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EDIT Fourth Periodic Activity Report (Month 36 to Month 47)

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Project no. 018340

Project acronym: EDIT

Project title: Toward the European Distributed Institute of

Taxonomy

Instrument: Network of Excellence

Thematic Priority: Sub-Priority 1.1.6.3: “Global Change and Ecosystems”

Periodic Activity Report

Period covered: from 03/01/2009 to 02/28/2010 Date of preparation: 04/03/2009 Start date of project: 03/01/2006 Duration: 5 years Project coordinator name: Simon TILLIER Project coordinator organisation name: Muséum National d’Histoire Naturelle (MNHN)


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CONTENT Publishable Executive Summary..........................................................................................3

Section 1 – Project objectives and major achievements during the reporting period ......7 1.1 Overview of general objectives .......................................................................................................7 1.2 Progress towards project objectives ...............................................................................................7 1.3 Solutions to overcome the problems encountered during the fourth period .......................13

Section 2 – Workpackage progress of the period ............................................................... 15 2.1 Workpackage 1: EDIT Coordination and Management ...........................................................15 2.2 Workpackage 2: Integrating and Reshaping the Expert and Expertise Basis.........................24 2.3 Workpackage 3: Integrating and Reshaping the Infrastructure Basis......................................30 2.4 Workpackage 5: Internet Platform for Cybertaxonomy............................................................41 2.5 Workpackage 6: Unifying revisionary Taxonomy on the Web.................................................52 2.6 Workpackage 7: Applying taxonomy for conservation .............................................................57 2.7 Workpackage 8: Training and Public Awareness........................................................................66 2.9 Deliverables list................................................................................................................................74

Section 3 – Consortium Management ................................................................................75 3.1. Consortium management tasks and their achievement; problems which have occurred and how they were solved. ...........................................................................................................................75 3.2. Contractors: Comments regarding contributions, changes in responsibilities and changes to consortium itself, if any....................................................................................................................75 3.3. The section should also provide short comments and information on co-ordination activities in the period, such as communication between partners, project meetings, possible co-operation with other projects/programmes etc. .........................................................................75 3.4. Project timetable and status, including an updated, frontlined barchart. ...............................77

ANNEX 1 – Plan for using and disseminating the knowledge..........................................79 Section 1 - Exploitable knowledge and its Use...............................................................79 Section 2 – Dissemination of knowledge........................................................................79 Section 3 - Publishable results ........................................................................................90

ANNEX 2 - Executive summary EDIT meetings ............................................................. 91 ANNEX 3 - Performance Indicators ..................................................................................92 ANNEX 4 - List of Acronyms.............................................................................................95


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Publishable Executive Summary The overall objective of EDIT is to significantly improve the capacity of the European Research Area by integrating the efforts of its major taxonomic institutions. EDIT pursues this by working to create and provide access to more, better quality taxonomic information and knowledge, best suited for application in conservation and resource management, to empower stakeholders of biodiversity in all of society. In its fourth year, EDIT stood up to be tested. Most of our projects and products have left the experimental phase to enter stress-testing, in the sense that they are no longer restricted to a small circle of people in the know. Indeed, in most cases we have received many more requests (for grants, training or participation to events) than we could support, and selection has become an important part of the process. EDIT’s work has become an integral part of the daily practice of taxonomists, and is identified as such.

• To reduce fragmentation and to transform taxonomy into an integrated science

− EDIT is bringing together researchers and users of scientific content in several ways. Scratchpad collaborative websites have continued their expansion, and our exemplar groups have tested many features of the Platform for Cybertaxonomy and provided feedback to the developer team.

− The EDIT Integration Research Grants (IRG) have been very successful at helping researchers work together, removing problems of distance and infrastructure in specific cases.

• To strengthen the scientific, technological and information capacities needed for Europe to understand how biodiversity is modified through Global change

− The second version of the Internet Platform for Cybertaxonomy was developed

and released. This incorporated feedback for many users to improve ergonomy, as well as added software and functions.

− EDIT contributes significantly to the global development of technological capacities for taxonomy and biodiversity science. Examples include the Global Names Architecture (GNA), Encyclopedia of Life (EoL), the International Barcode of Life (IBoL), or the CATE project.

− Finally, EDIT also experiments with future developments in standards and information technologies, such as our work on e-Flora or modern publishing pipelines.

• To progress toward a transnational entity by encouraging durable integration of the most important European taxonomic institutions, forming a nucleus of excellence around and from which institutions and taxonomists can integrate their activities


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− EDIT has developed an initial business plan for continued operation beyond 2011. This involved a detailed survey of individual activities and their successes and challenges.

− The EDITExpertNet database of experts, expertise and societies was released to the public this year. It is still being populated with data, but already holds stores of information about the human resources and knowledge available in Europe.

− Inter-institutional committees like the Information Science and Technology (ISTC) Committee and the Directors of Collections Committee (DoCC) have made strong advances in unifying practices and standards across the continent.

• To promote collaborative research to develop, improve and use the needed bioinformatics technologies

− The All-Taxa Biodiversity Inventory and Monitoring (ATBI+M) programme has once again been at the forefront of collaborative research. Significant methodological improvement has occurred and spread within the community thanks to the EDIT field manual, customised data entry forms and geographical visualisation software.

− The programme was expanded with formal or preparatory agreement with local partners on two new sites (one in Europe and one outside), as well as 253 new research visits to the existing sites.

− Collaboration agreements with ABRS (Australian Biological Resources Study) and SANBI (South African National Bioinformatics Institute) are helping to spread EDIT standards and methodologies beyond the borders of Europe.

• To create a forum for stakeholders and end-users for taxonomy in biodiversity and ecosystem research

− EDIT representatives liaised with stakeholders in numerous steering committees and boards, as well as co-organised several joint events. A stakeholder involvement assessment has revealed a staggering wealth of participation in EDIT meetings and programmes from all over the world.

− A new approach to public awareness work helps us spread information to potential stakeholders, through the creation of taxonomy success stories and taxonomist portraits.

− Hands-on training on EDIT tools and methodologies such as the Scratchpads or ATBI+M programmes help solidify interest and spread best practice.

• To promote the spreading of excellence to fulfil the needs of biodiversity and ecosystem research for taxonomy-based information.

− The second EDIT Summer School and Expert-in-Training programme have been

very successful and demonstrate a high demand for training in modern and rare aspects of taxonomy.

− Awareness of EDIT tools and methodologies has improved in the scientific community through the use of both general and specific newsletters, flyers and websites.


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− The International Year of Biodiversity has proved to be an amazing opportunity to promote taxonomy as a foundational science for biodiversity conservation. Our work with the BYSE (Biodiversity Year of Schedules Events 2010) website has been very successful in raising public awareness.

All deliverables and components planned for the 4th Periodic Activity Report are available at http://ww2.bgbm.org/edit/forms/cf_public.cfm/ / User: [email protected] / Password: Ju54gH Contractors involved :

Partic. no. Participant name Participant short

name Country

1 Caisse des Dépôts et Consignations – Coordinator CDC FR

2 Muséum national d’Histoire naturelle – Project Leader MNHN FR

3 Natural History Museum of Denmark, University of Copenhagen UKBH DK

4 MNCN : Museo nacional de Ciencias Naturales, RJB : Real Jardín Botánico, CEAB : Centro de Estudios de Blanes, ICM : Instituto de Ciencias del Mar

CSIC-MNCN ES

Netherland Consortium of Taxonomic Facilities NL – TAF

5 University of Amsterdam UvA NL

6 National Herbarium Netherlands NHN NL

7 Natural History Museum Naturalis NNM NL

8 Centraalbureau Schimmelcultures CBS NL

9 Freie Universitaet Berlin – Botanic Garden and Botanical Museum FUB–BGBM DE

10 Natural History Museum, London NHML UK

11 Royal Botanic Gardens Kew RBGK UK

12 Staatliches Museum für Naturkunde, Stuttgart SMNS DE

Belgian Consortium of Taxonomic Facilities BE – TAF

13 Royal Belgian Institute of Natural Sciences RBINS BE

14 Royal Museum for Central Africa, Tervuren RMCA BE

15 National Botanic Garden of Belgium NBGB BE

Polish Consortium of Taxonomic Facilities PL – TAF

16 Museum and Institute of Zoology, Polish Academy of Sciences MIZPAN PL

17 Institute of Botany, Polish academy of sciences IBPAN PL

18 Hungarian Natural History Museum HNHM H

National Consortium of Taxonomic Facilities, Slovakia NATAF


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19 Comenius University, Bratislava CUB SL

20 Institute of Botany, Slovakian Academy of Sciences IBSAS SL

21 Institut National de la Recherche Agronomique INRA FR

NETWORK ORGANISATIONS

22 Society for management of Electronic biodiversity data SMEBD IR

23 Species 2000 SP2000 UK

THIRD COUNTRIES PARTICIPANTS

24 Komarov Botanical Institute of the Russian Academy of Sciences BINRAS RU

25 Zoological Institute of the Russian Academy of Sciences ZINRAS RU

26 Missouri Botanical Garden, Saint Louis MO USA

27 US National Museum of Natural History, Smithsonian Institution, Washington USNM USA

29 Royal Botanical Gardens Edinburgh RBGE UK

30 Museum für Naturkunde MfN DE


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Section 1 – Project objectives and major achievements during the reporting period

1.1 Overview of general objectives

Taxonomy faces two major challenges. The first issue is that new taxonomic knowledge production is very slow compared to the needs of society and other fields of science. This is due to the antiquated methods and tools available to scientists as well as insufficient human resources. The other challenge is that relevant information is scattered across 250 years of literature, in countless collections all over the world, on a growing number of websites, and in the minds of taxonomists belonging to hundreds of institutions worldwide. Even descriptions of new species (ca. 20,000 each year) are scattered across specialist journals, in an archaic fashion. This further hinders researchers in increasing society’s understanding of biodiversity and ecosystems. The overall objective of EDIT is to integrate European taxonomic effort within the ERA and to build a world-leading capacity to provide better access to a more unified and higher quality taxonomic research information base, particularly for: [a] those users who assess changes in biodiversity and protect it against decline, [b] those who are dedicated to understanding ecosystem functioning, and [c] other taxonomists The operational and structural objectives of EDIT are: [1] To reduce fragmentation and to transform taxonomy into an integrated science [2] To strengthen the scientific, technological and information capacities needed for Europe to understand how biodiversity is modified through Global change [3] To progress toward a transnational entity by encouraging durable integration of the most important European taxonomic institutions, forming a nucleus of excellence around and from which institutions and taxonomists can integrate their activities [4] To promote collaborative research to develop, improve and use the needed bioinformatics technologies [5] To create a forum for stakeholders and end-users for taxonomy in biodiversity and ecosystem research [6] To promote the spreading of excellence to fulfil the needs of biodiversity and ecosystem research for taxonomy-based information.

1.2 Progress towards project objectives

In its fourth year, EDIT stood up to be tested. Most of our projects and products have left the experimental phase to enter stress-testing, in the sense that they are no longer restricted to a small circle of people in the know. Indeed, in most cases we have received many more requests (for grants, training or participation to events) than we could support, and selection has become an


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important part of the process. EDIT’s work has become an integral part of the daily practice of taxonomists, and is identified as such. This has served as the basis for our first designs of a lasting and sustainable working model. We have collated information on what activities were successful, established a first business plan for sustainable activity beyond 2011 and submitted it to the Board of Directors (BoD) to gain their engagement. This dialogue will continue, leading to a definite workflow and inter-institutional agreement by the close of the 5th year of the Network of Excellence. 1.2.1 Reduction of fragmentation and transformation of taxonomy into an integrated science A second round of Integration Grants was called for in September 2009. Out of the received 26 applications, 6 research projects were funded, allowing development of collaborative taxonomic research which enhances EDIT goals. The Scratchpads continue to prove successful: 38 new sites have been added this year, and the number of registered users has risen to more than 1600 (dev.scratchpads.eu/scratchpads/stats). The Scratchpad team led the development of a bid to the EU Infrastructure call under the acronym ViBRANT that will continue development of the Scratchpad system and continue efforts towards integration of web-based services for 3 further years. The Compositae exemplar group continued to develop and refine the Cichorieae portal with taxonomic data, images, descriptions and distribution data (http://wp6-cichorieae.e-taxonomy.eu/portal/). The insect exemplar group has followed its more diverse approach and is piloting a mechanism to publish species descriptions directly from a Scratchpad to a peer-reviewed journal. The palm exemplar group has imported into the Common Data Model (CDM) a large amount of content (a checklist, taxonomic treatments and protologues) which is displayed in Palmweb (www.palmweb.org). Feedback from palm scientists continues to guide the group's developments and collaboration with FP7 PALMS project has started. Different stakeholders from the scholarly publishing world have also been working together with representatives form EDIT partners on recommendations that should help enhance access and dissemination of taxonomic journals and series published by EDIT institutions. The implementation of a number of recommendations are on the way and will be reported in fifth periodic activity report (e.g. integration of journal archives in BHL - Biodiversity Heritage Library, to guarantee long term access; promotion of the Open Access model, a project on merging existing journals has been launched). 1.2.2 Strengthening the scientific, technological and information capacities needed for Europe to understand how biodiversity is modified through Global change


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Harnessing the most advanced but established information technologies, the Platform for Cybertaxonomy is a significant step towards integrating the information resources of EDIT institutions in a way directly useful for biodiversity research. Implementation work for the Internet Platform for Cybertaxonomy (WP5) was continued based on the Design Plan accepted in project year 2. Version 2 of the Platform for Cybertaxonomy delivered several software products as well as refined technological architecture, software for data output and input, security technology and further tools (see Project Deliverable 20). The developed applications are platform-independent, in order to allow institutions to continue using the underlying hardware, operating system, and database management systems of their choice. Collaboration was continued with the EU PESI (Pan European Species-directories Infrastructure) and the British CATE (Creating a Taxonomic e-Science) projects, focussing on the Common Data Model and the Java programming library underpinning the Platform. Global collaboration includes participation into the Global Names Architecture, connecting the pan-European species directories infrastructure with structures outside Europe; and ECBOL (European Consortum for the Barcode of Life) collaboration with CBOL (consortium for the barcode of Life), iBOL and the FP7 project QBOL (Quarantine Barcode of Life) . This will be continued in the next JPA. Many workshops were organised to develop a scientific and technical base for infrastructure integration: one plenary Directors of Collections committee (Leiden, July 2009) and several core group meetings; an e-Flora workshop (Leiden, Jan. 2010), and a meeting on scientific publishing in EDIT institutions (Bratislava). In addition, EDIT actively participated in many international meetings including SPNHC (Society for the Preservation of Natural history Collections), Scientific Collections International, and e-Biosphere. 1.2.3 Progress toward a transnational entity by encouraging durable integration of the most important European taxonomic institutions The online information service on taxonomic experts (EditExpertNet) has been further developed into a functioning database with more than 2500 entries of taxonomists, taxonomic societies and networks. Taxonomists from all EDIT institutions were invited, as well as numerous non-professional taxonomists who were invited through the EDIT scratchpads, exemplar groups, and taxonomic societies and networks. The EditExpertNet database is now developing into a comprehensive database which forms a valid basis for decision making with respect to research resources and recruitment strategies. The database is hosted by UKBH which will continue the hosting at least until the end of EDIT. The Database of Taxonomic Societies previously published on the webpages of EDIT and Comenius University, Bratislava was moved to be hosted by UKBH. It has been integrated in the EditExpertNet to facilitate the search for taxonomic work/experts and to involve the non-professionals, societies and networks. The further development of new functions and expansion


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of data will result in an information service with ample possibilities for gathering information on meetings, journals, faunistic records and similar data which are provided by the societies. Contact details of scientists from ATBI+M activities were also integrated into the EDIT expert database. A draft institutional agreement on sustained participation of EDIT staff was elaborated. The ISTC, which consists of the CIOs (Chief Information Officers) of EDIT institutions, continues to link WP5 developments with the people driving the IST process at the institutional level. ISTC members are evaluating Platform components at member institutions. The ISTC also discussed the organisation of future technical cooperation for maintaining the EDIT Platform components. We can also present concrete results in the first operational year of EDIT Directors of Collections committee and its core group:

• a first draft of a common scientific loan policy and a questionnaire on needs and wishes of European collection managers.

• First drafts of business plans were written for several components to be sustained after the EDIT contract: DoCC, European Taxonomic Information Service (a. expert communities infrastructure by PESI; b. data governance and provenance by SMEBD), ECBOL.

• Reports were written on the barriers and benefits of the EDIT physical and digital infrastructure and on scientific publishing in EDIT institutions.

Several proposals were prepared or submitted: to integrate and coordinate European DNA and tissue banks for biodiversity genomics1, a bid for a Caucasus Distributed Institute of Taxonomy2; organizing DNA-barcoding efforts into a Network of European Leading Labs3 (NELL); 5 M€ to establish EBOLD (European Barcode of Life Database), a European database system mirroring and complementing BOLD (Barcode of Life Database) in Canada, and to set up two DNA barcoding pipelines (NL, granted); to support e-taxonomy for botany, e-Flora, using the EDIT cybertaxonomy platform (submitted to EU-COST); the ViBRANT proposal4 to combine the taxonomic information backbone scratchpads (WP5), the cybertaxonomy platform (WP6) and the taxonomic information backbone and its user community (WP3.2 & PESI); to start join research activities with SANBI, using botanical data to quantify ecosystem services that support human well-being in South Africa5. 1.2.4 Promotion of the undertaking of collaborative research developing, improving and utilising the bio-informatics technologies needed Significant progress has taken place on the EDIT ATBI+M sites. A Memorandum of Cooperation (MoC) to establish a 2nd non-European ATBI+M site was signed. Negotiations to establish a 3rd European ATBI+M pilot site are underway. Revised data recording guidelines for

1 ESF RNP, submitted Oct. 2009 2 in preparation. 3 submitted. to EU-COST, failed 4 submitted to EC-FP7 Infrastructure 5 submitted to WOTRO of the Netherlands Organization for Scientific Research)


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ATBI+M pilot sites were released. Customized forms for species data recording on mobile devices were developed. Visualization of species distribution and detailed species sheets are functional in the ATBI+M websites. The manual on field recording techniques and protocols (22 chapters written by 70 authors) will be released by the end of March. More than 90 additional signed Terms of Reference (ToR) for individual participation at the European ATBI+M sites were received. 253 individual visits took place at both sites and 2808 additional species were recorded. The overall ATBI+M administrative concept was valued very positive by interviewed participants. The costs of generating a geo-referenced dataset from European pilot sites were calculated to be 6.0 € from the Mercantour/Alpi Marittime and 4.5 € from Gemer, respectively. The ATBI+M results helped to define the major orientation of the Mercantour National park for the next fifteen years and for educational issues. A European-Australian-South African Agreement to Collaborate (AtC) was signed and followed by an international EDIT e-Flora workshop (Leiden, Jan. 2010) to start cooperation activities (ie. participation in EDIT Summer Schools) and write joint networking and/or research proposals. Other international conferences scheduled include a Network of European Leading Labs (NELL) meeting (NL, with CBOL), ECBOL2 ( June 2010, Braga), and the 3rd Doc (May 2010, Tervuren). The ECBOL website will be upgraded and relaunched early 2010. 1.2.5 Creation of a forum for stakeholders and end-users for taxonomy in biodiversity and ecosystem research In addition to EDIT’s constant work with the scientific and conservation communities, as involved in the design of our tools and programmes, more specific efforts are devoted to fulfilling its responsibility as by far the largest taxonomic resource in the world. In WP 3 collaboration with SANBI and ABRS that was started in JPA3 was further formalised by signing the AtC. New contacts were made with representatives from scholarly publishing world (i.e. BioOne, IngentaConnect, CrossRef). In WP5 programmers met with end-users of the cyber taxonomic tools and gave tool demonstrations at different conferences. At several occasions WP6 organised Scratchpad training courses which were attended by a total number of 120 people from EDIT and non EDIT institutions. In the same WP a sociological survey of the Scratchpad user community was conducted to understand the motivations and benefits perceived by users when adopting the Scratchpad system and to identify the barriers (both social and technical) that may hinder wider uptake. Outcomes will feed into future development and outreach activities. WP7 continued to work with the national parks Mercantour (France), Alpi Maritime (Italy) and the Gemer Park in Slovakia. Additionally it has been working on a field methodology manual aimed professional taxonomists and scientific volunteers.

Figure 1: Participation at the ATBI+M pilot site Mercantour/Alpi Marittime (2007-2009)


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The EDIT field work manual will be released in year five. Within the context of WP8 users from the general public were targeted by the launch of webpage with portraits of researchers, zooming in on what drives them and why they think their work matters (see http://www.taxonomytraining.eu/content/portraits). From a similar perspective a new section “Taxonomic success stories” in the EDIT newsletter aims to put the taxonomic work in a broader context wherefore and how taxonomic information can be used. Furthermore the activities of WP8 have focused on the dissemination of knowledge to students during the EDIT summer school and to researchers by the facilitating tailored, training on the job courses. Finally EDIT representatives liaised with stakeholders in numerous steering committees or boards, as well as co-organised several joint events (see below, D12 and C1.4.5). Stakeholder involvement assessment has revealed a staggering wealth of participation in EDIT meetings and programmes from all over the world. See http://e-taxonomy.eu/WebSPEurope/StatPlanet.html and http://e-taxonomy.eu/WebSPWorld/StatPlanet.html for more detailed information. 1.2.6 Promotion of the spreading of excellence to fulfil the needs of biodiversity and ecosystem research for taxonomy based information The Internet Platform and particularly the Common Data Model is increasingly recognised as a model implementation for biodiversity informatics. EDIT’s approaches are discussed, inter alia, by the community standards body (TDWG - Biodiversity Information Standards) and by the preparatory project for the large-scale European research infrastructure, LifeWatch. The PESI and the CATE projects join forces with EDIT in using the CDM. Recently e-Flora projects intended to collaborate and make use of the developments of the EDIT platform. The ATBI+M approach was further promoted this year through active participation at international conferences and through dissemination of a re-designed flyer. A publication outline on flora and fauna of the ATBI+M pilot sites was prepared. More than 280 scientists interested in ATBI+M activities are registered at the web-based WP7 forum. A new electronic ATBI+M newsletter has also been designed and released. In training, the objective is to consolidate a high quality training that prepares students for future taxonomic careers. EDIT and other international partners are establishing a European state-of-the art School of Taxonomy: the Distributed European School of Taxonomy (DEST). The infrastructure outline of the DEST has been established. The Expert-in-training programme (EiT) and Summer School became operational in JPA-3; the Modern Taxonomy programme will be launched in May 2010. The DEST website is on-line since October 2009.


