Case Study: LifeWatch Italy Phytoplankton VRE

LifeWatch Italy, the Italian node of LifeWatch ERIC, has promoted and stimulated the debate on the use of semantics in biodiversity data management. Actually, biodiversity and ecosystems data are very heterogeneous and need to be better managed to improve the actual scientific knowledge extracted, as well as to address the urgent societal challenges concerning environmental issues. LifeWatch Italy has realized the Phytoplankton Virtual Research Environment (hereafter Phytoplankton VRE), a collaborative working environment supporting researchers to address basic and applied studies on phytoplankton ecology. The Phytoplankton VRE provides the IT infrastructure to enable researchers to obtain, share and analyse phytoplankton data at a level of resolution from individual cells to whole assemblages. A semantic approach has been used to address data harmonisation, integration and discovery: an interdisciplinary team has developed a thesaurus on phytoplankton functional traits and linked its concepts to other existing conceptual schemas related to the specific domain.

[1]  Meriç Albay,et al.  Shape and size in phytoplankton ecology: do they matter? , 2007, Hydrobiologia.

[2]  N. Salmaso,et al.  Functional classifications and their application in phytoplankton ecology , 2015 .

[3]  N. Salmaso,et al.  Morpho-Functional Groups and phytoplankton development in two deep lakes (Lake Garda, Italy and Lake Stechlin, Germany) , 2007, Hydrobiologia.

[4]  Nicola Fiore,et al.  A thesaurus for phytoplankton trait-based approaches: Development and applicability , 2017, Ecol. Informatics.

[5]  M. Sigovini,et al.  Open Nomenclature in the biodiversity era , 2016 .

[6]  A. Napiórkowska-Krzebietke,et al.  Assessment of the cell biovolume of phytoplankton widespread in coastal and inland water bodies. , 2016, Water research.

[7]  Jorge L. Sarmiento,et al.  Ocean Biogeochemical Dynamics , 2006 .

[8]  C. Violle,et al.  Ecological and biogeographical drivers of freshwater green algae biodiversity: from local communities to large-scale species pools of desmids , 2018, Oecologia.

[9]  J. Elser,et al.  Ecological Stoichiometry: The Biology of Elements from Molecules to the Biosphere , 2002 .

[10]  Jun Sun,et al.  Increasing the quality, comparability and accessibility of phytoplankton species composition time-series data , 2015 .

[11]  F. Capitanio,et al.  Using ZooImage automated system for the estimation of biovolume of copepods from the northern Argentine Sea , 2011 .

[12]  Irina Olenina,et al.  Biovolumes and size-classes of phytoplankton in the Baltic Sea , 2006 .

[13]  S. Taguchi.  RELATIONSHIP BETWEEN PHOTOSYNTHESIS AND CELL SIZE OF MARINE DIATOMS 1 2 , 1976 .

[14]  Erik Schultes,et al.  The FAIR Guiding Principles for scientific data management and stewardship , 2016, Scientific Data.

[15]  Zoe V. Finkel,et al.  Phytoplankton in a changing world: cell size and elemental stoichiometry , 2010 .

[16]  A. Basset,et al.  Marine phytoplankton size–frequency distributions: Spatial patterns and decoding mechanisms , 2008 .

[17]  Shawn Bowers,et al.  An ontology for describing and synthesizing ecological observation data , 2007, Ecol. Informatics.

[18]  M. Cellamare,et al.  Geometric shape as a trait to study phytoplankton distributions in aquatic ecosystems , 2012, Hydrobiologia.

[19]  G. Morabito,et al.  Strength and uncertainty of phytoplankton metrics for assessing eutrophication impacts in lakes , 2012, Hydrobiologia.

[20]  J. Baguley,et al.  A semi‐automated digital microphotographic approach to measure meiofaunal biomass , 2004 .

[21]  Jason G. Bragg,et al.  Allometry and stoichiometry of unicellular, colonial and multicellular phytoplankton. , 2009, The New phytologist.

[22]  S. F. Umani,et al.  Ability of phytoplankton trait sensitivity to highlight anthropogenic pressures in Mediterranean lagoons: A size spectra sensitivity index (ISS-phyto) , 2013 .

[23]  Elena Litchman,et al.  The role of functional traits and trade-offs in structuring phytoplankton communities: scaling from cellular to ecosystem level. , 2007, Ecology letters.

[24]  R. R. Strathmann,et al.  ESTIMATING THE ORGANIC CARBON CONTENT OF PHYTOPLANKTON FROM CELL VOLUME OR PLASMA VOLUME1 , 1967 .

[25]  G. Ferreyra,et al.  Seasonal phytoplankton dynamics in extreme southern South America (Beagle Channel, Argentina) , 2011 .

[26]  P. Falkowski,et al.  A universal driver of macroevolutionary change in the size of marine phytoplankton over the Cenozoic , 2007, Proceedings of the National Academy of Sciences.

[27]  Helmut Hillebrand,et al.  BIOVOLUME CALCULATION FOR PELAGIC AND BENTHIC MICROALGAE , 1999 .

[28]  P. R. Sloan,et al.  RELATIONSHIP BETWEEN CARBON CONTENT, CELL VOLUME, AND AREA IN PHYTOPLANKTON , 1966 .

[29]  Victor Smetacek,et al.  Pelagic ecosystem structure: Heterotrophic compartments of the plankton and their relationship to plankton size fractions 1 , 1978 .

[30]  T. Tinta,et al.  Pelagic habitats in the Mediterranean Sea: A review of Good Environmental Status (GES) determination for plankton components and identification of gaps and priority needs to improve coherence for the MSFD implementation , 2018, Ecological Indicators.

[31]  Snejana Moncheva,et al.  Application of a new multi-metric phytoplankton index to the assessment of ecological status in marine and transitional waters , 2012 .

[32]  P. A. Wheeler,et al.  CELL GEOMETRY REVISITED: REALISTIC SHAPES AND ACCURATE DETERMINATION OF CELL VOLUME AND SOURCE AREA FROM MICROSCOPIC MEASUREMENTS , 1999 .

[33]  J. Elser,et al.  Elements of ecology and evolution , 2005 .

[34]  Vincent S. Smith,et al.  Unifying European Biodiversity Informatics (BioUnify) , 2016 .

[35]  Marina Cabrini,et al.  Biovolume determination of phytoplankton guilds in transitional water ecosystems of Mediterranean Ecoregion , 2007 .

[36]  J. Randerson,et al.  Primary production of the biosphere: integrating terrestrial and oceanic components , 1998, Science.

[37]  S. Lehtinen,et al.  Cell volumes of marine phytoplankton from globally distributed coastal data sets , 2015 .

[38]  Dongyan Liu,et al.  Geometric models for calculating cell biovolume and surface area for phytoplankton , 2003 .

[39]  Steve Kelling,et al.  Participatory design of DataONE - Enabling cyberinfrastructure for the biological and environmental sciences , 2012, Ecol. Informatics.