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Journal articles on the topic 'GBIF repository'

Author: Grafiati

Published: 7 June 2025

Last updated: 2 August 2025

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1

Döring, Markus, Thomas Jeppesen, and Olaf Bánki. "Introducing ChecklistBank: An index and repository for taxonomic data." Biodiversity Information Science and Standards 6 (August 24, 2022): e93938. https://doi.org/10.3897/biss.6.93938.

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As a joint development between Catalogue of Life (COL) and the Global Biodiversity Information Facility (GBIF), ChecklistBank supports the publication and curation of checklists and provides a platform for their consistent discovery, use and citation. GBIF has for some time maintained ChecklistBank as its repository for its community to share species checklist data and to drive species searches on GBIF. The collaboration built on an earlierversion, to add functions needed to assemble the COL Checklist (Bánki et al. 2022) and to make it an independent system. Its data model is built around the

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Miller, Joe. "Evolution of GBIF's Taxonomic Backbone." Biodiversity Information Science and Standards 6 (August 1, 2022): e91092. https://doi.org/10.3897/biss.6.91092.

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GBIF (Global Biodiversity Information Facility) is an international research data infrastructure that mediates data from various sources such as museum collections, citizen science observations and machine generated data such as camera trap and environmental DNA. Data shared with GBIF comes with a taxonomic identification—normally a Linnaean binomial. Large data flows are now coming to GBIF without formal names but are identified by informal species hypotheses, usually based on DNA sequence similarity to a curated reference library.GBIF's task is to integrate all this data in a repository that

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Waller, John. "Processing Country Centroids at the Global Biodiversity Information Facility." Biodiversity Information Science and Standards 7 (August 9, 2023): e110728. https://doi.org/10.3897/biss.7.110728.

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The Global Biodiversity Information Facility (GBIF) is an international network and data infrastructure that promotes open access to biodiversity data. GBIF serves as a global hub for aggregating and disseminating biodiversity information from diverse sources, including museums, research institutions, and citizen science projects.I will present recent additions to GBIF data quality measures, focusing on the introduction of the country centroid filtering feature. Additionally, I explore the functionality and significance of GBIF data quality flags, which aid in assessing the reliability and usa

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Agosti, Donat, Terry Catapano, Guido Sautter, et al. "Biodiversity Literature Repository (BLR), a repository for FAIR data and publications." Biodiversity Information Science and Standards 3 (June 19, 2019): e37197. https://doi.org/10.3897/biss.3.37197.

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Scholarly publications in taxonomy are used as the sole carrier of the communication channel to publicize the description of new species, more generally any kind of taxon, their augmentations in form of re-descriptions to small notes such as additional observation records, or deprecations when the name of a taxon is changing. This is communicated in a highly standardized way. For nomenclatural issues, the Codes (e.g. International Code of Zoological Nomenclature) require certain elements, and for comparative reasons, highly formalized language, document structure, illustrations and citation sy

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Pando, Francisco, and Francisco Bonet. "Making LTER Data FAIR: A workbench using DEIMS datasets and GBIF Tools." Biodiversity Information Science and Standards 3 (June 19, 2019): e37257. https://doi.org/10.3897/biss.3.37257.

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DEIMS-SDR (Dynamic Ecological Information Management System - Site and dataset registry, Wohner et al. 2019) is one of the largest repositories of long-term ecological research (LTER) datasets. It provides sophisticated searching tools by metadata elements and identifiers for all the 930 contained datasets, most of them from European sites. Whereas datasets' metadata are highly structured and searchable, datasets themselves have little standardization in terms of content, identifiers or license, making data integration difficult or cumbersome. Adopting the data FAIR guiding principles(Wilkinso

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Alvares, Diego, Marcus Guidoti, Felipe Simoes, Carolina Sokolowicz, and Donat Agosti. "The BHL-Plazi Partnership: Getting data from the 1800s directly into 21st century, reused digital accessible knowledge." Biodiversity Information Science and Standards 5 (September 23, 2021): e75604. https://doi.org/10.3897/biss.5.75604.

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Plazi is a Swiss non-governmental organization dedicated to the liberation of data imprisoned in flat, dead-end formats such as PDFs. In the process, the data therein is annotated and exported in various formats, following field-specific standards, facilitating free access and reutilization by several other service providers and end-users. This data mining and enhancement process allows for the rediscovery of the known biodiversity since the knowledge on known taxa is published into an ever-growing corpus of papers, chapters and books, inaccessible to the state-of-the-art service providers, su

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Svenningsen, Cecilie, Marcos Gonzalez, and Tim Robertson. "GBIF's Vocabulary Server: A Tool to Create, Manage and Apply Controlled Vocabularies for Biodiversity." Biodiversity Information Science and Standards 8 (September 26, 2024): e137853. https://doi.org/10.3897/biss.8.137853.

