List of biodiversity databases

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This is a list of biodiversity databases. Biodiversity databases store taxonomic information alone or more commonly also other information like distribution (spatial) data and ecological data, which provide information on the biodiversity of a particular area or group of living organisms. They may store specimen-level information, species-level information, information on nomenclature, or any combination of the above. Most are available online.

Contents

Specimen-focused databases contain data about individual specimens, as represented by vouchered museum specimens, collections of specimen photographs, data on field-based specimen observations and morphological or genetic data. Species-focused databases contain information summarised at the species-level. Some species-focused databases attempt to compile comprehensive data about particular species (FishBase), while others focus on particular species attributes, such as checklists of species in a given area (FEOW) or the conservation status of species (CITES or IUCN Red List). Nomenclators act as summaries of taxonomic revisions and set a key between specimen-focused and species-focused databases. They do this because taxonomic revisions use specimen data to determine species limits.

NameFocusGroups includedCollection
Plants Birds Reptiles Fish Arthro­pods Other Euk. Prok. & Vir.
All Catfish Species Inventory  [1] Catfish Xinformation collated by genera, including estimated numbers of species, taxonomic experts
Arctos  [2] Specimen holdings of several natural history museums, agencies, and accessible private collectionsXXXXXXVertebrates, invertebrates, parasites, vascular and non-vascular plants, many with images and extensive usage data.
AntWeb  [3] Ants XSpecimen information, collection details, photographs, higher taxonomy
Avibase – the World Bird Database  [4] Birds, distribution, taxonomyXAvibase is an extensive database information system about all birds of the world, containing over 27 million records about 10,000 species and 22,000 subspecies of birds, including distribution information for 20,000 regions, taxonomy, synonyms in several languages and more.
ASEAN Biodiversity Information Sharing Service (BISS)  [5] Amphibians, birds, butterflies, dragonflies, edible plants, freshwater fishes, mammals, plants, reptiles and Malesian mosses of Southeast Asia XXXXXXIUCN status, habitat, regional presence/absence, description, classification
BioLib – Biological Library   [6] BioLib is an international encyclopedia of plants, fungi and animals.XXXXXXApart from taxonomic system you can visit the gallery, glossary, vernacular names dictionary, database of links and literature, systems of biotopes, discussion forum and several other functions related to biology.
CITES species database  [7] All species ever listed in CITES Appendices I, II or IIIXXXXXXScientific names, higher taxonomy, distribution, photos and CITES quotas
Fauna Europaea  [8] Europe's main zoological taxonomic indexXXXXQuality-checked data, 180,712 accepted taxon names, web portal also provide links to other key biodiversity services.
FishBase   [9] Fish XHigher taxonomy, common names, distribution, IUCN Redlist status
Fulgoromorpha Lists On the Web (FLOW)  [10] Planthoppers (Insecta: Hemiptera: Fulgoromorpha) – 15.000 speciesXTaxonomy and classification, nomenclature, type depository, bibliography, distribution, photos on actual and fossil planthoppers of the world and various associated biological information (host-plants, parasites, trophobiosis, etc.).
Freshwater Ecoregions of the World (FEOW)  [11] Freshwater ecoregionsXXXXXXXMaps of species and endemic numbers.
HerpNET  [12] Amphibians and reptiles XAmphibian and reptile distributions.
A Database of Plant Biodiversity of West Bengal (WBPBDIVDB)Plants of West Bengal Xrichness of floral diversity of West Bengal from Terai, Duars, Darjeeling, the eastern Himalayan region and in the mangrove forests of Sundarbans.
Reptile Database Reptiles XTaxonomic information, names, photos
iNaturalist All forms of lifeXXXXXXGeolocated observations, location checklists, taxonomic information, range maps
Integrated Botanical Information System (IBIS)  [13] Plants of Australia XTaxonomic information, collection details, photographs
iSpot All forms of life large enough to photographXxXXXXGeolocated individual observations and other information produced by citizen science participants
Integrated Taxonomic Information System (ITIS)  [14] all taxa of interest to North America, with other taxa included as availableXxXXXXTaxonomic information, including higher taxonomy
Natural History Information System [15] all forms of life, biotopes, rocksXxXXXXXFaunistic and floristic records (citizen science and other sources), phenology, ecology, biotopes, taxonomy, paleontology, stratigraphy
NatureServe   [16] plants, animals, and ecosystems of the United States and CanadaXxXXXXSource for information on more than 70,000 plants, animals, and ecosystems of the United States and Canada, including rare and endangered species.
Pl@ntNet Plants identification, observation, imagesXPlant identification, observations, citizen science project, photographs, distribution
Wikispecies   [17] All forms of lifeXxXXXXXHigher taxonomy, synonyms, vernacular names, references
A Pan-European Species-directories Infrastructure (PESI)  [18] European taxaXxXXXXAuthoritative taxonomic checklist of European species, including higher taxonomy, synonyms, vernacular names and European distribution
Naturdata  [19] Portuguese taxaXxXXXXChecklist of Portuguese species including mainland and islands with a page for each species including taxonomy, synonyms, vernacular names, images, videos and Portuguese distribution
Georgia (country) biodiversity website [20] Georgia Biodiversity DatabaseXxXXXXChecklists covering ca. 11,000 of plants and animals recorded for Georgia (Central and Western Caucasus)
ScaleNet [21] Scale insects (superfamily Coccoidea)XNomenclature, distribution, hosts, systematics, references
BacDive Metadatabase that provides strain-linked information about bacterial and archaeal biodiversity.XDifferent kind of metadata like taxonomy, morphology, physiology, environment and molecular-biology.
World Register of Marine Species Marine organismsXXXHigher taxonomy, scientific names, synonyms, distribution, attributes, references
AlgaeBase Algae and other oxygenic photosynthesisers other than embryophyte land plantsXXXHigher taxonomy, scientific names, common names, images, distribution, references
Tropicos [22] Taxonomy, distribution, and specimen data for Missouri Botanical Garden.XNearly 1.3 million scientific names and over 4.4 million specimen records, accumulated during the past 30 years.
iAMF [23] [24] Arbuscular Mycorrhizal Fungi Database for Phylogeny, Nomenclature, Taxonomy and Distribution in IndiaXXDistribution, phylogeny and taxonomy database of arbuscular mycorrhizal fungi was built in two phases: In the first phase of the study (2013–2015) occurrence of about 148 species of AM fungi was reported across 18 states of India namely: Andhra Pradesh, Assam, Bihar, Goa, Haryana, Jammu and Kashmir, Karnataka, Kerala, Madhya Pradesh, Maharashtra, Meghalaya, Orissa, Punjab, Rajasthan, Tamil Nadu, Uttarkhand, Uttar Pradesh and West Bengal (Gupta et al. 2014, under Delhi University innovation project) . In the second phase under UGC project (2015 onwards) the study has been extended to three more states namely Delhi, Tripura and Manipur reporting occurrence of 161 species. rRNA sequence data for these fungi is added as Phylogenetic Map and distribution data is available as Google Map.

