Scientific Advisory Council Padova 30-31/05/2007 Report from the Project Leader to the Scientific Advisory Council Simon Tillier, MNHN, Paris

Scientific Advisory CouncilPadova 30-31/05/2007

Report from the Project Leader to the Scientific Advisory Council

Simon Tillier, MNHN, Paris


Strategy elements

• Progress toward integration based upon– Making up tools for integrated research work, in relation with the

development of new distributed infrastructures– Providing a platform where directors can communicate and

make decisions in common, and administration tools (MoUs etc)– Proposing fora and projects where taxonomists can meet and

elaborate work in common– Inter- Network activities / participation in international initiatives – Communicating about taxonomy– Training

• Elaborate a vision for the future of taxonomy


1. Reduction of fragmentation

and transformation of taxonomy into an

integrated science


1.1. Building the Internet Platformfor Cybertaxonomy (WP5 + WP6/WP7/ WP2)

• Survey of partner institutions nearing completion [D5.01, 02, 04, 19 ]

• Modelling of taxonomic workflow for revisions [D5.08] and inventories [D5.10] nearing completion; interviews with over 20 taxonomists in 10 partner institutions. Modellers Group integrates models (workshop).

• Workflow to be used in user interface to locate informatics tools and services.

• Biodiversity Service and Application Tracker Website [D5.51, see Handout] has been launched and first test results are being submitted by personnel in Paris [D5.47] and Bratislava

• Basic platform design formulated and published in last EDIT Newsletter• Survey of communication tools completed [D5.51]. Pragmatic proposal for

common use of the content management system Drupal; used already for WP6 Scratchpads and WP5 Tracker

• For WP2 Expert database WP5 currently asses requirements; use of Drupal probable


1.1. Building the Internet Platform ..

• Taxonomic core (names / taxa) still under discussion [D5.44]. Proposal to use Berlin Model (WP6 exemplar group data successfully imported), alternative WP6 Scratchpads or combination of both. Requirements formulated by WP5 workshop. Conclusion now discussed in Developer Group and ISTC: to achieve true integration and openness for community efforts: design and implementation of new taxonomic core based on object oriented technologies (technical solution resembling approach of CATE). Strongly oriented towards TDWG Standard Architecture to provide cohesion with GBIF, EoL and other initiatives.

• Revisionary taxonomy data portals still being discussed within WP6. Webpage mock-ups have been constructed for exemplar groups by WP5 and 6. Development will continue based on existing databases to guide WP5 developers in building the output mechanisms for the platform. Drupal, CATE, Solanaceae Website candidates for interfacing.

• Inventorying data portal requirements tested by WP7/WP5 collaboration. For data capture tools existing solutions are evaluted that cover needs manifested in pilot software. Use of Drupal / Scratchpad-like approach for output envisioned (under discussion).


1.1. Building the Internet Platform ..

ViTaL (Virtual Taxonomic Library):• Report "Existing Digital Library Activity, Principles and Practice“ [D5.17]• IPR consultant appointed in April• Statement of requirements for bibliographic platform components to be

released [D5.18]. Incorporates user survey (64 taxonomists, 19 countries), will avoid duplication of efforts in BHL, and cover the needs of platform software interfacing, especially with literature scans (also single pages)

Geographic platform:• Development in Madrid started mid-February. • Extended catalogue of open-source European digital maps; standardized and

exported into GIS layers, will be made available by CSIC server. Drupal-Tracker considered for access, documentation and user annotation

• Beta version of application able to visualize georeferenced taxonomical data according to the Open Geospatial Consortium standards.

• A task group meeting with representatives of WP7 and Madrid, Tervuren, Warsaw and Berlin took place 14-16th May 2007 and delivered a report


1.2. Toward a common work model for taxonomic revisions (WP6)

• Exemplar groups and Web revisions

• Scratchpads available

• Meetings– integration with WP5– taxonomic commonalities

• Web site


1.3. Modalities for common work and integrated work flow for inventories (WP7)

• 2nd WP7 Workshop, Stuttgart, 14-16 March 2007

• WP7 / WP5 Modelling workshop, Budapest, 7-9 May 2007

• WP7 in conjunction with WP5 are testing appropriate tools for ATBI+M (i.e. Recorder, BioOffice)

• Planned WP4 / WP7 «ATBI+M field recording techniques and protocols workshop»,June 13-16 2007 El Ventorillo, Spain


2. Strengthening the scientific, technological and

information capacities needed for Europe to understand how biodiversity is modified through Global

change


• Follow-up from symposium on taxonomic networks and societies in Slovakia March 26-27 2007

• WP2 expert database will be built by WP5 developers

• Cooperation / coordination with existing and planned expert databases: SYNTHSYS NA B, ETI, German GTI, DAISIE, GBIF

• 2nd Symposium, planned ultimo 2007 / primo 2008, on taxonomic networks / societies

2.1. European taxonomic expert and expertise basis


2.2. Integration of infrastructures (1)

• Physical infrastructures (WP3.1.)– Integration

Inventory of opinions of directors (CETAF) about expectations, possibilities and mechanisms with respect the integration of various components in institutional operations.

