A data paper focus on the description of a scientific data set to improve accessibility and appropriate reuse of the data by other researchers. 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 24th March (NTNU VM)
On Tuesday we will be in the meeting room Stormrommet at NTNU University Museum downtown Trondheim at Erling Skakkes gate 47.
09:30 Coffee and registration
10:00 Introduction to the course
Overview course content and practical information.
Round-table presentation of your background (maximum 2 minutes each).
10:30 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).
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What & why
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The GBIF-IPT metadata profile & data paper guidelines
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Tools to use
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 10 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
Wednesday 25th March (NINA-building)
On Wednesday we be in the meeting room Toppskarven at the NINA-building located at the NTNU university campus Gløshaugen, in the northern part near Lerkendal, Høgskoleringen 9.
09:00 Introduction to day 2
09:30 Continue writing the data papers (all)
11:30 Lunch-seminar (max 30 minutes)
Introducing academic and peer-review publication for biodiversity data sets.
The Global Biodiversity Information Facility (GBIF) and the Norwegian Biodiversity Information Centre (Artsdatabanken) provides a framework for publishing primary biodiversity data. This lunch seminar presents recent developments on an integrated data publishing framework for primary biodiversity data. The seminar will present the new scientific journals from Pensoft and the Nature publishing group offering novel academic publication of (biodiversity) data set descriptions which is developed and recently released in collaboration with GBIF. We will also present options for persistent archiving of data sets using Norstore, B2SHARE (EUDAT) and Data One.
Popularized introduction to biodiversity data publishing open to the public.
12:00 Lunch
Hegstad Blakstad lunch restaurant in the NINA-building, Høyskoleringen 9.
13:00 Introduction to submitting the data papers
Pensoft BDJ, ZooKeys or PhytoKeys
15:00 Continue writing the data papers (all)
We aim at all data papers published before the summer holidays.
16:00 End of day 2
16:15 Workshop dinner at NINA-huset (proposed and if most of you can attend)
Hegstad Blakstad restaurant in the NINA-building, Høyskoleringen 9.
Organizers (contact persons)
- Dimitri Brosens (BeBIF, Belgian Biodiversity Platform) Skype: @dimevil
- Dag Endresen (GBIF Norway, UiO NHM, Oslo)
- Christian Svindseth (GBIF Norway, UiO NHM, Oslo)
- Gunnar Austrheim, Vegetation survey dataset, NTNU VM, Trondheim
- Dag-Inge Øien, NTNU VM, Trondheim
- Frank Hanssen, NINA, Trondheim
- Wouter Koch, Artsdatabanken, Trondheim
Participants (approximately 23 people)
- NTNU VM, 13 participants: Anders G. Finstad, Kristian Hassel, Tommy Presthus, Karstein Hårsaker, Marc Daverdin, Egil Aune, Maria Capa, Xio-long Lin, Olav H., Anders Lyngstad, Narjes Yousefi, Dag-Inge Øien, Gunnar Austrheim
- NINA, 7 participants: Erlend Nilsen (researcher), Siri Sæther (Ansvarlig for Bibliotek og open access), Roald Vang (Miljødataseksjonen), Frank Hanssen (Miljødataseksjonen), Graciela Rusch (forsker), Ishita Ahuja (forsker NINA/NTNU), Elisabet Forsgren (researcher, aquaculture)
- Artsdatabanken, 1 participant: Wouter Koch,
- [no participants attended from NTNU Institute for biology]
- GBIF, 3 people: Dimitri Brosens, Dag Endresen, Christian Svindseth
Please remember to prepare a short presentation of your own dataset! A round table presentation of datasets are included in the agenda after lunch on Tuesday.
Data paper template
Google Doc template
Google Documents provides an efficient platform for collaborative writing of a data paper. You can copy this document [save as] and share with your co-authors to start writing your own data paper.
Template with examples:
Github template link:
Another efficient tool for writing a collaborative data paper is provided by GitHub. GitHub is often used for collaborative development of software code. You can clone the template used by the Belgian GBIF network to start your own data paper.
Pensoft Writing Tool
Pensoft Publishers provides a useful writing tool for collaborative writing of a data paper and easy submission to the Pensoft Biodiversity Data Journal.