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Global Biodiversity Information Facility's (GBIF) global index of primary biodiversity data is based on contributions from more than 2,200 publishing institutions and over 100,000 datasets. Data originate from a broad variety of fields, from research to citizen science, from eDNA through specimen collections to observations and monitoring projects, across all taxonomic groups, and with a wide range of datasets and data types. Equally variable is the underlying motivation and focus for data collection and digitization. Even within commonly used domain concepts like Kingdom or OccurrenceStatus,

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Tattersall, Katherine, Peggy Newman, Sachit Rajbhandari, Dave Watts, and Mahmoud Sadeghi. "An Australian Model of Cooperative Data Publishing to OBIS and GBIF." Biodiversity Information Science and Standards 7 (September 7, 2023): e112228. https://doi.org/10.3897/biss.7.112228.

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The Australian Commonwealth Science and Industrial Research Organisation (CSIRO) hosts both the Australian Ocean Biodiversity Information System (OBIS) and Global Biodiversity Information Facility (GBIF) nodes within the National Collections and Marine Infrastructure (NCMI) business unit. OBIS-AU is led by the NCMI Information and Data Centre and publishes marine biodiversity data in the Darwin Core (DwC) standard via an Integrated Publishing Toolkit (IPT), with over 450 marine datasets at present. The Australian GBIF node is hosted by a separate team at the Atlas of Living Australia (ALA), a

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Agosti, Donat, Patrick Ruch, Gonzalez Lopez Jose Benito, and Lyubomir Penev. "Enabling Published Taxonomic Data to be used to Address the Biodiversity Crisis: Biodiversity Literature Repository and TreatmentBank." Biodiversity Information Science and Standards 6 (August 2, 2022): e91167. https://doi.org/10.3897/biss.6.91167.

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To understand the loss of species, a benchmark is needed, e.g. the status of biodiversity in 1992 when the Convention on Biological Diversity recognized biodiversity crisis to compare to its status in the successive year. Though we are far from knowning how many species there are on planet Earth, we keep track of their descriptions and number through the information kept in our libraries. Each species discovered is represented therein by at least one taxononic treatment. The library includes an estimated 500 million pages and is updated daily with an estimated 17–18,000 new species annually an

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DA SILVA, JAQUELINE SANTANA TAVARES FERREIRA, JOCELIA GRAZIA, and KIM RIBEIRO BARÃO. "Redescription of Steleocoris Mayr, 1864 and Theloris Thunberg, 1783 (Hemiptera: Pentatomidae), two poorly known African stink bugs." Zootaxa 4938, no. 4 (2021): 475–86. http://dx.doi.org/10.11646/zootaxa.4938.4.6.

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The knowledge about the monotypic genera Steleocoris Mayr and Theloris Thunberg is restricted to their original descriptions and subsequent nomenclatural acts. These genera are primarily distributed in South Africa and are two of the few genera of Carpocorini (Pentatomidae: Pentatominae) occurring in Africa. Here, we redescribe Steleocoris comma (Thunberg) and Theloris costata (Thunberg) and illustrate the genitalia of both sexes for the first time. Also, an occurrence map is provided based on collection labels from analyzed specimens and records available on GBIF and the web repository iNatur

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Agosti, Donat, Marcus Guidoti, Terry Catapano, Alexandros Ioannidis-Pantopikos, and Guido Sautter. "The Standards behind the Scenes: Explaining data from the Plazi workflow." Biodiversity Information Science and Standards 4 (October 9, 2020): e59178. https://doi.org/10.3897/biss.4.59178.

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As part of the CETAF COVID19 task force, Plazi liberated taxonomic treatments, figures, observation records, biotic interactions, taxonomic names, and collection and specimen codes involving bats and viruses from scholarly publications with the intention to create open access, findable, accessible, interoperable and reusable data (FAIR). The data is accessible via TreatmentBank and the Biodiversity Literature Repository (BLR) and it is continually harvested and reused by the Global Biodiversity Information Facility (GBIF) and Global Biotic Interactions (GloBI). This data was processed, enhance

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Shrestha, Lily, Vijay Barve, Chihjen Ko, et al. "Improving Access to Collection Information in Asia and Africa through the Global Registry of Scientific Collections." Biodiversity Information Science and Standards 7 (August 16, 2023): e111167. https://doi.org/10.3897/biss.7.111167.

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Global Registry of Scientific Collections, or GRSciColl, is a comprehensive registry of natural history collections maintained by the Global Biodiversity Information Facility (GBIF), building upon previous efforts developed by the Consortium of the Barcode of Life (CBOL) and other organizations. Its primary purpose is to provide a centralized platform for accessing information on institutions, their collections and associated staff members. While both GBIF and GRSciColl aim to encompass data from all around the globe, Asian and African collections are often underrepresented. To address this di

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Ioannidis-Pantopikos, Alexandros, and Donat Agosti. "Biodiversity Literature Repository: Building the customized FAIR repository by using custom metadata." Biodiversity Information Science and Standards 5 (September 14, 2021): e75147. https://doi.org/10.3897/biss.5.75147.

