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  • This step of the ARMS IJI workflow does the following: - Input: the OTU tables from the previous step (running the omics pipeline), containing taxa (usually genus or species names) obtained from the databases used by the pipeline; - Check: using the WoRMS taxon match webservice to check for the WoRMS match to those taxa; - Output: the WoRMS match (yes or not) and, if matched, the scientific name and aphiaID. It represents the Step 7 of the ARMS Workflow within the Internal Joint Initiative.

  • Following the FAIR principles and best practices, the LifeWatch ERIC Training Catalogue hosts the metadata of relevant learning resources so that these can be shared, searched, discovered, accessed and reused. The LifeWatch ERIC training catalogue’s accurate and descriptive metadata allow all users to find the most appropriate and well-suited educational resources for their needs. Metadata are based on a subset of the IEEE Standard for Learning Object Metadata (IEEE 2002). The detail page of each single metadata record includes all the descriptive information and, on the right side of the page, a button “Start the course” that allows to access the resource and hence to start the training.

  • This service aims to compute a list of taxa IDs detected from metabarcoding sequences of environmental DNA (eDNA) samples. This service contains eight substeps (1.1 to 1.8) implemented as a unique step. The eight substeps perform (1) sequencing error correction (using BayesHammer-SPAdes); (2) pairwise alignment, (3) pre-filtering, (4) dereplication, (5) attribute filtering, (6) clustering and OTU tab-producer (using OBITools); (7) taxonomic assignment (using blastn); (8) OTUs table generator. Several types of eDNA samples can be processed (i.e. water, feces, soil). It represents the Step 1 of the Metabarcoding Workflow within the Internal Joint Initiative.

  • This service aims at producing the zonal statistics. The Python and C++ codes provides a generic tool to extract the statistics from a geographic layer with quantitative values for each patch of a categorical map. For example, it is used in this workflow to compute the average vulnerability inside different administrative polygons. It represents the Step 7 (final step) of the Biotope vulnerability Workflow within the Internal Joint Initiative.

  • This service aims at checking which taxa detected and identified from eDNA metabarcoding sequences are listed as NIS and which taxa are not (i.e. native or unrecorded NIS). This service uses available GBIF (Global Biodiversity Information Facility) records of NIS for each Country provided by the Invasive Species Specialist Group (ISSG). it checks if a species is present in the checklist and if this is the case, the species is flagged as being invasive for that country by adding 1 (yes) or 0 (no) to the column isInChecklist of the data frame, and the checklist key or a note to the ref_checklistKey column, for the corresponding cases. It represents the Step 3 of the Metabarcoding Workflow within the Internal Joint Initiative.

  • 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.

  • This step of the ARMS IJI workflow does the following: - Input: the output from the previous step (running a taxon check on the input species names using the WoRMS taxon checker); - Input: geographical locations for the sample(s) that those species were found at; - Check: using the WRIMS taxon match webservice to check the known distribution of the species; - Output: information about whether the species are alien or native to the location they were found at. It represents the Step 8 of the ARMS Workflow within the Internal Joint Initiative.

  • An R package to get downloads from the EurOBIS database. In 2019, development started for the eurobis R package, to serve as an easy to use interface to download EurOBIS data in R. Currently, the main functions and documentation are being developed and are working, but need some further testing and user feedback before it can be officially released.

  • This service extracts from GBIF (Global Biodiversity Information Facility) taxa occurrence records that were not classified as NIS in Step 3 (GBIF NIS Verifier) of the Metabarcoding workflow. This step aims to verify if eDNA detections were identified outside the known distribution range using GBIF occurrences records. Additionally, for such eDNA detections, this step produces a geographical spatial polygon based on occurrence records available in GBIF. It represents the Step 4 of the Metabarcoding Workflow within the Internal Joint Initiative.

  • This service aims at creating a vector from the coordinates in the “Pop_troph_SIA.csv” file and convert it into a shapefile. It represents the Step 3.1 of the Crustaceans Workflow within the Internal Joint Initiative.