Establishment of an European Plant Genetic Resources Information Infra-Structure
EPGRIS
Report of the Start-up Coordination Meeting,
17-18 December 2000, IPGRI, Rome, Italy
Participants
Frank Begemann
Zentralstelle für Agrardokumentation und -information, Bonn, Germany
Eliseu Bettencourt
Instituto Nacional de Investigação Agrária, Oeiras, Portugal
Iva Faberova
Research Institute of Crop Production, Prague, Czech Republic
Theo van Hintum
CGN, Plant Research International, Wageningen, The Netherlands
Morten Hulden
Nordic Gene Bank, Alnarp, Sweden
Steve Katz
FAO, Rome, Italy
Brigitte Laliberté, Lorenzo Maggioni, Samy Gaiji, Thomas Metz, Elizabeth Goldberg
International Plant Genetic Resources Institute, Rome, Italy
Martine Mitteau, Véronique Jamilloux
Bureau des Ressources Génétiques, Paris, France
Welcoming address and introduction
Brigitte Laliberté welcomed all the participants on behalf of the IPGRI Regional Office for Europe and ECPGR and congratulated all the partners in EPGRIS for having produced such a successful EU project proposal. EPGRIS is an important model that should inspire other regional PGR networks to centralize or catalogue information on ex situ collections. The main impact expected out of EPGRIS is the development of national inventories and methodologies to develop such national coordination mechanisms. For the IPGRI Regional Office for Europe, EPRGIS is an important tool to bring in associated states and countries and build capacity in documentation. This project has been made known to IPGRIs partners during several visits namely to Albania and Armenia where commitments have been made to support documentation activities and participation in EPGRIS. IPGRI has recently revised a Memorandum of Understanding between with VIR in Russia. Article 3 of the MoU on documentation and information does not explicitly mentioned EPGRIS but it has clear intentions to bring in Russia into EPGRIS and ensure that national inventory is documented and completed. The Search Catalogue EURISCO together with other databases and catalogues such as SINGER, GRIN and many others will facilitate the access to information on some of the major ex situ collection around the world. Facilitating access to information is the first step to facilitating the use of the material and developing appropriate conservation strategies. EPGRIS is also a very important output for ECPGR and support to the work of the crop working groups without established Central Crop Databases. Additionally, in the context of a recent project proposal for EU funding in situ conservation of European crop wild relatives, EPGRIS has been mentioned as a possible model/approach to building national inventories.
Theo van Hintum, coordinator of EPGRIS also welcomed the participants and reiterated the importance of this project. The documentation of PGR in Europe is in the stage that the access to the individual sources can be streamlined. He thanked the partners for their constructive collaboration in the preparation phase of the project. It quite unusual that a project is accepted by the EU without any amendments. In this case it was possible thanks to the clear communication between the partners, amongst others during the project preparation meeting held already in 1999, also in Rome hosted by IPGRI. Finally, he thanked IPGRI for the efficient preparation of the meeting.
The EU scientific officer for this project Dr. Baig, has been invited to participate in the meeting, but could unfortunately not attend. In correspondence with Dr. Baig, it was agreed that the project could effectively start December 2000, although the contract was signed in September and the project could therefor start in October. If necessary, it would be possible to extend the duration of the contract with an extra few months at the end of the project (obviously without additional funding).
The participants agreed Theo van Hintum to chair the meeting.
The chairman presented the agenda, which was approved by the group. The agenda had been structured following the order of the workpackages (WP) which were to start in the first 18 months. A suggestion to include a session of 15 minutes on the BIG web site of ZADI was proposed and scheduled in the agenda of the Monday (see revised agenda in Annex I).
All participants introduced themselves and their respective institutes, summarized their particular tasks in EPGRIS and expressed their interest in this project.
Overview of the project
Theo van Hintum presented an overview of the EPGRIS project. Objective, expected achievements, project work plan, workpackages, project partners, main role of the participants, the details of the 10 different work packages and the relationships between the workpackages (for details refer to the project technical annex). The first achievement expected of EPGRIS are the national inventories and the second is the search catalogue, EURISCO with its estimated 70% of European PGR ex situ accessions by the end of the three-year project. Other important achievements expected are the improved collaboration between genebanks and the Clearing House Mechanism (CHM) of the CBD and improved capacity to manage PGR documentation and information.