Global Registry of Biorepositories (GRBio)
The Global Registry of Biorepositories (GRBio, http://grbio.org/) provides a collaborative registry of biorepositories where biorepository curators and contact persons can register their own collections and reserve their preferred institution code and collection codes.
- Darwin Core: instituteCode, instituteID, collectionCode, collectionID
Vegetation survey data
Some of you may have datasets based on survey data. This is a new data type in GBIF and methodology for improved support are under development. We recommend to start publishing your datasets following the current Darwin Core format. Enhanced support for this data type is under development and of high priority for the 2015 GBIF work plan.
- 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 vegetation survey dataset in GBIF: http://www.gbif.org/dataset/0b328835-ea95-4ec3-a0f4-dd2dba993f1f
- News story from GBIF, 25th March 2015: http://www.gbif.org/page/82105
Suggested reading list and examples
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
- https://dbh.nsd.uib.no/publiseringskanaler/KanalForlagInfo.action?id=22911 (Pensoft)
Editorial with an introduction to the objective of 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)
Examples of published data papers
Example data paper from Pensoft: BDJ (ISSN 1314-2828)
- Browse data paper in Biodiversity Data Journal
- Mitroiu M, Noyes J, Cetkovic A, Nonveiller G, Radchenko A, Polaszek A, Ronquist F, Forshage M, Pagliano G, Gusenleitner J, Bartalucci M, Olmi M, Fusu L, Madl M, Johnson N, Jansta P, Wahis R, Soon V, Rosa P, Osten T, Barbier Y, de Jong Y (2015) Fauna Europaea: Hymenoptera – Apocrita (excl. Ichneumonoidea). Biodiversity Data Journal 3: e4186. doi: 10.3897/BDJ.3.e4186
- Keklikoglou K, Faulwetter S, Chatzigeorgiou G, Badalamenti F, Kitsos M, Arvanitidis C (2013) MidMedPol: Polychaetes from midlittoral rocky shores in Greece and Italy (Mediterranean Sea). Biodiversity Data Journal 1: e961. doi:10.3897/BDJ.1.e961,
- http://biodiversitydatajournal.com/articles.php?id=961
- Faulwetter S, Markantonatou V, Pavloudi C, Papageorgiou N, Keklikoglou K, Chatzinikolaou E, Pafilis E, Chatzigeorgiou G, Vasileiadou K, Dailianis T, Fanini L, Koulouri P, Arvanitidis C (2014) Polytraits: A database on biological traits of marine polychaetes. Biodiversity Data Journal 2: e1024. doi:10.3897/BDJ.2.e1024,
- http://biodiversitydatajournal.com/articles.php?id=1024
- Sonké B, Couvreur T (2014) Tree diversity of the Dja Faunal Reserve, southeastern Cameroon. Biodiversity Data Journal 2: e1049. doi:10.3897/BDJ.2.e1049,
- http://biodiversitydatajournal.com/articles.php?id=1049
- Powney G, Brooks S, Barwell L, Bowles P, Fitt R, Pavitt A, Spriggs R, Isaac N (2014) Morphological and Geographical Traits of the British Odonata. Biodiversity Data Journal 2: e1041. doi:10.3897/BDJ.2.e1041, http://biodiversitydatajournal.com/articles.php?id=1041
Example data paper from Pensoft: PhytoKeys (ISSN 1314-2003)
- Browse data paper in PhytoKeys
- Alonso P, Iriondo JM (2014). URJC GB dataset: Community-based seed bank of Mediterranean high-mountain and semi-arid plant species at Universidad Rey Juan Carlos (Spain). PhytoKeys 35: 57–72. doi:10.3897/phytokeys.35.6746 Resource Key: http://www.gbif.org/dataset/59bf2c83-1e3c-40c8-9437-39ce3d3d462c
- García-Sánchez J, Cabezudo B (2013). Herbarium of the University of Malaga (Spain): Vascular Plants Collection. PhytoKeys 26: 7–19. doi:10.3897/phytokeys.26.5396, Resource ID: GBIF key: http://gbrds.gbif.org/browse/agent?uuid=962cceea-f762-11e1-a439-00145eb45e9a
- Espinosa M, López J (2013). Herbarium of Vascular Plants Collection of the University of Extremadura (Spain). PhytoKeys 25: 1–13. doi:10.3897/phytokeys.25.5341 Resource ID: GBIF key: http://gbrds.gbif.org/browse/agent?uuid=835d30de-f762-11e1-a439-00145eb45e9a
