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Astorga F, Groom Q, Shimabukuro PHF, Manguin S, Noesgaard D, Orrell T, Sinka M, Hirsch T, Schigel D. Biodiversity data supports research on human infectious diseases: Global trends, challenges, and opportunities. One Health 2023; 16:100484. [PMID: 36714536 PMCID: PMC9880238 DOI: 10.1016/j.onehlt.2023.100484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 12/06/2022] [Accepted: 01/05/2023] [Indexed: 01/19/2023] Open
Abstract
The unprecedented generation of large volumes of biodiversity data is consistently contributing to a wide range of disciplines, including disease ecology. Emerging infectious diseases are usually zoonoses caused by multi-host pathogens. Therefore, their understanding may require the access to biodiversity data related to the ecology and the occurrence of the species involved. Nevertheless, despite several data-mobilization initiatives, the usage of biodiversity data for research into disease dynamics has not yet been fully leveraged. To explore current contribution, trends, and to identify limitations, we characterized biodiversity data usage in scientific publications related to human health, contrasting patterns of studies citing the Global Biodiversity Information Facility (GBIF) with those obtaining data from other sources. We found that the studies mainly obtained data from scientific literature and other not aggregated or standardized sources. Most of the studies explored pathogen species and, particularly those with GBIF-mediated data, tended to explore and reuse data of multiple species (>2). Data sources varied according to the taxa and epidemiological roles of the species involved. Biodiversity data repositories were mainly used for species related to hosts, reservoirs, and vectors, and barely used as a source of pathogens data, which was usually obtained from human and animal-health related institutions. While both GBIF- and not GBIF-mediated data studies explored similar diseases and topics, they presented discipline biases and different analytical approaches. Research on emerging infectious diseases may require the access to geographical and ecological data of multiple species. The One Health challenge requires interdisciplinary collaboration and data sharing, which is facilitated by aggregated repositories and platforms. The contribution of biodiversity data to understand infectious disease dynamics should be acknowledged, strengthened, and promoted.
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Affiliation(s)
- Francisca Astorga
- Facultad de Ciencias, Universidad Mayor, Chile,Corresponding author.
| | - Quentin Groom
- Biodiversity Informatics, Meise Botanic Garden, Belgium Nieuwelaan 38, 1860, Meise, Belgium
| | | | - Sylvie Manguin
- HSM, University Montpellier, CNRS, IRD, 911 Av. Agropolis, 34394 Montpellier, France
| | - Daniel Noesgaard
- Global Biodiversity Information Facility, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark
| | - Thomas Orrell
- Smithsonian Institution, National Museum of Natural History, 10th St. & Constitution Ave. NW, Washington, DC 20560, USA
| | | | - Tim Hirsch
- Global Biodiversity Information Facility, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark
| | - Dmitry Schigel
- Global Biodiversity Information Facility, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark
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Peterson AT, Aiello-Lammens M, Amatulli G, Anderson R, Cobos M, Diniz-Filho JA, Escobar L, Feng X, Franklin J, Gadelha L, Georges D, Guéguen M, Gueta T, Ingenloff K, Jarvie S, Jiménez L, Karger D, Kass J, Kearney M, Loyola R, Machado-Stredel F, Martínez-Meyer E, Merow C, Mondelli ML, Mortara S, Muscarella R, Myers C, Naimi B, Noesgaard D, Ondo I, Osorio-Olvera L, Owens H, Pearson R, Pinilla-Buitrago G, Sánchez-Tapia A, Saupe E, Thuiller W, Varela S, Warren D, Wieczorek J, Yates K, Zhu G, Zuquim G, Zurell D. ENM2020: A Free Online Course and Set of Resources on Modeling Species' Niches and Distributions. Biodiv Inf 2022. [DOI: 10.17161/bi.v17i.15016] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The field of distributional ecology has seen considerable recent attention, particularly surrounding the theory, protocols, and tools for Ecological Niche Modeling (ENM) or Species Distribution Modeling (SDM). Such analyses have grown steadily over the past two decades—including a maturation of relevant theory and key concepts—but methodological consensus has yet to be reached. In response, and following an online course taught in Spanish in 2018, we designed a comprehensive English-language course covering much of the underlying theory and methods currently applied in this broad field. Here, we summarize that course, ENM2020, and provide links by which resources produced for it can be accessed into the future. ENM2020 lasted 43 weeks, with presentations from 52 instructors, who engaged with >2500 participants globally through >14,000 hours of viewing and >90,000 views of instructional video and question-and-answer sessions. Each major topic was introduced by an “Overview” talk, followed by more detailed lectures on subtopics. The hierarchical and modular format of the course permits updates, corrections, or alternative viewpoints, and generally facilitates revision and reuse, including the use of only the Overview lectures for introductory courses. All course materials are free and openly accessible (CC-BY license) to ensure these resources remain available to all interested in distributional ecology.
