Workshop Berlin 3: Coordination and routes for cooperation

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Full title: Coordination and routes for cooperation across organizations, projects and e-infrastructures
Date: 23rd of May 2013
Organisers: Plazi, JKI, MfN, Naturalis, FUB-BGBM, PENSOFT, RBGK

(For general information see: Workshops Berlin, May 2013)

Audience: Persons interested in specimen or observation data, standards, bibliographic references, digital publications, names, morphology, genes, media, annotations, identifiers.

Goal: The workshop aims at preparing the landscape for a future Biodiversity Knowledge Management System

Registration & Pre-workshop 3 Questionnaire

Registration & questionary of workshop 3 form

List of Participants of workshop 3

Participant list


08:00 – 8:30 Registration will take place in the room immediately in front the JKI big auditorium (i.e. JKI A300)

Part I: The challenge

Place: JKI auditorium (A300)

08:30 – 08:35 Welcome – Donat Agosti, Plazi
08:35 – 08:40 Introduction to pro-iBiosphere - vision, goals and objectives – Soraya Sierra, Naturalis
08:40 – 08:45 Overview of MoU – Gregor Hagedorn, Plazi/JKI
08:45 – 09:05 LifeWatch – Wouter Los, University of Amsterdam
09:05 – 09:25 250 Years of Monographs – The future of Botanical Monography – Karol Marhold, Slovak Academy of Sciences
09:25 – 09:45 World Flora Online – the global challenge for phytotaxonomists – Walter G. Berendsohn, FUB-BGBM

Part II: Preparing the landscape of a future BKMS

09:45 – 10:05 Workflows: What is needed to make all work together? – Norman Morrison, BioVeL - The University of Manchester
10:05 – 10:25 Publishing highly structured data – Norm Johnson, Ohio State University
10:25 – 10:40 Report on stakeholders requirement – Don Kirkup, RBGK
10:40 – 10:50 Questionnaire results meeting 3 – Jordan Biserkov, Pensoft
10:50 – 11:05 Tea/coffee break
11:05 – 11:20 The EU BON integration agenda – Hannu Saarenmaa, EU BON

Part III: Steps ahead - elements for an MoU

11:20 – 11:35 Open Access and data sharing – Willi Egloff, Plazi
11:35 – 11:50 Linked Open Data and Scientific knowledge management systems – Gregor Hagedorn, JKI/MfN
11:50 – 12:05 Persistent identifiers and links between them - building the cross-ref analogue for biodiversity data – Chuck Miller, MOBOT
12:05 – 12:20 Aspects of linking: uniqueness, stability, dereferencing and resolution – Jan Brase, DataCite
12:20 – 12:35 Questions and discussion
12:35 – 13:45 Lunch break
13:45 – 14:00 Annotation and feedback – Peter Hovenkamp, Naturalis
14:00 – 14:15 iMarine Gateway. Providing services for analyzing large and heterogeneous datasets in Virtual Research Environments – Nicolas Bailly, WorldFish Center
14:15 – 14:30 Names and Global Names Architecture (GNA) collaboration/integration with BKMS – Richard Pyle, Bishop Museum and Zoobank
14:30 – 14:45 Catalogue of Life – Alastair Culham, University of Reading
14:45 – 15:00 iDigBio – Deborah Paul, Florida State University, Tallahassee FL
15:00 – 15:15 Digitized collections – Vincent Smith / Vlad Blagoderov, NHM London (contacted)
15:15 – 15:30 Digital resources (images, audio) – Greg Riccardi, Florida State University
15:30 – 15:40 Questions and discussion
15:40 – 16:00 Tea/coffee break
16:00 – 16:15 Taxon treatments – Donat Agosti, Plazi
16:15 – 16:30 Bibliographic references – William Ulate, BHL
16:30 – 16:45 Bibliographic references – Jordan Biserkov, Pensoft
16:45 – 17:00 Piloting some of BKMS’s basic features through cybertaxonomic publications – Lyubomir Penev, Pensoft
17:00 - 17:15 Questions and discussion

Part IV Discussion of the previously prepared draft MoU, modified or extended with the results of today's workshop – Gregor Hagedorn, Plazi

17:15 – 18:30 Discussion
18:45 Dinner @ Seminaris Papillion Restaurant;
Please indicate your interest in the dinner by sending an email to Sabrina Eckert:
Cost: ca. 23 Euros, to be paid by participants (unless funding is required for this specific activity and has been agreed in advance with Plazi - Donat Agosti:

Concrete examples of ideas for potential points in a draft MoU

A primary purpose of the “Routes towards cooperation” meeting is to increase our reciprocal understanding and progress towards a multi-institutional Memorandum of Understanding (MoU). The following points are potential points in a draft MoU. It is welcome to comment them here on the wiki before the meeting takes place, or to add further points. The results would then have to be further discussed by the appropriate levels.

