Data publication presentation at SIL2013

Aaike De Wever, Astrid Schmidt-Kloiber

Biodiversity data publishing in freshwater sciences

© J. Freyhof, A. Hartl

RBINS – Royal Belgian Institute of Natural Sciences, BrusselsBOKU – University of Natural Resources & Life Sciences, Vienna

SIL2013 – August 2013 – Budapest, HUwww.freshwaterbiodiversity.eu

Freshwater biodiversity

• Freshwater species face a higher extinction rate than species in any other environment

• Need to improve capacity to protect and manage freshwater biodiversity in the face of ongoing changes to global climate and socioeconomics

Lipotes vexillifer

Recently extinct species

© Institute of HydrobiologyChinese Academy of Sciences

© M. Franzen

Incilius periglenes


Data publishing versus data sharing

• Data publishing paradigm– Both ‘traditional’

publishing through data paper as well as making data available on-line

– Stressing importance of providing a citation for data and citing data

– Assigning a Digital Object Identifier (DOI) to data

Mark J. Costello (2009) Motivating Online Publication of Data BioScience 59 (5): 418-427.


Building a global freshwater biodiversity information hub – www.freshwaterbiodiversity.eu

• Bringing data and information together in a central place – the BioFresh platform

• Making data more easily discoverable• Outlet for scientists to publish their data• Supporting large scale analysis and modelling using

these data


Building a global freshwater biodiversity information hub

• Focus on– information on datasets

(metadatabase)– occurrence data (or

primary biodiversity data)– distribution information– all kinds of thematic

biodiversity maps– other species information


Availability of data – general

• Large amounts of data are unavailable and we only have a vague idea of its volume

• Example for the data available through the Global Biodiversity Information Facility network– 20% of existing digitised data available through GBIF.

Saarenmaa (2006) ArcUser Online.

– 3% of natural history collections (digitised and non-digitised) are accessible through GBIF. Ariño (2010) Biodiversity Informatics, 7(2).

• There is a substantial volume of data we ‘know’ exists, but is hard to get by (e.g. data collected for monitoring the state of the environment or the impact of conservation efforts)


Availability of data – freshwater occurrences

• Based on the species names in the Freshwater Animal Diversity Assessment (FADA) database (currently covering about 1/3 of the global freshwater species) we harvested the available occurrence data from GBIF– 9M records, 7M geo-referenced (roughly 2% of the almost 400M

records)– Roughly 1/3 collection data and 2/3 observation data– Data from over 1200 datasets, but only 17 could be considered

being predominantly freshwater

• Data integrated in the BioFresh data portal data.freshwaterbiodiversity.eu

http://data.freshwaterbiodiversity.eu/


Availability of data – freshwater databases

• BioFresh constructed a metadatabase for documenting freshwater focused databases– 162 entries (54 under quality control)


Data publishing through BioFresh

• Establishing a thematic freshwater node for the Global Biodiversity Information Facility

• Data publishing efforts cover– Data from project partners including databases from major EU

projects on freshwater biodiversity including WISER, EFI+,…– Digitisation and compilation projects for completing data for

specific species groups: Odonata, EU fishes, Trichoptera, Plecoptera, Ostracoda

– Mobilisation of data gathered for the intercalibration of methods for the Water Framework Directive

– Encouraging the publication of your data…


Data publishing through BioFresh

• What can we offer data publishers– Biodiversity data publication offering

• visibility• citations• possibility for peer review both for metadata as for data

– Technical data quality review– Automatic integration of data in on-line database and

visualisation tools– But see also next slides…


Data publishing through freshwater journals

• We convinced editors of 19 journals to encourage the submission of biodiversity data associated with papers published in their journal

Bioscience, 62 (6): 529–530

• Submission of primary biodiversity data cfr. submission of sequence data to GenBank

• Step towards mandatory/default procedure

Aquatic BotanyAquatic Conservation: Marine and Freshwater EcosystemsAquatic EcologyAquatic SciencesCanadian Journal of Fisheries and Aquatic SciencesEcology of Freshwater FishFreshwater BiologyFreshwater ReviewsFundamental and Applied LimnologyHydrobiologiaInland WatersInternational Review of HydrobiologyFreshwater ScienceJournal of Fish BiologyJournal of Plankton ResearchLimneticaLimnologicaMarine and Freshwater Research River Systems


Data publishing through data papers

• Producing a data paper for a dataset that is publicly released (e.g. through the BioFresh data portal) produces a clear mechanism to cite the data and track its citation

• BioFresh is planning a theme issue focussing on freshwater databases

• All contributions are very welcome!

THANK YOU FOR YOUR ATTENTION!

Data publication presentation at SIL2013

Education

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