- Desmet P, Brouillet L (2013). Database of Vascular Plants of Canada (VASCAN): a community contributed taxonomic checklist of all vascular plants of Canada, Saint Pierre and Miquelon, and Greenland. PhytoKeys 25: 55–67. doi:10.3897/phytokeys.25.3100 Resource ID: GBIF key: http://gbrds.gbif.org/browse/agent?uuid=3f8a1297-3259-4700-91fc-acc4170b27ce
- Van Landuyt W, Vanhecke L, Brosens D (2012) Florabank1: a grid-based database on vascular plant distribution in the northern part of Belgium (Flanders and the Brussels Capital region). PhytoKeys 12: 59-67. doi:10.3897/phytokeys.12.2849
Example data paper from Pensoft: ZooKeys (ISSN 1313-2970)
- Browse data paper in ZooKeys
- Piazza P, Blazewicz-Paszkowycz M, Ghiglione C, Alvaro M, Schnabel K, Schiaparelli S (2014) Distributional records of Ross Sea (Antarctica) Tanaidacea from museum samples stored in the collections of the Italian National Antarctic Museum (MNA) and the New Zealand National Institute of Water and Atmospheric Research (NIWA). ZooKeys 451: 49-60. doi:10.3897/zookeys.451.8373
- Neubauer T, Kroh A, Harzhauser M, Georgopoulou E, Mandic O (2014) Synopsis of valid species-group taxa for freshwater Gastropoda recorded from the European Neogene. ZooKeys 435: 1-6. doi:10.3897/zookeys.435.8193
- Martínez-Morales M, Pinilla-Buitrago G, González-García F, Enríquez P, Rangel-Salazar J, Guichard Romero C, Navarro-Sigüenza A, Monterrubio-Rico T, Escalona-Segura G (2014) CracidMex1: a comprehensive database of global occurrences of cracids (Aves, Galliformes) with distribution in Mexico. ZooKeys 420: 87-115. doi:10.3897/zookeys.420.7050
- Morales Rozo A, Valencia F, Acosta A, Parra J (2014) Birds of Antioquia: Georeferenced database of specimens from the Colección de Ciencias Naturales del Museo Universitario de la Universidad de Antioquia (MUA). ZooKeys 410: 95-103. doi:10.3897/zookeys.410.7109
- Figueira R, Monteiro M, Reino L, Beja P, Mills M, Bastos-Silveira C, Ramos M, Rodrigues D, Queirós Neves I, Consciência S (2014) The collection and database of Birds of Angola hosted at IICT (Instituto de Investigação Científica Tropical), Lisboa, Portugal. ZooKeys 387: 89-99. doi:10.3897/zookeys.387.6412
- Neubauer T, Kroh A, Harzhauser M, Georgopoulou E, Mandic O (2014). Synopsis of valid species-group taxa for freshwater Gastropoda recorded from the European Neogene. ZooKeys 435: 1-6. doi:10.3897/zookeys.435.8193
- Gutt J, Piepenburg D, Voß J (2014). Asteroids, ophiuroids and holothurians from the southeastern Weddell Sea (Southern Ocean). ZooKeys 434: 1-15. doi:10.3897/zookeys.434.7622
- Brosens D, Vankerkhoven F, Ignace D, Wegnez P, Noé N, Heughebaert A, Bortels J & Dekoninck W (2013). FORMIDABEL: The Belgian Ants Database. ZooKeys 306: 59-70. doi:10.3897/zookeys.306.4898
- Brosens D, Breine J, Van Thuyne G, Belpaire C, Desmet P, Verreycken H (2015). VIS – A database on the distribution of fishes in inland and estuarine waters in Flanders, Belgium. ZooKeys 475: 119-145. doi:10.3897/zookeys.475.8556
Example data paper from Nature: Scientific Data (ISSN 2052-4436)
- Pigott DM, Golding N, Messina JP, Battle KE, Duda KA, Balard Y, Bastien P, Pratlong F, Brownstein JS, Freifeld CC, Mekaru SR, Madoff LC, George DB, Myers MF & Hay SI (2014). Global database of leishmaniasis occurrence locations, 1960–2012. Sci. Data 1:140036. doi:10.1038/sdata.2014.36. http://www.nature.com/articles/sdata201436
- Roquet F, Williams G, Hindell MA, Harcourt R, McMahon C, Guinet C, Charrassin J-B, Reverdin G, Boehme L, Lovell P & Fedak M (2014). A Southern Indian Ocean database of hydrographic profiles obtained with instrumented elephant seals. Sci. Data 1:140028. doi:10.1038/sdata.2014.28. http://www.nature.com/articles/sdata201428