The second coordination meeting will be organized by INIA in Portugal in the summer of 2002. The final project meeting is planned to be held in Prague in autumn 2003.
During the general discussion of the project, several issues came up that were to be considered during the detailed discussion of each WP, such as:
Workpackage A1 - Nomination Focal Persons
Brigitte Laliberté introduced WP-A1. In each European country the ECPGR national coordinator will be approached and asked to propose a National PGR Inventory Focal Person in liaison with the national Clearing House Mechanism focal point. This Focal Person will define the countries needs (help, training, etc.) and be responsible for establishing the National PGR Inventory, and providing the data to the European Search Catalogue. The focus of the project will be on the EU and associated states, but also other European countries will be invited to join the initiative (on a self-funding basis).
The discussion mainly concerned the mandate of the Focal Person (FP), how technical that person should be and the support that EPGRIS will provide to those FP and the national programs in general.
It was agreed that the invitation letter should clearly indicate what is expected of the FP. It is then up to the national coordinator to nominate who they think would be most appropriate. It should be made clear that a commitment should be made towards this project and in particular, data on a national inventory will be expected, even if a national inventory is at a very early stage of development. It was suggested to take some of the wording used in the original letter that was sent to the National Coordinators two years ago for the ECPGR survey on EPGRIS regarding the contribution to the Clearing House Mechanism.
A letter will be sent to all ECPGR National Coordinators, including an extract of the technical annex (brief summary of the project) with the objectives, excluding any financial information. The mechanism of sub-regional meetings, inventories of training needs and technical assistance will also be explained.
It was suggested to consult the list of FAO WIEWS focal points (available on-line) as a possibility to suggest that it be the same person to enhance complementarily with WIEWS.
It was also agreed that ECPGR countries would be considered but also the other European countries. The letter to the later could be simply addressed to the Ministry of Agriculture. There should be 2 types of letters. The first for the countries of the EU and Associated States eligible for funding and the second letter to the non-EU inviting them to nominate a FP but with the knowledge that the participation would be on a self-funding basis.
It was agreed that a draft letter (2 types, EU, non-EU) would be prepared by the ECPGR Coordinator (Lorenzo Maggioni) and circulated to the project partners for feedback. EPGRIS partners would be given a week to comment. A revised letter would then be sent to all ECPGR National coordinators and to EU countries not in ECPGR. (Action: L. Maggioni, by end of January 2001)
Workpackage A2 - Organization regional meetings
Iva Faberova introduced WP-A2. Her presentation covered the different sub-regions agreed on during the meeting in Rome in August 1999, and the estimated number of participants for each meeting considering the funded partners and the possibility of self-funded partners to attend. A very effective colored map of the different sub-regions was produced to visualize the division. Furthermore an overview of the European ex situ PGR collections with an estimated 750-800,000 accessions was presented. The ECCDB containing information on an estimated 424,812 accessions (July 2000). It is believed that there remains a large proportion of accession that is not included in any ECCDB.
The prerequisites of WP-A2 are that focal persons be nominated and this person should have clear duties and responsibilities for data supply (deliverable of WP-A1). Furthermore, data standards should be proposed (deliverable of WP-B1).
The length of the first sub-regional meetings was discussed and it was agreed that 2 days for the biggest groups should be sufficient, taking into consideration the country report of each participant. For small meetings, one day could be sufficient.
Concerns over the financial amount allocated to the organization of such meetings was expressed and it was felt that the funds could be insufficient in the light of continuously increasing airfares and other costs. It was proposed that, if there would be serious problems, money could possibly be moved from other activities. After the first round of regional meetings the necessity will be considered, but for the time being the coordinator strongly advised to try to stick to the budget. (Budget: for the hosting partner 1 person-month and 2000 for local costs per meeting, and 1000 per expected paid participant, for 'attending partners' (ZADI or CGN) .25 person month and 1000.)
The original timing of the meeting was discussed and it was proposed to postpone the date of the second meeting to allow some feedback from the second coordination meeting. The proposed dates for the first round of sub-regional meetings would be July 2001 (month 8) and the second round would be held in October 2002 (month 23).
