Mapping Nested Vegetation Plot Data to Darwin Core and the Humboldt Extension: Challenges and Open Questions

Vegetation plots (relevés)—records of all plant species with their abundance in fixed-size plots in terrestrial vegetation—might be independent, arranged in nested designs, or established as permanent plots for resurvey. Given their complexity, representing vegetation plot data in global infrastructures such as the Global Biodiversity Information Facility (GBIF) requires thoughtful use of Darwin Core (DwC) and extensions (Darwin Core Task Group 2009). In DwC, a relevé corresponds to a single dwc:Event, hence, the recommended way to publish such data in GBIF is using the Event Core with at least two additional extensions: Occurrence and Relevé (GBIF 2018). The GBIF Relevé extension provides standard measurements across vegetation layers, with explicitly defined units and precision (e.g., “tree cover (%)”). Other plot-level measurements (e.g., soil pH) can be described via the DwC Measurement or Facts extension. The recently ratified Humboldt extension (TDWG Humboldt Extension Task Group 2024) expands the DwC Event class to capture the sampling context of more complex plot designs by extending the descriptions of sampling events, making it especially relevant for nested and repeated sampling. However, recommendations are still evolving (Ingenloff et al. 2025) and it has not been extensively tested with vegetation plot data (Suppl. material 2). Out of the 374 databases listed in the Global Index of Vegetation‐Plot Databases (GIVD; accessed on 15.09.2025), only a few are currently published via GBIF (e.g., Hennekens 2018, Kuzemko et al. 2024, Swacha et al. 2025), and mostly as Occurrence class datasets. As a case study, we present the dataset by Palpurina (2025) exported from Turboveg 2 (Hennekens and Schaminée 2001), the standard software for vegetation data management in Europe. For this dataset, we used an R script*1 to directly access the database and export the data as Darwin Core Archive (DwC-A) using an Event Core with Occurrence, Relevé and Humboldt extensions. Regarding the Humboldt extension, field mapping required one-to-many and many-to-one relationships between Turboveg and DwC. Because some Turboveg 2 fields lacked sufficient detail, the script had to include hardcoded values and manual enrichment steps to populate missing DwC fields and ensure schema compliance. Our talk (Suppl. material 1) addresses challenges in applying the Humboldt extension to vegetation-plot data, focusing on common practices for capturing key data critical for vegetation data interoperability.

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Journal
Biodiversity Information Science and Standards
Published
2025-12-19
DOI
https://doi.org/10.3897/biss.9.182514
Primary Topic
Species Distribution and Climate Change
Type
article
Field-Weighted Citation Impact
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article

Mapping Nested Vegetation Plot Data to Darwin Core and the Humboldt Extension: Challenges and Open Questions

Salza Palpurina, Kate Ingenloff
Biodiversity Information Science and Standards
Species Distribution and Climate Change
article

Mapping Nested Vegetation Plot Data to Darwin Core and the Humboldt Extension: Challenges and Open Questions

Salza Palpurina, Kate Ingenloff
article en

Abstract

Vegetation plots (relevés)—records of all plant species with their abundance in fixed-size plots in terrestrial vegetation—might be independent, arranged in nested designs, or established as permanent plots for resurvey. Given their complexity, representing vegetation plot data in global infrastructures such as the Global Biodiversity Information Facility (GBIF) requires thoughtful use of Darwin Core (DwC) and extensions (Darwin Core Task Group 2009). In DwC, a relevé corresponds to a single dwc:Event, hence, the recommended way to publish such data in GBIF is using the Event Core with at least two additional extensions: Occurrence and Relevé (GBIF 2018). The GBIF Relevé extension provides standard measurements across vegetation layers, with explicitly defined units and precision (e.g., “tree cover (%)”). Other plot-level measurements (e.g., soil pH) can be described via the DwC Measurement or Facts extension. The recently ratified Humboldt extension (TDWG Humboldt Extension Task Group 2024) expands the DwC Event class to capture the sampling context of more complex plot designs by extending the descriptions of sampling events, making it especially relevant for nested and repeated sampling. However, recommendations are still evolving (Ingenloff et al. 2025) and it has not been extensively tested with vegetation plot data (Suppl. material 2). Out of the 374 databases listed in the Global Index of Vegetation‐Plot Databases (GIVD; accessed on 15.09.2025), only a few are currently published via GBIF (e.g., Hennekens 2018, Kuzemko et al. 2024, Swacha et al. 2025), and mostly as Occurrence class datasets. As a case study, we present the dataset by Palpurina (2025) exported from Turboveg 2 (Hennekens and Schaminée 2001), the standard software for vegetation data management in Europe. For this dataset, we used an R script*1 to directly access the database and export the data as Darwin Core Archive (DwC-A) using an Event Core with Occurrence, Relevé and Humboldt extensions. Regarding the Humboldt extension, field mapping required one-to-many and many-to-one relationships between Turboveg and DwC. Because some Turboveg 2 fields lacked sufficient detail, the script had to include hardcoded values and manual enrichment steps to populate missing DwC fields and ensure schema compliance. Our talk (Suppl. material 1) addresses challenges in applying the Humboldt extension to vegetation-plot data, focusing on common practices for capturing key data critical for vegetation data interoperability.

Biodiversity Information Science and StandardsVol. 9
Global Biodiversity Information Facility (DK), Bulgarian Academy of Sciences (BG), National Museum of Natural History (BG), Bulgarian Biodiversity Foundation (BG)
Openalex Percentile: Top 78%
Species Distribution and Climate Change
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