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The second Summer School, held in the Slovakian Murànska Planina NP, brought together 18 professional taxonomists and 20 students from all over Europe. The Expert-in-training programme 2009-2010 allows 17 students from European institutions to benefit from on-the-job training in EDIT institutions and other partner institutions. The third DEST training component, the Modern Taxonomy theoretical course programme, will provide future professionals with a solid basic taxonomic training. The IYB (International Year for Biodiversity) is the opportunity for Public Awareness actions to promote taxonomy and to exchange on best practices. EDIT-PA arranged the use of the official logo of IYB and Countdown 2010 for all partners. BYSE was promoted successfully. The success stories in the EDIT newsletter present best practices. The taxonomists’ portraits on the DEST website promote professional taxonomy and stimulate students to consider a career in this field. Finally, EDIT’s communication efforts have augmented. The EDIT newsletter brought together even more contributors from even more institutions than in the previous year (currently 37 authors from 26 institutions), and was expanded to a 500 print run due to high demand. Similarly, the EDIT websites have seen significant growth, as the following figures demonstrate: Website visits/year e-taxonomy.eu 31808 Mar 09-Feb 10 WP7 forum 4246 Jan 09-Dec 09 atbi.eu/gemer 843 Jan 09-Dec 10 atbi.eu/mercantour 6404 Jan 09-Dec 10 scratchpads.eu 70608 extrapolated from Nov 09 taxonomytraining.eu 1266 extrapolated from Jan-Feb 2010

1.3 Solutions to overcome the problems encountered during the fourth period

The time and effort spent in the fourth year on selecting which of EDIT’s activities to continue or not has paid off. We are facing less problems and a clearer way forward, and we are free to concentrate on the shape that continued joint activity will take. Nevertheless, corrective actions will continue in the last year of the contract, in order to provide excellence in all our endeavours. A regular concern along the years has been that integration of science policy progressed slowly. In year 4, changes transferring that activity from WP4 to WP 1.6 have helped speed up this activity, leading to the production of D16. In year 5, we expect this to gain even more traction as the sustainability architecture for integrated activity solidifies. Discussions in relation to the development of a transnational activity showed clearly that directors did not want a distinct structure from CETAF. Instead, many EDIT activities will


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continue and be organised within the umbrella of the Consortium of European Taxonomic Facilities. This will be pursued in year 5 and reflected in the updated EDIT business plans. Legal problems linked to the Expert database were finally solved by WP2 during year 4. Details are given in C2.1.10. The “Edit ExpertNet” is now available and getting regular input. Above all, collaboration with PESI has proven to accelerate its implementation, so that we can expect a fully-fledged and populated version around the time of the end of the contract. The low level of user engagement with the Internet Platform for Cybertaxonomy was largely due to its unfinished development up to now. WP 5 has now started to demonstrate and provide training to taxonomists. With this increase in marketing its products, we expect they will see much larger use once the word of mouth kicks in.


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Section 2 – Workpackage progress of the period

2.1 Workpackage 1: EDIT Coordination and Management

WP Leader: Simon Tillier Partner no. 2 - MNHN Other partners involved: all partners

2.1.1 Objectives

• Build up and operate a light but dynamic structure, involving the top executive level

of the partners, ensuring long-term operational and structural links between partners • Elaborate a common science policy and develop a joint research strategy to adapt to

changing demands on taxonomic science. • Coordinate the activities regarding research, infrastructures and expertise toward

common goals integrated at director’s level for implementation of further common decisions, aiming at combining all workpackages objectives into a single integrated sustainable structure

• Ensure interaction of EDIT activities with scientific activity in the field of biodiversity and with societal needs

• Coordinate interactions with stakeholders, including communication with institutional stakeholders

• Establish and actualise the roadmap for EDIT, including plans to enlarge the consortium

• Ensure internal and external communication of EDIT, and its visibility through the web

2.1.2 Progress towards objectives

Activity 1.1 establishment and operation of the administrating structure & Activity 1.2 Orientation, Sustainability and Development of exploitation strategies for EDIT

Besides operating the management structure (NSC meetings etc), the fourth year of EDIT has been marked by the continuation of the process leading to sustainability if consortium members wish so.

After having identified avenues for potential integration through consultation with workpackage leaders and directors, we have continued to explore the cost, feasibility and benefits of the potential integrated actions.


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Institution ABCD DRUPAL ViTaL GNOMA Gender Aspects EDIT ExpertNet

MNHN X X XUKBH X X X X XCSICUvA X X XNHN X X X XNNM X X X XCBS XFUB BGBM X X XNHML X X X XRBGKSMNS X XRBINS X X X XRMCA X X X XNGBG X XMIZPANIBPANHNHMCUBIBSAS X X X XINRASMEBDSP2000BINRASZINRASMO XUSNMRBGE X X X XMFN X X

TOTAL 14 10 10 13 2

Activities & bodies (Committees) to sustain have been clearly identified and we have asked institutions to identify their priorities, and whether they would be willing to commit resources (staff, funds…). The summary of this can be found in D1D2 update (Business Plan) and D17 Designs for Edit as a Supranational Entity.

In the meantime, further MoUs have been signed by partners, and a few others are submitted to directors for signature or are in preparation.

In parallel, and in addition to workshops and exchange with stakeholders described below, coordination with large taxonomic international initiatives has been developed, mainly through participation of their steering or institutional committees, and joint organizations of workshops or events.

Participating (poster/booth) Sponsoring/Co-sponsoring Design/Board participation

e-Biosphere 09 London 2009 e-Biosphere 09 London 2009 e-Biosphere 09 London 2009

Systematics Leiden 2009 GTI special fund workshop 2009 Diversitas CP1 SC (ongoing)

CETAF (ongoing) SPNHC Leiden 2009 Key2Nature associate participant (ongoing)

Diversitas OSC2 Symposium Cape Town 2009

LifeWatch PSB (ongoing)

Figure 2 : List of MoUs signed before February 28th 2010


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Activity 1.3 Communication

The EDIT Newsletter has established itself as a reputable and useful publication, with more and more submissions for publication coming from outside EDIT. JPA4, which covered issues 13 through 18, had the following breakdown:

400 copies of the newsletter were printed for each issue; this number will reach 500 in JPA5, due to high demand. It is sent to 1000 email addresses, ranging across Europe and the world (notably Global Taxonomic Initiative national focal points).

The central EDIT website continued to receive a high frequentation: 31.200 visits, with 97.700 page views over the 2009 period. More specialised tools also fulfilled specific functions: such as the ATBI+M internal forum (4.200 visits and 19.000 views), and general communication sites (for the Mercantour/Alpi Marittime inventory website, 6.400 visits, 40.000 views). A new website for the DEST was also launched. The EDIT 2d General Meeting (Carvoeiro, 14-16 Dec. 2009) brought together 140 participants and included side events ranging from the EDIT Young Taxonomist Symposium to special sessions by EDIT member Society for the management of Electronic Biodiversity Data. EDIT was also present at several major events gathering researchers and decision-makers during the target period. The e-biosphere 09 conference (London, 1-3 June 2009), was a great success with 503 participants from 69 countries. Similarly, EDIT was present at TDWG 2009 (Montpellier), the Third International Barcode of Life Conference (Mexico), two EPBRS (European Platform for Biodiversity and Research Strategy) meetings (Prague, Visby), the SYNTHESYS (Synthesis of Systematic Resources) final event (London), SPNHC 2 (Leiden), the BioNET GTI workshops (Paris), etc. Contributions from EDIT may be found in D12 (First report on scientific output). Indeed since it was launched EDIT has been presented at conferences (invitations, offered papersetc) and the number per year has increased steadily. The Biodiversity Year Schedule of Events, BYSE 2010 allowed the promotion of public biodiversity events of EDIT partners and other institutions 155 events from 27 countries and 75 institutions. Details of its promotion efforts are available at http://e-taxonomy.eu/node/610. EDIT also negotiated with the CBD (Convention for Biological Diversity) international so that all EDIT partners could use the official 2010 logo for non-commercial use. EDIT was also involved in the planning phase of the IYB on national levels. Other efforts include:

• EDIT Taxonomy Success Stories and Taxonomist portrait: http://e-taxonomy.eu/node/681.

• Press promotion of ATBIs also continued, with a second Mercantour (press day with more than 15 journalists, including television, radio and printed press).

Articles 23Authors 37EDIT contributing institutions 12Non-EDIT contributing institutions 14Event notices 56


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• EDIT Taxonomy Blogs: http://systematicsblog.myspecies.info/ Activity 1.4 Liaison with users of other stakeholders of taxonomic information

Liaison activities contribute to objective 5 of EDIT which aims to build partnerships with the

taxonomic stakeholder community. The network’s strategy has been to address the engagement with the user community as a two way process. The overall goals of these interactions are to spread excellence, to learn from others and to join forces with the wider user community on subjects of common interest. During the fourth year several liaison activities in different WP’s with the taxonomic stakeholder community took place. Representatives of EDIT travelled to meet end-users and other stakeholders and to present the work of the consortium. On the other side stakeholders were invited to participate in EDIT meetings. WP1 coordinates the liaison activities in EDIT which themselves were organised under the umbrella of other WPs.

Examples of stakeholder events where EDIT was represented are (but not limited to see also http://www.e-taxonomy.eu/node/412 ):

• European Platform for Biodiversity Research Strategy (EPBRS) (Prague, Czech Republic • eBiosphere conference (London, UK) • Society for the Preservation of Natural History Collections (SPNHC) Leiden, Netherlands • Gesellschaft für Informatik (Lübeck, Germany) • Second DIVERSITAS Open Science Conference (Cape town, South Africa) • Unesco (Paris, France)

• Examples of EDIT meetings where stakeholders were represented: • Scientific Publishing in Natural History Institutions (Bratislava, Slovakia) • e-Flora workshop (Leiden, The Netherlands) • 2nd General Meeting (Carvoeiro, Portugal) • Different training courses (Summer School and Scratchpad training sessions)

Data on liaison activities can be found in D12 Report on EDIT scientific output and C1.4.5 Networks of participation. Reports on end-users and other stakeholder interactions are described under the heading of the executing WP. For year four see for instance the work done in WP3, 6, 7 and 8.

Activity 1.5 Gender action plan

At the start of the current reporting period a new Chair has been appointed for the Gender Action Plan (GAP). The two instruments already initiated in 2008 were continued, namely Work/Life Balance travel grants for female and male taxonomists, and Fellowships for female scientists in early career.

• The Work/Life Balance travel grants action represents provisions for scientists (male of female) with babies or toddlers up to 3 years age. It provides more flexibility to the scientists in adapting timetables to make research conferences, training sessions and workshops more family friendly. In 2009, grants were attributed to 4 women and 2 men, in 2008 1 woman had benefited from the grant. From the 2009 grantees, 3 belong to the


- 19 -

NHN - NL, 1 to the HNHM - HU, 1 to RMCA - BE and 1 to the Institute of Botany and Microbiology - BE.

• The Fellowships for female scientists in early career are supporting outstanding women working in taxonomy or related fields and promoting them in their early career. In 2009, 16 women applied for this grant and 5 were accepted, 4 had benefited from it in 2008 out of 8. Among the 5 grantees in 2009, 2 came from Naturalis - NL, 1 from the Zoological Institute of Russian Academy of Sciences, 1 from Natural History Museum of Denmark and 1 from Zoological Museum of Amsterdam - NL. Their host institutions were for 2 of them the Smithsonian Institution - USA, for 2 other the Natural History Museum of Denmark and 1 visited the Natural History Museum - UK. 4 were post graduate students and 1 graduate student.

Among the activities and instruments to be implemented within the GAP throughout the project, a Memorandum of Understanding on Gender Issues validated by the Liaison Group was sent out to the EDIT partners’ board on 05 November for signature. Up to now, 2 partner institutions have signed it: Missouri Botanical Garden, St Louis and the Natural History Museum of Denmark. As one of the main sources of actions of the GAP, a survey enabling the analysis of the situation of the women participation and involvement within the various activities of the EDIT institutions was performed. The survey was coupled with a questionnaire asking for the partners’ interest in the development of an inter-institutional mentoring scheme. 13 institutions responded providing a fair background to pave the way for this next activity to be developed in 2010. Promotion of the EDIT GAP Participation to the conference organized by the Science and Society programme of the DG Research “Changing research landscapes to make the most of human potential: 10 years of EU activities in "Women and Science" and BEYOND”, 14 -15 May 2009 in Prague; Organization of the Belgian Women in Science General Assembly 2009; Participation to and organization of the European Platform of Women Scientists 2009 General Assembly in Brussels; Participation to the EDIT General Meeting and organization of a meeting on mentoring in order to expose the mentoring pre-programme and to collect advices, experiences and arouse potential mentees and mentors for the future activity. The meeting conveyed 18 participants from the EDIT institutions, 13 were females and several were PhD students. Activity 1.6 Developing Science Policy for European taxonomic institutions Building upon vision documents proposed for taxonomy the work of this EDIT activity aims at elaborating a common science policy and developing a joint research strategy that better integrates the current research activities of partner institutions. The second Science Policy Group (SPG) meeting in the end of the previous reporting period (February 2009) revealed that on the way towards the development of a common research proposal to be proposed to the EDIT BoD, there will be a number of items to be considered and taken into account: 1. A vision for the taxonomy of the future.


- 20 -

2. An agreed strategic framework or strategic themes around which common policies can be developed and implemented (defined by the SPG, see C1.6.1.2).

3. Information on institutional organisational structures and science policies (i.e. how the institutions worked). Most institution’s rules are relatively strict. The aim is therefore to identify areas of flexibility to enable cooperation.

4. Information on scientific activities of the EDIT partners to identify commonalities and complementarities.

The vision for taxonomy was already produced and used as the starting point of the SPG. This can be found based on two documents that had already been produced: • Taxonomy of the 21st Century (top-down approach): http://www.e-taxonomy.eu/files/Taxonomy21report.pdf ; and • Suggestions from the Symposium on Future Trends of Taxonomy (bottom-up approach): http://www.e-taxonomy.eu/files/FUTURE_TRENDS_OF_TAXONOMY.pdf These two documents were used by the SPG to define a number of strategic themes and propose new strategies for taxonomy where policies developments would be needed. Some of these strategic themes are already being covered within other activities of EDIT, while others will need to be further developed (see C1.6.1.2 and D15). The need for information on institutional organisational structures and policies what concerns science policy was identified during the second SPG meeting (C1.6.1.2) as it was concluded that that there was little practical prospect of standardisation of governance within EDIT – the funding models, administrative systems, staff employment, strategic drivers and many other factors were diverse and change often depended on external agencies in government or research councils. What was needed was appropriate harmonisation of policy within a common strategic framework to ensure effective and efficient collaboration. Standardisation, given current diversity, was agreed to be a potential result of a successful initial phase of integration rather than an essential precursor. In this same sense, for preparing a common research plan proposal it was absolutely necessary to have an overview of research activities each EDIT institution to identify points of harmonisation to be included in the proposal. The relative independence that most researchers have to work on their selected theme of research (a majority of the funding for research is obtained by competitive calls outside their own institution) makes that a direct top-down approach for a common research plan would most likely be unsuccessful. The only possible approach to develop a common research plan is by taking the current scientific activities of all partner institutions into consideration and by extracting shared approaches. To reach this goal the initial plan of compiling all partners’ research plans proved to be unrealistic due to the many shapes and heterogeneity of the information available and was therefore changed into a questionnaire/interview scheme developed by the SPG. This strategy ensured standardized outcome of all partners involved. Additional data were gathered through the internet and publications. Results were published in the relating component (C1.6.2.1). 2.1.3 Deviations from the project work programme and corrective actions


- 21 -

M1.2.1.7 and M1.2.1.8 were discontinued as priority was given to explore common grounds with CETAF structure. The adaptation of the legal structure has started in and with the CETAF Executive Committee. Several tasks in activity 1.6 were delayed due to the delay in hiring an additional staff member at the MfN Berlin. The task affected most was 1.6.4 (exploring and promoting new and emerging issues for joint taxonomic research) which has therefore been postponed to JPA5, including component C1.6.4.1 (report on workshop on new and emerging issues) and milestones (M1.6.4.1 & M1.6.4.2 proposal and implementation of a first workshop on new and emerging issues). Apart from this, when considering the strategy to be followed by the SPG until the end of EDIT, it was estimated that the original composition of the SPG was not optimal for the tasks to come. Due to both reasons, the third meeting of this group (due M39-41) did not take place but it was decided to set up a new SPG during the EDIT General Meeting in December 2009. This new SPG group was formed with the specific focus on completing the necessary steps to have the common research plan proposal for the continuity of EDIT beyond 2011 ready by the end of 2010. This new SPG has been designed considering the links with other activities in EDIT that will feed into the common research plan (strategic themes defined by the SPG that are already being covered) as well as the link with the BoD were the proposal will be ultimately presented. A first meeting of this new SPG group is planned for March 2010. 2.1.4 Lists of components6 & milestones A – WP1 components Deli

vera

ble

no.

Component number & name WP

no.

Dat

e

due

Actual

/Forecast

delivery

date

Link on public

website (if

component

public)

Lead

contractor

C1.1.7 Budget for months 35-53 submitted

by the NSC to the BoD WP1 M37 M37

MNHN

C1.1.8 Financial report WP1 M37

M42 M37, M42

MNHN

C1.2.4 Formalise the view of the BoD with

regard to future options WP1 M46

Merged

with D17 MNHN

C1.3.2 Newsletter, bimonthly issue WP1 ongo

ing ongoing MNHN

C1.3.4 1st implementation of action plan for

promotion of Taxonomy WP1 M47 M47 RE RBINS

C1.3.5 2nd report on implementation of

communication and PR strategy WP1 M47 M47

http://www.e-

taxonomy.eu/node

/745

MNHN

C1.3.6 Report on the joint planning of all

WP for the communication mechanisms WP1 M47 M47

http://www.e-

taxonomy.eu/nodeMNHN

6 Components are not part of the EC Contract no.018340.


- 22 -

Deli

vera

ble

no.


no.

Dat

e

due

Actual

/Forecast

delivery

date

Link on public

website (if

component

public)

Lead

contractor

/759

C1.4.2 Report on recommendations for

sustainable liaisons with users and other

stakeholders of taxonomy in the EDIT long

term structure

WP1 M45

Merged with

Business plan &

D17

MNHN

C1.4.5 Analyse and report on scope, scale

and nature of the networks where taxonomy

and taxonomists participate

WP1 M46 M47

http://www.e-

taxonomy.eu/node

/758

MNHN

C1.4.6 Poster presentation of results

workshop “meeting the needs of those that

use scientific names” at e-biosphere

conference

WP1 M39 M39

http://www.e-

taxonomy.eu/node

/760

MNHN

C1.5.5 Overview of existing GAP related

initiatives in EDIT institutions WP1 M47 M47

http://www.e-

taxonomy.eu/node

/773

RBINS

C1.5.6 Structure of EDIT mentoring

scheme and requirements WP1 M47

M47

http://www.e-

taxonomy.eu/node

/763

RBINS

C1.6.1.2 2nd report from Science Policy

Group including proposal for implementing

the research strategy to EDIT

WP1 M38 M47 RE MfN

C1.6.2.1 Report on research plans and

research activities of EDIT partner

institutions including analyses identifying

commonalities and complementarities

WP1 M45 M47 RE MfN

C1.6.4.1 Report on the outcome of first

dedicated workshops for new and emerging

issues

WP1 M47 Deferred

JPA5 (M55) MfN

B – WP1 Milestones

Milestone

no. Milestone name

WP

no. Date due

Actual

/Forecast

delivery date

Lead contractor

M1.1.13 Meeting of the NSC (13) WP1 M36 M36 MNHN




M1.2.14 Joint SAC & BoD meeting WP1 M45 M45 MNHN

M1.2.15 BoD working group meeting WP1 M39 M40 MNHN


- 23 -

Milestone

no. Milestone name

WP

no. Date due

Actual

/Forecast

delivery date

Lead contractor

M1.2.1.6 BoD meeting WP1 M45 M45 MNHN

M1.2.1.7 BoD workshop on infrastructure

components in cooperation with WP3 WP1 M39 cancelled MNHN

M1.2.1.8 BoD workshop on EDIT as a supranational

entity WP1 M45

Merged with

BoD meeting MNHN

M1.3.7 2nd General Meeting WP1 M45 M45 MNHN

M1.4.3

Promote, support and facilitate initiatives of

staff members institutions that contribute to

the transfer of taxonomic knowledge and

services towards the broader taxonomic

stakeholder community

WP1 M ongoing

M1.6.1.3 Second draft report of Science Policy Group for internal circulation & review WP1 M38 M38 MNCN, NHML

M1.6.1.4 Third meeting of the SPG WP1 M39-41 Cancelled MNCN, NHML

M1.6.2.1 Research plans from individual EDIT partners compiled WP1 M39 M39-45 MNCN, NHML

M1.6.2.2 Interviews with key person for research policy in EDIT partner institutions to complement analysis of research plans done

WP1 M42-43 M42-45 MNCN, NHML

M1.6.2.3 Preliminary analysis of institutional research plans undertaken WP1 M43-44 M45-47 MNCN, NHML

M1.6.3.1 Survey of current focal research activities of EDIT partners (review of institutional annual research reports) compiled

WP1 M38 M40 MfN, CSIC

M1.6.3.2 Participation in CBD/ABS working group 8 meeting WP1 M44 M44 MfN

M1.6.4.1 Proposals for dedicated workshop(s) for new and emerging issues WP1 M39 Postponed, JPA5

(M49) MfN

M1.6.4.2 First dedicated workshop on new and emerging issues WP1 M44 Postponed, JPA5

(M54) MfN


- 24 -

2.2 Workpackage 2: Integrating and Reshaping the Expert and Expertise Basis

WP Leader: Henrik Enghoff Partner n° 3 UKBH Other partners involved: 2- MNHN 5 - UvA 6 - NHN 7 - NNM 8 - CBS 9 - FUB-BGBM 10 - NHML 12 - SMNS 13 - RBINS 14 - RMCA 15 - NBGB 16 - MIZPAN 17 - IBPAN 18 - HNHM 19 - CUB 20 - IBSAS 21 - INRA 22 - SMEBD 23 - SP2000 24 - BINRAS 27 - USNM 29 - RBGE 30 - MFN 2.2.1 Objectives

• Providing an efficient online information service on European taxonomic experts, their expertise and ongoing and planned taxonomic research projects. The online information service (EditExpertNet.org) shall meet the needs for information by EDIT’s partners primarily by serving as a knowledge base for an integrated recruitment strategy within EDIT, constituting an integrated part of the EDIT internet platform for cyber-taxonomy, as wells as functioning as information backbone for other work packages. Involving non-professional taxonomists in an integrated European taxonomic workforce through promotion of taxonomic societies, networks and research teams within and outside EDIT. The taxonomic society- and network database will be integrated in the EditExpertNet. Furthermore, a field workshop for non-professional taxonomists participating in ATBI+M will be set up through collaboration with WP7.


- 25 -

• Promoting integration of taxonomic research teams within the field of descriptive/revisionary taxonomy. This is done by supporting exchange of researchers’ projects through the launch of the second call of Integrating Research Grants for taxonomy.

2.2.2 Progress towards objectives

Regarding the objective of proving an online information service on European taxonomic experts, their expertise and ongoing and planned taxonomic research projects, WP2 entered data on taxonomists belonging to EDIT’s different partner institutions into the EditExpertNet database. These taxonomists represented twenty-four of the twenty-eight partner institutions, corresponding to nearly the full complement of partner institutions (C2.1.4). Additionally, data on a whole range of other taxonomists associated with activities performed by the various EDIT workpackages were also registered in the EditExpertNet. These included participants of WP7’s (partner 30 MfN) ATBI+M inventory excursions to Alpi Maritime /Mercantour and Gemer national parks (C2.1.6), as well as the taxonomic experts associated with the first batch of WP6's (partner 10 NHML) exemplar group activities (C2.1.7). Further registration of taxonomists was conducted in collaboration with PESI (WP3, partner 6 NNM) and included taxonomists registered in the European species database (C2.1.12) in addition to the scientists of taxonomic relevance to EditExpertNet extracted from the lists of WP8’s (partner 13 RBINS) project on taxonomic training resources (C2.1.14) and the taxonomic experts participating in WP6’s scratchpads (C2.1.15). In relation to registering all these taxonomists, the question of security appeared. WP2 therefore forwarded a request to the European Data Protection Supervisor in order to clarify the legal aspects of making multinational personnel data available online. An answer pointing to the Danish Data Protection Agency (DPA) as the right authority monitoring legislation in this case was confirmed by DPA because the server holding the database is hosted by a Danish institution (C2.1.10). Consequently, a Memorandum of Understanding (MoU) has been signed accepting the housing of EditExpertNet by UKBH (partner 3) (C2.1.11). This signing and the sorting out of the legal responsibilities constitute the fulfilment of milestone 2.1.5 (M2.1.5).

Figure 3 : Edit ExpertNet portal


- 26 -

For tasks pertaining to the involvement of non-professional taxonomists through societies, networks and research teams see section 2.2.3. To promote integration of taxonomic research WP2 launched the second call for the Integrating Research Grant on EDIT’s web page (www.e-taxonomy.eu/node/156) and by e-mail with a dead line on the 30th September 2009. IRG holds a total amount of 100.000 € to be awarded to integrative research projects supporting the collaboration of researchers from EDIT institutions and associates within the field of descriptive/revisionary taxonomy. Of the twenty-one eligible applicants, six research projects were approved by the evaluation panel receiving funds ranging 8.000 -19.000 € (C2.4.4. and M2.4.4).