  1. Establishment of a multi-institutional focus group to coordinate software development to improve the efficiency of resource use by means of common Open Source based development projects using Open Source methodology.
  2. Agreements on specialization, e.g., one institution specializes in geographical analysis and visualization, providing services to other institutions or projects
    • perhaps ask which services institutions want to strengthen and share but also ask which activities they would rather like to use as services from others, in place of a missing, but also replacing an unsatisfying existing solution.
  3. Agreement on shared crowdsourcing activities to clean up data, e.g. bibliographic references, or markup content in legacy literature, e.g. scientific names, treatments, material citations.
  4. Agreement on long-term management procedures to provide stable identifiers. This agreement may be technology neutral (except that some way to use the identifiers in the human readable as well as semantic web should be specified). Both stable http-URIs (preferred in semantic web) and DOI technology (publishing industry) are possible implementations.
  5. Agreement on following the Linked Open Data example. (Note: Edinburgh may be a best practices example?)
  6. Agreement to communicate the data policies according to the Linked Open Data five star scoring
  7. Policy agreements on Open Access
  8. Agreement to register all biodiversity web services that are provided to other Biodiversity institutions in the Biodiversity Catalogue (Hosted @ Univ. Manchester)
  9. Agreement to register all workflows that are provided to other Biodiversity institutions in myExperiment (Hosted @ Univ. Manchester)
  10. Agreement to communicate the expected and planned stability of services by means of a standard vocabulary (e.g.: undecided, experimental, long-term service without fixed API, long-term service with stable and versioned API)
  11. Agreement to collaborate on the development of shared term definitions (glossary-style) with the understanding that new terms can be freely added, but an effort will be made to re-use or improve existing term definitions.
  12. Paul Kirk: Centrally 'cached' data should have a clear mechanism for providing usage statistics back to sources. (Norman Morrison: consider W3C PROV model.
  13. Norman Morrison: work towards specification and adoption of a common mechanism for data citation

Guidelines for speakers giving presentations

1. Presentation are limited to 15 minutes for each speaker plus 5 minutes for discussion.
2. Presentations should clearly answer the following questions (7-8 slides), definitely focusing on the interoperability problem:
2.1. Type of content we discuss (e.g., occurrences, genes, behaviour, morphology, etc.)
2.2. Sources of content (from where)
2.3. Formats of content (formats, standards)
2.4. Methods of gathering information (e.g., harvesting, ftp uploads, protocols)
2.5. Methods of delivery of information (e.g., free searches, API, web services, automated exports, linking mechanisms, etc.; provide links to API and web services documentation)
2.6. Identifiers used (type, persistence, dereferencing, resolvability)
2.7. Present or forthcoming interoperability features with other platforms
2.8. Constraints, needs and expectations to: a) Suppliers of content, and b) Users of content
3. Overall picture of what is needed within a certain domain (e.g., for names, references, genes, images, etc.) (2-3-slides)
4. The final outputs of presentations and discussions should be two-fold:
4.1. Summary table encompassing the answers to the above questions, that will be a basis for the whitepaper and future work
4.2. MoU draft discussed
4.3. Proposing an Advisory Board of key stakeholders that will form the ground for a consortium to develop and launch the future BKMS

Tasks involved:

Task 2.1. Coordination and routes for cooperation across organizations, projects and e-infrastructures (lead: Plazi). Encompassing the information gathered at Workshop 1 (Leiden, February 2013) and through the online questionnaire.

Task 4.1 Improve technical cooperation and interoperability at the e-infrastructure level (lead: FUB-BGBM).

Task 4.2 Promote and monitor the development and adoption of common mark-up standards and interoperability between schemas by identifying technical and societal constraints and needs to increase collaboration and interoperability between e-platforms and projects, and by envisioning practical solutions towards the Biodiversity Knowledge Management System (lead: Plazi).