AURORA Shiny App - streamlining biodiversity data sharing

An integrated Shiny application designed to streamline the preparation, validation, and export of both marine and terrestrial biodiversity datasets into Darwin Core tables for sharing on public repositories such as GBIF — the Global Biodiversity Information Facility.

Biodiversity data Darwin Core Standards Taxonomy matching Quality control Metadata Darwin Core Archive (DwC-A)
Tool workflow
1
Ingest
Import the source dataset and inspect its original structure before processing.
2
Field Mapping
Map original columns of the ingested dataset to Darwin Core terms with guidance and validation.
3
Identification Data Cleaning
Review and edit identification-related fields, especially scientificName and related Darwin Core terms, before taxonomic matching.
4
Taxonomy
Automatic matching of scientific names against authoritative taxonomic backbones such as WoRMS or GBIF.
5
Darwin Core Tables
Build structured Darwin Core tables for Event, Occurrence, and Extended Measurement or Fact (eMoF).
6
eMoF Editor
Review and edit eMoF-related fields and controlled vocabulary entries.
7
DwC Tables Overview & Quality Control (QC)
Inspect issues, diagnostics, summary outputs, and validation results for export.
8
Metadata
Streamline metadata creation and revision using an interface inspired by the GBIF IPT.
User manual

Step-by-step guidance covering ingestion, mapping, taxonomy, quality control, metadata, and export.

Open manual
Examples of supported tasks
📝
Map to Darwin Core
Align the original dataset fields with standardized Darwin Core (DwC) terms to ensure global interoperability.
📅
Standardize Temporal Data
Convert all event dates into ISO 8601 format for temporal consistency.
📍
Normalize Coordinates
Transform various coordinate formats into Decimal Degrees (WGS84).
🍃
Taxonomic Matching
Cross-reference scientific names with authoritative taxonomic databases such as WoRMS and GBIF to validate names and retrieve accepted classifications.
🗂️
Build Darwin Core Tables
Structure the data into relational Event, Occurrence, and eMoF tables to comply with the DwC-A star schema.
🔍
Data Quality Inspection
Review processed tables to identify inconsistencies, missing values, and other issues in the dataset.
📝
Metadata Preparation
Document dataset-level metadata to support revision, publication, and FAIR data sharing.
Data ingestion
Note
If your dataset is already in a tidy format, you can proceed directly by clicking Complete Ingestion .

What is a tidy format?
  • Each occurrence must correspond to a single row.
  • Do not store a single variable across multiple columns (e.g., species names split into separate columns).
 



                

                
              

            

            

              

                
Preview

                

                  
                  

                    

                      

                        
                      

                      

                        

                          

                            

                          

                        

                        

                          

                            

                          

                        

                        

                          

                            

                          

                        

                      

                      
                    

                  

                

                
              

            

          
        

        

          
          

            

              

                

                  
Field mapping to Darwin Core

                  
Map columns to Darwin Core terms, create fields, configure formatting options, and review the cleaned dataset.

                  

                    Darwin Core Quick Reference Guide
                  

                

                

                  
Validation

                  

                    

                  

                  
                

                

                  

                    

                      
                      

                        

                          

                            
Map each column to a Darwin Core term

                            

                            

                            

                              
                            

                            

                            

                            

                              
                            

                            

                            

                          

                        

                        

                          

                            

                              

                                Note: 
                                Create IDs and Create remarks can be used more than once.
                              

                            

                            
                              

                                

                                  
Create IDs

                                  

                                    

                                      
                                      

                                        
                                        
                                      

                                    

                                    

                                      
                                      

                                        
                                        
                                      

                                    

                                    

                                      
                                      
                                    

                                    

                                    

                                      

                                        
                                      

                                    

                                    
                                  

                                  
                                

                              

                              

                                

                                  
Create remarks

                                  

                                    

                                      
                                      

                                        
                                        
                                      

                                    

                                    

                                      
                                      

                                        
                                        
                                      

                                    

                                    

                                      
                                      
                                    

                                    

                                      

                                        
                                      

                                    

                                    
                                  

                                  
                                

                              

                            
                            

                            
                              

                                

                                  
Create / fill basisOfRecord

                                  

                                    

                                      
                                      

                                        
                                        
                                      

                                    

                                    

                                      

                                        
                                      

                                    

                                    
                                    
Use this only when all records in the dataset share the same basisOfRecord. Otherwise, the field should be filled correctly before import.

