SINGER Task Force report 2010

First SINGER Task Force Meeting

25 June 2010

Bioversity International, Rome, Italy

Report


Content

Session1: What is the scope of future information networks for crop genetic resources in the new CGIAR?                                                  p.3
Session 2: What kind of collective actions can we foresee for genetic resources information and informatics in the new CGIAR?                                        p.7


Summary of Recommendations                 p.12


Annex 1: Schema of the Integrated Molecular Breeding Platform p.14

Annex 2: Meeting Agenda                         p.15

Appendix: Report of the GIGA International Committee Meeting   




Summary of recommendations

Recommendation 1: SINGER and Genesys will share the same database. SINGER information management will be handled by Genesys; consequently, the database function will be lost and taken over by Genesys.

Recommendation 2: The future of the SINGER website needs to be further discussed by the Task Force and a way forward agreed, particularly for the transition period while Genesys is getting up and running.


Recommendation 3: The recommendations relating to the cost-benefit analysis for adopting GRIN-Global, the data attribution proposal and governance issues are still valid and should be considered by the SINGER Task Force in the ongoing implementation of the network.


Recommendation 4: Both cross-referencing tools mentioned above should be made available to the crop networks, acknowledging that expert validation is required in the process. The tools could be inserted into the Crop Genebank Knowledge Base.

Recommendation 5: The importance of pedigree information has been once again stressed to identify the parent of sample. There is a need for information on neighbourhood/duplicate/parental trees to be included in Genesys.

Recommendation 6: There is a need for Bioversity to promote only one system and to provide SINGER with a system like that of EURISCO that produces quality reports. No concrete decision was made in this regard and it was recommended that the Task Force discuss this issue in a separate meeting with the genebanks’ database managers.

Recommendation 7: An additional chapter should be added to the CGKB on data management and the upload mechanism could also be described here. The Generation Challenge Programme (GCP) would certainly be ready to publish their methodologies, such as the tools for crop registries, genotyping and phenotyping protocols or guidelines for core collections. An updated manual for collecting could be loaded on the CGKB. Increased awareness about this product is needed.


Recommendation 8: It was noted that pedigree management systems would serve as a key element for the integration of the GR management system and the IBP. It might also be further developed by GRIN-Global in Phase II.  This could also be an additional proposal for the Gates Foundation, as both projects are currently funded this donor.


Recommendation 9 : The Task Force needs to list all information components that already exist and outline the elements currently missing in order to produce a revised schema based on the one developed by  Ruaraidh for the SINGER consultation meeting.


Recommendation 10: Termination of collective actions would constitute a step backwards, and it must be put into perspective considering the new information needs of the world.  One key action is to raise awareness among ICWG-GR and the traditional SINGER audience and donors about the newly named portal Genesys (collectively developed). Genetic resources activities should be balanced against the breeding approach of MPs. The SINGER Task Force needs to demonstrate the advantage of global access to germplasm information in comparison to single, independent genebank databases.


Recommendation 11: The Task Force and the SINGER network members should provide key talking points and agree on a strong message to collectively convey when approached by consultants of the scoping study.  We could combine the ISC vision (Attached in Annex 2) with the Task Force recommendations.


The meeting was opened by David Williams, SGRP Coordinator, who reviewed the Task Force objectives and Meeting Agenda. 


Terms of Reference of the SINGER Task Force

 In view of the changes in the CGIAR and SGRP the ICWG-GR agreed that this is the appropriate time to review the needs for future system-wide information activities, taking a forward looking approach. A taskforce was established (based on the group nominated to look further at GRIN-Global) including Daniel Debouck, Luigi Guarino, Dave Ellis, Jan Konopka, Elizabeth Arnaud, Michael Mackay and Ruaraidh Sackville-Hamilton with the following terms of reference:

Define the scope of future information networks for crop genetic resources in the CGIAR. 
Determine and assess options that meet these needs and prepare a report.
Make a recommendation to the ICWG-GR on the way forward by 30 September 2010.


Rationale

The Task Force consultation and recommendations should feed into the larger discussions on scope of system-wide collaboration in genetic resources that we are expecting to be done by an external group following the directive from the Consortium Board. A thorough review of options, network assessment and preferences should be taken into account. With the Mega-programmes configuration, collective action is likely to be very different in future.

Collaboration may have to be based on what we really need to work together on and we may also have to raise funds to cover the costs of working together.


The meeting was organized according to two thematic sessions:

Session 1: What is the scope of future information networks for crop genetic resources in the new CGIAR?  