See also

Related Research Articles

<span class="mw-page-title-main">Royal Botanic Gardens, Kew</span> Government botanical research institute in the UK

Royal Botanic Gardens, Kew is a non-departmental public body in the United Kingdom sponsored by the Department for Environment, Food and Rural Affairs. An internationally important botanical research and education institution, it employs 1,100 staff. Its board of trustees is chaired by Dame Amelia Fawcett.

<span class="mw-page-title-main">Mycorrhiza</span> Fungus-plant symbiotic association

A mycorrhiza is a symbiotic association between a fungus and a plant. The term mycorrhiza refers to the role of the fungus in the plant's rhizosphere, its root system. Mycorrhizae play important roles in plant nutrition, soil biology, and soil chemistry.

<span class="mw-page-title-main">FishBase</span> Biological database about fish

FishBase is a global species database of fish species. It is the largest and most extensively accessed online database on adult finfish on the web. Over time it has "evolved into a dynamic and versatile ecological tool" that is widely cited in scholarly publications.

<span class="mw-page-title-main">Biological database</span>

Biological databases are libraries of biological sciences, collected from scientific experiments, published literature, high-throughput experiment technology, and computational analysis. They contain information from research areas including genomics, proteomics, metabolomics, microarray gene expression, and phylogenetics. Information contained in biological databases includes gene function, structure, localization, clinical effects of mutations as well as similarities of biological sequences and structures.

