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The GBIF Backbone Taxonomy is a single, synthetic management classification with the goal of covering all names GBIF is dealing with. It's the taxonomic backbone that allows GBIF to integrate name based information from different resources, no matter if these are occurrence datasets, species pages, names from nomenclators or external sources like EOL, Genbank or IUCN. This backbone allows taxonomic search, browse and reporting operations across all those resources in a consistent way and to provide means to crosswalk names from one source to another.
It is updated regulary through an automated process in which the Catalogue of Life acts as a starting point also providing the complete higher classification above families. Additional scientific names only found in other authoritative nomenclatural and taxonomic datasets are then merged into the tree, thus extending the original catalogue and broadening the backbones name coverage. The GBIF Backbone taxonomy also includes identifiers for Operational Taxonomic Units (OTUs) drawn from the barcoding resources iBOL and UNITE.
International Barcode of Life project (iBOL), Barcode Index Numbers (BINs). BINs are connected to a taxon name and its classification by taking into account all names applied to the BIN and picking names with at least 80% consensus. If there is no consensus of name at the species level, the selection process is repeated moving up the major Linnaean ranks until consensus is achieved.
UNITE - Unified system for the DNA based fungal species, Species Hypotheses (SHs). SHs are connected to a taxon name and its classification based on the determination of the RefS (reference sequence) if present or the RepS (representative sequence). In the latter case, if there is no match in the UNITE taxonomy, the lowest rank with 100% consensus within the SH will be used.
The GBIF Backbone Taxonomy is available for download at https://hosted-datasets.gbif.org/datasets/backbone/ in different formats together with an archive of all previous versions.
The following 105 sources have been used to assemble the GBIF backbone with number of names given in brackets:
The Global Invasive Species Database is a free, online searchable source of information about species that negatively impact biodiversity. The GISD aims to increase public awareness about invasive species and to facilitate effective prevention and management activities by disseminating specialist’s knowledge and experience to a broad global audience. It focuses on invasive alien species that threaten native biodiversity and covers all taxonomic groups from micro-organisms to animals and plants.
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The UF Fish Collection, dating to 1917, contains 214,205 lots and 2,300,803 specimens. Included are representatives of 8,250 species from 400 families. The collection includes 93 primary types and approximately 1,600 lots of secondary types representing 563 species. Also in the collection are 5,825 specimens of disarticulated and articulated skeletons representing 875 species. Especially notable are historic collections of large and important marine fishes as well as rapidly growing collections of freshwater fishes from Southeast Asia. In 2006, the museum expanded its program to archive frozen tissue samples with a newly established UF Genetic Resources Collection. Tissues of fishes are stored in -20ºC freezers and number 4,150 samples of 900 species. All specimens and tissues are databased online and available for loan.
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Observations from minka-sdg.org, MINKA Citizen Science Observatory is a community-based platform dedicated to biodiveristy and environmental data collection, utilising geolocalized images and observations uploaded by citizens through a mobile app and website. The dataset is produced by the BioPlatgesMet project, nested within MINKA, focuses on documenting and monitoring biodiversity in Barcelona's urban beach areas. This project highlights the dynamic dune ecosystems and engages the local community, naturalists, students, and enthusiasts in data collection. MINKA is a platform coordinated by the ICM-CSIC and the project BioPlatgesMet by AMB in Barcelona.
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The herbarium of the Academy of Natural Sciences (PH) is the oldest institutional herbarium in the United States. It is a national resource for material from 1750-1850. The diatom herbarium (ANSP) is managed separately.
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This dataset contains occurrence data of flora and fauna species. From the Netherlands on a 5 x 5 km scale, data from other countries are exact. Observations from Belgium are excluded and can be accessed on GBIF through Natuurpunt and Natagora. It summarizes the observations recorded by >175.000 volunteers.
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The extensive African Rodentia specimen and tissue collections of the Royal Museum for Central Africa (RMCA), the Royal Belgian Institute of Natural Sciences (RBINS) and the University of Antwerp (UA) provide taxonomical, ecological, geographical and genetic information, as well as measurements and data on parasitic and viral infections. The scientific importance of these collections is that, although numerous African rats and mice have been described over the last 150 years, many species descriptions are based on very few specimens.
