Implementing a Community Vision for the Future of Biodiversity Collections

Thiers, Barbara M.; Bates, John M.; Bentley, Andrew; Ford, Linda; Jennings, David; Monfils, Anna; Zaspel, Jennifer M.; Collins, James P.; Hazbón, Manzour Hernando; Pandey, Jyotsna L

doi:10.1093/biosci/biab036

Cited by 7 publications

(7 citation statements)

References 2 publications

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“…This is because of the siloed nature of the data and our inability to compile it into a single resource for machine readability, data manipulation or downstream use. This shortcoming is being addressed through various initiatives such as the Extended Specimen Network (ESN; Lendemer et al, 2020; Thiers et al, 2021), the Digital Extended Specimen (https://dissco.tech/2020/03/31/what-is-a-digital-specimen/), the Distributed System for Scientific Collections (DiSCCo; https://www.dissco.eu/), iSamples (N. Davies et al, 2021) and others. Such a system would require all actors in the data landscape (researchers, collections, data aggregators, publishers, etc.)…”

Section: Discussionmentioning

confidence: 99%

Metadata preservation and stewardship for genomic data is possible, but must happen now

Crandall

Toczydlowski

Liggins

et al. 2022

Preprint

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Genetic diversity within species represents a fundamental yet underappreciated level of biodiversity. Because genetic diversity can indicate species and population resilience to changing climate, its measurement is relevant to many national and global conservation policy targets. Many studies of evolutionary biology, molecular ecology and conservation genetics produce large amounts of genome-scale genetic diversity data for wild populations. While open data policies have ensured an abundance of freely available genomic data stored in the databases of the International Nucleotide Sequence Database Collaboration (INSDC), only about 13% of current accessions have the associated spatial and temporal metadata in INSDC necessary to be reused in monitoring programs, macrogenetic studies, or for acknowledging the sovereignty of nations or Indigenous Peoples. We undertook a “distributed datathon” to quantify the availability of these missing metadata in sources external to the INSDC and to test the hypothesis that these metadata decay with time. We also worked to remediate these missing metadata by extracting them, when present, from associated published papers, online repositories, and/or from direct communication with authors. Starting with 848 programmatically identified candidate datasets (INSDC BioProjects), we manually determined that 492 contained samples from wild populations. We successfully restored spatiotemporal metadata (locality name and/or geospatial coordinates and collection year) for 82% of these 492 datasets (N = 401 BioProjects comprising 42,104 individuals or BioSamples). We also quantified the availability of 33 additional categories of metadata in sources external to the INSDC. Information about associated publications and the type of habitat from which the samples were taken was the most easily found; information about sampling permits was the most challenging to locate. Looking at papers and online repositories was much more fruitful than contacting authors, who only replied to our email requests 45% of the time. Overall, 23% of our email queries to authors discovered useful metadata. Importantly, we found that the probability of retrieving spatiotemporal metadata declines significantly with the age of the dataset, with a 13.5% yearly decrease for metadata located in published papers or online repositories and up to a 22% yearly decrease for metadata that were only available from authors. This observable metadata decay, mirrored in studies of other types of biological data, should motivate swift updates to data sharing policies and researcher practices to ensure that the valuable context provided by metadata is not lost forever.

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Section: Discussionmentioning

confidence: 99%

Metadata preservation and stewardship for genomic data is possible, but must happen now

Crandall

Toczydlowski

Liggins

et al. 2022

Preprint

Self Cite

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“…The worldwide availability of data, including from efforts to digitize millions of specimens, has led to more engaged global stakeholders with research and educational users desiring more and higher quality data. Concepts such as the Extended Specimen Network endorsed by BCoN in the USA and the Digital Specimen emerging from the European Distributed System of Scientific Collections (DiSSCo) aim to further enhance the research and educational potential of specimens by linking associated extended data that exist in disparate databases (Webster 2017, Biodiversity Collections Network 2019, Lendemer et al 2019, Thiers et al 2021. Physical specimens would act as hubs to integrate data, such as genotype, phenotype, behavior, environment, biotic interaction networks, and multimedia components (e.g., specimen images, field images, videos).…”

Section: Discussionmentioning

confidence: 99%

“…This type of network would increase transparency for the community and provide numerous benefits to researchers, collections, and even providing countries. This example of an extended network for specimens has been called for in a broad strategy to enhance biodiversity collection for research and education (Biodiversity Collections Network 2019, Lendemer et al 2019, Thiers et al 2021.…”

Section: Challenges In Tracking Legal Documentationmentioning

confidence: 99%

The Need for Permit Management within Biodiversity Collection Management Systems to Digitally Track Legal Compliance Documentation and Increase Transparency About Origins and Uses

2021

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A growing number of domestic and international legal issues are confronting biodiversity collections, which require immediate access to information documenting the legal aspects of specimen ownership and restrictions regarding use. The Nagoya Protocol, which entered into force in 2014, established a legal framework for access and benefit-sharing of genetic resources and has notable implications for collecting, researchers working with specimens, and biodiversity collections. Herein, we discuss how this international protocol mandates operating changes within US biodiversity collections. Given the new legal landscape, it is clear that digital solutions for tracking records at all stages of a specimen's life cycle are needed. We outline how the Harvard Museum of Comparative Zoology (MCZ) has made changes to its procedures and museum-wide database, MCZbase (an independent instance of the Arctos collections management system), linking legal compliance documentation to specimens and transactions (i.e., accessions, loans). We used permits, certificates, and agreements associated with MCZ specimens accessioned in 2018 as a means to assess a new module created to track compliance documentation, a controlled vocabulary categorizing these documents, and the automatic linkages established among documentation, specimens, and transactions. While the emphasis of this work was a single year test case, its successful implementation may be informative to policies and collection management systems at other institutions.

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“…The workshop participants proposed that investments should be directed to maintain and modernize existing, decentralized biorepositories and should support virtual national and international networks to connect distributed biorepositories and researchers. Examples include the virtual community of practice model, Museums and Emerging Pathogens in the Americas (Colella et al 2021 ), and the community-derived Extended Specimen Network vision, which would link specimens with their genetic, phenotypic, geographical, and environmental data in alignment with FAIR data principles (for findability, accessibility, interoperability, and reuse; Thiers et al 2021 ).…”

Section: Increase Support For Capacity Building Collaboration Platfor...mentioning

confidence: 99%

The Case for Community Self-Governance on Access and Benefit Sharing of Digital Sequence Information

et al. 2022

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Implementing a Community Vision for the Future of Biodiversity Collections

Cited by 7 publications

References 2 publications

Metadata preservation and stewardship for genomic data is possible, but must happen now

Metadata preservation and stewardship for genomic data is possible, but must happen now

The Need for Permit Management within Biodiversity Collection Management Systems to Digitally Track Legal Compliance Documentation and Increase Transparency About Origins and Uses

The Case for Community Self-Governance on Access and Benefit Sharing of Digital Sequence Information

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