<span class="mw-page-title-main">Integrated Taxonomic Information System</span> Authoritative taxonomic information on plants, animals, fungi, and microbes

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 interagency group within the US federal government, involving several US federal agencies, and has now become an international body, with Canadian and Mexican government agencies participating. The database draws from a large community of taxonomic experts. Primary content staff are housed at the Smithsonian National Museum of Natural History and IT services are provided by a US Geological Survey facility in Denver. The primary focus of ITIS is North American species, but many biological groups exist worldwide and ITIS collaborates with other agencies to increase its global coverage.

<span class="mw-page-title-main">Glomeromycota</span> Phylum of fungi

Glomeromycota are one of eight currently recognized divisions within the kingdom Fungi, with approximately 230 described species. Members of the Glomeromycota form arbuscular mycorrhizas (AMs) with the thalli of bryophytes and the roots of vascular land plants. Not all species have been shown to form AMs, and one, Geosiphon pyriformis, is known not to do so. Instead, it forms an endocytobiotic association with Nostoc cyanobacteria. The majority of evidence shows that the Glomeromycota are dependent on land plants for carbon and energy, but there is recent circumstantial evidence that some species may be able to lead an independent existence. The arbuscular mycorrhizal species are terrestrial and widely distributed in soils worldwide where they form symbioses with the roots of the majority of plant species (>80%). They can also be found in wetlands, including salt-marshes, and associated with epiphytic plants.

Biodiversity informatics is the application of informatics techniques to biodiversity information, such as taxonomy, biogeography or ecology. It is defined as the application of Information technology technologies to management, algorithmic exploration, analysis and interpretation of primary data regarding life, particularly at the species level organization. Modern computer techniques can yield new ways to view and analyze existing information, as well as predict future situations. Biodiversity informatics is a term that was only coined around 1992 but with rapidly increasing data sets has become useful in numerous studies and applications, such as the construction of taxonomic databases or geographic information systems. Biodiversity informatics contrasts with "bioinformatics", which is often used synonymously with the computerized handling of data in the specialized area of molecular biology.

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 Information System. The Catalogue is used by research scientists, citizen scientists, educators, and policy makers. The Catalogue is also used by the Biodiversity Heritage Library, the Barcode of Life Data System, Encyclopedia of Life, and the Global Biodiversity Information Facility. The Catalogue currently compiles data from 165 peer-reviewed taxonomic databases that are maintained by specialist institutions around the world. As of September 2022, the COL Checklist lists 2,067,951 of the world's 2.2m extant species known to taxonomists on the planet at present time.

<i>Encyclopedia of Life</i> Free, online collaborative encyclopedia that documents species

The Encyclopedia of Life (EOL) is a free, online encyclopedia intended to document all of the 1.9 million living species known to science. It aggregates content to form "page"s for every known species. Content is compiled from existing trusted databases which are curated by experts and it calls on the assistance of non-experts throughout the world. It includes video, sound, images, graphics, information on characteristics, as well as text. In addition, the Encyclopedia incorporates species-related content from the Biodiversity Heritage Library, which digitizes millions of pages of printed literature from the world's major natural history libraries. The BHL digital content is indexed with the names of organisms using taxonomic indexing software developed by the Global Names project. The EOL project was initially backed by a US$50 million funding commitment, led by the MacArthur Foundation and the Sloan Foundation, who provided US$20 million and US$5 million, respectively. The additional US$25 million came from five cornerstone institutions—the Field Museum, Harvard University, the Marine Biological Laboratory, the Missouri Botanical Garden, and the Smithsonian Institution. The project was initially led by Jim Edwards and the development team by David Patterson. Today, participating institutions and individual donors continue to support EOL through financial contributions.

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 Infrastructure (PESI). As of June 2020, Fauna Europaea reported that their database contained 235,708 taxon names and 173,654 species names.

<i>Lygodium microphyllum</i> Species of fern

Lygodium microphyllum is a climbing fern originating in tropical Africa, Southeast Asia, Melanesia and Australia. It is an invasive weed in Florida where it invades open forest and wetland areas. The type specimen was collected in the vicinity of Nabúa, on the island of Luzon in the Philippines by Luis Née.

A taxonomic database is a database created to hold information on biological taxa – for example groups of organisms organized by species name or other taxonomic identifier – for efficient data management and information retrieval. 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 ; 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.

The Reptile Database is a scientific database that collects taxonomic information on all living reptile species. The database focuses on species and has entries for all currently recognized ~13,000 species and their subspecies, although there is usually a lag time of up to a few months before newly described species become available online. The database collects scientific and common names, synonyms, literature references, distribution information, type information, etymology, and other taxonomically relevant information.

