Data paper workshop, December 2014, Oslo

Data paper writing workshop organized during two days (2nd & 3rd December 2014) at the Natural History Museum in Oslo. Introduction to writing good dataset metadata and to the procedure for writing and submitting data paper manuscripts to the PENSOFT Biodiversity Data Journal. Participants bring their own dataset(s) and we will try to complete a good part of the writing for a complete data paper manuscript by the end of day 2.

Time and place: Dec. 2, 2014 9:00 AM – Dec. 3, 2014 4:00 PM, UiO Natural History Museum, Oslo

Data paper workshop, Oslo

Data paper workshop at UiO Natural History Museum in Oslo

A data manuscript may include the following information categories.

Dataset (Resource)

Project

People and Organisations

Keyword Set (General Keywords)

Taxonomic Coverage

Geographic Coverage

Temporal Coverage

Methods

Intellectual Property Rights

Additional Metadata

Tuesday 2nd December

09:00 Coffee and Danish bread

09:30 Introduction to the course

Overview course content and practical information.

Round-table presentation of your background (maximum 2 minutes each).

10:00 Introduction to data papers

What is a data paper? Why a data paper? The GBIF metadata profile! Tools to use (Pensoft writing tool and the use of Github).

What & why (Dimi)
The GBIF-IPT metadata profile (Dimi) & data paper guidelines
Tools to use (Dimi)

11:30 Introduction to journals accepting data papers

Pensoft: Biodiversity Data Journal, http://biodiversitydatajournal.com/;

Pensoft: ZooKeys; Pensoft: PhytoKeys

Nature: Scientific Data, http://www.nature.com/sdata/

12:15 Lunch break

13:00 Presentation of participants datasets

All participants, max 20 min each

15:00 Introduction to data cleaning, visualisation and mapping tools

OpenRefine, cartoDB, Mapbox, ...

16:00 Starting to write the data papers (all)

17:00 End of day 1

20:00 Workshop dinner (downtown Oslo)

Grand Hotel, Restaurant Palmen, Karl Johans gate 31, 0159 Oslo

140 meter from your hotel (Rica Travel Hotel) and is facing the parliament.

Reservation made for 20:00, please let me know if you will not attend the dinner!

Wednesday 3rd December

09:00 Introduction to day 2 (Dag/Dimitri)

09:30 Continue writing the data papers (all)

12:15 Lunch

13:00 Introduction to submitting the data papers

Pensoft BDJ, ZooKeys or PhytoKeys

15:00 Continue writing the data papers (all)

We agreed to aim at all data papers published by the end of January (2015).

16:00 End of day 2 (and course)

Participants (11 persons)

Dimitri Brosens (BeBIF, Belgian Biodiversity Platform)

Dag Endresen (GBIF-Norway)

Christian Svindseth (GBIF-Norway)

Einar Timdal, Lichen herbarium in Oslo, NHM Oslo

Tor Tønsberg, Lichen herbarium in Bergen, UiB [GBIF-dataset]

Lars Erik Johannesen, DNA collection and bird tissue collection, NHM Oslo

Kristine Dobbe, Polychaeta georeferencing project 2014, NHM Oslo

Ann-Helen Rønning, Polychaeta georeferencing project 2014, NHM Oslo

Gunnar Austrheim, Vegetation survey dataset, NTNU VM, Trondheim

Dag-Inge Øien, NTNU VM, Trondheim

-- unable to attend:

Wouter Koch, Fish dataset, Artsdatabanken, Trondheim

Marc Daverdin, NTNU VM, Trondheim

Anders Bryn, NHM-UiO & Forest and Landscape, forest survey data

Photos: https://www.icloud.com/photostream/#A25Uzl7VGBi7BT

Datasets to become data papers:

Google Doc template

https://docs.google.com/document/d/1mlxAQzfcJR4edRkRntQczaiGgqIiqxZolGzbiqhJ-z0/edit#heading=h.xlhcg1vdx731

Github template link: https://github.com/LifeWatchINBO/data-publication-guidelines/blob/master/occurrences/data-paper-template.md

Lichen herbarium in Bergen (UiB)

Home page: http://www.uib.no/en/universitymuseum/65821/herbarium-bg

Curator: Tor Tønsberg, UiB: http://www.uib.no/personer/Tor.T%C3%B8nsberg#

Institution ID: http://biocol.org/urn:lsid:biocol.org:col:15727

Institution code: BG

Collection code: BG-L

GBIF datasetID: www.gbif.org/dataset/fb1ecd28-f09e-4747-8bde-0b3d7a6f78d1

GBIF.no/ipt/: http://gbif.no/ipt/resource.do?r=bg_lichens

Lichen herbarium in Oslo (UiO NHM)

