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      Internet of Samples (iSamples): Toward an interdisciplinary cyberinfrastructure for material samples

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          Abstract

          Sampling the natural world and built environment underpins much of science, yet systems for managing material samples and associated (meta)data are fragmented across institutional catalogs, practices for identification, and discipline-specific (meta)data standards. The Internet of Samples (iSamples) is a standards-based collaboration to uniquely, consistently, and conveniently identify material samples, record core metadata about them, and link them to other samples, data, and research products. iSamples extends existing resources and best practices in data stewardship to render a cross-domain cyberinfrastructure that enables transdisciplinary research, discovery, and reuse of material samples in 21st century natural science.

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          Most cited references10

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          The FAIR Guiding Principles for scientific data management and stewardship

          There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders—representing academia, industry, funding agencies, and scholarly publishers—have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community.
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            The CARE Principles for Indigenous Data Governance

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              The Genomic Observatories Metadatabase (GeOMe): A new repository for field and sampling event metadata associated with genetic samples

              The Genomic Observatories Metadatabase (GeOMe, http://www.geome-db.org/) is an open access repository for geographic and ecological metadata associated with biosamples and genetic data. Whereas public databases have served as vital repositories for nucleotide sequences, they do not accession all the metadata required for ecological or evolutionary analyses. GeOMe fills this need, providing a user-friendly, web-based interface for both data contributors and data recipients. The interface allows data contributors to create a customized yet standard-compliant spreadsheet that captures the temporal and geospatial context of each biosample. These metadata are then validated and permanently linked to archived genetic data stored in the National Center for Biotechnology Information’s (NCBI’s) Sequence Read Archive (SRA) via unique persistent identifiers. By linking ecologically and evolutionarily relevant metadata with publicly archived sequence data in a structured manner, GeOMe sets a gold standard for data management in biodiversity science.
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                Author and article information

                Contributors
                Journal
                Gigascience
                Gigascience
                gigascience
                GigaScience
                Oxford University Press
                2047-217X
                07 May 2021
                May 2021
                07 May 2021
                : 10
                : 5
                : giab028
                Affiliations
                Gump South Pacific Research Station, University of California , BP 244, Moorea 98728, French Polynesia
                Berkeley Institute for Data Science, University of California , 190 Doe Library, Berkeley, CA 94720, USA
                Berkeley Natural History Museums, University of California , Valley Life Sciences Bldg, 3101, Berkeley, CA 94720, USA
                Open Context, The Alexandria Archive Institute , 125 El Verano Way, San Francisco, CA 94127, USA
                Open Context, The Alexandria Archive Institute , 125 El Verano Way, San Francisco, CA 94127, USA
                California Digital Library, University of California , Office of the President, 1111 Franklin Street, Oakland, CA 94607, USA
                National Museum of Natural History, Smithsonian Institution , 10th St. & Constitution Ave. NW, Washington, D.C., 20560, USA
                National Museum of Natural History, Smithsonian Institution , 10th St. & Constitution Ave. NW, Washington, D.C., 20560, USA
                Lamont-Doherty Earth Observatory, Columbia University , P.O. Box 1000 61 Route 9W Palisades, NY 10964, USA
                National Museum of Natural History, Smithsonian Institution , 10th St. & Constitution Ave. NW, Washington, D.C., 20560, USA
                Biodiversity Institute, The University of Kansas , Dyche Hall, 1345 Jayhawk Blvd, Lawrence, KS 66045, USA
                Bio5 Institute, University of Arizona , 1657 E Helen St, Tucson, AZ 85718, USA
                Lamont-Doherty Earth Observatory, Columbia University , P.O. Box 1000 61 Route 9W Palisades, NY 10964, USA
                Author notes
                Correspondence address.Neil Davies. Gump South Pacific Research Station, University of California, BP 244 98728, Moorea, French Polynesia. E-mail: ndavies@ 123456berkeley.edu
                Author information
                https://orcid.org/0000-0001-8085-5014
                https://orcid.org/0000-0002-5905-1617
                https://orcid.org/0000-0001-5620-4764
                https://orcid.org/0000-0001-7920-5321
                https://orcid.org/0000-0001-7604-8041
                https://orcid.org/0000-0003-2501-7952
                https://orcid.org/0000-0003-1038-3028
                https://orcid.org/0000-0003-1135-5942
                https://orcid.org/0000-0002-0028-6139
                https://orcid.org/0000-0002-6513-4996
                https://orcid.org/0000-0001-8815-0078
                https://orcid.org/0000-0001-7036-1977
                Article
                giab028
                10.1093/gigascience/giab028
                8103498
                33960385
                e940752f-defb-4b1d-9db6-ce62dc02568d
                © The Author(s) 2021. Published by Oxford University Press GigaScience.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 17 February 2021
                : 26 March 2021
                : 28 March 2021
                Page count
                Pages: 5
                Funding
                Funded by: National Science Foundation, DOI 10.13039/100000001;
                Award ID: 2004839
                Award ID: 2004562
                Award ID: 2004642
                Award ID: 2004815
                Categories
                Commentary
                AcademicSubjects/SCI00960
                AcademicSubjects/SCI02254

                material sample,specimen,data standards,cyberinfrastructure,unique identifiers,persistent identifiers,collections,geoscience,bioscience,archaeology

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