• Modifying SQL in some Dataviews
Adding the third administration in geography, adapt the format of genebank
accessions and correction the cooperator site on the website
Challenges and Achievements
GG adaptation to the routine processes

9. Outputs
Pilot data migration
• Document Plan data migration
• Tool for data migration (Java application stand
alone)
• Mapping rules
• Extraction
• Transformation
• Load
• Document Data Mapping
• Document Migration validations
• Document recommendations
Mobile synchronization with GRIN-Global
• Mobile application for Android Tablet
• Register inventory actions
• For one selected process for this pilot
• Web services for Synchronization (Java RestFul)
• Technical documentation
• Source code

10. Genebank - Conservation
5 Tubes x 3 explants: ~15 plants
Regeneration/Multiplication
Monitoring
(Viability)
Conservation
Safety
Duplication
Distribution Indexing
Availability : indexing + viability
Critical amount

11. Indexing (Inventory Quality Status)
Indexing
Results
Script load
Compile data
(Template)
Lab Coordinator
Documentation
Oracle DB
Data Validation
Availability Trigger
Results
Upload results
(DataView: Banco: Quality status)
Compile data
(Template)
GG DB
Data validation
(DataView: Banco)
Cooperator
Indexing
Update:
Trigger
Oracle: GRIN-Global:
Trigger: availability conditions

12. Genebank management (Inventory = Banco, …)
Oracle: GRIN-Global:
Coordinator
Technicians
Tablet’s
Oracle DB
MONITORIING
Multiplication
Regeneration
Subculturing for
Distribution
Subculturing for Indexing
Sub-culturing for safety
duplication
EVALUATION
Accepted
Rejected by
contamination
Rejected by low amount
Rejected by viability
SAFETY
DUPLICATES
CIP Monitoring
Bonsai I Monitoring
Bonsai II Monitoring
Cryo Monitoring
• Concept changed (Inventory = Bank)
To define actions:
• Create new dataviews.
• Definition of Inventory Maintenance
Policies for the genebank
management
• Definition of Inventory Maintenace
Policies for safety duplicates
Cooperator
GRIN-Global DB
Wi-Fi/GPRS
Web
services
Compile data
(DataView: Banco: Actions)

13. Inventories
Bank
Bonsai I
Bonsai II
CIP
Inventory Actions
MONITORIING
Multiplication
Regeneration
Subculturing for
Distribution
Subculturing for
Indexing
Sub-culturing for
safety duplication
EVALUATION
Accepted
Rejected by
contamination
Rejected by low
amount
Rejected by viability
SAFETY
DUPLICATE
S
CIP Monitoring
Bonsai I Monitoring
Bonsai II Monitoring
Cryo Monitoring

14. 14

15. Search Tool

16. Issues for a successful adoption
CIAT side should meet the needs of usability for the in vitro genebank :
The concepts of GRIN-Global are clearly oriented to the management of seed
collections which requires the completion of certain adaptations for the
management of in vitro collection for the adoption of this system.
• Improve usability and make adjustments necessary to facilitate data
management for in vitro collection
• Make adjustments to the dataviews, triggers
• Tablets and web services
• Using tablets to facilitate the identification of management QR codes

17. GRIN-Global
Seeds
GRIN-Global
in vitro
Middle tier
GRIN-Global
Curator Tool
Android
Mobile App
Admin
tool
Reports
Curating and handling of collections
Data entry
Lookup
tables
SQLite
Lookup
tables
Web site
Restful
(HTTP)
xml
json
Genesys
Web services
SOAP
Oracle DB

18. Conclusions
• Migration all available data was successfully achieved and valid in GRIN-
Global (Cassava Collection)
• Establish a plan and lessons learned for possible adoption
• GG offers more and useful attributes for collections documentation
• Mobile system integration with GG
• Usability of search tool is very low, therefore it needs to be improved
• As commonly observed by users, the usability of GG to manage Cassava
collection has an acceptable rating although there are many observations
and recommendations to get an optimal management of clonal
collections

19. Thank you!!