Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
13
datasets available to search
ShareScore release 0.7.1
Dataset results
13 results for “Global Biodiversity Information Facility”
Data licences and organization type of contributors to the Global Biodiversity Information Facility as of 19 January 2016
<p>Data from the Global Biodiversity Information Facility were extracted using R (version 3.2.0) on 9 July 2015 using the rgbif package (version 0.9.0) (Chamberlain, S., Ram, K., Barve, V. & Mcglinn, D. (2015) Package ‘rgbif’: Interface to the Global 'Biodiversity' Information Facility 'API' http://cran.r-project.org/web/packages/rgbif/rgbif.pdf). The ‘rights’ statements was extracted for all occurrence datasets with one or more observations. A total of 12,458 datasets were extracted, but only about 11% of the datasets have an explicit data-useage-rights statement at the dataset level. However, some datasets use the occurrence level ‘rights’ and ‘accessRights’ fields. To extract these data the rights information was obtained from the first record of each dataset where a rights statement was missing at the dataset level.</p> <p>The datasets were categorized into 13 different types depending on the origin of the observations.</p> <ol> <li>Biodiversity Information Facility or data centre</li> <li>Botanical Garden or Herbarium</li> <li>Citizen science</li> <li>Commercial</li> <li>Data publisher</li> <li>Educational</li> <li>Government</li> <li>Museum</li> <li>Network</li> <li>Parks Authority or Nature Reserve</li> <li>Research institution</li> <li>Society</li> <li>Foundations</li> </ol>
A Repackaged Taxonomic Backbone of Global Biodiversity Information Facility (GBIF)
<p>Publication date:<br> 2022-12-06T07:37:19-06:00</p> <p><br> A Repackaged Taxonomic Backbone of Global Biodiversity Information Facility (GBIF)<br> ---</p> <p>Global Biodiversity Information Facility (GBIF) facilitates access to billions of biodiversity data records. These records include detailed accounts of life on earth.</p> <p>To help records of specific life forms, GBIF provides a taxonomic backbone [1,2]. This backbone contains a long list of names used to describe species and associated hierarchies and taxonomic publications. These lists are sourced from datasets around the world.</p> <p>At time of writing (6 Dec 2022), GBIF publishes a simplified version of their taxonomic backbone at [https://hosted-datasets.gbif.org/datasets/backbone/](https://hosted-datasets.gbif.org/datasets/backbone/) [1].</p> <p>This repository provides script to pre-process https://hosted-datasets.gbif.org/datasets/backbone/current/simple.txt.gz to help facilitate access and improve performance of the creation of search indexes.</p> <p>Pre-process steps currently include:<br> 1. reducing amount of columns<br> 2. reverse sort by id<br> 3. reverse sort by name</p> <p><br> Contents<br> ---</p> <p>README:<br> this file</p> <p>repackage-gbif-backbone.sh:<br> script used to repackage GBIF Simple Backbone.</p> <p>repackage-gbif-backbone.log:<br> log of repackaging of GBIF Simple Backbone.</p> <p>backbone-current-simple.txt.gz:<br> original GBIF backbone archive</p> <p>gbif-backbone-by-name.tsv.gz:<br> two columns, gzipped, tab-separated text file with columns name, and id<br> reverse sorted by name </p> <p>gbif-backbone-by-name.tsv.sha256:<br> sha256 hash of the uncompressed gbif-backbone-by-name.tsv.gz</p> <p>gbif-backbone-by-id.tsv.gz:<br> 20 columns, gzipped, tab-separated text file with first 20 columns of repackaged GBIF backbone file<br> reverse sorted by id</p> <p>gbif-backbone-by-id.tsv.sha256:<br> sha256 hash of the uncompressed gbif-backbone-by-id.tsv.gz</p> <p>References<br> ---</p> <p>[1] Simplied GBIF Backbone Taxonomy. Accessed at https://hosted-datasets.gbif.org/datasets/backbone/ on 2022-12-06.<br> [2] GBIF Secretariat (2021). GBIF Backbone Taxonomy. Checklist dataset https://doi.org/10.15468/39omei accessed via GBIF.org on 2021-08-18.