grin global pilot data migration for in vitro cassava collection at ciat
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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!!
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