Tag: taxonomic classification

SILVA is a comprehensive, quality-controlled web resource for up-to-date aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains alongside supplementary online services. In addition to data products, SILVA provide ...

Chemical Entities of Biological Interest (ChEBI) is a free dictionary that describes 'small’ chemical compounds. These compound includes distinct synthetic or natural atoms, molecules, ions, ion pair, radicals, radical ions, complexes, conformers, et ...

The NCBI Taxonomy is a database of taxonomic information. It does not follow a single taxonomic treatise but rather attempts to incorporate phylogenetic and taxonomic knowledge from a variety of sources, including the published literature, web-based ...

The Genomes Online Database provides access to information regarding genome and metagenome sequencing projects, and their associated metadata, around the world. Information in GOLD is organized into four levels: Study, Biosample/Organism, Sequencing ...

The LIPID MAPS Lipid Classification System is comprised of eight lipid categories, each with its own subclassification hierarchy. All lipids in the LIPID MAPS Structure Database (LMSD) have been classified using this system and have been assigned LIP ...

The Barcode of Life Data Systems (BOLD) is an online workbench that aids collection, management, analysis, and use of DNA barcodes. It consists of 3 components (MAS, IDS, and ECS) that each address the needs of various groups in the barcoding communi ...

Database for identification and cataloguing of group II introns. All bacterial introns listed are full-length and appear to be functional, based on intron RNA and IEP characteristics. The database names the full-length introns, and provides informati ...

Darwin Core (DwC) is a vocabulary that includes a glossary of terms (in other contexts these might be called properties, elements, fields, columns, attributes, or concepts) intended to facilitate the sharing of information about biological diversity ...

The BIG Data Center at Beijing Institute of Genomics (BIG) of the Chinese Academy of Sciences provides a suite of database resources in support of worldwide research activities in both academia and industry. With the vast amounts of multi-omics data ...

PhylomeDB is a public database for complete catalogs of gene phylogenies (phylomes). Researchers are able to use this resource to visualise the history of genes with the available phylogentic trees and multiple sequence alignments.

SEA (Super-Enhancer Archive) is a web-based comprehensive resource focusing on the collection, storage and online analysis of super-enhancers. It focuses on integrating super-enhancers in multiple species and annotating their potential roles in the r ...

BacMap is a picture atlas of annotated bacterial genomes. It is an interactive visual database containing hundreds of fully labeled, zoomable, and searchable maps of bacterial genomes.

GBIF, the Global Biodiversity Information Facility, is an international open data infrastructure, funded by governments. It is not a data repository. Rather, GBIF indexes thousands of datasets shared freely by hundreds of institutions worldwide makin ...

TreeBASE is a repository of phylogenetic information, specifically user-submitted phylogenetic trees and the data used to generate them. TreeBASE accepts all types of phylogenetic data (e.g., trees of species, trees of populations, trees of genes) re ...

MycoBank is a database created for the mycological community (as well as scientific community more generally) to document new mycological names, combinations and associated data (such as descriptions and illustrations ). Pairwise sequence alignments ...

DPVweb provides a central source of information about viruses, viroids and satellites of plants, fungi and protozoa. Comprehensive taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences a ...

The Paleobiology Database seeks to provide researchers and the public with information about the entire fossil record. It stores global, collection-based occurrence and taxonomic data for marine and terrestrial animals and plants of any geological ag ...

The Biological Collections Ontology (BCO) supports the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys. The BCO covers distinctions between individuals, organisms, ...

The aim of a World Register of Marine Species (WoRMS) is to provide an authoritative and comprehensive list of names of marine organisms, including information on synonymy. While highest priority goes to valid names, other names in use are included s ...

Canadensys maintains this data repository, built using an installation of the GBIF Integrated Publishing Toolkit (IPT). Able to assign DOIs to datasets, it ensures the data is disseminated in standardized format in order to facilitate wider reuse and ...

The development of an abstract model for a taxonomic concept, which can capture the various models represented and understood by the various data providers, is central to this project. This model is presented as an XML schema document that is propose ...

This document defines how TDWG standards should be presented. Each standard is a logical directory or folder containing two or more files - a cover page outlining basic meta data for the standard and one or more normative files specifying the standar ...

Scratchpads are an online virtual research environment for biodiversity for the sharing of data and the creation of specific research networks. Sites can focus on specific taxonomic groups, the biodiversity of a biogeographic region, or any aspect of ...

GBIF Spain maintains this data repository, built using an installation of the GBIF Integrated Publishing Toolkit (IPT). Able to assign DOIs to datasets, it ensures the data is disseminated in standardized format in order to facilitate wider reuse and ...

The Integrated Taxonomic Information System (ITIS) provides taxonomic information on plants, animals, fungi, and microbes of North America and the world. The goal is to create an easily accessible database with reliable information on species names a ...