- Plooij FX, van de Rijt-Plooij H, Fischer M & Pusey A (2014). Longitudinal recordings of the vocalizations of immature Gombe chimpanzees for developmental studies. Scientific Data 1:140025. doi:10.1038/sdata.2014.25 http://www.nature.com/articles/sdata201425
- Mazzoldi C, Sambo A & Riginella E (2014). The Clodia database: a long time series of fishery data from the Adriatic Sea. Scientific Data 1:140018. doi:10.1038/sdata.2014.18. http://www.nature.com/articles/sdata201418
- Hao Z, AghaKouchak A, Nakhjiri N & Farahmand A (2014). Global integrated drought monitoring and prediction system. Scientific Data 1, Article number: 140001. doi:10.1038/sdata.2014.1 http://www.nature.com/articles/sdata20141
- Edgar GJ & Stuart-Smith RD (2014). Systematic global assessment of reef fish communities by the Reef Life Survey program. Scientific Data 1, Article number: 140007. doi:10.1038/sdata.2014.7 http://www.nature.com/articles/sdata20147
- Messina JP, Brady OJ, Pigott DM, Brownstein JS, Hoen AG & Hay SI ( 2014). A global compendium of human dengue virus occurrence. Scientific Data 1:140004. doi:10.1038/sdata.2014.4 http://www.nature.com/articles/sdata20144
References
- Chavan V, Penev L (2011) The data paper: a mechanism to incentivize data publishing in biodiversity science. BMC Bioinformatics 12: S2. doi:10.1186/1471-2105-12-S15-S2
- 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
- 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. http://dx.doi.org/10.1016/j.tree.2013.05.002
- 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
- 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
- Smith V, Georgiev T, Stoev P, Biserkov J, Miller J, Livermore L, Baker E, Mietchen D, Couvreur T, Mueller G, Dikow T, Helgen K, Frank J, Agosti D, Roberts D, Penev L (2013) Beyond dead trees: integrating the scientific process in the Biodiversity Data Journal. Biodiversity Data Journal 1: e995. doi:10.3897/BDJ.1.e995
Collection of relevant slides (on data papers)
GBIF Data publishing framework
- Chavan, V. (October 2013). Incentivising Biodiversity Data Publishing: GBIF - Pensoft partnership. [TDWG 2013] [21 slides] http://www.slideshare.net/vishwaschavan/data-papers-gbif-pensoft-workflow-tdwg-roma
- Chavan, V. (October 2013). Exploring the future of scholarly publishing of biodiversity data. [TDWG 2013] [49 slides] http://www.slideshare.net/vishwaschavan/final-future-scholarlypublishingbiodiversitydatatdwg2013
Pensoft: Biodiversity Data Journal
- http://www.slideshare.net/pensoft/presentations
- Penev, L. (May 2014). Authoring, peer-review and publishing in one place, for the first time. [17 slides]. http://www.slideshare.net/pensoft/pensoft-journal-system-20-washington-may-2014
- Penev, L. et al. (September 2013). Integrating data publishing with workflows in biodiversity research. http://www.slideshare.net/Daniel.Mietchen/integrating-data-publishing-with-workflows-in-biodiversity-research-potsdam-2013
- Penev, L. (September 2013). Authoring, peer-review and publication in one place, for the first time! Pensoft Journal System (PJS 2.0). [64 slides] http://www.slideshare.net/pensoft/authoring-peerreview-and-publication-in-one-place-for-the-first-time-pensoft-journal-system-pjs-20
- Penev, L. et al. (September 2013). Revolution in publication: Data and text publishing integrated in the Biodiversity Data Journal. [68 slides] http://www.slideshare.net/pensoft/revolution-in-publishing-bio-horizon-rome-2013
- Penev, L. et al. (February 2013). Pensoft writing tool: PWT. [55 slides] http://www.slideshare.net/pensoft/pwt-leiden-workshop-feb-2013-final-1
NPG: Scientific Data