2.2.3 Deviations from the project workprogramme and corrective actions

Concerning the objective of providing efficient online information service (the EditExpertNet.org), the task pertaining to Component 2.1.5 of entering data from test countries in the database has been delayed. However, information on the Danish and Norwegian taxonomists (professional and non-professional) (is being collected at this time of writing, and the task of registering these in the database is expected to be finished on a weekly scale). A second delay concerns the instalment of a Drupal module in the EditExpertNet database following the implementation of the CSSO identity provider component developed by WP5 (C2.1.13 = C5.84). The CSSO provides a heightened security infrastructure when accessing the database through the platform for cyber-taxonomy developed by WP5 (partner 9 FUB-BGBM) This task will too be carried out within a short time limit, as the contact between WPs 2 and 5 has been established and the work is now being performed on the server installed at UKBH. Regarding the tasks related to the involvement of non-professional taxonomists through societies, networks and research teams, some deviations have taken place, as the components C2.3.2 and C2.3.4 have been moved from JPA4 to JPA5, while C2.3.5 have been cancelled and C2.3.6 have been included in C2.3.2. In addition to the postponement of C2.3.2 to JPA5 there has been a change of title from “Second version of the online information service on societies and networks” to “Integration of networks and societies in the EditExpertNet database”). The postponement is a consequence of the serious delay which the first version of EditExpertNet suffered and the renaming is due to the decision to merge the Societies Database with EditExpertNet, which can be done rather straight forward without waiting all the software updating and testing procedures the second and final version demands. Accordingly, several new societies and networks have been included in EditExpertNet, but unfortunately not reaching the original ambition of 500 entries (M2.3.4) with the present 400 entries. However, this number is possible to reach as the entering of new taxonomic societies and networks in the database is an ongoing activity. The incorporation of C2.3.6 “Setting up a task force for a possible association of European taxonomic societies” in the re-formulated C2.3.2 is due to the double nature of these tasks. The aforementioned delay of the first version of the expert database and its cascading effect is regrettably also affecting milestone 2.1.3 (Responses received from selected users with questions


- 27 -

for the second version of the information service) and milestone 2.1.4 (Adoption by BoD of information service as the system for EDIT institutions to catalogue their human taxonomic resources), as both await a database clean of the bugs usually haunting first versions. Here it should be mentioned that M2.1.6 and M2.17 have been put twice in the JPA4 as well as M2.1.3 and M2.1.4. Hence, milestones 2.1.6 and 2.17 will be referring to new tasks being achieved in JPA5. Component C2.3.4 “Joint WP2-WP7 field workshop for non-professional taxonomist” has been postponed as the workshop was planned to consist of participants of the 2nd General Meeting, which should have taken place in Bratislava. However, the location of the meeting was changed but since there was a wish to promote field activities in the ATBI-M site “Gemer area” it was decided to keep the Slovakian location though it required postponing the event to JPA5 The cancellation of the symposium for existing taxonomic networks (C2.3.5 and associated milestone 2.3.3) was decided after the bleak prospects of it ever being held. There seemed to be a lack of interest in its implementation or so it must be interpreted as several request to initiate organizing the symposium remained fruitless.

2.2.4 Lists of components7 & milestones A – WP2 components

Deli

vera

ble

no.


no.

Date

due8

Actual

/Forecas

t delivery

date

Link on public

website (if

component

public)

Lead contractor

C2.1.4 Data on EDIT partner taxonomic

experts entered in information service

WP2 M40 M45 RE 3- UKBH

C2.1.5 Test data from test country/ies

entered in information service

WP2 M41 Deferred

to JPA 5

M 50

3- UKBH

C2.1.6 Data on experts associated with first

batch of ATBI+M’s entered in information

service

WP2 M38 M45 http://www.e-

taxonomy.eu/node

/705

3- UKBH

C2.1.7 Data on experts associated with first

batch of demonstrator group activities

entered in information service


D23 C2.1.8 Gap analysis on taxonomic expertise

in EDIT

WP2 M43 Deferred

to JPA 5 -

M50

3- UKBH

D20,

D23

C2.1.9 A business plan for WP2

information service on taxonomic experts,

their expertise and projects, in collaboration

with the newly funded PESI project

WP2 M42 Deferred

to JPA 5

M58

3- UKBH

7 Components are not part of the EC Contract no.018340. 8 Please indicate here the date as indicated in the Annex 1 – Description of work and/or the 4th JPA.


- 28 -

Deli

vera

ble

no.


no.

Date

due8

Actual

/Forecas

t delivery

date

Link on public

website (if

component

public)

Lead contractor

D23 C2.1.10 Report on legal aspects in relation

to making expert data available


D23 C2.1.11 MoU for information service

database on European taxonomic expertise


D23 C2.1.12 Collaboration with the newly

established PESI project on integrating

expert information from the European

species databases in the EDIT WP2


their expertise and projects


taxonomy.eu/node

/718

3-UKBH

D20,

D23

C2.1.13 (=C5.84) Integrate the CSSO

identity provider component with the

Experts-DB (FUB-INF with FUB-BGBM

& WP2)

WP2 M41 Deferred

to JPA 5

M49

3- UKBH

D23,

D6

C2.1.14 Inclusion of relevant data from

WP8 database on taxonomic training

resources in WP2 information service


D23 C2.1.15 Inclusion of data on experts

associated with (selected) WP6 sratchpads

in WP2 information service


C2.1.17 Sustainable mechanisms for the


their expertise and projects and the

information service on taxonomic societies

and networks


C2.3.2 Second version of the online

information service on societies and

networks

WP2 M46 Deferred

to JPA 5

M54

3- UKBH

D17,

D28

C2.3.5 Symposium for existing taxonomic

networks

WP2 M45 cancelled 3- UKBH

D1D

2

C2.3.6 Setting up a task force for a possible

association of European taxonomic

societies

WP2 M47 Incorpora

ted in

C2.3.2

3- UKBH

D12,

D16;

D1D

2

C2.4.4 call for integrating research grants

for taxonomy, evaluation of applications

and allocation of grants




- 29 -

Milestone

no.

Milestone name WP

no.

Date due9 Actual

/Forecast

delivery date

Lead contractor

M2.1.3 Responses received from selected users with

suggestions for the second version of the

information service

WP2 M42 Deferred to JPA

5 ( M56)

3- UKBH

M2.1.4 Adoption by the BoD of information service

as the system for EDIT institutions to

catalogue their human resources


5 (M52)

3- UKBH

M2.1.5 Memorandum of Understanding (MoU)

determining the hosting of the information

service database on European taxonomic

experts at the UKBH including a

specification on responsibilities and issues

regarding the transference and keeping of

data on European taxonomic experts in the

database


5 (M52)

3- UKBH

M2.1.6 Responses received from selected users with

suggestions for the second version of the

information service

WP2 M45 Cancelled Cf.

M2.1.3

3- UKBH

M2.1.7 Adoption by the BoD of information service

as the system for EDIT institutions to

catalogue their human taxonomic resources

WP2 M46 Cancelled Cf.

M2.1.4

3- UKBH

M2.3.3. Symposium for the existing taxonomic

networks

WP2 M45 cancelled 3- UKBH

M2.4.4 Integrating research grants for taxonomy

allocated

WP2 M40 M44 3- UKBH

9 Please indicate here the date as indicated in the Annex 1 – Description of work and/or the 4th JPA.


- 30 -

2.3 Workpackage 3: Integrating and Reshaping the Infrastructure Basis

WP Leader: Leo Kriegsman

Partner n° 7 NNM 10

Other partners involved: - all;

funded tasks:

2-MNHN

3-UKBH

5-UvA

6-NHN

7-NNM

8-CBS

9-FUB-BGBM

19-CUB

30-MfN (one task from 7-NNM since August 2009)

2.3.1 Objectives

General objectives from the Description of Work:

• Reduce the number of links in the chains of network decision making and in the operations of the (physical, equipment, digital, and administrative) infrastructure components.

• (ii) Add innovative analysing and modelling components, also from cooperating universities, to construct a new generation infrastructure.

• (iii) Promote that the integrated infrastructure will facilitate the mobilisation and organisation of innovative research excellence in Europe in strong and lasting networks.

• (iv) Establish agreements (commitments) at the level of institutional directors to achieve an integrated and dynamic approach.

2.3.2 Progress towards objectives Activity 3.1 Network of the physical taxonomic infrastructures (7-NNM) All WP3.1 tasks as listed in the DoW were ongoing. The Directors of Collections committee (DoC) proved to be a useful instrument in taking steps towards collections integration. Its

10 As indicated in the Annex 1 – Description of work.


- 31 -

organisational structure is now operational (DoW task 3.1.7). A second DoC workshop was held in Leiden in July 2009 (M3.1.6). Results from the DoC core group were presented and discussed (all DoW tasks). Specimen digitisation was added to the task list. Major achievements are:

- first proposal of a common scientific loans policy, presented to the BoD December 2009 (C3.1.6 & DoW task 3.1.8)

- co-organising the international conference of the Society for the Preservation of Natural History Collections (SPNHC); one day focused on EDIT (M3.1.7 & DoW task 3.1.10)

- a questionnaire distributed among European collections managers identified needs and wishes for a European collection managers forum; feedback was positive; a detailed analysis is expected to result in a proposal for an independent forum (DoW task 3.1.10)

A first draft business plan for the DoC beyond EDIT (C3.1.5 & DoW task 3.1.7) will serve as a basis for further discussions and refinement to investigate opportunities for and possible structure of a sustainable DoC after EDIT. Within tasks 3.1.7 and 3.1.9 a report (C3.1.4) was written on barriers and benefits in the operations of the physical and digital infrastructure components. An organisational model was designed in which EDIT and CETAF merge into a new organisation tentatively called CETAF 2.0. This model was discussed with the CETAF Executive Committee, but not yet with the EDIT BoD. The significance and role of natural history collections for the global research infrastructure landscape were addressed through activities within Scientific Collections International (SciColl), a new global organisation that is being initiated and fostered by the OECD Global Science Forum. Two steering group meetings were held (London, March 2009; Berlin, Sept. 2009) to discuss the SciColl strategic, outreach and governance plans. A SciColl outreach conference was held in Brussels (Feb. 2010). The ESF Research Network Programme proposal "European Network of DNA and Tissue banks for Biodviersity Genomics" was submitted Oct. 2009 to establish a European network with a strong global outreach that will become an essential component of the EDIT infrastructure. Focal areas envisaged include facilitating research; enabling easy, coordinated and sustainable access; improved collection quality and safety. Activity 3.2 Taxonomic information infrastructure (5-UvA) Task 3.2.1 Collaborate with other EDIT WPs and relevant other partners and programs on the design of the scope of a common web-based European biodiversity information infrastructure, especially investigating the efficient use of taxon names as keywords to cross-link biology information. As part of the Global Names Architecture (GNA) participation during JPA4 a document was drafted presenting the linkage of the pan-European species directories infrastructure with infrastructures outside Europe (C.3.2.4). The Nomina 6 meeting at Santa Cruz (Feb. 2010) was attended to discuss the further development and implementation of the Global Names Usage Bank (GNUB) within the GNA. Main focus of the meeting was to agree on a definitive GNUB datamodel and to discuss potential user cases (EDIT M3.2.5d – in prep.). A first import of the pan-European checklists within the EDIT CDM-store has been established (C3.2.7). Task 3.2.2 Start of implementation of (national) institutional bases for a common and durable organisation and management approach for the maintenance and updating of European species lists. Contributions have been drafted supporting the stability and continuity in the performance of the European Taxonomic Information Service (M3.2.4a, M3.2.4b), including a common management approach for maintenance and updating of pan-European species lists. Plans were discussed at the BoD (Dec. 2010). The ESF proposal on disseminating taxonomic and methodological standards submitted in JPA 3 (C3.2.5) was positively evaluated by the ESF and sent to member countries for approval. WP3.1 contributed to the EPBRS "World Biodiversity and European Taxonomy" meeting (as e-conference and session chair), preparing a common agenda on the sustainability of biodiversity research in Europe (M3.2.6). An associated activity is


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setting up a common agenda on prioritised taxa, meaning those that play a role within European legislation on habitat protection, nature conservation, pest control, etc. (C3.2.8 – in prep.). Task 3.2.3 Describe the model for the set up of an advanced pan-European species-directories infrastructure supporting the reach of a next (higher) level of completeness, quality, consistency, integration, incorporation, and (e-science) application. Travels to relevant East European institutes in Georgia, Turkey, Ukraine, Russia. To support the dissemination of taxonomic and methodological standards from the European knowledge infrastructures to national focal points and other biodiversity communities, a bid was prepared for a Caucasus Distributed Institute of Taxonomy (C.3.2.3). To further integrate outer European countries of the Western Palaearctic into the EDIT work program, the network of national focal points has been further extended. EDIT will contribute to the organisation of the next National Focal Points meeting at Edirne (Turkey) in May 2010. Other proposals to support the continuation of PESI are in preparation (C3.2.9 – in prep.). Activity 3.3 Sustaining the cybertaxonomy process (5-UvA) C3.3.1 Report on sustainable mechanisms for cybertaxonomy in WP3 (M47) Instead of a report, real action was taken to safeguard the future of the cybertaxonomy platform. A team consisting of, amongst others, leaders of WP3.2, WP5 and WP6, submitted a proposal (ViBRANT) to the EU-FP7 Infrastructure call (Dec 2009). The proposal combines elements of scratchpads (WP5), cybertaxonomy platform (WP6) and the FE/PESI community (WP3.2). Activity 3.4 Large-scale networked instrumental facilities (8-CBS) Task 3.4.1 Continue joint activities of the Consortium Barcode of Life by involving scientific committee members of CBoL and other (global) initiatives in ECBoL activities Collaboration with CBOL and iBOL, an international campaign based in Canada for establishing a global DNA barcoding network (http://www.dnabarcoding.org/), are ongoing. Collaboration was initiated with the recently established QBOL, Quarantine Barcoding of Life (http://www.qbol.org/UK/), a project financed by the 7th Framework Program of the European Union (2009-2012). National funds in the Netherlands were secured Sept. 2009 to establish EBOLD as the European node in iBOL. Task 3.4.2 Proposals for COST money or similar funds to organise workshop(s) on joint barcoding proposals As a follow-up to the EuroBioForum meeting (Strasbourg, Sept 2008), phone conferences were held with CBOL and iBOL to discuss future collaboration with Genome Canada, and to re-orientate on the reality of the world-wide economic crisis, which has diminished interest from potential funders in industry. ECBOL also prepared an unsuccessful COST proposal (Sept 2009). However, national funds in the Netherlands allow CBS and the new NCB Naturalis to establish two centres for DNA Barcoding as well as EBOLD, a database system for Europe to mirror or complement the BOLD database in Canada. EBOLD is envisaged to be part of the sustainable EDIT infrastructure (see Task 3.4.8). Other large (1 M€ or more) barcoding proposals were succesful in Poland (EU Grant), Bavaria (state level), Germany (federal level), France (national), Belgium (national). The QBOL project was supported by a 3 M€ grant from EU-FP7. Task 3.4.3 Involvement in the scientific organisation of the one-day-meeting on DNA Barcoding in conjunction with General EDIT meeting in month 40 The EDIT symposium was restructured into a young systematist meeting. The ECBOL-2 meeting is scheduled for June 2010 (http://ecbol2.bio.uminho.pt/ECBOL_2.html). To prepare this meeting and the ECBOL workplan for 2010, ECBOL and CBOL met in Portugal (15 Dec 2009). A scientific committee was assembled for ECBOL2, a programme determined, and a


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steering group meeting planned. A Network of European Leading Labs meeting will be held in Utrecht. A plan was drafted for ECBOL after the EDIT contract. Task 3.4.4 Development of MycoBank and associated software as a model approach for local data repository The MycoBank software that was developed for the Dutch FES Plant Health barcoding project, was also successfully employed in Europe as part of the QBOL project. Furthermore, it was decided to place servers in a data centre in Belgium, allowing remote data curation throughout Europe (CITRIX software), and to make the software freely available as part of EBOLD. Meetings were held to discuss how to mirror EBOLD with the Canadian BOLD system (CBOL Mexico, Nov 2009) and with the Chinese hub of BOLD (Beijing, Dec 2009), and how to integrate software development and data synchronisation. Task 3.4.5. Contribute to the promotion and further development of the BOLD data system, and integration with the European data systems The Netherlands Centre of Biodiversity (NCB = EDIT partners NNM, NHN and ZMA) was granted 30 million Euro in September 2009, and together with affiliated CBS two centres for DNA Barcoding will be established. Some 1.1 million Euro has been reserved by NCB to establish EBOLD, a database system for Europe to mirror or complement the BOLD database in Canada. CBS will coordinate the software development of this system. EBOLD is envisaged to be part of the sustainable EDIT infrastructure. Task 3.4.6 Start liaisons with industry for specific applications of barcoding technology Together with 19 partners, CBS and various members of ECBOL successfully established QBOL, coordinated by Plant Research International (Wageningen, the Netherlands). QBOL aims at assembling collections of all quarantine regulated plant pathogenic organisms in Europe, and to develop DNA-barcodes for identification. CBS coordinates a workpackage on barcoding of Fungi, and one on database, software and informatics developments. The programme will result in an internet-based database system with taxonomic features and barcode sequences allowing improved identifications of plant pathogens. QBOL will be extended globally in 2010. Task 3.4.7 Involve European industries in the development and funding of DNA barcoding and related products Although the ECBOL workshop at the Eurobiofund Forum in Stassbourg (M 27, so see also 3rd PAR) and the subsequent ECBOL-1 workshop were well attended and succeeded in awakening and increasing the interest of grant agencies and ministries in DNA barcoding, the interest shown afterwards by these parties as well as industrial attendees turned out to be disappointing, possibly due to the financial crisis. At national level, several proposals involving EDIT partners were successful at national level (see 3.4.2). Task 3.4.8 Continue maintainance of the ECBOL website and stimulate the participation of partners and third parties involved in barcoding by using the website as a platform for exchange and cooperation EDIT kept funding this activity. See Task 3.4.9. The website is now being revamped to be relaunched early 2010. An ECBOL coordinator will update the website with current information, and link various barcoding labs, keeping them abreast of the latest information. Task 3.4.9 Developing a business plan for ECBOL to continue after EDIT Based on a feasibility study and group discussion, the most appropriate organisation model for ECBOL at this stage of development was decided to be a virtual network. A quick scan for funding revealed that the COST-system would be an option to explore (see also task 3.4.11). The proposal was, however, not successful, and thus a new funding mechanism must be found. CBS and NCB Naturalis have agreed that they will co-fund an ECBOL coordinator for two years after the EDIT contract, i.e. until 2013. Tasks will include maintenance of the ECBOL-website and


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editing a Barcoding Newsletter. Sustainable funding beyond 2013 will be discussed at the ECBOL-2 meeting (Braga, June 2010). Task 3.4.10 Coordination of funded European projects in the context of iBOL iBOL is an international campaign based in Canada for establishing a global DNA barcoding network (http://www.dnabarcoding.org/). The European barcoding partners in ECBOL (EDIT) investigated MoU possibilities, but this was postponed due to legal and organizational constraints. ECBOL and iBOL will nonetheless informally collaborate on various levels, including coordination of work and data sharing (sequences). Task 3.4.11 EU proposal for coordinating DNA barcoding in Europe (Network of Leading Labs) The ECBOL partners (both from EDIT and outside) jointly prepared a COST 1st phase proposal application, submitted Sept 2009, to build up expertise in DNA barcoding, supporting biodiversity and taxonomy, through an integrated Network of European Leading Laboratories (NELL) (www.ecbol.org). Tools and protocols would be developed, labs would coordinate barcoding efforts to reduce duplication, and public awareness of new technologies in biodiversity research would be raised. Unfortunately, the proposal did not pass the first phase. Nevertheless, a NELL meeting is planned for Lab managers in April (CBS Utrecht). Activity 3.5 Liaisons with international infrastructures (6-NHN) Tasks 3.5.3 and 3.5.4 In conjunction with the most recent SPNHC meeting held in Leiden (July, 2009), the directors of ABRS (Australian Biological Resources Study), SANBI (South African National Biodiversity Institute) and EDIT Workpackages 3.5, 6 and 8 met to discuss short and long term collaboration opportunities, to work out projects and link them to specific funding possibilities in more detail. A report was written (C3.5.4-5) that includes detailed information on the major areas where collaboration is pursued. Formalisation of envisaged cooperation documents will be by means of a European-Australian-South African Agreement to Collaborate (AtC). Task 3.5.5 Stimulate and facilitate the development of projects between EDIT and international infrastructures The signatories of an Agreement to Collaborate (AtC = component C3.5.6), including EDIT partners, ABRS and SANBI, agreed that a co-ordinated international effort is needed to establish a basis for collaboration among the partners in areas of taxonomic and biodiversity research, natural history collections maintenance, improvement and expansion, and capacity building. The AtC provides evidence of concrete and specific development in international collaboration. Tasks 3.5.6 and 3.5.7 An e-Flora workshop was organized in Leiden (January, 2010) to discuss the needs of different flora projects for electronic tools, to create a consortium of international institutions committing to the various e-Flora activities and to discuss network funding opportunities. Representatives of flora projects lacking an elaborate electronic data management tool or online data presentation will collaborate with technology developers to advance in their e-Flora developments. For this purpose various exemplar groups have been selected (activity coordinated by the NBGB). The exemplar groups will provide feedback to the EDIT CDM platform (WP5) and, subsequently, provide the building blocks needed for developing an e-Flora platform. Activity 3.6 Integration of institutions’ taxonomic publications (2-MNHN)


- 35 -

The objective of this activity is to create a platform for exchange of technical and strategic issues related to scientific publishing of scientific journals and series by EDIT institutions. In year four the following network activities among scientific publishing representatives were launched and useful information was put together and disseminated among EDIT partners:

- A document with all scientific publications (journals and series) published by or on behalf of EDIT partners was further updated (Duin, D. (2009, April 29), Scientific titles published in EDIT institutions http://www.e-taxonomy.eu/journals. A following update is planned for May 2010.

- A mailing list for EDIT publishing staff (desk editors, scientific editors, librarians and other people interested in scholarly publishing) was launched to discuss technical and strategic publishing issues (M3.6.2)

- A webpage with the address http://www.e-taxonomy.eu/publishing covering the publishing activities in EDIT, reports and other documentation was launched

- A 2nd meeting on Scientific Publishing in Natural History Institutions was held in Bratislava, which gathered 40 people to discuss how the access and dissemination of taxonomic information could be further enhanced (M3.6.3) a report on the meetings’ outcomes was drafted (C3.6.2).

- A document was published with recommendations to publishing representatives, libraries, and directors of Natural History Institutions (C3.6.3).

2.3.3 Deviations from the project workprogramme and corrective actions Task 3.1.7 Liaising with SPG and other WPs to specify research visions of EDIT and refine requirements for the physical infrastructure components C3.1.3 Report on the requirements for the physical infrastructure, stemming from research and stakeholder needs and needs from other WPs (M44) => postponed till M51 This task and report needed input from former WP1.6 and the Science Policy Group (SPG). To speed up the interaction, the WP3 leader has now joined the SPG and pariticipated in a two-day meeting in the first month of JPA5 (11-12 March 2010, Berlin). The report is expected to be delivered before the June 2010 BoD (M51). C3.1.4 Identification of barriers and benefits in the operations of the (physical, equipment, digital and administrative) infrastructure component (M44) => delivered M46-M47 WP3.1 suffered from the departure of the project manager from Leiden to Berlin which increased the administrative burden to the WP leader. A first version of this component was delivered in M46 and ditributed for comments. A second, improved version was delivered in M47. The report is expected to serve as one of the basic documents for discussions on the design of the EDIT infrastructure at the next BoD (June 2010).

