Species_occ_biotope.csv

Output file of the "Biotope GBIF Extractor" service (step 1a) of the Biotope vulnerability Workflow within the Internal Joint Initiative. It represents also the output file of the "Occurrences Dataset Uploader" service (step 1b) when the input comes from the user. It is a CSV file with species occurrences in one country. It contains at least 5 columns: - decimalLatitude (numeric) : the latitude of the observed specimen expressed in decimal degree in WGS 84 coordinate system (EPSG:4326) - decimalLongitude (numeric) : the longitude of the observed specimen expressed in decimal degree in WGS 84 coordinate system (EPSG:4326) - acceptedScientificName (text) : the name of the species - ClassKey (numeric): the GBIF taxonomic class key - TaxonKey (numeric): the GBIF taxonomic class key - year (numeric) : the year of the observation - coordinateUncertaintyInMeters (numeric) : the CE 95 uncertainty on the location of the observation, expressed in meter.

SPEDInstabR R package - Estimation of the Relative Importance of Factors Affecting Species Distribution Based on Stability Concept

The package estmates the importance and the relative contribution of factors to explain species distribution by using several plots. A global geographic raster file for each environmental variable may be also obtained with the mean relative contribution, considering all species present in each raster cell, of the factor to explain species distribution. Finally, for each variable it is also possible to compare the frequencies of any variable obtained in the cells where the species is present with the frequencies of the same variable in the cells of the extent.

GBIF Spain Regions module

Portal to explore records in specific regions such as Protected Natural Areas, Provinces, National Biogeographical Regions, Special Protection Areas (SPA) and Natura 2000.

Biotope GBIF extractor

The service aims at harvesting species occurrences from GBIF based on a keyword for the geographic region (two letter country code) and a time interval, both entered by the user. It represents the Step 1a of the Biotope vulnerability Workflow within the Internal Joint Initiative.

Occurrences Dataset Uploader

This service aims at enabling the dataset uploading from the user. It represents the Step 1b of the Biotope vulnerability Workflow within the Internal Joint Initiative.

occurrences.txt

Output file of the "Occurrences Syntax Normalizer" service (step 3) of the Biotope vulnerability Workflow within the Internal Joint Initiative. It represents also the input file of the "Occurrence Datacube Builder" service (step 4) if incidence is considered, or the input file of the "CIMPAL Calculator" service (step 6) if impact is considered. It is a TXT file that contains TSV data with species occurrences in one country. It contains at least 5 columns: - CoordN (numeric) : the latitude of the observed specimen expressed in decimal degree in WGS 84 coordinate system (EPSG:4326) - CoordE (numeric) : the longitude of the observed specimen expressed in decimal degree in WGS 84 coordinate system (EPSG:4326) - Name (text) : the name of the species - ClassKey (numeric): the GBIF taxonomic class key - TaxonKey (numeric): the GBIF taxonomic class key - Year (numeric) : the year of the observation - CoordPrecision (numeric) : the CE 95 uncertainty on the location of the observation, expressed in meter.

SDMselect R package - Cross-validation model selection and species distribution mapping

A set of functions for covariate selection and model specifications with cross-validation and forward model selection. It selects GAM, GLM models using a multiple k-fold cross-validation and map species distribution while accounting for model uncertainties. Multiple families are possible and compared all together using RMSE or AUC as a result of cross-validation procedure. Covariates correlation may be tested. The model selection procedure will test different combinations of covariates with LM, GLM, GLM natural splines and GAM models, with different distributions (Gaussian, Gamma, Log-Normal, Tweedie; Binomial) and with different maximum degrees of freedom for GLM with polynoms or natural splines. Calculations are parallelized when possible. Outputs are numerous, allowing for summary of the model selection and the comparison of the different models all together. The final model selected is used to map species distribution along with maps of uncertainty.

Alien_taxa_Cube.csv

Output file of the "Occurrences DataCube Builder" service (step 4) of the Biotope vulnerability Workflow within the Internal Joint Initiative. It represents also the input of the "Occurrences DataCube Analyst" service (step 5). It is the invasive species datacube that is a CSV file including spatially aggregated invasive taxa and structured as follows: - Date - Geolocation code - Species name - Frequency - Minimum uncertainty.

Azorean Biodiversity Portal

The University of Azores hosts the Azores Bioportal (http://azoresbioportal.uac.pt/) a regional E-Infrastructure. The Azorean Biodiversity Portal (ABP) is an e-infrastructure now associated with Portuguese PORBIOTA and LIFEWATCH. The ABP is a key e-infrastructure for the integrated management of biodiversity data of the Azores, providing a large number of specialized services supporting research, policy and education. The 3000 visits per day, the numerous international scientific collaborations, resulting in publications and academic thesis, and the connection with other prestigious databases demonstrate the Portal’s scientific quality as well as its general appeal. Several Natural History Collections are also managed by University of Azores, namely of Algae, Bryophytes, Vascular Plants, Molluscs and Arthropods.The Azorean Biodiversity Portal shares all the information available on the biodiversity of the Azores, one of the five Macaronesian archipelagos (the other being Madeira, Salvage Islands, the Canary Islands and Cape Verde). Macaronesia is recognized as an important part of the Mediterranean hotspot of biodiversity; however, a comprehensive systematic revision of its biodiversity was still lacking at the end of the 20th century.Based in two European INTERREG IIIB projects, an unprecedented collaboration of more than 200 taxonomists and other scientists resulted in accurate and comprehensive lists of terrestrial species in the Canary Islands (Izquierdo et al., 2001, 2004; Moro et al., 2003), Cape Verde (Arechavaleta et al., 2005), the Azores (Borges et al., 2005b, 2010) and Madeira–Selvagens (Borges et al., 2008). This unique collaboration was fundamental for creating the baseline taxonomic information for the ABP, updating the taxonomic information, listing synonyms.

FOR-PLAT: Forestry data Platform

FOR-PLAT is a first step of establishment of high-throughput data centre for collecting, modelling and analysis of forest ecosystem biotic diversity data in the frame of LifeWatch Slovenia. It is an upgrade of present research infrastructure of the Slovenian Forestry Institute on the fields of biodiversity monitoring and response of terrestrial ecosystem to changing climate as well as monitoring of other processes in forests in the national mesh of research plots. The database is part of the national data hub RI-SI-LifeWatch ERIC VRE.