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As part of the Antarctic Site Inventory (e.g. Lynch et al. 2012, Naveen and Lynch 2011), we have developed a database and gathered photographic information on lichen richness for sites that are frequently visited by tourists on the Antarctic Peninsula.
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The Purdue Entomological Research Collection (PERC) is an integral part of the Department of Entomology at Purdue University. Specimens housed in the collection are the basis for research in systematic entomology at Purdue and by specialists worldwide. The PERC also serves as a reference to facilitate the accurate and timely identification of insects for extension and teaching needs. Approximately 2 million specimens are held, representing more than 140,000 species. This includes mainly dry-mounted pinned material as well as many specimens stored in liquid preservative or mounted on slides.
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[Spanish] Esta colección está integrada por un pequeño grupo ejemplares pertenecientes a diversos fila de invertebrados, menos artrópodos o moluscos. Históricamente, las muestras más antiguas tienen su origen en la década de los años 1920 hasta el momento. Actualmente hay previsiones de incremento gracias a acuerdos con instituciones de investigación. La gran mayoría de muestras se conservan en alcohol y sólo algunos esqueletos de esponjas, corales o equinodermos se han preservado en seco. Algunos ejemplares procedían del Laboratorio de Biología Marina de Santander y otros de la Estación Biológica de Nápoles.
[English] This collection is integrated by a small group of specimens belonging to phyla of invertebrates except to Arthropoda and Mollusca. The smaller number of specimens of this collection doesn't facilitate an independent administration of this collection. Specimens basically belong to Porifera, Cnidaria, Ctenophora, Platyhelmintha, Annelida, Briozoa and Echinodermata. Some specimens come from the Laboratory of Biology Marina from Santander and the Biological Station of Naples.
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Databases and Geographical Information Systems are becoming increasingly popular tools for biogeographic analysis. The reliability of the analysis depends on the accuracy of the entered data and the ability to add changes in systematics and taxonomy. The main aim of the Southern Ocean Mollusc Database (SOMBASE) project is to set up a database linked with a GIS and user-friendly front end. This system allows for the inclusion of other taxa in the future. Currently the database consists of records for 950 shelled gastropod and 136 bivalve species and 2800 sites from the Southern Ocean.The database contains fields including: 1) Taxonomic authorship, synonyms, higher level classifications, diagnostic morphological characters, and ecological features; 2) Distributional information including substrate and depth; 3) Bibliographic information.The maps can display selected sites based on any query of any field or combination of fields in the database. An online version of the database is available with distribution maps for all taxonomic levels (www.antarctica.ac.uk/SOMBASE). SOMBASE is a contribution to the Biogeiegraphic Atlas of the Southern Ocean
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The Entomological collections contain research material of all extant terrestrial and aquatic arthropod groups except crustaceans:Hexapoda, Myriopoda, Tardigrada, Arachnoidea and Cheliceratea.
More than 430 000 needle mounted insects have been identified with genus or species names and an additional number identified to family level. Moreover, the collection contains about 42,000 tubes with ethanol-fixed insects identified to genus or species level, and 29,000 slides (mainly aphids and chironomids).
Of other terrestrial arthropods we have more than 15,000 tubes with ethanol-fixed material of spiders determined to species or genus. In addition, we have more than 1200 dried galls and mines.
The bulk of the material is from the last 70-80 years and is available for loan to other scientific institutions for the purpose of scientific studies. Other persons must make arrangement with a local institution that may be willing to take responsibility for the loan.