A letter of invitation to attend these sub-regional meetings will be sent by the hosting partners. Two types of letters will be sent; one to those funded and the other to those on a self-funding basis. (Action: Organizers sub-regional meeting, at least 3 months before the meetings). It will be then up to IPGRI regional office for Europe and ECPGR to contact non funded FPs individually to provide some additional support. This will be done at their discretion but in consultation with the EPGRIS partners. A draft a letter of invitation (2 types) would be prepared and circulated to the group for comments. (Action: I. Faberova, at the latest May 2001)
It was proposed that a common agenda for all the sub-regional meetings be developed. The agenda of the first meeting could include following points:
Issues to be discussed during the meeting are
A short paper on these issues will be prepared and circulated. (Action: F. Begemann, draft circulated at the end of Januari 2001)
It was proposed to get a clear picture of what the "legal status" of EURISCO and the information provided by it would be, to be prepared to face questions from the participants on this point. S. Gaiji explained the documentation for SINGER and proposed that something similar be used for EURISCO. It was also suggested to consult the rules that the EU might have on this subject. Part of it is covered under WP-C1. Concerns were expressed over the legal status of EPGRIS with its 7 partners over the legal status of EURISCO with its many national partners. It was however emphasized that partners provide the information on a voluntary basis. The terms and conditions of the data should be clear, for example the data in EURISCO are the public domain but cannot be used for commercial purposes. It was therefore suggested to study the SINGER model and see if it can be made suitable for EURISCO. However, some partners expressed concern about making it too 'heavy'; for example if a "copyright" statement is to be used it should not have the "I accept" button such as the one on the SINGER site. A short paper on these issues will be prepared and circulated. (Action: T v Hintum, draft circulated at the latest April 2001)
Workpackage A3 - Staff visits and individual support
Frank Begemann introduced WP-A3. There are resources available to take away bottlenecks in the development of national inventories: direct financial support for investments and staff exchanges with ZADI, NGB or CGN.
There need to be clear criteria for the selection of candidates for staff exchange or individual support. These could include:
Existence of national inventory, based on information collated in the list of national inventories produced. (Action: F. Begemann) For the inventories that are accessible on-line, the links will be made from the ECPGR web site, germplasm database page. (Action: B. Laliberté, when links become available)
These criteria should be established before the next meeting. (Action: F. Begemann & T. van Hintum, draft circulated at the latest June 2001) Own knowledge of situation through contacts, country visits and meeting would be also used to select potential candidates, in consultation with the ECPGR National Coordinators. But these criteria could then be used to justify the selection. The decision would then be taken by the three hosting institutes, ZADI, CGN and NGB, to arrange for bilateral invitation procedures.
The question was raised whether non-EU countries could benefit from funding even if indirectly through staff exchange. Possibilities will be checked and results will be circulated. (Action: T. van Hintum, at the latest April 2001)
Welcome second day, brief introduction to new participants
The chairman introduced the new participants (Steve Katz from FAO and Lorenzo Maggioni the ECPGR Coordinator) and gave a brief introduction to the project.
Overview related FAO activities
Steve Katz gave an overview of the activities of the FAO, especially in regards to information and knowledge management (the World Agricultural Information Centre - WAICENT), and put this in the light of the World Food Summit (November 1996). He elaborated on FAO's principles of information management: strategic use of metadata and content repositories, separation of content, presentation and processing, controlled vocabularies, categorization schemes, and the use of international and non-proprietary standards such as XML. The technical structure behind the FAO web-site was presented. This site had in November 2000 and impressive number of 11.5 million hits with over 500.000 user sessions! Also the problem of finding material on the WWW was discussed, and the possible solution provided by the Dublin Core (an agreed set of core metadata) was presented.
(see
www.fao.org/waicent and www.fao.org/)
Presentation of the 'Bundesinformationssystem Genetische Ressourcen' (BIG)
Frank Begemann briefly presented BIG, the integrated system developed at ZADI, to give access to a wide spectrum of genetic resources maintained in Germany. The system uses a distributed database approach in which a user defined query is transferred to several locally maintained databases, and all results are translated in one form using the XML protocol.
The use of this kind of approach in EPGRIS is considered an option that can be developed; it would provide the partners to get acquainted with the technology, and since it is generally considered to be the 'next technology', it would prepare EURISCO for the future. However, since the objective of EPGRIS is not to develop new technology, but to develop a new infrastructure, EPGRIS will be conservative in applying it in the 'production database'.
