100+ datasets found
  1. GBIF Backbone Taxonomy

    • gbif.org
    • smng.net
    • +4more
    Updated Nov 17, 2023
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    GBIF (2023). GBIF Backbone Taxonomy [Dataset]. http://doi.org/10.15468/39omei
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    Dataset updated
    Nov 17, 2023
    Dataset provided by
    Global Biodiversity Information Facilityhttps://www.gbif.org/
    License

    Attribution 4.0 (CC BY 4.0)https://creativecommons.org/licenses/by/4.0/
    License information was derived automatically

    Description

    The GBIF Backbone Taxonomy is a single, synthetic management classification with the goal of covering all names GBIF is dealing with. It's the taxonomic backbone that allows GBIF to integrate name based information from different resources, no matter if these are occurrence datasets, species pages, names from nomenclators or external sources like EOL, Genbank or IUCN. This backbone allows taxonomic search, browse and reporting operations across all those resources in a consistent way and to provide means to crosswalk names from one source to another.

    It is updated regulary through an automated process in which the Catalogue of Life acts as a starting point also providing the complete higher classification above families. Additional scientific names only found in other authoritative nomenclatural and taxonomic datasets are then merged into the tree, thus extending the original catalogue and broadening the backbones name coverage. The GBIF Backbone taxonomy also includes identifiers for Operational Taxonomic Units (OTUs) drawn from the barcoding resources iBOL and UNITE.

    International Barcode of Life project (iBOL), Barcode Index Numbers (BINs). BINs are connected to a taxon name and its classification by taking into account all names applied to the BIN and picking names with at least 80% consensus. If there is no consensus of name at the species level, the selection process is repeated moving up the major Linnaean ranks until consensus is achieved.

    UNITE - Unified system for the DNA based fungal species, Species Hypotheses (SHs). SHs are connected to a taxon name and its classification based on the determination of the RefS (reference sequence) if present or the RepS (representative sequence). In the latter case, if there is no match in the UNITE taxonomy, the lowest rank with 100% consensus within the SH will be used.

    The GBIF Backbone Taxonomy is available for download at https://hosted-datasets.gbif.org/datasets/backbone/ in different formats together with an archive of all previous versions.

    The following 105 sources have been used to assemble the GBIF backbone with number of names given in brackets:

