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opencc-zeroMar 2024View details →

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>

opencc-zeroSep 2022View details →

Supplementary material 2 from: Woodburn M, Buschbom J, Droege G, Grant S, Groom Q, Jones J, Trekels M, Vincent S, Webbink K (2022) Latimer Core: A new data standard for collection descriptions. Biodiversity Information Science and Standards 6: e91159. https://doi.org/10.3897/biss.6.91159

Standards with LtC alignments

opencc-zeroSep 2022View details →

Supplementary material 1 from: Woodburn M, Buschbom J, Droege G, Grant S, Groom Q, Jones J, Trekels M, Vincent S, Webbink K (2022) Latimer Core: A new data standard for collection descriptions. Biodiversity Information Science and Standards 6: e91159. https://doi.org/10.3897/biss.6.91159

A summary of the classes in the Latimer Core standard.

opencc-zeroSep 2022View details →

Supplementary material 1 from: Martin-Cabrera P, Perez Perez R, Irrison J-O, Lombard F, Ove Möller K, Rühl S, Creach V, Lindh M, Stemmann L, Schepers L (2022) Establishing Plankton Imagery Dataflows Towards International Biodiversity Data Aggregators. Biodiversity Information Science and Standards 6: e94196. https://doi.org/10.3897/biss.6.94196

Imagery dataset example

opencc-ncJun 2009View details →

Biodiversity information retrieval across networked data sets

<p>Recording of presentation. An approach to integrate data through wrapping of various datasets stored in relational databases located on networked platforms. It is designed to overcome copyright problems in data sharing.</p>

opencc-zeroSep 2021View details →

Supplementary material 1 from: Woodburn M, Droege G, Grant S, Groom Q, Jones J, Trekels M, Vincent S, Webbink K (2021) A Data Standard for Dynamic Collection Descriptions. Biodiversity Information Science and Standards 5: e73902. https://doi.org/10.3897/biss.5.73902

Provisional list of classes.

Figure 2 from: Miyazaki Y, Teramura A, Senou H (2016) Biodiversity data mining from Argus-eyed citizens: the first illegal introduction record of Lepomis macrochirus macrochirus Rafinesque, 1819 in Japan based on Twitter information. ZooKeys 569: 123-133. https://doi.org/10.3897/zookeys.569.7577

Figure 2 - Photographs of Lepomis macrochirus macrochirus collected from the outdoor pool of Chigasaki Park, Yokohama City, Kanagawa Prefecture, Japan on 14 June 2015. A voucher specimen, juvenile, KPM-NI 38654 (photo: KPM-NR 164120 by AT), 22.6 mm SL B voucher specimen, juvenile (right side), KPM-NR 108928 by YM (the same individual as KPM-NI 38654) C adult specimens, photograph, KPM-NR 164118 by AT.

Figure 3 from: Miyazaki Y, Teramura A, Senou H (2016) Biodiversity data mining from Argus-eyed citizens: the first illegal introduction record of Lepomis macrochirus macrochirus Rafinesque, 1819 in Japan based on Twitter information. ZooKeys 569: 123-133. https://doi.org/10.3897/zookeys.569.7577

Figure 3 - Photograph of the outdoor pool of Chigasaki Park, Yokohama City, Kanagawa Prefecture, Japan.

Figure 1 from: Miyazaki Y, Teramura A, Senou H (2016) Biodiversity data mining from Argus-eyed citizens: the first illegal introduction record of Lepomis macrochirus macrochirus Rafinesque, 1819 in Japan based on Twitter information. ZooKeys 569: 123-133. https://doi.org/10.3897/zookeys.569.7577

Figure 1 - A tweet including two fish images posted by AT on 14 June 2015. The image on the left shows two adults of Lepomis macrochirus macrochirus, while the one on the right shows juveniles of Lepomis macrochirus macrochirus and two young of Carassius auratus (however, the specimens in the latter image are not able to be identified even to family level from the image alone). The comments are translated into English as follows: "The results of a pool cleaning. I cannot believe the foolishness of the person who introduced these fish into the pool." https://twitter.com/orca_lf/status/610088107476516864 [Accessed on 25 November 2015]

Figure 5 from: Miyazaki Y, Teramura A, Senou H (2016) Biodiversity data mining from Argus-eyed citizens: the first illegal introduction record of Lepomis macrochirus macrochirus Rafinesque, 1819 in Japan based on Twitter information. ZooKeys 569: 123-133. https://doi.org/10.3897/zookeys.569.7577

Figure 5 - The voucher specimens and photographs of Carassius auratus collected from the outdoor pool of Chigasaki Park, Yokohama City, Kanagawa Prefecture, Japan, on 14 June 2015. A voucher specimen, KPM-NI 38655 (photo: KPM-NR 108929 by YM), 64.9 mm SL B voucher specimen (live), KPM-NI 38656 (photo: KPM-NR 164119 by AT), 61.3 mm SL C voucher specimen (fresh), KPM-NR 108930 by YM (the same individual as KPM-NI 38656).

Figure 4 from: Miyazaki Y, Teramura A, Senou H (2016) Biodiversity data mining from Argus-eyed citizens: the first illegal introduction record of Lepomis macrochirus macrochirus Rafinesque, 1819 in Japan based on Twitter information. ZooKeys 569: 123-133. https://doi.org/10.3897/zookeys.569.7577

Figure 4 - A portion of gut components of Lepomis macrochirus macrochirus collected from the outdoor pool of Chigasaki Park, Yokohama City, Kanagawa Prefecture, Japan, on 14 June 2015. Dragonfly nymphs, Sympetrum sp., were included.