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El DICTUS mantiene la colección de peces nativos de Sonora que incluye la totalidad de la representación de los peces nativos y exóticos del Estado. A pesar de ser nodo de la REMIB, esta colección no se ha computarizado e incorporado a este nodo. La colección representa el 6% con respecto al territorio nacional. Está ordenada bajo la clasificación de Eschmeyer (1998). Se encuentra arreglada de acuerdo a números de catálogo progresivos por especie por localidad a lo largo del tiempo. La colección cuenta con mas de 35,000 ejemplares repartidos en 1000 registros. Las recolectas datan desde los años 1960 hasta el presente y se encuentran mantenidos en frascos de cristal en alcohol etílico al 70%. Cuenta con registro de recolectores, números de individuos, fechas y observaciones de recolecta, localidades georreferenciadas, autoridad y fecha de determinación. La Colección de Peces Nativos de Sonora mantiene las 64 especies que habitan actualmente las aguas continentales del Estado de Sonora, y las extirpadas de territorio nacional. Los peces nativos comprenden 43 especies registradas a largo de recolectas iniciadas a finales del siglo antepasado hasta la actualidad. Casi el 67% de los peces que habitan en Sonora son nativos, el restante 33% son peces introducidos con fines acuiculturales, de ornato y de control biológico. Sonora representa el 8.9% de las especies de peces nativos del país y el 19.5, 33.3 y 38.8% de los géneros, familias y órdenes a nivel nacional. Dentro de las especies con distribución actual para Sonora, el 53.48% se encuentra incluido bajo alguna categoría de protección de acuerdo a la NOM-059-2002. Ocho están en especies en peligro de extinción, sin embargo 7 de ellas ya han sido extirpadas de territorio nacional. Como amenazadas se encuentran 11 y como Sujetas a Protección especial. Tres especies son endémicas dentro de los límites del estado, sin embargo, Sonora comparte un número importante de endemismos restringidos a las provincias biogeográficas Sonorense, Madrense y Sinaloense. Este proyecto pretende computarizar la colección de peces nativos de Sonora, poner a disposición y dar permanente actualización a la información de la colección a través del Nodo de la REMIB que mantiene en DICTUS.
Reino: 1 Filo: 1 Clase: 1 Orden: 15 Familia: 22 Género: 54 Especie: 85
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The Royal Belgian Institute of Natural Sciences houses a precious collection of zoological, anthropological, paleontological, mineralogical and geological materials and data. The renowned Iguanodons from Bernissart, ambassadors of the Belgian science institute in Brussels, represent a natural history collection currently estimated to hold over 37 million specimens. The roots of the present day collection reach far back in history. It evolved from the Natural History collection of Karel of Lotharingen, governor of The Netherlands (1712-1780) and was part of didactic materials owned by the Central School of the City of Brussels. After the independence of Belgium, the City of Brussels donated the collection to the Belgian Government and became part of the autonomous Royal Natural History Museum in 1846, known as the Royal Belgian Institute of Natural Sciences since 1948. Fieldwork by researchers and collaborators, in Belgium and abroad, donations and purchases have been expanding the assets ever since. The data presented in this dataset are coming from the DaRWIN database, the collection management tool of the RBINS. Today, DaRWIN manages information on about 550.000 specimens stored in the institute's repositories. This number rises on a daily basis thanks to the continued efforts of curators and their adjuncts that are responsible for maintaining the stored specimens and information. The dataset is made available on GBIF and covers the complete collection, as well as subcollections within Vertebrates (mammals, birds, reptiles, amphibians and fish), Invertebrates (acarines, arachnids, Belgian marine invertebrates, brachiopods, bryozoans, marine chelicerates, cnidarians, crustaceans, echinoderms, molluscs and rotifers) and Entomology (beetles, dipterans, heterocerans, hymenopterans, orthopterans and rhopalocerans).
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Data set about the annual monitoring of the effect of herbivorism on the conservation status of endangered species Androcymbium europaeum. Since 2010, the SERPAM Department (Evaluation, Restoration and Protection of Mediterranean Agrosystems Service) of the Zaidin Experimental Station belonging to Spanish National Research Council (CSIC-EEZ), has been carrying out annual sampling to evaluate the effect of domestic and wild livestock (eg. rabbits) on the pastures inhabited by Androcymbium europaeum. A randomized block design with three treatments (type of management: rabbit and domestic herbivorism; only excluded to livestock; and excluded to rabbit and livestock) was performed. In each treatment, two types of monitoring were carried out: abundance estimation of A. europaeum by counting individuals on 50 x 50 cm squares; and plant species diversity in 2-m long transects using the modified Point-Quadrat method. This study was carried out in the "Rambla de las Amoladeras" (Almería) within the Cabo de Gata-Níjar protected area (southern Spain). The dataset describes information from 2010 to 2022. Monitoring is performed annually.