    • Catalogue of Life Checklist - 4766428 names
    • International Barcode of Life project (iBOL) Barcode Index Numbers (BINs) - 635951 names
    • UNITE - Unified system for the DNA based fungal species linked to the classification - 611208 names
    • The Paleobiology Database - 212054 names
    • World Register of Marine Species - 188857 names
    • The Interim Register of Marine and Nonmarine Genera - 183894 names
    • The World Checklist of Vascular Plants (WCVP) - 131891 names
    • GBIF Backbone Taxonomy - 114350 names
    • TAXREF - 109374 names
    • The Leipzig catalogue of vascular plants - 75380 names
    • ZooBank - 73549 names
    • Integrated Taxonomic Information System (ITIS) - 68377 names
    • Plazi.org taxonomic treatments database - 61346 names
    • Genome Taxonomy Database r207 - 60545 names
    • International Plant Names Index - 52329 names
    • Fauna Europaea - 45077 names
    • The National Checklist of Taiwan (Catalogue of Life in Taiwan, TaiCoL) - 36193 names
    • Dyntaxa. Svensk taxonomisk databas - 35892 names
    • The Plant List with literature - 32692 names
    • United Kingdom Species Inventory (UKSI) - 29643 names
    • Artsnavnebasen - 29208 names
    • The IUCN Red List of Threatened Species - 21221 names
    • Afromoths, online database of Afrotropical moth species (Lepidoptera) - 13961 names
    • Brazilian Flora 2020 project - Projeto Flora do Brasil 2020 - 13829 names
    • Prokaryotic Nomenclature Up-to-Date (PNU) - 10079 names
    • Checklist Dutch Species Register - Nederlands Soortenregister - 8814 names
    • ICTV Master Species List (MSL) - 7852 names
    • Cockroach Species File - 6020 names
    • GRIN Taxonomy - 5882 names
    • Taxon list of fungi and fungal-like organisms from Germany compiled by the DGfM - 4570 names
    • Catalogue of Afrotropical Bees - 3623 names
    • Catalogue of Tenebrionidae (Coleoptera) of North America - 3327 names
    • Checklist of Beetles (Coleoptera) of Canada and Alaska. Second Edition. - 3312 names
    • Systema Dipterorum - 2850 names
    • Catalogue of the Pterophoroidea of the World - 2807 names
    • The Clements Checklist - 2675 names
    • Taxon list of Hymenoptera from Germany compiled in the context of the GBOL project - 2496 names
    • IOC World Bird List, v13.2 - 2366 names
    • Official Lists and Indexes of Names in Zoology - 2310 names
    • National checklist of all species occurring in Denmark - 1922 names
    • Myriatrix - 1876 names
    • Database of Vascular Plants of Canada (VASCAN) - 1822 names
    • Taxon list of vascular plants from Bavaria, Germany compiled in the context of the BFL project - 1771 names
    • Orthoptera Species File - 1742 names
    • A list of the terrestrial fungi, flora and fauna of Madeira and Selvagens archipelagos - 1602 names
    • Aphid Species File - 1565 names
    • World Spider Catalog - 1561 names
    • Taxon list of Jurassic Pisces of the Tethys Palaeo-Environment compiled at the SNSB-JME - 1270 names
    • Backbone Family Classification Patch - 1143 names
    • GBIF Algae Classification - 1100 names
    • International Cichorieae Network (ICN): Cichorieae Portal - 975 names
    • Psocodea Species File - 803 names
    • New Zealand Marine Macroalgae Species Checklist - 787 names
    • Annotated checklist of endemic species from the Western Balkans - 754 names
    • Taxon list of animals with German names (worldwide) compiled at the SMNS - 503 names
    • Catalogue of the Alucitoidea of the World - 472 names
    • Lygaeoidea Species File - 462 names
    • Catálogo de Plantas y Líquenes de Colombia - 422 names
    • GBIF Backbone Patch - 317 names
    • Phasmida Species File - 259 names
    • Cortinariaceae fetched from the Index Fungorum API - 234 names
    • Coreoidea Species File - 233 names
    • GTDB supplement - 139 names
    • Mantodea Species File - 119 names
    • Endemic species in Taiwan - 93 names
    • Taxon list of Araneae from Germany compiled in the context of the GBOL project - 88 names
    • Species of Hominidae - 78 names
    • Taxon list of Sternorrhyncha from Germany compiled in the context of the GBOL project - 77 names
    • Taxon list of mosses from Germany compiled in the context of the GBOL project - 75 names
    • Mammal Species of the World - 73 names
    • Plecoptera Species File - 71 names
    • Species Fungorum Plus - 64 names
    • Catalogue of the type specimens of Cosmopterigidae (Lepidoptera: Gelechioidea) from research collections of the Zoological Institute, Russian Academy of Sciences - 47 names
    • Species named after famous people - 41 names
    • Dermaptera Species File - 36 names
    • Taxon list of Trichoptera from Germany compiled in the context of the GBOL project - 34 names
    • True Fruit Flies (Diptera, Tephritidae) of the Afrotropical Region - 33 names
    • Range and Regularities in the Distribution of Earthworms of the Earthworms of the USSR Fauna. Perel, 1979 - 32 names
    • Taxon list of Diplura from Germany compiled in the context of the GBOL project - 30 names
    • Lista de referencia de especies de aves de Colombia - 2022 - 24 names
    • Taxon list of Auchenorrhyncha from Germany compiled in the context of the GBOL project - 20 names
    • Catalogue of the type specimens of Polycestinae (Coleoptera: Buprestidae) from research collections of the Zoological Institute, Russian Academy of Sciences - 19 names
    • Taxon list of Thysanoptera from Germany compiled in the context of the GBOL project - 19 names
    • Lista de especies de vertebrados registrados en jurisdicción del Departamento del Huila - 18 names
    • Taxon list of Microcoryphia (Archaeognatha) from Germany compiled in the context of the GBOL project - 15 names
    • Catalogue of the type specimens of Bufonidae and Megophryidae (Amphibia: Anura) from research collections of the Zoological Institute, Russian Academy of Sciences - 12 names
    • Grylloblattodea Species File - 11 names
    • Coleorrhyncha Species File - 9 names
    • Taxon list of liverworts from Germany compiled in the context of the GBOL project - 9 names
    • Embioptera Species File - 7 names
    • Taxon list of Pisces and Cyclostoma from Germany compiled in the context of the GBOL project - 6 names
    • Taxon list of Pteridophyta from Germany compiled in the context of the GBOL project - 6 names
    • Taxon list of Siphonaptera from Germany compiled in the context of the GBOL project - 5 names
    • The Earthworms of the Fauna of Russia. Perel, 1997 - 5 names
    • Taxon list of Zygentoma from Germany compiled in the context of the GBOL project - 4 names
    • Asiloid Flies: new taxa of Diptera: Apioceridae, Asilidae, and Mydidae - 3 names
    • Taxon list of Protura from Germany compiled in the context of the GBOL project - 3 names
    • Taxon list of hornworts from Germany compiled in the context of the GBOL project - 2 names
    • Chrysididae Species File - 1 names
    • Taxon list of Dermaptera from Germany compiled in the context of the GBOL project - 1 names
    • Taxon list of Diplopoda from Germany in the context of the GBOL project - 1 names
    • Taxon list of Orthoptera (Grashoppers) from Germany compiled at the SNSB - 1 names
    • Taxon list of Pscoptera from Germany compiled in the context of the GBOL project - 1 names
    • Taxon list of Pseudoscorpiones from Germany compiled in the context of the GBOL project - 1 names
    • Taxon list of Raphidioptera from Germany compiled in the context of the GBOL project - 1 names

  2. Data from: GBIF Occurrence Download

    • search.datacite.org
    Updated Sep 6, 2016
    + more versions
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    Occdownload Gbif.Org (2016). GBIF Occurrence Download [Dataset]. http://doi.org/10.15468/dl.iz7pw4
    Explore at:
    Dataset updated
    Sep 6, 2016
    Dataset provided by
    DataCitehttps://www.datacite.org/
    The Global Biodiversity Information Facility
    Authors
    Occdownload Gbif.Org
    License

    Attribution 4.0 (CC BY 4.0)https://creativecommons.org/licenses/by/4.0/
    License information was derived automatically

    Description

    A dataset containing 90 species occurrences available in GBIF matching the query: DatasetKey: Plasm bearing foraminifera counts of multinet M21/2_MSN648. The dataset includes 90 records from 1 constituent datasets: 90 records from Plasm bearing foraminifera counts of multinet M21/2_MSN648. Data from some individual datasets included in this download may be licensed under less restrictive terms.

  3. GBIF for CREST database for crestr -- Version 3

    • figshare.com
    zip
    Updated Jan 28, 2025
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    Manuel Chevalier (2025). GBIF for CREST database for crestr -- Version 3 [Dataset]. http://doi.org/10.6084/m9.figshare.6743207.v12
    Explore at:
    zipAvailable download formats
    Dataset updated
    Jan 28, 2025
    Dataset provided by
    Figsharehttp://figshare.com/
    Authors
    Manuel Chevalier
    License

    Attribution 4.0 (CC BY 4.0)https://creativecommons.org/licenses/by/4.0/
    License information was derived automatically