(see
www.big-flora.de/)
Workpackage B1 - Definition of data and standards
Morten Hulden introduced WP-B1, showing what standards need to be set, and what issues need to be considered when setting these. He gave a comprehensive overview of options available.
A brief discussion on the type of data to include was concluded by leaving this decision to the national partners and be inclusive as opposed to being exclusive at this stage, within the range of PGRFA. If PGRFA information is available and there is a unique identifier (such as accession number), then it can be included.
The data format generated more discussion, as this is the crucial element of the project. The main points of discussion were on the following:
Regarding the issue of language, it was concluded that the content (field containing descriptive text) should be accepted in original languages but field names should be in English only (according to an agreed list). The field names will depend on the final list of descriptors agreed. The content could be transferred to the 'centralized' database using the Unicode character set that avoids the problem of regional language settings and thus covers the symbols used in all languages.
The export file format should be as much as possible in XML which already includes a tag delimiter. But it was felt that data transfer should not be waiting for files to be in XML as this might delay the process too much. Fields should therefore be accepted with both, tab delimited and XML and partners should be encouraged to move towards XML format (<field>content</field>).
Wherever there is an FTP site available, the data can be stored there and uploaded in Rome. In cases where no FTP sites are available, other solutions can be found.
It was agreed to use the IPGRI/FAO Multi-Crop Passport Descriptors (MCPD) as a starting point. But the main criticism of the MCPD were that there are inconsistencies in the names of the fields. It was suggested to use a naming system proposed by M. Hulden:
The last part of the name indicates the type of the field (_name, _number, _acronym). The middle part _together_ with the last part indicates the domain of the field, i.e. the pool from which the field draws its values (accession_name, accession_number, institude_acronym). The first part is a qualifier that makes the field name unique within the database (genebank_accession_name, collector_accession_number, donor_institute_acronym). Short versions of such field names (gbkaccnam, colaccnum, doninsacr) are convenient when longer names are impossible because of db software restrictions or otherwise inconvenient in tabular output. For example: gbkaccnum = accession number given by the genebank; doncouacr = acronym of the donors country.
This suggestion was strongly supported by some. However others opposed the idea since - it might be too late at this stage as the MCPD are used by a vast range of users, including the ECCDB and in other regions, -it would have to be discussed within the ECPGR Crop Working Groups, and - field names are not meant to include metadata and therefore it should not matter what they are called as long as the definition (description of the field content) is clear.
Also on the individual descriptors, no agreement could be reached within the scope of this meeting. Therefore the following steps were agreed:
If this process is not successful, the current MCPD will be used as a basis for the sub-regional meetings.
Two main models of data conversion were presented: (1) conversion at the central catalogue "centralized conversion" where one place does the conversion of more than 40 files and (2) conversion at the providers side "decentralized conversion" where 40 people do their own conversion. The advantages and disadvantages of each option was discussed and are summarized below:
|
Option 1: centralized conversion |
Option 2: decentralized conversion |
|
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Advantages |
|
|
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Disadvantages |
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It was then agreed that a decentralized conversion would be preferable, mainly because of the resource requirement and therefore low sustainability of the centralized option.
Workpackage B2 - Creation database
Samy Gaiji introduced WP-B2, presenting the requirements, and options for creating the database system. SINGER will provide the technical support to the IPGRI regional office for Europe to implement the EURISCO search catalogue.
The requirements for the development of EURISCO are:
The inclusion of ancillary data such as GIS, map standards, climatic and soil data sets and references (URLs) should be considered as a second step to EURISCO. The ultimate objective of EURISCO is to access information on a particular accession and continue the search on the national database.
One of the obstacles for effective use of the catalogue is the taxonomy; taxonomic references should be used. SINGER uses a range of them such as Species2000, GRIN. BIG used BIGTax as a solution. It was agreed that the taxonomic authority should not be required; it should be strongly encouraged but at this stage should not be mandatory. This should be taken into consideration for data quality improvement and could be done as a second step to the project, part of the public awareness.
Over the last year, SINGER has been involved in developing the SINGER Tool Kit (TK), a software to web enable databases, particularly designed for genebank management databases but can be used for a wide range of databases. The TK replicator has therefore been developed based on SQL/ODBC allowing replication between data sources (MS SQL7). Data integrity is automatically checked. If data is rejected, then a message is generated with the reasons for rejection. If corrected, the data is re-submitted. The front-end design would be left for the partners but the TK design forms and queries.