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El herbario EMMA (acrónimo de Escuela de Montes de Madrid) es el herbario de la Escuela Técnica Superior de Ingeniería de Montes, Forestal y del Medio Natural (Universidad Politécnica de Madrid). La colección principal es un herbario de plantas vasculares dedicado especialmente a la flora leñosa de la Península Ibérica. Otras floras representadas en menor grado son la Macaronésica (con especial atención a las Islas Canarias) y la Norteafricana, siempre en su vertiente más forestal. También posee pliegos de especies ornamentales, obtenidas a partir de material procedente de parques y jardines. Consta aproximadamente de unos 40.000 pliegos que abarcan cerca de 5.000 especies.
Entre algunos materiales históricos que conserva el herbario EMMA se encuentra la colección de Rafael Areses, de más de 1.500 pliegos que en su mayoría son de procedencia exótica, colectada en los pazos y jardines gallegos donde este ingeniero de montes ejerció su profesión. Aún más interés tienen los materiales testigo del trabajo de los prestigiosos botánicos forestales Luis Ceballos y Fernández de Córdoba (1896-1967), Manuel Martín Bolaños (1897-1970) y Carlos Vicioso (1886-1978), procedentes principalmente de sus herborizaciones en las islas Canarias y en las provincias de Cádiz, Málaga y Huelva. De Juan Ruiz de la Torre (1928-2015), catedrático de Botánica desde 1968 a 1997, se conservan infinidad de pliegos, tanto de su etapa de trabajo en Marruecos, como de sus múltiples recorridos por toda la geografía española, que culminaron con la realización del Mapa Forestal de España, escala 1:200.000
Actualmente se pueden consultar por medio de GBIF más de 19000 registros que corresponden a la totalidad de Pteridophyta, Gymnospermae, Angiospermae y Monocotyledoneae (a excepción de Gramineae, familia que, en su mayoría, se encuentra sin informatizar)
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This dataset contains INSDC sequence records not associated with environmental sample identifiers or host organisms. The dataset is prepared periodically using the public ENA API (https://www.ebi.ac.uk/ena/portal/api/) by querying data with search parameters: `environmental_sample=False & host=""`
EMBL-EBI also publishes other records in separate datasets (https://www.gbif.org/publisher/ada9d123-ddb4-467d-8891-806ea8d94230).
The data was then processed as follows:
1. Human sequences were excluded.
2. For non-CONTIG records, the sample accession number (when available) along with the scientific name were used to identify sequence records corresponding to the same individuals (or group of organism of the same species in the same sample). Only one record was kept for each scientific name/sample accession number.
3. Contigs and whole genome shotgun (WGS) records were added individually.
4. The records that were missing some information were excluded. Only records associated with a specimen voucher or records containing both a location AND a date were kept.
5. The records associated with the same vouchers are aggregated together.
6. A lot of records left corresponded to individual sequences or reads corresponding to the same organisms. In practise, these were "duplicate" occurrence records that weren't filtered out in STEP 2 because the sample accession sample was missing. To identify those potential duplicates, we grouped all the remaining records by `scientific_name`, `collection_date`, `location`, `country`, `identified_by`, `collected_by` and `sample_accession` (when available). Then we excluded the groups that contained more than 50 records. The rationale behind the choice of threshold is explained here: https://github.com/gbif/embl-adapter/issues/10#issuecomment-855757978
7. To improve the matching of the EBI scientific name to the GBIF backbone taxonomy, we incorporated the ENA taxonomic information. The kingdom, Phylum, Class, Order, Family, and genus were obtained from the ENA taxonomy checklist available here: http://ftp.ebi.ac.uk/pub/databases/ena/taxonomy/sdwca.zip
More information available here: https://github.com/gbif/embl-adapter#readme
You can find the mapping used to format the EMBL data to Darwin Core Archive here: https://github.com/gbif/embl-adapter/blob/master/DATAMAPPING.md
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This database contains information on the algae specimens registered so far in the herbarium of the Swedish Museum of Natural History.