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In the landscape of general-purpose repositories, <u>Zenodo</u> was built at the European Laboratory for Particle Physics' (<u>CERN</u>) data center to facilitate the sharing and preservation of the long tail of research across all disciplines and scientific domains. Given Zenodo's long tradition of making research artifacts <u>FAIR</u> (Findable, Accessible, Interoperable, and Reusable), there are still challenges in applying these principles effectively when serving the needs of specific research domains.<u>Plazi</u>'s biodiversity taxonomic literature processing pipeline liberates data from

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Lecoq, Marie-Elise, Fabien Cavière, and Régine Vignes-Lebbe. "Living Atlases: tips and advices." Biodiversity Information Science and Standards 1 (August 14, 2017): e20252. https://doi.org/10.3897/tdwgproceedings.1.20252.

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Atlas of Living Australia (ALA), Australian node of the Global Biodiversity Information Facility (GBIF), provides information on all the known species in Australia. Since 2010, ALA has developed an open source framework providing different tools to help users from various sectors. The ALA technical team, with the help of GBIF, has reorganized the architecture of ALA tools into several modules to help other institutions to re-use the code. The three first sessions of this workshop focuses on data indexation, occurrence search engine and metadata registry. The last session delves into more techn

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Cornwell, Peter. "Progress with Repository-based Annotation Infrastructure for Biodiversity Applications." Biodiversity Information Science and Standards 7 (September 14, 2023): e112707. https://doi.org/10.3897/biss.7.112707.

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Rapid development since the 1980s of technologies for analysing texts, has led not only to widespread employment of text 'mining', but also to now-pervasive large language model artificial intelligence (AI) applications. However, building new, concise, data resources from historic, as well as contemporary scientific literature, which can be employed efficiently at scale by automation and which have long-term value for the research community, has proved more elusive.Efforts at codifying analyses, such as the Text Encoding Initiative (TEI), date from the early 1990s and were initially driven by

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Bánki, Olaf, Donald Hobern, and Markus Döring. "Building on the Functionalities of GBIF-COL ChecklistBank." Biodiversity Information Science and Standards 7 (August 28, 2023): e111668. https://doi.org/10.3897/biss.7.111668.

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ChecklistBank, co-developed by Catalogue of Life (COL) and the Global Biodiversity Information Facility (GBIF), provides a suite of functionalities for building taxonomic data solutions. In addition to serving as a publishing platform and open data repository for taxonomic and nomenclatural data, ChecklistBank includes tools for managing the assembly of new species lists from other datasets published to the platform. The ChecklistBank API provides access to all data sources, including the COL Checklist, all mediated through ChecklistBank. It also allows for (bulk) matching of names, and provid

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Agosti, Donat, Marcus Guidoti, and Guido Sautter. "Liberating the Richness of Facts implicit in taxonomic Publication: The Plazi Workflow." Biodiversity Information Science and Standards 4 (October 9, 2020): e59179. https://doi.org/10.3897/biss.4.59179.

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The growing corpus of hundreds of millions of pages of taxonomic literature reporting research results based on specimens is very rich in facts. In order to make them reusable, Plazi, Pensoft and Zenodo are building and maintaining the Biodiversity Literature Repository which includes a workflow to discover, describe, store, in order to making these facts open access, findable, accesible, interoperable and reusable (FAIR). Currently, 43,000 articles have 406,000 material citations, and around 50% of annually new described species are made accessible and immediately reused by the Global Biodive

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Seregin, Alexey, and Nina Stepanova. "MHA Herbarium: Eastern European collections of vascular plants." Biodiversity Data Journal 8 (October 23, 2020): e57512. https://doi.org/10.3897/BDJ.8.e57512.

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World herbaria with 387.5M specimens (Thiers 2019) are being rapidly digitised. At least 79.9M plant specimens (20.6%) are already databased throughout the globe in the standard form of GBIF-mediated data. The contribution of smaller herbaria has been steadily growing over the last few years due to cost reduction, usage of platforms and solutions developed by the leaders. A web-resource the Moscow Digital Herbarium (Seregin 2020b) was launched by the Lomonosov Moscow State University in October, 2016 for publication of specimens imaged and databased in the Moscow University Herbarium (MW). As

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Zudin, Sergey, Wilfried Heintz, Daniel Kraus, Frank Krumm, Laurent Larrieu, and Andreas Schuck. "A spatially-explicit database of tree-related microhabitats in Europe and beyond." Biodiversity Data Journal 10 (October 12, 2022): e91385. https://doi.org/10.3897/BDJ.10.e91385.

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Tree to tree interactions are important structuring mechanisms for forest community dynamics. Forest management takes advantage of competition effects on tree growth by removing or retaining trees to achieve management goals. Both competition and silviculture have, thus, a strong effect on density and distribution of tree related microhabitats which are key features for forest taxa at the stand scale. In particular, spatially-explicit data to understand patterns and mechanisms of tree-related microhabitats formation in forest stands are rare. To train and eventually improve decision-making cap

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Penev, Lyubomir, Teodor Georgiev, Viktor Senderov, Mariya Dimitrova, and Pavel Stoev. "The Pensoft Data Publishing Workflow: The FAIRway from articles to Linked Open Data." Biodiversity Information Science and Standards 3 (June 13, 2019): e35902. https://doi.org/10.3897/biss.3.35902.

