Diego Gonzalezd.f.gonzalez@cgiar.org

Angela Hernándeza.hernandez@cgiar.org

GRIN-Global Pilot Data Migration for in vitro Cassava Collection

Joint National Plant Germplasm System Meeting

June 14-16, 2016Fort Collins, Colorado-USA

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

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

Ericson Aranzales Coordinator of the in vitro Cassava

Collection

Monica VelezResearch Assistance of the in vitro Cassava Laboratory

Diego GonzalezIT Engineer of the Genebank

documentationDr. Daniel DebouckLeader of the Genetic Resources Program

May 2015, GG TrainingBy Marty and Juan Carlos

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 DBStaging 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

Ericson Aranzales, Coordinator of the in vitro Cassava Collection

• 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 AchievementsGG adaptation to the routine processes

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

Genebank - Conservation5 Tubes x 3 explants: ~15 plants

Regeneration/Multiplication

Monitoring(Viability)

Conservation

Safety Duplication

Distribution Indexing

Availability : indexing + viability

Critical amount

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

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)

InventoriesBank

Bonsai I

Bonsai II

CIP

Inventory Actions

MONITORIING

MultiplicationRegenerationSubculturing for DistributionSubculturing for Indexing

Sub-culturing for safety duplication

EVALUATION

AcceptedRejected by contaminationRejected by low amountRejected by viability

SAFETY DUPLICATES

CIP MonitoringBonsai I MonitoringBonsai II Monitoring

Cryo Monitoring

14

Search Tool

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

GRIN-GlobalSeeds

GRIN-Globalin vitro

Middle tierGRIN-Global

Curator Tool

AndroidMobile App

Admin tool

ReportsCurating and handling of collections

Data entry

Lookup tables

SQLiteLookup tables

Web site

Restful(HTTP)

xml

json

Genesys

Web services

SOAP

Oracle DB

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

Thank you!!