Workshops Leiden February 2013

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The participants of the pro-iBiosphere workshops

Contents

Date and venue

11th of February (Monday) to 14th of February (Thursday) 2013, Leiden, the Netherlands.

At the Hilton Garden Inn Hotel

Directions to the venue can be found here.

Participants

Please refer to the separate Participant list.

Before the meeting

Hotels

Accommodation in Leiden

Public transport in the Netherlands

Public transport

Agenda

Day 1: 11th of February 2013

Workshop #1: e-platforms & e-tools for taxonomy

Organisers: NBGB, FUB-BGBM, Naturalis, Plazi, RBGK

Audience:

  • Editors of Floras and Faunas who are interested in adopting e-platforms and e-tools
  • Taxonomists who are interested in using the e-tools

Objectives:

  • Promote digital taxonomic tools amongst taxonomists
  • Understand the software requirements of users
  • Provide exemplar training

Expected results:

  • Improved understanding of the current use of the infrastructure by suppliers and consumers
  • Documentation of requirements for potential costumers (by means of a questionnaire that has been previously distributed)
  • Identification of barriers to take-up use of e-tools (by means of a questionnaire that has been previously distributed)

Agenda

8.30 – 9.00 Registration

PART I: Introduction

Chair: Jan van Tol

9.00 – 9.05 Welcome and short introduction — Erik Smets, Naturalis
9.05 – 9.10 EU FP7 pro-iBiosphere project — Soraya Sierra, Naturalis
9.10 – 9.35 Why do we need open access and exchangeable taxonomic information? — Donat Agosti, Plazi
9.35 – 10.05 Existing digital standards — Terence H. Catapano, Plazi
10.05 – 10.10 Questions

PART II: e-platforms for taxonomy: Background information

Chair: Jan van Tol

10.10 – 10.35 Scratchpads — Dave Roberts, ViBRANT
10.35 – 10.45 Tea/coffee break
10.45 – 11.05 EDIT Platform for Cybertaxonomy — Anton Güntsch, FUB-BGBM
11.05 – 11.20 Linnaeus NG & BioPortals for species data management and harvesting — Peter Schalk, ETI
11.20 – 11.35 Open community platforms on the Biowikifarm — Gregor Hagedorn, JKI & Plazi
11.35 – 11.50 Mediawiki-based KOS — Andru Vallance, Practicalplants.org
11.50 – 12.00 Questions

PART III: e-tools for taxonomy: purpose, uses

Chair: Quentin Groom

12.00 – 12.30 Pensoft Writing Tool (PWT) — Pavel Stoev, Pensoft
12.30 – 13.10 Lunch break
13.10 – 13.35 EDIT Taxonomic Editor — Patricia Kelbert, FUB-BGBM
13.35 – 14.00 Xper2 — Régine Vignes Lebbe, UPMC
14.00 – 14.40 CharaParser and associated software — Hong Cui, University of Arizona
14.40 – 15.10 Building apps for smart phones and tablets to enhance the reach and transfer of taxonomic research effort — Alexander Krings, N. Carolina State University, USA
15.10 – 15.30 Questions
15.30 – 15.40 Tea/coffee break

PART IV: Examples of projects using the e-tools

Chair: Don Kirkup

15.40 – 16.00 Communicating information on alien plants using Scratchpads — Quentin Groom & Filip Verloove, NBGB
16.00 – 16.20 CDM data portal: applications and projects — Eckhard von Raab-Straube, FUB-BGBM
16.20 – 16.40 Parsing morphological descriptions to support semantic-based access — Hong Cui, University of Arizona
16.40 – 17.00 The Flora of Zimbabwe project – progress to date and the way forward — Mark Hyde
17.00 – 17.10 Questions

PART V: Discussion of Day 1

17.10 – 18.00
What is the current use of the e-infrastructure by suppliers and consumers?
What are possible ways to encourage the use of standards?

PART VI: Icebreaker session

18.00 – 19.00

Day 2: 12th of February 2013

Continuation of Workshop #1: e-platforms & e-tools for taxonomy

PART V: Training and demonstration

Training sessions will take place in parallel sessions. Participants will be able to join a total of three training sessions during the day. The maximum number of participants per training is 20.