- http://www.slideshare.net/SusannaSansone/presentations
- Sansone, S.-A. (November 2014). Better data through better curation. [Scientific Data, data paper] [25 slides]http://www.slideshare.net/SusannaSansone/better-data-through-better-curation-ssansone-npg-event-on-data-publication-nov
- Sansone, S.-A. (November 2014). Data papers and their applications: examples from Nature Publishing Group and Ubiquity Press. [51 slides] http://www.slideshare.net/SusannaSansone/scidatacon-2014-data-papers-and-their-applications-workshop-npg-scientific-data
- Sansone, S.-A. (November 2014). What is big data in biomedicine? Data types to be considered. [Big data, small data, data papers] [13 slides] http://www.slideshare.net/SusannaSansone/sansone-statement-bdebatetue11nov2014, http://blogs.nature.com/scientificdata/2014/10/13/size-doesnt-matter/
- Sansone, S.-A. et al. (May 2014). Scientific data: A new open-access, online-only publication for descriptions of scientifically valuable datasets. Focusing initially on datasets from the life, biomedical and environmental science communities. http://www.slideshare.net/SusannaSansone/rda-long-tail-data-interest-group
ViBRANT, Scratchpads and the Natural History Museum in London
- Baker, E. et al. (November 2013). A paradigm shift in biodiversity publishing: The new Biodiversity Data Journal. [20 slides] http://www.slideshare.net/edwbaker/baker-bdj-28708706
- Smith V. et al. (June 2013). Don’t make me think: Biodiversity data publishing made easy. [12 slides] [ViBRANT, Scratchpads] http://www.slideshare.net/vsmithuk/2013-i-evobio-smith-dont-make-me-thinknotext
- Koureas, D.N. et al. (February 2013). Publishing biodiversity: The interplay between Scratchpads and the new Biodiversity Data Journal. [42 slides] http://www.slideshare.net/dimitriskoureas/publishing-biodiversity-koureas
- Smith V. et al. (September 2012). Making your data work for you: Scratchpads, publishing & the Biodiversity Data Journal. [33 slides] http://www.slideshare.net/vsmithuk/making-your-data-work-for-you-scratchpads-publishing-the-biodiversity-data-journal, http://www.slideshare.net/vsmithuk/making-your-data-work-for-you-scratchpads-publishing-the-biodiversity-data-journal-14455301
Other useful slides to consult
- Desmet, P. & Brosens, D. (October 2014). Occurrence data at the INBO: opening up our data publication workflow. [TDWG 2014] [46 slides] https://speakerdeck.com/peterdesmet/occurrence-data-at-the-inbo-opening-up-our-data-publication-workflow
- Kunze, J. (February 2012). New metaphors: data papers and data citations. [31 p] http://n2t.net/ark:/13030/m58050wd, https://merritt.cdlib.org/d/ark%3A%2F13030%2Fm58050wd/2/producer%2Fjakdatametaphorsfeb12-120229173050-phpapp01.pdf
Mapping tools and resources
- CartoDB: http://cartodb.com/
- MapBox: https://www.mapbox.com/
- QGIS: http://qgis.org/en/site/
- Norwegian Mapping Agency (freely available map data for Norway) http://www.kartverket.no/kart/gratis-kartdata/lisens/
Practical information
GBIF Norway will cover the costs of travel and accommodation for invited participants travelling from outside of Trondheim.
Travel reimbursement forms (Norwegian):
- http://www.uio.no/for-ansatte/ansettelsesforhold/reise/reiseskjemaer-oversikt.html
- http://www.uio.no/for-ansatte/skjema/opa/reiseregning.doc - [pdf]
- http://www.uio.no/for-ansatte/skjema/opa/vedlegg-utland.docx - [odt]
Travel reimbursement forms (English):
- http://www.uio.no/english/for-employees/employment/travel/travel-forms-overview.html
- http://www.uio.no/english/for-employees/employment/salary-payment/reimbursements/index.html
- http://www.uio.no/for-ansatte/skjema/opa/utleggsrefusjon-eng.rtf - [pdf]
- http://www.uio.no/for-ansatte/skjema/opa/vedlegg-utland.docx - [odt]