Filter
Reset all

Subjects

Content Types

Countries

AID systems

API

Certificates

Data access

Data access restrictions

Database access

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 314 result(s)

UniRef

UniProt Reference Clusters

Subject(s)
Content type(s)
Country
The UniProt Reference Clusters (UniRef) provide clustered sets of sequences from the UniProt Knowledgebase (including isoforms) and selected UniParc records in order to obtain complete coverage of the sequence space at several resolutions while hiding redundant sequences (but not their descriptions) from view.

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 >>>!!!>>>

e!DAL - electronic Data Archive Library

Subject(s)
Content type(s)
Country
!!! <<< this record is no longer maintained, please use https://www.re3data.org/repository/r3d100011876 or https://www.re3data.org/repository/r3d100011647 >>> !!!: e!DAL stands for electronic Data Archive Library. It is a lightweight open source software software framework for publishing and sharing research data. e!DAL was developed based on experiences coming from decades of research data management and has grown towards being a general data archiving and publication infrastructure [https://doi.org/10.1186/1471-2105-15-214]. First research data repository is "Plant Genomics and Phenomics Research Data Repository" [https://doi.org/10.1093/database/baw033].

InterPro

protein sequence analysis & classification

Subject(s)
Content type(s)
Country
InterPro collects information about protein sequence analysis and classification, providing access to a database of predictive protein signatures used for the classification and automatic annotation of proteins and genomes. Sequences in InterPro are classified at superfamily, family, and subfamily. InterPro predicts the occurrence of functional domains, repeats, and important sites, and adds in-depth annotation such as GO terms to the protein signatures.

Antimicrobial Peptide Database

APD

Subject(s)
Content type(s)
Country
The Antimicrobial Peptide Database (APD) was originally created by a graduate student, Zhe Wang, as his master's thesis in the laboratory of Dr. Guangshun Wang. The project was initiated in 2002 and the first version of the database was open to the public in August 2003. It contained 525 peptide entries, which can be searched in multiple ways, including APD ID, peptide name, amino acid sequence, original location, PDB ID, structure, methods for structural determination, peptide length, charge, hydrophobic content, antibacterial, antifungal, antiviral, anticancer, and hemolytic activity. Some results of this bioinformatics tool were reported in the 2004 database paper. The peptide data stored in the APD were gleaned from the literature (PubMed, PDB, Google, and Swiss-Prot) manually in over a decade.

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.

pSILAC

pulsed SILAC

Subject(s)
Content type(s)
Country
database of pSILAC data – information about changes in mRNA levels and protein synthesis following microRNA misexpression in HeLa cells

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.

Rhea

Subject(s)
Content type(s)
Country
Rhea is a freely available and comprehensive resource of expert-curated biochemical reactions. It has been designed to provide a non-redundant set of chemical transformations for applications such as the functional annotation of enzymes, pathway inference and metabolic network reconstruction. There are three types of reaction participants (reactants and products): Small molecules, Rhea polymers, Generic compounds. All three types of reaction participants are linked to the ChEBI database (Chemical Entities of Biological Interest) which provides detailed information about structure, formula and charge. Rhea provides built-in validations that ensure both mass and charge balance of the reactions. We have populated the database with the reactions found in the enzyme classification (i.e. in the IntEnz and ENZYME databases), extending it with additional known reactions of biological interest. While the main focus of Rhea is enzyme-catalysed reactions, other biochemical reactions (including those that are often termed "spontaneous") also are included.

UCSD Signaling gateway

Subject(s)
Content type(s)
Country
<<<!!!<<< This repository is no longer available. >>>!!!>>>

Carbohydrate-Active enZYmes Database

CAZy

Subject(s)
Content type(s)
Country
CAZy is a specialist database dedicated to the display and analysis of genomic, structural and biochemical information on Carbohydrate-Active Enzymes (CAZymes). CAZy data are accessible either by browsing sequence-based families or by browsing the content of genomes in carbohydrate-active enzymes. New genomes are added regularly shortly after they appear in the daily releases of GenBank. New families are created based on published evidence for the activity of at least one member of the family and all families are regularly updated, both in content and in description.

