• LifeWatch ERIC Metadata Catalogue
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Phytoplankton Virtual Research Environment

The LifeWatch Italy national node has realised the Phytoplankton Virtual Research Environment (Phyto VRE) for supporting researchers to address basic and applied studies on phytoplankton ecology at a level of resolution going from individual cells to whole assemblages.

The Phyto VRE enables researchers to:

- produce harmonised data on taxonomy and morphological traits by using the Atlas of Phytoplankton, Atlas of Shapes and Phytoplankton Traits Thesaurus;

- access, download, and select LifeWatch Italy datasets (published through the LifeWatch Italy Data Portal and distributed by the LifeWatch ERIC Metadata Catalogue) or upload their own datasets structured according to the Phyto template based on the LifeWatch Italy Data Schema in order to execute the services included in the VRE;

- faciliatate the computation of morphological and demographic traits (such as hidden dimension, biovolume, surface area, surface-volume ratio, cell carbon content, etc.) and investigate their distribution patterns at different levels of data aggregation (i.e. spatial, temporal, taxonomic) by means of services, which automate a set of operations written in the R language.

Default

Identification

Date ( Creation )
2016
Date ( Publication )
2020
Date ( Revision )
2021
Status
Under development / Pre operational
Version
1.1
Keywords
Virtual Research Environment
Keywords
phytoplankton
Keywords
functional traits
Keywords
atlas of shapes
Keywords
taxonomy
Keywords
controlled vocabulary
Keywords
computational services
Keywords
data analysis
Access constraints
License
Use limitation
Metadata records are freely available under a Public Domain (CC0 1.0) License; while the VRE is licensed under a Creative Commons Attribution (CC-BY 4.0) License.
Access constraints
Copyright
Other constraints
LifeWatch Italy 2021
Creator
  Italian Agency for the Environmental Prevention and Protection · Centro Regionale Mare (CRM)- Bari - Elena Stanca
Creator
  Stazione Zoologica Anton Dohrn, Naples (Italy) - Leonilde Roselli
Creator
  Institute of Research on Terrestrial Ecosystems (IRET), National Research Council (CNR) - Francesco Cozzoli
Creator
  LifeWatch ERIC Service Centre - Nicola Fiore
Creator
  LifeWatch ERIC Service Centre - Lucia Vaira
Creator
  Institute of Research on Terrestrial Ecosystems (IRET), National Research Council (CNR) - Ilaria Rosati
Creator
  LifeWatch ERIC Service Centre - Maria Teresa Manca
Principal investigator
  University of Salento, LifeWatch Italy - Alberto Basset
 
OnLine resource
Link to the VRE ( WWW:LINK-1.0-http--link )
OnLine resource
Info page ( WWW:LINK-1.0-http--link )
Service Name
Atlas of Phytoplankton
Service Description
It is a guide for the identification of marine and freshwater species. It includes pictures, synonyms, morphological, morphometrical and ecological characters and geographical distribution of the taxa. It also provides formulas to calculate the biovolume and surface area based on linear dimensions according to the organism view (e.g., lateral, frontal, etc.).
Service Reference (id)
https://metadatacatalogue.lifewatch.eu/srv/eng/catalog.search#/metadata/3ca7867c-0178-4310-a825-5c8bedaf5465
Service Name
Atlas of Shapes
Service Description
It is a catalogue of geometrical models for calculating biovolume and surface area of phytoplankton taxa. It includes illustrative schemes of simple and complex shapes.
Service Reference (id)
https://metadatacatalogue.lifewatch.eu/srv/eng/catalog.search#/metadata/97b3148e-368a-423d-85dd-654efd38cdc3
Service Name
Phytoplankton Traits Thesaurus
Service Description
It is a compilation of standardized definitions and semantic properties of approximately 120 morpho-functional and demographic traits (i.e., abundance, cell carbon content, etc.).
Service Reference (id)
https://metadatacatalogue.lifewatch.eu/srv/eng/catalog.search#/metadata/88e5ea76-b6cb-4d53-9902-926a60363ad2
Service Name
Traits Computation
Service Description
It is a web service to calculate phytoplankton traits such as biovolume, surface area, surface/volume ratio, density, cell carbon content, total biovolume, total carbon content.
Service Reference (id)
https://metadatacatalogue.lifewatch.eu/srv/eng/catalog.search#/metadata/ae7bc525-6358-4568-b8d1-b72686b3d575
Service Name
Size Class Distribution
Service Description
It is a web service to visualize the distribution of individuals in different size classes selected on the basis of logarithmic values of biovolume or carbon content.
Service Reference (id)
https://metadatacatalogue.lifewatch.eu/srv/eng/catalog.search#/metadata/e21b8d5e-11c5-4545-b205-a34d207f959b
Service Name
Size Density Relationships
Service Description
It is a web service to calculate and describe the relationships between size (total biovolume and total carbon content) and abundance.
Service Reference (id)
https://metadatacatalogue.lifewatch.eu/srv/eng/catalog.search#/metadata/ec5bca8e-cf11-4b5c-b032-c8f0ba13f9af
Publications about this VRE
Stanca, E., Cellamare, M., & Basset, A. (2013) "Geometric shape as a trait to study phytoplankton distributions in aquatic ecosystems". Hydrobiologia, 701(1), 99-116.
Publications about this VRE
Stanca E., Roselli L., Cozzoli F., Rosati I., Fiore N. and Basset A. (2017) "Phytoplankton morphological and demographic traits computation in a virtual research environment Phyto VRE", Abstract book of 52nd European Marine Biology Symposium, September 2017 Slovenia. ISBN 978-961-93486-5-9.
Publications about this VRE
Stanca, E.; Fiore, N.; Rosati, I.; Vaira, L.; Cozzoli, F.; Basset, A. (2020) "Case study: LifeWatch Italy Phytoplankton VRE", in: Zhao, Z. et al. Towards interoperable research infrastructures for environmental and earth sciences. Lecture Notes in Computer Science, 12003: pp. 324-341. https://hdl.handle.net/10.1007/978-3-030-52829-4_18.
Publications about this VRE
Ilaria Rosati et al., 2017, A thesaurus for phytoplankton trait-based approaches: Development and applicability, Ecological Informatics, 42, 129-138, DOI: https://doi.org/10.1016/j.ecoinf.2017.10.014.
VRE Helpdesk
https://helpdesk.lifewatchitaly.eu/
 

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