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  • The World Register of Introduced Marine Species (WRiMS) records which marine species in the World Register of Marine species (WoRMS) have been introduced deliberately or accidentally by human activities to geographic areas outside their native range. As a user or developer you can use the WoRMS webservice to feed your own application with standard WoRMS data, including WRiMS data. A non-exhaustive list of applications: - get the AphiaID for your taxon - check the spelling of your taxa - get the authority for your taxa - get the full classification for your taxa - resolve your unaccepted names to accepted ones - get all synonyms for a taxon - fuzzy/near match your species list - resolve a common name/vernacular to a scientific name - get the common name(s)/vernacular(s) for a taxon - get the sources/references for a taxon - get the WoRMS citation for a taxon - get the direct children for a taxon - get all taxa modified during a time interval - get an external identifier for a taxon - get the AphiaID for an external identifier/database - get all distributions for a taxon - get all attributes for a taxon

  • To address the today’s ecological challenges, it is necessary to use data coming from different disciplines and providers. Discovery and integration of data, especially from the ecological domain, is highly labour-intensive and often ambiguous in semantic terms. To improve the location, interpretation and integration of data based on its inherent meaning vocabularies can help in harmonizing and enriching descriptions of data, providing a formal mechanism for the definition of terms and their relationships. To satisfy these emerging needs LifeWatch ERIC developed a Semantic Resources Catalogue (EcoPortal) focused on the Biodiversity and Ecosystem Research. This effort will help to support the community in the management and integration/alignment of their semantics and subsequently also of their data. The main goal of the EcoPortal initiative is to provide a unique platform for vocabularies in the ecological and domain for different kinds of stakeholders.

  • As a user or developer you can use the WoRMS webservice to feed your own application with standard WoRMS data. A non exhaustive list of applications: - get the AphiaID for your taxon - check the spelling of your taxa - get the authority for your taxa - get the full classification for your taxa - resolve your unaccepted names to accepted ones - get all synonyms for a taxon - fuzzy/near match your species list - resolve a common name/vernacular to a scientific name - get the common name(s)/vernacular(s) for a taxon - get the sources/references for a taxon - get the WoRMS citation for a taxon - get the direct children for a taxon - get all taxa modified during a time interval - get an external identifier for a taxon - get the AphiaID for an external identifier/database - get all distributions for a taxon - get all attributes for a taxon

  • This service provides a user-friendly Graphical User Interface (GUI) that allow researchers to run a workflow wrapped into R code for: - the reshaping of the input dataset in order to obtain alien species and native specie richness for each family at the habitat and site level. If more that 1 EUNIS habitat is present in a site, the richness will be calculate for the two (or more that 2) habitats in the site; - the selection of the best fitting model, by calling a set of R functions from the packages lme4 and MuMIn. Initially, a full GLMM model is calculated including both richness and level-1 EUNIS habitat as fixed factor. Subsequently, reduced models are calculated and compared with the full model using the Akaike Information Criteria (AIC). The model showing the best AIC is used to create the output (tables and graph); - the plot of the rarefaction curves on the reshaped dataset.

  • The Atlas of Phytoplankton provides a reference point for marine, transitional and freshwater scientists and students involved in phytoplankton identification and classification. It includes illustrative cards with information about i) taxonomy, with pictures and schematic drawings, information on similar species and/or synonyms, references; ii) ecological characteristics and geographical distribution of species; and iii) morphological features, such as shape association, linear dimensions association and formulae for cell volume and surface computation thanks to the integration with the Atlas of Shapes.

  • The Phytoplankton Traits Computation service provides a user-friendly Graphical User Interface (GUI) that allow researchers to run a workflow wrapped into R code for the computation of morphological and demographic traits, such as hidden dimension, biovolume, surface area, surface-volume ratio, cell carbon content, density, carbon content and total biovolume. The service works on datasets structured according to the Phyto template based on the "LifeWatch Italy Data Schema" that can be selected by the GUI or uploaded by the researchers. The input file is in CSV format with some mandatory fields according to the computation type. Before selecting or uploading the input file, users have to specify some parameters (e.g., the computation type, the traits to be computed, the aggregation level, etc.). The service provides as output a file that includes the original records with the computed traits. Moreover, users can restrict the set of records of the output file by exploiting the "Data Selecting" service, which is integrated in the workflow, that allows to exclude rare taxa based on their ranked distribution considering the density (n of cells per liter), or the biovolume per liter (μm3 of cells per liter) or the carbon content per liter (pgC per liter) as size unit. To do that, users need to specify the threshold value (between 0 and 1) and to choose the size unit (density, biovolume per liter or carbon content per liter). Both output files could be used in the other services provided within the Phyto VRE.

  • The Atlas of Shapes represents a reference point for marine, transitional and freshwater scientists and students involved in phytoplankton morphological traits association and measurement. It provides a schematic protocol for calculating biovolume of phytoplankton species detectable with the Utermöhl method in transitional ecosystems of the different world ecoregions. The Atlas includes the illustrative scheme of the shape classification subdivided in “Simple Shapes” and “Complex Shapes”, clicking on a specific shape, users are able to see: the shape views (e.g., lateral, frontal, etc.) with the corresponding linear dimensions and the biovolume and surface area computational models.

  • PEMA is a HPC-centered, containerized assembly of key metabarcoding analysis tools. It supports the downstream analysis of four marker genes (16S/18S rRNA, ITS and COI) but also, by allowing the user to train the classifiers with custom reference databases, it can be used for further marker genes. By combining state-of-the art technologies and algorithms with an easy to get-set-use framework, PEMA allows researchers to tune thoroughly each study thanks to roll-back checkpoints and on-demand partial pipeline execution features.

  • Data Services provide the users with tools in order to: a) publish their datasets and make them available to the community by providing information that allows a user to locate and access the resource and its curator/creator, b) import their datasets to the Lifewatch Greece Infrastructure and to GBIF or MedOBIS, c) perform biodiversity data and information quality improvement, and d) search about datasets of interest by providing an efficient way of querying semantic networks. The schema of the data that is provided by the users is mapped to the semantic model of the LWI and the data is transformed to LWI format before it is stored to the Infrastructure. The semantic model is based on CIDOC CRM (http://www.cidoc-crm.org/), CRM dig, CRM geo, CRM sci and MarineTLO (http://www.ics.forth.gr/isl/MarineTLO/). Login is required to access the service.