MS12 - Workshop on mark-up of biodiversity literature

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Notes have been taken collaboratively and are archived here.
Workshop participants in front of MfN.


One of the pro-iBiosphere Milestones is MS12, a workshop on the interoperability of mark-up approaches used for legacy and recent biodiversity literature across organismic domains. It is part of Workpackage 3 and took place at MfN in Berlin on February 10-11, 2014.


Aims/objectives are (with % of workshop time):

  • (5%) Review of the pilot: "Interoperability between taxon treatments from both legacy and prospective literature from three organismic domains (fungi, plants and animals)"
  • (5%) Review of D3.3.1 - Report on state-of the art and research horizons of semantic integration of biodiversity literature.
  • (5%) Review of D4.2 - Report on a strategy for improvement & interoperability of the XML schemas.
  • (75%) Brain storming and consensus building on development priorities for tools/services to allow and facilitate the mark-up of biodiversity literature and integration of marked-up literature into a future iBiosphere system.
  • use cases for markup, e.g. semantic search
  • identify roadmap, workplan, potential projects and responsibilities
    • integration with Wikidata?
  • should be compatible with both legacy and prospective literature
  • cybertypes
  • (10%) Produce outline and some draft elements for D3.3.2 - Report on progress during the coordination process of partners and non consortium partners.


We aim at gathering about 15 participants from within and outside the pro-iBiosphere project who are actively involved with efforts of semantic markup of recent or legacy biodiversity literature, e.g.:

  • Mark-up & text mining experts (IT developers & researchers)
  • BHL experts
  • Scientists active in the area
  • Companies operating in this environment or offering services that could be used in such contexts
  • Developers of semantic search technologies


Please put your name here if you will attend the workshop. Please order alphabetically by last names.

  1. Donat Agosti (Plazi)
  2. Philippa J. Benson (PJB Consulting)
  3. Terry Catapano (Plazi)
  4. Sabrina Eckert (FUB-BGBM)
  5. Bruno Jehle (BJ Institue, Aaarau)
  6. Quentin Groom (NBGB)
  7. Anton Güntsch (FUB-BGBM)
  8. Gregor Hagedorn (MfN)
  9. Charlotte Johns (RBGK)
  10. Don Kirkup (RBGK)
  11. Dimitris Koureas (NHM London)
  12. Chris Maloney (NCBI, contractor, A-Tek, Inc. - remotely)
  13. Daniel Mietchen (MfN)
  14. Jeremy Miller (Naturalis)
  15. Andreas Müller (FUB-BGBM)
  16. Rod Page (University of Glasgow - remotely)
  17. Lyubomir Penev (Pensoft)
  18. Guido Sautter (Plazi)
  19. Soraya Sierra (Naturalis)
  20. William Ulate (BHL, MOBOT)
  21. Florian Wetzel (MfN, EU-BON)

Expected results:

  • Identify use cases for structured data generated on the basis of biodiversity literature
  • Outline of the structure and focus of D3.3.2 - report on progress during the coordination process of partners and non consortium partners


February 10

HOMEWORK: fill in this questionnaire

February 11

Warming up: sign participant list
  • 8:30 - 9:00 Registration and coffee
  • 9:00 - 10.30 Presentation (Chris Maloney, remotely, slides, on Vimeo; Philippa Benson)
  • 10:30 - 10:50 Coffee break
    • 10:45 PHOTO in front of main entrance
  • 10:50 - 12:50 Synthesis
  • 12:50 - 14:00 Lunch together with MS23 participants
  • 14:00 - 18:00 Optional (e.g. work on report D3.3.2)
  • 19:00 Dinner


  • September 25, 2013: Invitations to potential participants
  • October 8, 2013: Initial outline of D3.3.1 Semantic integration of the biodiversity literature
  • October 11, 2013: Preliminary agenda for MS12 - Workshop on mark-up of biodiversity literature
  • November 11, 2013: Preliminary list of participants for MS12 - Workshop on mark-up of biodiversity literature
  • December 10, 2013: Comments from partners on D3.3.1
  • December 15, 2013: Final formatting of D3.3.1
  • December 20, 2013: Submission of D3.3.1
  • February 7, 2014: Preparatory materials for workshop sent out - questionnaire
  • February 9, 2014: Soft deadline for submission of responses to preparatory materials

The default room for the two workshops is HS 3330, for the management meeting the Seminarraum Paläontologie. For most of the time, one other room is available for breakout sessions and other forms of group work, as detailed here.


If funding has been approved in advance between the organisers of the workshops and you, a maximum of 400/1300Euros (inside/outside EU) can be funded for flights/train travel (cheapest economy choice), and accommodation as indicated above. Overnight stay will be paid from the day previous of the meeting to the night following the meeting. Breakfast is also covered, if included in the hotel. Lunch/coffee is free. Dinner, taxi and additional hotel charges have to be paid by participants themselves. Reimbursement claims must be sent to Gregor Hagedorn (who has to approve them) with original receipts (not electronic copies thereof) by March 15. This includes boarding tickets if you came by plane. Do not forget to add your IBAN and BIC/SWIFT codes (help) under your bank details in the reimbursement form. Otherwise, delays in reimbursements will result. The reimbursement forms will be uploaded soon.


For practical information, see Workshops Berlin, February 2014.