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7 results for “taxonomic backbone”
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>
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>
African wood density database with matches to the taxonomic backbone data sets of World Flora Online (version 2023.12) and the World Checklist of Vascular Plants (version 11)
<p>The <strong><span>African Wood Density Database </span></strong><span>provides air-dry wood density data for over 750 tree species grown in Africa.</span></p> <p>This archive provides taxonomic matches with recent versions of <strong>World Flora Online</strong> (WFO; <a href="../records/10425161">version 2023.12 downloaded from Zenodo</a>; Borch et al. <a href="https://onlinelibrary.wiley.com/doi/10.1002/tax.12373">2020</a>) and the <strong>World Checklist of Vascular Plants</strong> (WCVP; <a href="https://sftp.kew.org/pub/data-repositories/WCVP/Archive/">version 11 downloaded from the Kew data depository</a>; Govaerts et al. <a href="https://doi.org/10.1038/s41597-021-00997-6">2021</a>). Matching was done via the <strong>WorldFlora</strong> package (<a href="https://cran.r-project.org/package=WorldFlora">version 1.14-3</a>; Kindt <a href="https://bsapubs.onlinelibrary.wiley.com/doi/full/10.1002/aps3.11388">2020</a>), using similar scripts as documented in this Rpub: <a href="https://rpubs.com/Roeland-KINDT/1134151">https://rpubs.com/Roeland-KINDT/1134151</a>.</p> <p> </p> <ul> <li><span>Carsan, S. Orwa, C. Harwood, C. Kindt, R. Stroebel, A. Neufeldt, H. and Jamnadass, R. 2012. African Wood Density Database. World Agroforestry Centre, Nairobi. <a href="https://apps.worldagroforestry.org/treesnmarkets/wood/">https://apps.worldagroforestry.org/treesnmarkets/wood/#</a> </span></li> <li><span>Borsch, T., Berendsohn, W., Dalcin, E., Delmas, M., Demissew, S., Elliott, A., Fritsch, P., Fuchs, A., Geltman, D., Güner, A., Haevermans, T., Knapp, S., le Roux, M.M., Loizeau, P.-A., Miller, C., Miller, J., Miller, J.T., Palese, R., Paton, A., Parnell, J., Pendry, C., Qin, H.-N., Sosa, V., Sosef, M., von Raab-Straube, E., Ranwashe, F., Raz, L., Salimov, R., Smets, E., Thiers, B., Thomas, W., Tulig, M., Ulate, W., Ung, V., Watson, M., Jackson, P.W. and Zamora, N. (2020), World Flora Online: Placing taxonomists at the heart of a definitive and comprehensive global resource on the world's plants. TAXON, 69: 1311-1341. <a href="https://doi.org/10.1002/tax.12373">https://doi.org/10.1002/tax.12373</a></span></li> <li><span>Govaerts, R., Nic Lughadha, E., Black, N. <em>et al.</em> The World Checklist of Vascular Plants, a continuously updated resource for exploring global plant diversity. <em>Sci Data</em> <strong>8</strong>, 215 (2021). <a href="https://doi.org/10.1038/s41597-021-00997-6">https://doi.org/10.1038/s41597-021-00997-6</a></span></li> <li><span>Kindt, R. 2020. WorldFlora: An R package for exact and fuzzy matching of plant names against the World Flora Online taxonomic backbone data. <em>Applications in Plant Sciences</em> 8(9): e11388. <a href="https://doi.org/10.1002/aps3.11388">https://doi.org/10.1002/aps3.11388</a></span></li> </ul> <p> </p> <p>Original funding for the database was provided <span>by the Carbon Benefits Project (CBP) supported by The Global Environment Facility (GEF). Development of the 2024 version </span>was supported by the <strong>Darwin Initiative</strong> to project DAREX001 of <em>Developing a Global Biodiversity Standard certification for tree-planting and restoration</em>, by <strong>Norway’s International Climate and Forest Initiative through the Royal Norwegian Embassy in Ethiopia</strong> to the <em>Provision of Adequate Tree Seed Portfolio</em> project in Ethiopia, by the <strong>Green Climate Fund</strong> through the IUCN-led <em>Transforming the Eastern Province of Rwanda through Adaptation</em> project and through the <em>Readiness proposal on Climate Appropriate Portfolios of Tree Diversity for Burkina Faso</em>, by the <strong>Bezos Earth Fund</strong> to the <em>Bezos Quality Tree Seed for Africa in Kenya and Rwanda</em> project and by the <strong>German International Climate Initiative (IKI)</strong> to the regional tree seed programme on <em>The Right Tree for the Right Place for the Right Purpose in Africa</em>. When using <strong>African Wood Density database</strong> in your work, cite the 2012 version (Carsan et al. <a href="https://apps.worldagroforestry.org/treesnmarkets/wood/">2012</a>) as well as this repository using the DOI.</p>
Data from: Plastome-based subgenus-level phylogenetic backbone of hawthorns: insights into the maternal position and taxonomic synopsis of Crataegus shandongensis (Rosaceae, Maleae)
Open the record for dataset details and reuse information.
Data from: Utilizing next-generation sequencing to resolve the backbone of the Core Goodeniaceae and inform future taxonomic and floral form studies
Though considerable progress has been made in inferring phylogenetic relationships of many plant lineages, deep unresolved nodes remain a common problem that can impact downstream efforts, including taxonomic decision-making and character reconstruction. The Core Goodeniaceae is a group affected by this issue: data from the plastid regions trnL-trnF and matK have been insufficient to generate adequate support at key nodes along the backbone of the phylogeny. We performed genome skimming for 24 taxa representing major clades within Core Goodeniaceae. The plastome coding regions (CDS) and nuclear ribosomal repeats (NRR) were assembled and complemented with additional accessions sequenced for nuclear G3PDH and plastid trnL-trnF and matk. The CDS, NRR, and G3PDH alignments were analyzed independently and topology tests were used to detect the alignments' ability to reject alternative topologies. The CDS, NRR, and G3PDH alignments independently supported a Brunonia (Scaevola s.l. (Coopernookia (Goodenia s.l.))) backbone topology, but within Goodenia s.l., the strongly-supported plastome topology (Goodenia A (Goodenia B (Velleia + Goodenia C))) contrasts with the poorly supported nuclear topology ((Goodenia A + Goodenia B) (Velleia + Goodenia C)). A fully resolved and maximally supported topology for Core Goodeniaceae was recovered from the plastome CDS, and there is excellent support for most of the major clades and relationships among them in all alignments. The composition of these seven major clades renders many of the current taxonomic divisions non-monophyletic, prompting us to suggest that Goodenia may be split into several segregate genera.
Data from: Utilizing next-generation sequencing to resolve the backbone of the Core Goodeniaceae and inform future taxonomic and floral form studies
Open the record for dataset details and reuse information.
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
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
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International Brain Laboratory public data
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OpenNeuro
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