    Description

    This database contains all the presence records of plants, beetles, chironomids, foraminifera and diatoms contained in the GBIF database in September 2024. This new version of the database has a new, refined spatial resolution at 5min (each grid cell in the previous version is now parted in 9 sub grid cells). The curation of the input data has also been largely improved.The coordinates of the presence records have been homogenised on a 0.083x0.083° grid, and corresponding bioclimatic values from the Worldclim2.0 database have been added.These data are formatted and ready to use by the crestr R package. More information about the data is available https://www.manuelchevalier.com/crestr/articles/calibration-data.html.To download the latest version of the database, please follow this link: https://figshare.com/articles/GBIF_for_CREST_database/6743207Please cite all the appropriate datasets from the following list:GBIF.org (23 August 2024) GBIF Occurrence Download Part 1. https://doi.org/10.15468/dl.7bvejkGBIF.org (23 August 2024) GBIF Occurrence Download Part 2. https://doi.org/10.15468/dl.mpfc47GBIF.org (23 August 2024) GBIF Occurrence Download Part 3. https://doi.org/10.15468/dl.nuq5tnGBIF.org (23 August 2024) GBIF Occurrence Download Part 4. https://doi.org/10.15468/dl.q8zuhhGBIF.org (24 August 2024) GBIF Occurrence Download Part 5. https://doi.org/10.15468/dl.qwcs68GBIF.org (24 August 2024) GBIF Occurrence Download Part 6. https://doi.org/10.15468/dl.y9kpwcGBIF.org (24 August 2024) GBIF Occurrence Download Part 7. https://doi.org/10.15468/dl.uk2xv6GBIF.org (25 August 2024) GBIF Occurrence Download Part 8. https://doi.org/10.15468/dl.zgmnq9GBIF.org (26 August 2024) GBIF Occurrence Download Part 9. https://doi.org/10.15468/dl.68hqxg

  4. Z

    Global Biodiversity Information Facility (GBIF): an exhaustive list of gbif...

    • data.niaid.nih.gov
    Updated Jun 2, 2023
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    Poelen, Jorrit (2023). Global Biodiversity Information Facility (GBIF): an exhaustive list of gbif record ids, dataset keys, and their associated Occurrence IDs, Institution Code, Collection Codes and Catalog Numbers. hash://sha256/ea88f03a7bfd1ba853fdbea3203d54ab81ac3cdc8e8da7c96bbbba9c4b05d933 hash://md5/c49fe34785354847b37ea4509261e130 [Dataset]. https://data.niaid.nih.gov/resources?id=zenodo_7789865
    Explore at:
    Dataset updated
    Jun 2, 2023
    Dataset authored and provided by
    Poelen, Jorrit
    License

    CC0 1.0 Universal Public Domain Dedicationhttps://creativecommons.org/publicdomain/zero/1.0/
    License information was derived automatically

    Description

    The Global Biodiversity Information Facility (GBIF) indexes thousands of biodiversity datasets from Natural History Collections, citizen science initiatives (e.g., iNaturalist, eBird), and other sources. As part of the index process, GBIF associates at least two identifiers with indexed records: a record id (aka gbifID) and a dataset id (aka dataset key). These ids are central to do lookup, reference data, and package interpreted data products.

    This publication contains an exhaustive list of GBIF IDs and ids associated by their data providers as derived from:

    GBIF.org (01 March 2023) GBIF Occurrence Download https://doi.org/10.15468/dl.pk3trq

    The resource (size: ~260GB) provided by GBIF had content id hash://sha256/c8bac8acb28c8524c53589b3a40e322dbbbdadf5689fef2e20266fbf6ddf6b97 and was used to generate the resource included in this publication using

    preston cat 'zip:hash://sha256/c8bac8acb28c8524c53589b3a40e322dbbbdadf5689fef2e20266fbf6ddf6b97!/0015281-230224095556074.csv'
    | cut -f 1,2,3,37,38,39
    | gzip\

    gbifid.tsv.gz

    with the content id of gbifid.tsv.gz (size: ~35GB) being hash://sha256/a339e32e10edaad585f61f2ded06cbb23e0618c65a6360db18d7d729054940a8 .

    the first 10 lines of gbifid.tsv.gz as extracted via

    preston cat --remote https://zenodo.org/record/7789866/files,https://linker.bio hash://sha256/a339e32e10edaad585f61f2ded06cbb23e0618c65a6360db18d7d729054940a8
    | gunzip
    | head

    are:

    gbifID datasetKey occurrenceID institutionCode collectionCode catalogNumber 2997162320 c71c8000-9fc7-422c-804a-ce6abe751771 3399442 CEPEC CEPEC CEPEC00109669 2997162309 c71c8000-9fc7-422c-804a-ce6abe751771 2733085 CEPEC CEPEC CEPEC00000818 2997162317 c71c8000-9fc7-422c-804a-ce6abe751771 2733086 CEPEC CEPEC CEPEC00000888 2997162313 c71c8000-9fc7-422c-804a-ce6abe751771 3399443 CEPEC CEPEC CEPEC00109744 2997162306 c71c8000-9fc7-422c-804a-ce6abe751771 2733087 CEPEC CEPEC CEPEC00000889 2997162316 c71c8000-9fc7-422c-804a-ce6abe751771 3399440 CEPEC CEPEC CEPEC00109605 2997162324 c71c8000-9fc7-422c-804a-ce6abe751771 2733088 CEPEC CEPEC CEPEC00000890 2997162308 c71c8000-9fc7-422c-804a-ce6abe751771 3399441 CEPEC CEPEC CEPEC00109615 2997162303 c71c8000-9fc7-422c-804a-ce6abe751771 2733089 CEPEC CEPEC CEPEC00000891

    Note that at time of writing, the html resource associated with the occurrence id 2997162320, and data set key c71c8000-9fc7-422c-804a-ce6abe751771 (extracted from of the first data row example above) are available via:

    https://gbif.org/occurrence/2997162320

    and

    https://gbif.org/dataset/c71c8000-9fc7-422c-804a-ce6abe751771

    respectively.

    This resource was initially created to help integrate with Bionomia (https://bionomia.net) to help associate people identifiers provided by bionomia to their original records via their GBIF ids. Bionomia re-uses GBIF records ids as a way to define links between records and the people (e.g., curators, collectors, identifiers) that worked on them.

    In other words, this resource provides a versioned translation table from the GBIF data universe (as defined by GBIF record ids, and dataset keys) to the data collections that exist (and evolve) independent of it.

