Data publishing workshop October 2015, Trondheim

Workshop agenda

The workshop will be organized in the meeting room Libella, NINA-building located at the NTNU university campus Gløshaugen, in the northern part near Lerkendal, at address Høgskoleringen 9, NO-7034 Trondheim.

Thursday 29th October 2015

09:30 Coffee and registration

10:00 Introduction to the course

    Overview course content and practical information (10 min, Dag Endresen)

    Round-table presentation of your background (maximum 1 minute each).

10:30 Getting started with data publication

    Data publishing landscape, publishing software (20 min, Dag Endresen)

    Introduction to data publishing at NINA (20 min, Roald Vang)

    Dataset registration and data publishing at the GBIF portal (20 min, Jan Legind)

    Darwin Core data standard and the Darwin Core archive format (20 min, Dag Endresen)

12:15 Lunch break

13:15 Demo: Data publishing using the IPT software (20 min, Christian Svindseth)

    Occurrence data, multimedia, measurements.

    Hands-on exercise with IPT for all participants using an Occurrence core demo-dataset.

14:15 What is survey based monitoring data (event core) (15 min, Dag Endresen)

14:30 Publication of survey based monitoring data (event core) (30 min, Anders Finstad)

    Hands-on exercise with IPT for all participants using an Event core demo-dataset.

16:00 End of day 1

Friday 30th October 2015

09:00 Dataset metadata and long-term data archiving and data management plan (20 min, Dag Endresen)

09:30 Survey-based data (continued)

10:00 Presentation of participants own datasets (max 10 minutes each)

    Organization of participants into groups, each group working with one of the participants own datasets.

12:15 Lunch break

13:15 Hands-on work in groups with own datasets.

16:00 End of day 2 (Evaluation form)

Getting started with data publishing

This session provides an introduction to publishing biodiversity data through the GBIF network.

• http://www.gbif.org/publishing-data/summary

• GBIF Secretariat (2015). Getting Started: An overview of data publishing in the GBIF network, version 1.1. Copenhagen: Global Biodiversity Information Facility, 17 pp. ISBN: 87-92020-28-3 (for version 1.0). http://www.gbif.org/resource/80635

Long-term data archiving and data management plan

GBIF and the Data Observation Network for Earth (DataONE) collaborate to support long-term persistence of the biodiversity data shared through the GBIF network. The collaboration is part of a commitment in the GBIF Work Programme to explore data archival services offering redundancy to handle scenarios such as technical failure and the disappearance of projects or institutions that share data through the network.

• NorStore: https://www.uninett.no/datalagring

• EUDAT: http://eudat.eu/

• EUDAT B2FIND: http://b2find.eudat.eu/group/about/gbif

• DataONE: http://www.gbif.org/page/8199

• NeIC B2Share Nordic: https://wiki.neic.no/wiki/B2Share_Nordic

Dataset metadata

Documenting the provenance and scope of datasets is required in order to publish data through the GBIF network. Dataset documentation is referred to as ‘resource metadata’ that enable users to evaluate the fitness-for-use of a dataset. This session provides recommended practices and instruction on publishing metadata.

Dataset (Resource)
Project
People and Organisations
Keyword Set (General Keywords)
Taxonomic Coverage
Geographic Coverage
Temporal Coverage
Methods
Intellectual Property Rights
Additional Metadata

Darwin Core data standard

The Darwin Core is body of standards that includes a glossary of terms. The Darwin Core is primarily based on taxa, their occurrence in nature as documented by observations, specimens, and samples, and related information. A printable reference guide to the ratified Darwin Core terms found at:

• http://rs.tdwg.org/dwc/terms/index.htm

Publication of multimedia data

This session provides basic information about the multimedia resources metadata schema called the Audubon Core. Large volumes of biodiversity-related multimedia objects, held in repositories, have a huge potential to be used in scientific analysis and interpretations.

• http://www.gbif.org/occurrence/search?MEDIA_TYPE=*

Publication of survey-based monitoring data

Sample-based data come from thousands of different kinds of environmental, ecological, and natural resource investigations. These events range from one-off surveys to ongoing monitoring and include activities like freshwater and marine sampling, plant cover and vegetation plots, and citizen science bird counts, among others. The Darwin Core extension for sample data is a major advancement that will enable data holders publishing through the GBIF network to share population abundance data (including time series population data) or presence/absence data, and also to document the sampling protocol.

• http://www.gbif.org/newsroom/news/sample-based-data
• GBIF and EUBON (2015). Publishing sample data using the GBIF IPT. Latest version 23 March 2015. Available at http://www.gbif.org/sites/default/files/gbif_IPT-sample-data-primer_en.pdf

Venue and local information, Trondheim

• Workshop location: NINA-bulding, Høgskoleringen 9, NO-7034 Trondheim, Norway

• Lunch at the cantina of the NINA building: Hegstad & Blakstad AS, http://www.hegstadblakstad.no/

• Trondheim: http://en.wikipedia.org/wiki/Trondheim; http://en.wikivoyage.org/wiki/Trondheim

• Airport, Værnes, TRD: https://avinor.no/flyplass/trondheim/

• Airport bus: http://flybussen.no/Trondheim/, http://vaernesekspressen.no/

• Airport train (35 min travel time to Trondheim): https://www.nsb.no/en/our-destinations/stations/vaernes-station?id=1299

Participants (24 people)

• NINA (11 participants):
  • Roald Vang (organizer)
  • Frank Hanssen (co-organizer)
  • Erlend B. Nilsen
  • Jens Åström
  • Elisabet Forsgren
  • Knut Andreas Eikland Bækkelie
  • Signe Nybø (only attending 29 Oct)
  • Ishita Ahuja
  • Laila Saksgård
  • Gunnel Østborg
  • Sigrid Skoglund
• NTNU VM (7 participants):
  • Anders G. Finstad (organizer)
  • Dag-Inge Øien
  • Marc Daverdin
  • James David Mervyn Speed
  • Karstein Hårsaker
  • Hanna-Kaisa Lakka
  • Anders Kolstad
• Tromsø and Bergen (3 participants):
  • André Frainer, Department of Arctic and Marine Biology, University of Tromsø (UiT) 
  • Elina Halttunen, Havforskningsinstituttet i Tromsø 
  • Arnfinn Morvik, Havforskningsinstituttet i Bergen, IMR.no
• GBIF Norway & GBIF secretariat (3 participants):
  • Dag Endresen, GBIF Norway (organizer)
  • Christian Svindseth, GBIF Norway (organizer)
  • Jan Legind, GBIF Secretariate, Copenhagen (co-organizer) 

References

1. Austrheim G, Endresen DTF, Finstad AG, Grytnes J-A, Koch W, Lindgaard A, Mathisen IE, Speed JDM, and Øien D-I (2015). Deling av vegetasjonsdata: Forslag til infrastruktur for å sikre faglige og tekniske standarder som kan lette datautveksling. NTNU Vitenskapsmuseet naturhistorisk rapport 2015-4:1-23. ISBN 978-82-8322-044-5. [URL]

2. Chavan V, Penev L, & Hobern D (2013) Cultural Change in Data Publishing Is Essential BioScience 63(6): 419-420. doi:10.1525/bio.2013.63.6.3

3. Costello MJ, Michener WK, Gahegan M, Zhang ZQ, Bourne PE (2013) Biodiversity Data Should Be Published, Cited, and Peer Reviewed. Trends in Ecology & Evolution Volume 29, Issue 8, Pages 454–461. doi:10.1016/j.tree.2013.05.002

4. GBIF (2010). Darwin Core Quick Reference Guide, version 1.3, released on 9 March 2012, (contributed by Wieczorek J, De Giovanni R, Vieglais D, Remsen DP, Döring M, Robertson T), Copenhagen: Global Biodiversity Information Facility, 41 pp. http://www.gbif.org/resource/80633