BioModels

Subject(s)
Content type(s)
Country
BioModels is a repository of mathematical models of biological and biomedical systems. It hosts a vast selection of existing literature-based physiologically and pharmaceutically relevant mechanistic models in standard formats. Our mission is to provide the systems modelling community with reproducible, high-quality, freely-accessible models published in the scientific literature.

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.

BeetleBase

Subject(s)
Content type(s)
Country
<<<!!!<<< This database doesn't exist anymore. 2017-09-05 >>>!!!>>>

FlyReactome

a curated knowledgebase of drosophila melanogaster pathways

Subject(s)
Content type(s)
Country
<<<!!!<<< This repository is no longer available. This record is out dated >>>!!!>>>- eir fields, maintained by the FlyReactome staff.

Bioconductor

Open Source Software for Bioinformatics

Subject(s)
Content type(s)
Country
Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.

MGnify

formerly: EBI Metagenomics

Subject(s)
Content type(s)
Country
MGnify (formerly: EBI Metagenomics) offers an automated pipeline for the analysis and archiving of microbiome data to help determine the taxonomic diversity and functional & metabolic potential of environmental samples. Users can submit their own data for analysis or freely browse all of the analysed public datasets held within the repository. In addition, users can request analysis of any appropriate dataset within the European Nucleotide Archive (ENA). User-submitted or ENA-derived datasets can also be assembled on request, prior to analysis.

BioPortal

Subject(s)
Content type(s)
Country
BioPortal is an open repository of biomedical ontologies, a service that provides access to those ontologies, and a set of tools for working with them. BioPortal provides a wide range of such tools, either directly via the BioPortal web site, or using the BioPortal web service REST API. BioPortal also includes community features for adding notes, reviews, and even mappings to specific ontologies. BioPortal has four major product components: the web application; the API services; widgets, or applets, that can be installed on your own site; and a Virtual Appliance version that is available for download or through Amazon Web Services machine instance (AMI). There is also a beta release SPARQL endpoint.

TopFIND

The public knowledgebase for protein termini and protease processing

Subject(s)
Content type(s)
Country
TopFIND is a protein-centric database for the annotation of protein termini currently in its third version. Non-canonical protein termini can be the result of multiple different biological processes, including pre-translational processes such as alternative splicing and alternative translation initiation or post-translational protein processing by proteases that cleave proteases as part of protein maturation or as a regulatory modification. Accordingly, protein termini evidence in TopFIND is inferred from other databases such as ENSEMBL transcripts, TISdb for alternative translation initiation, MEROPS for protein cleavage by proteases, and UniProt for canonical and protein isoform start sites.

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.

WormBase

facilitating insights into nematode biology

Subject(s)
Content type(s)
Country
Launched in 2000, WormBase is an international consortium of biologists and computer scientists dedicated to providing the research community with accurate, current, accessible information concerning the genetics, genomics and biology of C. elegans and some related nematodes. In addition to their curation work, all sites have ongoing programs in bioinformatics research to develop the next generations of WormBase structure, content and accessibility

ErythronDB

Erythron Database

Subject(s)
Content type(s)
Country
<<<!!!<<< The original ErythronDB site is now retired! Code for generating the web site is available here https://github.com/ErythronDB/erythrondb-docker. >>>!!!>>>

Mechanism and Catalytic Site Atlas

CSA (formerly)

Subject(s)
Content type(s)
Country
M-CSA is a database of enzyme reaction mechanisms. It provides annotation on the protein, catalytic residues, cofactors, and the reaction mechanisms of hundreds of enzymes. There are two kinds of entries in M-CSA. 'Detailed mechanism' entries are more complete and show the individual chemical steps of the mechanism as schemes with electron flow arrows. 'Catalytic Site' entries annotate the catalytic residues necessary for the reaction, but do not show the mechanism. The M-CSA (Mechanism and Catalytic Site Atlas) represents a unified resource that combines the data in both MACiE and the CSA

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.