Figure 4 : Scientific Publishing meeting - Bratislava


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C3.2.6 Contribute to meeting, organised by WP2, on taxonomic networks and GSDs involvement (with WP2, Sp2000, and PESI) (M 44) For details on deviations for this activity, see Work Package 2. M3.2.5 Set up of a common EDIT agenda on prioritised taxa (M 43) This acitvity needs input from the Science Policy Group that has been increasing its activity since Dec 2009. A draft document on prioritised taxa (C3.2.8), due in JPA5, was prepared Oct 2009 and all relevant European prioritised species lists were collected and merged, but a release of the document is postponed until a stable, uniform and user-friendly implementation is possible within the PESI portal. C3.3.1 Report on sustainable mechanism for the cybertaxonomy in WP3 (M47) Instead of a report, real action was taken to safeguard the future of the cybertaxonomy platform. A team consisting of, amongts others, leaders of WP3.2, WP5 and WP6, submitted a proposal called ViBRANT to the EU-FP7 Infrastructure call in December 2009. The proposal combines elements of the scratchpads (WP5), the cybertaxonomy platform (WP6) and the FE/PESI community (WP3.2). Another proposal submitted, i4Life, will also be important for sustaining these products and communities for a longer period. M3.4.7 Organise a meeting to work out formal proposal(s) to establish one or more major barcoding factories in Europe, and discuss lobbying strategies => postponed till M51 Emphasis shifted towards funding applications for national barcoding centres in 2009 (Netherlands, Germany, Poland; see Task 3.4.2). CBS and NCB are establishing two barcoding labs in the Netherlands. Coordination will be discussed at ECBOL-2 (Braga, June 2010). C3.4.8 Proposal for ATBI+M combined with DNA-barcoding submitted for EU or other funding WP3 (M44) => report delivered M46 WP3 could not submit the proposal, because it requires 50% matching at national level that could not be raised by 15 September. In this particular case, we suffered from the change of annual deadline of LIFE+ from mid-November (2007, 2008) to mid-September (2009). Had it stayed at mid-November, new NCB funds in the Netherlands would have given us the chance to submit the proposal. A report on the issue has been delivered M46. C3.4.10 Report on mechanisms to maintain ECBOL after EDIT (M 47) => postponed till M51 At the barcoding meeting in Carvoeiro, Portugal (Dec. 2009), several options for sustainable development were discussed, but the results were not sufficient to serve as basis for a report on this critical issue. The report has therefore been postponed until after the ECBOL-2 meeting in Braga, Portugal (June 2010) where possibilites of organizing sustainable funding beyond 2011 will be discussed among a large barcoding community during. C.3.5.7 Proposal for a communication mechanism with other networks of excellence and international networks within Europe and South/North America or East Asia (M45) This report was submitted one month later, because key participants of the workshop could only travel to the Netherlands in January 2010. The e-Flora workshop (Jan. 2010) led to increased contacts with Australia and South Africa and more interaction between workpackages (EDIT Platform for Cybertaxonomy, Scratchpads, NBGB, RBGE, MO, RBGK). The appendices of the AtC are currently being signed by ABRS, SANBI and interested partner institutions. A COST pre-proposal for networking (App. 6) and a WOTRO pre-proposal for joint research (App. 2) have been submitted. If granted, we envisage signing an MoU in the final year of the EDIT contract.


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Relevant additional work not planned in JPA4 The fouth year of EDIT also saw positive deviations from the original workplan. The following relevant additional activities were pursued: 1. Wild flowers of Europe: A European public awareness project to stimulate common plant knowledge, with European school children as target group, led by the Hortus Botanicus Leiden and National Botanic Garden of Belgium, Meise. Scientific background data and educative fact sheets (in Dutch) are now available. The project will be implemented as a pilot study into outreach activities. 2.Role of palaeontology in EDIT As a follow-up to an ESF workshop held in Crete. it became clear that additional workshops would be needed to discuss the future of palaeontology in Europe, with emphasis on its role in EDIT. WP3 suggested to provide a platform for one or two workshops, the first of which will be held in Stuttgart, March 2010 (M48). Some preparation was required within JPA4. 2.3.4 Lists of components11 & milestones A – WP3 components Deliv

erabl

e no.


no.

Date

due

12

Actual

/Forecast

delivery

date

Link on public

website (if

component

public)

Lead contractor

D17 C3.1.3 Report on the requirements for the

physical infrastructure, stemming from

research and stakeholder needs and needs

from other WPs

WP3 M44 M55

(delayed

JPA 5)

7-NNM

D17 C3.1.4 Identification of barriers and

benefits in the operations of the (physical,

equipment, digital and administrative)

infrastructure component

WP3 M44 M46 7-NNM

D17 C3.1.5 Report on sustainable mechanisms

for the EDIT natural history collections as

an integrated infrastructure (M47)

WP3 M47 M47 PP 7-NNM

D17 C3.1.6 At least one MoU on collection

policies proposed to the directors (M47)

WP3 M47 M45 PP 7-NNM

C.3.1.9 Create a taskforce to prepare the

formation of a European network of DNA

and tissue banks

WP3 M47 M43 CO 3-UKBH

D16 C.3.2.3 Proposal(s) for funding of Pan-

European species directories

WP3 M46 M46 CO 5-UvA



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Deliv

erabl

e no.


no.

Date

due

12

Actual

/Forecast

delivery

date

Link on public

website (if

component

public)

Lead contractor

infrastructures, extending the geographical

scope

D17 C.3.2.4 Linking pan-European species

directories infrastructure with structures

outside Europe

WP3 M40 M47 RE 5-UvA

D28 C3.2.6 Contribute to meeting, organised by

WP2, on taxonomic networks and GSDs

involvement (with WP2, Sp2000, and

PESI)

WP3 M46 see WP2

report -

cancelled

5-UvA

D17 C3.2.7 CDM import tools for the pan-

European species registers

WP3 M43 M47

(postponed)

JPA5

http://www.e-

taxonomy.eu/nod

e/786

9- FUB-BGBM

D17 C3.3.1 Report on sustainable mechanism

for the cybertaxonomy in WP3

WP3

WP5

WP6

M47 Delayed

M53

5-UvA

9-BGBM

10-NHML

D16 C3.4.4 Proposal(s) for funding of

European DNA-barcoding projects and

facilities

WP3 M36 M45 CO 8-CBS

D16 C3.4.5 Seeking funding to organise

workshop(s) on joint barcoding proposals


D16 C3.4.6 Establish liaisons with industry;

coordinate current and foreseen initiatives

for barcoding proposals by groups

focussing on user and stakeholder needs


D16 C.3.4.7 European contribution as central

node in iBOL


D17 C3.4.8. Proposal for ATBI+M combined

with DNA-barcoding submitted for EU or

other funding

WP3 M44 M44 CO 7-NNM

D16 C.3.4.8a European contribution as central

node in iBOL


D17 C3.4.8b. Proposal for ATBI+M combined

with DNA-barcoding submitted for EU or

other funding

WP3 M44 M44 CO 7-NNM

D16 C 3.4.9 Seeking funding for a European

Network of Leading Labs


D17 C3.4.10 Report on mechanisms to maintain

ECBOL after EDIT

WP3 M47 Delayed

JPA 5 M55

8-CBS

D17 C.3.5.4 Report on cooperation between

EDIT partner institutions and ABRS,

including ALA and TRIN


taxonomy.eu/nod

e/650

6-NHN


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Deliv

erabl

e no.


no.

Date

due

12

Actual

/Forecast

delivery

date

Link on public

website (if

component

public)

Lead contractor

D17 C.3.5.5 Report on cooperation between

EDIT partner institutions and SANBI

WP3 M43 M42 Merged with

C3.5.4

6-NHN

D17 C.3.5.6 Agreements, preferably MoU’s, for

cooperation with ABRS (incl. ALA and

TRIN) and SANBI


taxonomy.eu/nod

e/669

6-NHN

D17 C.3.5.7 Proposal for a communication

mechanism with other networks of

excellence and international networks

within Europe and South/North America

or East Asia


taxonomy.eu/nod

e/748

6-NHN

D17 C.3.6.2 Report on second workshop on

scientific publishing by NHI


taxonomy.eu/nod

e/710

2-MNHN

D17 C.3.6.3 Recommendations for scientific

publishing in EDIT institutions, based on

workshop and discussion platform


taxonomy.eu/nod

e/755

2-MNHN


Milestone

no.

Milestone name WP

no.

Date due13 Actual

/Forecast

delivery date

Lead contractor

M3.1.5 Second workshop of the EDIT Directors of

Collections with focus on loan policies,

compatibility of management structures and

collections rescue task force

WP3 M40 M40 7-NNM

M3.1.6 Co-organising the SPNHC 2009 conference,

state of the art and dissemination of skills in

collection management

WP3 M40 M40 7-NNM

M3.1.7 Directors of Collections core group

workshop with external experts

WP3 M43 M45 7-NNM

M3.1.8 Directors of Collections task group meeting

on collections policy and scope and mandate

of a collections rescue task force

WP3 M49 Forecast M49 7-NNM

M3.2.4a Stability and continuity in the performance

of the European Taxonomic Information

Services (part 1)

WP3 M42 M44 5-UvA

M3.2.4b Stability and continuity in the performance

of the European Taxonomic Information

WP3 M45 M46 5-UvA



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Milestone

no.

Milestone name WP

no.

Date due13 Actual

/Forecast

delivery date

Lead contractor

Services (part 2)

M3.2.5 Set up of a common EDIT agenda on

prioritised taxa

WP3 M43

M3.2.6 Contribute to EPBRS "World Biodiversity

and European Taxonomy"

WP3 M38 M38 5-UvA

M3.4.7 Organise a meeting to work out formal

proposal(s) to establish one or more major

barcoding factories in Europe, and discuss

lobbying strategies

WP3 M36 See 2.2.3

Deviations

8-CBS

M3.5.3 Meetings with EDIT partner institutions,

ABRS and SANBI to work out projects for

collaboration

WP3 M 36-41 M36-46 6-NHN

M3.6.2 Create a mailing list to discuss scientific

publishing issues

WP3 M36 M36 2-MNHN

M3.6.3 workshop scientific publishing by NHI WP3 M39 M40 2-MNHN


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2.4 Workpackage 5: Internet Platform for Cybertaxonomy

WP Leader: Walter G. Berendsohn Partner n° 9 FUB-BGBM Other partners involved: 2 MNHN 4 CSIC–MNCN 5 UvA 7 NNM 8 CBS 9 FUB–BGBM 10 NHML 11 RBGK 12 SMNS 13 RBINS 14 RMCA 15 NBGB 16 MIZPAN 18 HNHM 19 CUB 20 IBSAS 29 RBGE 30 MfN 2.4.1 Objectives The general Workpackage objectives for the entire project period are (i) the integration of the participating institutions’ biodiversity informatics and IT resources, and (ii) the creation of the Internet Platform for Cybertaxonomy, a collection of interoperable tools and services oriented towards practical use for revisionary taxonomy and taxonomic biodiversity inventories. The following objectives were set for the fourth 18 month period: (a) Integrate newly developed and existing taxonomic software using the Common Data Model (CDM), the Java Library based on the CDM, and standard data and communication interfaces. Roll out the second and third version of the Figure 5 : Cybergate


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Internet Platform, cumulating in a fully functional virtual environment for cybertaxonomy. (b) Continue the development of co-operative processes among the institutions by means of collaboration in the ISTC (Information Science and Technology Commission), bilateral exchanges of personnel, joint development and application of software, and the conclusion of Memoranda of Understanding on common practices in the IST sector and agreement on ways to sustain the Internet Platform software beyond the project period At the outset of year 4 of the project, decisions of the ISTC and results from its third meeting formed the base for further efforts regarding objective (i/a). For objectives (ii/b), the strategy for the implementation of the Internet Platform for Cybertaxonomy including the technologies to be used had been decided, a list of components that had to be developed was fixed, version 2 of the CDM was available, and application development was continued in all areas defined. In the following, numbering of activities and tasks corresponds to the DoW in the 4th JPA. 2.4.2 Progress towards objectives Activity 5.1 Integration of Information Science and Technology (IST) departments This task corresponds to objectives (i/b). The Liaison with Board of Directors and Scientific Advisory Committee (5.1.1.) was carried out by the WP5 lead. [9 FUB-BGBM]. The Information Science & Technology Committee (5.1.3) had its fourth meeting in September 2009; the importance of this body for linking EDIT with the people driving the IST process at the institutional level was once more confirmed. The ISTC discussed the developments of platform version 2, procedures of user testing and standardised evaluation procedures. Furthermore the ISTC discussed needs and requirements for the 5th JPA such as platform introduction sessions at EDIT institutions [All cooperating Partners]. . The MoUs (approved by the BoD) have now been signed by 14 institutions: Drupal (9x), ABCD (12x), Libraries Cooperation (9x), Global Names and Classification service (10x). Management, coordination and liaison with other WPs (5.1.4). In a substantial way, WP5 collaborated with: WP7 through the identification of field tools (components of D20, i.e. Platform Version 2), through species information sheets and the integration of the geoplatform and the ATBI field sites, and through the construction of Drupal-based ATBI web portals [4 CSIC, 9 FUB-BGBM, 12 SMNS, 14 RMCA]; with WP6 through close cooperation with the Exemplar Groups [9 FUB-BGBM, 10 NHML]; with WP3 through the development of taxonomic infrastructure (with the PESI project as one of the most promising developments for Platform adoption and with building new collaborations with tropical e-Floras). [5 UvA, NHN, NNM] and through building cross-links with GBIF via the Specimen Explorer portal [7 NNM]; with WP2 through software development and potential “prospecting” of users in the context of the experts database (another interface implemented in Drupal) [3 UKBH, 9 FUB-BGBM]. Promote scientific standards and standard tools (5.1.5). In the course of developing the Common Data Model, EDIT staff substantially contributed to several TDWG standardisation efforts, in particular to TCS (Taxonomic Concept Schema), SDD (Structured Descriptive Data) and the TDWG Ontology. The subject of one of the approved MoU is the application of the ABCD standard by EDIT institutions. The CDM has a potential to become a base for standards e.g. in the LifeWatch initiative [9 FUB-BGBM and several partners]. The following activities refer to general objective (ii), JPA objectives (a):


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Activity 5.2 Creating the Internet Platform for Cybertaxonomy [Lead: FUB-BGBM] The core developments in this activity were the continued refinement of the CDM Library as well as improvements in the Common Data Model itself. Both developments were driven by general requirements of the CDM Framework architecture as well as by concrete requirements that arose in the course of application development, particularly of the taxonomic editor (Activity 5.5) and the data portals (5.8). Besides adaption of library functionalities EDIT web services were implemented and adapted. These services collect data from the community store and expose it to the web. PESI datasets (Fauna Europaea, the Euro+Med Plantbase, European Register of Marine Species) were prepared for integration. Collaboration with CATE project was continued. This resulted in further functionalities of the CDM library and refinement of the CDM. The EDIT Cybergate, a graphical user interface offering a single entry point to the entire Platform was refined. Activity 5.3 Virtual Library of Taxonomic Literature (ViTaL) [Lead: NHML] After the developer of activity 5.3 has left the EDIT project and the NHML in February 2009, no replacement to fill the position was found. Basic developments were continued by non EDIT personnel. As the situation did not improve in the last months it was decided by the WP5 leader and agreed by NHM London to shift the activity 5.3 tasks from the NHM London to MfN Berlin (coordinators of BHL Europe, a project directly related to EDIT 5.3). It is expected that cooperation of BHL and EDIT at one place will result in substantial synergies. The tasks of activity 5.3 were evaluated by MfN (budget channeled through BGBM because of administrative difficulties), looking at solutions. Next the steps that were to be taken with respect to integration with the BHL Europe project were investigated. A solution has been developed that will firmly integrate EDIT and BHL, recognising that the environment in which ViTaL would function had moved on from the state of affairs more than 4 years ago, both technically and community-wise. The major development in the community is the BHL Europe project. Technically, the solution using the MetaLib software had proven to be complicated, not well supported by the company, and costly in the long term. There are new opportunities to link to existing solutions in the library sector, which will now be tested and than exploited, together with BHL Europe. Concrete steps were included in the workplan for JPA5. Through the BHL Europe project further developments are guaranteed - BHL-E will have a developer working on further integration of BHL services with the EDIT Platform library. Chances for long term sustainability are also much enhanced by this close liaison. Activity 5.4 Geographic Platform Components [Lead: RMCA] The development of the platform continued during the 4th year of the project. The platform features 2 types of interfaces: a REST webservice (queried by the means of HTTP URL and producing images in JPG format) and a graphical application with an interactive map and menu allowing the production and printing of thematic maps. The REST webservices provide the following functionalities: • Production of map in image format (JPG) for which type of outlines and fill colours can be

dynamically defined by the means of HTTP GET parameters.


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• Production of maps in image format (JPG) with occurrence data transmitted via HTTP GET parameters. These data can be displayed with satellite images and vector representation of the ATBI+M site as background.

These 2 REST services can be used by any external website needing to dynamically display maps. The graphical interface offers the following functionalities: • dynamic upload of occurrence data to the portal, and visualization with tailor-made legends

and symbols. • querying of geoferenced data from the GBIF portal (searched by taxon of interest) and

visualisation through freely defined symbols and legends. • reprojection of these occurrence data in several reference systems. • analysis of these occurrence data (calculation of the richness and variety of values inside

dynamically defined bounding boxes) • export of these maps into image format (intended for printed publications) The portal also features several background layers (TDWG zones, Google Earth and Yahoo satellite images, integration of freely available layers for rivers and lakes) and allows the dynamic querying of external Web Map Servers. Since February 2010 James Davy and Franck Theeten are installing with the help of Pere Roca Ristol a replica of this portal on a server managed by the RMCA. They will in the following year of the project maintain this site as a backup for production, complete the documentation of the code and functionalities of the portal and fine-tune server-side code in order to improve the portability of the application. To spread the excellence and enhance user involvement, a joint GIS workshop was realized as part of the EDIT summer school 2009 (from field to the web). The material is included in EDIT's training directory, and contributes to the (WP8) DEST as a means to assure long-term continuity and use of the tools. Activity 5.5 Taxonomic core tools [Lead: FUB-BGBM]

This activity is now almost entirely focused on the development of a new generation of advanced taxonomic editing software, which will significantly speed up the taxonomic work process. The activity does also give key input to the continued development of the Common Data Model from an (editor) user perspective. Version 2 of the Taxonomic Editor (the “EDITor”) has been finalized. It offers functions for creating taxonomic trees, organizing synonymies, and maintaining factual data and it provides new functionalities such as organizing concept relations, search functions, de-duplication of references and names, setting of user preferences (e.g. nomenclatural code), and connecting external data sources. Furthermore, a prototype of a “Power user interface” for editorial data cleaning and integrity checking was integrated into the Taxonomic editor. The latest version of the Editor runs on Microsoft Windows XP and Vista, as well as Mac OS 10. The software includes a pre-installed H2 Java Database Engine for local use but can also communicate with a server database. Activity 5.6 Descriptive and identification tools [Lead: MNHN] The major computational development of activity 5.6 in year 4 was the development of the SDD/CDM import/export module (SDD – Structured Descriptive Data – is the new standard for this type of data). The module establishes the communication between the current software


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tools for the management of descriptive data with the CDM. This data flow will be tested in year 5 with real examples, in collaboration with an exemplar group. Communication and exchange with the taxonomic community (5.6.7) were continued through some participations to several international congresses (E-biosphere conference, Systematics Association meeting, TDWG conference) where posters or presentations (exclusively “taxonomists oriented”) have been presented. The master courses “Systématique, Evolution et Paléontologie” at Paris University as well as the courses during the second Summer School were performed once again. Moreover, an inventory of existing descriptive datasets and identification keys has been initiated through the participative wiki-like website called SpeciesID and some resources (videos, training manual, etc.) on the concrete use of all the tools have been collected in order to continue the updating of the BDTracker. During year 4 we have solved the main issues with regards to the organization of the congress on identification: “Identifying biodiversity: progress and problems” will take place at MNHN on year 5 thanks to these background efforts. Activity 5.7 Security Infrastructure [Lead: FUB-INF] The design of a common security infrastructure within EDIT was already planned at the time of D7 (Aug. 2007) and a preliminary decision was taken to use the Shibboleth standard-based application framework to implement a single-sign-on mechanism (SSO) and identity providers within the EDIT network. The software now developed will allow developers to adapt their biodiversity informatics applications to become part of a large network, to which users can sign on with a single username and password. Development of the security infrastructure was continued and a number of problems have been solved (C5.085 Integrate further platform components with the CSSO security infrastructure). In a next step the single sign on can be implemented for all EDIT applications. Activity 5.8 Publication tools [Lead: FUB-BGBM]

The CDM Data Portal demonstrates the data output capabilities of the EDIT Platform, as well as the integration of CDM functionality into the Drupal Content Management System. The EDIT CDM Data Portal has been further developed following user requirements from the EDIT exemplar groups with improved stability, increased functionality of web services, implementation of multiple taxonomic views, improved search functionality and taxonomic tree browsing (C5.126 Data portal update for Platform version 2) Individual themes were developed for the three WP6 exemplar groups. For the printed publication output, a functional description for service to generate printed publication for the CDM was made available. Activity 5.9 Specimen access as a platform component [Lead: FUB-BGBM] The specimen access portal has been operational since year 3: EDIT Specimen and Observation Explorer (http://search.biocase.org/edit/). Further developments including the incorporation of direct access to the search results via the taxonomic editor are features of Platform version 3 and will be incorporated in due course.

Activity 5.10 Software quality and usability testing

Besides user input for software development obtained throughout the project a systematic approach on testing was needed. For this reason software quality and usability testing started in May 2009 lead by the RGBE. A “test plan discussion document” was circulated to developers


- 46 -

and other members of the EDIT community to obtain agreement on the methods and scope of the structured testing. For structured procedures it was decided to use the TestLink framework to document the results of the test cases. Automated testing may be used if possible (C.5.130 Reliability and usability testing summary report for Platform version 2). A detailed manual for the Taxonomic Editor was produced. Furthermore a plan for testing of the taxonomic editor within several EDIT institutions was developed. The testing will start in JPA5 and is based on international testing standards. 2.4.3 Deviations from the project workprogramme and corrective actions With one exception (activity 5.3), the work proceeded with relatively few deviations from the plan. In particular, project deliverable 20, which depended on the timely delivery of 29 components (24 from WP5) and 5 milestones was produced and delivered in time. As described above, Activity 5.3 (Virtual Taxonomic Library [NHML]) incurred considerable difficulties due to staffing problems at the NHML, eventually leading to a transfer of responsibility to MfN, where synergies with the BHL Europe project can be fully exploited. The workplan of the activity was evaluated and redressed, however, the objectives were fully maintained and will be now be pursued by a different technical approach in JPA5. The following JPA4 components were cancelled or transferred to JPA5: C5.030 (Launch of ViTaL as a functioning component of EDIT Platform for Cybertaxonomy), C5.102 (ViTaL User Review), C5.103 (ViTaL Sustainability review), C5.104 (ViTaL technical review and roadmap), and C5105 (Specification of im-/export data interface to and from CDM). Uncritical delays occurred in the following activities: • In activity 5.1 [FUB-BGBM], component C5.093 (Report to the BoD with respect to

integration of IST departments in EDIT institutions) was delayed by one month. • In activity 5.2 [FUB-BGBM], component C5.140 (CDM_PESI integration accomplished and

tested) was postponed to M48 in JPA5 due to parental leave of the responsible programmer. • In Activity 5.4 [RMCA] two components were delayed by 1-4 months (C5.073, C5.110),

however, without affecting project deliverables or milestones. The main reason identified for the delays was the strong engagement of the responsible staff in educative activities of EDIT.

• In Activity 5.5 [FUB-BGBM], the 1-month delays in components C5.078 (Fully functional version to the CDM editor available) and C5.113 (CDM power user interface design study and pilot implementation) were actually due to a delay in report writing.