Session 2: What kind of collective actions can we foresee for genetic resources information and informatics in the new CGIAR?


A series of questions listed in the Meeting Agenda (see Annex 2) guided the discussion reported hereunder.


Participants:

Task Force Members


1.Elizabeth Arnaud

SINGER Coordinator, SGRP, Bioversity international

3. Daniel Debouck by Skype

Head of Genetic Resources Unit, CIAT

4. Luigi Guarino

Science Coordinator, Global Crop Diversity Trust

5. Michael Mackay

GIGA PI, Bioversity international

6. Ruaraidh Sackville-Hamilton

Head of Genetic Resources Unit , IRRI

TF members not able to attend


7. Dave Ellis

Supervisory Plant Physiologist, USDA-ARS

8.. Jan Konopka

ICARDA


Invited attendees


9. Adriana Alercia

Key descriptors development, Bioversity international

10. Harold Bockelman

Supervisory Agronomist , USDA-ARS

11. Audrey Chaunac

Project assistant, Bioversity international

12. Hannes Gaisberger

GPG2 - 4.1: scanning mission reports, programme specialist, Bioversity international

13. Alexandra Jorge

GPG2 coordinator ,Bioversity international

14. Graham McLaren

GCP informatics project leader

15. Fawzy Nawar

Genesys web developer, Bioversity international

16. Federico Mattei

GPG2 - 4.1: scanning mission reports, project assistant

17. David Williams

SGRP Coordinator




Session 1 : 

What is the scope of future information networks for crop genetic resources in the new CGIAR? 


Session Chair:  Graham MacLaren


1.1 General discussion about the future of SINGER in the context of the CGIAR Mega-programmes (MPs) and Genesys development


1.1.1 Database

Recommendation 1: SINGER and Genesys will share the same database. SINGER information management will be handled by Genesys; consequently, the database function will be lost and taken over by Genesys.

1.1.2 Website

It was generally agreed that SINGER should continue as a network. The question was raised as to whether SINGER will still need a website. A website is important for the network’s visibility and to facilitate system-wide efforts, particularly within the context of the CGIAR change process; however a cost-benefit analysis should be conducted to answer this question. The SINGER website provides an identity for the network, which represents a particular group of data providers and addresses the needs of a specific users, so what additional functions would this portal (accessible via the SINGER website) have with regard to Genesys? One difference is that the SINGER website presently gives more visibility to countries where germplasm collecting has taken place. There is an ethical duty to make this information publically available. Such information should also be visible on Genesys, which should also include the distribution data available in SINGER.


Recommendation 2: The future of the SINGER website needs to be further discussed by the Task Force and a way forward agreed, particularly for the transition period while Genesys is getting up and running.


1.1.3 Governance of SINGER

The termination of the System-wide Genetic Resources Programme (SGRP) in December 2010 has been announced; this will impact the future management of SINGER. To date, it is unclear as to what will happen with regard to the maintenance of a comparable system-wide programme. There is an assumption that the ICWGR-GR will remain, even if SGRP is terminated.


1.1.4 Vision of the GIGA International Steering Committee 

A PowerPoint presentation on the draft vision of the GIGA International Steering Committee for Genesys was presented by Michael Mackay. Genesys should contribute to alleviating the global food crisis and addressing climate change (see Annex 1). A question was raised as to whether FIGS should be locally available. The Focused Identification of Germplasm Strategy (FIGS) is an approach which can be used locally with subsets of data downloaded from Genesys.

It was mentioned that emphasis should now be placed on including more information/data in Genesys and that the portal’s additional functionalities should be considered in the subsequent phase of development.

How flexible should Genesys be with regard to the accessibility of subsets of data addressing various interest groups? Should this data also be included in different portals? While this may not be necessary at the present time, it was noted that in the future (medium-term), it might be useful to employ different functionalities, e.g. in different languages for various interest groups.


1.1.5
Recommendations of the SINGER/GPG2 Consultation and Planning Meeting held from 24-28 August at USDA in Beltsville, Maryland (see Meeting Report for further information)

Some recommendations are now obsolete as work has already commenced to address these; for other recommendations, the wording should be revised to ensure these are up to date. For example, ‘SINGER team’ should be amended to ‘SINGER network’. 


Recommendation 3: The recommendations relating to the cost-benefit analysis for adopting GRIN-Global, the data attribution proposal and governance issues are still valid and should be considered by the SINGER Task Force in the ongoing implementation of the network.



