BioFresh project

Member of the

Freshwater Information Platform

Submitting data to the Freshwater Biodiversity Data Portal

The Freshwater Biodiversity Data Portal – initiated through the BioFresh project – strongly encourages scientists to submit any primary biodiversity data published in a scientific paper to national nodes of GBIF or to thematic initiatives such as the Freshwater Biodiversity Data Portal. This initiative is discussed in the paper: De Wever, A, Schmidt-Kloiber, A, Gessner, MO and K Tockner (2012) Freshwater Journals Unite to Boost Primary Biodiversity Data Publication. Bioscience, 62 (6): 529–530. doi:10.1525/bio.2012.62.6.2.

Collaboration with freshwater journals

In collaboration with freshwater journal editors we developed the following statement, which will widely be published in the instructions for authors and on the journals websites:

Authors are encouraged to place all species distribution records in a publicly accessible database such as the national Global Biodiversity Information Facility (GBIF) nodes ( or data centres endorsed by GBIF, including BioFresh (

This statement is currently (March 2012) approved by the editors and publishers of the following journals: Aquatic Botany, Aquatic Conservation: Marine and Freshwater Ecosystems, Aquatic Ecology, Aquatic Sciences, Canadian Journal of Fisheries and Aquatic Sciences, Ecology of Freshwater Fish, Freshwater Biology, Freshwater Reviews, Fundamental and Applied Limnology, Hydrobiologia, Inland Waters, International Review of Hydrobiology, Freshwater Science (Journal of the North American Benthological Society until January 2012), Journal of Fish Biology, Journal of Plankton Research, Limnetica, Limnologica, Marine and Freshwater Research and River Systems. Discussions are in progress with an additional 9 major journals in the field.

Proposed procedure

As the Freshwater Biodiversity Data Portal is not the only possible outlet for publishing primary biodiversity data to the Global Biodiversity Information Facility (GBIF) network, data providers should first identify whether publishing through the Freshwater Biodiversity Data Portal is the most suitable option, e.g. for national datasets from countries with an active GBIF node, their national node (see list) may be a more suitable option, for freshwater datasets from countries which are currently not a member of GBIF on the other hand, publication through the Freshwater Biodiversity Data Portal would definitely be a good solution. If you are convinced that publishing through the Freshwater Biodiversity Data Portal is the way to go or you are interested to learn more about the publication procedure we propose, please read on…

Submitting data to the Freshwater Biodiversity Data Portal and the GBIF-network involves providing a basic description of the dataset (for the metadatabase) and organising the data in a standard format (Darwin Core). For organising (or mapping) the data, there is a range of technical options going from sending the data in an Excel template to installing a server-tool for hosting your institute’s data. For primary biodiversity data used in a scientific paper, submitting data in a spreadsheet is probably the best option, but in case of doubt, have a look at the other options or contact us for more information or assistance.

Submit data in spreadsheet format

Submitting data in a spreadsheet template will be the most straightforward option for most small datasets and is especially suitable for a ‘finished’ dataset from an individual researcher. If you want to publish data from a database that is constantly being updated or if you want complete control over the data publishing process, please consider the next two options.

The following video provides a basic explanation of this procedure:

Tutorial: Using the BioFresh Data Submission Spreadsheet from BioFresh Oxford on Vimeo.

Data can be submitted using the BioFresh-spreadsheet templates as documented in this overview of the different fields and their recommendation (97.7kb xls document hosted on Google code) (in this case, metadata should be completed using the Freshwater Metadatabase). The full template can be downloaded here (44kb xls document hosted on Google code) For simple datasets we have also produced a minimal template (42kb xls document hosted on Google code). Alternatively, we also accept data exported in the GBIF template for occurrence data available from (this template includes a worksheet for completing the metadata).

Simply send the data to for processing.

Submit data using the Freshwater Biodiversity Data Portal/BioFresh Integrated Publishing Toolkit (IPT) page

If you prefer to take control over all steps of the data publishing process and plan to release updates of your data, you can request login and password for the BioFresh IPT. Send us an email at with the name and description of your dataset (the latter is not required if you already completed a metadatabase entry for this dataset).
Full instructions on how to use the IPT are available from GBIF, for data publishing, we suggest you immediately jump to the quick reference section. We plan to compile a brief instructions guide for users of the BioFresh IPT, but, in the meantime, have a look at the instructions compiled for Canadensys and please don’t hesitate to contact us for any assistance.

Submit data using your own IPT

Institutions wanting to publish several datasets which are regularly updated should consider installing their own IPT. This allows them to host any data they want to provide to the Freshwater Biodiversity Data Portal and/or GBIF (after endorsement by a GBIF node). Full instructions on how to install and use the IPT are available from GBIF.