• Activity 5.6 [MNHN] had to postpone and transfer to JPA5 the milestone 5.39 (Meeting with Key2Nature project with the aim of federating the European taxonomic identification community). This had to be postponed, because M 54 was the only date to be agreed on all partners of the meeting. There was an uncritical delay of two months in C121 “SDD-CDM2 import/export module finalised”.

• Component C5.127 (Prototype of service to generate printed publication for the CDM) in activity 5.8 [FUB-BGBM], was postponed to Month 49 in JPA5, in order to include needs and requirements which will result from a meeting of important user groups in March 2010 (M48).


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2.4.4 Lists of components14 & milestones A – WP5 components

Deliv

erable

no.


no.

Date

due

15

Actual

/Forecast

delivery

date

Link on public website

(if component public)

Lead

contractor

20 C5.069 E-conference on requirements of

geospatial services for taxonomists

5 M36 M36 14- RMCA

20 C5.076 Taxonomic sample data available

(data)

5 M36 M36 http://www.e-

taxonomy.eu/node/616

9- FUB-

BGBM

20 C5.077 CDM data interface components

available (software)



9 - FUB-

BGBM

20 C5.107 Specification for the application of

EDIT Geo-Software for taxonomic

inventory sites (WP7)



14-RMCA

20 C5.081 Use case model and functional

description of CDM descriptive data

editor (Model/Report).



2 -

MNHN-

20 C5.096 Report on WP7 data management 5 M40 M40 30 - MfN

20 C5.060 (deferred from 5.2 to 5.4) ATBI

site data linked to geoplatform



14 -

RMCA

20 C5.070-2 Report on converter webservice

that transforms point occurrence data to

distribution data (based on the

documentation of requirements: report 1;

M33)

5 M40 M40 14 -

RMCA

20 C5.072 Dynamically link GBIF data to

core geoplatform allowing GBIF data to

be visualised in addition to custom user

data.



14 -

RMCA

20 C5.078 Fully functional version of the

CDM editor available (software)



9 – FUB -

BGBM

20 C5.113 CDM power user interface design

study and pilot implementation (report

and software)



9 – FUB -

BGBM

20 C5.116 Inventory of descriptive

knowledge bases.



2 –

MNHN-

20 C5.117 Specification of a CDM Library

functionality for the output of structured

descriptive content in structured and

textual form (ASAP).



2 –

MNHN-



- 48 -

Deliv

erable

no.


no.

Date

due

15

Actual

/Forecast

delivery

date



Lead

contractor

20 C5.126 Data portal update for Platform

version 2 ready



2 –

MNHN-

20 C5.130 Reliability and usability testing

summary report for Platform version 2



29 - RBGE

20 C5.058 CDM2 Framework

Implementation available



9 – FUB-

BGBM

20 C5.059 CDM2 Community store interfaces

documented



9 – FUB-

BGBM

20 C5.097 First report on integration of

software developments in partner

institutions



9 – FUB-

BGBM

20 C5.098 Report: List of additional software

applications requiring interface definitions



9 – FUB-

BGBM

20 C5.030 Launch of ViTaL as a functioning

component of the EDIT Platform for

Cybertaxonomy including system and user

documentation to enable effective access –

not accepted

5 M41 M41 (not

accepted) -

cancelled

10 -

NHML

20 C5.108 MapViewer version 2: The EDIT

MapViewer with enhanced functionality

available.



14 -

RMCA

20 C5.109 Map REST Services version 2:

The EDIT Map Web Services for

occurrence and distribution data with

enhanced functionality available



14 -

RMCA

20 C5.118 Pilot implementation of a CDM

Library functionality for the output of

structured descriptive content in

structured and textual form.



2 –

MNHN-

20 C5.085 Integrate further platform

components with the CSSO security

infrastructure



9 – FUB-

BGBM

20 C5.088 Functional description for service

to generate printed publication from the

CDM



9 – FUB-

BGBM

21 C5.120 User documentation and training

manual.



2 –

MNHN-

21 C5.102 ViTaL User Review. A review of

user feedback submitted during the pilot

phase and after the launch of ViTaL -

5 M44 cancelled 10 -

MHML


- 49 -

Deliv

erable

no.


no.

Date

due

15

Actual

/Forecast

delivery

date



Lead

contractor

cancelled

21 C5.092 Report on the 4th ISTC meeting

and Draft Workplan for JPA-5



9 – FUB-

BGBM

1/2 C5.094 Report on MoU development to

BoD



9 – FUB-

BGBM

C5.103 ViTaL Sustainability review. A

review of the commitments already made

and the further commitments necessary to

ensure the sustainability of ViTaL. -

cancelled


NHML

21 C5.039 Report on the application of

geoplatform software to map inventory



4 – CSIC-

MNCN

21 C5.040 Application to select vector units

by environmental and spatial criteria (ED

application)



4 – CSIC-

MNCN

21 C5.073 Workshop with WP7 contributors

to geo-Platform to review geo-platform

functionality (report 2 on requirements)

5 M45 M48 14 -

RMCA

21 C5.122 Metadatabase for the resource

catalogue.



2 –

MNHN-

21 C5.127 Prototype of service to generate

printed publication from the CDM -

postponed to M 49

5 M45 M49

(postponed)

9 – FUB-

BGBM

21 C5.104 ViTaL Technical review and

roadmap - cancelled


NHML

21 C5.121 SDD-CDM2 import/export

module finalised. - Postponed from M 45



2 –

MNHN-

21 C5.140 CDM-PESI integration

accomplished and tested: (PESI) Import

interface for Fauna Europaea and

Euro+Med Data, export to PESI UI

database M 46 s.a. C3.2.7 postponed to M

48

5 M46 M48

(postponed)

9 – FUB-

BGBM

17 C3.2.7 CDM import tools for the pan-

European species registers (European

Register of Marine Species, Fauna

Europaea and Euro+Med PlantbaseI -

postponed from M43 to M46

3 M43 M47

(postponed)

JPA5

9- FUB-

BGBM

17 C5.119 Report on sustainability of

Platform software

5 M47 M47 9 – FUB-

BGBM

21 C5.093 Report to the BoD with respect to 5 M47 cancelled 9 – FUB-


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Deliv

erable

no.


no.

Date

due

15

Actual

/Forecast

delivery

date



Lead

contractor

integration of IST departments in EDIT

institutions

BGBM

21 C5.105 Specification of im-/export data

interface to and from CDM - cancelled


NHML

21 C5.110 Design document for a prototype

software for data completeness assessment

(gap analysis) for selected test data (e.g.

ATBI and other datasets) – postponed to

M49

5 M47 M49

(postponed)

14 -

RMCA

21 C5.125 Concept to provide EDIT Service

Providers with suitable Shibboleth policy

mapping tools

5 M47 M47 9 – FUB-

BGBM


Milest

one

no.

Milestone name WP

no.

Date due16 Actual

/Forecas

t delivery

date

Lead

contractor

5.22 Revised CDM frozen and documented for

Platform release 2.

5 M36 M36 9 – FUB-

BGBM

5.32 Three significant taxonomic initiatives

setup as CDM projects (e.g. EDIT

exemplar groups)

5 M36 M36 9 – FUB-

BGBM

5.19b Functional description for descriptive user

interface (i.e. for descriptive data CDM 2

editor incl. SDD import).

5 M38 M38 2 –

MNHN-

UPMC

5.26 Soft launch of ViTaL (formerly M09) 5 M40 M40 10 -

NHML

5.33 CDM Toolkit Bundle (data store, editor,

conversion tools) available and

documented to be used by EDIT partner

institutes and beyond

5 M40 M40 9 – FUB-

BGBM

5.34 4th ISTC Meeting held 5 M43 M43 9 – FUB-

BGBM

5.37 Successful integration of a first existing

software tool for descriptive data (keys and

5 M41 M41 2 –

MNHN-



- 51 -

Milest

one

no.

Milestone name WP

no.

Date due16 Actual

/Forecas

t delivery

date

Lead

contractor

taxon descriptions) with the CDM. UPMC

5.39 Meeting with Key2Nature project with the

aim of federating the European taxonomic

identification community - Postponed

M54

5 M46 M54

(postpone

d)

2 –

MNHN-

UPMC

5.38 Report on data completeness assessment

(gap analysis) for selected test data (ATBI)

5 M46 M47 14 -

RMCA


- 52 -

2.5 Workpackage 6: Unifying revisionary Taxonomy on the Web

WP Leader: Dr Dave Roberts

Partner no. 10 NHML

Other partners involved: -9 FUB -BGBM

- 11 RGBK

2.5.1 Objectives

• Define and develop the means to provide access to the currently highly fragmented taxonomic information source.

• Facilitate and support communities of taxonomic experts.

• Define what is needed from the cyber-environment for taxonomic Web content to be delivered.

• Assess barriers to implementation.

2.5.2 Progress towards objectives Cooperation within the “International Cichorieae Network” (ICN) has been further intensified (http://wp6-cichorieae.e-taxonomy.eu/blog/home). Several taxonomic novelties published by members of the ICN have been integrated into the Common Data Model, photographs of rarely depicted taxa have been added. Important data sets, e.g. on published illustrations, have been contributed by ICN members. Services to the community and the scientific public have also continued, e.g. by the literature review on the ICN blog. Close cooperation with the Euro+Med Plantbase (http://www.emplantbase.org/home.html) and PESI (http://www.eu-nomen.eu/pesi/) continued.

Again, several revised prototype versions of the Cichorieae portal have been developed, tested and further improved in close co-operation with WP5. Some fundamental novelties will be available in April 2010 after migration of the complete data set to the new CDM. One innovation, the testing of alternative taxonomic views for one taxon, will be displayed soon. Data received by Euro+Med Plantbase and PESI resp. have been modified for that purpose. Many details have been discussed with external users to meet the requirements of professional and amateur botanists. Basic data such as names, protologues (currently c. 4100), morphological descriptions, images (c. 950), distribution data and data on systematics have continuously been updated and added. Apart from morphological descriptions cited from floras and monographs, standardised descriptions (Delta Access) are now available for 52 taxa. An illustrated glossary has been compiled and will be incorporated in spring 2010. A set of standardised descriptions has been tested by WP 5 in Paris (MNHN) to create multi access keys (Xper2).


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The palm taxonomy content available online through Palmweb (www.palmweb.org) has substantially increased during the last year. The site now holds taxonomic descriptions for over 30% of the accepted species, gives access to protologues for more than 60% of accepted species and around 15% of synonyms, and includes a gallery of over 2000 images that illustrates around a third of the taxon pages. In addition, the first versions of an interactive dichotomous key and of a multi-access key to all palm genera have been completed. These are currently hosted at the RBG Kew’s website and will be linked to Palmweb shortly.

Taking advantage of the functionality provided by the Content Management System in which the portal has been implemented, the palm exemplar groups has also added several pages of general information about palms, including links to relevant resources such as a bibliography list and an online illustrated glossary of palm terms. Supplementing the taxonomic content in this way makes the portal more user-friendly and improves its outreach.

As usual, the exemplar group has worked closely with WP5 developers to enhance the layout and functionality of the portal. New features include a search of taxon names in external databases, citations in the taxon pages, and the display of metadata in the image gallery.

A significant amount of time has been put into obtaining permission to use content from copyright holders. Many authors and publishers have been contacted to request use of photos or printed publications. As a result of this effort, the palm exemplar group has access to new material highly relevant for the website. This new content is currently being processed, and will be incorporated into the Palmweb database with the Taxonomic Editor.

The palm scientific community was given an update on the portal during the EUNOPS 9 meeting, held at the Royal Botanic Gardens at Kew on the 25-26 April 2009. The members of EUNOPS maintain their interest in eTaxonomy and strongly support Palmweb. However, concern was expressed about the slow progress with developments. An update on the portal was also given to the staff of the Herbarium in the RBG, Kew.

The palm exemplar group developed an Access database as part of the collaboration with the EU-funded project "Palm harvest impacts in tropical forests" (EU-PALMS). This database was designed to hold ethnobotany data compiled from publications by the EU-PALMS project. Data gathering is completed, therefore the palm exemplar group has started exploring the options to make the information available in Palmweb.

The insect exemplar group is mainly using the Scratchpads system to bring taxonomy to the web. As of January 2010, over 30 insect Scratchpads have been developed (e.g. http://taygetis.myspecies.info, http://phthiraptera.myspecies.info/ and http://blattodea-culture-group.org/). Insect Scratchpads offer diverse data. For example pages about entomological societies, species pages, bibliographies, taxonomic classifications, distribution maps, and images. Several Scratchpads have developed into community websites for their taxa.

Focal taxon of the insect exemplar group are the Diptera (www.diptera.myspecies.info, www.sciaroidea.info). The family Milichiidae serves as a zoological testbed for the portal (http://dev.e-taxonomy.eu/dataportal/diptera/) and taxonomic editor developed by WP5 as well as demonstrating the many options Scratchpads offer (www.milichiidae.info).

The revision of the genus Milichiella (Diptera: Milichiidae) was published in on paper as well as online (www.milichiidae.info/content/milichiella-online-revision) with the online version including an interactive key and photos of all 110 species. Additionally two faunistic online-only


- 54 -

articles were published (http://diptera.myspecies.info/content/carnidae-lake-kerkini-region-greece, http://milichiidae.info/content/milichiidae-lake-kerkini-region-greece), pushing the boundaries of publication.

One of the barriers to publication of taxonomic data on the web is the need for compliance with the codes of nomenclature, which don't allow pure online publication of nomenclatural acts. The EDIT IRG project "Streamlining Fungus Gnat (Diptera: Sciaroidea: Lygistorrhinidae) Taxonomy", which was funded in November 2009, solves this issue by developing new automated workflows for online and print publication of taxonomic papers as a collaboration between Scratchpads and Pensoft publishing. This will dramatically reduce the time and cost of print publications, encourage online collaboration and benefit all Scratchpad users. Automatic submission, review and publication of species descriptions and nomenclatural acts between the Scratchpads and the taxonomic journal ZooKeys, will be achieved, providing a prototype for rapid print publication of descriptive taxonomy that conforms to the ICZN rules of nomenclature. This approach may serve as a model for other publishers.

Scratchpad development has continued with 155 sites now supported and over 1700 registered users (over 700 added this year, by comparison to 500 added in Year 3). There are mostly taxon-specific sites as well as regional sites (taxon-focused and geographically restricted, e.g. the lichens of Bermuda). We also have information and service sites (providing services to the taxonomic community, and sites for Societies, journals or demonstration functions. Five sites are private and used for pre-publication collaborative work. They support 160k nodes (i.e. pages). We recorded 163,203 unique visits last year with 639,141 pages being viewed. Individuals look at an average of 4 pages per visit (cf 5 in Year 3) and a visit lasts an average of 3 minutes (cf 4 minutes in Year 3). There has been 84.51% increase in traffic over the year. [data from Google Analytics].

The most significant achievement in the Scratchpads this year was migration to Drupal 6 undertaken

Figure 6 : Scratchpad Usage Statistics


- 55 -

primarily to align activities with the development of LifeDesks in EoL. Such an alignment offered the opportunity for significant synergistic benefit on both sides, although the benefit has been more political than practical. Nevertheless we have adopted the LifeDesk taxonomic editor's user interface that, with additional development is now a central part of the Scratchpad infrastructure. Most significantly we are able to handle very large numbers of taxa (>2 million in tests) and to support large rearrangements of taxonomic hierarchy (moving whole orders and classes for example) in real time. The capacity to handle such large taxonomies means that the Scratchpad infrastructure is suitable for a taxonomy of all life, as might be needed for an ecological or geographically focussed project, for instance an ATBI.

A sociological survey of the Scratchpad user community was conducted with the aim to understand the motivations and benefits perceived by users when adopting the Scratchpad system and to identify the barriers (both social and technical) that may hinder wider uptake). A summary of the outcomes was presented during the EDIT General Meeting with the title “Why people engage” http://www.e-taxonomy.eu/files/EDITGenMeet2_DDuin.zip.

2.5.3 Deviations from the project workprogramme and corrective actions Deliverable D12, First report on EDIT Scientific output, was delayed by 3 months due to conflicting demands on the author's time. The development of a metric to provide a statistic useable in career management (C6.11) was not completed. This was being undertaken jointly with GBIF (Global Biodiversity Information Facility) and has become a very active area of work. The Scratchpad system developed aggregated statistics, but the development of usage statistics for each contributing individual was not of sufficient priority within the available development resource. The report on sustainability of exemplar groups and their data (C6.18) has been put back to M50 following intensive work (code sprints), that have only just drawn to a close, to enhance the portal component of the platform. The organisation of an International Cichorieae Conference has been abandoned because it would have been overshadowed by the upcoming International Compositae meeting scheduled for Montreal in 2010. 2.5.4 Lists of components17 & milestones A – WP6 components Deli

vera

ble

no.


no.

Date

due

18

Actual

/Forecast

delivery

date

Link on public

website (if

component

public)

Lead contractor



- 56 -

Deli

vera

ble

no.


no.

Date

due

18

Actual

/Forecast

delivery

date

Link on public

website (if

component

public)

Lead contractor

D25 C6.13 Revision of genus Milichiella

(Diptera: Milichiidae) effectively complete


taxonomy.eu/no

de/700

NHML

D25 C6.14 Cichorieae are effectively complete

(excluding microspecies)


taxonomy.eu/no

de/701

FU-BGBM

D25 C6.15 Rattans effectively complete 6 M44 M44 http://www.e-

taxonomy.eu/no

de/676

RGBK

D26 C6.16 Functional TAPIR interface from

Scratchpads


taxonomy.eu/no

de/651

NHML

D26 C6.17 To report on a developers workshop

at the TDWG symposium to gather

opinions about sustainability

mechanisms


taxonomy.eu/no

de/747

NHML

B – WP6 Milestones Milestone

no.

Milestone name WP

no.

Date due19 Actual

/Forecast

delivery date

Lead contractor

M6.32 Produce a list of evaluated data sources for

potential integration into the CDM/data

portals

6 M36 M36 FU-BGBM

M6.33 Deliver an enhanced Scratchpad capacity for

external data integration and display.

6 M36 M36 NHML

M6.36 Offer an integrated suite of tools to

facilitate data compilation.

6 M40 M40 NHML

M6.38 Evaluate progress in XML mark-up tools as

mechanisms for data capture

6 M42 M42 NHML

M6.40 2000 images digitised and annotated 6 M44 M44 FU-BGBM

M6.43 Meeting with WP5 to refine portal design 6 M37 M37 RGBK

M6.44 Meeting with WP5 to refine portal design 6 M40 M40 FU-BGBM

M6.45 Meeting with WP5 to refine portal design 6 M43 M43 RGBK

M6.46 Meeting with WP5 to refine portal design 6 M46 M46 NHML

M6.48 Organize IX meeting of the European

Network of Palm Scientists (EUNOPS

6 M40 M40 RGBK



- 57 -

2.6 Workpackage 7: Applying taxonomy to conservation

WP Leader: Christoph Häuser Partner no. 30 - MfN Other partners involved: -2 MNHN -3 UKBH -4 CSIC – MNCN -7 NNM -9 FUB – BGBM -12 SMNS -13 RBINS -14 RMCA -19 CUB -27 USNM 2.6.1 Objectives • Objective 1: Raise public awareness and strengthen utilisation of European capacities for end

users of taxonomic information in biodiversity conservation, particularly for biodiversity inventories, assessments, and monitoring;

• Objective 2: Mobilise and integrate European taxonomic expertise for undertaking and contributing to biodiversity inventories, assessments, and monitoring, especially in areas of conservation concern;

• Objective 3: Develop and refine standards, techniques and tools for both rapid and repeated all taxa biodiversity inventories and monitoring (ATBI+M) programs, also for world wide application;

• Objective 4: Establish a European ATBI+M task force for conducing biodiversity inventories, assessments and monitoring both within and outside Europe;

• Objective 5: Provide and update comprehensive biodiversity inventories as a sound baseline for monitoring of selected areas of conservation concern, especially towards the 2010 target.

2.6.2 Progress towards objectives Activity 7.1: Assessing biodiversity inventory and monitoring needs, evaluating relevant taxonomic capacities, and raising stakeholder awareness The ATBI+M approach was further promoted in two ways: 1. Active participation at international conferences (ALTERnet, Leipzig; German Society for General and Applied Entomology Conference, Göttingen; BioSTRAT IPBES workshop, Brussels; E-biosphere Conference, London; GEO-Day of Biodiversity, Ebern; SPNHC Conference, Leiden; 4th Symposion for Research in Protected Areas of the Hohe Tauern National Park, Salzburg; TDWG Conference, Montpellier; Int. Biodiversity Conference on Sustainable Development,


- 58 -

Papua, Indonesia; UNESCO Biodiversity Conference, Paris), and 2. The already released ATBI+M flyer (see Component C7.1.7) was re-designed into a more general form that makes it also suitable for reaching non-professional taxonomists, field biologists, conservation managers and park rangers (Component C7.1.9).

As the number of recorded species between 2007 and 2009 has reached a level that justifies publication efforts for some groups, a tentative outline for a series of monographs has been prepared for the ATBI+M pilot site Mercantour/Alpi Marittime (Component C7.1.10). Potential coordinators for the single groups have been identified and a definitive publication plan will be elaborated during the 5th JPA.

The available taxonomic expertise, the work force for individual taxa and regions as well as scientists that may contribute in some way to ATBI+M activities have been continuously recorded and updated, with the inclusion of more than 850 entries so far. This represents the addition of more than 100 new contacts during the 4th year of activities. The number of registered individual members with specific interests for one of the ATBI+M sites exceeds 280 at the special web-based WP7 forum (www.atbi.eu/forum). This is an increase of more than 60 experts in comparison to the 3rd year. Activity 7.2: Mobilising taxonomic resources and establishing the ATBI+M task force network As part of a coordination plan for human resource management of ATBI+M task forces based on the EDIT taxonomic expert information system developed by WP2 and WP5 (www.editexpertnet.org), contact details and affiliations of scientists that participated at ATBI+M activities thus far have been delivered to WP2 (Component C7.2.7). These scientists have been invited to join the EDIT expert database. Constitution of expert teams for future ATBI+M activities is intended to run through this information system. A further step to warrant the engagement of scientists at ATBI+M activities consisted of elaborating an institutional agreement on sustained participation of EDIT staff (Component C7.2.8). This draft document will be circulated among the BoD for revision and the final version is to be signed during the 5th JPA. The former e-mail updates sent to all relevant WP7 contacts were replaced by a newsletter in a more reader-friendly layout in PDF format (Components C7.2.10 and C7.2.15). The newsletter offer up-to-date information about ATBI+M activities, WP7 relevant short reports and announcements on past and upcoming meetings as well as short news. In June 2009, a Memorandum of Cooperation (MoC) was signed between the DFG Research Unit “Biodiversity and Sustainable Management of a Megadiverse Mountain Ecosystem in South Ecuador” and EDIT WP7 (Component C7.2.11). This opens the opportunity of joint ATBI+M fieldwork in the Reserva Biológica San Francisco, for which over 60 researchers have already indicated interest. Draft Terms of Reference (ToR) for individual participation in this second non-European ATBI+M pilot site have been elaborated (Component C7.2.13), and the final version will be released once negotiations regarding fees for collecting permits are concluded. The WP7 management has been approached by the Bantimurung Bulusaraung National Park, Sulawesi, Indonesia, to express interest in becoming a non-European ATBI+M site. At present, consultations with relevant Indonesian authorities are underway for elaborating a Memorandum of Understanding (MoU) and to adapt the Terms of Reference (ToR) for individual participation to the local requirements.