1.2 Present status of the collective information products and the future of these under the CGIAR MPs


1.2.1. Crop registries – The Rice registry example

Crop registries support global crop conservation strategies by cross-referencing accessions maintained in different genebanks. Each crop registry is particular to a specific crop and some need to be improved in terms of user-friendliness. In the Rice registry,  based on ICIS, 223,397 rice samples have been analyzed from six current and one historical rice collection: IRRI Genebank, USDA, INGER, AfricaRice, CAAS, CIAT and IITA. It was mentioned that that Ontology terms and definitions are needed globally in ICIS to enable queries and data annotation. There was an expression of interest from NPGR, India and EMBRAPA, Brazil to join the registry and this request will be pursued. Each crop registry is coordinated by one centre as part of the genebank’s activities.

The Wheat and Rice registries share a common approach to implementation with regard to their crop databases. Duplicates are identified using a tool developed by Tom Hazekamp, mainly based on Excel macros. ICARDA has also developed a cross-referencing tool.  However, the tool cannot be used alone and results must be validated by an expert with access to additional sources of information (e.g. collecting forms).

In the Rice registry, when searching a name, returned occurrences are displayed and grouped per entity. This grouping highlights data curation problems such as an error in connecting the sample to the wrong parent. The clustering tree traces back to the original collected sample in order to identify such errors and improve data quality.  Duplicates, in the genetic sense, are indentified and neighbourhood clustering is possible. The next step is to add images to the registry.

Recommendation 4: Both cross-referencing tools mentioned above should be made available to the crop networks, acknowledging that expert validation is required in the process. The tools could be inserted into the Crop Genebank Knowledge Base.

Crop registries are collection management tools. Cross-referencing is interesting for CGIAR centres and for other genebanks. Users can see what duplicates are available for request and where these can be obtained. Unique accessions are also identified. This information could be transferred to Genesys, thus linking the crop registries to the global portal (as the link with Genesys still needs to be developed). 

Recommendation 5: The importance of pedigree information in the identification of a sample’s parent has been emphasized once again. There is a need for information on neighbourhood/duplicate/parental trees to be included in Genesys.

Should Genesys include the same data as that which is maintain in the crop registries?  A limiting factor is that other registries have been developed and are implemented in different ways. There is no neighbourhood relation for other registries.

1.2.2 SINGER data upload and scanning collecting mission reports

Some datasets received from centres were not as complete as the data presently included in SINGER and not all data were formatted. Data received will be uploaded into SINGER and Genesys, and we should have a versioning of SINGER. Centres have requested a system for data exchange that is easy to install, does not require much training or interactions and remains sustainable even when IT staff are no longer available.  Templates have been sent to centres, and databases should be mapped against these templates.  

Criticisms were made regarding the fact that three different upload methods are used within Bioversity: EURISCO model, Genesys upload tool (DDC) and SINGER manual upload. The question, ‘why not adapt the EURISCO upload and connectivity system historically used by several European genebanks?’ was raised. It was indicated that different requirements and data flows need different mechanisms. The DDC was made to upload updates of characterization and evaluation data into Genesys, while the EURISCO system was developed to upload large scale sets of Passport data. 

Recommendation 6: There is a need for Bioversity to promote only one system and to provide SINGER with a system like that of EURISCO that produces quality reports. No concrete decision was made in this regard and it was recommended that the Task Force discuss this issue in a separate meeting with the genebanks’ database managers.

1.2.3 The Crop Genebank Knowledge Base

The Crop Genebank Knowledge Base (CGKB) will contribute to more efficient and effective ex situ conservation of crop genetic resources by facilitating easy access to knowledge and best practices for genebank management of selected crops, as well as for many aspects of general genebank management (see http://cropgenebank.sgrp.cgiar.org/). The website was developed using a content management system, Joomla. 


The CGKB also has training objectives. Tutorials and instructional videos are can be downloaded from the website.  Each crop contact person is responsible for loading content into the CGKB.


Recommendation 7: An additional chapter should be added to the CGKB on data management and the upload mechanism could also be described here. The Generation Challenge Programme (GCP) would certainly be ready to publish their methodologies, such as the tools for crop registries, genotyping and phenotyping protocols or guidelines for core collections. An updated manual for collecting could be loaded on the CGKB. Increased awareness about this product is needed. 