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Abstract
The accessibility of global biodiversity information has surged in the past two decades, notably through widespread funding initiatives for museum specimen digitization and emergence of large-scale public participation in community science. Effective use of these data requires the integration of disconnected datasets, but the scientific impacts of consolidated biodiversity data networks have not yet been quantified. To determine whether data integration enables novel research, we carried out a quantitative text analysis and bibliographic synthesis of >4,000 studies published from 2003 to 2019 that use data mediated by the world's largest biodiversity data network, the Global Biodiversity Information Facility (GBIF). Data available through GBIF increased 12-fold since 2007, a trend matched by global data use with roughly two publications using GBIF-mediated data per day in 2019. Data-use patterns were diverse by authorship, geographic extent, taxonomic group, and dataset type. Despite facilitating global authorship, legacies of colonial science remain. Studies involving species distribution modeling were most prevalent (31% of literature surveyed) but recently shifted in focus from theory to application. Topic prevalence was stable across the 17-y period for some research areas (e.g., macroecology), yet other topics proportionately declined (e.g., taxonomy) or increased (e.g., species interactions, disease). Although centered on biological subfields, GBIF-enabled research extends surprisingly across all major scientific disciplines. Biodiversity data mobilization through global data aggregation has enabled basic and applied research use at temporal, spatial, and taxonomic scales otherwise not possible, launching biodiversity sciences into a new era.
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Affiliation(s)
- J Mason Heberling
- Section of Botany, Carnegie Museum of Natural History, Pittsburgh, PA 15213;
| | - Joseph T Miller
- Global Biodiversity Information Facility, Secretariat, DK-2100 Copenhagen Ø, Denmark
| | - Daniel Noesgaard
- Global Biodiversity Information Facility, Secretariat, DK-2100 Copenhagen Ø, Denmark
| | - Scott B Weingart
- Digital Humanities Program, University Libraries, Carnegie Mellon University, Pittsburgh, PA 15213
| | - Dmitry Schigel
- Global Biodiversity Information Facility, Secretariat, DK-2100 Copenhagen Ø, Denmark
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Hobern D, Baptiste B, Copas K, Guralnick R, Hahn A, van Huis E, Kim ES, McGeoch M, Naicker I, Navarro L, Noesgaard D, Price M, Rodrigues A, Schigel D, Sheffield CA, Wieczorek J. Connecting data and expertise: a new alliance for biodiversity knowledge. Biodivers Data J 2019; 7:e33679. [PMID: 30886531 PMCID: PMC6420472 DOI: 10.3897/bdj.7.e33679] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 03/04/2019] [Indexed: 11/12/2022] Open
Abstract
There has been major progress over the last two decades in digitising historical knowledge of biodiversity and in making biodiversity data freely and openly accessible. Interlocking efforts bring together international partnerships and networks, national, regional and institutional projects and investments and countless individual contributors, spanning diverse biological and environmental research domains, government agencies and non-governmental organisations, citizen science and commercial enterprise. However, current efforts remain inefficient and inadequate to address the global need for accurate data on the world's species and on changing patterns and trends in biodiversity. Significant challenges include imbalances in regional engagement in biodiversity informatics activity, uneven progress in data mobilisation and sharing, the lack of stable persistent identifiers for data records, redundant and incompatible processes for cleaning and interpreting data and the absence of functional mechanisms for knowledgeable experts to curate and improve data. Recognising the need for greater alignment between efforts at all scales, the Global Biodiversity Information Facility (GBIF) convened the second Global Biodiversity Informatics Conference (GBIC2) in July 2018 to propose a coordination mechanism for developing shared roadmaps for biodiversity informatics. GBIC2 attendees reached consensus on the need for a global alliance for biodiversity knowledge, learning from examples such as the Global Alliance for Genomics and Health (GA4GH) and the open software communities under the Apache Software Foundation. These initiatives provide models for multiple stakeholders with decentralised funding and independent governance to combine resources and develop sustainable solutions that address common needs. This paper summarises the GBIC2 discussions and presents a set of 23 complementary ambitions to be addressed by the global community in the context of the proposed alliance. The authors call on all who are responsible for describing and monitoring natural systems, all who depend on biodiversity data for research, policy or sustainable environmental management and all who are involved in developing biodiversity informatics solutions to register interest at https://biodiversityinformatics.org/ and to participate in the next steps to establishing a collaborative alliance. The supplementary materials include brochures in a number of languages (English, Arabic, Spanish, Basque, French, Japanese, Dutch, Portuguese, Russian, Traditional Chinese and Simplified Chinese). These summarise the need for an alliance for biodiversity knowledge and call for collaboration in its establishment.
