Natural history collections are invaluable repositories of biological information that provide an unrivaled record of Earth's biodiversity. Museum genomics—genomics research using traditional museum and cryogenic collections and the infrastructure supporting these investigations—has particularly enhanced research in ecology and evolutionary biology, the study of extinct organisms, and the impact of anthropogenic activity on biodiversity. However, leveraging genomics in biological collections has exposed challenges, such as digitizing, integrating, and sharing collections data; updating practices to ensure broadly optimal data extraction from existing and new collections; and modernizing collections practices, infrastructure, and policies to ensure fair, sustainable, and genomically manifold uses of museum collections by increasingly diverse stakeholders. Museum genomics collections are poised to address these challenges and, with increasingly sensitive genomics approaches, will catalyze a future era of reproducibility, innovation, and insight made possible through integrating museum and genome sciences. more »« less
Cicero, Carla; Koo, Michelle S; Braker, Emily; Abbott, John; Bloom, David; Campbell, Mariel; Cook, Joseph A; Demboski, John R; Doll, Andrew C; Frederick, Lindsey M; et al
(, PLOS ONE)
Meloro, Carlo
(Ed.)
More than tools for managing physical and digital objects, museum collection management systems (CMS) serve as platforms for structuring, integrating, and making accessible the rich data embodied by natural history collections. Here we describe Arctos, a scalable community solution for managing and publishing global biological, geological, and cultural collections data for research and education. Specific goals are to: (1) Describe the core features and implementation of Arctos for a broad audience with respect to the biodiversity informatics principles that enable high quality research; (2) Highlight the unique aspects of Arctos; (3) Illustrate Arctos as a model for supporting and enhancing the Digital Extended Specimen concept; and (4) Emphasize the role of the Arctos community for improving data discovery and enabling cross-disciplinary, integrative studies within a sustainable governance model. In addition to detailing Arctos as both a community of museum professionals and a collection database platform, we discuss how Arctos achieves its richly annotated data by creating a web of knowledge with deep connections between catalog records and derived or associated data. We also highlight the value of Arctos as an educational resource. Finally, we present the financial model of fiscal sponsorship by a nonprofit organization, implemented in 2022, to ensure the long-term success and sustainability of Arctos.
Ellwood, Elizabeth R.; Addink, Wouter; Bates, John; Bentley, Andrew; Buschbom, Jutta; Freire-Fierro, Alina; Fortes, Jose; Jennings, David; Lehnert, Kerstin; Ludäscher, Bertram; et al
(, Biodiversity Information Science and Standards)
Thanks to substantial support for biodiversity data mobilization in recent decades, billions of occurrence records are openly available, documenting life on Earth and enabling timely research, awareness raising, and policy-making. Initiatives across local to global scales have been separately funded to serve different, yet often overlapping audiences of data users, and have developed a variety of platforms and infrastructures to meet the needs of these audiences. The independent progress of biodiversity data providers has led to innovations as well as challenges for the community at large as we move towards connecting and linking a diversity of information from disparate sources as Digital Extended Specimens (DES). Recognizing a need for deeper and more frequent opportunities for communication and collaboration across the globe, an ad-hoc group of representatives of various international, national, and regional organizations have been meeting virtually since 2020 to provide a forum for updates, announcements, and shared progress. This group is provisionally named International Partners for the Digital Extended Specimen (IPDES), and is guided by these four concepts: Biodiversity, Connection, Knowledge and Agency. Participants in IPDES include representatives of the Global Biodiversity Information Facility (GBIF), Integrated Digitized Biocollections (iDigBio), American Institute of Biological Sciences (AIBS), Biodiversity Collections Network (BCoN), Natural Science Collections Alliance (NSCA), Distributed System of Scientific Collections (DiSSCo), Atlas of Living Australia (ALA), Biodiversity Information Standards (TDWG), Society for the Preservation of Natural History Collections (SPNHC), National Specimen Information Infrastructure of China (NSII), and South African National Biodiversity Institute (SANBI), as well as individuals involved with biodiversity informatics initiatives, natural science collections, museums, herbaria, and universities. Our global partners group strives to increase representation from around the globe as we aim to enable research that contributes to novel discoveries and addresses the societal challenges leading to the biodiversity crisis. Our overarching mission is to expand on the community-driven successes to connect biodiversity data and knowledge through coordination of a globally integrated network of stakeholders to enable an extensible technical and social infrastructure of data, tools, and working practices in support of our vision. The main work of our group thus far includes publishing a paper on the Digital Extended Specimen (Hardisty et al. 2022), organizing and hosting an array of activities at conferences, and asynchronous online work and forum-based exchanges. We aim to advance discussion on topics of broad interest to our community such as social and technical capacity building, broadening participation, expanding social and data networks, improving data models and building a backbone for the DES, and identifying international funding solutions. This presentation will highlight some of these activities and detail progress towards a roadmap for the development of the human network and technical infrastructure necessary to support the DES. It provides an opportunity for feedback from and engagement by stakeholder communities such as TDWG and other initiatives with a focus on data standards and biodiversity informatics, as we solidify our plans for the future in support of integrated and interconnected biodiversity data and credit for those doing the work.
Davis, Courtney L.; Guralnick, Robert P.; Zipkin, Elise F.
