Digital Extended Specimens: Enabling an Extensible Network of Biodiversity Data Records as Integrated Digital Objects on the Internet

Hardisty, Alex; Ellwood, Elizabeth R.; Nelson, Gil; Zimkus, Breda M.; Buschbom, Jutta; Addink, Wouter; Rabeler, Richard K.; Bates, John M.; Bentley, Andrew; Fortes, José A. B.; Hansen, Sara; Macklin, James; Mast, Austin; Miller, Joseph T.; Monfils, Anna; Paul, Deborah; Wallis, Elycia; Webster, Michael S.

doi:10.1093/biosci/biac060

Cited by 39 publications

(23 citation statements)

References 33 publications

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“…Due to its focus on data interoperability, GBIF is well positioned to lead the community in a shift from domain‐specific databases to data hubs for biodiversity informatics. The concept of the Digital Extended Specimen, or DES, describes the emerging paradigm in which specimen data from natural history collections are digitally linked to ecological, environmental and refined biological data from other domains (Wilkinson et al, 2016; Macklin et al, 2022). Outside the context of GBIF, however, motivation to normalize biodiversity data and support DES development is low when the emphasis is on sharing results from analysis or data aggregations rather than sharing the underlying data.…”

Section: The Potential and Power Of Biodiversity Databasesmentioning

confidence: 99%

The role of systematics for understanding ecosystem functions: Proceedings of the Zoologica Scripta Symposium, Oslo, Norway, 25 August 2022

et al. 2023

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On 25 August 2022, the Zoologica Scripta -An International Journal of Systematic Zoology and the Norwegian Academy of Sciences and Letters arranged a symposium entitled 'The role of systematics for understanding ecosystem functions' in the Academy's premises in Oslo, Norway. The symposium aimed at offering a forum for exploring and discussing trends and future developments in the field of systematics. Eleven international experts contributed expertise on various issues related to global challenges, such as biodiversity assessments, databases, cuttingedge analysis tools, and the consequences of the taxonomic impediment. Here, we compiled a multi-author proceedings paper of the symposium contributions

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Section: The Potential and Power Of Biodiversity Databasesmentioning

confidence: 99%

The role of systematics for understanding ecosystem functions: Proceedings of the Zoologica Scripta Symposium, Oslo, Norway, 25 August 2022

et al. 2023

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Section: Introductionmentioning

confidence: 99%

“…Currently, there is a global impetus toward an interconnected network to link other sources of biodiversity and environmental data and in this way provide interdisciplinary information (Hardisty et al, 2022). Hardisty et al (2022) use specimens as a digital anchor connecting other discipline-specific data. A recent example is modelling, understanding, and preventing potential pandemics, following COVID-19 (Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services [IPBES], 2020).…”

Section: Introductionmentioning

confidence: 99%

South Africa’s initiative toward an integrated biodiversity data portal

Daly

Ranwashe

2023

Front. Ecol. Evol.

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Researchers and policymakers have called on the South African National Biodiversity Institute (SANBI), in its role as the statutory biodiversity organisation of South Africa, to develop a coordinated and integrated biodiversity informatics hub. While biodiversity information is increasingly available from several providers, there is no platform through which to access comprehensive biodiversity information from a single source. In response, SANBI is redeveloping the Biodiversity Advisor platform, which will integrate geospatial, species and ecosystem data, literature and other data made available by a wide variety of data partners. To do so it has adopted a Service Orientated Architecture, whereby existing, independent biodiversity datasets are integrated. Consolidating such an extensive and varied set of databases, however, introduces some significant operational challenges. Solutions had to be found to address limited infrastructure, the complexity of the system, the lack of taxonomic identifiers, as well as the need for access and attribution. Solutions had to be pragmatic, given limited financial resources and limited capacity for information technology. The emerging outcome is a system that will easily allow users to access most biodiversity data within South Africa from a single, recognised platform.

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“…Making genomic material digitally discoverable to researchers, and linking them and data generated from these samples back to the associated voucher specimens is another challenge. Fortunately, there is a current international initiative to collate the different forms of data surrounding a voucher specimen, as a Digital Extended Specimen (DES), across multiple institutions worldwide (Hardisty et al 2022).…”

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confidence: 99%

“…This could result in a second researcher borrowing the sample and publishing it as a "new" sequence. Researchers already have difficulties in submitting sequences to GenBank, as several have confused field numbers for catalog numbers from the National Museum of Natural History, Smithsonian Institution (Mulcahy et al 2022). Some museums, using modifiable codes, can append a primary code (from the specimen voucher) for additional "parts" of that specimen.…”

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confidence: 99%

Specimen Identifiers: Linking tissues, DNA samples, and sequence data to voucher specimens in publicly accessible databases