The list of participants for each training

Place: Room nr 1

8.30 – 11.20 Pensoft Writing Tool (PWT) — Teodor Georgiev & Jordan Biserkov, Pensoft
11.20 – 11.30 Tea/coffee break
11.30 – 12.30 Xper2 — Régine Vignes Lebbe, UPMC
12.30 – 13.20 Lunch break
13.20 – 15.20 (continuation) Xper2 — Régine Vignes Lebbe, UPMC
15.20 – 15.30 Tea/coffee break
15.30 – 18.20 Bring your key to your mobile device (Android) — Gregor Hagedorn, JKI & Plazi

Place: Room nr 2

8.30 – 11.20 Scratchpad taster session* — Dimitris Koureas, Isa van de Velde & Dave Roberts, ViBRANT
11.20 – 11.30 Tea/coffee break
11.30 – 12.30 Scratchpad taster session repeat of previous session* — Dimitris Koureas, Isa van de Velde & Dave Roberts, ViBRANT
12.30 – 13.20 Lunch break
13.20 – 15.20 (continuation) Scratchpad taster repeat — Dimitris Koureas, Isa van de Velde & Dave Roberts, ViBRANT
15.20 – 15.30 Tea/coffee break
15.30 – 18.20 Developing organism identification apps for Android devices* — Alexander Krings, N. Carolina State University, USA
*note: a copy of the Scratchpad training manual will be distributed among participants

Place: Room nr 3

8.30 – 11.20 EDITor session 1 — Sabrina Eckert, Patricia Kelbert, Eckhard von Raab-Straube, FUB-BGBM
11.20 – 11.30 Tea/coffee break
11.30 – 12.30 Developing organism identification apps for Android devices* — Alexander Krings, N. Carolina State University, USA
12.30 – 13.20 lunch break
13.20 – 15.20 (continuation) Developing organism identification apps for Android devices — Alexander Krings, N. Carolina State University, USA
15.20 – 15.30 Tea/coffee break
15.30 – 18.20 EDITor repeat of morning session — Sabrina Eckert, Patricia Kelbert, Eckhard von Raab-Straube, FUB-BGBM
*note: the minimal background required for the identification apps is basic knowledge of HTML and CSS

Place: Room nr 4

8.30 – 12.30 Golden Gate — Guido Sautter, Plazi
12.30 – 13.20 lunch break
13.20 – 15.00 Introduction to BioVel & Workflow demo's — Elisabeth Paymal, BioVel
15.00 – 15.30 BioVel discussion — Yde de Jong, BioVel
15.30 – 18.20 Charparse — Hong Cui, The University of Arizona

Day 3: 13th of February 2013

Workshop #2: Legacy literature – Semantic mark-up generation, data quality and user-participation infrastructure

Organisers: Plazi, FUB-BGBM, Naturalis, NBGB, RBGK

Audience:

  • People interested in mark-up
  • Editors of Floras and Faunas
  • Scientists
  • Commercial vendors
  • IT Developers, mark-up experts

Objective:

  • Define the road ahead on the field of semantic mark-up, data quality and user-participation infrastructure

Expected result:

  • Generation of semantic mark-up in respective document collections (i.e. recognition of treatment boundaries, of feature descriptions and of other characteristics of species)

Agenda

PART I: Biosystematic literature: Where are we and where do we want to go?

Chair: Donat Agosti

8:30 – 9:00 What is a "flora"? – Peter Hovenkamp, Naturalis
9:00 – 9:30 Surfacing the deep data of taxonomy – Rod Page, University of Glasgow
9:30 – 9:45 Incentives for editors – Laurence Bénichou, EJT, Muséum Nationale d'Histoire Naturelle
9:45 – 10:00 Discussion

PART II: Mark-up and semantic enhancement of biosystematics literature Chair: Rod Page

10:00 – 10:15 Zootaxa / European Journal of Taxonomy pathway – Terance H. Catapano, Plazi
10:15 – 10:30 Pensoft Markup Tool (PMT) – Teodor Georgiev, Pensoft
10:30 – 10:45 Tea/coffee break
10:45 – 11:00 Semantic publishing: the revolution is here – David Shotton, Oxford University
11:00 – 11:15 A proposal for the use of a semantic vocabulary, taxpub as a starting point – Terance H. Catapano, Plazi
11:15 – 11:30 Questions & Discussion

Chair: Terry Catapano

11:30 – 11:50 Mark-up and parsing with Perl scripts – Thomas Hamann, Naturalis
11:50 – 12:10 Mark-up tools / GoldenGate – Guido Sautter, Plazi
12:10 – 12:30 Charparse – Hong Cui, The University of Arizona
12:30 – 12:45 Questions & Discussion
12:45 – 13:30 Lunch break

PART II (ctd): Mark-up and semantic enhancement of biosystematics literature

Chair: Donat Agosti

13:30 - 13:40 The BHL way to content - William Ulate & Chuck Miller, BHL, Missouri Botanical Garden
13:40 – 13:50 BioStor - Rod Page, University of Glasgow
13:50 - 14:00 Ontologies – Bob Morris, Harvard
14:00 - 14:10 Annotations – James Macklin, Agriculture and Agrifood Canada
14:10 - 14:30 What is and how to measure quality? – Christiana Klingenberg, Plazi
14:30 - 14:50 Discussion and way ahead

Potential topics:

  • Where do we want to go?
  • Lessons learned
  • The issue of scaling
  • How to get more content or how to get the crowd involved
14:50 – 15:05 Tea/coffee break
15:05 - 17:00 Discussion and way ahead (ctd.)