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Affiliation(s)
- Donald Hobern
- Global Biodiversity Information Facility Secretariat, Copenhagen, Denmark Global Biodiversity Information Facility Secretariat Copenhagen Denmark
| | - Brigitte Baptiste
- Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Bogotá, Colombia Instituto de Investigación de Recursos Biológicos Alexander von Humboldt Bogotá Colombia
| | - Kyle Copas
- Global Biodiversity Information Facility Secretariat, Copenhagen, Denmark Global Biodiversity Information Facility Secretariat Copenhagen Denmark
| | - Robert Guralnick
- Vertnet, Florida, United States of America Vertnet Florida United States of America.,University of Colorado, Boulder; University of Colorado Museum of Natural History, Boulder, United States of America University of Colorado, Boulder; University of Colorado Museum of Natural History Boulder United States of America.,Univ. of Florida, Gainesville, United States of America Univ. of Florida Gainesville United States of America
| | - Andrea Hahn
- Global Biodiversity Information Facility Secretariat, Copenhagen, Denmark Global Biodiversity Information Facility Secretariat Copenhagen Denmark
| | - Edwin van Huis
- Naturalis, Amsterdam, Netherlands Naturalis Amsterdam Netherlands
| | - Eun-Shik Kim
- Kookmin University, Seoul, South Korea Kookmin University Seoul South Korea
| | - Melodie McGeoch
- Monash University, Clayton, Australia Monash University Clayton Australia
| | - Isayvani Naicker
- African Academy of Sciences, Nairobi, Kenya African Academy of Sciences Nairobi Kenya
| | - Laetitia Navarro
- German Centre for Integrative Biodiversity Research, Leipzig, Germany German Centre for Integrative Biodiversity Research Leipzig Germany
| | - Daniel Noesgaard
- Global Biodiversity Information Facility Secretariat, Copenhagen, Denmark Global Biodiversity Information Facility Secretariat Copenhagen Denmark
| | - Michelle Price
- Conservatoire et Jardin botaniques de la Ville de Genève, Geneva, Switzerland Conservatoire et Jardin botaniques de la Ville de Genève Geneva Switzerland
| | - Andrew Rodrigues
- Global Biodiversity Information Facility Secretariat, Copenhagen, Denmark Global Biodiversity Information Facility Secretariat Copenhagen Denmark
| | - Dmitry Schigel
- Global Biodiversity Information Facility Secretariat, Copenhagen, Denmark Global Biodiversity Information Facility Secretariat Copenhagen Denmark
| | - Carolyn A Sheffield
- Smithsonian Libraries/Biodiversity Heritage Library, Washington, DC, United States of America Smithsonian Libraries/Biodiversity Heritage Library Washington, DC United States of America
| | - John Wieczorek
- VertNet, Bariloche, Argentina VertNet Bariloche Argentina.,Museum of Vertebrate Zoology, University of California, Berkeley, United States of America Museum of Vertebrate Zoology, University of California Berkeley United States of America
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