</p> <p><br> Hash URIs<br> ---<br> This publication includes the following content uris:</p> <p>hash://sha256/82d5f2153b4533322692d95eeb18b0f103e1b2297e38bd9ea935b07ba86cd7d5<br> hash://sha256/50c155f66efb2efba0b8b624f8541e81cbe16a701d420a5073791fb993f72919<br> hash://sha256/9cd7d4c91292d86c726210446cd6fe45602505a7c0ea3b7c4f4f481f85f193ad (uncompressed)<br> hash://sha256/f950dde25cce9ba9cce67caa1c68ce0c99cb31fe2dc9658fec85a987d9f31654<br> hash://sha256/f21c6b90f17c6083fcfb4853f3c581dcc2aadd291691fa128392a205321f420b (uncompressed)<br> hash://sha256/5e0a4d1d2d1cccbdcc6b2c9831fafe61c54eb055f2d13ec40d9ac161889b9f89<br> hash://sha256/f6e477133d0585706ee5522963b204200cb3cd198f011cbf62be0fa8519763b5 (uncompressed)<br> </p>
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
<p>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.</p> <p>This publication contains an exhaustive list of GBIF IDs and ids associated by their data providers as derived from:</p> <p>GBIF.org (01 March 2023) GBIF Occurrence Download https://doi.org/10.15468/dl.pk3trq</p> <p>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</p> <pre><code class="language-bash">preston cat 'zip:hash://sha256/c8bac8acb28c8524c53589b3a40e322dbbbdadf5689fef2e20266fbf6ddf6b97!/0015281-230224095556074.csv'\ | cut -f 1,2,3,37,38,39\ | gzip\ > gbifid.tsv.gz </code></pre> <p>with the content id of gbifid.tsv.gz (size: ~35GB) being hash://sha256/a339e32e10edaad585f61f2ded06cbb23e0618c65a6360db18d7d729054940a8 .</p> <p>the first 10 lines of gbifid.tsv.gz as extracted via</p> <pre><code>preston cat --remote https://zenodo.org/record/7789866/files,https://linker.bio hash://sha256/a339e32e10edaad585f61f2ded06cbb23e0618c65a6360db18d7d729054940a8\ | gunzip\ | head</code></pre> <p>are:</p> <pre><code>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</code></pre> <p>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:</p> <p>https://gbif.org/occurrence/2997162320</p> <p>and</p> <p>https://gbif.org/dataset/c71c8000-9fc7-422c-804a-ce6abe751771</p> <p>respectively.</p> <p>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. </p> <p>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. </p> <p>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 .</p>
Supplementary material 1: Global Biodiversity Information Facility: Taxa and Records from: Integrating and visualizing primary data from prospective and legacy taxonomic literature - Biodiversity Data Journal 3: e5063 (12 May 2015) https://doi.org/10.3897/BDJ.3.e5063
All records in GBIF with taxonomic ranks (kingdom, phylum, class, order, and species), basis of record (e.g., preserved specimen), and count of records, exported from GBIF on 7 December 2014.
Fig. 5 in Freier Zugang zu den Informationen der Artenvielfalt - Wie werde ich Teil der Global Biodiversity Information Facility (GBIF)?
Fig. 5: Das Suchportal des Botanik-Knotens von GBIF-Deutschland, einer der mehreren im Internet verfügbaren Zugangspunkte zu den Daten des GBIF-Netzwerks.
Fig. 2 in Freier Zugang zu den Informationen der Artenvielfalt - Wie werde ich Teil der Global Biodiversity Information Facility (GBIF)?
Fig. 2:Tatenflüsse über das Internet im GBIF-Netzwerk zwischen Nutzer, Suchportal und Datenlieferant.
Fig. 3 in Freier Zugang zu den Informationen der Artenvielfalt - Wie werde ich Teil der Global Biodiversity Information Facility (GBIF)?
Fig. 3: Die Zuordnung der Daten aus dem relationalen Datenschema der Sammlungsdatenbank zu den ABCD-Elementen wird im Mapping festgelegt und ist in einer komfortablen Oberfläche mit dem Internet- Browser möglich.
Fig. 1 in Freier Zugang zu den Informationen der Artenvielfalt - Wie werde ich Teil der Global Biodiversity Information Facility (GBIF)?
Fig. 1: Die Wrapper-Software umgibt die bestehenden Sammlungsdatenbanken mit einer zusätzlichen Abstraktionsschicht und bietet so eine definierte Schnittstelle zwischen den existierenden Datenbanksystemen und den GBIF-Suchportalen.