(, Journal of Animal Ecology)
Abstract Natural history collections (NHC) provide a wealth of information that can be used to understand the impacts of global change on biodiversity. As such, there is growing interest in using NHC data to estimate changes in species' distributions and abundance trends over historic time horizons when contemporary survey data are limited or unavailable.However, museum specimens were not collected with the purpose of estimating population trends and thus can exhibit spatiotemporal and collector‐specific biases that can impose severe limitations to using NHC data for evaluating population trajectories.Here we review the challenges associated with using museum records to track long‐term insect population trends, including spatiotemporal biases in sampling effort and sparse temporal coverage within and across years. We highlight recent methodological advancements that aim to overcome these challenges and discuss emerging research opportunities.Specifically, we examine the potential of integrating museum records and other contemporary data sources (e.g. collected via structured, designed surveys and opportunistic citizen science programs) in a unified analytical framework that accounts for the sampling biases associated with each data source. The emerging field of integrated modelling provides a promising framework for leveraging the wealth of collections data to accurately estimate long‐term trends of insect populations and identify cases where that is not possible using existing data sources.
Boldgiv, Bazartseren; Lkhagva, Ariuntsetseg; Edwards, Scott; Stenseth, Nils C; Bayarsaikhan, Jamsranjav; Altangerel, Dondog; Usukhjargal, Dorj; Dovchin, Badamgarav; Gombobaatar, Sundev; Batsaikhan, Nyamsuren; et al
(, Proceedings of the National Academy of Sciences)
Amid global challenges like climate change, extinctions, and disease epidemics, science and society require nuanced, international solutions that are grounded in robust, interdisciplinary perspectives and datasets that span deep time. Natural history collections, from modern biological specimens to the archaeological and fossil records, are crucial tools for understanding cultural and biological processes that shape our modern world. At the same time, natural history collections in low and middle-income countries are at-risk and underresourced, imperiling efforts to build the infrastructure and scientific capacity necessary to tackle critical challenges. The case of Mongolia exemplifies the unique challenges of preserving natural history collections in a country with limited financial resources under the thumb of scientific colonialism. Specifically, the lack of biorepository infrastructure throughout Mongolia stymies efforts to study or respond to large-scale environmental changes of the modern era. Investment in museum capacity and training to develop locally-accessible collections that characterize natural communities over time and space must be a key priority for a future where understanding climate scenarios, predicting, and responding to zoonotic disease, making informed conservation choices, or adapting to agricultural challenges, will be all but impossible without relevant and accessible collections.
Neang, Andrew B.; Sutherland, Will; Beach, Michael W.; Lee, Charlotte P.
(, Proceedings of the ACM on Human-Computer Interaction)
Recent CSCW research on the collaborative design and development of research infrastructures for the natural sciences has increasingly focused on the challenges of open data sharing. This qualitative study describes and analyzes how multidisciplinary, geographically distributed ocean scientists are integrating highly diverse data as part of an effort to develop a new research infrastructure to advance science. This paper identifies different kinds of coordination that are necessary to align processes of data collection, production, and analysis. Some of the hard work to integrate data is undertaken before data integration can even become a technical problem. After data integration becomes a technical problem, social and organizational means continue to be critical for resolving differences in assumptions, methods, practices, and priorities. This work calls attention to the diversity of coordinative, social, and organizational practices and concerns that are needed to integrate data and also how, in highly innovative work, the process of integrating data also helps to define scientific problem spaces themselves.
Card, Daren C., Shapiro, Beth, Giribet, Gonzalo, Moritz, Craig, and Edwards, Scott V. Museum Genomics. Retrieved from https://par.nsf.gov/biblio/10349206. Annual Review of Genetics 55.1 Web. doi:10.1146/annurev-genet-071719-020506.
Card, Daren C., Shapiro, Beth, Giribet, Gonzalo, Moritz, Craig, & Edwards, Scott V. Museum Genomics. Annual Review of Genetics, 55 (1). Retrieved from https://par.nsf.gov/biblio/10349206. https://doi.org/10.1146/annurev-genet-071719-020506
@article{osti_10349206,
place = {Country unknown/Code not available},
title = {Museum Genomics},
url = {https://par.nsf.gov/biblio/10349206},
DOI = {10.1146/annurev-genet-071719-020506},
abstractNote = {Natural history collections are invaluable repositories of biological information that provide an unrivaled record of Earth's biodiversity. Museum genomics—genomics research using traditional museum and cryogenic collections and the infrastructure supporting these investigations—has particularly enhanced research in ecology and evolutionary biology, the study of extinct organisms, and the impact of anthropogenic activity on biodiversity. However, leveraging genomics in biological collections has exposed challenges, such as digitizing, integrating, and sharing collections data; updating practices to ensure broadly optimal data extraction from existing and new collections; and modernizing collections practices, infrastructure, and policies to ensure fair, sustainable, and genomically manifold uses of museum collections by increasingly diverse stakeholders. Museum genomics collections are poised to address these challenges and, with increasingly sensitive genomics approaches, will catalyze a future era of reproducibility, innovation, and insight made possible through integrating museum and genome sciences.},
journal = {Annual Review of Genetics},
volume = {55},
number = {1},
author = {Card, Daren C. and Shapiro, Beth and Giribet, Gonzalo and Moritz, Craig and Edwards, Scott V.},
}
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