- 59 -

To establish a 3rd European ATBI+M pilot site (Component C7.2.12), negotiations have been initiated with the Trust of the German National Park ‘Unteres Odertal’ (Lower Oder Valley NP) and the Ministry of Environment of the German Federal State Brandenburg. The National Park ‘Unteres Odertal” is located in northeast Germany in the Federal State Brandenburg at the Oder river valley at the border to Poland. The end version of the Terms of Reference (ToR) for individual participation at the 1st non-European ATBI+M pilot site at the Udzungwa Mountains National Park in Tanzania is available (Component C7.2.9). Activity 7.3: Developing standards, protocols, and tools for conducting an ATBI+M program Remarkable progress has been made regarding IT-tasks: Revised data recording guidelines for ATBI+M pilot sites have been released (Component C7.3.9) and are under continuous review, based also on the feedback given by participants. Customized forms for mobile devices have been developed for electronic species data recording in the ATBI+M sites (Component C7.311). These forms were developed for mobile devices with a GPS receiver and the software ArcPad (a tool from ESRI Inc.). They include locality, event and species forms and were tested preliminarily during the 2nd EDIT summerschool at the ATBI+M site Gemer Area in Slovakia. Further tests with improved forms will take place during the 5th JPA.

A web service developed by WP5 for map visualization has been embedded in the dedicated websites for the European ATBI+M sites to illustrate the distribution of species recorded during field activities (Component C7.3.7). Furthermore, a detailed species sheet is generated, a picture of the selected species – if available – and detailed information is scrolled up for each record, including the locality name, macrohabitat notes, collection method, determinator and the deposit of the record (Component C7.3.10).

Following the 2nd workshop held in Las Palmas de Gran Canaria in January 2009 to outline the contents of the Manual on ATBI+M field recording techniques and protocols with 32 prospective authors (see Component 7.3.5), negotiations were conducted with the Journal Abc Taxa (www.abctaxa.be) to publish the manual as a especial volume (Component C7.3.8). Abc Taxa is a product of the Belgian National Focal Point to the Global Taxonomy Initiative and consists of a series of peer-reviewed manuals dedicated to capacity building in zoological and botanical taxonomy, in collection management and in good practices in taxonomic and curatorial research. The manual consists of 22 chapters written by 70 authors and it is expected to be released by the end of March 2010. Activity 7.4: Operating the ATBI+M task force and evaluating relevant methods and techniques More than 90 signed Terms of Reference (ToR) for individual participation were received during the 4th JPA. Activities on the 1st ATBI+M pilot site, Mercantour/Alpi Marittime, were scaled up during 2009, resulting in 212 individual visits. This implies an increase of almost 100% as compared with 2008 (Components C7.4.6 and C7.4.9). Second year activities at the second European ATBI+M site in the Gemer area concluded with 41 individual visits of 21 participants. Participation of scientists from EDIT partner institutions at ATBI+M activities differed at both pilot sites: While 65.9% of the participants at the Gemer Area came from EDIT institutions, this


- 60 -

proportion further decreased in Mercantour/Alpi Marittime (27.4%). Increasing participation of scientists from non-EDIT partner institutions in 2009 is however an indication that the ATBI+M approach has been well accepted beyond the framework of EDIT.

As of February 2010, a total of 6476 species have been reported from both ATBI+M sites, Mercantour/Alpi Marittime and Gemer Area (Component C7.4.9). The most numerous group is represented by the kingdom Animalia (4224 species), followed by plants (1466) and fungi (610). Ten different sampling techniques have been applied, with the Coleoptera (Insecta) as the group being sampled with the largest number of different delivered data sets on their techniques (Component C7.4.9).

A web-based content management system (CMS) is available for each of the active

ATBI+M pilot sites (Component C7.4.7). The CMS for all websites is based on a Drupal installation (version 5.12) and the access for administration is restricted to user groups (see 7.3 for details). Number of visits since the 1st of September 2007 reached 11743 and 1406 as of February 2010 for the Mercantour/Alpi Marittime and for the Gemer Area websites, respectively, thus indicating that the website contents, though very specific, have received good attention. Activity 7.5: Sustaining the European ATBI+M task force and long term study sites As part of reviewing the ATBI+M concept, a questionnaire was sent to 162 participants of both European ATBI+M pilot sites to evaluate the WP7 services (administration and on-site, Component C7.5.5). In general, the overall administrative concept for the ATBI+M activities was valued very positive by the participants that sent back the questionnaire, although it is unfortunate that they represented only 40% of the contacted experts. However, it is important to note that the large majority of the interviewees do consider benefiting from their participation and is willing to further participate in the coming years.

The costs for sustained ATBI+M operations at established European pilot sites were calculated on the basis of the actual WP7 working scheme (Component C7.5.7). As expected, level of field activities and country-specific living costs largely influence the amount of funds required to operate the ATBI+M pilot sites, assuming that administrative and IT-relevant aspects are not taken over by the management of the respective protected area. The amount calculated rely on the actual number of field days for the ATBI+M site Mercantour/Alpi Marittime in 2009 (576) and accounts for 71,654.4 € for this site. If the lower costs for accommodation and daily allowances at the ATBI+M site Gemer Region are taken into account for the same level of field activities, then this amount is reduced by 18.144,0 €. More importantly, the costs for generating a complete geo-referenced dataset (starting from registration of expert up to online presentation) could be estimated to be 6.0 € and 4.5 € for the ATBI+M sites Mercantour/Alpi Marittime and Gemer Region, respectively.

The survey from user feedback of ATBI+M results by conservation community and stakeholders (Component C7.5.6) revealed a variety of data usage. The Mercantour National Park

Figure 7: Number of identified species and distribution between 2007 and 2009 in Mercantour/AlpiMarittime


- 61 -

could benefit from the data collected for the definition of a list of its natural heritage (endemic, rare and\or protected species). This list is included in the Charta, an official document which defines the major orientations of the park for the next fifteen years. Moreover the ATBI+M results were used for education issues, e.g. for a university lecture about “Analyses and Techniques of Biodiversity Inventories” in France and a one-year-course on natural biodiversity for primary school pupils in Italy. The feedback of the Slovakian conservation community and stakeholders about their use of the ATBI+M results was rather restrained, but also here the results are used for a Slovakian taxonomic database at the Comenius University in Bratislava. In addition the ATBI+M results were also used for education purposes such as the international Summerschool “From field to Web - studying biodiversity with the taxonomist's toolbox” which was hosted in Muránska Planina in 2009. 2.6.3 Deviations from the project work programme and corrective actions The conservation managers and stakeholders workshop on added value of ATBI+M activities for conservation & protected area management (Component C7.1.8) had to be postponed to M52, as it was not possible to find a time frame that suited all invited participants, especially those coming from the USA. Likewise, the review of the EDIT ATBI+M approach and cost model (Component C7.5.9), planned to take place subsequent to the stakeholder workshop was postponed to M52 too, because part of the review team is composed of experts from the USA.

The inventory and monitoring field work at the first non-European ATBI+M pilot site in Tanzania could not be initiated, as the high bureaucratic hurdles posed by the Tanzanian counterparts for issuing group collecting permits could not be taken yet. Hence it was also not possible to conclude a Material Transfer Agreement(s) (MTA) for specimens and materials collected (Component C7.2.6)

The Terms of reference for individual participation at a 3rd European ATBI+M pilot site (Component C7.2.14) can be first drafted when the negotiations with the Trust of the German National Park ‘Unteres Odertal’ and the Ministry of Environment of the German Federal State Brandenburg have been finalized. This component is schedule for M50.

The non-European ATBI+M pilot site planning workshop for Madagascar (Component C7.2.17), for which WP7 had offered financial support never took place due to difficulties for finding suitable dates and venues by the (non-EDIT) organizing committee. 2.6.4 Lists of components20 & milestones A – WP7 components

Deli

vera

ble

no.


no.

Date

due

21

Actual

/Forecast

delivery

date

Link on public

website (if

component

public)

Lead contractor

D22 C7.1.8 Report from conservation managers

and stakeholders meeting on added value of

7 45 Deferred to

JPA 5

MfN/SMNS



- 62 -

Deli

vera

ble

no.


no.

Date

due

21

Actual

/Forecast

delivery

date

Link on public

website (if

component

public)

Lead contractor

ATBI+M activities for conservation &

protected area management

(M52)

D22 C7.1.9 ATBI+M flyer targeting non-

professionals [in cooperation with WP1,

WP2, WP8]

7 40 44 http://www.e-

taxonomy.eu/nod

e/717

MfN/SMNS

D12

updat

e

C7.1.10 Publication outline for individual

ATBI+M pilot sites

7 44 M47 http://www.e-

taxonomy.eu/nod

e/764

MfN/SMNS

D1D

2

C7.2.6 Material Transfer Agreement(s)

(MTA) concluded for specimens and

materials collected at first non-European

ATBI+M pilot site

7 37 Deferred to

JPA 5

(M50)

MfN/SMNS

D23 C7.2.7 Coordination plan for human

resource management of ATBI+M task

forces based on EDIT taxonomic expert

information system [in cooperation with

WP2 and WP5]

7 43 45 http://www.e-

taxonomy.eu/nod

e/749

MfN/SMNS

D17 C7.2.8 Draft institutional agreement on

sustained participation of EDIT staff in

ATBI+M activities

7 42 45 PP MfN/SMNS

D6

updat

e

C7.2.9 Terms of reference for individual

participation at 1st non-European ATBI+M

pilot site

7 37 44 http://www.e-

taxonomy.eu/nod

e/679

MfN/SMNS

D28 C7.2.10 First ATBI+M electronic

newsletter [in cooperation with WP1]

7 39 40 http://www.e-

taxonomy.eu/nod

e/647

MfN/SMNS

D1D

2

C7.2.11 Signed agreement for establishment

of a 2nd non-European ATBI+M pilot site

7 40 39 http://www.e-

taxonomy.eu/nod

e/673

MfN/SMNS

D1D

2

C7.2.12 Signed agreement for establishment

of a 3rd European ATBI+M pilot site

7 41 46 http://www.e-

taxonomy.eu/nod

e/750

MfN/SMNS

D6

updat

e


participation at a 2nd non-European

ATBI+M pilot site

7 42 drafted MfN/SMNS

D6

updat

e


participation at a 3rd European ATBI+M

pilot site

7 43 deferred to

JPA 5

(M52)

MfN/SMNS

D28 C7.2.15 Second ATBI+M electronic

newsletter [in cooperation with WP1]

7 46 46 http://www.e-

taxonomy.eu/nod

e/753

MfN/SMNS


- 63 -

Deli

vera

ble

no.


no.

Date

due

21

Actual

/Forecast

delivery

date

Link on public

website (if

component

public)

Lead contractor

D20 C7.3.7 Report on usability of ATBI+M map

visualization tools for scientists and

stakeholders

7 37 39 PP MfN/SMNS

D12

updat

e

C7.3.8 Manual on ATBI+M field recording

techniques and protocols [in cooperation

with WP1]

7 46 Deferred to

JPA 5

(M48)

MfN/SMNS

D19 C7.3.9 Revised data recording guidelines for

ATBI+M pilot sites

7 36 36 PP MfN/SMNS

D20 C7.3.10 Prototype of web-based species

information sheets with detailed

information of the distribution within the

ATBI+M pilot sites

7 38 37 PP MfN/SMNS

D20 C7.3.11 Report on field testing of

customized data recording tools

7 43 40 PP MfN/SMNS

D12 C7.4.6 Progress report on inventory and

monitoring activities at established

European ATBI+M pilot sites

7 36 36 http://www.e-

taxonomy.eu/nod

e/620

MfN/SMNS

D20 C7.4.7 Content management system for

ATBI+M administration and outreach

implemented for ATBI+M pilot sites

7 36 36 http://www.e-

taxonomy.eu/nod

e/621

MfN/SMNS

D12 C7.4.9 Update of participation, target taxa

and applied inventory and monitoring

techniques for established ATBI+M pilot

sites

7 45 M46 http://www.e-

taxonomy.eu/nod

e/765

MfN/SMNS

D1D

2

C7.5.5 Survey from feedback of ATBI+M

participants

7 38 45 http://www.e-

taxonomy.eu/nod

e/752

MfN/SMNS

D22 C7.5.6 Survey from user feedback of

ATBI+M results by conservation

community and stakeholders

7 44 46 http://www.e-

taxonomy.eu/nod

e/751

MfN/SMNS

D19 C7.5.7 Cost assessment of sustained

ATBI+M operations at established

European pilot sites

7 45 47 PP MfN/SMNS

D19 C7.5.9 Review of the EDIT ATBI+M

approach and cost model

7 47 deferred to

JPA 5

(M52)

MfN/SMNS



- 64 -

Milestone

no.

Milestone name WP

no.

Date due22 Actual

/Forecast

delivery date

Lead contractor

M7.1.7 Workshop for presenting ATBI+M concept

and first results to conservation managers

and stakeholders [in cooperation with WP1]

7 43 Deferred to JPA

5 ( M51)

MfN/SMNS

M7.1.9 Draft ATBI+M flyer targeting non-

professionals [in cooperation with WP1,

WP2, WP8]

7 38 38 MfN/SMNS

M7.1.10 Taxonomic publication coordinators for

individual ATBI+M pilot sites identified

7 42 M42 MfN/SMNS

M7.2.1 Meetings with relevant authorities for

European ATBI+M pilot site(s) (ongoing)

7 ongoing ongoing MfN/SMNS

M7.2.2 Meetings with relevant authorities for non-

European ATBI+M pilot site(s) (ongoing)

7 ongoing ongoing MfN/SMNS

M7.2.3 Draft Terms of reference for participation in

first non-European ATBI+M pilot site

7 36 36 MfN/SMNS

M7.2.4 Draft Material Transfer Agreement (MTA)

for specimens and materials collected at first

non-European ATBI+M pilot site

7 36 Deferred to JPA

5 ( M48)

MfN/SMNS

M7.2.5 Data on taxonomic experts from ATBI+M

activities entered in EDIT taxonomic expert

information service [in cooperation with

WP2 and WP5]

7 41 41 MfN/SMNS

M7.2.6 Draft institutional agreement on

participation of EDIT staff in ATBI+M

activities

7 38 40 MfN/SMNS

M7.2.7 Draft agreement for establishment of a 2nd

non-European ATBI+M pilot site

7 38 38 MfN/SMNS

M7.2.8 Draft agreement for establishment of a 3rd

European ATBI+M pilot site

7 39 44 MfN/SMNS

M7.2.9 Draft terms of reference for individual

participation at a 2nd non-European

ATBI+M pilot site

7 40 40 MfN/SMNS

M7.2.10 Draft terms of reference for individual

participation at a 3rd European ATBI+M

pilot site

7 41 41 MfN/SMNS

M7.2.11 Non-European ATBI+M pilot site planning

workshop

7 41 cancelled MfN/SMNS

M7.3.10 Manuscript drafts delivered for manual on

ATBI+M field recording techniques and

protocols

7 37 37 MfN/SMNS

M7.3.11 Meeting of editorial committee for manual 7 39 39 MfN/SMNS



- 65 -

Milestone

no.

Milestone name WP

no.

Date due22 Actual

/Forecast

delivery date

Lead contractor

on ATBI+M field recording techniques and

protocols [in cooperation with WP1]

M7.3.12 Revised manuscript delivered for manual on

ATBI+M field recording techniques and

protocols

7 41 42 - 44 MfN/SMNS

M7.3.13 Draft manual on ATBI+M field recording

techniques and protocols

7 43 ongoing since

M46

MfN/SMNS

M7.3.14 Demonstration of geo-referencing tools and

geospatial analytical components for

ATBI+M participants [in cooperation with

WP5.4 and WP8]

7 40 40 MfN/SMNS

M7.3.15 Draft recommendations for application of

new data recording tools and protocols for

ATBI+M participants

7 46 47 MfN/SMNS

M7.4.2 Inventory and monitoring field work at

established European ATBI+M pilot sites

continued

7 36 - 43 36 - 43 MfN/SMNS

M7.4.4 Inventory and monitoring field work

initiated at first non-European ATBI+M

pilot site

7 38 - 45 Deferred to JPA

5 ( M50-57)

MfN/SMNS

M.7.4.8 Data about participation, target taxa and

inventory and monitoring techniques applied

for established ATBI+M pilot sites collected

7 44 44 MfN/SMNS

M7.4.9 Meeting of review team for methods and

techniques applied at European ATBI+M

pilot sites

7 46 delayed MfN/SMNS

M7.4.10 Data collection for gap analysis of higher

taxa for established European ATBI+M

pilot site(s)

7 47 47 MfN/SMNS

M7.5.9 Participation at second EDIT General

Meeting

7 45 45 MfN/SMNS

M7.5.10 Participation at second EDIT "summer

school" at European ATBI+M pilot site [in

cooperation with WP8]

7 40 40 MfN/SMNS

M7.5.11 Distribution of survey for feedback on

ATBI+M results from conservation

community and stakeholders

7 42 44 MfN/SMNS

M.7.5.12 Constitution of ATBI+M review team 7 44 delayed MfN/SMNS

M7.5.13 Meeting of review team to assess ATBI+M

approach and cost model

7 46 delayed MfN/SMNS


- 66 -

2.7 Workpackage 8: Training and Public Awareness

WP Leader: Thierry Backeljau Partner no. 13-RBINS Other partners involved: - 2 MNHN - 3 UKBH - 4 CSIC-MINCN - 5 UvA - 6 NHN - 7 NNM - 8 CBS - 9 FUB-BGBM - 10 NHML - 11 RBGK - 12 SMNS - 14 RMCA - 15 NBGB - 16 MIZPAN - 17 IBPAN - 19 CUB - 20 IBSAS - 30 MfN 2.7.1 Objectives

Training

• Assess European strengths and weaknesses in the current offer of training in taxonomy. • Improve dissemination of information on training opportunities. • Promote collaboration between training providers and encourage them to participate into

DEST. • Establish mechanisms for integration of training resources into DEST. • Develop student and professional access to the DEST and provide opportunities for

training.

Public Awareness

• Raise public awareness on key issues in taxonomy. • Sustain PR activities of EDIT. • Integrate EDIT partners’ staff devoted to the disseminating of scientific knowledge.

Establish mechanisms allowing sustainability of training and PA beyond EDIT 2.7.2 Progress towards objectives


- 67 -

Activity 8.1 Assessment of the training resources for taxonomy in Europe A prototype of the system for an interactive on-line catalogue of training resources for taxonomy has been developed and will be fully operational with continuity for the future and updateable by all concerned parties in M48 instead of M46, due to the departure of a staff member. The service is implemented under Drupal to be compatible with the CMS used in the EDIT network and is fully portable. The rights of the users are also managed by Drupal. The service will be added to the EDIT federation using the Single Sign On System deployed by WP5 (CSSO). In that way EDIT users that have already a login name and password for an EDIT service will be able to use the same credentials. New Users who ask access to the on-line catalogue can then also have access to the other services of the EDIT project if allowed by the other EDIT service providers. Activity 8.2 Mobilisation of European training providers into the Distributed European School of Taxonomy Continued in Activity 8.4. Activity 8.3 Establishment of pilot schemes for integration In 2008 (JPA-3), the Expert-in-training programme and Summer School were launched. Both training programmes will underpin the development of the DEST and serve as flagship initiatives to increase students’ interest in taxonomy and raise the awareness of the general public. Summer Schools The Summer Schools train students in ‘Best Field Practices’ for basic

taxonomic research, biodiversity studies, and conservation biology. It provides a unique opportunity for students to work with professional taxonomists and experience firsthand the challenges and rewards of fieldwork. The Summer School is open to MSc students and early stage PhD students from EDIT institutions or European universities / institutes. The Second EDIT Summer School 2009 was held in the period 19/07 – 02/08/2009

in the biodiversity-rich region of the Murànska Planina national park, (Gemer Region) Muráň, Slovakia. In response to the feedback received from participants of the First Summer School, a central theme was set forth: ‘From Field to Web - Studying biodiversity with the taxonomist's toolbox’,

Figure 8: GIS training

Figure 9: Collecting Fungi


- 68 -

covering the full work flow from specimen datasets to biodiversity insight. Several EDIT institutes were actively involved in the organisation (13-RBINS, 14-RMCA, 15-NBGB, 19-CUB, 12-SMNS). The programme brought together students and training providers from all over Europe. 18 professional taxonomists, affiliated to 13 institutes / universities in 10 European countries, gave lectures and field work to 20 students (9♀/11♂ - 13 nationalities) from 16 European universities / institutes in 11 European countries. The Summer School website gives background information, general organisational info, training programme, reports, Summer School video 2009, etc. (http://atbi.eu/summerschool) More detailed information can be found in the report C8.3.1.4 Report on the Second EDIT Summer School ‘From Field to Web - Studying biodiversity with the taxonomist's toolbox’ at www.atbi.eu/summerschool/?q=node/177. Expert-in-training programme The Expert-in-training programme provides young graduate students and early career researchers with an opportunity to acquire, and to strengthen, taxonomic research skills through individual on-the-job training. EDIT covers the costs of travel, accommodation, and provides a per diem to contribute towards living costs and training-related costs. The 2009-2010 programme (call 2) was launched in May 2009 and offered 31 trainings in 13 EDIT institutions and in 8 other partner institutions for trainees from European universities / institutes. Sixty one applications were submitted. Within the anticipated budget, 17 applicants were granted, equivalent to 36 weeks of training. Out of the 31 training offers, 18 different training subjects were solicited by the trainees. Most applied for (≥ 5) were ‘Advanced Biosystematics, Phylogenetics and Biogeography’ (NHN Leiden), ‘On the job training in family level identification of a hyperdiverse insect group: The Beetles (Coleoptera)’ (NHM London), Systematics of freshwater subterranean Malacostraca: Morphology, molecular systematics, and web-taxonomy (Univ. Ljubljana), Tropical Plant Identification Course (RBGK).