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As one of the first advocates of open access and open data in the field of biodiversity publishiing, Pensoft has adopted a multiple data publishing model, resulting in the ARPHA-BioDiv toolbox (Penev et al. 2017). ARPHA-BioDiv consists of several data publishing workflows and tools described in the Strategies and Guidelines for Publishing of Biodiversity Data and elsewhere: Data underlying research results are deposited in an external repository and/or published as supplementary file(s) to the article and then linked/cited in the article text; supplementary files are published under their own

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Takahashi, Miwa, and Oliver Berry. "Amplifying the Power of eDNA by Making it FAIR." Biodiversity Information Science and Standards 7 (September 13, 2023): e112553. https://doi.org/10.3897/biss.7.112553.

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Environmental DNA (eDNA) is a fast-growing biomonitoring approach to detect species and map their distributions, with the number of eDNA publications exponentially increasing in the past decade. While millions of DNA sequences are often generated and assigned to taxa in each publication, these records are stored in numerous locations (e.g., supplementary materials at journals' servers, open data publishing platforms such as Dryad) and in various formats, which makes it difficult to find, access, re-use and integrate datasets. Making eDNA data FAIR (findable, accessible, interoperable, re-usabl

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Agosti, Donat, Laurence Benichou, Lyubomir Penev, and Roger Hyam. "A Possible Workflow from New and Legacy Publications to keep the World Flora Online up to date with New Species and Augmenting Taxonomic Treatments." Biodiversity Information Science and Standards 6 (August 23, 2022): e91241. https://doi.org/10.3897/biss.6.91241.

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Thousands of new species are discovered each year, and new results are published to add to the knowledge of existing species. A growing number of these are immediately accessible through the Biodiversity Literature Repository (BLR) and reused by Global Biodiversity Information Facility (GBIF), bringing the number of treatments covering plant species to over 25,000 treatments. This includes the findable, accessible, interoperable, and resuable (FAIR) treatments and related figures, and in many cases the material citation of the holotype, and links to the collection, specimen and gene sequences

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Grosjean, Marie, Morten Høfft, Marcos Gonzalez, Tim Robertson, and Andrea Hahn. "GRSciColl: Registry of Scientific Collections maintained by the community for the community." Biodiversity Information Science and Standards 5 (September 13, 2021): e74354. https://doi.org/10.3897/biss.5.74354.

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<u>GRSciColl</u>, the Registry of Scientific Collections, is a comprehensive, community-curated clearinghouse of collections information originally developed by the Consortium of the Barcode of Life (<u>CBOL</u>) and hosted by the <u>Smithsonian Institution</u> until 2019. It is now hosted and maintained in the <u>Global Biodiversity Information Facility</u> (GBIF) <u>registry</u> (see <u>this news item</u>).GRSciColl aims to improve access to information about institutions, the scientific collections they hold, and to facilitate access to the staff members who manage them. Anyone can use GRSc

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van der Kolk, Henk-Jan, Peter Desmet, Kees Oosterbeek, et al. "GPS tracking data of Eurasian oystercatchers (Haematopus ostralegus) from the Netherlands and Belgium." ZooKeys 1123 (October 3, 2022): 31–45. http://dx.doi.org/10.3897/zookeys.1123.90623.

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We describe six datasets that contain GPS and accelerometer data of 202 Eurasian oystercatchers (Haematopus ostralegus) spanning the period 2008–2021. Birds were equipped with GPS trackers in breeding and wintering areas in the Netherlands and Belgium. We used GPS trackers from the University of Amsterdam Bird Tracking System (UvA-BiTS) for several study purposes, including the study of space use during the breeding season, habitat use and foraging behaviour in the winter season, and impacts of human disturbance. To enable broader usage, all data have now been made open access. Combined, the d

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van, der Kolk Henk-Jan, Peter Desmet, Kees Oosterbeek, et al. "GPS tracking data of Eurasian oystercatchers (Haematopus ostralegus) from the Netherlands and Belgium." ZooKeys 1123 (October 3, 2022): 31–45. https://doi.org/10.3897/zookeys.1123.90623.

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We describe six datasets that contain GPS and accelerometer data of 202 Eurasian oystercatchers (Haematopus ostralegus) spanning the period 2008–2021. Birds were equipped with GPS trackers in breeding and wintering areas in the Netherlands and Belgium. We used GPS trackers from the University of Amsterdam Bird Tracking System (UvA-BiTS) for several study purposes, including the study of space use during the breeding season, habitat use and foraging behaviour in the winter season, and impacts of human disturbance. To enable broader usage, all data have now been made open access. Combined, the d

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Simoes, Felipe, Donat Agosti, and Marcus Guidoti. "Delivering Fit-for-Use Data: Quality control." Biodiversity Information Science and Standards 5 (September 20, 2021): e75432. https://doi.org/10.3897/biss.5.75432.