Home page: http://nhm2.uio.no/lav/web/index.html

Curator: Einar Timdal, UiO NHM: http://www.nhm.uio.no/om/organisasjon/forskning-samlinger/personer/einarti/index.html

Institution ID: http://grbio.org/cool/2knt-7f1r

Institution code: NHMO

Collection code: O-L

GBIF datasetID: http://www.gbif.org/dataset/7948250c-6958-4a29-a670-ed1015b26252

GBIF.no/ipt/: http://gbif.no/ipt/resource.do?r=o_lichens

DNA bank & Bird tissue collection (UiO NHM)

Home page: http://www.nhm.uio.no/english/research/infrastructure/dna-bank/

Curator: Lars Erik Johannessen: http://www.nhm.uio.no/om/organisasjon/konservering-forskningsteknikk/personer/larsejo/

Curator: Arild Johnsen: http://www.nhm.uio.no/english/about/organization/research-collections/people/arilj/index.html

Institution ID: http://grbio.org/cool/2knt-7f1r

Institution code: NHMO

Collection code: BI

Collecion ID: http://grbio.org/cool/wes0-t2ie

GBIF datasetID: http://www.gbif.org/dataset/341e0c37-0153-4108-b222-021ea770fdd3

GBIF.no/ipt/: http://gbif.no/ipt/resource.do?r=o_aves_d

Vegetation survey data

Proposed new survey data format for Darwin Core archives: http://terms.tdwg.org/wiki/Vegetation_Survey

DEMO IPT for exploring the new Darwin Core format: http://eubon-ipt.gbif.org/

Example of a vegetaion survey dataset in GBIF: http://www.gbif.org/dataset/0b328835-ea95-4ec3-a0f4-dd2dba993f1f

Suggested reading list

Pensoft: Biodiversity Data Journal (ISSN 1314-2828)

http://biodiversitydatajournal.com/

http://biodiversitydatajournal.com/browse_articles

http://pwt.pensoft.net/ (Pensoft Writing Tool)

Biodiversity Data Journal is classified as a level 1 (nivå 1) journal in Norway:

https://dbh.nsd.uib.no/publiseringskanaler/KanalTidsskriftInfo?id=480894&bibsys=0

Editorial med en introduksjon til hensikten med BDJ:

Smith et al. (2013) Beyond dead trees: integrating the scientific process in the Biodiversity Data Journal. doi:10.3897/BDJ.1.e995, http://biodiversitydatajournal.com/articles.php?id=995

Nature: Scientific Data (ISSN 2052-4436)

Nature Publishing Group has launched a similar data paper journal, Scientific Data:

http://www.nature.com/sdata/

http://www.nature.com/press_releases/scientific-data.html (launched in May 2014)

http://blogs.nature.com/scientificdata/ (Scientific Data blog)

Not yet registered in the Norwegian scientific journal classification system:

https://dbh.nsd.uib.no/publiseringskanaler/KanalTreffliste?enkeltSok=2052-4436

In collaboration with GBIF: http://www.gbif.org/page/2997 (November 2013)

Global Registry of Biorepositories (GRBio): http://grbio.org/

Darwin Core: instituteCode, instituteID, collectionCode, collectionID

Hotel:

Participants traveling to Oslo will stay at the Rica Travel Hotel.

Rica Travel Hotel in Arbeidergate 4, 0159 Oslo (+47 22 00 33 00)

Airport transport:

The Airport train (http://www.flytoget.no/) departures with 10 minute interval, 19 minutes travel time to Oslo central station. The station “Nasjonalteateret” (National Theatre) is 550 meters from the Rica Travel Hotel and reached by every second departure of the airport train (those with end station Drammen). The ticket cost is NOK 170 kr.

Local transport:

The subway (http://www.tbanen.no/) station “Stortinget” is located 150 meter from the Rica Travel Hotel and the station “Tøyen” is located 500 meter from the Natural History Museum (Lids hus) [subway line map.pdf].

Alternatively, the museum is located 2.2 km walking distance from the hotel.

Travel reimbursement forms (Norwegian):

Travel reimbursement forms (English):

Organizer

GBIF Norway and The Belgian Biodiversity Platform

Tags: biodiversity, workshop, data paper

Published Apr. 23, 2015 8:39 AM - Last modified Sep. 8, 2015 3:03 PM