data editors meeting at sefs

Aaike De Wever, Mark Gessner

Data publication discussion

© J. Freyhof, A. Hartl

SEFS7 – June 2011 – Girona, ESP www.freshwaterbiodiversity.eu

Context (1/3)

• The EU-FP7 BioFresh-project aims to improve capacity to protect and manage freshwater biodiversity by (among others) building a Dedicated Freshwater Biodiversity Information Platform (BioFresh data portal)

• BioFresh wants to encourage the publication of freshwater biodiversity data in a broad sense

• There is a growing tendency from funding agencies and scientific institutes to encourage open data initiatives

SEFS7 – June 2011 – Girona, ESP www.freshwaterbiodiversity.eu

Context (2/3)

• EMBL/GenBank/DDBJ provides a very good example on how primary research data can be centrally stored and made available to other researchers

• Sequence data submission to EMBL/GenBank/DDBJ is a prerequisite for publishing in most SCI journals.

• Strains

SEFS7 – June 2011 – Girona, ESP www.freshwaterbiodiversity.eu

Context (3/3)

• The GBIF network acts as a repository for basic biodiversity data (taxon identity, occurrence, reference)

• BioFresh offers assistance to data holders who wish to publish basic freshwater biodiversity data, through the GBIF network.

• BioFresh promotes publication of research data, by compiling a metadatabase to document freshwater related databases and will also consider making ‘richer’ datasets available through its portal (http://data.freshwaterbiodiversity.eu/)

• A concerted action of journal editors would greatly foster data publication

SEFS7 – June 2011 – Girona, ESP www.freshwaterbiodiversity.eu

GBIF

SEFS7 – June 2011 – Girona, ESP www.freshwaterbiodiversity.eu

Basic biodiversity data

• Occurrence information– Species– Location (description and coordinates)– Type of record: observation/specimen/sound recording/…– + metadata: dataset, collection, institute,…

• Teaser to richer dataset– Occurrence data may be accompanied by environmental data,

but these are not included in the ‘basic biodiversity data’

• Standards and tools to exchange these data through a system of interoperable databases are readily available

• BioFresh as a facilitator to ease the data submission to GBIF

SEFS7 – June 2011 – Girona, ESP www.freshwaterbiodiversity.eu

Questions / Goals

• Collect opinions on the initiative• What would be required to make this work?• What are the worries?

• Have a preliminary agreement by the meeting Thursday night

SEFS7 – June 2011 – Girona, ESP www.freshwaterbiodiversity.eu

Example papers - Hydrobiologia

1. Clear example

2. Yes, but cites dataset

3. Depends

SEFS7 – June 2011 – Girona, ESP www.freshwaterbiodiversity.eu

Example papers

• Aquatic Conservation: Marine and Freshwater Ecosystems

• No, link to GenBank

• Aquatic siences

SEFS7 – June 2011 – Girona, ESP www.freshwaterbiodiversity.eu

Example papers

• Marine &Freshwater Research

• Depends, any original data?

• Limnetica

• Clear example!

SEFS7 – June 2011 – Girona, ESP www.freshwaterbiodiversity.eu

• Information on databases could be stored in a central metadatabase. This should be seen as an archiving initiative that makes sure that datasets can be easily traced. BioFresh is planning to built such a metadatabase for freshwater. Obviously this initiative will also get stronger if it gets backed by journal editors. In addition, BioFresh is considering to provide a ‘ready-to-publish-overview’ export for users of its metadatabase who want to make their full database available and publish a metadata paper (see next option).

SEFS7 – June 2011 – Girona, ESP www.freshwaterbiodiversity.eu

• Full databases, which go beyond the basic biodiversity and are not organized in a standard way, could be documented in ‘metadata papers’ (i.e. papers describing the database) in either (online) data journals, theme issues of a regular journal or as more elaborated regular papers. Hereby the data itself would be made available as supplementary material and the database can be unambiguously cited. BioFresh would integrate the information in such papers in its metadatabase and where relevant/possible BioFresh could also integrate the data itself in its data portal to give the data and the paper more visibility.

SEFS7 – June 2011 – Girona, ESP www.freshwaterbiodiversity.eu

• Data available as on-line supplementary material to papers could be made available as non-copyrighted material (regardless whether the paper itself is open access or not) and be documented in a metadatabase with archiving functionality. This would be an extension to the current BioFresh metadatabase.