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Automatic data mining is not an easy task and its success in the biodiversity world is deeply tied to the standardization and consistency of scientific journals' layout structure. The various formatting styles found in the over 500 million pages of published biodiversity information (Kalfatovich 2010), pose a remarkable challenge towards the goal of automating the liberation of data currently trapped on the printed page. Regular expressions and other pattern-recognition strategies invariably fail to cope with this diverse landscape of academic publishing. Challenges such as incomplete data and

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Tretyakova, A. S., N. Yu Grudanov, and D. S. Shilov. "INVENTORY AND ANALYSIS OF THE FLORA OF THE VISIMSKIY RESERVE." Ботанический журнал 108, no. 1 (2023): 66–75. http://dx.doi.org/10.31857/s0006813623010088.

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The vascular plant flora of the Visimskiy State Natural Biosphere Reserve was studied. It comprises 530 species, 238 genera and 69 families of vascular plants. 510 species were classified as native plants and 20 species as alien plants (4% of the species composition). The top families in terms of the number of species are Asteraceae, Rosaceae, Poaceae, Ranunculaceae. The top genera in terms of the number of species are Alchemilla, Ranunculus, Carex, Poa, Hieracium. The geographical analysis revealed the dominance of Holarctic, Eurasian, boreal and boreal-nemoral species. The analyzed flora als

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Vaz, Stephanie, Mariana Mendes, Gabriel Khattar, et al. "Firefly (Coleoptera, Lampyridae) species from the Atlantic Forest hotspot, Brazil." Biodiversity Data Journal 11 (March 23, 2023): e101000. https://doi.org/10.3897/BDJ.11.e101000.

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We compiled a database of firefly species records from the Atlantic Forest hotspot in Brazil and made it available at GBIF. Data were gathered from literature and from several key entomological collections, including: Coleção entomológica Prof. José Alfredo Pinheiro Dutra (DZRJ/UFRJ) and Coleção do Laboratório de Ecologia de Insetos from Universidade Federal do Rio de Janeiro (CLEI/UFRJ); Coleção Entomológica do Instituto Oswaldo Cruz (CEIOC); Museu de Zoologia da Universidade de São Paulo (MZSP); Coleção Entomológica Pe. Jesus Santiago Moure from Universidade Federal do Paraná (DZUP/UFPR); an

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REQUENA-ZUÑIGA, Edwin, Maria E. CANO, María V. MICIELI, Gerardo A. MARTI, Walter LEÓN-CUETO, and Abraham G. CÁCERES. "Geographical distribution of mosquitoes of the genera Haemagogus and Sabethes (Diptera: Culicidae), potential vectors of the Yellow fever virus in Peru." Revista de la Sociedad Entomológica Argentina 83, no. 02 (2024): 81–86. https://doi.org/10.25085/rsea.830210.

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The aim of this work is to present bibliographic records and technical reports of mosquitoes collected after sylvatic yellow fever outbreaks. Records were analyzed according to their distribution with respect to administrative divisions and Perú ecoregions and were organized in a database published in the GBIF repository. Distribution maps were made based on the mosquito database. In total, 282 records (9 mosquito species) distributed in 13 departments are presented. The most important are Cusco (n= 168), Loreto (n= 33), Puno (n= 31) and Junín (n= 14). Regarding the analysis by ecoregions, it

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Dias, David, Fonseca Clara Baringo, Luiza Correa, et al. "Repatriation Data: More than two million species occurrence records added to the Brazilian Biodiversity Information Facility Repository (SiBBr)." Biodiversity Data Journal 5 (May 30, 2017): e12012. https://doi.org/10.3897/BDJ.5.e12012.

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Primary biodiversity data records, available on-line, are essential for conservation planning. Of the mega diversity countries, Brazil have reached a high level of scientific research in describing their biodiversity. However, there still remain significant limitations in recovering, collating and organizing available information on Brazil's biological diversity and its distribution. Since the colonial period, biological material were often collected and transferred to other countries, which were characterized, stored and maintained. As a result, natural history museums worldwide possess large

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Baker, Ed, Benjamin Price, Simon Rycroft, and Martin Villet. "Global Cicada Sound Collection I: Recordings from South Africa and Malawi by B. W. Price & M. H. Villet and harvesting of BioAcoustica data by GBIF." Biodiversity Data Journal 3 (September 2, 2015): e5792. https://doi.org/10.3897/BDJ.3.e5792.

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Sound collections for singing insects provide important repositories that underpin existing research (e.g. Price et al. 2007 at http://bio.acousti.ca/node/11801; Price et al. 2010) and make bioacoustic collections available for future work, including insect communication (Ordish 1992), systematics (e.g. David et al. 2003), and automated identification (Bennett et al. 2015). The BioAcoustica platform (Baker et al. 2015) is both a repository and analysis platform for bioacoustic collections: allowing collections to be available in perpetuity, and also facilitating complex analyses using the BioV

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Agosti, Donat, and Alexandros Ioannidis-Pantopikos. "Taxonomic Treatments as Open FAIR Digital Objects." Research Ideas and Outcomes 8 (August 25, 2022): e93709. https://doi.org/10.3897/rio.8.e93709.

