Taxonomic treatment

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]

Taxonomic treatment of Apis mellifera, Linnaeus 1758

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.

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.
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