Introducing guidelines for publishing DNA-derived occurrence data through biodiversity data platforms

Abstract

DNA sequencing efforts of environmental and other biological samples disclose unprecedented and largely untapped opportunities for advances in the taxonomy, ecology, and geographical distributions of our living world. To realise this potential, DNA-derived occurrence data (notably sequences with dates and coordinates) – much like traditional specimens and observations – need to be discoverable and interpretable through biodiversity data platforms. The Global Biodiversity Information Facility (GBIF) recently headed a community effort to assemble a set of guidelines for publishing DNA-derived data. These guidelines target the principles and approaches of exposing DNA-derived occurrence data in the context of broader biodiversity data. They cover a choice of terms using a controlled vocabulary, common pitfalls, and good practices, without going into platform-specific details. Our hope is that they will benefit anyone interested in better exposure of DNA-derived occurrence data through general biodiversity data platforms, including national biodiversity portals. This paper provides a brief rationale and an overview of the guidelines, an up-to-date version of which is maintained at https://doi.org/10.35035/doc-vf1a-nr22. User feedback and interaction are encouraged as new techniques and best practices emerge.

Sharing insect data through GBIF: novel monitoring methods, opportunities and standards

“…(ii) DNA metabarcoding DNA metabarcoding datasets can be published to GBIF with the occurrence core and publishers can apply the DNA-derived data extension to increase the richness of their datasets, e.g. by sharing sequences and relevant metadata from laboratory protocols and bioinformatics pipelines [23]. However, several datasets are published without the use of the extension and/or by using the event core instead, e.g.…”

“…Researchers can link media files to individual occurrence records or event records, providing visual or auditory evidence to support their observations and enriching the dataset. Provision of primary media alongside its data and biological interpretation allows re-interpretations (such as re-identification) using improved reference libraries.DNA-derived data extension: For DNA-derived data, GBIF has developed the DNA-derived data extension [23]. This extension enables researchers to include DNA-specific information, such as DNA sequences, genetic markers used, or laboratory protocols followed.…”

“…Also, determining what constitutes a species unit can be highly influenced by the chosen pre-processing and annotation method. For example, the DNA-derived data extension [ 23 ] enables the sharing of DNA-derived occurrences obtained by various methods (eDNA, PCR detection etc. ); however, the taxonomy associated with sequences risks being quickly outdated unless sequences are regularly re-interpreted according to updated reference databases.…”

“…DNA-derived data extension: For DNA-derived data, GBIF has developed the DNA-derived data extension [ 23 ]. This extension enables researchers to include DNA-specific information, such as DNA sequences, genetic markers used, or laboratory protocols followed.…”

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“…New digitalisation technologies are rapidly being adopted in ecology, with drones, high-frequency biologgers, automatic species identification (e.g., through DNA metabarcoding [22], camera-trap sampling [23], or passive acoustic sampling [24]), digitisation of natural history and other scientific collections [25,26], and citizen science [27] through apps [28] and social media platforms [29] as recent examples. Also, many observational and monitoring networks utilising these new methods are in place to provide data flows on biodiversity and ecosystems.…”