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Found 63 result(s)

BacDive

Bacterial Diversity Metadatabase

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BacDive is a bacterial metadatabase that provides strain-linked information about bacterial and archaeal biodiversity. The database is a resource for different kind of phenotypic data like taxonomy, morphology, physiology, environment and molecular-biology. The majority of data is manually annotated and curated. With the release in April 2019 BacDive offers information for 80,584 strains. The database is hosted by the Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH and is part of de.NBI the German Network for Bioinformatics Infrastructure.

FungiDB

The Fungal and Oomycete Genomics Resource

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FungiDB belongs to the EuPathDB family of databases and is an integrated genomic and functional genomic database for the kingdom Fungi. FungiDB was first released in early 2011 as a collaborative project between EuPathDB and the group of Jason Stajich (University of California, Riverside). At the end of 2015, FungiDB was integrated into the EuPathDB bioinformatic resource center. FungiDB integrates whole genome sequence and annotation and also includes experimental and environmental isolate sequence data. The database includes comparative genomics, analysis of gene expression, and supplemental bioinformatics analyses and a web interface for data-mining.

TriTrypDB

kinetoplastid genomics resource

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TriTrypDB is an integrated genomic and functional genomic database for pathogens of the family Trypanosomatidae, including organisms in both Leishmania and Trypanosoma genera. TriTrypDB and its continued development are possible through the collaborative efforts between EuPathDB, GeneDB and colleagues at the Seattle Biomedical Research Institute (SBRI).

GiardiaDB

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Giardia lamblia is a significant, environmentally transmitted, human pathogen and an amitochondriate protist. It is a major contributor to the enormous worldwide burden of human diarrheal diseases, yet the basic biology of this parasite is not well understood. No virulence factor has been identified. The Giardia lamblia genome contains only 12 million base pairs distributed onto five chromosomes. Its analysis promises to provide insights about the origins of nuclear genome organization, the metabolic pathways used by parasitic protists, and the cellular biology of host interaction and avoidance of host immune systems. Since the divergence of Giardia lamblia lies close to the transition between eukaryotes and prokaryotes in universal ribosomal RNA phylogenies, it is a valuable, if not unique, model for gaining basic insights into genetic innovations that led to formation of eukaryotic cells. In evolutionary terms, the divergence of this organism is at least twice as ancient as the common ancestor for yeast and man. A detailed study of its genome will provide insights into an early evolutionary stage of eukaryotic chromosome organization as well as other aspects of the prokaryotic / eukaryotic divergence.

VectorBase

Bioinformatics Resource for Invertebrate Vectors of Human Pathogens

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VectorBase provides data on arthropod vectors of human pathogens. Sequence data, gene expression data, images, population data, and insecticide resistance data for arthropod vectors are available for download. VectorBase also offers genome browser, gene expression and microarray repository, and BLAST searches for all VectorBase genomes. VectorBase Genomes include Aedes aegypti, Anopheles gambiae, Culex quinquefasciatus, Ixodes scapularis, Pediculus humanus, Rhodnius prolixus. VectorBase is one the Bioinformatics Resource Centers (BRC) projects which is funded by National Institute of Allergy and Infectious Diseases (NAID).

BsubCyc

a member of the BioCyc Database Collection

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BsubCyc is a model-organism database for the bacterium Bacillus subtilis and is based on the updated B. subtilis 168 genome sequence and annotation published by Barbe et al. in 2009. Gene function annotations are being updated when new literature is available. Subscriptions are now required to access BsubCyc. For more information on obtaining a subscription, click here: http://www.phoenixbioinformatics.org/biocyc/subscriptions.html

Cefas Data Hub

Cefas Data Portal

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The Centre for the Environment, Fisheries and Aquaculture Science (Cefas), as one of the world's longest-established marine research organisations, has provided advice on the sustainable exploitation of marine resources since 1902. Today Cefas works in support of a healthy environment and a growing blue economy providing innovative solutions for the aquatic environment, biodiversity and food security. The Cefas Data Hub provides access to over 2080 metadata records, with over 5500 data sets available to download and connect to in support of commitments to Open Science through the Data Portal. Datasets available are increasingly diverse and include many legacy datasets including those from fish, shellfish and plankton surveys from the 1980's to the present day. Other increasingly international datasets made available include species migration data from tagging activities and data on habitat and sediment, ecosystem change, human activities including marine litter, otolith sampling and fish stomach contents, oceanography, acoustics, health and water quality. Data is provided under Open Government License by default where feasible.

ATCC Genome Portal

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Database and knowledgebase of authenticated microbial genomics data with full data provenance to physical materials held within American Type Culture Collection's (ATCC) biorepository and culture collections. Data includes whole genome sequencing data for bacterial, viral and fungal strains at ATCC, their genome assemblies, metadata, drug susceptibility data, and more. All data is freely available for non-commercial research use only (RUO) applications via the web portal interface or via a REST-API. The goal is to provide the research community with provenance information and authentication between the biological source materials and reference genome assemblies derived from them.

enviPath

The enironmental contaminant biotransormation pathway resource

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enviPath is a database and prediction system for the microbial biotransformation of organic environmental contaminants. The database provides the possibility to store and view experimentally observed biotransformation pathways. The pathway prediction system provides different relative reasoning models to predict likely biotransformation pathways and products.