Fig.1 in Die Global Biodiversity Information Facility (GBIF) - Struktur, Aufgaben und Ziele
Fig.1: Das Knotensystem GBIF Deutschland und seine Anbindung an GBIF International. Die Daten fliessen aus den Teilprojekten in die Datenbanksysteme der einzelnen Knoten, denen ein BioCASE-Wrapper aufgesetzt ist, der auf dem ABCD-Datenmodell basiert. Damit ist es möglich, alle angebundenen Daten über das Datenportal von GBIF International im Internet abzurufen bzw. verfügbar zu machen. GBIF International stellt ausserdem die Wrapper-Software DiGIR, welche auf dem Darwin Core 2 aufbaut, zur Verfügung. Einzelne Teilprojekte, wie z.B. DIG mit BIODAT im Knoten Evertebraten I, setzen eigene Datenbanklösungen ein und fungieren daher als direkte GBIF Datenprovider. Die Angaben entsprechen dem Stand Anfang April 2005.
A Repackaged Taxonomic Backbone of Global Biodiversity Information Facility (GBIF) - 2021-11-26
<p>A Repackaged Taxonomic Backbone of Global Biodiversity Information Facility (GBIF)<br> ---</p> <p>Global Biodiversity Information Facility (GBIF) facilitates access to billions of biodiversity data records. These records include detailed accounts of life on earth.</p> <p>To help records of specific life forms, GBIF provides a taxonomic backbone [1,2]. This backbone contains a long list of names used to describe species and associated hierarchies and taxonomic publications. These lists are sourced from datasets around the world.</p> <p>At time of writing (18 Aug 2021), GBIF publishes a simplified version of their taxonomic backbone at [https://hosted-datasets.gbif.org/datasets/backbone/](https://hosted-datasets.gbif.org/datasets/backbone/) [1].</p> <p>This repository provides script to pre-process https://hosted-datasets.gbif.org/datasets/backbone/backbone-current-simple.txt.gz to help facilitate access and improve performance of the creation of search indexes.</p> <p>Pre-process steps currently include:</p> <p>1. reducing amount of columns<br> 2. reverse sort by id<br> 3. reverse sort by name</p> <p><br> Contents<br> ---</p> <p>README:<br> this file</p> <p>repackage-gbif-backbone.sh:<br> script used to repackage GBIF Simple Backbone.</p> <p>backbone-current-simple.txt.gz:<br> original GBIF backbone archive</p> <p>gbif-backbone-by-name.tsv.gz:<br> two columns, gzipped, tab-separated text file with columns name, and id<br> reverse sorted by name</p> <p>gbif-backbone-by-name.tsv.sha256:<br> sha256 hash of the uncompressed gbif-backbone-by-name.tsv.gz</p> <p>gbif-backbone-by-id.tsv.gz:<br> 20 columns, gzipped, tab-separated text file with first 20 columns of repackaged GBIF backbone file<br> reverse sorted by id</p> <p>gbif-backbone-by-id.tsv.sha256:<br> sha256 hash of the uncompressed gbif-backbone-by-id.tsv.gz</p> <p>References<br> ---</p> <p>[1] Simplied GBIF Backbone Taxonomy. Accessed at https://hosted-datasets.gbif.org/datasets/backbone/ on 2021-08-18.<br> [2] GBIF Secretariat (2021). GBIF Backbone Taxonomy. Checklist dataset https://doi.org/10.15468/39omei accessed via GBIF.org on 2021-08-18.</p> <p><br> Hash URIs<br> ---<br> This publication includes the following content uris:</p> <p>repackage-gbif-backbone.sh:<br> hash://sha256/073ac5490252c4ccbbd4f516d391faebe62c9fde9e4d75ae870441a86c382527</p> <p>backbone-current-simple.txt.gz:<br> hash://sha256/15cbfc038e666356af27248935f79e408ed51fd8c0b49a668fed8dbf72591502<br> hash://sha256/1f78788a4a046dcbcf1e36c7658a1e333ca60e7586a372238d58b938d91fde51 (uncompressed)</p> <p>gbif-backbone-by-name.tsv.gz:<br> hash://sha256/6e11ae9961a9498b60d4bdeb489d6c1f5da9c2732310edaecdc79bd287b79ef4<br> hash://sha256/934ce05dbd067abb209168bd1d9389f122d051e1b7374b5d757a12e86f8da9a5 (uncompressed)</p> <p>gbif-backbone-by-id.tsv.gz:<br> hash://sha256/c434c7d3622421b17dadcd119391b32a66edee59f484d4cab924d92fd17713e2<br> hash://sha256/e2cf9116a21966315b0482d391052223e21c8e916ae0c097dfd37bed017b815b (uncompressed)</p>
Fig. 4 in Freier Zugang zu den Informationen der Artenvielfalt - Wie werde ich Teil der Global Biodiversity Information Facility (GBIF)?
