Realm and Biome

A task group of the Darwin Core maintenance group working on vocabularies to describe the ecological context of a sampling or observing event.

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Realm and Biome Charter </br >

A Task Group of the Darwin Core Maintenance Group

Convenor

  • Cecilie Svenningsen – Global Biodiversity Information Facility (GBIF) Secretariat

Core Members

  • Kate Ingenloff – Global Biodiversity Information Facility (GBIF) Secretariat
  • John Wieczorek – providing support for the process of Vocabulary enhancements as the Darwin Core convenor.
  • Pier Luigi Buttigieg – Alfred Wegener Institute - Board member of the GSC, Chief editor of the Environment Ontology (ENVO), Chair of IOC-UNESCO’s Ocean Data and Information System

Motivation

Species occurrence data, in its most basic form, provides essential details about the species observed, including names, dates, and geographic location of observations. While geographic information captures the location, metadata about the ecological context of the observation site can offer invaluable insights for users in their downstream analysis.

Three terms are currently available to capture habitat information associated with species occurrences: Darwin Core’s habitat and targetHabitatScope and excludedHabitatScope in Humboldt extension for ecological inventories. Two additional terms, env_broad_scale and env_local_scale, in the DNA-derived data GBIF extension (adapted from the Minimum Information about any (x) Sequence (MIxS) standard), capture system-level environmental information implementing the Environment Ontology (ENVO) as a controlled vocabulary. However, none of the existing cores or extensions includes a term that provides a means to report the broader categories of realm and biome to describe sampling sites. It is also currently not possible to report which environmental material surrounds the sample at the time of sampling, except in the context of a DNA-derived sample for which the term env_medium from the DNA-derived data extension can be applied. Adding the terms biome, realm, and environmentalMaterial to DwC will give data publishers and data users methods of broadly considering the biogeography of available data from a climatic (biome) and a geographic (realm) perspective and the medium in which a sample was collected (environmentalMaterial).

This task group aims to integrate the terms realm, biome, and environmentalMaterial with controlled vocabularies into the Darwin Core standard in the Event class. Enriching the environmental context of biodiversity data by including these terms with associated controlled vocabularies can enhance data curation and provide biodiversity data users with deeper analytical capabilities.

Goals Outputs and Outcomes

The main goal of the task group will be to propose another new term, realm, to the Darwin Core standard and evaluate the proposal of two other terms, biome and environmentalMaterial, including the possibility of implementing controlled vocabularies for all terms. The primary deliverables will be:

  • A review of the appropriateness of ENVO, IUCN, or other sources for deriving a controlled vocabulary for proposed terms realm and biome.
    • Potentially include use cases to examine which resource best covers user needs
  • An assessment of how the inclusion of the terms relates to other TDWG standards, including the Latimer Core standard, which currently includes the terms ltc:biogeographicRealm, ltc:biome and ltc:material.
  • A proposal to extend the Darwin Core standard to include realm and potentially biome and environmentalMaterial as terms with associated controlled vocabularies. This includes
    • a formal definition of the term realm following the Darwin Core Term proposal template.
    • a formal definition of the term biome following the Darwin Core Term proposal template.
    • a formal definition of the term environmentalMaterial following the Darwin Core Term proposal template.
    • formal definitions of the controlled vocabularies and their concepts following the Vocabulary Maintenance Standard.
    • updates to the relevant GBIF schemas (Event, Occurrence, DNA-derived data) used to publish Darwin Core Archives.

Strategy

The task group deliverables will be maintained in a GitHub repository and communication will be conducted via email. The task group will work closely with the Darwin Core Maintenance Group and the Genomics Standards Consortium to coordinate changes that may affect both standards.

Becoming Involved

Motivated individuals with the following skills and knowledge are encouraged to join the task group:

  • Data holders with information on realms, biomes, and environmental material (for use in the development of any potential use cases)
  • Data users who can help scope the need for specific values in the proposed terms - Specialists with an ecology background
  • Individuals with knowledge of potential resources that can support the development of a controlled vocabulary for the terms

Individuals interested in contributing to the task group should contact the convenor and are invited to participate in the GitHub repository for the task group.

Please join the mailing list to contact the group [link to mail list].

History/Context

Proposals to include the biome and environmentalMaterial terms in the Darwin Core Standard have been open on the DwC GitHub repository since 2014, with the conclusion that a task group is needed to resolve the remaining issues.

ENVO was initially proposed as an ontology for a biome term. More recently, however, the IUCN Global Ecosystem Typology superseded that recommendation and the suggestion that the addition of two new terms, biome and realm, be considered.

Summary

The motivation is to improve the Darwin Core standard to increase the accessibility of metadata related to survey sites. In support of this goal, this task group is established to define three potential new Darwin Core terms, realm, biome, and environmentalMaterial, and controlled vocabularies for each of these.

Resources