                                  

                                  
                                

                              

                              

                                

                                  

                                    organismQuantity and sampleSizeValue Dependency Fields 
                                    
                                      
                                      
                                        
                                      
                                    
                                  

                                  

                                    

                                  

                                  
                                

                              

                            
                            

                            

                              
                            

                          

                        

                        

                          

                            
                              

                                

                                  
Original coordinate system

                                  

                                    
Identify the original CRS (EPSG) of the dataset. Coordinates will be transformed into EPSG:4326 (WGS 84).

                                    

                                      
                                      
                                    

                                    

                                      

                                        
                                      

                                    

                                    

                                      

                                        
                                      

                                    

                                    

                                    Target CRS EPSG:[4326]
                                    
Coordinates will be stored in decimal degrees.

                                  

                                  
                                

                              

                              

                                

                                  
Date formatting

                                  

                                    

                                      

                                        
                                      

                                    

                                    

                                      
                                      Note:
                                      While our date-formatting engine works hard, it isn't flawless. 
                                      Handling every possible date and time combination is complex. 
                                      It will do its best, but please review the results carefully. If your 
                                      eventDate
                                       is too messy, please preprocess values before ingestion.
                                    

                                    

                                      
                                      

                                        

                                          
                                        

                                        

                                          
                                        

                                      

                                    

                                    

                                      This option is only used for ambiguous numeric dates such as 01/02/2024. 
                                      If you choose dd/mm, that value is interpreted as 1 February 2024. 
                                      If you choose mm/dd, it is interpreted as 2 January 2024. 
                                      Dates already in ISO format, such as 2024-02-01 or 2019-10-01T22:39:12, are not affected.
                                    

                                  

                                  
                                

                              

                            
                            

                            

                              
                            

                          

                        

                        

                          

                            
Preview of the cleaned dataset after mapping, create-fields, and formatting.

                            

                          

                        

                        

                          

                            

                          

                        

                      

                    

                  

                  
                

              

            

            
            
            
          

        

        

          
          
          

            

              
Identification Data Cleaning

              

                

                  

                    According to the 
                    Darwin Core
                     standard, when scientific names include open nomenclature qualifiers such as 'cf.', 'aff.', or informal placeholders (e.g., 'sp.'), these qualifiers should not be included in the 
                    scientificName
                     field, but rather in the 
                    identificationQualifier
                     term. The 
                    scientificName
                     should contain the lowest possible taxon rank that can be confidently determined, while the 
                    identificationQualifier
                     field captures the determiner's uncertainty or relationship to a known taxon.
                  

                  

                    For example, for 
                    Gadus cf. morhua
                    :
                  

                  
    
                    
  • 
                      scientificName
                      : 'Gadus'
                    
    • 
                    
  • 
                      taxonRank
                      : 'genus'
                    
    • 
                    
  • 
                      identificationQualifier
                      : 'cf. morhua'
                    
    • 
                  

                  

                    To ensure data traceability, the original identification is retained in the 
                    verbatimIdentification
                     field as a historical record.
                  

                

                

                  Warning: 
                  The 
                  Reviewed scientificName
                   column (red) must be completed manually or by accepting the suggestion for every row before applying changes.
                  

                  Optional fields shown below are Darwin Core terms that were not selected during Field Mapping. They can be reviewed and edited here if needed. 
                  Please review all entries for accuracy.
                

                
                  

                    

                      
Settings

                      

                        

                        

                        

                          
                          
                          
                        

                        

                        

                        

                        
                          
                          Download decisions (CSV)
                        
                      

                      
                    

                  

                  

                    

                      
Editable lookup table

                      

                        

                        

                      

                      
                    

                  

                
              

              
            

          

        

        

          
          

            

              
Taxonomy match

              

                

                  
Notes

                  

                    
    
                      
  • 
                        Taxonomic Matching
                         — Matches are generated from the scientificName field.
                      
    • 
                      
  • 
                        Database Authorities
                         — Marine taxa are validated against the World Register of Marine Species (worrms package, wm_records_taxamatch()). Terrestrial taxa are matched against the GBIF Backbone Taxonomy via the rgbif package.
                      
    • 
                      
  • 
                        Ambiguity Resolution
                         — The results table contains one row per unique scientificName. When a match is uncertain, a manual selection is required to confirm the correct taxon.
                      
    • 
                      
  • 
                        Inclusion Rules
                         — Only records with a confirmed match are included in the final dataset and passed to subsequent processing steps. Unresolved names are excluded from the output but retained in the validation log for review.
                      
