Tag: taxonomy

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 National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed database of citations and abstracts publish ...

The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. Data available from TAIR includes the complete genome sequence along with gene structure, gene pro ...

The Entrez Global Query Cross-Database Search System is a federated search engine, or web portal that allows users to search many discrete health sciences databases at the National Center for Biotechnology Information (NCBI) website. Entrez can effic ...

Curated classification and nomenclature for all of the organisms in the public sequence databases. This currently represents about 10% of the described species of life on the planet.

A public resource for knowledge on the timescale and evolutionary history of life.A search utility allows exploration of the thousands of divergence times among organisms in the published literature. A tree-based (hierarchical) system is used to iden ...

BacDive—the Bacterial Diversity Metadatabase merges detailed strain-linked information on the different aspects of bacterial and archaeal biodiversity. BacDive contains entries for over 63,000 strains and provides information on their taxonomy, morph ...

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 ...

The MAR databases is a collection of manually curated marine microbial contextual and sequence databases, based at the Marine Metagenomics Portal. This was developed as a part of the ELIXIR EXCELERATE project in 2017 and is maintained by The Center f ...

BCCM/MUCL is a generalist fungal culture collection of over 30 000 filamentous fungi, yeasts and arbuscular mycorrhizal fungi including type, reference and test strains. The collections activities include the distribution of its holdings, the accessi ...

proGenomes is a database providing consistent taxonomic and functional annotations for 87,920 bacterial and archaeal genomes belonging to over 12,000 species. These can be interactively explored and downloaded, whereby subsets can be customized, e.g. ...

WDCM 10K sequencing projects

dbPSP (database of Phosphorylation Sites in Prokaryotes) is an updated resource for annotating protein phosphorylation sites (p-sites) in prokaryotes (bacteria and archaea).

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 ...

Human metagenomic extrachromosomal mobile genetic elements

anti-CRISPR operons

Fast and easy retrieval of r-protein sequences from publicly available complete prokaryotic genome sequences.

An open-access curated barcode library for diatoms. Diatoms (Bacillariophyta) are ubiquitous microalgae which produce a siliceous exoskeleton and which make a major contribution to the productivity of oceans and freshwaters. They display a huge dive ...

CpGDB (Chloroplast Genome Database) is a user friendly, freely available and dynamic relational database which allows search and download of complete chloroplast genome sequences, individual gene sequences and feature records of different plant speci ...

Development and implementation of common data elements for venous thromboembolism research. Data Standards for Clinical Research. The International Society on Thrombosis and Haemostasis' Common Data Elements (CDE) provides pre-defined data standard ...

New open data resource for comparative studies of an old insect order. The Odonate Phenotypic DataBase is a resource for dragonfly and damselfly phenotypes. The database consists of a variety of morphological, behavioural, and bio-geographical infor ...

AciDB is a database of about 600 manually curated acidophilic organisms, their genomic information and associated metadata.

Genome database that is purely based on the Semantic Web technology, which enables the integration of heterogeneous data and flexible semantic searches.

CANNUSE is a database containing the traditional uses of Cannabis.

WCO-Lite is an online nomenclatural catalogue of harvestmen of the world (Arachnida, Opiliones) curated in TaxonWorks.

Is an online platform focuses on providing an up-to-date account of Botryosphaeriales with notes on orders, families and genera and species, keeping abreast of the current literature.

an online database of unspecific peroxygenases. UPObase: Unspecific Peroxygenase Database : Homepage. Unspecific Peroxygenase Database (UPObase) is a genome mining pipeline based database which consists of all the sequences of fungal unspecific per ...

Plant & Fungal Carbohydrate Structure Database (PFCSDB) stores published data on glycans and glycoconjugates of plant and fungal origin. It provides data on structures, bibliography, taxonomy, 1H and 13C NMR spectrum assignment, methods used for stru ...

Bacterial Carbohydrate Structure Database (BCSDB) stores published data on glycans and glycoconjugates of bacterial and archaean origin. It provides data on structures, bibliography, taxonomy, 1H and 13C NMR spectrum assignment, methods used for stru ...