Tropicos is an online botanical database containing taxonomic information on plants, mainly from the Neotropical realm. It is maintained by the Missouri Botanical Garden and was established over 25 years ago. The database contains images and taxonomical and bibliographical data on more than 4.2 million herbarium specimens. In addition, it contains data on over 49,000 scientific publications. The database can be queried in English, French, and Spanish. The oldest records in the database go back to 1703.

Catalog of Fishes is a comprehensive on-line database and reference work on the scientific names of fish species and genera. It is global in its scope and is hosted by the California Academy of Sciences. It has been compiled and is continuously updated by the curator emeritus of the CAS fish collection, William N. Eschmeyer.

Yolande Dalpé is a former Research Scientist with Agriculture and Agri-Food Canada. She became the first mycologist in Ottawa to study the taxonomy of mycorrhizal fungi. Her research focuses on developing new information on taxonomy, phylogeny, distribution and biology of fungi, including systematic research related to biosecurity/alien invasive species as well as species involved in the development of bioproducts. She was awarded the Lawson Medal by the Canadian Botanical Association for her "cumulative, lifetime contributions to Canadian botany, for the research she has performed in mycology, and has been recognized nationally and internationally." The standard author abbreviation Dalpé is used to indicate this person as the author when citing a botanical name.

<span class="mw-page-title-main">Interim Register of Marine and Nonmarine Genera</span> Taxonomic database

The Interim Register of Marine and Nonmarine Genera (IRMNG) is a taxonomic database which attempts to cover published genus names for all domains of life, from 1758 in zoology up to the present, arranged in a single, internally consistent taxonomic hierarchy, for the benefit of Biodiversity Informatics initiatives plus general users of biodiversity (taxonomic) information. In addition to containing just over 500,000 published genus name instances as at May 2023, the database holds over 1.7 million species names, although this component of the data is not maintained in as current or complete state as the genus-level holdings. IRMNG can be queried online for access to the latest version of the dataset and is also made available as periodic snapshots or data dumps for import/upload into other systems as desired. The database was commenced in 2006 at the then CSIRO Division of Marine and Atmospheric Research in Australia and, since 2016, has been hosted at the Flanders Marine Institute (VLIZ) in Belgium.

<span class="mw-page-title-main">Fish DNA barcoding</span>

DNA barcoding methods for fish are used to identify groups of fish based on DNA sequences within selected regions of a genome. These methods can be used to study fish, as genetic material, in the form of environmental DNA (eDNA) or cells, is freely diffused in the water. This allows researchers to identify which species are present in a body of water by collecting a water sample, extracting DNA from the sample and isolating DNA sequences that are specific for the species of interest. Barcoding methods can also be used for biomonitoring and food safety validation, animal diet assessment, assessment of food webs and species distribution, and for detection of invasive species.

<span class="mw-page-title-main">Ocean Biodiversity Information System</span> Online marine biology database

The Ocean Biodiversity Information System (OBIS), formerly Ocean Biogeographic Information System, is a web-based access point to information about the distribution and abundance of living species in the ocean. It was developed as the information management component of the ten year Census of Marine Life (CoML) (2001-2010), but is not limited to CoML-derived data, and aims to provide an integrated view of all marine biodiversity data that may be made available to it on an open access basis by respective data custodians. According to its web site as at July 2018, OBIS "is a global open-access data and information clearing-house on marine biodiversity for science, conservation and sustainable development." 8 specific objectives are listed in the OBIS site, of which the leading item is to "Provide [the] world's largest scientific knowledge base on the diversity, distribution and abundance of all marine organisms in an integrated and standardized format".

