genebank data and information management system

A member of CGIAR consortium www.iita.org

Genebank data and information management

system

TCHAMBA Marimagne

2015 IITA R4D week


Outline

• Genebank context

• Data management systems

• Challenges

• Way forward


Genebank context

in vitro bank Field bank Seed bank

Data & information management system


Crops Number of

accessions (%)

Cowpea (Vigna unguiculata L.) 15,552 51

Soybean (Glycine max L. Merr) 1,909 6

Cassava (Manihot esculenta Crantz) 3,746 12

Yam (Dioscorea spp.) 3,222 11

Bambara groundnut (Vigna subterranea L. Verdc) 2,055 7

Maize (Zea Mays L.) 1,561 5

Miscellaneous legumes 296 1

Wild Vigna (Vigna species L.) 1,686 6

Banana/plantain (Musa spp.) 283 >0

African yam bean [Sphenostylis stenocarpa (Hochst.)

Harms] 161 >0

Genebank context


• Acquisition

• Regeneration

• Conservation

• Characterization

• Evaluation

• Distribution

• Utilization

Genebank context

Documentation

and Data

Management

Priority on routine works and research to support genebanking


• Genebank Inventory System

• Accessions database

• Genesys

• Easy-SMTA

Data management systems

http://www.google.com.ng/url?sa=i&rct=j&q=&esrc=s&frm=1&source=images&cd=&cad=rja&uact=8&ved=0CAcQjRxqFQoTCNOV2-X0hckCFUZiDwodDdsMlA&url=http%3A%2F%2Fmoderninformatics.com%2Fdatabase.html&psig=AFQjCNF42PxZnMV2JHPe61LohBwC6zuDaw&ust=1447246761263663


Genebank Inventory System

Only accessible

to GRC staff and

few IITA

collaborators

(e.g. breeders)

http://tomcat1.iita.cgiarad.org/inventory/login.jspx

http://tomcat1.iita.cgiarad.org/inventory/login.jspx


Genebank operations • Constantly identifying the samples or accessions,

• Tracking, and updating the information.

• Conventional hand registration (with paper records) is time-consuming and prone to

human error


Medium Term Storage (MTS)

Bar-codes used to track the handling of Cowpea accessions in MTS (5 °C)


Long Term Storage (LTS)

Cowpea accessions conserved in Long Term Storage (-20°C)


Safety duplication in Cotonou (Benin rep.)

Inventory system available for remote accessibility and management

http://gi.iita.org/inventory

http://gi.iita.org/inventory


Bar code equipment and system


Winged bean at flowering stage



• Genesys

• Easy-SMTA



Accessions database

http://my.iita.org/accession2/

http://my.iita.org/accession2/





• Genesys

• Easy-SMTA


Genesys

https://www.genesys-pgr.org

https://www.genesys-pgr.org/







• Genesys

• Easy-SMTA (online reporting tool)


Easy-SMTA

https://mls.planttreaty.org/itt/index.php?r=site/login

https://mls.planttreaty.org/itt/index.php?r=site/login


Challenges

• Maintaining and improving the inventory and accessions

databases system,

• E-Research initiative (GRC open data, open access),

• Reinforce and expand Wi-Fi coverage of fields and screen

houses for remote data collection and transfer into the

central database.

• Linking accessions database with BMS and other breeders

databases.


Way Forward

• GRIN-Global

• Focused Identification of Germplasm Strategy(FIGS)

• Laboratory Information Management System(LIMS) for plant

tissue culture lab

• Implementing Radio Frequency Identification(RFID)


GRIN-Global

GRIN: NPGS Genebank information management system

GRIN-Canada: Canadian genebank information management system

Enhanced and expanded to address global germplasm information

management needs

By USDA-Agricultural Research Service (ARS) and Bioversity International funded

by Global Crop Diversity Trust (GCDT)

Many national and international genebanks moving to GRIN-Global

http://www.ars-grin.gov/

Source: USDA/ARS National Plant Germplasm System presentation











Focused Identification of Germplasm Strategy

(FIGS)

– Identifying accessions potentially useful to breeders

– Eco geographical information coupled with traits of interest

e.g. For drought tolerance, select material collected from drought environments

(potentially tolerant)