Most syndromic surveillance systems use data from ED visits, often free-text chief complaints. Classification of chief complaints into syndromes is often inconsistent, due to the lack of agreement about the concepts that define a syndrome and how ind ...

The eLibrary of Microbial Systematics and Genomics (eLMSG) database provides a platform for microbial systematics, genomics and phenomics (polyphasic taxonomy related phenotypes). It includes information in areas such as microbial taxonomy, ecology, ...

The Ag Data Commons is a public, government, scientific research data catalog and repository available to help the agricultural research community share and discover research data funded by the United States Department of Agriculture and meet Federal ...

Biological collections are replete with taxonomic, geographic, temporal, numerical, and historical information. This information is crucial for understanding and properly managing biodiversity and ecosystems, but is often difficult to access. Data pu ...

The iDigBio IPT is a website that hosts biodiversity data and serves it in a standardised format, allowing aggregators such as iDigBio to index it into their portals whenever the data is applicable to that portal.

GBIF France hosts this data repository on behalf of GBIF Togo in collaboration with the GBIF Secretariat, built using an installation of the GBIF Integrated Publishing Toolkit (IPT).

GBIF France hosts this data repository on behalf of GBIF Benin in collaboration with the GBIF Secretariat, built using an installation of the GBIF Integrated Publishing Toolkit (IPT).

GBIF Norway is the Norwegian participant node in the Global Biodiversity Information Facility, GBIF. They make primary data on biological diversity from the Norwegian collections and observation databases freely available and coordinate and support G ...

GBIF Portugal promotes the free and open sharing of primary biodiversity data and enriches knowledge of Portuguese and World biodiversity. It promotes the integration of Portuguese data publishers and resources of biodiversity information on the GBIF ...

GBIF France aims to collect all primary biodiversity data hosted in France, regardless of whether they concern the biodiversity of French territory or the rest of the world. GBIF France also supports additional countries' nodes with the hosting of th ...

OBIS provides data hosting and helpdesk support to publishers of marine data around the globe. EurOBIS/Flanders Marine Institute (VLIZ) hosts multiple IPT installations on behalf of various OBIS Nodes. Currently, there are more than 20 OBIS Nodes aro ...

In taxonomy, descriptive data takes a number of very different forms. The goal of the Structured Descriptive Data (SDD) standard is to allow capture, transport, caching and archiving of descriptive data in all of its varied forms, using a platform- a ...

The Belgium Biodiversity Platform hosts this data repository on behalf of BioFresh in collaboration with the GBIF Secretariat, built using an installation of the GBIF Integrated Publishing Toolkit (IPT). Biofresh is an EU-funded international project ...

VertNet uses the Integrated Publishing Toolkit (IPT) to host published biodiversity data on the VertNet IPT for its participating institutions. The IPT is a free, open source web application designed to publish primary occurrence data, species checkl ...

When taxonomic descriptions are prepared for input to computer programs, the form of the coding is usually dictated by the requirements of a particular program or set of programs. This restricts the type of data that can be represented, and the numbe ...

The Belgium Biodiversity Platform maintains this data repository in collaboration with the GBIF Secretariat, built using an installation of the GBIF Integrated Publishing Toolkit (IPT). The Belgian Biodiversity Platform is a science-policy interface ...

The Colombian Biodiversity Information System (SiB Colombia) maintains this data repository, built using an installation of the GBIF Integrated Publishing Toolkit (IPT). Able to assign DOIs to datasets, it ensures the data is disseminated in standard ...

The Belgium Biodiversity Platform hosts this data repository on behalf of the SCAR Antarctic Biodiversity Portal biodiversity.aq in collaboration with the GBIF Secretariat, built using an installation of the GBIF Integrated Publishing Toolkit (IPT). ...

DanBIF maintains this data repository in collaboration with the GBIF Secretariat, built using an installation of the GBIF Integrated Publishing Toolkit (IPT). DanBIF carries out the work on making accessible the Danish, Faroese and Greenlandic resour ...

OBIS-USA brings together marine biological occurrence data – recorded observations of identifiable marine species at a known time and place, collected primarily from U.S. Waters or with U.S. funding. OBIS-USA is part of an international data sharing ...

The U.S. node to GBIF represents an integral part of the U.S. Geological Survey’s activities to collect, organize and share biological information. As with other initiatives, the U.S. GBIF node streamlines access to U.S. biodiversity information and ...

The Nonindigenous Aquatic Species (NAS) information resource for the United States Geological Survey has been established as a central repository for spatially referenced biogeographic accounts of introduced aquatic species. The program provides scie ...

Finnish Biodiversity Information Facility (FinBIF) maintains this data repository in collaboration with the GBIF Secretariat, built using an installation of the GBIF Integrated Publishing Toolkit (IPT). FinBIF compiles Finnish biodiversity informatio ...