Fig. 4: Anzahl der im GBIF-Netzwerk verfügbaren Datensätze (Belege und Beobachtungen) in Millionen.
Leafcutter ants of the genus Atta in the Insects Collection at the Field Museum of Natural History. The field data on the attached tags are transcribed for entry into databases such as AntWeb and the Global Biodiversity Information Facility. Photograph: Matthew Nelsen. in The Evolution of Natural History Collections
Leafcutter ants of the genus Atta in the Insects Collection at the Field Museum of Natural History. The field data on the attached tags are transcribed for entry into databases such as AntWeb and the Global Biodiversity Information Facility. Photograph: Matthew Nelsen.
A Repackaged Taxonomic Backbone of Global Biodiversity Information Facility (GBIF)
<div> <div>Publication date:</div> <div>2024-03-12T14:26:33-03:00</div> <br><br> <div>A Repackaged Taxonomic Backbone of Global Biodiversity Information Facility (GBIF)</div> <div>---</div> <br> <div>Global Biodiversity Information Facility (GBIF) facilitates access to billions of biodiversity data records. These records include detailed accounts of life on earth.</div> <br> <div>To help records of specific life forms, GBIF provides a taxonomic backbone [1,2]. This backbone contains a long list of names used to describe species and associated hierarchies and taxonomic publications. These lists are sourced from datasets around the world.</div> <br> <div>At time of writing (18 Aug 2021), GBIF publishes a simplified version of their taxonomic backbone at [https://hosted-datasets.gbif.org/datasets/backbone/](https://hosted-datasets.gbif.org/datasets/backbone/) [1].</div> <br> <div>This repository provides script to pre-process https://hosted-datasets.gbif.org/datasets/backbone/backbone-current-simple.txt.gz to help facilitate access and improve performance of the creation of search indexes.</div> <br> <div>Pre-process steps currently include:</div> <div>1. reducing amount of columns</div> <div>2. reverse sort by id</div> <div>3. reverse sort by name</div> <br><br> <div>Contents</div> <div>---</div> <br> <div>README:</div> <div>this file</div> <br> <div>repackage-gbif-backbone.sh:</div> <div>script used to repackage GBIF Simple Backbone.</div> <br> <div>backbone-current-simple.txt.gz:</div> <div>original GBIF backbone archive</div> <br> <div>gbif-backbone-by-name.tsv.gz:</div> <div>two columns, gzipped, tab-separated text file with columns name, and id</div> <div>reverse sorted by name</div> <br> <div>gbif-backbone-by-name.tsv.sha256:</div> <div>sha256 hash of the uncompressed gbif-backbone-by-name.tsv.gz</div> <br> <div>gbif-backbone-by-id.tsv.gz:</div> <div>20 columns, gzipped, tab-separated text file with first 20 columns of repackaged GBIF backbone file</div> <div>reverse sorted by id</div> <br> <div>gbif-backbone-by-id.tsv.sha256:</div> <div>sha256 hash of the uncompressed gbif-backbone-by-id.tsv.gz</div> <br> <div>References</div> <div>---</div> <br> <div>[1] Simplied GBIF Backbone Taxonomy. Accessed at https://hosted-datasets.gbif.org/datasets/backbone/ on 2023-08-28.</div> <div>[2] GBIF Secretariat (2021). GBIF Backbone Taxonomy. Checklist dataset https://doi.org/10.15468/39omei accessed via GBIF.org on 2023-08-28.</div> <br><br> <div>Hash URIs</div> <div>---</div> <div>This publication includes the following content uris:</div> <br> <div>hash://sha256/82d5f2153b4533322692d95eeb18b0f103e1b2297e38bd9ea935b07ba86cd7d5</div> <div>hash://sha256/fde017e1315b4ae6fc1e1bae79f9cfd234b8ba40f6f4fb5ac031084a3b1763f0</div> <div>hash://sha256/1804594be92a0e9a7b60c245925a1a488d4d98a4a38028cb0c8a420faefa36c2 (uncompressed)</div> <div>hash://sha256/480926c8a1f218f8d5d76db7b4687c09ea11ab1c7ee9b0788238f2ff1eab7298</div> <div>hash://sha256/8184f1e96d306ba5355e3e229d8e93eacd3fee4ab19107ae99b71bc4b9d523b6 (uncompressed)</div> <div>hash://sha256/6241ffc32d0e1dbd826b36e45dfa469046ce69e671224bbb43f89996ca577955</div> <div>hash://sha256/6df36a48615d9a3d7541995c6fc01da7f3ee34679d560ec619212a2c5f037679 (uncompressed)</div> </div>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.