1.3 The Integrated Breeding Platform (IBP) in the GCP transition phase and MPs – What the IBP requires from collective actions in genetic resources information? (see Annex 1)


The Integrated Breeding Platform (IBP) will provide access to breeding services and well characterized and useful genetic resources. It will use the maize field book system and the IRRI ICIS tools. The workflow will be configurable. Capacity development and support will be provided.  Ten breeding projects serve as use cases.


The IBP can also utilize information from the Ontology, Central Registry, Genesys, the Ordering System and the CGKB. The Ordering System, as developed on SINGER, is critical for the IBP to provide access to reference sets with certified quality data. It was proposed that the reference sets of the GRSS be included in Genesys.


How can genetic resources management be integrated into the IBP system? 


Recommendation 8: It was noted that pedigree management systems would serve as a key element for the integration of the GR management system and the IBP. It might also be further developed by GRIN-Global in Phase II.  This could also be an additional proposal for the Gates Foundation, as both projects are currently funded this donor.


The GCP will come to an end by 2013. The development of the IBP has been secured in the CGIAR MP3 and coordination of the IBP will function in a manner similar to that of the SGRP.



1.4 GRIN-Global progress and perspective for the next three years


The final version of the curator and web tools for GRIN-Global will be available at the end of 2010. The second release of the curator tool will be administered in the summer of 2010. At the end of September 2010, a Technical Advisory Committee meeting will be held, as well as an additional training for trainers. The USDA Genebank is still using GRIN Classic at the moment.



Session 2: 

What kind of collective actions can we foresee for genetic resources information and informatics in the new CGIAR?


Session Chair:  Ruaraidh Sackville-Hamilton

Participation of Daniel Debouck by Skype



2.1 What are the priority collective actions/decisions to undertake? What is the message SINGER wants to convey to management of the CGIAR centres?

It is necessary to secure the GPG2 products.


1. SINGER: the database will be now same as Genesys database. For the web interface, future plans need to be decided with the network members.

2. GPG2 Passport data quality: Georeferences obtained with Biogoemancer are still affected by errors and need to be checked and validated by each curator. A comparison with the latitude/longitude originally indicated in the collecting report is often necessary. Thus, this is a centre-specific activity and is no longer considered as a collective action. Ruaraidh Sackville-Hamilton raised important points about the quality of georeferences obtained from Biogeomancer that need to be discussed further. Validation of metadata for the georeferences is also necessary.

1. Revision of the current MCPD:  Following modifications suggested from crop registries, EURISCO and CGP, the standards validation must be applicable for a wider community than just SINGER.
2. Testing GRIN-Global according to selected standards.
3. Awareness: The target audience will be the Director Generals of CGIAR centres.  Awareness efforts should focus on the following points:
4. Is Genesys convincing enough as a system-wide product? We need to ask partners to be the spoken voice for Genesys.
a. Genesys and associated systems (GRIN-Global) are part of a global system. 
b. Approach the Treaty Governing Body: Benefit-sharing fund could be spent on information system.
c. GRIN-Global adoption linked to Genesys.


The scoping study defined by the Consortium Board should identify whether collaboration between CGIAR centres is needed across crops or along the crop-specific value chain. The collective collaboration in sharing genebank information is valuable for germplasm users and a platform across crops could be developed so genebank databases can be linked to this facility, but the content could be organized and provided by each MP. SINGER members should provide the scoping study with examples of the advantages of accessing across crop information for development actors, environmentalists and extension workers.

Two concepts need to be discussed further: the centralized database for all crops and the decentralized model like that of the IBP which provides configuration per crop. Each element of the information workflow needs to be identified, e.g. the crop registries’ role is at the level of GRIN-Global. 

Recommendation 9 : The Task Force needs to list all information components that already exist and outline the elements currently missing in order to produce a revised schema based on the one developed by  Ruaraidh for the SINGER consultation meeting.


2.2 Recommendations of  the Task Force to support collective actions

A strong case for collaboration needs to be made, including for non-technical issues. Are we just individually part of the global system or/and are there activities we want to do together? Should collective action development be continued? The long-term strategic consequences of working individually or collectively should be demonstrated. The MP8 concept, based on the outputs of the Mombasa meeting, includes all genetic resources information services that the outside community expects from CGIAR centres.


Providing genebank information to breeders and curators, which represent a relatively small audience, should not prevent the provision of important information to other types of users in order to extend the benefits of genebank services. Genebanks should seek to engage the wider public. SINGER members must explain the type of system they wish to establish and what type of data should be included. How global would a system be that only addresses users’ needs for two or three crops?