A prototype of EURISCO could be tested on the EPGRIS Intranet web site (private site accessible only by the project partners. Address: http://141.ipgri.cgiar.org/EPGRIS Username: EPGRIS. Password: EPGRISpartner.)
It was suggested that data be accepted in both formats, pipe-delimited and XML to test the procedures. SINGER would be ready to start in February 2001 with national inventories already available such as from ZADI, RICP, BRG, INIA and CGN. ZADI would provide the format in XML to test the physical transfer. It can provide data for Germany but also for Russia (VIR). This trial would also feedback information for the needs for 'standards'.
The establishment of a project Internet site to be used as a public awareness tool was discussed. It was proposed that the information about the project would be the responsibility of the project coordinator. The front-end should include:
The issue of replication and the archiving of old files was discussed. It was agreed that the complete set of data from a national inventory should be replaced with the new set and the old files be archived. This would avoid the problem of updating record by record and the problem of deleting redundant records would be solved this way. Downloading protocols should be established for the "distributed" databases. To facilitate the searches, it would be preferable to search data stored locally. Frequent updates is not considered to be problematic (could be done as an automatic procedure daily).
The agreed timeframe for the development of EURISCO is:
|
Task |
Month from the start of EPGRIS |
|
Data standards |
2 (up to 8 - see discussion WP-B1) |
|
Creation of database |
6 |
|
Demo web site |
7 |
|
Feedback from EPGRIS partners (1) |
8 |
|
Data replication |
10 |
|
Feedback from EPGRIS partners (2) |
12 |
|
Frant-end design |
14 |
|
Feedback from EPGRIS partners (3) |
16 |
|
Finalisation |
36 |
Workpackage C1 - General coordination
Theo van Hintum gave some additional information about the management of the project:
Other business
The project should create a web Intranet site with the following information (Action: B. Laliberté, by end of January 2001)
An EPGRIS Intranet has been created to post the minutes of the meeting, circulate the demo site during the development. (Address: http://141.ipgri.cgiar.org/EPGRIS Username: EPGRIS. Password: EPGRISpartner)
The issue of the future of the ECCDB was raised. The ECCDB managers are preempting that EPGRIS might take over the roles of the DB managers. It was felt that the ECCDB can bring value to the data and the crop collections. These database can be linked to particular projects and or expertise. Furthermore, they can be used to identify duplicates. A discussion paper could be produced to explain the objectives of EPGRIS and the complementarily with the ECCDBs. The new web site could be used to publish this information. A letter could be sent to all DB managers to also clarify this issue, including a diagram of where all the components fit in together. DB managers should be encouraged to concentrate efforts into characterization and evaluation. T. van Hintum agreed to produce such a letter, since he is both a DB manager and coordinator of EPGRIS. (Action: T. v. Hintum, by April 2001)
Closing of meeting
The chairman thanked the participants for their contributions to this productive meeting. Important decisions have been made that were critical for the development of the project. The collaboration of the host and organizers of the meeting IPGRI, and especially Brigitte, was gratefully acknowledged.
Note: the minutes of the Meeting of the ECPGR Internet Advisory Group, Sunday 17/12/00 will be produced as a separate document.
ANNEX I
Revised agenda
Sunday 17 December 9:00 - 17:30
|
Time |
Topics |
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9:00 10:30 |
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10:30 11:00 |
Coffee break |
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11:00 12:30 |
|
|
12:30 14:00 |
Lunch |
|
14:00 15:30 |
|
|
15:30 16:00 |
Coffee break |
|
16:00 17:30 |
|
|
20:00 onwards |
Social dinner at the Restaurant Al Callarello Via Salvatore Rosa 8, Rome, Tel: (39-06) 5747575 |
Monday 18 December 9:00 - 17:00
|
Time |
Topics |
|
9:00 10:30 |
|
|
10:30 11:00 |
Coffee break |
|
11:00 12:30 |
|
|
12:30 - 14:00 |
Lunch |
|
14:00 15:30 |
|
|
15:30 16:00 |
Coffee break |
|
16:00 18:00 |
|