5. GBIF (2011a). Publishing and Registering Data with GBIF, version 1.0, released on 11 April 2011, (contributed by Remsen D, Hahn A, Ko B, Chavan V, Raymond M), Copenhagen: Global Biodiversity Information Facility, 9 pp. http://www.gbif.org/resource/80644

6. GBIF (2011b). GBIF Metadata Profile – How-to Guide, (contributed by Ó Tuama, E, Braak K, Remsen D), Copenhagen: Global Biodiversity Information Facility, 11 pp. http://www.gbif.org/resource/80641

7. GBIF (2011c). GBIF Metadata Profile, Reference Guide, Feb 2011, (contributed by O Tuama E, Braak K, Copenhagen: Global Biodiversity Information Facility, 19 pp. http://www.gbif.org/resource/80640

8. GBIF (2015). The story of GBIF data publshing [comic]. Global Biodiversity Information Facility, Copenhagen. http://community.gbif.org/pg/file/read/48774/comic-how-to-publish-data-using-gbif

9. GBIF and EUBON (2015). Publishing sample data using the GBIF IPT. Latest version 23 March 2015. http://www.gbif.org/sites/default/files/gbif_IPT-sample-data-primer_en.pdf

10. Morris RA, Barve V, Carausu M, Chavan V, Cuadra J, Freeland C, Hagedorn G, Leary P, Mozzherin D, Olson A, Riccardi G, Teage I, and Whitbread G (2013) Discovery and publishing of primary biodiversity data associated with multimedia resources: The Audubon Core strategies and approaches. Biodiversity Informatics 8(2):185-197. doi:10.17161/bi.v8i2.4117

11. Piwowar HA, Day RS, Fridsma DB (2007) Sharing Detailed Research Data Is Associated with Increased Citation Rate. PLoS ONE 2(3): e308. doi:10.1371/journal.pone.0000308

12. Robertson T, Döring M, Guralnick R, Bloom D, Wieczorek J, Braak K, Otegui J, Russell L, Desmet P (2014) The GBIF Integrated Publishing Toolkit: Facilitating the Efficient Publishing of Biodiversity Data on the Internet. PLoS ONE 9(8): e102623. doi:10.1371/journal.pone.0102623

13. Wieczorek J, Bloom D, Guralnick R, Blum S, Döring M, Giovanni R, Robertson T, and Vieglais D (2012) Darwin Core: An Evolving Community-Developed Biodiversity Data Standard. PLoS ONE 7(1): e29715. doi:10.1371/journal.pone.0029715

Tutorial videos

• Braak K (2015). How to install the GBIF Integrated Publishing Toolkit (IPT). GBIF Secretariat, Copenhagen. [Vimeo video, 7m24s]. https://vimeo.com/116142276
• GBIF (2015). GBIF videos on Vimeo. https://vimeo.com/gbif/videos
• Giddens M (2010). GBIF - Darwin Core Archive publishing. [YouTube video, 6m6s]. https://www.youtube.com/watch?v=hYbDN2jCCoc
• Noé N (2015). Basic Biodiversity Publishing at GBIF using the IPT. [YouTube video, 1h40m]. https://www.youtube.com/watch?v=s_ofkEBtK2U see also: http://community.gbif.org/pg/bookmarks/read/48862/precourse-activity-webinar-about-basic-use-of-the-ipt
• Remsen D (2011). GBIF Tutorial: Darwin Core Archive Assistant. [YouTube Video, 10m44s]. GBIF secretariat, Copenhagen. https://www.youtube.com/watch?v=_hF0sslw-B4

Preparations before the workshop

GBIF organized a training workshop on data publishing during the global nodes meeting 3 weeks ago (4-5 October). We will reuse and adapt some of the training material from the nodes training workshop for our workshop in Trondheim. We recommend to study the training material from the nodes meeting in advance of the workshop in Trondheim.
http://community.gbif.org/pg/pages/view/48270/gb22-training-event-for-nodes