The Belgium Biodiversity Platform hosts this data repository on behalf of GBIF Mauritania (MrBIF) in collaboration with the GBIF Secretariat, built using an installation of the GBIF Integrated Publishing Toolkit (IPT). More specifically, MrBIF aims t ...

The Atlas of Living Australia (GBIF Australia) maintains this data repository in collaboration with the GBIF Secretariat, built using an installation of the GBIF Integrated Publishing Toolkit (IPT). Able to assign DOIs to datasets, it ensures the dat ...

GBIF France hosts this data repository on behalf of Madagascar Biodiversity Information Facility (MadBIF) in collaboration with the GBIF Secretariat, built using an installation of the GBIF Integrated Publishing Toolkit (IPT). Most data collected wit ...

The South African National Biodiversity Institute (SANBI) leads and coordinates research, and monitors and reports on the state of biodiversity in South Africa. The institute provides knowledge and information, gives planning and policy advice and pi ...

GBIF France hosts this data repository on behalf of GBIF Guinea in collaboration with the GBIF Secretariat, built using an installation of the GBIF Integrated Publishing Toolkit (IPT). GBIF-GUINEE is established within the Centre d'Observation de Sur ...

GBIF-Sweden serves researchers, public authorities and others interested in biodiversity as the Swedish hub for information and international exchange of data on the biological diversity of the world. The ambition of GBIF-Sweden is to continuously ha ...

TaiBIF (Taiwan Biodiversity Information Facility) is the Taiwan portal of GBIF. Although Taiwan’s land is not spacious, it possesses extraordinarily abundant biodiversity resources and many endemic species. TaiBIF is in charge of integrating Taiwan's ...

This is an ontology of taxonomic terms (names of taxonomic groups) used in the systematics of fish, including non-teleost groups such as Chondrichthys (sharks and rays), Sarcopterygii (lungfish and coelacanths), lampreys, and hagfish.

This is a vocabulary of taxonomic ranks intended to replace the sets of rank terms found in the Teleost Taxonomy Ontology, the OBO translation of the NCBI taxonomy and similar OBO taxonomy ontologies. It provides terms for taxonomic ranks drawn from ...

An ontology for animal life history and natural history characteristics suitable for populations and higher taxonomic entities.

An Ontology describing resources with different formats. This Ontology can be used to annotate and describe terminological / ontological knowledge resources.

This ontology was designed to help integrate species concepts with species occurrences, gene sequences, images, references and geographical information.

The Encyclopedia of Life (EOL) is a collaborative encyclopedia to describe all known living species. It identifies sources of biodiversity knowledge that are legally and practically shareable; integrates them with other sources and adds metadata; pro ...

The International Plant Names Index (IPNI) provides nomenclatural information (spelling, author, types and first place and date of publication) for the scientific names of Vascular Plants from Family down to infraspecific ranks.

The Face Of Fungi database allows deposition of taxonomic data, phenotypic details and other useful data. Its aim is to enhance current taxonomic understanding and ultimately enable mycologists to gain better and updated insights into the current fun ...

The Catalog of Fishes is the authoritative reference for taxonomic fish names, featuring a searchable on-line database.

The Geospatial extension of the Darwin core.

The Japan Collection of Microorganisms (JCM) collects, catalogues, and distributes cultured microbial strains, restricted to those classified in Risk Group 1 or 2.

The Catalogue of Life (COL) stores information on species and their distribution across the globe. It consists of a single integrated species checklist and taxonomic hierarchy. The Catalogue holds essential information on the names, relationships and ...

To provide attractive biological resources with useful information attached, the NITE Biological Resource Center (NBRC) actively collects potentially useful biological resources (microorganisms and cloned genes) and distributes them to promote basic ...

Gramene Taxonomy Ontology (GR-TAX) is a representation of the taxonomy tree in the ontology format. Each term in this ontology can represent subspecies, species, genus, order, class or any rank in the classification. Primarily derived from NCBI Taxon ...

LIAS is a global information system for Lichenized and Non-Lichenized Ascomycetes. It includes several interoperable data repositories. In recent years, the two core components ‘LIAS names’ and ‘LIAS light’ have been enlarged. LIAS light stores pheno ...

The taxonomy database that is maintained by the UniProt group is based on the NCBI taxonomy database, which is supplemented with data specific to the UniProt Knowledgebase (UniProtKB). While the NCBI taxonomy is updated daily to be in sync with GenBa ...

The mission of this project was to built a virtual herbarium to display the images of Brazilian plants that are housed in foreign herbaria and was presented by the Brazilian Research Council (CNPq) to the Rio de Janeiro Botanical Garden (JBRJ) in Dec ...

In 2010, Brazil published the Catalog of Plants and Fungi of Brazil and launched the first online version of the List of Species of the Brazilian Flora, meeting Target 1 of the Global Strategy for Plant Conservation (GSPC-CBD). This botanical milesto ...