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TwitterThe Global Biodiversity Information Facility (GBIF) is an international network and data infrastructure funded by the world's governments providing global data that document the occurrence of species. GBIF currently integrates datasets documenting over 1.6 billion species occurrences, growing daily. The GBIF occurrence dataset combines data from a wide array of sources including specimen-related data from natural history museums, observations from citizen science networks and environment recording schemes. While these data are constantly changing at GBIF.org, periodic snapshots are taken and made available on AWS.
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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
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Species occurrence records for native and non-native bees, wasps and other insects collected using mainly pan, malaise, and vane trapping; and insect netting methods in Canada, Mexico, the non-contiguous United States, U.S. Territories (specifically U.S. Virgin Islands), U.S. Minor Outlying Islands and other global locations with the bulk of the specimens coming from the Eastern United States often from Federal lands such as USFWS, NPS, DOD, USFS. Some records also contain notes regarding plants or substrates from which insects were collected or that were present and/or in flower at the time the insects were collected. Unless otherwise noted, taxonomic determinations (identifications) were completed by Sam Droege (USGS Eastern Ecological Science Center- EESC, Native Bee Laboratory) and Clare Maffei (USFWS, Inventory and Monitoring Branch).
The EESC Native Bee Lab currently keeps only a small synoptic collection, rare and voucher specimens are deposited in the Smithsonian National Collection (NMNH) and widely distributed to other institutions for DNA, revisions, and augmentation of existing collections. Surplus specimens are also made available to students to learn their identifications. Corrections to any of our determinations are always welcomed. Common species that are not in demand for surplus are usually destroyed and the pins recycled. Recent revisions to Lasioglossum, Ceratina, and to a much lesser extent Triepeolus and Epeolus and other small groups have rendered determinations prior to those revisions out of date for species involved in name changes and users should account for that during analyses. Current data (included information on specimen codes without identifications) are always available without charge directly from Sam Droege.
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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.
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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.
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The dataset comprises occurrencies of the selected phyla and classes / subclasses for the Turks and Caicos Islands. This data has been extracted from GBIF database on December 4th, 2020. The GBIF database is available for download at: https://www.gbif.org
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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 .
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This dataset provides a direct internet link to FSM's data hosted on the GBIF website / records.
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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
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TwitterBiologists recognize the Caribbean archipelago as a biodiversity hotspot and employ it for their research as a “natural laboratory”, but do not always appreciate that these ecosystems are in fact palimpsests shaped by multiple human cultures over millennia. We discuss two case studies of the Caribbean’s fragmented natural history collections, the effects of differing legislation and governance by the region’s multiple nation states. We use digital natural history specimen data from GBIF to demonstrate how colonial history has influenced specimen collection patterns in Trinidad & Tobago, The Bahamas, and the Greater Antilles.
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The FLOTROP dataset contains numerous plant observations (around 340,000 occurrences) in northern tropical Africa (from the 5 th to 25th parallel north) in open ecosystems (savannah and steppe). They were collected by multiple collectors between 1920 and 2012 and were managed by Philippe Daget. These observations are probably the most important and unique source of plant distribution over the Sahel area. The data are now available in the Global Biodiversity Information Facility (GBIF), Tela Botanica website, and as maps in the African Plant Database. For the overall area involved, this dataset has increased by 40% the data available in the GBIF. For some countries between the 15th and 21st parallel north, the FLOTROP dataset has increased available occurrences 10-fold compared to the data existing in the GBIF.
Tropical northern Africa (herein defined as between the 5th and 25th parallel north) is mostly occupied by open ecosystems, such as steppe and savannah. The vegetation in these ecosystems is consumed by animals, either wildlife or livestock, and is also used by the local communities for food, energy or medicinal purposes. The open ecosystems in tropical northern Africa are of great importance to the economy, food security and human well-being. Plant diversity within these ecosystems is driven by many factors, such as the climate, soil, fire and grazing. Plant diversity in these regions is being greatly impacted by global change. Historical data are needed to understand species and diversity dynamics. The database presented in this work is the collection of numerous datasets gathered over the years. At the outset, the FLOTROP database was intended to store all the data recorded by IEMVT (French institute for tropical livestock production and veterinary medicine, now part of CIRAD) in the sixties. In 1993, CIRAD and CNRS set up a project to collect a maximum of botanical surveys within these regions. Two software packages were created by the team to manage the database. The first was created under DOS then a second was started under Windows using the APL DYALOG language. Data were collected and scanned between 1993 and 2016. We extracted the data from the software version. We shared the species occurrences recorded in the database on the Tela Botanica website (http://www.tela-botanica.org/) and on the GBIF database.
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This FAIRsharing record describes: GBIF, the Global Biodiversity Information Facility, is an international open data infrastructure, funded by governments. It is not a data repository. Rather, GBIF indexes thousands of datasets shared freely by hundreds of institutions worldwide making it the biggest biodiversity database on the Internet. GBIF.org makes the data discoverable and citable, assigning each download a DOI and storing it for an extended period of time. More than 1 peer-reviewed research publication citing GBIF as a source of data is published every day, in studies spanning the impacts of climate change, the spread of pests and diseases, priority areas for conservation and food security. To share your data with GBIF follow this quick guide: http://www.gbif.org/publishing-data/quick-guide To deposit/host your data, it is recommended you use one of the trusted IPT data hosting centres (DHC) listed in FAIRsharing.org. The DHC will provide you with an account on their IPT, which will allow you to manage your own datasets and publish them through GBIF.org.
