Introduction to taxonomic concepts
Treatment: The taxonomic treatment is a well-defined part of a scientific publication documenting the features of a particular taxon, including a diagnosis of the taxon, a reference to previous work, an extended description, notes on the distribution and habitat, citation of material, and general comments about the taxon.
Species: There are several different definitions of species. In the taxonomic context, a species is the most basic unit of classification and taxonomic rank of a biological organism, grouped based on their shared characteristics.
Specimen: A gathering, or part of a gathering, of a single species or infraspecific taxon, disregarding admixtures, mounted either as a single preparation or as more than one preparation with the parts clearly labeled as being part of the same specimen or bearing a single, original label in common. A specimen may not be a living organism or an active culture.
Material citation: A citation of a testimony material (specimen) that was collected, deposited in a scientific collection, and linked to a given treatment. The material citation is used to testify to the presence of that taxon in that location and to enable the verification of the morphological, ecological, and biological features of the same specimen.
Protologue: the original description of the taxon, which brings everything associated with a name to its valid publication, e.g. description, diagnosis, illustrations, references, synonymy, geographical data, citation of specimens, discussion, and comments.
Original material: comprises the following elements:
(a) those specimens and illustrations (both unpublished and published before the publication of the protologue) that the author associated with the taxon, and that were available to the author before, or at the time of, preparation of the description, diagnosis, or illustration with analysis validating the name;
(b) any illustration published as part of the protologue;
(c) the holotype (see Glossary) and those specimens which, even if not seen by the author of the description or diagnosis validating the name, were indicated as types (syntypes or paratypes, see Glossary) of the name at its valid publication;
(d) the isotypes or isosyntypes (see Glossary) of the name irrespective of whether such specimens were seen by either the author of the validating description or diagnosis or the author of the name.
The original material forms the set of specimens and illustrations from which a lectotype may be chosen.
Types: the application of scientific names at the rank of family or below is determined using nomenclatural types. A nomenclatural type is that element (usually a collected specimen, but sometimes an illustration) to which the name of a taxon is permanently attached, whether as a valid name or as a synonym. A nomenclatural type is considered original material because it represents the author’s concepts regarding the scientific name proposed and was most likely cited in the protologue. The main types are holotype, isotype, syntype, paratype, lectotype, neotype, and type.
Here you can get a detailed presentation on Basic Concepts and Definitions.
TreatmentBank
TreatmentBank is a service provided by Swiss Plazi GmbH. Its primary purpose is to liberate data from scholarly publications and convert it into a format that is findable, accessible, interoperable, and reusable (FAIR). This includes various data types such as taxonomic treatments, treatment citations, figures, tables, material citations, and bibliographic information.
The Plazi TreatmentBank focuses on scientific, published, biosystematic literature, particularly documenting and describing the world's approximately 1.9 million known species, which are covered in an estimated corpus of over 500 million published pages. All the cited publications within Plazi are accessible at the Biodiversity Literature Repository at Zenodo/CERN.
TreatmentBank also serves as a European Research Infrastructure, where it annotates taxonomic publications. This process includes quality control, which is done as much as possible through automated means and, when necessary, through human curation.
The service is designed to extract and manage data from publications. It offers several functionalities:
Data Liberation and Management: TreatmentBank liberates data from scholarly publications, converting, enhancing, linking, storing, and disseminating it as Findable, Accessible, Interoperable, and Reusable (FAIR) data. This includes taxonomic treatments, citations, figures, tables, material citations, and bibliographic references. The process can be highly automated, and suitable for processing both historical journal back-issues and current publications. A combination of automated processes and manual checks ensures the quality of the data.
Search Capabilities: Users can search TreatmentBank using a full-text search or an extended search. The extended search provides more precision, allowing users to find information related to specific taxonomic names, bibliographic records, or observation records.
GoldenGATE Document Editor: This is a visual editor for marking up documents in XML format, designed to automate most of the markup process. This tool is likely integral to the data extraction and management process within TreatmentBank.
These features collectively enable TreatmentBank to serve as a comprehensive tool for managing and accessing data derived from a wide range of taxonomic and biodiversity-related scholarly publications.
VIDEO Tutorials
Plazi also has tutorials as screencasts posted on YouTube:
Last modified: Sunday, 19 November 2023, 10:47 PM