Missouri Botanical Garden Open Conference Systems, TDWG 2014 ANNUAL CONFERENCE

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Centralising thematic (freshwater) biodiversity data using the Darwin Core standard and GBIF’s Integrated Publishing Toolkit (IPT)
Aaike De Wever, Astrid Schmidt-Kloiber, Sylvain Renaudier, Michel Kapel, Robert Vogl, Koen Martens

Last modified: 2014-09-29


In order to encourage open access data publication and to support active mobilisation of biodiversity data in the freshwater research realm, the EU-funded BioFresh project created an information platform [1] for centralising such data and related freshwater biodiversity information. The data portal [2] component of the BioFresh platform consists of an occurrence database and a metadatabase on freshwater datasets.

For the occurrence database, we selected a number of recommended fields from the Darwin Core standard, which were considered as relevant in the context of freshwater (documented as “freshwater core” [3]). We assisted data holders of individual datasets to publish their data through a central BioFresh installation of GBIF’s Integrated Publishing Toolkit (IPT) and encouraged institutional partners to set up their own IPT for data publication.

To centralise the data and incorporate them in a freshwater occurrence database, we developed a “Data Portal Import Tool”. This data-harvesting tool allows users to (1) perform a taxonomic review of the dataset and (2) link the occurrence data to a central taxonomic backbone, in this case the FADA (Freshwater Animal Diversity Assessment [4]) database. In addition, we built a module to incorporate additional occurrence data available through the GBIF network. These data are filtered on dataset and species information during import (to exclude e.g. marine datasets and non-freshwater species).

As a means to encourage the publication of occurrence data and the documentation of datasets in the metadatabase, we fully endorse the release of such data and information through the publication of a (meta-) data paper. To motivate the documentation of a wide range of freshwater-related datasets, we therefore developed an automated workflow for publishing the information entered in the BioFresh metadatabase as an article of the recently launched Freshwater Metadata Journal [5].

The Data Portal Import Tool and Freshwater Metadata Journal are fully functional since October 2014 and will be demoed on-request during the poster presentation at TDWG 2014.

[1] http://www.freshwaterbiodiversity.eu/

[2] http://data.freshwaterbiodiversity.eu/

[3] https://code.google.com/p/freshwatercore/

[4] http://fada.biodiversity.be/

[5] http://freshwaterjournal.eu/