Discussion and small presentation to clarify points

17:00 - 17:15 Summary – Donat Agosti, Plazi

PART III: Hands on

13:20 – 14:50 GoldenGate, Crowdsource, Authorsource – Guido Sautter, Plazi
14:50 – 15:05 Tea/coffee break
15:05 - 16:35 Charparse – Hong Cui, The University of Arizona

Day 4: 14th of February 2013

Workshop #3: Prospective Literature – Toward Best Practices for data acquisition and curation using e-tools for taxonomy

Organisers: Naturalis, NBGB, FUB-BGBM, RBGK

Audience:

  • IT institutions
  • Editors of Floras, Faunas and Mycotas
  • Online data curators

Objective:

  • Identify and promote good practices for entering new field data and collaboratively writing of taxonomic treatments

Expected results:

  • Collect data that will facilitate writing the Best Practices e-Guide on Editorial Policies by establishing:
  • What are the new and standardized editorial policies that are needed for the curation and publication of biodiversity data in an e-environment?


Agenda:

PART I: Why do we need Flora, Fauna or Mycota works?

Chair: Gregor Hagedorn

8:30 – 9:00 Introduction – Gregor Hagedorn, JKI & Plazi
9.00 – 10.00 Discussion (to be continued at 16.40 hours)
  • Do we need Flora, Fauna or Mycota publications in a digital age?
  • Is quick access to scientific journal literature with semantic mark-up sufficient?
  • Do we need a new landscape to write/curate/synthesize the future floras sensu lato?
  • Which elements of traditional Flora/Fauna/etc. should be carried into digital knowledge management?

PART II: Uses of extracting semantic data

Chair: Gregor Hagedorn

10.00 – 10.30 Deconstructing PDFs into SVG to extract semantic data, phylogeny-extraction as an example – Ross Mounce, University of Bath & Open Knowledge Foundation Panton Fellow
10.30 – 10.35 Questions
10.35 – 10.45 Tea/coffee break

PART III: Improving the XML workflow between registers and queries

Chair: Richard Pyle

10.45 – 10.55 A common XML query/response model for automated publication-to-registration pipeline – Jordan Biserkov, Pensoft
10.55 – 11.05 IPNI - Nicky Nicolson, Royal Botanical Gardens Kew
11.05 – 11.15 Index Fungorum – Paul Kirk, CABI
11.15 – 11.25 MycoBank – Vincent Roberts, CBS-KNAW Fungal Biodiversity Center
11.25 – 11:35 ZooBank – Rich Pyle, Bishop Museum
11.35 – 11.40 Questions

PART IV: Synergies between pro-iBiosphere and other global initiatives/projects

Chair: Richard Pyle

11.40 – 12.00 Linking the Global Names Project with pro-iBiosphere – David Patterson, GN project
12.00 – 12.20 GNA compatible names backbon – Nicky Nicolson, RBGK
12.20 – 12.40 Floras in the 21st Century: The Flora of North America Saga (common goals, future collaboration) – James Macklin, Agriculture and Agri-Food Canada Ottawa, Ontario, Canada
12.40 - 13.00 Discussion
12.40 – 13.30 Lunch

PART V: Moving Flora's, Fauna's and Funga into an advanced XML based journal production workflow

Chair: Donat Agosti

13.30 – 14.00 European Journal of Taxonomy (vision, aims, approach) – Laurence Bénichou, Muséum Nationale d'Histoire Naturelle
14.00 – 14.30 Biodiversity Data Journal (vision, aims, approach) – Jordan Biserkov, Pensoft
14.30 – 14.45 Questions
14.45 – 15.00 Tea/coffee break

PART VI: Demonstration of workflows for publishing

Chair: Donat Agosti

15.00 – 15.45 TaxPub – Terance H. Catapano, Plazi
15.45 – 16.30 Pensoft Journal System (PJS 1.0 and 2.0): A complete XML-based collaborative online platform for authoring, peer-review, editing, publishing and dissemination – Jordan Biserkov, Pensoft
16.30 – 16.40 Questions

PART VII: CONCLUSION

Chair: Gregor Hagedorn

16.40 – 17.30 Discussion
  • How do you publish your data?
  • How to produce more timely publications?
  • How to maintain the actuality of a flora/fauna/monograph?
  • How to coordinate the flora/fauna/monograph activities and sharing of resources?

See also: Management Meetings Leiden 15th February 2013

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