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Taxonomy is the science of charting and describing the worlds biodiversity. Organisms are grouped into taxa which are given a given rank building the taxonomic hierarchy. The taxa are described in taxonomic treatments, well defined sections of scientific publications (Catapano 2019). They include a nomenclatural section and one or more sections including descriptions, material citations referring to studied specimens, or notes ecology and behavior. In case the treatment does not describe a new discovered taxon, previous treatments are cited in the form of treatment citations. This citation can

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Bánki, Olaf, Markus Döring, Thomas Jeppesen, and Donald Hobern. "Demonstration of Taxonomic Name Data Services through ChecklistBank." Biodiversity Information Science and Standards 7 (September 12, 2023): e112544. https://doi.org/10.3897/biss.7.112544.

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ChecklistBank is a publishing platform and open data repository focused on taxonomic and nomenclatural datasets. It was launched at the end of 2020, and is a joint development by Catalogue of Life (COL) and the Global Biodiversity Information Facility (GBIF). Close to 50K datasets, mostly originating from published literature mediated through Plazi's TreatmentBank, Pensoft Publishers and the European Journal of Taxonomy, are openly accessible through ChecklistBank. Data sets also include sources with (Molecular) Operational Taxonomic Units, such as from UNITE / PlutoF, National Center for Biot

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Sandramo, Domingos, Enrico Nicosia, Silvio Cianciullo, Bernardo Muatinte, and Almeida Guissamulo. "Unlocking the Entomological Collection of the Natural History Museum of Maputo, Mozambique." Biodiversity Data Journal 9 (April 21, 2021): e64461. https://doi.org/10.3897/BDJ.9.e64461.

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The collections of the Natural History Museum of Maputo have a crucial role in the safeguard of Mozambique's biodiversity, representing an important repository of data and materials about the natural heritage of the Country. In this paper is described a dataset based on the Museum's Entomological Collection recording 409 species belonging to 7 orders and 48 families. Each specimen's available data, such as geographical coordinates and taxonomic information, have been digitized to build the dataset. The specimens included in the dataset were acquired between 1914–2018 by collectors and research

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Bénichou, Laurence, Marcus Guidoti, Isabelle Gérard, Donat Agosti, Tony Robillard, and Fabio Cianferoni. "European Journal of Taxonomy: a deeper look into a decade of data." European Journal of Taxonomy 782 (December 17, 2021): 173–96. http://dx.doi.org/10.5852/ejt.2021.782.1597.

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The European Journal of Taxonomy (EJT) is a decade-old journal dedicated to the taxonomy of living and fossil eukaryotes. Launched in 2011, the EJT published exactly 900 articles (31 778 pages) from 2011 to 2021. The journal has been processed in its entirety by Plazi, liberating the data therein, depositing it into TreatmentBank, Biodiversity Literature Repository and disseminating it to partners, including the Global Biodiversity Information Facility (GBIF) using a combination of a highly automated workflow, quality control tools, and human curation. The dissemination of original research al

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Lemos, Valéria M., Marianna Lanari, Margareth Copertino, et al. "Patos Lagoon estuary and adjacent marine coastal biodiversity long-term data." Earth System Science Data 14, no. 3 (2022): 1015–41. http://dx.doi.org/10.5194/essd-14-1015-2022.

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Abstract. Estuaries are among the most productive aquatic ecosystems and provide important ecological and economic services in coastal areas. However, estuarine systems have been threatened worldwide by natural and anthropogenic impacts acting on local, regional, and global scales. Long-term ecological studies contribute to the understanding and management of estuarine functioning and provide the baseline information for detection changes and modeling of predictive scenarios. Here, we describe long-term data on the biodiversity and physico-chemical parameters obtained from 1993 to 2016 for the

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Agosti, Donat, Terry Catapano, Guido Sautter, and Willi Egloff. "The Plazi Workflow: The PDF prison break for biodiversity data." Biodiversity Information Science and Standards 3 (June 13, 2019): e37046. https://doi.org/10.3897/biss.3.37046.

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The Swiss NGO Plazi (http://plazi.org) has developed an automated workflow for liberating data, including images and text, from new taxonomic publications issued in PDF format. This stepwise process extracts, article metadata, illustrations and their captions, bibliographic references, scientific names, named geographic entities such as coordinates and country names, collection codes, and finally, taxonomic treatments. These extracted data are enhanced and published in TreatmentBank (http://plazi.org) and deposited in Biodiversity Literature Repository (https:/biolitrepo.org) respectively, in

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Bánki, Olaf, Markus Döring, and Thomas Jeppesen. "Name IDs and Name Matching for Catalogue of Life: Existing Services and Prospects." Biodiversity Information Science and Standards 7 (August 28, 2023): e111662. https://doi.org/10.3897/biss.7.111662.