    • 
                      
  • 
                        Workflow Restart
                         — To process unresolved names, corrections must be made in the Identification Data Cleaning tab and the taxonomic matching step must be rerun.
                      
    • 
                    

                  

                  
                

                

                

                  
                    

                      

                        
Settings

                        

                          

                          

                            
                            

                              

                                
                              

                              

                                
                              

                            

                          

                          

                            
                          

                          

                          

                        

                        
                      

                    

                    

                      

                        
Columns to keep in final dataset

                        

                          

                            

                          

                          

                            Only Darwin Core output terms are available for selection. The 
                            inputName
                             and 
                            taxonMatchStatus
                             fields are strictly technical and are excluded from the final dataset. When using WoRMS, the 
                            scientificNameID
                             is populated with the identifier returned by the matching source (i.e., the LSID). Conversely, when the GBIF backbone is used, the 
                            scientificNameID
                             field is currently ignored (see: 
                            GBIF Issue #217
                            ).
                          

                        

                        
                      

                    

                    

                      

                        
Summary

                        

                          

                        

                        
                      

                    

                  
                

              

              
            

            

              
Name lookup table

              

                

                  

                

                

                  
                    
                    Export lookup (CSV)
                  
                  
                

              

              
            

            

              
Issues (taxonomy)

              

                

              

              
            

          

        

        

          

            

              

                
Build Darwin Core Tables

                
Choose the archive resource type and review the allowed fields step by step before building the Darwin Core tables.

              

              

                
Build settings

                

                  

                

                
              

              

                
Selection warnings / status

                

                  

                

                
              

              

                

                  

                

                

                  

                  

                    

                    

                      

                    

                  

                

                
              

              

                
Quality report

                

                  

                    

                  

                

                
              

              

                
Table previews

                

                  

                    
                    

                      

                        

                          

                        

                      

                      

                        

                          

                        

                      

                      

                        

                          

                        

                      

                    

                  

                

                
              

            

          

        

        

          
          

            

              
eMoF Data Editor

              

                

                  

                    This editor helps standardize the core measurement vocabulary fields in the 
                    Extended Measurement or Fact (eMoF)
                     table after the Darwin Core tables have already been built.
                  

                  
    
                    
  • Repeated non-numeric measurement rows are grouped into a single editable row.
    • 
                    
  • 
                      Rows containing numeric 
                      measurementValues
                       are grouped, and their values are locked to prevent accidental bulk edits.
                    
    • 
                    
  • Edits remain as a draft until you click Apply changes to eMoF.
    • 
                  

                

                

                  Note: 
                  Consult the controlled vocabulary at 
                  BODC-NERC controlled vocabulary.
                

                
                  

                    

                      
Status

                      

                        

                        

                        

                        

                          
                          
                        

                      

                      
                    

                  

                  

                    

                      
Editable lookup table

                      

                        

                        

                      

                      
                    

                  

                
              

              
            

          

        

        

          
          

            Note: 
            This section provides a brief summary of the DwC tables content and issues still present that need to be solved. For a more rigorous assessment, you can perform a comprehensive quality control check using the 
            LifeWatch & EMODnet Biology QC tool.
          

          

            

              

                Data overview
                
              

              

                

                  

                    

                      
Data Overview & Summary

                    

                    

                      

                        

                          
Export status

                          

                            

                          

                        

                      

                      

                        

                          
Errors

                          

                            

                          

                        

                      

                      

                        

                          
Warnings

                          

                            

                          

                        

                      

                      

                        

                          
Records (occurrence)

                          

                            

                          

                        

                      

                    

                    

                    

                      

                    

                    

                      

                    

                    

                    
Overview of measurement or fact records

                    

                      

                    

                    

                    
Geographic coverage of the dataset

                    

                    

                      

                    

                    

                    

                      

                    

                    

                      

                    

                    

                    
Taxonomic coverage of the dataset

                    

                      

                        

                      

                    

                  

                

                

                  

                    
Overview of all issues

                    

                      

                    

                    

                    
Details

                    

                      

                    

                    

                    
eMoF issues

                    

                      

                    

                  

                

              

              
            

          

        

        

          
          
          
Dataset Metadata

          
The sections follow the structure of the GBIF IPT metadata form. Fields can be completed to facilitate metadata review among dataset authors, and then copied and pasted into the metadata form of the selected IPT for dataset submission.

          

            

              

                
              

              

                

                  

                    

                      

                        

                          

                            Resource identity
                          

                        

                        

                          

                            

                              

                                

                                  
                                  
                                

                                
Descriptive title of the resource.