Mulcahy¹

2022

BISS

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Nearly all disciplines of biology now have some form of molecular genetic analyses incorporated into areas of their research, from systematics, ecology, and behavior, to physiology and conservation. In order for science to be transparent, the source and provenance of the genetic material used must be easily identifiable and traceable, following the FAIR principles of being Findable Accessible, Interoperable, and Reusable (Wilkinson et al. 2016). Natural history collections are ever-increasingly facilitating the use of genetic components from collection objects, and in some cases increasing the number and types of collection objects under their care (i.e., tissue/DNA-only, e.g., blood, feather, skin- fin-clips, environmental samples). Most natural history collections are now making their holdings available online, either on their own platforms or via aggregate search engines like the Global Biodiversity Information Facility (GBIF) and the Global Genome Biodiversity Network (GGBN). Many natural history collections are also now using digital management systems, where digital identifiers such as Digital Object Identifiers (DOIs) and Uniform Resource Identifiers (URIs) are assigned to objects in collections (Güntsch et al. 2017), including multiple objects derived from the same individual organism (e.g., voucher specimen, images, and genomic samples). Associated objects may receive different digital identifiers in order to be uniquely identifiable in the digital management system, but sharing this information on third-party platforms (e.g., GBIF, GGBN) is challenging, especially in avoiding duplicate entries. Furthermore, genetic materials are often sought out by researchers external to the holding collection institution, and molecular sequence data are then generated and deposited in third-party public repositories, such as GenBank and the Barcode of Life Database (BOLD). Making genomic material digitally discoverable to researchers, and linking them and data generated from these samples back to the associated voucher specimens is another challenge. Fortunately, there is a current international initiative to collate the different forms of data surrounding a voucher specimen, as a Digital Extended Specimen (DES), across multiple institutions worldwide (Hardisty et al. 2022). The National Center for Biotechnology Information (NCBI), which hosts GenBank, has created a BioCollections Database to curate metadata for natural history collections and linking sequence data to voucher specimens (Sharma et al. 2018). Institution codes, collection codes, and catalog numbers are linked to create a “structured voucher” annotation (following the Darwin Core Triplet) to standardize usage across interconnected databases (e.g., GenBank, European Nucleotide Archive, and the DNA Databank of Japan). However, duplicate institution codes can make this complicated, and collection institutions that use digital identifiers instead of traditional catalog numbers make this even more challenging. The NCBI BioCollections Database curators have resolved the duplicate institution codes problem, by adding the three-letter country code (or state code, within the same country). However, this database is used only for sequence data, in GenBank, and related databases (e.g., ENA, DDBJ), which raises the question, is there a need for a more universal biocollection codes database? Additionally, as museums move towards using digital identifiers, in the place of catalog numbers, confusion can arise when multiple digital identifiers are assigned to parts of the same “specimen” (e.g., specimen voucher, tissue, DNA, images, etc.). For instance, if a given specimen has unique URIs for the voucher specimen, the DNA, and an image, a researcher borrowing the DNA, might use the DNA URI as an identifier for the genetic database. A different researcher, at a later date, might see that specimen (or image) in the museum’s collection, and think it is a different specimen of that species, when in fact it is the same specimen. This could result in a second researcher borrowing the sample and publishing it as a “new” sequence. Researchers already have difficulties in submitting sequences to GenBank, as several have confused field numbers for catalog numbers from the National Museum of Natural History, Smithsonian Institution (Mulcahy et al. 2022). Some museums, using modifiable codes, can append a primary code (from the specimen voucher) for additional “parts” of that specimen. For example, if the primary code for an insect specimen ends in “…6d15ce”, a leg taken for DNA extraction could be modified as “…6d15ce_leg” and “…6d15ce_dna” for the extract. This minimizes the chances for mistaking these as being from different specimens. However, if completely different codes are assigned to different parts of the same specimen, the chance increases for mistaking two objects from the same specimen as being from different specimens. Collections staff must carefully consider the hierarchical relationships of objects in their collections, and how they are assigned URIs, especially when considering long-term operability in current and future aggregate database structures (e.g., GBIF, GGBN, NCBI, and the DES). In this presentation, these issues are raised and the difficulties in linking specimens, genomic resources, and associated data in aggregate databases and data repositories are discussed.

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Digital Extended Specimens: Enabling an Extensible Network of Biodiversity Data Records as Integrated Digital Objects on the Internet

Cited by 39 publications

References 33 publications

The role of systematics for understanding ecosystem functions: Proceedings of the Zoologica Scripta Symposium, Oslo, Norway, 25 August 2022

The role of systematics for understanding ecosystem functions: Proceedings of the Zoologica Scripta Symposium, Oslo, Norway, 25 August 2022

South Africa’s initiative toward an integrated biodiversity data portal

Specimen Identifiers: Linking tissues, DNA samples, and sequence data to voucher specimens in publicly accessible databases

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