0

10

20

30

40

50

60

70

call 1 call 2

training subjectsEDIT institutionsother partnersapplicationsgranted trainees

Figure 10: Call 1 versus call 2


- 69 -

The complete list of traineeships offered during call 2 and a detailed description of the training are available at: http://www.taxonomytraining.eu. Training institutions and applicants’ institution country are illustrated in the maps hereunder. The report C8.3.2.3 Evaluation report on the pilot expert-in-training programme (Call 1&2) can be consulted at: www.taxonomytraining.eu/content/reports. Future perspectives: sustain the Expert-in-training programme beyond EDIT In addition to the large number of applications received in call 2, the evaluation feedback of the trainees shows that there is an overwhelming interest in these intensive trainings. Another positive outcome is that, to our knowledge, at least 2 trainees obtained a job thanks to the completion of an EDIT Expert-in-training! Furthermore, the programme generates future research cooperation. Activity 8.4 Implementation of EDIT's Distributed European School of Taxonomy This task will have its full development of activities in JPA5 with the launch of the 3rd DEST training component: the ‘Modern Taxonomy’ theoretical course programme (May 2010). The programme has been defined in dialogue with EDIT partners and other partners. The courses cover topics in basic taxonomy such as: nomenclature, identification tools and methods, describing species, phylogeny and evolutionary biology, data analysis and management, collection conservation, and relevance of taxonomy to other disciplines and to society in general. The ‘Modern Taxonomy’ programme will provide future professionals with a solid basic taxonomic training. The programme will be modular so that courses can be offered at several institutions. Still, one of the challenges will be to integrate the course programme into university curricula. In October 2009, the ‘DEST Taxonomy Training’ website (www.taxonomytraining.eu) was launched to inform on the EDIT training products and future training developments. Future plans are to develop a virtual campus with a communication zone for collaborative teaching and training. It is the intention to continue the DEST trainings beyond EDIT and even to extend the


- 70 -

programme by involving overseas partners (cfr Agreement to Collaborate with ABRS (Australian Biological Resources Study) and SANBI (South African National Biodiversity Institute). Activity 8.5 Public Awareness for the promotion of Taxonomy The IYB: planning, communication & launch The International Year of Biodiversity in 2010 is the opportunity to promote taxonomy to a large audience, including the general public and policy makers. It is also a good opportunity for the EDIT institutions to exchange and collaborate on PA matters. The planning phase for the IYB started early in the EDIT institutions. The communication campaigns had to be prepared. EDIT-PA arranged the partnership with the IUCN organisation Countdown 2010 and the use of the Countdown 2010 logo for all EDIT institutions. EDIT-PA obtained from the CBD International the permission of the non-commercial use of the official IYB logo and guidelines which were distributed to all EDIT partners. In this way EDIT-PA supported the individual communication campaigns of the EDIT institutions. The IYB programme of the institutions with the different outreach activities was planned well ahead as well. Here, EDIT-PA was able to participate to some planning meetings of the institutions and to inform about the BYSE calendar. EDIT-PA was invited to the IYB launches of the EDIT institutions, and was able to compare the diverse communication strategies. The IYB is a unique chance to study the communication about taxonomy/biodiversity in Europe and will be further analysed during 2010. BYSE 2010 The BYSE calendar remains the main integration tool for PA. Here, all partners can participate with their local programme. They receive a promotion of their events on European level and get an overview of events of the partner institutions and allied. The promotion and implementation has been very successful with over 150 events from 30 countries registered within the first 8 months. The calendar can be consulted at: www.countdown2010.net/byse. The calendar has been promoted via press releases of RBINS and Countdown 2010 (the collaborator of the calendar). Also the newsletters of the Ecsite network, BGCI, and BioNET International promoted the calendar. The Vifabio webpage lists BYSE among the top ten biodiversity websites (www.vifabio.de). Component reporting C8.5.6 deals with the implementation of BYSE. The EDIT Success Stories and Taxonomists’ Portraits The EDIT success stories have been launched and received their proper section within the EDIT newsletter. The topic is ‘best practices in engaging citizens into biodiversity/modern taxonomy’. The stories are based on outreach activities from EDIT and allied institutions. Here different outreach events are valorized and made known to a larger public. The engagement of citizens into biodiversity is needed for a well functioning society. Institutions as NHM and BG with their outreach programmes play an important role. The first stories have been published in newsletters 18 and 19 dealing with programmes to reconnect children to their local environment. One story takes place in Benin, the other targets all UK primary schools (www.taxonomy.eu/newsletter). Another type of success stories are the EDIT taxonomists’ portraits published on the DEST website. Short portraits about engaged taxonomists present this fascinating, diverse and joyful profession and stimulate students to consider a career in this field. The portraits are found at


- 71 -

www.taxonomytraining.eu under the heading: ‘Meet the EDIT taxonomists’. Component reporting C.8.5.7 explains the concept of the success stories. A taxonomy blog has been set up in collaboration with WP1 and WP6. Here scientists are invited to share their experiences and thoughts. The blog has been launched in December 2009 and is placed on http://systematicsblog.myspecies.info/. 2.7.3 Deviations from the project workprogramme and corrective actions C8.1.4.4 Report on the fully operational on-line catalogue of training resources for taxonomy with continuity for the future (due for M46) and M8.12 Fully operational on-line catalogue of training resources for taxonomy with continuity for the future (due for M46). The catalogue of training resources will be fully operational with a two month delay due to the departure of the staff member who was responsible for this milestone. M8.9 Second meeting of the committee of training providers (due for M44) has been postponed to M49 as all issues could be discussed and agreed by e-mail or phone. M8.11 MoU on PA (due for M41) has been postponed (M58) and will be discussed and validated by EDIT-PA officers during the discussion forum and will be sent to the BoD for approval (M58). JPA5 has been revised accordingly. 2.7.4 Lists of components23 & milestones A – WP8 components Delive

rable

no.


no.

Date

due

24

Actual

/Forecast

delivery

date

Link on

public

website (if

component

public)

Lead

contract

or

D27 C.8.1.4.2 Report on the consultation

interface for the on-line catalogue of

training resources for taxonomy

WP8 M41 M41 http://ww

w.e-

taxonomy.e

u/node/63

8

14-

RMCA

D27 C8.1.4.3 Report on the input interface for

the on-line catalogue of training resources

for taxonomy


w.e-

taxonomy.e

u/node/68

0

14-

RMCA

D27 C8.1.4.4 Report on the fully operational on-

line catalogue of training resources for

taxonomy with continuity for the future

WP8 M46 M48 Deferred

JPA 5

14-

RMCA

D27 C8.3.1.4 Report of the Second EDIT

Summer School


w.e-

13-15

BETAF



- 72 -

Delive

rable

no.


no.

Date

due

24

Actual

/Forecast

delivery

date

Link on

public

website (if

component

public)

Lead

contract

or

taxonomy.e

u/node/68

2

D27 C8.3.1.5 Status report of the Third EDIT

Summer School is available (outline and

curriculum)


w.e-

taxonomy.e

u/node/75

4

13-15

BETAF

D27 C8.3.2.3 Evaluation report on the pilot

expert in training programme (Call1&2)


w.e-

taxonomy.e

u/node/71

4

13-

RBINS

D27 C8.4.1.1 Text of draft course prospectus,

ready for its consideration by the BoD

WP8 M46 M46 RE 13-

RBINS

D27 C8.4.1.2 Draft agreement on course

prospectus of the DEST

WP8 M41 M41 RE 13-

RBINS

D27 C8.4.2.2 Report on identified sustainability

mechanisms for DEST beyond EDIT

WP8 M47 M47 RE 13-

RBINS

D28 C8.5.5 Recommendations and guidelines for

integrated approaches of PA activities

towards 2010 and beyond

WP8 M45 M45 CO 13-

RBINS

D28 C8.5.6 Promotion and edition of the BYSE

calendar including learnings for best

practices sharing and recommendation for

2010 implementation of partners initiatives

in a common framework


w.e-

taxonomy.e

u/node/61

0

13-

RBINS

D28 C8.5.7 Production of modern taxonomy

"success stories" showing the global value of

taxonomy research, European collections,

and the results obtained by cooperation


w.e-

taxonomy.e

u/node/68

1

13-

RBINS

D13 C5.071 Specification of a joint geospatial

training course (with WP5.4, WP7, WP8)


w.e-

taxonomy.e

u/node/63

7

14-

RMCA



- 73 -

Milestone no.

Milestone name WP no. Date due25

Actual /Forecast

delivery date

Lead contractor

M8.8 Second Summer School is conducted at European ATBI+M sites in liaison with WP7

WP8 M40 M40 13-15 BETAF

M8.9 Second meeting of committee of training providers

WP8 M44 M49 13-RBINS

M8.11 MoU on PA WP8 M41 M58 13-RBINS M8.12 Fully operational on-line catalogue of

training resources for taxonomy with continuity for the future

WP8 M46 M48 14-RMCA

M8.13 Second call of Expert-in-training programme is operational

WP8 M38 M38 13-RBINS

M8.14 Delivery of scratchpad courses (WP6) WP8 M44 M44 10-NHML M8.15 Delivery of georeferencing courses (in

liaison with WP5 & WP7) WP8 M40 M40 14-RMCA

25 Please indicate here the date as indicated in the Annex 1 – Description of work and/or the 3rd JPA.


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2.9 Deliverables list

Deliv.

no. Deliverable name Date due

Actual

/Forecast

delivery

date

Link on

public

website (if

deliverable

public)

Lead

participant

D12 1st report on EDIT Scientific output

M 40 M43 http://www.e-taxonomy.eu/node/678

NHML

D13 First report on Integrated Training for taxonomy


RBINS

D15 (update)

Final Report: Elements for research policy – new strategies for Taxonomy

M 43 M43 CO Chair of SPG ,

NHML

D16 Mechanism for Identifying Funding Opportunities and Streamlining Response

M 40 M 40 CO NNM

D17 Designs for EDIT as a

sustainable supranational entity M 47 M 47 RE MNHN

D20 Version 2 of the Internet platform for Cybertaxonomy


FUB-BGBM

D22 Report on progress toward stakeholder forum

M 47 M47 PP MfN

D23 Operational Pilot Information Service on European Taxonomic Workforce

M 36 M 42

UKBH

D21D2 update

Updated Roadmap - A business plan

M 47 M47 Merged with D17

MNHN


- 75 -

Section 3 – Consortium Management

3.1. Consortium management tasks and their achievement; problems which have occurred and how they were solved.

Progress follows on the lines established during the third year. Deliverables are syntheses of achievement, introduced by an executive summary. Most of them were delivered to meet the deadlines set in the 4th JPA, with a few exceptions duly justified in relevant work package reports. Regarding financial management, underspending is just under 350 000€ euros for a planned total spending of 3,010 000 million euros. This amount allows the flexibility requested for implementation of JPA 5 and of to finish of the planned activities. Partners are continuing to improve their use of the Information Management Tool, allowing a better follow-up during the year of the costs they incurred and the time they spent. Indeed the year 4 mid-term report showed better use of the resources in coherence with the planned budget. It also allowed to alert partners on the use of resources. The problem of Staff turnover identified in WP3, 5 and 7 for the previous years has not been a major problem in this fourth year.

3.2. Contractors: Comments regarding contributions, changes in responsibilities and changes to consortium itself, if any.

Regarding membership, during the 4th reporting period the Museum für Naturkunde (MfN) and the Royal Botanical Gardens Edinburgh (RBGE) joined the consortium, while UBER (Universität Berlin) withdrew. Regarding change in responsibilities, as from February 2010, WP2 leadership changed from Henrik Enghoff to Henrik AErenlund Peterson, while remaining within partner 2 UKBH. Christiane Quaisser, in charge of WP3.1 moved from Naturalis (partner 7-NNM) to partner 30 MfN, and joined the coordination of WP1.6 Simon Mayo, Team Leader from RBGE retired and was replaced by Alan Paton.

3.3. The section should also provide short comments and information on co-ordination activities in the period, such as communication between partners, project meetings, possible co-operation with other projects/programmes etc.


- 76 -

The nature of EDIT and its member institutions require an intensive work of coordination and communication to maintain the political and scientific will to work together. This has never been more important as now, when this will needs to be formalised into sustainable plans for the future. Formal institutional cooperation is formalised through Board of Directors and Network Steering Committee meetings, while a more general culture of collaboration is fostered by the internal side of the EDIT communication plan (through newsletters, websites and email communication). EDIT’s spin-off projects have reached a point in maturity and independence such that the network can now work with them to unlock potential far beyond the NoE’s initial range. For example, PESI will help maintain and structure the EDIT Expert and Expertise database. Similarly, ECBOL is in a consolidation phase, symbolised by the second ECBOL conference next June in Braga (Portugal). We also directly support our member institutions’ involvement in projects such as LifeWatch, CATE and Tree of Life. Specific elements of collaboration include participation in the workshops of the Global Science Forum of the OECD, notably with the steering group on scientific collections, as well as the Global Names Architecture initiative.


- 77 -

Mon

th 0

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th 1

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onth

2M

onth

3M

onth

4M

onth

5M

onth

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onth

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onth

8M

onth

9M

onth

10

Mon

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th 1

3M

onth

14

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onth

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th 2

7M

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th 2

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th 3

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th 3

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th 3

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th 3

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th 3

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onth

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th 4

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onth

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th 4

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onth

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th 4

5M

onth

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th 4

7M

onth

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Mon

th 4

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onth

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WP1 EDIT coordination and managment

from WP43.6. Integration of institutions taxonomic publications (new) (from WP4

3.5 Liaisons with international infrastructures

3.4 Large-scale networked instrumental facilities

3.3 Sustaining the cybertaxonomy process: Not yet applicable in months 12-30. Waits for progress in WP5.

3.2 The taxonomic information infrastructure network

3.1 Network of the physical taxonomic infrastructures

WP8 Training and public awareness

7.4 Operating the ATBI+M task force and evaluating relevant methods and techniques

7.3 Developing standards, protocols, and tools for conducting an ATBI+M programme

7.5 Sustaining the European ATBI+M task force and long term study sites

WP6 Unifying revisionary taxonomy

5.8 Publication support as platform components

5.7 Communication tools as platform components

8.3 Pilot schemes for integration

8.2 Mobilisation of training providers into the Distributed European School of Taxonomy

8.4 Implementation of EDIT's Distributed European School of Taxonomy

8.1 Assessment of training resources for taxonomy in Europe

1st year 2nd year

2.1 Information service on taxonomic experts, their expertise and ongoing and planned taxonomic research projects

2.3 Involving non-professional taxonomists, taxonomic societies and networks

(2.2 Information service on ongoing and planned taxonomic projects) - Now included in 2.1

1.6 Implementation of research strategy & science policy for taxonomy

2.4 Supporting integration of taxonomic research

WP3 Integrating and reshaping the infrastructure basis

7.2 Mobilising taxonomic resources and establishing the ATBI+M task force network

1.1 Establishment and operation of the administrating structure, incl coordination of the WPs1.2 Orientation, Sustainability and development of exploitation strategies for EDIT1.3 Communication (Internal/External)

WP2 Integrating and reshaping the expert and expertise base

1.4 Liaison programme1.5 Gender action plan

WP5 Internet platform for cybertaxonomy: tools, sharing, networking and integration5.1 Integration of information and science and technology (IST) departments; overall WP5 coordination

5.2 Creating the Internet Platform for Cybertaxonomy

5.3 Virtual Library of Taxonomic Literature and Documentation

5.4 Geographical platform components

5.5 Taxonomic-core Platform components

5.6 Descriptive and identification platform components

5.9 Specimen access platform components

6.1 Content development and expert taxonomic networks

5.10. Software quality and usability testing

6.2 Define what is needed from the cyber-environment

6.3 Community structuring by management committees and expert taxonomic networks

5th Year

8.5 Public Awareness for the promotion of Taxonomy

WP7 Application of taxonomy to biodiversity conservation

7.1 Assessing biodiversity inventory and monitoring needs, evaluating relevant taxonomic capacities, and raising stakeholder awareness

relay from WP4

3rd year 4th Year

3.4. Project timetable and status


- 78 -


- 79 -

ANNEX 1 – Plan for using and disseminating the knowledge Section 1 - Exploitable knowledge and its Use Not concerned. Section 2 – Dissemination of knowledge cat1: EDIT closed meeting / workshop cat2: EDIT organised meeting cat3: EDIT co-organised/sponsored cat4: EDIT represented / invited (talk / presentation)

Planned /

actual date Type Type & name

Type of

audience

countries

addressed

Size of

audience

Partner responsible

/ invovled Category

28 February

2009 infoday

Master info day of the Royal Belgian

Society of Belgium Bachelor students Belgium 120 RBINS/RMCA 4

3-6 March

2009 Conf ALTERnet Conference (Leipzig) policy-makers Europe MfN 4

9 March 2009 meeting UK Fungus Barcoding Workshop,

Edinburgh Research Europe 30

RBGE, CBS/RBGK,

NHML 3

9 March 2009 meeting Wageningen round table discussion on

DNA-B researchers national CBS, NNM 4

16-19 March

2009 Conf

DGaaE Conference, Göttingen

(German Society for General and

Applied Entomology)

student/researchers Europe 400 SMNS 4

17-19 March

2009 meeting PESI meeting WP4,5,6 (Oostende) researchers Europe 10 BGBM 4

19-20 March

2009 Meeting OECD-GSF SciColl (NHM London)

general directors,

collections directors,

science foundations

international 25 NHML, MfN, NNM 4

23-25 March

2009 Meeting CETAF 25 (RBG Kew) Research Europe 25 MfN, SMNS 4

24-25 March

2009 meeting CETAF (Kew) researchers Europe 25 all partners 4

26 March

2009 Meeting EDIT NSC (Kew) researchers Europe 15

MNHN, UKBH, CSIC,

NNM, BGBM, NHML,

RBINS, MfN, SMNS

1

27 March

2009 meeting Science Policy Group Meeting

Researchers /

Managers / Europe 10 CSIC, MNHN, 1

7-9 April

2009

worksho

p TRACEAM Summerschool Workshop Research, Education Europe 50 CBS 4

6-8 April Meeting CBD ABS7 (Paris) policy-makers International MfN 4


- 80 -

2009

21-23 April

2009

worksho

p

LifeWatch Workshop Network

Engagement (Zandvoort) policy-makers Europe 40 UvA, NNM, BGBM 4

27-28 April

2009 meeting GBIF (Copenhagen) researchers international BGBM 4

28 April 2009 infoday Lifewatch info day for Belgium scientists, decision

maker Brussels 50 RBINS,RMCA, NBGB 4

29 April meeting WP1/WP3 meeting (Amsterdam) researchers Europe 5 MNHN, UvA, CBS,

NNM 1

5 May 2009 infoday Ecosystem assessment policy at EU

level

scientists, decision

maker Brussels, EU 100 many 4

5-6 May 2009 worksho

p DFG Strategie Workshop (Bonn)

researchers, funding

body Germany 50 4

6 May 2009 Brainsto

rming

EPBRS meeting for strategies beyond

2010


maker Brussels, EU 100 many 4

6 May 2009 Worksh

op

BioSTRAT IPBES workshop

(Brussels) Europe MfN 4

11-12 May

2009 Meeting

OECD SciColl WG3 draft meeting

(NHM, London)

Researchers,

decision maker International MfN 4

11-14 May

2009 Meeting BHL-Europe kick off research/PA Europe

MfN, RBINS, RMCA,

NGBG, BGBM 4

13-15 May

2009

worksho

p

A Global Setting for European

Environmental Monitoring – Measuring

What We Must Manage (Copenhagen)

researchers, funding

bodies, ESF, ESA,

etc.

Europe 100 BGBM 4

14 April 2009

- 3rd May

2009

Conf EPBRS e-conference researchers Europe N/A all partners 4

19-22 May

2009 Conf EPBRS conf (Prague) policy-makers Europe N/A MNHN… 4

18-19 May

2009

worksho

p

LifeWatch semantic data integration

workshop

Researchers /

Managers international 40 BGBM, UvA, 4

19-20 May

2009 meeting LifeWatch WP5 meeting (Amsterdam)

Researchers /

Managers Europe 10 BGBM, UvA, 4

28-30 May

2009 Meeting

Lifewatch Management Committee &

Policy & Science Board (Bruxelles)

Researchers /

Managers Europe 30

MNHN, BGBM, UvA,

CSIC,… 4

30 May 2009 Meeting DIVERSITAS-D (Berlin) researchers Germany 25 BGBM, MfN 4

30-31 May

2009 Meeting

CBoL management Committee

(London) researchers International MNHN… 4

1-6 June 2009 Conf E-biosphere conference (London) researchers International

MNHN, NHML,

BGBM, SMNS, CSIC,

RBINS, RMCA…

3

17-18 June

2009

worksho

p GTI workshop (Paris) with BIONET researchers International MNHN … 3

20 June 2009 GEO-Day of Biodiversity (Ebern,

Germany) General Public National MfN, 4


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22 June 2009 Conf

DNA-Barcoding - the future of

taxonomy? 3e cycle Science

Symposium, University of Geneva,

Switzerland

Research Europe 60 CBS 4

22-23 June

2009

worksho

p

EDIT Scientific Publishing Meeting

(Bratislava)

Natural history

Publishing / editing

staff

Europe /

International 40

MNHN, RBINS,

RMCA, MfN, BGBM,

CUB, IBSAS…

2

24-25 June

2009 meeting EDIT NSC (Bratislava) researchers Europe 15

MNHN, UKBH, CSIC,

NNM, BGBM, NHML,

RBINS, MfN, SMNS

1

25-26 June

2009 Meeting CETAF EC (Bratislava) Research Europe MfN, SMNS 4

29 June 2009 DIVERSITAS-D (Leipzig) researchers Germany 40 BGBM, MfN 4

8-11 July

2009 Conf SPNHC Conf (Leiden) researchers International 4

10 July 2009 meeting EDIT DoCC (Leiden) Directors of

Collections Europe 20 EDIT partners 1

19 July - 2

August 2009

summer

school EDIT 2nd Summer School (Slovakia)

students /

researchers Europe 40

EDIT partners & non

EDIT partners 1

24 July 2009 Conf SYNTHESYS final event (London) Researchers /

Managers Europe 4

24 June 2009 worksho

p

Countdown2010 - European partner

assembly stakeholders Europe 50 RBINS 4

6-8 July 2009 Meeting EDIT international liaisons meeting

(Leiden)

directors/researcher

s International 6

NHN, NHML, RBINS,

NNM, SANBI, ABRS 2

8-11 July

2009 Conf

SPNHC conference incl. EDIT Session

(Leiden)

Researchers /

Directors of

Collections

International 250 NNM, UvA 4

6-7 July 2009 meeting

International Collaboration Meeting

SANBI/ABRS/WP3/WP6/WP8 on

AtC, Leiden

researchers, training International 6 NHN, NHML, RBINS 1

23. July 2009 Meeting Kick off meeting for the UK network:

IYB UK biodiversity for life

stakeholders

(museums,

organisations,

ministry)

national 100 NHML, RBGK, RBGE,

RBINS

4

10-12 August

2009 meeting BHL fall meeting

scientific managers,

librarians, IT Europe 30 RBINS, RMCA, NBGB 4

10-14 August

2009 Conf

Biosys Systematics Association meeting

(Leiden) researchers RMCA, RBINS, NBGB 4

28-29

August2009

symposi

um European Bird curator meeting

cuators, scientists,

collection manager Europe 50

RMCA, RBINS, NNM

& non EDIT partners 4

9-10

September

2009

meeting EDIT NSC meeting (Berlin) researchers Europe 15

MNHN, UKBH, CSIC,

NNM, BGBM, NHML,

RBINS, MfN, SMNS

1

29 sept - 1

October 2009 meeting EPBRS meeting (Visby, sweden) policy-makers Europe


- 82 -

2/ septembre

2009 meeting GSAP-DNHC meeting researchers global 10 BGBM 4

3-4

September

2009

meeting LifeWatch WP5 meeting (Berlin) researchers Europe 9 BGBM, 4

4 September

2009 infoday Lifewatch info day for Belgium


maker Brussels 50 RBINS,RMCA, NBGB 4

3-4 Sept 2009 meeting 4th OECD-GSF meeting on scientific

collections, Berlin

general directors,


science foundations

international 25 NHML, MfN, NNM 4

7-10

September

2009

Conf

Darwin’s Tree of Life Symposium,

Society for General Microbiology,

Edinburgh, UK

Research International 400 CBS 4

14-15

September

2009

meeting ViBRANT proposal preparatory

meeting researchers Europe 30 NHML, BGBM, UvA... 1

15-16

September meeting 4th ISTC meeting researchers Europe 21

BGBM, CBS, CUB,

HNHM, MfN, MNHN,

NBGB, NHM, RBGK,

RBINS, RMCA, SMNS,

UvA

1

17-19

September

2009

Symposi

um

4th Symposion for Research in

Protected Areas of the Hohe Tauern

National Park (Salzburg, Austria)

researchers International SMNS 4

17 September

2009 infoday

FP7 environment and climate change

call


maker Europe 3000 many 4

18 September

2009 infoday FP7 Africa call



27-29

September

2009

conferen

ce

/worksh

op

39. annual meeting GI researchers Europe 50 BGBM 4

28-29

September

2009

meeting SYNTHESYS II kick-off NA2

(London) researchers Europe 25 BGBM 4

28-29

September

2009

meeting ViBRANT proposal preparatory

meeting researchers Europe 4 NHML, UvA 1

28-29

September

2009

meeting kick-off of SYNTHESYS II NA 2 scientists, decision

maker Europe 25 BGBM, NHML… 4

1 October

2009 meeting review of KeytoNature


maker Europe 50 several 4

5-9 October

2009 meeting GBIF governing board (Copenhaguen)

scientists,

researchers intenational 4


- 83 -

7-8 October

2009 meeting LINCAOCNET (edible insects online)


maker intenational 10 RMCA, RBINS 4

9 October

2009 infoday FP7 ICT call on digital libraries



10-16

October 2009 conf Diversitas OSC (Cape town) researchers international MNHN… 4

13 October

2009 meeting PESI mid-term review (Brussels) researchers Europe 10 BGBM, UVA, 4

14-15

October 2009 meeting

Q-BOL Meeting, Dept of Primary

Industries Melbourne, Australia research unknown 50 CBS 4

14-16


Lifewatch Management Committee and

Policy and science board (Stockholm)

Researchers,

scientists managers Europe 35

MNHN, BGBM, UvA,

CSIC... 4

20-21

October 2009 Meetings

CETAF EC and General meeting

(Helsinki)

policy-makers,

researchers,

Directors

Europe All CETAF members 4

4 November

2009 Conf

Biodiversity Research Conference of

EU parlament (Brussels)


maker Europe MfN 4


CEPA meeting (Belgian communication

and education partners for the national

organisation of the IYB)

stakeholders,

education ministry national 20 RBINS 4

6 November

2009 infoday Marie Curie initiatives and fellowships



8-15

November

2009

Conf CBoL conference (Mexico city) scientists managers international MNHN… 4

9-11

November

2009

worksho

p

LifeWatch Data Providers Platform

meeting (Zandvoort) policy-makers Europe 40 UvA, NNM 4

9-13

November

2009

Conf TDWG Conf (montpellier) researchers international

MNHN, NHML,

BGBM, RMCA,

NBGB…

4

11-14

November Conf

Int.Biodiversity Conf. on Sustainable

Development (Papua, Indonesia) researchers international MfN 4

12-20

November

2009

LAPI (Medellin) researchers interanational BGBM 4

15-19

November

2009

Conf

Asian Mycological Congress, National

Museum of Natural Science, Taichung,

Taiwan


16-18

November

2009

meeting BHL meeting scientists, decision

maker Europe 40 RBINS,RMCA, NBGB 4

17.