Article in 2nd EDIT newsletter, April 2007.

Report on EDIT website (24 May 2007)

Preparation of a call for advice on the structure, finance, and operating system of EDIT as a virtual European organisation

In-depth interviews at the director’s level.

– Biological Resources CentresWP 3.1b discussion report to be presented at the Workshop Scientific Collections (12, 13 June 2007) of the OECD Global Science Forum.


• Information backbone (WP3.2a)– Architecture of an information backbone

Contributions to a ‘globally unified access system’ for unamgious cross-linking of (taxon) name objects and their attached data types Presented at EoL summit at Crete (Feb 2007) with the proposal for a 3-layercross-reference structure concept. Agreed by GBIF, EoL, ZooBank, COL and TDWG representatives

– Identification of the components, and definition of functionalities for a new generation infrastructureContributions to the proposal for a preparatory project “Life Watch” biodiversity research infrastructure

– Preparation (also with other partners) of funding plansContributions to the SpeciesBase proposal

Drafting of a FP7 proposal for a ‘pan-European Species-directories Infrastructure’ (PESI), to be submitted early 2008.

Integration of infrastructures (2)


• European Taxonomic Information Services (WP3.2b)– Common management approach for the continuation,

maintenance and integration of the Pan-European species checklists

- Workshop “The future of taxonomy - the role of focal points in taxonomic information infrastructure networks” in Smolenice (Slowakia), March 2007.

- Outline of national focal point network and interim board meeting (terms of reference) to be discussed in Tromsø (July 2007)

– Promotion of checklist updates and validation- Preparation of action plans by the checklist programs.

- Mitigation of Fauna Europaea service to a new server for a more sophisticated and stable (Linux) platform. (Investments not paid by EDIT). New update server currently being tested to support update and validated procedures

– Preparation of plans (and funding proposals) to expand the checklist services (in data and in geographical scope)

- Inclusion considered in the plan for a ‘pan-European Species-directories Infrastructure’.



• Bioinformatics toolbox (WP 3.2c)

Design of a user-friendly bioinformatics toolbox for interpolating and processing phylogenetic trees, matrices, DNA barcodes, and other relevant biodiversity data to facilitate research and conservation outcomes.

Finished with submission of report.

Inclusion in WP6 products in discussion.




• DNA barcoding (WP3.4)– Coordination of DNA-barcoding in Europe for all

organism groups (also in support of CBOL)• Website ECBOL launched: http://www.ecbol.org/• Feeding the website with data about current and planed European activities

are ongoing. • EDIT - DNA Barcoding in Europe, conference in Leiden, 3-5 October 2007• Flyer is out and registration started

– Models for DNA banks and testing of new storage system

– Starting plans for macro/micro arrays and bio-sensors• Both subjects to be addressed by various speakers at the

conference.

http://www.ecbol.org/



• Liaison with international infrastructures (WP 3.5)

– Towards communication, cooperation and information exchange to develop a reference framework for EDIT

• Plan developed for established communication with other European and international infrastructures.

• Ongoing inventory of networks, organisations, contact persons to prepare for selected site visits

• Contributions to WP1


2.3. Integration of IT departments

• Meeting of the Information Science and Technology Commission (ISTC) in Month 8 had 14 of the 27 EDIT partner institutions attending (plus a delegate from RBG Edinburgh)

• The ISTC has published its recommendations

• The ISTC has endorsed the second WP5 18 month plan as described at the time of the meeting

• WP5.1 IT report is nearing completion – 15 EDIT partner institutions have been interviewed


• Assessment of the training resources for taxonomy in Europe

– 143 answers exploitable. Interviews and surveys provided 94 additional courses and 60 additional contact persons

– Northern and southern European countries are less represented – An important part of courses are held in English– Many respondents target a European and international audience as well as a national one. 7%

held in countries outside Europe– Closer collaboration between museums and the academic world is recommended. – Societies and networks little represented, their inclusion in EDIT should be encouraged. – Sustainability to be explored– Teaching methods highly conventional : set-up of an e-learning facility should be explored. – A large proportion not exclusively focus on taxonomy (only 29% is exclusively taxonomic). – Many courses do not cover nomenclatural rules

• Strategy and Call to potential training providers

• Planned «EDIT summer school» WP7 + WP8 Summer 2008, Mercantour/Alpi Marittime, France/Italy, for students from taxonomy related disciplines, on European taxonomy: methods and networking

2.4. Integration of training


3. Progress toward a transnational entity

by encouraging durable integration of the most

important European taxonomic institutions


• Board of Directors (SAC, Network Office, NSC)

• Legal– CSIC report– ESFRI report on the pros and cons of about 10 options– Should be considered together with the CETAF (two levels

structure?)