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ChecklistBank, developed by Catalogue of Life (COL) and the Global Biodiversity Information Facility (GBIF), is a publishing platform and open data repository focused on taxonomic and nomenclatural data sets (checklists). It contains close to 50K datasets, mostly originating from digitised peer reviewed scientific articles mediated by Plazi, amongst others. The COL Checklist (Bánki et al. 2023) is assembled out of a selection of the data sources in ChecklistBank. The Catalogue of Life Checklist is issued with name usage identifiers, as well as a digital object identifier for the Checklist vers

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Liu, Melissa Jean-Yi, Lily Shrestha, Marie Grosjean, Morten Høfft, Marcos Gonzalez, and Tim Robertson. "An Introduction to the Global Registry of Scientific Collections (GRSciColl)." Biodiversity Information Science and Standards 8 (August 12, 2024): e134257. https://doi.org/10.3897/biss.8.134257.

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The Global Registry of Scientific Collections (GRSciColl) is a comprehensive community-curated repository of scientific collections, their host institutions, and associated staff members. GRSciColl was adopted by the Global Biodiversity Information Facility (GBIF) in 2018, after being developed and hosted at the Smithsonian Institution.GRSciColl houses data on various institutional or personal scientific collections such as natural history collections, archeological collections, and cell culture collections. Users can access information about the collection location, content, accessibility sta

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Agosti, Donat, Lyubomir Penev, Patrick Ruch, Laurence Benichou, and Alexandros Ioannidis-Pantopikos. "The Ecosystem of Linked Biodiversity Publications: General picture of tools and services created by Plazi, Pensoft, MNHN, CETAF, Zenodo, and SIBiLS." Biodiversity Information Science and Standards 7 (August 8, 2023): e110681. https://doi.org/10.3897/biss.7.110681.

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A goal of natural history institutions is to contribute to the understanding of biodiversity and disseminate this knowledge through scholarly publications and other public activities. In today's world, it is expected that this knowledge, imprisoned in separated silos of millions of publications scattered through ca. 500 million published pages, is readily available for exploring and reusing by humans and artificial intelligence tools. The goal of the BiCIKL project and its key product, the Biodiversity Knowledge Hub (BKH), is to put together novel tools and services to publish and extract data

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Cordero, Sebastián, Manuel López-Aliste, Francisca Gálvez, and Francisco Fontúrbel. "Herbarium collection of the Pontificia Universidad Católica de Valparaíso (PUCV), Chile." Biodiversity Data Journal 10 (September 29, 2022): e90591. https://doi.org/10.3897/BDJ.10.e90591.

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This database gathers 10,721 specimens, belonging to 2,578 species from the Chilean vascular flora (angiosperms, gymnosperms and pteridophytes) deposited in the Herbarium of the Pontificia Universidad Católica de Valparaíso (PUCV) in Chile. The PUCV botanical collection was started by the renowned botanist Otto Zöllner and represents a major natural historical legacy for central Chile, with decades of information represented through preserved specimens. This collection is currently deposited in the Curauma campus of the PUCV. This digitisation effort is part of the PUCV's endeavour to mobilise

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Adamova, V. V. "USING SDM FOR MODELING THE POTENTIAL RANGE OF COCHLODINA LAMINATA (GASTROPODA, PULMONATA, CLAUSILIIDAE) IN EUROPE." Ecology. Economy. Informatics.System analysis and mathematical modeling of ecological and economic systems 1, no. 6 (2021): 66–69. http://dx.doi.org/10.23885/2500-395x-2021-1-6-66-69.

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The study presents a model of the potential distribution of the land snail Cochlodina laminata (Clausiliidae), created using the SDM (species distribution modeling) methods. The forecast was made on the basis C. laminata records from GBIF repository. This species has the wide distribution in of this and wide ecological valence in comparison with the most of the european clausilids. Climatic parameters and altitude from the open database WorldClim.org were selected as predictors. For the forecast, the models with the best statistical indicators were selected, and the ensemble forecast procedure

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Penev, Lyubomir, Daniel Mietchen, Vishwas Chavan, et al. "Strategies and guidelines for scholarly publishing of biodiversity data." Research Ideas and Outcomes 3 (February 28, 2017): e12431. https://doi.org/10.3897/rio.3.e12431.

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The present paper describes policies and guidelines for scholarly publishing of biodiversity and biodiversity-related data, elaborated and updated during the Framework Program 7 EU BON project, on the basis of an earlier version published on Pensoft's website in 2011. The document discusses some general concepts, including a definition of datasets, incentives to publish data and licenses for data publishing. Further, it defines and compares several routes for data publishing, namely as (1) supplementary files to research articles, which may be made available directly by the publisher, or (2) p

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Kandaurov, Andrei, Alexander Bukhnikashvili, Giorgi Sheklashvili, and Ioseb Natradze. "The occurrence of insectivores (Mammalia, Eulipotyphla) in Georgia from 1864 through to 2022." Biodiversity Data Journal 11 (July 11, 2023): e106256. https://doi.org/10.3897/BDJ.11.e106256.