    Note that the resource identified by hash://sha256/c8bac8acb28c8524c53589b3a40e322dbbbdadf5689fef2e20266fbf6ddf6b97 was not included in this publication it was too big (260GB) to fit. You may be able to retrieve the resource from its original location at https://api.gbif.org/v1/occurrence/download/request/0015281-230224095556074.zip .

  5. Data from: GBIF Occurrence Download

    • search.datacite.org
    Updated Nov 6, 2018
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    Occdownload Gbif.Org (2018). GBIF Occurrence Download [Dataset]. http://doi.org/10.15468/dl.or9eef
    Explore at:
    Dataset updated
    Nov 6, 2018
    Dataset provided by
    DataCitehttps://www.datacite.org/
    The Global Biodiversity Information Facility
    Authors
    Occdownload Gbif.Org
    License

    Attribution-NonCommercial 4.0 (CC BY-NC 4.0)https://creativecommons.org/licenses/by-nc/4.0/
    License information was derived automatically

    Description

    A dataset containing 18 species occurrences available in GBIF matching the query: TaxonKey: Puya obconica L.B.Sm.. The dataset includes 18 records from 7 constituent datasets: 1 records from SysTax - Botanical Gardens. 9 records from Tropicos Specimen Data. 1 records from NMNH Extant Specimen Records. 1 records from The AAU Herbarium Database. 3 records from University of Vienna, Institute for Botany - Herbarium WU. 2 records from Field Museum of Natural History (Botany) Seed Plant Collection. 1 records from Harvard University Herbaria. Data from some individual datasets included in this download may be licensed under less restrictive terms.

  6. North American Apidae Occurrence Data Filtered from GBIF

    • zenodo.org
    csv
    Updated Nov 10, 2024
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    Lucas Jeremiah Sharrett; Lucas Jeremiah Sharrett (2024). North American Apidae Occurrence Data Filtered from GBIF [Dataset]. http://doi.org/10.5281/zenodo.14062445
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    csvAvailable download formats
    Dataset updated
    Nov 10, 2024
    Dataset provided by
    Zenodohttp://zenodo.org/
    Authors
    Lucas Jeremiah Sharrett; Lucas Jeremiah Sharrett
    License

    Attribution 4.0 (CC BY 4.0)https://creativecommons.org/licenses/by/4.0/
    License information was derived automatically

    Description

    This is a filtered dataset from GBIF including all Apidae observations identified to the species level in the North American range. Data was downloaded using rgbif::occ_download and accessed from R via rgbif (https://github.com/ropensci/rgbif) on 2024-11-10. The original unfiltered GBIF occurrences can be download at https://doi.org/10.15468/dl.5k8kue, and https://api.gbif.org/v1/occurrence/download/request/0005473-241107131044228.zip. The data is filtered to have coordinates in North America, no geospatial issues, no duplicates across species and coordinates, no coordinate uncertainty greater than 1 kilometer, and no occurrences lying within 1km of a college or university. This dataset is incomplete as it does not include ALL observations that occur in North American countries as observations lacking a continent field of "north_america" in GBIF are not included. The data was uploaded to Zenodo after filtering with the following DOI: 10.5281/zenodo.14062444.

  7. o

    Occurrence Download

    • explore.openaire.eu
    Updated Jan 1, 2020
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    GBIF.Org User (2020). Occurrence Download [Dataset]. http://doi.org/10.15468/dl.7yssak
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    Dataset updated
    Jan 1, 2020
    Authors
    GBIF.Org User
    Description

    A dataset containing 11981835 species occurrences available in GBIF matching the query: { "and" : [ "HasCoordinate is false", "TaxonKey is Insecta" ] } The dataset includes 11981835 records from 5404 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044746-200221144449610/datasets/export for details. Data from some individual datasets included in this download may be licensed under less restrictive terms.

  8. o

    Occurrence Download

    • explore.openaire.eu
    Updated Jan 1, 2016
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    GBIF.Org User (2016). Occurrence Download [Dataset]. http://doi.org/10.15468/dl.mbyghv
    Explore at:
    Dataset updated
    Jan 1, 2016
    Authors
    GBIF.Org User
    Description

    A dataset containing 3826495 species occurrences available in GBIF matching the query: { "Country" : [ "is Colombia" ] } The dataset includes 3826495 records from 1068 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018098-160910150852091/datasets/export for details. Data from some individual datasets included in this download may be licensed under less restrictive terms.

  9. Data from: GBIF Occurrence Download

    • search.datacite.org
    Updated Jun 24, 2018
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    Occdownload Gbif.Org (2018). GBIF Occurrence Download [Dataset]. http://doi.org/10.15468/dl.smroup
    Explore at:
    Dataset updated
    Jun 24, 2018
    Dataset provided by
    Global Biodiversity Information Facilityhttps://www.gbif.org/
    DataCitehttps://www.datacite.org/
    Authors
    Occdownload Gbif.Org
    License

    Attribution-NonCommercial 4.0 (CC BY-NC 4.0)https://creativecommons.org/licenses/by-nc/4.0/
    License information was derived automatically

    Description

    A dataset containing 987117827 species occurrences available in GBIF matching the query: All data. The dataset includes 987117827 records from 19784 constituent datasets: Please see https://www.gbif.org/occurrence/download/0032137-180508205500799 for full list of all constituents.

  10. o

    Occurrence Download

    • explore.openaire.eu
    Updated Jan 1, 2023
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    GBIF.Org User (2023). Occurrence Download [Dataset]. http://doi.org/10.15468/dl.96g5sv
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    Dataset updated
    Jan 1, 2023
    Authors
    GBIF.Org User
    Description

    A dataset containing 20655509 species occurrences available in GBIF matching the query: { "Country" : [ "is Colombia" ] } The dataset includes 20655509 records from 4013 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0259663-220831081235567/datasets/export for details. Data from some individual datasets included in this download may be licensed under less restrictive terms.