The International Collection of (Vesicular) Arbuscular Mycorrhizal Fungi (INVAM) is the largest collection of living arbuscular mycorrhizal fungi (AMF) and includes Glomeromycotan species from 6 continents. Curators of INVAM acquire, grow, identify, and elucidate the biology, taxonomy, and ecology of a diversity AMF with the mission to expand availability and knowledge of these symbiotic fungi. Culturing AMF presents difficulty as these fungi are obligate biotrophs that must complete their life cycle while in association with their plant hosts, while resting spores outside of the host are vulnerable to predation and degradation. Curators of INVAM have thus developed methods to overcome these challenges to increase the availability of AMF spores. The inception of this living collection of germplasm occurred in the 1980s and it takes the form of fungi growing in association with plant symbionts in the greenhouse, with spores preserved in cold storage within their associated rhizosphere. AMF spores acquired from INVAM have been used extensively in both basic and applied research projects in the fields of ecology, evolutionary biology, agroecology, and in restoration. INVAM is umbrellaed under the Kansas Biological Survey at The University of Kansas, an R1 Research Institution. The Kansas Biological Survey is also home to the well-known organization Monarch Watch. INVAM is currently located within the tallgrass prairie ecoregion, and many collaborators and researchers associated with INVAM study the role of AMF in the mediation of prairie biodiversity. James Bever and Peggy Schultz are the Curator and Director of Operation team, with Elizabeth Koziol and Terra Lubin as Associate Curators.

References

  1. ↑ "All Catfish Species Inventory" . Retrieved 4 June 2010.
  2. ↑ "Arctos". Archived from the original on 4 May 2017. Retrieved 9 June 2011.
  3. ↑ "AntWeb". Archived from the original on 27 October 2014. Retrieved 4 June 2010.
  4. ↑ "Avibase – the World Bird Database". Archived from the original on 19 January 2022. Retrieved 9 March 2019.
  5. ↑ "ASEAN Biodiversity Information Sharing Service". Archived from the original on 6 June 2024. Retrieved 4 June 2010.
  6. ↑ "BioLib – Biological Library – Home". January 1997. Archived from the original on 27 February 2021. Retrieved 1 April 2019.
  7. ↑ "CITES-listed species database". Archived from the original on 9 January 2014. Retrieved 4 June 2010.
  8. ↑ "Fauna Europaea – All Europaean Animal Species Online". Archived from the original on 4 May 2022. Retrieved 4 June 2010.
  9. ↑ "FishBase : A Global Information System on Fishes". Archived from the original on 17 October 2017. Retrieved 4 June 2010.
  10. ↑ "FLOW: Fulgoromorpha Lists on The Web". Archived from the original on 4 October 2017. Retrieved 1 January 2018.
  11. ↑ "Freshwater Ecoregions of the World". Archived from the original on 19 March 2018. Retrieved 4 June 2010.
  12. ↑ "HerpNET". Archived from the original on 10 May 2020. Retrieved 4 June 2010.
  13. ↑ "Integrated Biodiversity Information System". Archived from the original on 4 March 2016. Retrieved 2 April 2015.
  14. ↑ "Integrated Taxonomic Information System". Archived from the original on 10 June 2013. Retrieved 4 June 2010.
  15. ↑ "Natural History Information System". Archived from the original on 7 January 2014. Retrieved 22 January 2014.
  16. ↑ "NatureServe Explorer: An online encyclopedia of life". Archived from the original on 15 March 2006. Retrieved 4 June 2010.
  17. ↑ "Wikispecies, free species directory". Archived from the original on 4 December 2012. Retrieved 5 June 2010.
  18. ↑ "A Pan-European Species-directories Infrastructure (PESI)". Archived from the original on 29 May 2020. Retrieved 3 January 2011.
  19. ↑ "Naturdata – Biodiversidade online". Archived from the original on 1 January 2012. Retrieved 13 December 2011.
  20. ↑ "Georgian Biodiversity database". www.biodiversity-georgia.net. Archived from the original on 17 September 2020. Retrieved 13 June 2022.
  21. ↑ "ScaleNet: Scale insect web catalog". Archived from the original on 7 January 2014. Retrieved 3 June 2014.
  22. ↑ "Tropicos". www.tropicos.org. Archived from the original on 17 June 2022. Retrieved 13 June 2022.
  23. ↑ "Gupta, M., Naqvi, N., Kumar, P. (2017). i AMF – Centralized database of arbuscular mycorrhizal distribution, phylogeny and taxonomy. Journal of Recent Advances in Applied Sciences, 30 (1). 1 - 5 < http://www.jraas.org/ >". Archived from the original on 6 June 2024. Retrieved 16 August 2020.{{cite web}}: External link in |title= (help)
  24. ↑ "The state of arbuscular mycorrhizal fungal diversity in India: An analysis | Request PDF". Archived from the original on 6 June 2024. Retrieved 16 August 2020.
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