Figure 3 from: Michel E (2016) Anchoring Biodiversity Information: From Sherborn to the 21st century and beyond. In: Michel E (Ed.) Anchoring Biodiversity Information: From Sherborn to the 21st century and beyond. ZooKeys 550: 1–11. https://doi.org/10.3897/zookeys.550.7460

Figure 3 - The full panel of symposium speakers under the heading WWSD? What would Sherborn Do? From left to right: Suzanne Pilsk, Chris Lyal, Henning Scholz, Edward Dickinson, Neil Evenhuis, Daphne Fautin, Sandy Knapp, Lyubomir Penev, Rod Page, Chris Thompson, Chris Freeland, Gordon McOuat, (behind podium Richard Pyle, David Remsen).

Figure 2 from: Michel E (2016) Anchoring Biodiversity Information: From Sherborn to the 21st century and beyond. In: Michel E (Ed.) Anchoring Biodiversity Information: From Sherborn to the 21st century and beyond. ZooKeys 550: 1–11. https://doi.org/10.3897/zookeys.550.7460

Figure 2 - Sherborn's land and freshwater mollusc collections, with specimen labels in his own handwriting A Gastropods B Bivalves.

Figure 10 from: McOuat G (2016) Naming and Necessity: Sherborn's Context in the 19th Century. In: Michel E (Ed.) Anchoring Biodiversity Information: From Sherborn to the 21st century and beyond. ZooKeys 550: 57–69. https://doi.org/10.3897/zookeys.550.7399

Figure 10 - An iconographic picture of Sherborn in later years – staged, but revealing and taken at about the time of the final quote.

Figure 4 from: Dickinson EC (2016) Reinforcing the foundations of ornithological nomenclature: Filling the gaps in Sherborn's and Richmond's historical legacy of bibliographic exploration. In: Michel E (Ed.) Anchoring Biodiversity Information: From Sherborn to the 21st century and beyond. ZooKeys 550: 107–134. https://doi.org/10.3897/zookeys.550.10170

Figure 4 - An example of two-state publication. Here the Proceedings of the Zoological Society of London, 1887, demonstrates a two-state situation. Left image: "first state". Right image: "second state". Images from Dickinson et al. (2011: 36) reproduced with permission from The Natural History Museum, London.

Figure 2 from: Dickinson EC (2016) Reinforcing the foundations of ornithological nomenclature: Filling the gaps in Sherborn's and Richmond's historical legacy of bibliographic exploration. In: Michel E (Ed.) Anchoring Biodiversity Information: From Sherborn to the 21st century and beyond. ZooKeys 550: 107–134. https://doi.org/10.3897/zookeys.550.10170

Figure 2 - Bibliographic publications per decade, 1970 to late 2011, by subject. Treating books, periodicals and general works such as catalogues (source: references cited by Dickinson et al. 2011).

Figure 3 from: Dickinson EC (2016) Reinforcing the foundations of ornithological nomenclature: Filling the gaps in Sherborn's and Richmond's historical legacy of bibliographic exploration. In: Michel E (Ed.) Anchoring Biodiversity Information: From Sherborn to the 21st century and beyond. ZooKeys 550: 107–134. https://doi.org/10.3897/zookeys.550.10170

Figure 3 - The wrapper for the 13th part of the Planches Coloriées showing vernacular and scientific names. All the wrappers for the first twenty parts, all that were published without supporting texts, have been depicted in Zoological Bibliography: 10 in vol. 1, No. 4, pp. 144–148 and 10 in Vol. 2, No. 1, 37–41 pp. These pages were published under the terms of the Creative Commons Attribution Licence and may be reproduced with proper attribution.

Figure 4 from: Taylor MA (2016) 'Where is the damned collection?' Charles Davies Sherborn's listing of named natural science collections and its successors. In: Michel E (Ed.) Anchoring Biodiversity Information: From Sherborn to the 21st century and beyond. ZooKeys 550: 83–106. https://doi.org/10.3897/zookeys.550.10073

Figure 4 - Differing treatments of Thomas Hawkins. A The original Sherborn entry in Where is the – Collection? (p. 67) B The much more extensive entry in World Palaeontological Collections (Cleevely 1983, p. 147).

Figure 2 from: Taylor MA (2016) 'Where is the damned collection?' Charles Davies Sherborn's listing of named natural science collections and its successors. In: Michel E (Ed.) Anchoring Biodiversity Information: From Sherborn to the 21st century and beyond. ZooKeys 550: 83–106. https://doi.org/10.3897/zookeys.550.10073

Figure 2 - The final bill from Cambridge University Press, tipped into a copy of Where is the – Collection? in the NHM Library. Photo courtesy R. J. Cleevely, NHM.

Figure 3 from: Welter-Schultes F, Görlich A, Lutze A (2016) Sherborn's Index Animalium: New names, systematic errors and availability of names in the light of modern nomenclature. In: Michel E (Ed.) Anchoring Biodiversity Information: From Sherborn to the 21st century and beyond. ZooKeys 550: 173–187. https://doi.org/10.3897/zookeys.550.10041

Figure 3 - Example of a new name established in a chaotically arranged early zoological work. Detail of Hartmann (1821: p. 231), with the original description of Helix ruderata Hartmann, 1821 (currently Discus ruderatus). For the non-insider it is very difficult to see that a new name was established here. It is necessary to understand precisely the content of the German text: "s. meine Tab. II. f. 11. Der vorigen ähnlich, aber aufgeblasener, rauher, weniger Umgänge" (= see my plate II, figure 11. Similar to the previous one, but more inflated, rougher, fewer whorls).