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.

A curated repository of cell types with multifaceted characterization.

Committee for developing, refining, and maintaining a universal virus taxonomy. The goal is to categorize the multitude of known viruses into a single classification scheme that reflects their evolutionary relationships, i.e. their individual phyloge ...

Diatoms.org represents such a content curation community, providing open, online access to a vast amount of recent and historical information on North American diatom taxonomy and ecology.

Web-based platform of nucleotide sequence alignments of plants.

Morphbank :: Biological Imaging is a continuously growing database of images that scientists use for international collaboration, research and education. Images deposited in Morphbank :: Biological Imaging document a wide variety of research includin ...

LOTUS (naturaL prOducTs occUrrence databaSe) is one of the biggest and best annotated resources for NPs occurrences available free of charge and without any restriction. Natural Products Online is an open source project for Natural Products (NPs) sto ...

A public library of bat calls

DetR DB is a database of ionizing radiation resistance determinants contains a comprehensive catalog of radioresistant microbes and their molecular and genetic determinants of enhanced ionizing radiation tolerance. The database provides search tools ...

Avibase is an extensive database information system about all birds of the world, containing over 55 million records about 10,000 species and 22,000 subspecies of birds, including distribution information, taxonomy, synonyms in several languages and ...

A comprehensive database for profiling prokaryotic pan-genome dynamics.

A centralized datasource for all data relevant for the understanding of viral fusion peptides.

A comprehensive repetitive sequence database of over 80 000 species.

FRCD (Food Risk Component Database) is a comprehensive food risk component database with molecular scaffold, chemical diversity, toxicity, and biodegradability analysis.

Compilation of all names of Bacteria and Archaea which have been validly published according to the Bacteriological Code since 1. Jan. 1980, and nomenclatural changes which have been validly published since.

!!! >>> the repository is offline >>> !!! GOBASE is a taxonomically broad organelle genome database that organizes and integrates diverse data related to mitochondria and chloroplasts. GOBASE is currently expanding to include information on represent ...

Tropicos® was originally created for internal research but has since been made available to the world’s scientific community. All of the nomenclatural, bibliographic, and specimen data accumulated in MBG’s electronic databases during the past 30 year ...

Retrieving contents of BacDive and related information resources in a machine-readable form. BacDive is the Bacterial Diversity Metadatabase and provides strain-linked information about bacterial and archaeal biodiversity. The web-service offers seve ...

A comprehensive organelle genomes database for algae cpDNA and mtDNA. Algae is the earliest evolutionary biological group on the earth, are thought to have appeared at least 2.6 billion years ago. As the most complex biological group, algae have sho ...

The Alberta Food Composition Database (AFCDB) is the first comprehensive resource on food constituents, chemistry and biology dedicated to major Alberta-grown produce. It provides information on both macronutrients and micronutrients, including many ...

The PLANTS Database provides standardized information about the vascular plants, mosses, liverworts, hornworts, and lichens of the U.S. and its territories. It includes names, plant symbols, checklists, distributional data, species abstracts, charact ...

BioVeL is a virtual e-laboratory that supports research on biodiversity issues using large amounts of data from cross-disciplinary sources. BioVeL supports the development and use of workflows to process data. It offers the possibility to either use ...

TAED is a database of phylogenetically indexed gene families. It contains multiple sequence alignments from MAFFT1, maximum likelihood phylogenetic trees from PhyML2, bootstrap values for each node, dN/dS ratios for each lineage from the free ratios ...

The Barcode of Life Data Systems (BOLD) provides DNA barcode data. BOLD's online workbench supports data validation, annotation, and publication for specimen, distributional, and molecular data. The platform consists of four main modules: a data port ...

The PLANKTON*NET data provider at the Alfred Wegener Institute for Polar and Marine Research is an open access repository for plankton-related information. It covers all types of phytoplankton and zooplankton from marine and freshwater areas. PLANKT ...