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Of the 108 species that occur in Georgia, ten species are insectivores belonging to the order Eulipotyphla. Forty percent of them are endemic to the Caucasus and sixty percent are endemic to the Middle East, including the Caucasus. Up to now, no comprehensive data on the distribution of insectivores in Georgia have been available.The aggregated standardised data on the occurrence of small mammals can be applied to resource management, biogeography, ecological and systematic studies and to the planning of nature conservation efforts. Hereafter, the attempt to provide accumulated in one paper al

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Benichou, Laurence, Marianne Salaün, Iva Boyadzhieva, Seyhan Demirov, Teodor Georgiev, and Lyubomir Penev. "Pre-publication Data Linking in Taxonomy and Biodiversity: The ARPHA and Metotaxa-Metostem publishing systems." Biodiversity Information Science and Standards 7 (August 9, 2023): e110919. https://doi.org/10.3897/biss.7.110919.

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The traditional way of publishing in PDF makes it difficult to retrospectively convert the legacy literature into data. This presentation will discuss pre-publication tagging as an alternative solution for publishing FAIR (Findable, Accessible, Interoperable, Resuable) biodiversity data.The Metotaxa-Metostem workflow Тhe MetoTaxa project aims to create a new digital production chain for the <em>European Journal of Taxonomy</em>, which enables the pre-publication semantic structuring of text, automatic tagging and semantic enrichment (annotation).The system is based on a single-source publishin

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Santamaria, Erika, Marco Súarez, Gallego Ricardo Ortiz, Patricia Fuya, Geraldine Páez, and Catalina Marceló-Díaz. "Culicoides Latreille (Diptera, Ceratopogonidae) of Colombia: records from the collection of insects of medical importance from National Institute of Health." Biodiversity Data Journal 12 (June 13, 2024): e72511. https://doi.org/10.3897/BDJ.12.e72511.

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The collection of insects of medical importance from the Instituto Nacional de Salud, INS (Bogotá, Colombia: https://www.ins.gov.co/Paginas/Inicio.aspx), was started in 1934 with the aim of being an institutional and national repository of the biodiversity of insects involved in vector-borne diseases of importance in public health. Today, the entomological collection includes more than 7,500 specimens.The ceratopogonid insects are one group of Diptera that are represented in this collection. Within the Ceratopogonidae, the genus <i>Culicoides</i> Latreille, 1809 is relevant in public health be

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Krimmel, Erica, Austin Mast, Deborah Paul, Robert Bruhn, Nelson Rios, and David Shorthouse. "Rapid Creation of a Data Product for the World's Specimens of Horseshoe Bats and Relatives, a Known Reservoir for Coronaviruses." Biodiversity Information Science and Standards 4 (October 2, 2020): e59067. https://doi.org/10.3897/biss.4.59067.

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Genomic evidence suggests that the causative virus of COVID-19 (SARS-CoV-2) was introduced to humans from horseshoe bats (family Rhinolophidae) (Andersen et al. 2020) and that species in this family as well as in the closely related Hipposideridae and Rhinonycteridae families are reservoirs of several SARS-like coronaviruses (Gouilh et al. 2011). Specimens collected over the past 400 years and curated by natural history collections around the world provide an essential reference as we work to understand the distributions, life histories, and evolutionary relationships of these bats and their v

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Lenzi, Alice, Silvia Gisondi, Marco Bardiani, et al. "Protected insect species in Italy: occurrence data from a 10-year citizen science initiative." Biodiversity Data Journal 13 (May 7, 2025): e151742. https://doi.org/10.3897/BDJ.13.e151742.

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Occurrence data provide an important baseline for the planning of conservation strategies and for the protection of species and habitats. However, collecting such data usually requires energy and it is time-consuming. Recently, citizen science has been shown to be a suitable approach for the study and monitoring of biodiversity, as it allows for the collection of a large number of records, distributed spatially and over time. Additionally, this approach enable the generation of new knowledge and fosters environmental awareness in the participating volunteers.The present paper describes the dat

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Newman, Peggy, David Martin, and Javier Molina. "Building Software for Hierarchical Events in Biodiversity Informatics." Biodiversity Information Science and Standards 7 (August 29, 2023): e111770. https://doi.org/10.3897/biss.7.111770.

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In 2019, the Atlas of Living Australia (ALA) ran a national consultation, clarifying a long-held suspicion that while simple occurrence records provide invaluable discoverability and analysis for biodiversity data, the lack of contextual information on data collection methodology and protocols limits its usefulness for species abundance estimation and time-series analysis. The consultation recognised that the ALA has strong leadership in biodiversity standards and development, and that our 12-year history and investment in projects and engagement demonstrates a clear capacity to transition to

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Bánki, Olaf, Donald Hobern, Markus Döring, et al. "Towards a Quality Assurance and Quality Control Mechanism for Species List Building." Biodiversity Information Science and Standards 7 (August 28, 2023): e111665. https://doi.org/10.3897/biss.7.111665.

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Catalogue of Life (COL) brings together the efforts and contributions of taxonomists from around the world, and addresses the needs of researchers, policy-makers, environmental managers and the wider public for a consistent, up-to-date and authoritative listing of all the world's known species. The names that science gives to species are fundamental tools that allow us to refer to these units of biodiversity. Knowing the name for a species unlocks everything that has been learned about its biology, distribution and relevance to humans. Every day, taxonomists continue to publish new scientific

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