                              

                            

                          

                          

                            

                              

                                

                                  
                                  
                                

                                
Short name of the resource.

                              

                            

                            

                              

                                

                                  
                                  

                                    
                                    
                                  

                                

                                
Organization responsible for publishing the resource.

                              

                            

                          

                        

                        
                      

                      

                        

                          

                            Resource type
                          

                        

                        

                          

                            

                              

                                

                                  
                                  

                                    
                                    
                                  

                                

                              

                            

                            

                              

                                

                                  
                                  

                                    
                                    
                                  

                                

                              

                            

                            

                              

                                

                                  
                                  

                                    
                                    
                                  

                                

                              

                            

                          

                        

                        
                      

                      

                        

                          

                            Languages and licence
                          

                        

                        

                          

                            

                              

                                

                                  
                                  

                                    
                                    
                                  

                                

                              

                            

                            

                              

                                

                                  
                                  

                                    
                                    
                                  

                                

                              

                            

                            

                              

                                

                                  
                                  

                                    
                                    
                                  

                                

                              

                            

                          

                        

                        
                      

                      

                        

                          

                            Narrative fields
                          

                        

                        

                          

                            

                              
                              
                            

                            
Overview of the resource.

                          

                          

                            

                              
                              
                            

                            
General description of resource maintenance.

                          

                          

                            

                              
                              
                            

                            
Description of the maintenance frequency.

                          

                        

                        
                      

                      

                        

                        

                          
                        

                      

                    

                  

                  

                    

                      

                        

                          

                            Resource contacts
                          

                        

                        

                          

                            
                            
                          

                          

                        

                        
                      

                      

                        

                          
                        

                        

                          
                        

                      

                    

                  

                  

                    

                      

                        

                          

                            Acknowledgements
                          

                        

                        

                          

                            

                              
                              
                            

                            
Acknowledgements to funders and main contributors.

                          

                        

                        
                      

                      

                        

                          
                        

                        

                          
                        

                      

                    

                  

                  

                    

                      

                        

                          

                            Bounding box
                          

                        

                        

                          

                            

                              

                                
                                
                              

                            

                            

                              

                                
                                
                              

                            

                            

                              

                                
                                
                              

                            

                            

                              

                                
                                
                              

                            

                          

                          

                            

                              
                              
                            

                            
Geographic description of the study area.

                          

                        

                        
                      

                      

                        

                          
                        

                        

                          
                        

                      

                    

                  

                  

                    

                      

                        

                          

                            Taxonomic scope
                          

                        

                        

                          

                            

                              
                              
                            

                            
Description of the taxonomic scope.

                          

                          

                            

                              

                                

                                  
                                  
                                

                              

                            

                            

                              

                                

                                  
                                  
                                

                              

                            

                          

                        

                        
                      

                      

                        

                          
                        

                        

                          
                        

                      

                    

                  

                  

                    

                      

                        

                          

                            Temporal extent
                          

                        

                        

                          

                            

                              

                                

                                  
                                  
                                

                              

                            

                            

                              

                                

                                  
                                  
                                

                              

                            

                          

                        

                        
                      

                      

                        

                          
                        

                        

                          
                        

                      

                    

                  

                  

                    

                      

                        

                          

                            Extended narrative
                          

                        

                        

                          

                            

                              
                              
                            

                          

                          

                            

                              
                              
                            

                          

                          

                            

                              
                              
                            

                          

                        

                        
                      

                      

                        

                          
                        

                        

                          
                        

                      

                    

                  

                  

                    

                      

                        

                          

                            Keyword sets
                          

                        

                        

                          

                            
                            
                          

                          

                        

                        
                      

                      

                        

                          
                        

                        

                          
                        

                      

                    

                  

                  

                    

                      

                        

                          

                            Project description
                          

                        

                        

                          

                            

                              
                              
                            

                          

                          

                            

                              
                              
                            

                          

                          

                            

                              
                              
                            

                          

                          

                            

                              
                              
                            

                          

                        

                        
                      

                      

                        

                          

                            Project personnel
                          

                        

                        

                          

                            
                            
                          

                          

                        

                        
                      

                      

                        

                          
                        

                        

                          
                        

                      

                    

                  

                  

                    

                      

                        

                          

                            Sampling methodology
                          

                        

                        

                          

                            

                              
                              
                            

                          

                          

                            

                              
                              
                            

                          

                          

                            

                              
                              
                            

                          

                          

                            

                              
                              
                            

                          

                        

                        
                      

                      

                        

                          
                        

                        

                          
                        

                      

                    

                  

                  

                    

                      

                        

                          

                            Main citation
                          

                        

                        

                          

                            

                              
                              
                            

                          

                          

                            

                              
                              
                            

                          

                        

                        
                      

                      

                        

                          

                            Bibliographic citations
                          

                        

                        

                          

                            
                            
                          

                          

                        

                        
                      

                      

                        

                          
                        

                        

                          
                        

                      

                    

                  

                  

                    

                      

                        

                          

                            Collections
                          

                        

                        

                          

                            
                            
                          

                          

                        

                        
                      

                      

                        

                          

                            Specimen preservation methods
                          

                        

                        

                          

                            
                            
                          

                          

                        

                        
                      

                      

                        

                          

                            Curatorial units
                          

                        

                        

                          

                            
                            
                          

                          

                        

                        
                      

                      

                        

                          
                        

                        

                          
                        

                      

                    

                  

                  

                    

                      

                        

                          

                            Links
                          

                        

                        

                          

                            

                              
                              
                            

                          

                          

                            
                            
                          

                          

                        

                        
                      

                      

                        

                          
                        

                        

                          
                        

                      

                    

                  

                  

                    

                      

                        

                          

                            Additional metadata
                          

                        

                        

                          

                            

                              
                              
                            

                          

                          

                            

                              
                              
                            

                          

                          

                            

                              
                              
                            

                          

                          

                            

                              
                              
                            

                          

                        

                        
                      

                      

                        

                          

                            Alternative identifiers
                          

                        

                        

                          

                            
                            
                          

                          

                        

                        
                      

                      

                        

                          
                        

                        

                          
                        

                      

                    

                  

                  

                    

                      

                        

                          

                            Export metadata
                          

                        

                        

                          
                            
                            Export workbook
                          
                        

                        
                      

                      

                        

                          
                        

                        

                      

                    

                  

                

              

            

          

        

        

          

            

              
The AURORA project

              

                

                  

                    
                  

                  

                    

                      The AURORA R Shiny application
                       was developed as a core output of the 
                      project AURORA - bringing deep-sea biodiversity data to light
                      , an initiative dedicated to streamline the mobilization of deep-sea biodiversity data.
                    

                    
Although the deep sea covers 65% of the planet, it remains Earth’s least understood biome. Within European marine waters, deep-sea data (depths >200 m) account for only 11% of records in the Ocean Biogeographic Information System (OBIS), dropping to a mere 1% for depths below 3500 meters.

                    
To address this knowledge gap, the Digital Marine Biodiversity Lab at the University of Aveiro is mobilizing its collections of deep-sea data, starting with the Aurora seamount on the Gakkel Ridge in the Central Arctic Ocean.

                    
This data mobilisation to open repositories, such as EMODnet Biology, will directly contribute to the development of the European Digital Twin of the Ocean.

                  

                

              

              
            

            

              
Disclaimer

              

                
This application is provided as a tool to assist in the standardization of biodiversity datasets into Darwin Core (DwC) archives. While every effort is made to ensure the accuracy of the underlying mapping logic and transformation scripts, the outputs are provided "as is" without any guarantees of completeness, accuracy, or fitness for a specific purpose.

              

              
            

            
              

                

                  
How to cite

                  

                    
Magnenti, Á. S., Araújo, S. M., … Matos, F. L. (2026). Aurora Shiny App: Streamlining biodiversity data sharing (Version 1.0).

                    

                      http://bio-shiny.ua.pt:3838/aurora
                    

                    

                      License: 
                      CC-BY 4.0
                       — This work may be shared and adapted, including for commercial purposes, provided appropriate credit is given.
                    

                  

                  
                

              

              

                

                  
Support and bug reports

                  

                    

                      Technical support: 
                      For technical support or to suggest new feature enhancements for the AURORA Shiny App, please reach out to us directly via email at 
                      fmatos@ua.pt
                      .
                    

                    

                      Bug reports: 
                      If you encounter any bugs or functional glitches, please report them by opening a new issue on the AURORA GitHub repository: 
                      AURORA GitHub repository
                      .
                    

                  

                  
                

              

            
            

              
Institutional support

              

                

                  Participating institutions logos
                

              

              
            

            

              
Funding

              

                
AURORA project is funded by the Flanders Marine Institute (VLIZ) through the DTO-BioFlow project funded by the European Union.