Vega

Vertebrate Genome Annotation database

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A repository for high-quality gene models produced by the manual annotation of vertebrate genomes. The final update of Vega, version 68, was released in February 2017 and is now archived at vega.archive.ensembl.org. We plan to maintain this resource until Feb 2020.

QTL Archive

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This site provides access to raw data from various QTL (quantitative trait loci) studies using rodent inbred line crosses. Data are available in the .csv format used by R/qtl and pseudomarker programs. In some cases analysis scripts and/or results are posted to accompany the data.

PlutoF

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An online data management workbench and computing service provider for biology and related disciplines.

Columbia University Academic Commons

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Academic Commons provides open, persistent access to the scholarship produced by researchers at Columbia University, Barnard College, Jewish Theological Seminary, Teachers College, and Union Theological Seminary. Academic Commons is a program of the Columbia University Libraries. Academic Commons accepts articles, dissertations, research data, presentations, working papers, videos, and more.

European Chemical Biology Database

ECBD

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The European Chemical Biology Database (ECBD) is a prototype database, currently being developed for EU-OPENSCREEN. The purpose of ECBD is to store and integrate screening data from EU-OPENSCREEN partners and contributors.

AmoebaDB

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AmoebaDB belongs to the EuPathDB family of databases and is an integrated genomic and functional genomic database for Entamoeba and Acanthamoeba parasites. In its first iteration (released in early 2010), AmoebaDB contains the genomes of three Entamoeba species (see below). AmoebaDB integrates whole genome sequence and annotation and will rapidly expand to include experimental data and environmental isolate sequences provided by community researchers . The database includes supplemental bioinformatics analyses and a web interface for data-mining.

DRYAD

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Dryad is an open data publishing platform and a community committed to the open availability and routine re-use of all research data. We publish data in any format and any discipline. All Dryad data undergoes a curation process and is published under a CC0 waiver to promote reuse.

Project Tycho: Data for Health

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Project Tycho is a repository for global health, particularly disease surveillance data. Project Tycho currently includes data for 92 notifiable disease conditions in the US, and up to three dengue-related conditions for 99 countries. Project Tycho has compiled data from reputable sources such as the US Centers for Disease Control, the World Health Organization, and National health agencies for countries around the world. Project Tycho datasets are highly standardized and have rich metadata to improve access, interoperability, and reuse of global health data for research and innovation.

AIMS Data Repository

formerly: AIMS Data Centre

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The Australian Institute of Marine Science (AIMS) is a tropical marine research centre. The AIMS Data Repository preserves experimental and survey data, sensor data, research analyses and other types of data collected by projects conducted by the Australian Institute of Marine Science (AIMS). Contributors to the repository are primarily AIMS researchers from various science disciplines including ecology, biology, environmental sciences, microbiology, geosciences and oceanography, geochemistry, biodiversity conservation, evolutionary environmental studies, climate and oceanic change, fisheries, biochemistry and molecular biology, limnology and functions of inland waters, genetics and hereditary, observing network

Immuno Polymorphism Database

IPD

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Established by the HLA Informatics Group of the Anthony Nolan Research Institute, IPD provides a centralized system for studying the immune system's polymorphism in genes. The IPD maintains databases concerning the sequences of human Killer-cell Immunoglobulin-like Receptors (KIR), sequences of the major histocompatibility complex in a number of species, human platelet antigens (HPA), and tumor cell lines. Each subject has related, credible news, current research and publications, and a searchable database for highly specific, research grade genetic information.

COVID-19 Data Portal

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The COVID-19 Data Portal was launched in April 2020 to bring together relevant datasets for sharing and analysis in an effort to accelerate coronavirus research. It enables researchers to upload, access and analyse COVID-19 related reference data and specialist datasets as part of the wider European COVID-19 Data Platform.

BIGG Database

Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions

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BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. BiGG integrates several published genome-scale metabolic networks into one resource with standard nomenclature which allows components to be compared across different organisms. BiGG can be used to browse model content, visualize metabolic pathway maps, and export SBML files of the models for further analysis by external software packages. Users may follow links from BiGG to several external databases to obtain additional information on genes, proteins, reactions, metabolites and citations of interest.

SWISS-MODEL Repository

SMR

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The SWISS-MODEL Repository is a database of annotated three-dimensional comparative protein structure models generated by the fully automated homology-modelling pipeline SWISS-MODEL.

doRiNA

database of RNA interactions in post-transcriptional regulation

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doRiNA is a database of transcriptome-wide binding site data for RNA binding proteins and microRNAs

Environmental Data Initiative Repository

EDI Data Portal

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We preserve environmental data for open and reproducible science, to promote synthesis across space and time, and to aid in the assessment of environmental change and its consequences.

CryptoDB

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CryptoDB is an integrated genomic and functional genomic database for the parasite Cryptosporidium and other related genera. CryptoDB integrates whole genome sequence and annotation along with experimental data and environmental isolate sequences provided by community researchers. The database includes supplemental bioinformatics analyses and a web interface for data-mining.