November

2009

Launch RBINS Launch for the IYB Press, policy makers,

stakeholders national 150

RBINS, NBGB, RMCA,

, MNHN 4


- 84 -

20-21

November

2009

Conf Biologentag (Berlin) students /

researchers / teachernational 150 MfN 4

22-23

November

2009

meeting Caucusus proposal preparatory meeting Research Europe 6 BGBM, UvA 1

25.

November

2009

Launch IYB UK net launch of the IYB at the

NHML

Press, policy makers,

stakeholders national 250

NHML, RBGK, RBGE,

RBINS 4

25 November

2009

conf/pri

ze

Lifelong Learning

Programme,innovation and creativity

price europe


maker Belgium 100 RBINS,RMCA, NBGB 4

30 November

- 4 December

2009

Conf CBD Business&Biodiversity (Jarkarta) scientists, decision

maker international MfN 4

1 December

2009

worksho

p communicate biodiversity


maker Belgium 30 RBINS,RMCA 4

1-2

December

2009

worksho

p

NSF Dimensions of Biodiversity

workshop in Washington


maker International 50 MNHN, UvA 4

1-3

December

2009

worksho

p

Rome meeting on collections

digitisation

directors, curators,

local politicians national 70 outside EDIT 4

7 December

2009

Informat

ion stand

Lifelong Learning Programme, Info

Days (EU)

researchers/educatio

n specialists

International/

EU >250 RMCA,NBGB 4

9 December

2009

Worksh

op

Software development: Applikationen

for Smartphones to assess biodiversity

data (Munich)

students /

researchers / teachernational 12 MfN 4

10 December

2009 infoday

Lifelong Learning Programme, Info

Days Belgium french community

researchers/educatio

n specialists Belgium 40 RMCA, NBGB 4

15 December

2009 Meeting CETAF EC (Carvoeiro) Researchers Europe MfN, SMNS 4

15-16

December

2009

Conf EDIT Young taxonomist symposium &

second General Meeting Researchers international all EDIT partners 2

15 December

2009 meeting EDIT DoC core group meeting

Directors of

Collections Europe 10

MNHN, NHML, NNM,

RBGK, MfN 1

15-16

December

2009

poster

Moving toward sustainable cooperation

between EDIT, ABRS and SANBI

(Carvoeiro)

Researchers international NHN, NHML, RBINS 1

17 December

2009 meeting 6th meeting of the EDIT BoD Directors Europe all EDIT partners 1

17 December

2009 meeting 15th EDIT NSC meeting Researchers Europe 16 EDIT NSC members 1


- 85 -

23 December

2009 Conf

The 5th International Day of

Microbiology & 2009 Annual Scientific

Meeting of IMCAS. Beijing, China


11 January

2010 Conf

Kick Off IYB in Berlin (Internationales

Year Biodiversity) science-policy international 300 MfN 4

11-15 January

2010 meeting

Life Watch MC meeting, WP5 meeting

(Rome) Rresearchers Europe 30

BGBM, UvA, MNHN,

CSIC, 4

12 January

2010

worksho

p networking with KeyToNature

organisers of the

Summer School Belgium 7 RMCA 3

14 January

2010 infoday ICT-PSP general info day



19 January

2010 Meeting

Naturwissenschaftlicher Verein

Steiermark, Fachgruppe Entomologie

(Graz, Austria)

Research national 4

20-21 January

2010 Meeting EOL Governance (Leiden) science-policy international MfN 4

21-22 January

2010

worksho

p

EDIT tropical E-flora platfrom meeting

(Leiden)

directors/researcher

s international 30

NHN, NNM, NHML,

BGBM, NBGB, RBGE,

RBGK, SANBI, ABRS,

MOBOT

2

21-22 January

2010 Meeting UNESCO IYB (Paris)

science-policy,

researchers,

Directors, Decision

makers

international MfN 4

22 January

2010 conf

20 years of the Adrien Bauchau fonds

(grants for students, projects)


maker Belgium 100 RMCA 4

22-23

February

2010

Worksh

op Lifewatch workshop (Berlin) Researchers Europe MfN 4

25-29 January

2010 Conf

UNESCO Biodiversity Conference

(Paris)

science-policy,

researchers,

Directors, Decision

makers

international MfN 4

28 January

2010 Conf

Hidden Treasure Symposium, NCB-

Naturalis. Leiden, The Netherlands Research Europe 40 NHML, CBS 3

28 January

2010

Launch

&

worksho

p

Launch of the NCB - Naturalis

Biodiversity center & Workshop: A new

visitor group for NCB Naturalis

Launch: NL

stakeholders,

ministry. Workshop:

NL museum

directors

national

Launch: 800,

Workshop:

27

RBINS, Naturalis, CBS,

NHN, UVA, NHML 4

2 February

2010 infoday FP7 Led ERA infoday


maker Belgium 100 RMCA, NBGB 4


- 86 -

4 February

2010 infoday ICT-PSP info day on digital libraries


maker Europe 500 CETAF members 4

8-9 February

2010 Conf SciColl conference

general directors,


science foundations

international 80 RBINS, MNHN 4

8-12 February

2010 meeting Nomina 6 meeting researchers International 9 UvA 4

22 February

2010 meeting Diversitas Meeting researchers international BGBM 4

22-23

February

2010

worksho

p Life Watch D Workshop

researchers, policy

makers Germany 55

BGBM, MfN, UvA,

CSIC, 4

23 February

2010 meeting BioFresh kick-off meeting researchers Europe 40 UvA 4

25 February

2010 meeting CETAF executive meeting

scientific managers,

librarians, IT Europe 10 several 4

future

activities

12 March

2010

worksho

p

e-Flora exemplar groups (BGBM

Berlin) researchers international 15

BGBM, RBGK, RBGE,

NHN, NBGB 2

25 March

2010

worksho

p

The components of the EDIT Platform

for Cybertaxonomy (introduction) researchers France 25

BGBM, MNHN,

RMCA 2

24-25 March

2010 Meeting EDIT 16th NSC Meeting researchers Europe 16

All EDIT NSC

members 1

26-28 March

.2010 meeting Life Watch MC meeting (Aarhus) researchers Europe

BGBM, RBINS,

MNHN, UvA

18-21 May

2010 meeting

PESI meeting, steering committee, WP3

focal point meeting (Erdine, Istanbul) researchers Europe BGBM, ,UvA a

27 May 2010 meeting BHL Review researchers International BGBM

31 May 2010 meeting SPNHC (Ottawa, Canada) researchers International BGBM

2-4 June 2010 Conf

ECBOL 2 - International Year of Biodiversity, University of Minho, Braga, Portugal

http://ecbol2.bio.uminho.pt/ECBOL_

2.html

researchers Europe

EDIT participants and

other barcoding

intitiatives

2

21-22 June

2010 Meeting 17th EDIT NSC researchers Europe 16 EDIT NSC members 1

22-23 June

2010 Meeting EDIT 6th BoD Meeting Directors

Europe /

International 30 All EDIT institutions 1

25-26 August

2010 meeting Flora Malesiana (Singapur) researchers BGBM 4

13-15

September

2010

meeting LifeWatch MC meeting Researchers,

Managers BGBM 4


- 87 -

20-22

September

2010

meeting Tools for identifying biodiversity:

progress and problems

researchers, policy

makers, general

public on education

Europe 150

MNHN (collaboration

with Key2Nature and

STERNA)

3

5-6 October

2010 meeting CETAF scientific managers All CETAF partners

11 October

2010 GBIF governing board

Researchers,

managers BGBM 4

24-24

November

2010

Life Watch MC meeting Researchers,

Managers

BGBM, RBINS,

MNHN, UvA 4

January 2011 Confere

nce

EDIT General meeting and scientific

Conference

Researchers, policy

makers, press International 200 All EDIT participants 2

17-18 January

2011 meeting LifeWatch MC meeting

Researchers,

Managers

BGBM, RBINS,

MNHN, UvA 4

Planned /

actual date Type Type & name Type of audience

countries

addressed

Size of

audience

Partner

responsible

/ partner

involved

Category

18 May 2009 Web

launch BYSE Catalogue launch web users International web RBINS 2

18 May 2009 Press

release

BYSE Catalogue launch by

RBINS and Countdown 2010 journalists

Belgium and

International RBINS

From May

2009 on Flyer

BYSE information flyer (paper

and digital version) EDIT institutions and allied

all over

Europe 1500 RBINS

25-26 June

2009 Press event ATBI press day journalists France 20

SMNS,

MNHN 3

June 2009 Article Piemonte PARCHI (186): "Ho

un nome quindi eisto" researcher, tourists International

SMNS,

MfN

June 2009 flyer

EDIT modern tools for

taxonomy: Plaform for

Cybertaxonomy - The

taxonomic workflow brought

to the internet

researchers/policy makers International BGBM 4

June 2009 flyer


taxonomy: International

Cichorieae network - An

Exemplar group for modern

taxonomy

reaearchers/policy makers International BGBM 4

June 2009 flyer


taxonomy: Cybertaxonomy

Geoplatform -Mapping out

researchers / policy makers International BGBM 4

Media & Press events


- 88 -

the diversity of life

June 2009 flyer


taxonomy: Specimen Explorer

for taxonomists - Primary

biodiversity data and the

Common Data Model


June 2009 flyer


taxonomy: Desktop

Taxonomic Editor - A word

processor for taxonomists


July 2009 Brochure

WGL Brochure about

Evaluation of the Sixth EU

Framework Programme

policy-maker Germany MfN

July 2009 Newsletter ATBI newsletter researchers International web SMNS,

MfN

August 2009 video clip EDIT Summerschool in

Slovakia students/researcher International

CUB, MFN,

SMNS

September

2009 Publication

EDIT-Training the next

generation of taxonomists. In

Practice - Bulletin of the

Institute of Ecology and

Environmental management:

Sept. 2009, N°65, p.15-16.

students/researchers (field

biologists & ecologists) International RBINS

22 October Web

launch

DEST Taxonomy Training

www.taxonomytraining.eu web users International web RBINS 2

October 2009 Web

launch

update website of the Summer

School web users International web RMCA 2

October 2009 Newsletter BioNET International

promotes BYSE web users Global RBINS

November &

December

2009

Newsletter Ecsite newsletter promotes

BYSE

Science centers and museums in

Europe Europe RBINS

December

2009 Web page

Vifabio lists BYSE among

Top Ten Biodiversity pages web users Global RBINS

December

2009 poster

not only bird migrate (mobility

programs) participants International RMCA 4

1 December

2009 Article

EDIT Newsletter 18: EDIT

reaching out to southern

counterparts: perspectives

from the ABRS and SANBI all international

SANBI,

ABRS

2

10 December

2009

flyers &

posters

Flyers Summer School + A3

posters

students/researchers/participants

at conferences International

web and at

meetings RMCA 2

18 January Web video of the Summer School web users International web RMCA 2


- 89 -

2010 launch

February 2010 Book ABCTaxa: ATBI+M field

methods manual

field biologists, students, park

managers International

SMNS,

MFN

February 2010 web site

update EDIT WP5 site:

http://wp5.e-

taxonomy.eu/blog/

web users International web BGBM

February 2010 web site

update developer Wiki:

http://dev.e-

taxonomy.eu/trac/wiki/

web users International web BGBM

February 2010 Web

launch

New Platform access site:

http://wp5.e-taxonomy.eu/ researchers, web users International web BGBM

February 2010 Web

launch

Bundles setup site:

http://wp5.e-

taxonomy.eu/cdm-setups/

researchers, web users International web BGBM

future activities

March 2010 newletter SPNHC newsletter researchers International BGBM 4

March 2010 newletter GfBS newsletter researchers International BGBM 4

2009 "popular"

article

Stuttgarter Beiträge zur

Naturkunde, Serie C, 68:

"EDIT in Mercantour" (p.40-

41)

researcher, greater public Germany SMNS


- 90 -

Section 3 - Publishable results Not applicable


- 91 -

ANNEX 2 - Executive summary EDIT meetings

See annex 2 separate document.


- 92 -

ANNEX 3 - Performance Indicators

Key performance Indicators 3rd RP 4th RP

1 To reduce fragmentation and to transform taxonomy into an integrated science

1.1 Number field days of EDIT institutions actively involved in ATBI+M pilot sites (new 1.2)

218 (2007), 310 (2008) 325 (2009) Gemer=159, PNM/PNAM=166

1.2 Number of institutions, organisations, SME's, individuals involved in EDIT training programmes (new1.3)

summer school: 21 trainers from 13 inst.: 6 EDIT - 7 non-EDIT; expert-in-training: 21 training offers from 9 EDIT inst.

summer school 18 trainers from 13 inst.: 14 EDIT - 4 non-EDIT; expert-in-training: 31 training offers from 21 inst.: 13 EDIT inst. - 8 non-EDIT inst.

1.4 Examplar expert networks (number of participants, number of co-operating institutions – taxonomical input & data provider) for scratchpads (new 1.5)

94 Scratchpads, 754 Users 155 scratchpads, 1700 registered users

1.5 Number of hits on the EDIT website => see 5.2.1 approx 2000 per months approx 3700 per months

2 To strengthen the scientific, technological and information capacities needed for Europe to understand how biodiversity is modified through Global change

2.1 Number of ATBI+M records available through GBIF 10619 23542

2.2. Number of downloads of EDIT platform components

CDM Dataportal (2); CDM Community Store & CDM Library (19); EDIT Desktop Taxonomic Editor (65); Security Components - Shibboleth Proxy (4)

CDM Dataportal (14); CDM Community Store & CDM Library (4787); EDIT Desktop Taxonomic Editor (2896); Security Components - Shibboleth Proxy (0)

2.3 Number of jointly developed platform components (web services, web applications, desktop applications)

5 jointly developed platform components 8 jointly developed platform components

2.4 Number of talks / presentation on EDIT activities presented outside of EDIT 62 105

2.5 Number of MoUs for improving collaboration and integration of IT departments within EDIT, and number of signatories (old 2.4)

Number of MoUs: 2 (Drupal, ABCD); Number of Signatures: 16 (signed by 10 Institutions)

Number of MoUs: 4 (Drupal, ABCD, Libraries, Global Names); Number of Signatures: 40 (signed by 14 Institutions)

2.6 Number of public visitors to CDM-based portals, e.g. Exemplar Groups (average stay, number of pages viewed)

Cichorieae Portal (visits: 410; visitors: 223; average stay [seconds]: 253); Diptera Portal (visits: 460; visitors: 118; average stay [seconds]: 275); Palmae Portal (visits: 1476; visitors: 358; average stay [seconds]: 313)

Cichorieae Portal (visits: 9108; visitors: 2361; average stay [seconds]: 689); Diptera Portal (visits: 2643; visitors: 326; average stay [seconds]: 1040); Palmae Portal (visits: 7949; visitors: 2412; average stay [seconds]: 726)

2.7 Quantity of data accessible through CDM-based portals (no. of names, number of taxa, no. of images, etc.)

539539 data accessible through CDM-based portals. Data items please see annex 4566526

2.8 Number of Scratchpads, number of registered users, number of pages. (Could extend 2.10 by adding mean time on site, mean time on page, number of first-time visitors. But we can't break that between registered and pubic. )

94 Scratchpads, 754 Users, 130828 data objects (pages) 155 scratchpads, 1700Users, 166664 data objects

3 To progress toward a transnational entity by encouraging durable integration of the most important European taxonomic institutions, forming the nucleus of excellence around and from which institutions and taxonomists can integrate their activities.


- 93 -

3.1. sum of institutional budgets (incl. personnel) allocated to EDIT" (current project and later sustainable infrastructure) ?

Y1: 3.278.462,40 total costs (of which 1.797.655,01 eligible); Y2 5.391.347,60 total costs (of which 3.532.940,26 eligible) and Y3 5.421.855,18total costs (of which 3,557,484,11 eligible costs)

Y4: 5102744,03 total costs (of which 3431306,58 eligible)

3.2 Number of MoU signed by EDIT institutions ABCD: 10; DRUPAL: 7; ViTAL: 1

ABCD: 14, DRUPAL: 10; ViTAL 10; GNOMA: 13; GAP: 2

3.3 Number of experts entered in database and number of hits on the database (new)

0 but building 2500 entries

4 To promote the undertaking of collaborative research developing, improving and utilising the bio-informatics technologies needed

4.1 Number of papers co-authored by at least two EDIT institutions (new) ask Daphne

4.2 Number of individual contributors to scratchpads 754

1700

4.3 Number of individuals contributing data to CDM 6

6

4.4 Number of applications for EDIT grants / number of exchange grants

4 women in science grants out of 4 (8000€ total) 1 life/ work balance grant out of 4 (200€) for 2008. In 2009, 6 awards out of 16 application received will be granted for the 2nd women in science call. 1st round of Integrating Research Grants in 2008, 13 application were received and 9 received. For Summer School 1 : 30 applications were received online and 20 grants were awarded, For the expert in training, 10 applications were received and 9 grants awarded

For Summer School: 30 applications were received online and 20 grants were awarded, For the expert-in-training, 61 applications were received and 17 grants awarded, For GAP activities: 6 Work/life balance grants awarded out of 7 (2 males & 4 females). 16 Applications for the Women in Science scheme were received, 5 were awarded.

5 To create a forum for stakeholders and end-users for taxonomy in biodiversity and ecosystem research

5.1 Number of public visitors to the scratchpads, average stay, number of pages viewed (new)

84,893 visits, 5.1 Pages/Visit (staying for 4 minutes), 433,206 pages viewed

163,203 visits, 3,92 pages/visit, 639,641 pages viewed

5.2.1 Number of visits to the EDIT website, length of stay, number of pages visited (new)

(over 3.5 months): 6,587 visits, 24,787 pages viewed, 3.76 pages/visit

32,356 visits, 93,028 pages viewed, average length of sta of 3mn11s.

5.2.2 Number of newsletters distributed (paper + number of downloads). (new) 400 distributed in print, 1000 online per issue

500 print run, 1000 online per issue.; 2x ATBI-newsletter (online), each issue distributed electronically to 850 addresses

5.2.3 Number of visitis to WP5, WP6 & WP 7 websites

WP5 Blog: 45376 visits; WP5 Wiki: 38678 visits; WP5 CDM-Model: 2818 visits / editwebrevisions.info: 5670 views; scratchpads.eu: 11300 views / WP7: 5032 since 01.09.07

WP8: in 2 month period: 212 visits, 948 pageviews / WP5 Blog: 49914 visits; WP5 Wiki: 31728 visits; WP5 CDM-Model: 18991 visits / editwebrevisions.info: xxx views; scratchpads.eu: xxx views / WP7: 11561

5.3. Number (/ percentage) of non-EDIT researchers actively involved in ATBI+M assessment teams (non EDIT researchers / total number of researchers)

2007: 12 (32.4%) 2008: 37 (43.0%) 2009: 98 (70.5%); Gemer 15 (57.7%) out of 26, PNM/PNAM 83 (73.4 %) out of 113

5.4. Access (number of visits) to the ATBI+M websites 5313 (PNM/PNAM), 540 (Gemer), both since 01.09.07 11743 (PNM/PNAM), 1406 (Gemer), both

since 01.09.07 5.5. Number of scratchpads WP6 94 155

6 To promote the spreading of excellence to fulfil the needs of biodiversity and ecosystem research for taxonomy based information


- 94 -

6.1. Participation of staff from outside the network in EDIT meetings 141 visits from non EDIT participants,

from 95 non EDIT institutions

6.2 Number of international conferences, workshops etc. in which EDIT participates as such

74 73

6.2.1 Number of international meetings (co)-organised by EDIT 8 21

6.3 Evolution of respectively, number of EDIT trainees and of non-EDIT trainees

summer school 3 EDIT and 17 non EDIT / expert-in-traing: 9 EDIT trainings. In JPA4 this call will be open to non EDIT applicants

summer school: 2 EDIT and 18 non EDIT / expert-in-training: submitted applications: 28 EDIT 33 non EDIT - granted applications: 8 EDIT 9 non EDIT

6.4 Evolution of number of new training opportunities (course modules) organised specifically by EDIT

2007: 0; 2008: 2 programmes running (summer school, expert-in-training)

2009: 2 programmes running (summer school, expert-in-training) /summer school: one per year / expert-in-training: training offer went from 21 (2008) to 31 training subjects

6.5 new webpages produced by EDIT about EDIT (counting n° of nodes, different subwebsites etc.) => measure of webimpact by EDIT

Central website: appr. 500 nodes.

Central ATBI website : appr. 1000 nodes (concerns following webpages: http://www.atbi.eu/wp7/ ; http://www.atbi.eu/mercantour-marittime/ ; http://www.atbi.eu/gemer/ ; http://www.atbi.eu/summerschool/ )

6.6 Number of IT departments represented in the ISTC 18 institutions 18 institutions


- 95 -

ANNEX 4 - List of Acronyms

A

ABRS (Australian Biological Resources Study)

Agreement to Collaborate (AtC)

All-Taxa Biodiversity Inventory and Monitoring (ATBI+M)

B

BHL - Biodiversity Heritage Library

Board of Directors (BoD)

BOLD (Barcode of Life Database)

BYSE (Biodiversity Year of Schedules Events 2010)

C

CATE (Creating a Taxonomic e-Science)

CBD (Convention for Biological Diversity)

CBOL (consortium for the barcode of Life)

Committee and the Directors of Collections Committee

(DoCC)

Common Data Model (CDM)

content management system (CMS)

D

Danish Data Protection Agency (DPA)

Distributed European School of Taxonomy (DEST)

E

EBOLD (European Barcode of Life Database)

ECBOL (European Consortum for the Barcode of Life)

Encyclopedia of Life (EoL)

EPBRS (European Platform for Biodiversity and Research

Strategy)

Expert-in-training programme (EiT)

G

GBIF (Global Biodiversity Information Facility)

Gender Action Plan (GAP)

Global Names Architecture (GNA)

I

Information Science and Technology (ISTC)

Integration Research Grants (IRG)

International Barcode of Life (IBoL)

International Cichorieae Network” (ICN)

IYB (International Year for Biodiversity)

M

Material Transfer Agreement(s) (MTA)

Memorandum of Understanding (MoU)

N

Network of European Leading Labs (NELL)

P

PESI (Pan European Species-directories Infrastructure)

Q

QBOL (Quarantine Barcode of Life)

S

SANBI (South African National Bioinformatics Institute)

Science Policy Group (SPG)

Scientific Collections International (SciColl)

SDD (Structured Descriptive Data)

SPNHC (Society for the Preservation of Natural history

Collections)

SYNTHESYS (Synthesis of Systematic Resources)

T

TCS (Taxonomic Concept Schema)

TDWG - Biodiversity Information Standards

Terms of Reference (ToR)

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