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The present historical paper deals with the pelagic Polychaetes except the Tomopterids collected on the cruises of the "Thor", 1908-1910 in the Mediterannenan and adjacent waters. The tables included in this report present also the scientific results from other research vessels such as "Dana" (years 1921 and 1930) and "S/S Pangan" (1911).
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A dataset contains contain 22,600+ records of vascular plants from the Meshchera National Park (Vladimir Oblast, Russia) and its buffer zone made by Alexey P. Seregin. The dataset is based on grid scheme with 80 squares ranging from 24.1 to 24.5 km2 (2.5 minutes lat. x 5 minutes long., WGS84). This grid scheme is coherent with a grid used for mapping of Vladimir Oblast using larger squares ranging from 94.7 to 98.2 km2 (5 minutes lat. x 10 minutes long.). In 1999–2004 (mainly in 2002), I studied 61 grid squares in the Meshchera National Park and recorded 11,721 occurrences of 683 species. In 2011–2012 (mainly in 2012), I made 1124 km of foot trips studying the flora. As a result, I visited 80 grid squares and recorded 20,034 species occurrences. Few records were extracted from relevant literature. Thereby, the presented dataset consists of 22,651 unique occurrences of 812 species. Records of the first survey confirmed in 2012 are not duplicated. The dataset was used to produce grid maps in “Vascular flora of Meshchera National Park (Vladimir Province of Russia)” (Seregin, 2004) and in its revised and enlarged edition entitled “New flora of the Meshchera National Park (Vladimir Oblast, Russia): Checklist, distribution atlas, peculiarities, and distributional changes in species over the last decade (2002–2012)” (Seregin, 2013). In the latter publication, one can find habitat details, spatial patterns within the park, distribution map, and grid frequency reported for each species as well as precise localities for the rarest species. New records include 43 species from Gus-Krustalny District, 8 species from Sobinsky District, and 4 species from Sudogodsky District (including Raduzhny Urban Okrug). Bidens connata, Senecio dubitabilis, Petunia ×atkinsiana, Monarda didyma, Prunus avium are reported for the first time for Vladimir Oblast.
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The GBIF Backbone Taxonomy is a single, synthetic management classification with the goal of covering all names GBIF is dealing with. It's the taxonomic backbone that allows GBIF to integrate name based information from different resources, no matter if these are occurrence datasets, species pages, names from nomenclators or external sources like EOL, Genbank or IUCN. This backbone allows taxonomic search, browse and reporting operations across all those resources in a consistent way and to provide means to crosswalk names from one source to another.
It is updated regulary through an automated process in which the Catalogue of Life acts as a starting point also providing the complete higher classification above families. Additional scientific names only found in other authoritative nomenclatural and taxonomic datasets are then merged into the tree, thus extending the original catalogue and broadening the backbones name coverage. The GBIF Backbone taxonomy also includes identifiers for Operational Taxonomic Units (OTUs) drawn from the barcoding resources iBOL and UNITE.
International Barcode of Life project (iBOL), Barcode Index Numbers (BINs). BINs are connected to a taxon name and its classification by taking into account all names applied to the BIN and picking names with at least 80% consensus. If there is no consensus of name at the species level, the selection process is repeated moving up the major Linnaean ranks until consensus is achieved.
UNITE - Unified system for the DNA based fungal species, Species Hypotheses (SHs). SHs are connected to a taxon name and its classification based on the determination of the RefS (reference sequence) if present or the RepS (representative sequence). In the latter case, if there is no match in the UNITE taxonomy, the lowest rank with 100% consensus within the SH will be used.
The GBIF Backbone Taxonomy is available for download at https://hosted-datasets.gbif.org/datasets/backbone/ in different formats together with an archive of all previous versions.
The following 105 sources have been used to assemble the GBIF backbone with number of names given in brackets: