AURORA Shiny App: Streamlining Biodiversity Data Sharing - User Manual

Overview This manual provides comprehensive guidance for using the AURORA Shiny App, a user-friendly web-based application designed to streamline the mobilization of biodiversity data. The tool addresses common barriers to data publication by assisting researchers and data managers in converting unstructured datasets into standards-compliant Darwin Core (DwC) formats. Developed as a core output of the AURORA – Bringing Deep-Sea Biodiversity Data to Light project, the application specifically targets the improvement of data quality, interoperability, and global visibility for biodiversity data. The AURORA Shiny App was primarily designed to assist in structuring raw data following the DwC OBIS-ENV or Sampling Event data formats; this includes generating an Event Core (also known as a Sampling-event core) as the primary table, which is then linked to an Occurrence Extension and an eMoF Extension table. Additionally, the AURORA Shiny App supports the simpler Occurrence Core data format, where individual observations or specimens serve as the primary records without a hierarchical event structure. While it does not generate a final DwC-Archive (.zip) file directly, it produces the necessary standardized data tables for publication through tools like the GBIF IPT. Main Features The manual details a step-by-step workflow for data standardization: Data Ingestion & Tidy Formatting: Supports uploading CSV files and provides tools to pivot "wide-format" datasets into the "tidy" format required for Darwin Core compliance. Field Mapping: Includes an auto-suggest feature using fuzzy matching to map original column headers to standard DwC terms. Taxonomic Validation: Enables cleaning of identification data and matching scientific names against the WoRMS or GBIF taxonomic backbones. Standardization of Coordinates & Dates: Automatically converts geographical coordinates to decimal degrees (WGS84) and formats date-related fields to ISO 8601 standards. Controlled Vocabularies (eMoF): Facilitates the population of the Extended MeasurementOrFact (eMoF) table using standardized BODC-NERC controlled vocabularies. Metadata Documentation: Includes a form for metadata that is compatible with the GBIF Integrated Publishing Toolkit (IPT) to enhance sharing and revisions. Funding The development of this tool was funded through the DTO-BioFlow Project, contributing to the development of the European Digital Twin of the Ocean