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EPOCA data management

EPOCA data management activities: a summary


 Nisumaa A.-M.1,2, Schlitzer R.3, Hansson L.1,2 & Gattuso J.-P.1,2


  1. CNRS-INSU, Laboratoire d'Océanographie de Villefranche, BP 28, 06234 Villefranche-sur-Mer Cedex, France
  2. Université Pierre et Marie Curie-Paris 6, Observatoire Océanologique de Villefranche, BP 28, 06230 Villefranche-sur-Mer, France
  3. Alfred Wegener Institute for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany

Corresponding author: gattuso@obs-vlfr.fr

1. Introduction

The EU FP7 Integrated Project EPOCA (European Project on OCean Acidification) was launched in May 2008 for four years. The overall goal was to advance our understanding of the biological, ecological, biogeochemical, and societal implications of ocean acidification. The EPOCA consortium brought together more than 160 researchers from 32 institutes and 10 European countries (Belgium, France, Germany, Iceland, Italy, The Netherlands, Norway, Sweden, Switzerland, the United Kingdom).During the last four years, a considerable amount of ocean acidification data has been generated by the international community. The following is a summary of the observational and experimental data that were archived as part of the EPOCA data management activities and which are publicly available. Model data are archived separately (http://tinyurl.com/epoca-model) and are not covered in this article. Data management consisted of two parts: (1) the management of data created by EPOCA and (2) the archiving of data on the biological response to ocean acidification that have been published in the literature. The latter is known as the EPOCA/EUR-OCEANS data compilation on the effects of ocean acidification (Nisumaa et al., 2010).The aim of this article is to briefly describe the data available, as EPOCA management activities came to an end on 30 April 2012.

2. Infrastructure used

EPOCA data have been archived in the information system PANGAEA (The Publishing Network for Geoscientific & Environmental Data), which is operated as an open access library aimed at archiving, publishing and distributing georeferenced data from earth system research. The system guarantees long-term availability of its content through a commitment of the operating institutions (http://www.pangaea.de/about/). The archived data can be accessed on the EPOCA web site at http://tinyurl.com/epoca-data.

3. Data products

3.1. EPOCA data

EPOCA had strong data management activities and the data policy required that data be submitted within three months of measurement. While EPOCA strongly encouraged data sharing and co-authorship, access to the data was restricted if requested by the authors.In total, 137 data sets were archived. They were produced using various methods (observations, perturbation experiments in the laboratory and mesocosms, etc.; Fig. 1) and disciplines (e.g. chemical oceanography, paleooceanography, biology; Fig. 1).


Figure 1. Number of EPOCA data sets from experiments, cruises, paleo and observational studies

The largest portion of data originated from laboratory experiments, including a total of  99 of data sets, from which 82 have been published as scientific articles. Experimental data have focussed on many different groups of organisms: corals, bacteria, phytoplankton, zooplankton, bryozoans, echinoderms, mollusks, and fish.The largest EPOCA experimental effort was the Svalbard 2010 mesocosm experiment, that was carried out in Kongsfjorden, Svalbard, Norway (see Biogeosciences special issue; http://www.biogeosciences.net/). It included nine mesocosms with five different pCO2 treatments. Many different measurements were performed including the following major groups: viruses, protista, bacteria, phytoplankton, zooplankton, gases and seawater chemistry (http://epocaarctic2010.wordpress.com/the-experiments/). This effort resulted in seven data sets, from 25 scientists, including 182 variables and 3199761 data points.Data from some sediment core records have been also archived, including 18 data sets from nine papers. Data from two time series were archived: from Point B station in the Bay of Villefranche (France; since 2007) and the North Atlantic continuous plankton recorder survey (1960-2007). Cruise data are also represented with a total of 11 cruises in the North-Eastern Atlantic and Arctic Ocean spanning the period 2008 to 2011.


