Taxonomic database
Encyclopedia
A taxonomic database is a database
created to hold information related to biological taxa
- for example groups of organisms organized by species name
or other taxonomic identifier - for efficient data management
and information retrieval
as required. Today, taxonomic databases are routinely used for the automated construction of biological checklists such as floras and faunas, 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 museums
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
.
, algae, bryophytes
and higher plants would need to encode conventions from the International Code of Botanical Nomenclature while their counterparts for animals
and most protists
would encode equivalent rules from the International Code of Zoological Nomenclature
; 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 additional 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.
(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
. 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, 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.
), 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 Taxonomic Database Working Group
.
Database
A database is an organized collection of data for one or more purposes, usually in digital form. The data are typically organized to model relevant aspects of reality , in a way that supports processes requiring this information...
created to hold information related to biological taxa
Taxon
|thumb|270px|[[African elephants]] form a widely-accepted taxon, the [[genus]] LoxodontaA taxon is a group of organisms, which a taxonomist adjudges to be a unit. Usually a taxon is given a name and a rank, although neither is a requirement...
- for example groups of organisms organized by species name
Species
In biology, a species is one of the basic units of biological classification and a taxonomic rank. A species is often defined as a group of organisms capable of interbreeding and producing fertile offspring. While in many cases this definition is adequate, more precise or differing measures are...
or other taxonomic identifier - for efficient data management
Data management
Data management comprises all the disciplines related to managing data as a valuable resource.- Overview :The official definition provided by DAMA International, the professional organization for those in the data management profession, is: "Data Resource Management is the development and execution...
and information retrieval
Information retrieval
Information retrieval is the area of study concerned with searching for documents, for information within documents, and for metadata about documents, as well as that of searching structured storage, relational databases, and the World Wide Web...
as required. Today, taxonomic databases are routinely used for the automated construction of biological checklists such as floras and faunas, 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 museums
Museum
A museum is an institution that cares for a collection of artifacts and other objects of scientific, artistic, cultural, or historical importance and makes them available for public viewing through exhibits that may be permanent or temporary. Most large museums are located in major cities...
and herbaria
Herbarium
In botany, a herbarium – sometimes known by the Anglicized term herbar – is a collection of preserved plant specimens. These specimens may be whole plants or plant parts: these will usually be in a dried form, mounted on a sheet, but depending upon the material may also be kept in...
); 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
Biodiversity Informatics is the application of informatics techniques to biodiversity information for improved management, presentation, discovery, exploration and analysis...
.
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 fungiFungus
A fungus is a member of a large 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, Fungi, which is separate from plants, animals, and bacteria...
, algae, bryophytes
Bryophyte
Bryophyte is a traditional name used to refer to all embryophytes that do not have true vascular tissue and are therefore called 'non-vascular plants'. Some bryophytes do have specialized tissues for the transport of water; however since these do not contain lignin, they are not considered to be...
and higher plants would need to encode conventions from the International Code of Botanical Nomenclature while their counterparts for animals
Animal
Animals are a major group of multicellular, eukaryotic organisms of the kingdom Animalia or Metazoa. Their body plan eventually becomes fixed as they develop, although some undergo a process of metamorphosis later on in their life. Most animals are motile, meaning they can move spontaneously and...
and most protists
Protist
Protists are a diverse group of eukaryotic microorganisms. Historically, protists were treated as the kingdom Protista, which includes mostly unicellular organisms that do not fit into the other kingdoms, but this group is contested in modern taxonomy...
would encode equivalent rules from the International Code of Zoological Nomenclature
International Code of Zoological Nomenclature
The International Code of Zoological Nomenclature is a widely accepted convention in zoology that rules the formal scientific naming of organisms treated as animals...
; in both cases modelling the relevant taxonomic hierarchy
Biological classification
Biological classification, or scientific classification in biology, is a method to group and categorize organisms by biological type, such as genus or species. Biological classification is part of scientific taxonomy....
for any taxon is a natural fit with the relational
Relational database
A relational database is a database that conforms to relational model theory. The software used in a relational database is called a relational database management system . Colloquial use of the term "relational database" may refer to the RDBMS software, or the relational database itself...
model employed in almost all database systems. In additional 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 SystemIntegrated Taxonomic Information System
The Integrated Taxonomic Information System is a partnership designed to provide consistent and reliable information on the taxonomy of biological species. ITIS was originally formed in 1996 as an interagency group within the U.S...
(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
Catalogue of Life
The Catalogue of Life, started in June 2001 by Species 2000 and Integrated Taxonomic Information System , is planned to become a comprehensive catalogue of all known species of organisms on Earth by the year 2011. 66 taxonomic databases with contributions from more than 3,000 specialists from...
. 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, 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), multiple non-current names for the same taxon (synonymsSynonym (taxonomy)
In scientific nomenclature, a synonym is a scientific name that is or was used for a taxon of organisms that also goes by a different scientific name. For example, Linnaeus was the first to give a scientific name to the Norway spruce, which he called Pinus abies...
), 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 Taxonomic Database Working Group
Taxonomic Database Working Group
"Biodiversity Information Standards " is a non profit scientific and educational association that is affiliated with the International Union of Biological Sciences...
.
See also
- List of biodiversity databases
- DatabaseDatabaseA database is an organized collection of data for one or more purposes, usually in digital form. The data are typically organized to model relevant aspects of reality , in a way that supports processes requiring this information...
- Biological classificationBiological classificationBiological classification, or scientific classification in biology, is a method to group and categorize organisms by biological type, such as genus or species. Biological classification is part of scientific taxonomy....
- Biodiversity informaticsBiodiversity InformaticsBiodiversity Informatics is the application of informatics techniques to biodiversity information for improved management, presentation, discovery, exploration and analysis...
- Taxonomic Database Working GroupTaxonomic Database Working Group"Biodiversity Information Standards " is a non profit scientific and educational association that is affiliated with the International Union of Biological Sciences...
- Integrated Taxonomic Information SystemIntegrated Taxonomic Information SystemThe Integrated Taxonomic Information System is a partnership designed to provide consistent and reliable information on the taxonomy of biological species. ITIS was originally formed in 1996 as an interagency group within the U.S...
- Catalogue of LifeCatalogue of LifeThe Catalogue of Life, started in June 2001 by Species 2000 and Integrated Taxonomic Information System , is planned to become a comprehensive catalogue of all known species of organisms on Earth by the year 2011. 66 taxonomic databases with contributions from more than 3,000 specialists from...
- A Pan-European Species-directories Infrastructure (PESI)