Biodiversity Time Series Analyses from European Marine Ecosystems

<div>This workflow evaluates temporal trends in taxonomic community metrics for European marine ecosystems. It has user-provided data as input, that is filtered in order to evaluate temporal trends in the taxonomic community metrics for each site.</div><div><br></div><div>This workflow is part of Marco-Bolo project task 5.1.</div>

Date ( Publication): 2025-11-05

Status: On going / operational

Version: 1

Keywords: time series analysis

Keywords: European marine ecosystems

Keywords: Marco-Bolo

Keywords: taxonomic community metrics

Owner

Senckenberg Society For Nature Research - Andrés Peredo Arce

Access constraints: License

Use limitation: <span data-ng-bind-html="shouldApplyLinky(value) | newlines | textToHtml" class="text-muted ng-binding">MIT License</span>

OnLine resource: Link to the workflow in NaaVRE (
WWW:LINK-1.0-http--link
)

OnLine resource: Deliverable 5.1 Scientific document determining biodiversity trends, underlying drivers and essential observations for predictive modelling V1.0 (
WWW:LINK-1.0-http--link
)

Contain Services

Service Name: Biodiversity data from excel retriever

Service Description: This is a NaaVRE workflow component / building block written in R that retrieves, validates, and saves biodiversity data and metadata from an Excel file for further processing. If the input file is not found in either location, the script stops with an error. It reads two sheets from the Excel file: Metadata and Data. It defines required columns for both data and metadata and checks if all required columns are present in the dataframes. If columns are missing or extra columns are present, the script stops with an error message. Finally, it writes the metadata and data to separate CSV files (metadata.csv and data.csv) in the temporary directory.

Service Reference (id): https://metadatacatalogue.lifewatch.eu/srv/eng/catalog.search#/metadata/d9fc8450-10d0-4774-92af-257a1fc4e488

Service Name: Parameter validator

Service Description: This is a NaaVRE workflow component / building block that validates user-provided parameters to ensure they are numeric and fall within specified ranges. It keeps a counter for validation errors and creates a timestamped log file in a specified cloud storage path. It validates the following parameters: 1) param_09_years: must be between 0 and 1000. 2) param_10_upper_limit_max_depth, param_11_lower_limit_max_depth, param_12_upper_limit_min_depth, and param_13_lower_limit_min_depth: must be between -10000 and 10000. 3) param_07_first_month, and param_08_last_month: must be between 1 and 12. If any validation errors occur, the script stops and links the user to the log file for details.

Service Reference (id): https://metadatacatalogue.lifewatch.eu/srv/eng/catalog.search#/metadata/df300e45-ad42-4901-9025-b5c870a216d8

Service Name: Species occurence data cleaner

Service Description: This is a NaaVRE workflow component / building block that acts as a species occurrence data cleaner. It reports on parameters set by reading (meta)data from input files, and filtering by year, depth and season. Finally it writes data to output files.

Service Reference (id): https://metadatacatalogue.lifewatch.eu/srv/eng/catalog.search#/metadata/258e222b-5945-4efd-8292-b4dea4b1308c

Service Name: Trend analyzer

Service Description: This is a NaaVRE workflow component / building block that calculates, visualises, and stores temporal trends in biodiversity metrics, enabling users to analyse changes over time and interpret results through customisable plots and exported data.