Taxonomic treatment

Last updated
Taxonomic treatment of Apis mellifera, Linnaeus 1758 ApisMellifera treatment.png
Taxonomic treatment of Apis mellifera, Linnaeus 1758

A taxonomic treatment is a section in a scientific publication documenting the features of a related group of organisms or taxa. [1] Treatments have been the building blocks of how data about taxa are provided, ever since the beginning of modern taxonomy by Linnaeus 1753 for plants [2] and 1758 for animals. [3] Each scientifically described taxon has at least one taxonomic treatment. In today’s publishing, a taxonomic treatment tag [4]

Contents

is used to delimit such a section. [5] It allows to make this section findable, accessible, interoperable and reusable FAIR data. This is implemented in the Biodiversity Literature Repository, where upon deposition of the treatment a persistent DataCite digital object identifier (DOI) is minted. This includes metadata about the treatment, the source publication and other cited resources, such as figures cited in the treatment. This DOI allows a link from a taxonomic name usage to the respective scientific evidence provided by the author(s), both for human and machine consumption.

Treatments are considered data and thus copyright is not applicable [6] and thus can be made available even from closed access publications.

Etymology

The term taxonomic treatment has been coined because the term description has two meanings in species or taxonomic descriptions. One is equivalent to treatment, the second as subsection in treatments describing the taxon, complementing diagnosis, materials examined, distribution, conservation and other subsections. [7]

History

This term has been introduced during a national US NSF digital library project, [8] and has been further developed into Taxpub, [9] a taxonomy specific version of the Journal Article Tag Suite by Plazi, National Center for Biotechnology Information, and Pensoft Publishers. It was prototyped by the taxonomic journal ZooKeys , [10] which adopted Taxpub from its volume 50 onwards, followed by PhytoKeys. [11] Taxpub is now used by journals published by Pensoft Publishers, European Journal of Taxonomy [12] by Consortium of European Taxonomic Facilities (CETAF), and the National Museum of Natural History, France. [13] The TreatmentBank [14] service provided by Plazi to convert taxonomic publications into FAIR data provides access to over 500,000 taxonomic treatments, [15] including over 7,700 treatments for new described species in 2020. [16] They will eventually become accessible in BLR after passing quality control to avoid artifacts due to the complex conversion of unstructured, mainly PDF based publications.

Related Research Articles

<span class="mw-page-title-main">National Center for Biotechnology Information</span> Database branch of the US National Library of Medicine

The National Center for Biotechnology Information (NCBI) is part of the (NLM), a branch of the National Institutes of Health (NIH). It is approved and funded by the government of the United States. The NCBI is located in Bethesda, Maryland, and was founded in 1988 through legislation sponsored by US Congressman Claude Pepper.

HaXml is a collection of utilities for parsing, filtering, transforming, and generating Extensible Markup Language (XML) documents using the programming language Haskell.

PubMed is a free database including primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine (NLM) at the National Institutes of Health maintains the database as part of the Entrez system of information retrieval.

<span class="mw-page-title-main">Entrez</span> Cross-database search engine for health sciences

The Entrez Global Query Cross-Database Search System is a federated search engine, or web portal that allows users to search many discrete health sciences databases at the National Center for Biotechnology Information (NCBI) website. The NCBI is a part of the National Library of Medicine (NLM), which is itself a department of the National Institutes of Health (NIH), which in turn is a part of the United States Department of Health and Human Services. The name "Entrez" was chosen to reflect the spirit of welcoming the public to search the content available from the NLM.

PubMed Central (PMC) is a free digital repository that archives open access full-text scholarly articles that have been published in biomedical and life sciences journals. As one of the major research databases developed by the National Center for Biotechnology Information (NCBI), PubMed Central is more than a document repository. Submissions to PMC are indexed and formatted for enhanced metadata, medical ontology, and unique identifiers which enrich the XML structured data for each article. Content within PMC can be linked to other NCBI databases and accessed via Entrez search and retrieval systems, further enhancing the public's ability to discover, read and build upon its biomedical knowledge.

<span class="mw-page-title-main">Mycobacteriophage</span> Virus infecting mycobacteria

A mycobacteriophage is a member of a group of bacteriophages known to have mycobacteria as host bacterial species. While originally isolated from the bacterial species Mycobacterium smegmatis and Mycobacterium tuberculosis, the causative agent of tuberculosis, more than 4,200 mycobacteriophage species have since been isolated from various environmental and clinical sources. 2,042 have been completely sequenced. Mycobacteriophages have served as examples of viral lysogeny and of the divergent morphology and genetic arrangement characteristic of many phage types.