  11. Data from: imr_mareano_grab

    • gbif.org
    • erddap.eurobis.org
    • +4more
    Updated Apr 30, 2025
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    Sten-Richard Birkely; Sten-Richard Birkely (2025). imr_mareano_grab [Dataset]. http://doi.org/10.15468/dlaxsw
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    Dataset updated
    Apr 30, 2025
    Dataset provided by
    Global Biodiversity Information Facilityhttps://www.gbif.org/
    Institute of Marine Research
    Authors
    Sten-Richard Birkely; Sten-Richard Birkely
    License

    Attribution 4.0 (CC BY 4.0)https://creativecommons.org/licenses/by/4.0/
    License information was derived automatically

    Time period covered
    Jan 1, 2006 - May 5, 2021
    Area covered
    Description

    Dataset contains species name, their number of specimen and wet-weight for each taxa (0,1 mg). Samples were originally preserved in formaline and later converted to ethanol. After identification samples are stored at Bergen Museum/University of Bergen.

  12. o

    Occurrence Download

    • explore.openaire.eu
    Updated Jan 1, 2023
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    GBIF.Org User (2023). Occurrence Download [Dataset]. http://doi.org/10.15468/dl.eucdj8
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    Dataset updated
    Jan 1, 2023
    Authors
    GBIF.Org User
    Description

    A dataset containing 6572299 species occurrences available in GBIF matching the query: { "and" : [ "Country is Ecuador", "TaxonKey is Animalia" ] } The dataset includes 6572299 records from 1504 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0089934-230530130749713/datasets/export for details. Data from some individual datasets included in this download may be licensed under less restrictive terms.

  13. Data from: GBIF Occurrence Download

    • search.datacite.org
    Updated Dec 13, 2017
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    Occdownload Gbif.Org (2017). GBIF Occurrence Download [Dataset]. http://doi.org/10.15468/dl.ohpzhm
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    Dataset updated
    Dec 13, 2017
    Dataset provided by
    Global Biodiversity Information Facilityhttps://www.gbif.org/
    DataCitehttps://www.datacite.org/
    Authors
    Occdownload Gbif.Org
    License

    Attribution-NonCommercial 4.0 (CC BY-NC 4.0)https://creativecommons.org/licenses/by-nc/4.0/
    License information was derived automatically

    Description

    A dataset containing 875010368 species occurrences available in GBIF matching the query: All data. The dataset includes 875010368 records from 18477 constituent datasets: Please see http://www.gbif.org/occurrence/download/0008114-171124123535762 for full list of all constituents.

  14. North American Syrphidae Occurrence Data Filtered from GBIF

    • zenodo.org
    csv
    Updated Nov 10, 2024
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    Lucas Jeremiah Sharrett; Lucas Jeremiah Sharrett (2024). North American Syrphidae Occurrence Data Filtered from GBIF [Dataset]. http://doi.org/10.5281/zenodo.14062632
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    csvAvailable download formats
    Dataset updated
    Nov 10, 2024
    Dataset provided by
    Zenodohttp://zenodo.org/
    Authors
    Lucas Jeremiah Sharrett; Lucas Jeremiah Sharrett
    License

    Attribution 4.0 (CC BY 4.0)https://creativecommons.org/licenses/by/4.0/
    License information was derived automatically

    Description

    This is a filtered dataset from GBIF including all Syrphidae observations identified to the species level in the North American range. Data was downloaded using rgbif::occ_download and accessed from R via rgbif (https://github.com/ropensci/rgbif) on 2024-11-10. The original unfiltered GBIF occurrences can be download at https://doi.org/10.15468/dl.p97dt2, and https://api.gbif.org/v1/occurrence/download/request/0005496-241107131044228.zip. The data is filtered to have coordinates in North America, no geospatial issues, no duplicates across species and coordinates, no coordinate uncertainty greater than 1 kilometer, and no occurrences lying within 1km of a college or university. This dataset is incomplete as it does not include ALL observations that occur in North American countries as observations lacking a continent field of "north_america" in GBIF are not included. The data was uploaded to Zenodo after filtering with the following DOI: 10.5281/zenodo.14062632.

  15. o

    Occurrence Download

    • explore.openaire.eu
    Updated Jan 1, 2021
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    GBIF.Org User (2021). Occurrence Download [Dataset]. http://doi.org/10.15468/dl.dmrgbk
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    Dataset updated
    Jan 1, 2021
    Authors
    GBIF.Org User
    Description

    A dataset containing 3835796 species occurrences available in GBIF matching the query: { "and" : [ "Country is China", "Year 1950-2021" ] } The dataset includes 3835796 records from 2309 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0271528-200613084148143/datasets/export for details. Data from some individual datasets included in this download may be licensed under less restrictive terms.

  16. f

    Full Dataset prior to Cleaning

    • figshare.com
    zip
    Updated Mar 31, 2023
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    Paige Chesshire (2023). Full Dataset prior to Cleaning [Dataset]. http://doi.org/10.6084/m9.figshare.22455616.v1
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    zipAvailable download formats
    Dataset updated
    Mar 31, 2023
    Dataset provided by
    figshare
    Authors
    Paige Chesshire
    License

    Attribution 4.0 (CC BY 4.0)https://creativecommons.org/licenses/by/4.0/
    License information was derived automatically

    Description

    This dataset includes all of the data downloaded from GBIF (DOIs provided in README.md as well as below, downloaded Feb 2021) as well as data downloaded from SCAN. This dataset has 2,808,432 records and can be used as a reference to the verbatim data before it underwent the cleaning process. The only modifications made to this datset after direct download from the data portals are the following:

    1) for GBIF records, I renamed the countryCode column to be "country" so that the column title is consistent across both GBIF and SCAN 2) A source column was added where I specify if the record came from GBIF or SCAN 3) Duplicate records across SCAN and GBIF were removed by identifying identical instances "catalogNumber" and "institutionCode" 4) Only the Darwin core columns (DwC) that were shared across downloaded datasets were retained. GBIF contained ~249 DwC variables, and SCAN data contained fewer, so this combined dataset only includes the ~80 columns shared between the two datasets