• Funding

• General meeting 2008


4. Promotion of the undertaking of collaborative

research


4.1. Emerging technologies and challenges for taxonomic research

• Workshops on new techniques / methods relevant to WPs: WP4-WP7 on collecting methods (june 2007), geographical components (WP5, WP7), barcode (WP3, oct 2007) etc.

• General symposium on Perspectives and future trends in Taxonomy (Conceptual challenges and technical opportunities) planned 2008 (WP4). Topics already planned but Steering Committee will be able to interact with Future Scoping Group.

• Participation in workshops : TDWG, Diversitas AToL/CBoL (Duke Univ), EMBO (Roma)


4.2. Taxonomic Inventories

• 2nd WP7 Workshop, Stuttgart, 14-16 March 2007

• Preparations for ATBI+M fieldwork: 250 scientists from > 70 institutions already subscribed to stay informed

• Activities start this field season in Mercantour/Alpi Marittime– The MoU to be signed – Terms of Reference available for individual signature– The permits are underway

• Gemer (Slovakia) and Spessart (Germany) are ready to go

• Activities in marine habitats will follow, through pro-active MarBEF-EDIT network overlap


4.3. Inter networks collaboration

• MarBEF General Assembly, May 14-16 – WP6 : MARBEF will use one WP6 scratchpad to

mount a data-gathering template, with a view to linking back to ERMS when development time allows.

– WP7: decision to work together in two EU marine sites (Rhine delta, plus Mediterranea)

• Alter-net LTER workshop, march 2007

• Life Watch elaborated through inter-network collaboration


5. Creation of a forum for stakeholders and end users for

taxonomy


5.1. The EDIT website(s)

http://www.e-taxonomy.eu• general information, calendar, events, documents, fora, access to WP sites

http://wp5.e-taxonomy.eu • “blog”, “wiki” to document all WP5 activities and operations, forums stemming from ISTC

debates on definitions of terms, certification categories and platform components

http://wp6.e-taxonomy.eu • scratchpads, web revisions, meetings

http://wp7.e-taxonomy.eu • Up-to-date ATBI+M information, All proposed ATBI+M sites, Workshop reports, Interactive

forum, Online fieldwork reports

Set-up of the WP7 webserver: www.atbi.eu• Close WP5-WP7 collaboration, Databases with connection to off-line interfaces, Connection

with WP5 (cyberplatform) and GBIF

http://www.e-taxonomy.eu/

http://wp5.e-taxonomy.eu/


5.2. The bimonthly EDIT newsletter

• Announced by email on various lists, downloadable

• Sections : news, events, articles

• Contents rapidly increasing


6. Promotion of the spreading of excellence

to fulfil the needs of biodiversity and ecosystem research for taxonomy based information


6.1. International and national fora

• EPBRS/BIOTA workshop, Leipzig, 8 May

• Sustainable Neighbourhood – from Lisbon to Leipzig through Research (L2L), Leipzig, 9-10 May

• CBD SBSTTA, Paris 1-9 july 2007


6.2. International networking

• WP7: Jakarta, Indonesia: extra-EU networking, 2-5 AprilEDIT presented to 6 institutions in 4 days as « portal » for non-EU countries to EU expertise

• WP3: link with CBoL (workshop planned Leiden, oct 2007) + Ex Com

• Diversitas BioGenesis

• EoL?


6.3. Interfaces with society

• Upon SAC recommendation

• Interfaces with society

• Stakeholder Liaison Officer

• Work plan: addressing interfaces


• Analysis and development of strategies for interaction with stakeholders, PR and PA

Look Inside and outside the taxonomic community-Stakeholder / user map-Investigation strengths and weaknesses-Integration study

PR and communication plan with RBGK (+ WP8)

• Implementation Advise, support and initiating Workshops and other activities with stakeholders

Interfacing with society: work plan


7. Providing a vision for the future


7.1. Future Scoping Group• Decided by the BoD

• 6-8 people, Chair Ricahrd Lane

• Advice requested:– Scope of the task force– Identify key people– Definitive timetable

• Nov 2007 report to the SAC

• Late 2007 / early 2008 present 3-4 page proposal to Board of Directors for adoption


7.2. Engaging young researchers

• Encourage participation in workshops and activities

• Constitue working groups


Documents

Scientific Advisory Council Padova 30-31/05/2007 Report from the Project Leader to the Scientific Advisory Council Simon Tillier, MNHN, Paris