<i>Chionomys</i> Genus of rodents

Chionomys is a genus of rodent in the family Cricetidae.

<i>Trichocereus macrogonus</i> Species of cactus

Trichocereus macrogonus, synonym Echinopsis macrogonus, is a species of cactus found in Ecuador, Peru and Bolivia. Two varieties are accepted as of September 2023: var. macrogonus and var. pachanoi. Plants contain varying amounts of the psychoactive alkaloid mescaline. They have been used both ritually and in traditional medicine from pre-Columbian times. Trichocereus macrogonus is one of a number of similar species that may be called San Pedro cactus. Indigenous names include achuma and huachuma, although these too may be applied to similar species.

John S. Clark was a Scottish-born Australian entomologist and myrmecologist known for his study of Australian ants. Born in Glasgow, he developed an interest in entomology at a young age. Clark first arrived in Australia in 1905 and originally worked for the state railways in Queensland. He developed an interest in ants shortly afterwards, collecting his first specimens in North Queensland. He married his first wife, Maggie Forbes in 1908, who bore four children, and died in 1935. He married his second wife, Phyllis Marjorie Claringbulls in 1939 and had two daughters with her. On her suicide in 1943, Clark sent his daughters to an orphanage.

ZooKeys is a peer-reviewed open access scientific journal covering zoological taxonomy, phylogeny, and biogeography. It was established in 2008 and the founding editor-in-chief was Terry Erwin until his death in 2020. In December 2023, Torsten Dikow was appointed the new editor-in-chief. It is published by Pensoft Publishers.

Plazi is a Swiss-based international non-profit association supporting and promoting the development of persistent and openly accessible digital bio-taxonomic literature. Plazi is cofounder of the Biodiversity Literature Repository and is maintaining this digital taxonomic literature repository at Zenodo to provide access to FAIR data converted from taxonomic publications using the TreatmentBank service, enhances submitted taxonomic treatments by creating a version in the XML format Taxpub, and educates about the importance of maintaining open access to scientific discourse and data. It is a contributor to the evolving e-taxonomy in the field of Biodiversity Informatics.

<i>Gelasimus vocans</i> Species of fiddler crab

Gelasimus vocans is a species of fiddler crab. It is found across the Indo-Pacific from the Red Sea, Zanzibar and Madagascar to Indonesia and the central Pacific Ocean. It lives in burrows up to 50 centimetres (20 in) deep. Several forms of G. vocans have been recognised, with their authors often granting them the taxonomic rank of full species or subspecies.

<span class="mw-page-title-main">Journal Article Tag Suite</span>

The Journal Article Tag Suite (JATS) is an XML format used to describe scientific literature published online. It is a technical standard developed by the National Information Standards Organization (NISO) and approved by the American National Standards Institute with the code Z39.96-2012.

Pensoft Publishers are a publisher of scientific literature based in Sofia, Bulgaria. Pensoft was founded in 1992, by two academics: Lyubomir Penev and Sergei Golovatch. It has published over 1000 academic and professional books and currently publishes over 60 peer-reviewed open access scientific journals including ZooKeys, PhytoKeys, Check List, Comparative Cytogenetics, Journal of Hymenoptera Research, Deutsche Entomologische Zeitschrift, and Zoosystematics and Evolution.

The World Spider Catalog (WSC) is an online searchable database concerned with spider taxonomy. It aims to list all accepted families, genera and species, as well as provide access to the related taxonomic literature.

<i>Macleania insignis</i> Species of flowering plant

Macleania insignis, family Ericaceae is a member of the blueberry family—its most common ancestors in North America include blueberries and cranberries. The family Ericaceae is spread across the world, with a large concentration found in South America. This plant falls within the Neotropical subgroup and then Andean clade of this family. The Psammisia II section shares the closest common ancestor to this plant, and its closest split on a family tree is shared with Macleania coccoloboides and Macleania bullata. Phylogenic classification of M. insignis has primarily been carried out through an examination of morphological traits as well as genetic analysis. Macleania is an angiosperm eudicot, in the order of Ericales and the family Ericaceae.

<span class="mw-page-title-main">Gregor Hagedorn</span> German botanist (born 1965)

Gregor Hagedorn is a German botanist and academic director at the Natural History Museum, Berlin.

The Biodiversity Literature Repository (BLR) is a biodiversity dedicated community created in November 11, 2013, in Zenodo, the open science repository at CERN and part of the European project OpenAIRE. The goal of BLR is to provide a long-term, stable, open repository that allows deposition of bio-taxonomic articles enhanced with custom metadata and links to data extracted from therein and deposited in BLR. As of April 25, 2021, this includes 94,443 taxonomic treatments and 293,457 figures from 48,993 articles which are made findable, accessible, interoperable and reusable FAIR data. Most of the data is uploaded on a continuous basis by Plazi using its TreatmentBank service based on their Plazi workflow, and Pensoft Publishers using BLR as repository for data published in their journals. The largest single re-user of data is the Global Biodiversity Information Facility (GBIF), using data from within 33,623 processed articles.

