Filter
Reset all

Subjects

Content Types

Countries

AID systems

API

Certificates

Data access

Data access restrictions

Database access

Database access restrictions

Database licenses

Data licenses

Data upload

Data upload restrictions

Enhanced publication

Institution responsibility type

Institution type

Keywords

Metadata standards

PID systems

Provider types

Quality management

Repository languages

Software

Syndications

Repository types

Versioning

  • * at the end of a keyword allows wildcard searches
  • " quotes can be used for searching phrases
  • + represents an AND search (default)
  • | represents an OR search
  • - represents a NOT operation
  • ( and ) implies priority
  • ~N after a word specifies the desired edit distance (fuzziness)
  • ~N after a phrase specifies the desired slop amount
Found 51 result(s)

Pathogen Portal

the Bioinformatics Resource Centers Portal

Subject(s)
Content type(s)
Country
Pathogen Portal is a repository linking to the Bioinformatics Resource Centers (BRCs) sponsored by the National Institute of Allergy and Infectious Diseases (NIAID) and maintained by The Virginia Bioinformatics Institute. The BRCs are providing web-based resources to scientific community conducting basic and applied research on organisms considered potential agents of biowarfare or bioterrorism or causing emerging or re-emerging diseases. The Pathogen Portal supports and links to five Bioinformatics Resource Centers (BRCs). Each BRC specializes in a different group of pathogens, focusing on, but not limited to, pathogens causing (Re-)Emerging Infectious Diseases, and those in the NIAID Category A-C Priority Pathogen lists for biodefense research. The scope of the BRCs also includes Invertebrate Vectors of Human Disease. Pathogen Portal covers EuPathDB, IRD, PATRIC, VectorBase and ViPR.

PATRIC

Pathosystems Resource Integration Center

Subject(s)
Content type(s)
Country
<<<!!!<<< This repository is no longer available. >>>!!!>>> PATRIC will go offline by mid-December2022. Here is what you need to know. As announced previously, PATRIC, the bacterial BRC, and IRD / ViPR, the viral BRCs, are being merged into the new Bacterial and Viral Bioinformatics Resource Center (BV-BRC). BV-BRC combines the data, tools, and technologies from these BRCs to provide an integrated resource for bacterial and viral genomics-based infectious disease research.

FungiDB

The Fungal and Oomycete Genomics Resource

Subject(s)
Content type(s)
Country
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.

EMBL-EBI

European Molecular Biology Laboratory - European Bioinformatics Institute

Subject(s)
Content type(s)
Country
The European Bioinformatics Institute (EBI) has a long-standing mission to collect, organise and make available databases for biomolecular science. It makes available a collection of databases along with tools to search, download and analyse their content. These databases include DNA and protein sequences and structures, genome annotation, gene expression information, molecular interactions and pathways. Connected to these are linking and descriptive data resources such as protein motifs, ontologies and many others. In many of these efforts, the EBI is a European node in global data-sharing agreements involving, for example, the USA and Japan.

ALSoD

ALS Online Database

Subject(s)
Content type(s)
Country
ALSoD is a freely available database that has been transformed from a single gene storage facility recording mutations in the SOD1 gene to a multigene ALS bioinformatics repository and analytical instrument combining genotype, phenotype, and geographical information with associated analysis tools. These include a comparison tool to evaluate genes side by side or jointly with user configurable features, a pathogenicity prediction tool using a combination of computational approaches to distinguish variants with nonfunctional characteristics from disease-associated mutations with more dangerous consequences, and a credibility tool to enable ALS researchers to objectively assess the evidence for gene causation in ALS. Furthermore, integration of external tools, systems for feedback, annotation by users, and two-way links to collaborators hosting complementary databases further enhance the functionality of ALSoD.

DTU Bioinformatics

Center for Biological Sequence Analysis (formerly)

Subject(s)
Content type(s)
Country
<<<!!!<<< DTU Bioinformatics was closed on 31 December 2018 as part of a reorganization at DTU >>>!!!>>>

ProteomeXchange

PX

Subject(s)
Content type(s)
Country
The ProteomeXchange consortium has been set up to provide a single point of submission of MS proteomics data to the main existing proteomics repositories, and to encourage the data exchange between them for optimal data dissemination. Current members accepting submissions are: The PRIDE PRoteomics IDEntifications database at the European Bioinformatics Institute focusing mainly on shotgun mass spectrometry proteomics data PeptideAtlas/PASSEL focusing on SRM/MRM datasets.