– Material must be geo-referenced


Radio Frequency Identification (RFID)

Barcode/ UPC RFID Tag/EPC

Efficiency Ability to read one tag at a time (line

of sight required)

Ability to read multiple tags simultaneously

(no line of sight required)

Dependability Labels easily damaged Tags less susceptible to damage

Can be used in harsher environments

Data Capacity Limited amount of data can be

assigned

Significantly higher data capacity to capture

detailed information about product

Accuracy close to 100%

Flexibility Static information Potential for read/ write capability, making

tags reusable

A step towards Internet of Things (IoT) in Genebank

A means of identifying a unique object or person using a radio frequency

transmission


GRC new web-based Genebank documentation system

Integration with Global

systems

Database

Server

Web services/APIs

btn the database

server and any

application

Mobile devices used to

collect/document data

on the fields/screen

houses and submit to

the server

Web interfaces and mobile

apps to access, manage,

manipulate and admin data

Annual report SMTAs report

Pass. C&E data uploading

Germplasm backup list

BMS

CassavaBase

YamBase

?IITABase

http://www.google.com.ng/url?sa=i&rct=j&q=&esrc=s&frm=1&source=images&cd=&cad=rja&uact=8&ved=&url=http://www.interactivelion.com/database-architecture.aspx&psig=AFQjCNGz2ecK-PytfVSuBJCZXPgmlcNYgg&ust=1447148478418779

https://www.google.com.ng/url?sa=i&rct=j&q=&esrc=s&frm=1&source=images&cd=&cad=rja&uact=8&ved=0CAcQjRxqFQoTCKbGj5KHg8kCFcxxFAod134Gow&url=https://www.croptrust.org/&psig=AFQjCNEYUQ-FBxoF7jFurTi4nH9eH3MTkg&ust=1447148693308226

https://www.google.com.ng/url?sa=i&rct=j&q=&esrc=s&frm=1&source=images&cd=&cad=rja&uact=8&ved=0CAcQjRxqFQoTCJb9_L6Hg8kCFcdOFAodfzIDug&url=https://www.croptrust.org/2014/topics/information-systems/&bvm=bv.106923889,d.ZWU&psig=AFQjCNG3LJti2SYiBeCOF7PhAFt5-TmhBw&ust=1447148777835996

http://www.google.com.ng/url?sa=i&rct=j&q=&esrc=s&frm=1&source=images&cd=&cad=rja&uact=8&ved=0CAcQjRxqFQoTCPOUv-mIg8kCFcKRDwodrb0JcQ&url=http://www.zigersnead.com/current/blog/post/svalbard-global-seed-vault/03-23-2008/903/&bvm=bv.106923889,d.ZWU&psig=AFQjCNEA3D67m1_Kr6OarAqKiu4xDxZrHA&ust=1447149053139166

https://www.google.com.ng/url?sa=i&rct=j&q=&esrc=s&frm=1&source=images&cd=&cad=rja&uact=8&ved=0CAcQjRxqFQoTCIfx5NqHg8kCFUw8FAod8dAFkg&url=https://en.wikipedia.org/wiki/File:Svalbard_Global_Seed_Vault_logo.svg&bvm=bv.106923889,d.ZWU&psig=AFQjCNHhRvvUS96Objl4JAut9CJyhlsCNA&ust=1447148836758853

https://www.google.com.ng/url?sa=i&rct=j&q=&esrc=s&frm=1&source=images&cd=&cad=rja&uact=8&ved=0CAcQjRxqFQoTCO2GhZeIg8kCFYRCFAod8QIAcw&url=https://passel.unl.edu/pages/printinformationmodule.php?idinformationmodule=1130447292&bvm=bv.106923889,d.ZWU&psig=AFQjCNH8TuAicOmrim7TgeJMg1i1rYAXKw&ust=1447148967524651


GRC Team & Collaborators

“As far as the laws of mathematics refer to reality, they are not certain; and as far as they are certain, they do not refer to reality.”

— Albert Einstein

Address to Prussian Academy of Sciences (1921)

Acknowledgement