References

  1. ↑ Catapano, Terry (2010). "TaxPub: An Extension of the NLM/NCBI Journal Publishing DTD for Taxonomic Descriptions". Proceedings of the Journal Article Tag Suite Conference 2010. 2010. doi: 10.5281/zenodo.3484285 .
  2. ↑ Linnaeus, Carolus (1753). Species plantarum: exhibentes plantas rite cognitas, ad genera relatas, cum differentiis specificis, nominibus trivialibus, synonymis selectis, locis natalibus, secundum systema sexuale. Stockholm: Laurentis Salvius. doi: 10.5281/zenodo.3931989 .
  3. ↑ Linnaeus, Carolus (1758). Systema Naturae per regna tria naturae: secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis. Stockholm: Laurentis Salvius. doi: 10.5962/bhl.title.542 .
  4. ↑ Catapano, Terry (2010). "TaxPub: An Extension of the NLM/NCBI Journal Publishing DTD for Taxonomic Descriptions". Proceedings of the Journal Article Tag Suite Conference 2010. 2010. doi: 10.5281/zenodo.3484285 .
  5. ↑ Penev, Lyubomir; Catapano, Terry; Agosti, Donat (2012). "Implementation of TaxPub, an NLM DTD extension for domain-specific markup in taxonomy, from the experience of a biodiversity publisher". Journal Article Tag Suite Conference (JATS-Con) Proceedings 2012. 2012. doi: 10.5281/zenodo.804247 .
  6. ↑ Patterson, David J.; Egloff, Willi; Agosti, Donat; Eades, D; Franz, Niko; Hagedorn, Gregor; Rees, J.; Remsen, David P. (2012). "Scientific names of organisms: attribution, rights, and licensing". BMC Research Notes. 7 (79): 79. doi: 10.1186/1756-0500-7-79 . PMC   3922623 . PMID   24495358.
  7. ↑ Catapano, Terry (2010). "TaxPub: An Extension of the NLM/NCBI Journal Publishing DTD for Taxonomic Descriptions". Proceedings of the Journal Article Tag Suite Conference 2010. 2010. doi: 10.5281/zenodo.3484285 .
  8. ↑ Moritz, Tom (2003). "Collaborative Research: Development of new digital library applications in the context of a basic ontology for biosystematics information using the literature of entomology (ants)". zenodo.org/communities/biosyslit/. doi:10.5281/zenodo.580296 . Retrieved 2020-02-09.
  9. ↑ Catapano, Terry. "Taxpub". Plazi. Retrieved 27 October 2009.
  10. ↑ Penev, Lyubomir; Roberts, Dave; Smith, Vince S.; Agosti, Donat; Erwin, Terry (2010). "Taxonomy shifts up a gear: New publishing tools to accelerate biodiversity research". ZooKeys (50): 1–4. doi: 10.3897/zookeys.50.543 .
  11. ↑ Kress, W.; Penev, Lyubomir (2011). "Innovative electronic publication in plant systematics: PhytoKeys and the changes to the "Botanical Code" accepted at the XVIII International Botanical Congress in Melbourne". PhytoKeys (6): 1–4. doi: 10.3897/phytokeys.6.2063 . PMC   3261036 . PMID   22287917.
  12. ↑ "About the Journal". europeanjournaloftaxonomy.eu. Retrieved 2021-04-26.
  13. ↑ Côtez, Emmanuel; Mabille, Anne; Chester, Chloé; Rocklin, Emmanuelle; Deroin, Thierry; Desutter-Grandcolas, Laure; Lesur, Joséphine; Merle, Didier; Robillard, Tony; Bénichou, Laurence (2018). "1802–2018 : 220 ans d'histoire des périodiques au Muséum". Adansonia. 40 (1): 1. doi: 10.5252/adansonia2018v40a1 .
  14. ↑ "TreatmentBank". plazi.org. Retrieved 2020-02-09.
  15. ↑ "Plazi: Treatments". plazi.org. Retrieved 2021-04-26.
  16. ↑ "New species in 2020 in Plazi TreatmentBank". tb.plazi.org/GgServer/srsStats. Retrieved 2021-04-26.
This page is based on this Wikipedia article
Text is available under the CC BY-SA 4.0 license; additional terms may apply.
Images, videos and audio are available under their respective licenses.