    For GBIF, we downloaded the data in three separate chunks, therefore there are three DOIs. See below:

    GBIF.org (3 February 2021) GBIF Occurrence Downloadhttps://doi.org/10.15468/dl.6cxfsw GBIF.org (3 February 2021) GBIF Occurrence Downloadhttps://doi.org/10.15468/dl.b9rfa7 GBIF.org (3 February 2021) GBIF Occurrence Downloadhttps://doi.org/10.15468/dl.w2nndm

  17. Data from: Bugbase, Lepidopterological Society

    • gbif.org
    • demo.gbif.org
    Updated Feb 20, 2023
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    Per Stadel Nielsen; Per Stadel Nielsen (2023). Bugbase, Lepidopterological Society [Dataset]. http://doi.org/10.15468/fhqj1a
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    Dataset updated
    Feb 20, 2023
    Dataset provided by
    Global Biodiversity Information Facilityhttps://www.gbif.org/
    Lepidopterological Society, Denmark
    Authors
    Per Stadel Nielsen; Per Stadel Nielsen
    License

    Attribution-NonCommercial 4.0 (CC BY-NC 4.0)https://creativecommons.org/licenses/by-nc/4.0/
    License information was derived automatically

    Time period covered
    Jan 1, 1900 - Apr 1, 2020
    Area covered
    Description

    Database on the recordings of Lepidoptera and Trichoptera by the Lepidopterological Society of Denmark (https://www.lepidoptera.dk). Occurrences are based on observations and collecting by any means, trapping, photos etc. Society specialist groups check data for errors and unusual records, mostly by contacting the observer/recorder. To assure quality of data, only members of the society are given access to enter records in the database.

  18. s

    Occurrence records from the GBIF Database (Walvis Ridge)

    • dataportal.saeri.org
    Updated Jul 23, 2022
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    (2022). Occurrence records from the GBIF Database (Walvis Ridge) [Dataset]. https://dataportal.saeri.org/dataset/occurrence-records-from-the-gbif-database-walvis-ridge
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    Dataset updated
    Jul 23, 2022
    License

    Attribution 4.0 (CC BY 4.0)https://creativecommons.org/licenses/by/4.0/
    License information was derived automatically

    Description

    The dataset comprises occurrencies of the selected phyla and classes / subclasses for the Walvis Ridge Project AOI. This data has been extracted from GBIF database on July 19th and 20th, 2022. The download covered the following groups of species: Procellariiformes, Testudines, Mollusca Polychaeta Crustacea Echinodermata Elasmobranchii Mammalia Actinopterygii The GBIF database is available for download at: https://www.gbif.org

  19. A GBIF download test

    • zenodo.org
    zip
    Updated Aug 27, 2020
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    Robertson; Robertson (2020). A GBIF download test [Dataset]. http://doi.org/10.15468/dl.5xuttz
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    zipAvailable download formats
    Dataset updated
    Aug 27, 2020
    Dataset provided by
    Zenodohttp://zenodo.org/
    Authors
    Robertson; Robertson
    License

    Attribution 4.0 (CC BY 4.0)https://creativecommons.org/licenses/by/4.0/
    License information was derived automatically

    Description

    Test of DOI linking

  20. Species occurrence and occupancy in protected areas of the Natura2000...

    • zenodo.org
    • data.niaid.nih.gov
    csv
    Updated Mar 28, 2024
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    Damiano Oldoni; Damiano Oldoni; Peter Desmet; Peter Desmet; Tim Adriaens; Tim Adriaens (2024). Species occurrence and occupancy in protected areas of the Natura2000 network in Belgium [Dataset]. http://doi.org/10.5281/zenodo.3784227
    Explore at:
    csvAvailable download formats
    Dataset updated
    Mar 28, 2024
    Dataset provided by
    Zenodohttp://zenodo.org/
    Authors
    Damiano Oldoni; Damiano Oldoni; Peter Desmet; Peter Desmet; Tim Adriaens; Tim Adriaens
    License

    CC0 1.0 Universal Public Domain Dedicationhttps://creativecommons.org/publicdomain/zero/1.0/
    License information was derived automatically

    Area covered
    Belgium
    Description

    Context

    Invasive alien species have been pointed out as an important driver of biodiversity loss. Many policy responses are being developed to address this threat. Protected areas often represent and preserve hotspots of biological diversity and ensure the maintenance of ecosystem services crucial to human livelihoods. The impact of biological invasions can be particularly severe in protected areas and their occurrence and impact in such areas is an important element of the risk they pose. To address this, there is a need for data on the occurrence and extent of alien species invasions in protected areas.

    Description

    This dataset contains species occurrence and occupancy in protected areas of the Natura2000 network in Belgium (Special Conservation Areas sensu Habitat Directive and Special Protection Areas sensu Bird Directive). The dataset was generated using the Belgian occurrence cube at species level and the Belgian occurrence cube for non-native taxa (both containing GBIF data aggregated using Oldoni et al. 2020), the 1x1km EEA reference grid and the Natura2000 protected areas shapefiles from the European Environment Agency.

    Data are grouped by protected area (SITECODE), year (year) and (infra)species (taxonKey, speciesKey). For each group, it provides the number of occurrences found in GBIF (n), the area of occupancy (aoo: number of 1 km2 squares), the coverage (coverage: % of 1 km2 squares), the minimum coordinateUncertaintyInMeters (min_coord_uncertainty), and the alien status (is_alien) based on the Global Register of Introduced and Invasive Species - Belgium. For infraspecific taxa in the latter, the alien status of the species is looked up and included.

    The dataset is built on open science principles and intended to be completely reproducible:

    • The input data are publicly available on Zenodo, with the download DOIs listed in the related identifiers of this dataset package.
    • The code to process the data is publicly available and documented on GitHub.