UniSave

UniProtKB Sequence/Annotation Version Archive

Subject(s)
Content type(s)
Country
The UniProtKB Sequence/Annotation Version Archive (UniSave) has the mission of providing freely to the scientific community a repository containing every version of every Swiss-Prot/TrEMBL entry in the UniProt Knowledge Base (UniProtKB). This is achieved by archiving, every release, the entry versions within the current release. The primary usage of this service is to provide open access to all entry versions of all entries. In addition to viewing their content, one can also filter, download and compare versions.

Virus Pathogen Resource

ViPR

Subject(s)
Content type(s)
Country
<<<!!!<<< This repository is no longer available. >>>!!!>>> Migration of the data, tools, and services from IRD and ViPR to BV-BRC is complete! We are now in the sunsetting phase of the transition. Starting on October 31, 2022, launching the IRD or ViPR home pages will redirect you to the new BV-BRC home page. The current plan is to completely shut down IRD and ViPR by the end of this calendar year. Although it will still be possible to use those sites until shutdown, we strongly encourage you to start using BV-BRC now.

ChEMBL

Subject(s)
Content type(s)
Country
ChEMBL is a database of bioactive drug-like small molecules, it contains 2-D structures, calculated properties (e.g. logP, Molecular Weight, Lipinski Parameters, etc.) and abstracted bioactivities (e.g. binding constants, pharmacology and ADMET data). The data is abstracted and curated from the primary scientific literature, and cover a significant fraction of the SAR and discovery of modern drugs We attempt to normalise the bioactivities into a uniform set of end-points and units where possible, and also to tag the links between a molecular target and a published assay with a set of varying confidence levels. Additional data on clinical progress of compounds is being integrated into ChEMBL at the current time.

UCSC Genome Browser

University of California Santa Cruz Genome Bioinformatics

Subject(s)
Content type(s)
Country
It is an interactive website offering access to genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations. The Browser is a graphical viewer optimized to support fast interactive performance and is an open-source, web-based tool suite built on top of a MySQL database for rapid visualization, examination, and querying of the data at many levels.

Electron Microscopy Data Bank

EMDB

Subject(s)
Content type(s)
Country
The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps of macromolecular complexes and subcellular structures. It covers a variety of techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography.

DNA Data Bank of Japan

DDBJ

Subject(s)
Content type(s)
Country
DDBJ; DNA Data Bank of Japan is the sole nucleotide sequence data bank in Asia, which is officially certified to collect nucleotide sequences from researchers and to issue the internationally recognized accession number to data submitters.Since we exchange the collected data with EMBL-Bank/EBI; European Bioinformatics Institute and GenBank/NCBI; National Center for Biotechnology Information on a daily basis, the three data banks share virtually the same data at any given time. The virtually unified database is called "INSD; International Nucleotide Sequence Database DDBJ collects sequence data mainly from Japanese researchers, but of course accepts data and issue the accession number to researchers in any other countries.

T3DB

Toxin and Toxin Target Database

Subject(s)
Content type(s)
Country
The Toxin and Toxin Target Database is a unique bioinformatics resource that combines detailed toxin data with comprehensive toxin target information. The focus of the T3DB is on providing mechanisms of toxicity and target proteins for each toxin. This dual nature of the T3DB, in which toxin and toxin target records are interactively linked in both directions, makes it unique from existing databases.

Influenza Research Database

IRD

Subject(s)
Content type(s)
Country
<<<!!!<<< The migration of the data, tools, and services from the legacy IRD and ViPR applications to BV-BRC is now complete. All web traffic from the IRD and ViPR resources is also being forwarded to the BV-BRC home page https://www.re3data.org/repository/r3d100014100 >>>!!!>>>

MetaboLights

Subject(s)
Content type(s)
Country
MetaboLights is a database for Metabolomics experiments and derived information. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations and concentrations, and experimental data from metabolic experiments.