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Dataset that provides a direct link to PNG's data hosted on the GBIF website/ records.
Contact emails: info@gbif.org / helpdesk@gbif.org
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This database contains all the presence records of plants, beetles, chironomids, foraminifera and diatoms contained in the GBIF database in April 2018.The coordinates of the presence records have been homogenised on a 0.25x0.25° grid, and corresponding bioclimatic values from the Worldclim2.0 database have been added.These data are formatted and ready to use by the CREST software. Additional python scripts have been added to group plant species into pollen types.To download the latest version of the database, please follow this link: https://figshare.com/articles/GBIF_for_CREST_database/6743207
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To achieve large geographic coverage, species occurrence databases that are composed of ad hoc species data collections such as that provided by the Global Biodiversity Information Facility (GBIF) are often used. A drawback to using these data is their geographic sampling bias, in which some regions are more intensively sampled than others, while other areas have very little to none reported sampling effort. Uneven sampling effort can mislead conclusions about biodiversity patterns and species distributions (Gotelli & Colwell, 2001; Lobo, 2008).
Here we provide taxonomic occurrence grids to help mitigate the effects of sampling bias in species distribution modeling. These grids can be used to exclude areas of (a custom-defined) low sampling effort from the background when sampling for pseudo-absences’ (Phillips et al., 2009; Barbet-Massin et al.,2012). The occurrence grids have a 1 degree spatial resolution using WGS 84 as the geographic coordinate system. Each 1 degree grid cell contains the number of records present in GBIF corresponding to a specific taxonomic group: plants, mammals, reptiles, amphibians, birds and molluscs.
To construct the occurrence grids, we used the 1- by 1-degree world latitude and longitude vector grid provided by ESRI (Redlands, California). It has a custom license which permits it reuse as long as ESRI is cited. It was downloaded from : https://www.arcgis.com/home/item.html?id=f11bcdc5d484400fa926dcce68de3df7
To map spatial sampling effort, the number of georeferenced occurrences corresponding to each taxonomic group contained by each 1- by 1-degree grid cell were counted. The grids were then converted to GeoTIFFs. The raster values correspond to the number of occurrences reported for the grid cells. For the purposes of the TrIAS project, grid cells with fewer than 5 occurrences were removed. The TrIAS taxonomic occurrence grids are used as inputs to the TrIAS risk modelling and mapping workflow: https://github.com/trias-project/risk-modelling-and-mapping. Full (with all grid cells containing at least one occurrence) taxonomic occurrence grids are also provided.
GBIF data for each taxonomic group were downloaded using the following criteria: “Basis of Record”: Observation, Machine Observation, Human Observation, Specimen, Material sample, Literature Occurrence, Unknown evidence., "HasCoordinate is true", "HasGeospatialIssue is false", "TaxonKey is Amphibia", "Year 1975-2005".
Raster Attributes
Attribute
Description
OID
numeric row ID
Value
the number of records contained in the grid cell
Count
the number of times the value appears in the raster
The extent of each taxonomic occurrence grid:
longitude -180.0; latitude -90.0 (southwest corner)
longitude 180.0; latitude 90.0 (northeast corner)
Files:
TrIAS taxonomic occurrence grids
amphib_1deg_min5.tif
birds_1deg_min5.tif
mammals_1deg_min5.tif
molluscs_1deg_min5.tif
reptiles_1deg_min5.tif
Raw taxonomic occurrence grids
amphib_1deg_grid.tif
birds_1deg_grid.tif
mammals_1deg_grid.tif
molluscs_1deg_grid.tif
reptiles_1deg_grid.tif
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A dataset containing 11644510 species occurrences available in GBIF matching the query: DatasetKey: Dutch Vegetation Database (LVD). The dataset includes 11644510 records from 1 constituent datasets: 11644510 records from Dutch Vegetation Database (LVD). Data from some individual datasets included in this download may be licensed under less restrictive terms.
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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:
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Twitterhttps://pacific-data.sprep.org/dataset/data-portal-license-agreements/resource/de2a56f5-a565-481a-8589-406dc40b5588https://pacific-data.sprep.org/dataset/data-portal-license-agreements/resource/de2a56f5-a565-481a-8589-406dc40b5588
Dataset that provides a direct link to Kiribati's data hosted on the GBIF website/ records.
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TwitterThe purpose of this dataset is to evaluate herptile species' biodiversity in California's southwest desert. Species data was downloaded from the Global Diversity Information Facility (GBIF). GBIF.org (21 September 2022) GBIF Occurrence Download https://doi.org/10.15468/dl.5jhd82
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Twitterhttps://pacific-data.sprep.org/dataset/data-portal-license-agreements/resource/de2a56f5-a565-481a-8589-406dc40b5588https://pacific-data.sprep.org/dataset/data-portal-license-agreements/resource/de2a56f5-a565-481a-8589-406dc40b5588
Dataset that provides a direct link to Nauru's data hosted on the GBIF website/records.
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TwitterThe Global Biodiversity Information Facility (GBIF) is an international network and data infrastructure funded by the world's governments providing global data that document the occurrence of species. GBIF currently integrates datasets documenting over 1.6 billion species occurrences, growing daily. The GBIF occurrence dataset combines data from a wide array of sources including specimen-related data from natural history museums, observations from citizen science networks and environment recording schemes. While these data are constantly changing at GBIF.org, periodic snapshots are taken and made available on AWS.