    Files

    • protected_areas_species_occurrence.csv: number of occurrences (n), area of occupancy (aoo) and coverage of taxa (taxonKey) in Natura2000 areas of Belgium (SITECODE). Other columns included: speciesKey (for species is speciesKey = taxonKey), SITETYPE containing the site type of the Natura2000 area (one of A, B or C), min_coord_uncertainty with the lowest coordinate uncertainty in meters, is_alien containing the alien status (TRUE or FALSE) and remarks containing, if present, the infraspecific alien taxa whose occurrences contribute to the calculated aoo (only for species).
    • protected_areas_species_info.csv: taxonomic information of taxa in protected_areas_species_occurrence.csv as retrieved from GBIF Backbone Taxonomy. Columns: taxonKey, speciesKey, scientificName, kingdom, phylum, order, class, genus, family, species, rank and includes. The latter contains the infraspecific taxa and synonyms whose occurrences contribute to the number of occurrences at species level.
    • protected_areas_metadata.csv: protected area information for areas included in protected_areas_species_occurrence.csv. Columns: SITECODE as in protected_areas_species_occurrence.csv (BE*******), SITENAME containing the name of the protected area, SITETYPE as in protected_areas_species_occurrence.csv, flanders, wallonia and brussels containing whether the area is situated respectively in Flanders, Wallonia or Brussels-Capital Region (TRUE or FALSE). Field codes are in line with EEA element definitions for Natura 2000 sites.

    Potential use of the dataset

    Currently, there is no comprehensive reporting system for invasive alien species in Natura 2000 sites. This dataset provides a baseline as to which species occur in which protected area. We envisage this dataset can be an interesting starting point for various types of analyses on alien species in protected areas in Belgium, but that it can also be used in complement to other data on alien species in protected areas to study more general patterns. Some examples of research questions:

    • Which protected areas are most invaded by alien species
    • Which alien species are most distributed in protected areas and which traits do they have
    • How does the proportion of alien species in protected areas change in time
    • How does the occurrence/occupancy of alien species in protected areas match lists of regulated species (e.g. Union List, EPPO lists)
    • To what extent can the network of protected areas contribute to providing safe refuge to native species from the impacts of invasive alien species
    • How widespread are the impacts of certain alien species on protected areas

    Acknowledgements

    This work has been funded under the Belgian Science Policies Brain program (BelSPO BR/165/A1/TrIAS), the European Union's LIFE program (LIFE19 NAT/BE/000953 - LIFE RIPARIAS).

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GBIF (2023). GBIF Backbone Taxonomy [Dataset]. http://doi.org/10.15468/39omei
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GBIF Backbone Taxonomy

Explore at:
Dataset updated
Nov 17, 2023
Dataset provided by
Global Biodiversity Information Facilityhttps://www.gbif.org/
License

Attribution 4.0 (CC BY 4.0)https://creativecommons.org/licenses/by/4.0/
License information was derived automatically

Description

The GBIF Backbone Taxonomy is a single, synthetic management classification with the goal of covering all names GBIF is dealing with. It's the taxonomic backbone that allows GBIF to integrate name based information from different resources, no matter if these are occurrence datasets, species pages, names from nomenclators or external sources like EOL, Genbank or IUCN. This backbone allows taxonomic search, browse and reporting operations across all those resources in a consistent way and to provide means to crosswalk names from one source to another.

It is updated regulary through an automated process in which the Catalogue of Life acts as a starting point also providing the complete higher classification above families. Additional scientific names only found in other authoritative nomenclatural and taxonomic datasets are then merged into the tree, thus extending the original catalogue and broadening the backbones name coverage. The GBIF Backbone taxonomy also includes identifiers for Operational Taxonomic Units (OTUs) drawn from the barcoding resources iBOL and UNITE.

International Barcode of Life project (iBOL), Barcode Index Numbers (BINs). BINs are connected to a taxon name and its classification by taking into account all names applied to the BIN and picking names with at least 80% consensus. If there is no consensus of name at the species level, the selection process is repeated moving up the major Linnaean ranks until consensus is achieved.

UNITE - Unified system for the DNA based fungal species, Species Hypotheses (SHs). SHs are connected to a taxon name and its classification based on the determination of the RefS (reference sequence) if present or the RepS (representative sequence). In the latter case, if there is no match in the UNITE taxonomy, the lowest rank with 100% consensus within the SH will be used.

The GBIF Backbone Taxonomy is available for download at https://hosted-datasets.gbif.org/datasets/backbone/ in different formats together with an archive of all previous versions.

The following 105 sources have been used to assemble the GBIF backbone with number of names given in brackets:

  • Catalogue of Life Checklist - 4766428 names
  • International Barcode of Life project (iBOL) Barcode Index Numbers (BINs) - 635951 names
  • UNITE - Unified system for the DNA based fungal species linked to the classification - 611208 names
  • The Paleobiology Database - 212054 names
  • World Register of Marine Species - 188857 names
  • The Interim Register of Marine and Nonmarine Genera - 183894 names
  • The World Checklist of Vascular Plants (WCVP) - 131891 names
  • GBIF Backbone Taxonomy - 114350 names
  • TAXREF - 109374 names
  • The Leipzig catalogue of vascular plants - 75380 names
  • ZooBank - 73549 names
  • Integrated Taxonomic Information System (ITIS) - 68377 names
  • Plazi.org taxonomic treatments database - 61346 names
  • Genome Taxonomy Database r207 - 60545 names
  • International Plant Names Index - 52329 names
  • Fauna Europaea - 45077 names
  • The National Checklist of Taiwan (Catalogue of Life in Taiwan, TaiCoL) - 36193 names
  • Dyntaxa. Svensk taxonomisk databas - 35892 names
  • The Plant List with literature - 32692 names
  • United Kingdom Species Inventory (UKSI) - 29643 names
  • Artsnavnebasen - 29208 names
  • The IUCN Red List of Threatened Species - 21221 names
  • Afromoths, online database of Afrotropical moth species (Lepidoptera) - 13961 names
  • Brazilian Flora 2020 project - Projeto Flora do Brasil 2020 - 13829 names
  • Prokaryotic Nomenclature Up-to-Date (PNU) - 10079 names
  • Checklist Dutch Species Register - Nederlands Soortenregister - 8814 names
  • ICTV Master Species List (MSL) - 7852 names
  • Cockroach Species File - 6020 names
  • GRIN Taxonomy - 5882 names
  • Taxon list of fungi and fungal-like organisms from Germany compiled by the DGfM - 4570 names
  • Catalogue of Afrotropical Bees - 3623 names
  • Catalogue of Tenebrionidae (Coleoptera) of North America - 3327 names
  • Checklist of Beetles (Coleoptera) of Canada and Alaska. Second Edition. - 3312 names
  • Systema Dipterorum - 2850 names
  • Catalogue of the Pterophoroidea of the World - 2807 names
  • The Clements Checklist - 2675 names
  • Taxon list of Hymenoptera from Germany compiled in the context of the GBOL project - 2496 names
  • IOC World Bird List, v13.2 - 2366 names
  • Official Lists and Indexes of Names in Zoology - 2310 names
  • National checklist of all species occurring in Denmark - 1922 names
  • Myriatrix - 1876 names
  • Database of Vascular Plants of Canada (VASCAN) - 1822 names
  • Taxon list of vascular plants from Bavaria, Germany compiled in the context of the BFL project - 1771 names
  • Orthoptera Species File - 1742 names
  • A list of the terrestrial fungi, flora and fauna of Madeira and Selvagens archipelagos - 1602 names
  • Aphid Species File - 1565 names
  • World Spider Catalog - 1561 names
  • Taxon list of Jurassic Pisces of the Tethys Palaeo-Environment compiled at the SNSB-JME - 1270 names
  • Backbone Family Classification Patch - 1143 names
  • GBIF Algae Classification - 1100 names
  • International Cichorieae Network (ICN): Cichorieae Portal - 975 names
  • Psocodea Species File - 803 names
  • New Zealand Marine Macroalgae Species Checklist - 787 names
  • Annotated checklist of endemic species from the Western Balkans - 754 names
  • Taxon list of animals with German names (worldwide) compiled at the SMNS - 503 names
  • Catalogue of the Alucitoidea of the World - 472 names
  • Lygaeoidea Species File - 462 names
  • Catálogo de Plantas y Líquenes de Colombia - 422 names
  • GBIF Backbone Patch - 317 names
  • Phasmida Species File - 259 names
  • Cortinariaceae fetched from the Index Fungorum API - 234 names
  • Coreoidea Species File - 233 names
  • GTDB supplement - 139 names
  • Mantodea Species File - 119 names
  • Endemic species in Taiwan - 93 names
  • Taxon list of Araneae from Germany compiled in the context of the GBOL project - 88 names
  • Species of Hominidae - 78 names
  • Taxon list of Sternorrhyncha from Germany compiled in the context of the GBOL project - 77 names
  • Taxon list of mosses from Germany compiled in the context of the GBOL project - 75 names
  • Mammal Species of the World - 73 names
  • Plecoptera Species File - 71 names
  • Species Fungorum Plus - 64 names
  • Catalogue of the type specimens of Cosmopterigidae (Lepidoptera: Gelechioidea) from research collections of the Zoological Institute, Russian Academy of Sciences - 47 names
  • Species named after famous people - 41 names
  • Dermaptera Species File - 36 names
  • Taxon list of Trichoptera from Germany compiled in the context of the GBOL project - 34 names
  • True Fruit Flies (Diptera, Tephritidae) of the Afrotropical Region - 33 names
  • Range and Regularities in the Distribution of Earthworms of the Earthworms of the USSR Fauna. Perel, 1979 - 32 names
  • Taxon list of Diplura from Germany compiled in the context of the GBOL project - 30 names
  • Lista de referencia de especies de aves de Colombia - 2022 - 24 names
  • Taxon list of Auchenorrhyncha from Germany compiled in the context of the GBOL project - 20 names
  • Catalogue of the type specimens of Polycestinae (Coleoptera: Buprestidae) from research collections of the Zoological Institute, Russian Academy of Sciences - 19 names
  • Taxon list of Thysanoptera from Germany compiled in the context of the GBOL project - 19 names
  • Lista de especies de vertebrados registrados en jurisdicción del Departamento del Huila - 18 names
  • Taxon list of Microcoryphia (Archaeognatha) from Germany compiled in the context of the GBOL project - 15 names
  • Catalogue of the type specimens of Bufonidae and Megophryidae (Amphibia: Anura) from research collections of the Zoological Institute, Russian Academy of Sciences - 12 names
  • Grylloblattodea Species File - 11 names
  • Coleorrhyncha Species File - 9 names
  • Taxon list of liverworts from Germany compiled in the context of the GBOL project - 9 names
  • Embioptera Species File - 7 names
  • Taxon list of Pisces and Cyclostoma from Germany compiled in the context of the GBOL project - 6 names
  • Taxon list of Pteridophyta from Germany compiled in the context of the GBOL project - 6 names
  • Taxon list of Siphonaptera from Germany compiled in the context of the GBOL project - 5 names
  • The Earthworms of the Fauna of Russia. Perel, 1997 - 5 names
  • Taxon list of Zygentoma from Germany compiled in the context of the GBOL project - 4 names
  • Asiloid Flies: new taxa of Diptera: Apioceridae, Asilidae, and Mydidae - 3 names
  • Taxon list of Protura from Germany compiled in the context of the GBOL project - 3 names
  • Taxon list of hornworts from Germany compiled in the context of the GBOL project - 2 names
  • Chrysididae Species File - 1 names
  • Taxon list of Dermaptera from Germany compiled in the context of the GBOL project - 1 names
  • Taxon list of Diplopoda from Germany in the context of the GBOL project - 1 names
  • Taxon list of Orthoptera (Grashoppers) from Germany compiled at the SNSB - 1 names
  • Taxon list of Pscoptera from Germany compiled in the context of the GBOL project - 1 names
  • Taxon list of Pseudoscorpiones from Germany compiled in the context of the GBOL project - 1 names
  • Taxon list of Raphidioptera from Germany compiled in the context of the GBOL project - 1 names

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