3.2. EPOCA/EUR-OCEANS data compilation

The number of ocean acidification papers has increased considerably within the last 15 years, with a total number of more than 800 articles, 79% of them published after 2003 (Gattuso and Hansson, 2011). Data comparisons were hampered by the fact that few papers provided information on carbonate chemistry and auxiliary data. Additionally, variables are often reported in different units, calculated using different sets of constants and on different pH scales. There was therefore, a dire need for an organized data harmonization and archiving effort. To address this issue, EPOCA and EUR-OCEANS (European Network of Excellence for Ocean Ecosystems Analysis) started a compilation of experimental and observational data on the effects of ocean acidification on marine organisms.



Figure 2. Summary of the data compilation. LE: laboratory experiments; FM: field measurements; ME: mesocosm experiments; NE: not enough carbonate chemistry parameters measured; ND: data not provided by authors; Lost: data lost by authors.

The compilation process included a search of the EPOCA ocean acidification blog (http://oceanacidification.wordpress.com/) for papers describing the biological effects of ocean acidification on marine organisms and communities. Data were checked according to two criteria. First, the pCO2 or pH levels used needed to be relevant to past or for future scenarios (i.e. pCO2 values ranging from about 100 to 1700 μatm and pHT values from about 7.5 to 8.5). Second, salinity and temperature, and at least two variables of the carbonate system, had to be available (Nisumaa et al., 2010). Data requests for this effort were stopped at the beginning of April and by the end of EPOCA, 227 data sets had been archived from 247 scientific publications. Data were obtained either directly from the authors as numerical files (Excel or text) or were extracted from tables or figures in the original paper. This compilation also includes relevant EPOCA data sets.


Figure 3. Biological processes reported in the papers: G: calcification rate; Size: size related variables; N: nutrients; E: elements measured in the tissue; PP: primary production; μ: growth rate; Pi: pigments; R: respiration; S: survival; Pr: proteins; M: mobility processes; RP: reproductive processes; OBP: other biological variables.

The compilation includes 175 laboratory experiments, 28 mesocosm experiments and 30 field measurements (Fig. 2). The most studied biological variable is calcification, representing 14% of the papers from which data have been archived. Size and growth related parameters are also well covered, followed by elemental composition, primary production, respiration, survival, pigments and reproductive processes (Fig. 3). Phytoplankton and corals are the best represented taxonomic groups, followed by mollusks, bacteria, zooplankton, macroalgae, fish, crustaceans and echinoderms (Fig. 4). The most covered geographical areas are the NE Atlantic, E and NW Pacific, followed by the W Pacific, Mediterranean and Black Seas, W Indian Ocean and W Atlantic.


Figure 4. Taxonomic coverage of the papers included in the data compilation.

4. Conclusion

Several other ocean acidification projects were launched after the start of EPOCA. These include the German project BIOACID (http://www.bioacid.de/), the UK ocean acidification programme (UKOA; http://www.oceanacidification.org.uk/) and the EU project MedSeA (http://medsea-project.eu/). Each of these projects has a data management component. The data from BIOACID and MedSeA are archived in Pangaea, as is the EPOCA data, whereas UKOA data are archived in BODC (British Oceanographic Data Centre). It is hoped that the compilation that was started as part of EPOCA and EUR-OCEANS will be continued through one of the existing projects or ideally, via a future international coordination office - allowing for a more perennial data product.


This work is a contribution to the "European Project on Ocean Acidification" (EPOCA) which received funding from the European Community's Seventh Framework Programme (FP7/2007-2013) under grant agreement n° 211384. We are grateful for the help and support from all the staff at Pangaea, especially Hannes Grobe. Stéphane Pesant and Nassim Taalba are thanked for the launch of the data compilation effort. We would like to also thank all the authors who have provided their data.


Gattuso J.-P. & Hansson L., 2011. Ocean acidification: background and history. In: Gattuso J.-P. & Hansson L. (Eds.), Ocean acidification, pp. 1-20. Oxford: Oxford University Press.

Nisumaa A.-M., Pesant S., Bellerby R. G. J., Middelburg J. J., Orr J. C., Riebesell U., Tyrrell T., Wolf-Gladrow D. & Gattuso J.-P., 2010. EPOCA/EUR-OCEANS data compilation on the biological and biogeochemical responses to ocean acidification. Earth System Science Data 2:167-175.