Originally, SINGER was created to capture global information regarding all flows of germplasm and to enable a global analysis of distribution data. This role supports the implementation of the International Treaty and continues to remain relevant. In-Trust collections must be fully documented for their germplasm transfers. SINGER has an advocacy role within the global system for genetic resources and information produced by our genebanks should be freely and publically available.


The International Treaty aims to collect all germplasm transfers in addition to SMTA information.  What does this change with regard to the SINGER rationale?

    • CGIAR Centres must continue to lead in this domain and document all SMTAs, making the information publicly available.
    • This role remains a collective responsibility even if the Treaty agreement was signed with each genebanks individually.
    • CGIAR needs to commit to the international public goods concept.


A unanimous decision to maintain our collective achievements and commitment from the Treaty is needed. The historical motivation to maintain SINGER with regard to information distribution largely depends on whether the Treaty will take over this responsibility in a comprehensive way. Genebanks’ legal obligations are also important.


We did not exhaust all possible means for information data curatorship; additional efforts should have been made. Further, SINGER did not pay enough attention to data analysis in the past. We need to underline the responsibility of the CGIAR for the curatorship of information, which is not only based on technical solutions. We can collectively perform assessments of the status of data completeness and point out gaps in CGIAR genebank information regarding passport, characterization and evaluation data. We can also analyze the reasons for such gaps and determine actions and next steps for improvement. 


SINGER should be aligned with long-term strategic results and we need to promote the products of the network, provide users with definitions and demonstrate the strategic objectives of Genesys.


Recommendation 10: Termination of collective actions would constitute a step backwards, and it must be put into perspective considering the new information needs of the world.  One key action is to raise awareness among ICWG-GR and the traditional SINGER audience and donors about the newly named portal Genesys (collectively developed). Genetic resources activities should be balanced against the breeding approach of MPs. The SINGER Task Force needs to demonstrate the advantage of global access to germplasm information in comparison to single, independent genebank databases.



2.3   Target audience and scoping study responses

The Task Force was asked to produce recommendations for ICWG-GR regarding the future of system-wide actions and to re-engage the original funding agencies of SINGER, explaining the new situation with regard to Genesys. It is critical that the importance of maintaining the SINGER network and the website be emphasized.  A better definition of the user community for CGIAR products needs to be provided, as well as an explanation of how to adapt these products to changing user needs.


SINGER was initially funded by the Inter-Centre Working Group, with additional support from other donors. SINGER, as a network, needs to be engaged in collective actions to build the future in terms of access to PGR data. The long-term vision of SINGER is to continue with the development and maintenance of an information system according to the most cost-efficient means. In addition to making recommendations for action, the CGIAR should also provide additional funds. SINGER should not be abandoned by donors. Who will be the future funders of SINGER once SGRP has ended? The SINGER Task Force report must underline the lead function of the CGIAR regarding the documentation of all germplasm flows. CGIAR genebank information should be made public; the terms of confidentiality will be determined by the Treaty’s decision.


We need to think collectively, ensure the sustainability of our collaborative work, continue the exchange of information using standards and seek to implement cost-efficient activities.  We need to address all aspects of SINGER:

1. SINGER database will be the same as Genesys database.
2. SINGER members must define what do we need to do together? Provide a List!
3. SINGER portal: Will Genesys interface be a unique interface or is there still a visibility     needed?


It is important to participate in, and contribute ideas to, the development of the cross-cutting genetic-resources MP component and to respond to scoping study questions

Recommendation 11: The Task Force and the SINGER network members should provide key talking points and agree on a strong message to collectively convey when approached by consultants of the scoping study.  We could combine the ISC vision (Attached in Annex 2) with the Task Force recommendations.


Election of the Task Force Chair

Graham (who is not a Task Force member) and Daniel received an equal number of votes, but both declined the position. The Chair still needs to be identified to present this report in September. A proposal was made that the SINGER Coordinator serve as the Acting Chair for the time being.

Timeline

 Deadline for distribution of these minutes to Task Force members: 2 July 2010.
Feedback on draft minutes received by 11 July 2010 to allow Luigi (who will be in Mongolia) to send his response.
 Elizabeth will liaise with Task Force members between now and 15 September 2010 to organize further consultations by mail or Skype.
 The original deadline for the full proposals for the MP is the 30 September 2010



Annex 1

Schema of the Integrated Breeding Platform



Annex 2

SINGER Task Force Meeting






ĉ
Elizabeth Arnaud,
Feb 2, 2011, 3:34 PM
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