Highlight on Coffee and Information Systems
21 June 2016
Marie Haga | Marie's Corner
We have decided to tweak my corner a little this time, and give you an update on recent developments in two areas of our work. More specifically I will focus on information systems and technology for genebanks and innovative ways to safeguard the diversity of coffee. Let us start with the latter.
Building the global system for conservation of coffee
The Crop Trust was very happy to announce our collaboration with World Coffee Research on the Development of a Global Conservation Strategy for Coffee. It is clear that we are not the only ones with excitement for our collaboration. See below for coffee related media coverage of our collaboration:
The strategy, to be created jointly by World Coffee Research and the Crop Trust, will develop a current understanding of the status of major coffee collections, identify major gaps, develop the understanding of the complementarity of ex situ and in suit collections of coffee, and identify high priority actions that need to be taken ensure the conservation and availability of coffee genetic resources.
Sarada Krishnan, World Coffee Research’s consultant, recently dove into a desk study that will analyze the history of coffee collections and coffee diversity, the use and impact of coffee resources, and the vulnerability of coffee genetic resources. Daniela Horna, the Crop Trust’s consultant on the project, created and sent out a survey to major collections of coffee globally to paint a picture of the status of coffee collections. We have already received completed surveys from quite a few collections.
The strategy will be completed in October this year, following feedback from the 117th Session of the International Coffee Council. The Crop Trust will use the strategy to encourage the coffee community and industry to come together to help conserve the world’s coffee diversity through the Crop Trust’s Endowment Fund.
Information Systems and Technology for Genebanks
Just like any complex operation, a genebank needs help from information technology to keep it functioning properly, and to communicate its work to the outside world. At the Crop Trust, we’ve long recognized this, following the lead of the Global Plan of Action. Over the years, we’ve supported the development and deployment of information systems both at national and global level. This continues, and has been intensifying of late.
CRP Barcoding Workshop will be held in Berlin on 20-24 June. The workshop targets CGIAR genebank documentation specialists and key IT staff involved in development and maintenance of genebank databases. We will attempt to link the “experts” within the system with “beginners”. Together, they will develop detailed plans for enhanced use of mobiles, barcoding and other IT in genebank daily operations based on established procedures in their genebanks.
The Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) in Gatersleben, Germany, the German federal genebank, has kindly agreed to demonstrate the use of IT tools for data acquisition in day-to-day operations. A one-day visit to IPK will provide extra inspiration to develop comprehensive plans for improved data management and use of IT in each participating CGIAR genebank.
All the 11 CGIAR genebanks are sending two of their data management specialists or experts in genebank procedures, which closely relate to data management.
A look-and-feel upgrade for Genesys was started earlier in 2016 and the updated graphics have just been received. We expect to have the updated version of the portal published in July.
Discussions about CIAT sharing their data were revitalized during a recent visit by Fiona Hay (IRRI) in the context of the CRP’s Seed Longevity Initiative, and we have resumed negotiations with the centre about publishing their data on Genesys.
We have also agreed to host the AVRDC database manager, who will spend two weeks at the Crop Trust (22 August - 2 September) and will focus on documenting their databases, learning about genebank data management practices and updating data on Genesys. AVRDC is also one of the key partners in the two-year project that was submitted for funding to the German government (BLE), and for which we are awaiting final approval. The “Genesys Catalog of Phenotypic Datasets” project will look at how Genesys can manage complex evaluation data.
Taxonomic data validation is an important aspect of genebank data curation. We contracted ICARDA in 2015 to develop a proof-of-concept tool that suggests corrections to existing accession taxonomic data, based on similarity with “approved” names. We have agreed with USDA to use their current database of taxonomic names, as used in GRIN-Global, and have developed the Genesys Taxonomy Validator -- a tool that will, once embedded into Genesys, generate an on-demand report on invalid data in taxonomies reported by data providers. This new Genesys tool is an addition to our existing GIS data validation toolkit, which identifies incorrectly geo-referenced accessions.
Inclusion of accession imagery will enhance the Genesys experience and eventually make Genesys a source of crop images for publications. The first image in the gallery for this banana accession showcases the metadata display. Each accession image will be annotated with the relevant Copyright, Ownership, Licensing and Title information. ILRI, IRRI and Bioversity were approached to help test and improve the initial functionality.
We supported the Centre for Pacific Crops and Trees genebank at SPC in their first test upload of the passport data of their collection to the Genesys test environment. This is a major milestone in collaboration with CePaCT on data! We expect Albert Fiu, their new database manager, will be in position to upload at least the minimum passport data on their entire collection to Genesys in July.
Upgrading IT infrastructure
As part of the CWR project, we are engaging in IT infrastructure audits of 25 national genebanks around the world, and we also have funds for significant upgrades for 15 of these. Some recent milestones:
- PRC Vietnam project finished.
- ICTA, Guatemala, Upgrading genebank IT infrastructure: agreement signed.
- INIAF, Bolivia, Upgrading genebank IT infrastructure: agreed on the terms, waiting to sign.
- CORPOICA, Colombia, IT Upgrading project: agreeing on terms of the donation.
- INIFAT, Cuba, Upgrading genebank IT infrastructure: Tito Franco is assisting with discussions with INIFAT on their IT needs and their acceptance of our terms of the Donation Agreement. Tito will likely travel to Havana soon to finalize the proposal and provide on-site assistance in getting the agreement signed.
- We have approached the national genebank of the Philippines with an offer to assist them in updating their information systems infrastructure. Documentation specialists from IRRI’s genebank kindly agreed to assist and visit the national genebank to discuss options. We expect their response within a month.
- NACGRAB, Nigeria, IT Upgrading project: initiated discussions.
The genebank database management tool is growing: with Chile already online, Tunisia reporting they will be online in July, Colombia in December, and Uruguay and many CGIAR genebanks expressing interest in deploying GRIN-Global.
We are now engaging the community, with CIAT and CIP leading, in implementation of GRIN-Global user interfaces that will allow for much better integration with mobile devices (when running around the genebank and out in the field).
We are also preparing with Martin Reisinger of USDA a set of on-line training tools for GRIN-Global administrators and users.
There are of course tons of things going on in other areas – we’ll be back with more in a month’s time.
Best regards from all of us in Bonn,