PhytoPath

Subject(s)
Content type(s)
Country
<<<!!!<<< This site is no longer maintained and is provided for reference only. Some functionality or links may not work. For all enquiries please contact the Ensembl Helpdesk http://www.ensembl.org/Help/Contact >>>!!!>>> PhytoPath is a new bioinformatics resource that integrates genome-scale data from important plant pathogen species with literature-curated information about the phenotypes of host infection. Using the Ensembl Genomes browser, it provides access to complete genome assembly and gene models of priority crop and model-fungal, oomycete and bacterial phytopathogens. PhytoPath also links genes to disease progression using data from the curated PHI-base resource. PhytoPath portal is a joint project bringing together Ensembl Genomes with PHI-base, a community-curated resource describing the role of genes in pathogenic infection. PhytoPath provides access to genomic and phentoypic data from fungal and oomycete plant pathogens, and has enabled a considerable increase in the coverage of phytopathogen genomes in Ensembl Fungi and Ensembl Protists. PhytoPath also provides enhanced searching of the PHI-base resource as well as the fungi and protists in Ensembl Genomes.

Health Atlas

Leipzig Health Atlas

Subject(s)
Content type(s)
Country
The Health Atlas is an alliance of medical ontologists, medical systems biologists and clinical trials groups to design and implement a multi-functional and quality-assured atlas. It provides models, data and metadata on specific use cases from medical research projects from the partner institutions.

European Chemical Biology Database

ECBD

Subject(s)
Content type(s)
Country
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.

GeneCards

The Human Gene Database

Subject(s)
Content type(s)
Country
GeneCards is a searchable, integrative database that provides comprehensive, user-friendly information on all annotated and predicted human genes. It automatically integrates gene-centric data from ~125 web sources, including genomic, transcriptomic, proteomic, genetic, clinical and functional information.

European Variation Archive

EVA

Subject(s)
Content type(s)
Country
The European Variation Archive is an open-access database of all types of genetic variation data from all species. The EVA provides access to highly detailed, granular, raw variant data from human, with other species to follow. As of September 2017, EMBL-EBI will maintain reliable accessions for non-human genetic variation data through the European Variation Archive (EVA). NCBI's dbSNP database will continue to maintain stable identifiers for human genetic variation data only. This change will enable a more rapid turnaround for data sharing in this burgeoning field.

NCBI Third Party Annotation

TPA

Subject(s)
Content type(s)
Country
TPA is a database that contains sequences built from the existing primary sequence data in GenBank. TPA records are retrieved through the Nucleotide Database and feature information on the sequence, how it was cataloged, and proper way to cite the sequence information.

The European Genome-phenome Archive

EGA

Subject(s)
Content type(s)
Country
The European Genome-phenome Archive (EGA) is designed to be a repository for all types of sequence and genotype experiments, including case-control, population, and family studies. We will include SNP and CNV genotypes from array based methods and genotyping done with re-sequencing methods. The EGA will serve as a permanent archive that will archive several levels of data including the raw data (which could, for example, be re-analysed in the future by other algorithms) as well as the genotype calls provided by the submitters. We are developing data mining and access tools for the database. For controlled access data, the EGA will provide the necessary security required to control access, and maintain patient confidentiality, while providing access to those researchers and clinicians authorised to view the data. In all cases, data access decisions will be made by the appropriate data access-granting organisation (DAO) and not by the EGA. The DAO will normally be the same organisation that approved and monitored the initial study protocol or a designate of this approving organisation. The European Genome-phenome Archive (EGA) allows you to explore datasets from genomic studies, provided by a range of data providers. Access to datasets must be approved by the specified Data Access Committee (DAC).

1000 Genomes

Thousand Genomes

Subject(s)
Content type(s)
Country
The 1000 Genomes Project is an international collaboration to produce an extensive public catalog of human genetic variation, including SNPs and structural variants, and their haplotype contexts. This resource will support genome-wide association studies and other medical research studies. The genomes of about 2500 unidentified people from about 25 populations around the world will be sequenced using next-generation sequencing technologies. The results of the study will be freely and publicly accessible to researchers worldwide. The International Genome Sample Resource (IGSR) has been established at EMBL-EBI to continue supporting data generated by the 1000 Genomes Project, supplemented with new data and new analysis.

The Taenia solium Genome Project

T. solium Genome Project

Subject(s)
Content type(s)
Country
>>>!!!<<< 2021-08; The repository is no longer available. >>>!!!<<< Archived page of Taenia solium genome project see https://web.archive.org/web/20160309194611/http://www.taeniasolium.unam.mx/taenia