A taxonomic database is a

database In computing, a database is an organized collection of data stored and accessed electronically. Small databases can be stored on a file system, while large databases are hosted on computer clusters or cloud storage. The design of databases ...

created to hold information on biological

taxa In biology, a taxon (back-formation from ''taxonomy''; plural taxa) is a group of one or more populations of an organism or organisms seen by taxonomists to form a unit. Although neither is required, a taxon is usually known by a particular nam ...

– for example groups of organisms organized by

species name In taxonomy, binomial nomenclature ("two-term naming system"), also called nomenclature ("two-name naming system") or binary nomenclature, is a formal system of naming species of living things by giving each a name composed of two parts, bot ...

or other taxonomic identifier – for efficient

data management Data management comprises all disciplines related to handling data as a valuable resource. Concept The concept of data management arose in the 1980s as technology moved from sequential processing (first punched cards, then magnetic tape) to ...

and

information retrieval Information retrieval (IR) in computing and information science is the process of obtaining information system resources that are relevant to an information need from a collection of those resources. Searches can be based on full-text or other c ...

. Taxonomic databases are routinely used for the automated construction of biological checklists such as

floras Flora is all the plant life present in a particular region or time, generally the naturally occurring ( indigenous) native plants. Sometimes bacteria and fungi are also referred to as flora, as in the terms ''gut flora'' or ''skin flora''. Et ...

and

faunas Fauna is all of the animal life present in a particular region or time. The corresponding term for plants is ''flora'', and for fungi, it is ''funga''. Flora, fauna, funga and other forms of life are collectively referred to as '' biota''. Z ...

, both for print publication and online; to underpin the operation of web-based species information systems; as a part of biological collection management (for example in

museum A museum ( ; plural museums or, rarely, musea) is a building or institution that cares for and displays a collection of artifacts and other objects of artistic, cultural, historical, or scientific importance. Many public museums make th ...

s and herbaria); as well as providing, in some cases, the taxon management component of broader science or biology information systems. They are also a fundamental contribution to the discipline of

biodiversity informatics Biodiversity informatics is the application of informatics techniques to biodiversity information, such as taxonomy, biogeography or ecology. Modern computer techniques can yield new ways to view and analyze existing information, as well as predict ...

Goal

The goal of a taxonomic database is (or should be) to accurately model the characteristics of interest that are relevant to the organisms which are in scope for the intended coverage and usage of the system. For example, databases of

fungi A fungus ( : fungi or funguses) is any member of the group of eukaryotic organisms that includes microorganisms such as yeasts and molds, as well as the more familiar mushrooms. These organisms are classified as a kingdom, separately fr ...

alga Algae (; singular alga ) is an informal term for a large and diverse group of photosynthetic eukaryotic organisms. It is a polyphyletic grouping that includes species from multiple distinct clades. Included organisms range from unicellular mic ...

bryophyte The Bryophyta s.l. are a proposed taxonomic division containing three groups of non-vascular land plants (embryophytes): the liverworts, hornworts and mosses. Bryophyta s.s. consists of the mosses only. They are characteristically limited in s ...

s and higher plants would need to encode conventions from the

International Code of Botanical Nomenclature The ''International Code of Nomenclature for algae, fungi, and plants'' (ICN) is the set of rules and recommendations dealing with the formal botanical names that are given to plants, fungi and a few other groups of organisms, all those "trad ...

while their counterparts for

animal Animals are multicellular, eukaryotic organisms in the biological kingdom Animalia. With few exceptions, animals consume organic material, breathe oxygen, are able to move, can reproduce sexually, and go through an ontogenetic stage ...

s and most

protist A protist () is any eukaryotic organism (that is, an organism whose cells contain a cell nucleus) that is not an animal, plant, or fungus. While it is likely that protists share a common ancestor (the last eukaryotic common ancestor), the e ...

s would encode equivalent rules from the

International Code of Zoological Nomenclature The International Code of Zoological Nomenclature (ICZN) is a widely accepted convention in zoology that rules the formal scientific naming of organisms treated as animals. It is also informally known as the ICZN Code, for its publisher, the I ...

; in both cases modelling the relevant taxonomic hierarchy for any taxon is a natural fit with the relational model employed in almost all database systems. In addition to encoding organism identifiers (most frequently a combination of scientific name, author, and – for zoological taxa – year of original publication), a taxonomic database may frequently incorporate additional taxonomic information such as synonyms and taxonomic opinions, literature sources or citations, plus a range of biological of attributes as desired for each taxon such as geographic distribution, ecology, descriptive information, threatened or vulnerable status, etc.

History

Possibly the earliest documented management of taxonomic information in computerised form comprised the taxonomic coding system developed by Richard Swartz et al. at the Virginia Institute of Marine Science for the Biota of Chesapeake Bay and described in a published report in 1972. This work led directly or indirectly to other projects with greater profile including the NODC Taxonomic Code system which went through 8 versions before being discontinued in 1996, to be subsumed and transformed into the still current

Integrated Taxonomic Information System The Integrated Taxonomic Information System (ITIS) is an American partnership of federal agencies designed to provide consistent and reliable information on the taxonomy of biological species. ITIS was originally formed in 1996 as an interagen ...

(ITIS). A number of other taxonomic databases specializing in particular groups of organisms that appeared in the 1970s through to the present jointly contribute to the Species 2000 project, which since 2001 has been partnering with ITIS to produce a combined product, the

Catalogue of Life The Catalogue of Life is an online database that provides an index of known species of animals, plants, fungi, and microorganisms. It was created in 2001 as a partnership between the global Species 2000 and the American Integrated Taxonomic In ...

. While the Catalogue of Life currently concentrates on assembling basic name information as a global species checklist, numerous other taxonomic database projects such as

Fauna Europaea Fauna Europaea is a database of the scientific names and distribution of all living multicellular European land and fresh-water animals. It serves as a standard taxonomic source for animal taxonomy within the Pan-European Species directories Infr ...

, the Australian Faunal Directory, and more supply rich ancillary information including descriptions, illustrations, maps, and more. Many taxonomic database projects are currently listed at the TDWG "Biodiversity Information Projects of the World" site.

Issues

The representation of taxonomic information in machine-encodable form raises a number of issues not encountered in other domains, such as variant ways to cite the same species or other taxon name, the same name used for multiple taxa (

homonyms In linguistics, homonyms are words which are homographs (words that share the same spelling, regardless of pronunciation), or homophones ( equivocal words, that share the same pronunciation, regardless of spelling), or both. Using this definition ...

), multiple non-current names for the same taxon (

synonyms A synonym is a word, morpheme, or phrase that means exactly or nearly the same as another word, morpheme, or phrase in a given language. For example, in the English language, the words ''begin'', ''start'', ''commence'', and ''initiate'' are ...

), changes in name and taxon concept definition through time, and more. One forum that has promoted discussion and possible solutions to these and related problems since 1985 is the Biodiversity Information Standards (TDWG), originally called the Taxonomic Database Working Group.

References

{{reflist * Catalogues Information science

Database In computing, a database is an organized collection of data stored and accessed electronically. Small databases can be stored on a file system, while large databases are hosted on computer clusters or cloud storage. The design of databases ...

Goal

History

Issues

See also

References