Filter
Reset all

Subjects

Content Types

Countries

AID systems

API

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
  • 1 (current)
Found 23 result(s)

Online Mendelian Inheritance in Animals

OMIA

Subject(s)
Content type(s)
Country
Online Mendelian Inheritance in Animals (OMIA) is a catalogue/compendium of inherited disorders, other (single-locus) traits, and genes in 218 animal species (other than human and mouse and rats, which have their own resources) authored by Professor Frank Nicholas of the University of Sydney, Australia, with help from many people over the years. OMIA information is stored in a database that contains textual information and references, as well as links to relevant PubMed and Gene records at the NCBI, and to OMIM and Ensembl.

Stanford Microarray Database

SMD

Subject(s)
Content type(s)
Country
>>>!!!<<< SMD has been retired. After approximately fifteen years of microarray-centric research service, the Stanford Microarray Database has been retired. We apologize for any inconvenience; please read below for possible resolutions to your queries. If you are looking for any raw data that was directly linked to SMD from a manuscript, please search one of the public repositories. NCBI Gene Expression Omnibus EBI ArrayExpress All published data were previously communicated to one (or both) of the public repositories. Alternatively, data for publications between 1997 and 2004 were likely migrated to the Princeton University MicroArray Database, and are accessible there. If you are looking for a manuscript supplement (i.e. from a domain other than smd.stanford.edu), perhaps try searching the Internet Archive: Wayback Machine https://archive.org/web/ . >>>!!!<<< The Stanford Microarray Database (SMD) is a DNA microarray research database that provides a large amount of data for public use.

Autism Chromosome Rearrangement Database

ACRD

Subject(s)
Content type(s)
Country
The Autism Chromosome Rearrangement Database is a collection of hand curated breakpoints and other genomic features, related to autism, taken from publicly available literature: databases and unpublished data. The database is continuously updated with information from in-house experimental data as well as data from published research studies.

NCBI Gene

Gene

Subject(s)
Content type(s)
Country
The Gene database provides detailed information for known and predicted genes defined by nucleotide sequence or map position. Gene supplies gene-specific connections in the nexus of map, sequence, expression, structure, function, citation, and homology data. Unique identifiers are assigned to genes with defining sequences, genes with known map positions, and genes inferred from phenotypic information. These gene identifiers are used throughout NCBI's databases and tracked through updates of annotation. Gene includes genomes represented by NCBI Reference Sequences (or RefSeqs) and is integrated for indexing and query and retrieval from NCBI's Entrez and E-Utilities systems.

Database of Genomic Variants Archive

DGVa

Subject(s)
Content type(s)
Country
<<<!!!<<< Phasing out support for the Database of Genomic Variants archive (DGVa). The submission, archiving, and presentation of structural variation services offered by the DGVa is transitioning to the European Variation Archive (EVA) https://www.re3data.org/repository/r3d100011553. All of the data shown in the DGVa website is already searchable and browsable from the EVA Study Browser. Submission of structural variation data to EVA is done using the VCF format. The VCF specification allows representing multiple types of structural variants such as insertions, deletions, duplications and copy-number variants. Other features such as symbolic alleles, breakends, confidence intervals etc., support more complex events, such as translocations at an imprecise position. >>>!!!>>>

Ensembl Metazoa

e!EnsemblMetazoa

Subject(s)
Content type(s)
Country
Ensembl Metazoa is a genome-centric portal for metazoan species of scientific interest.

Ensembl Plants

e!EnsemblPlants

Subject(s)
Content type(s)
Country
EnsemblPlants is a genome-centric portal for plant species. Ensembl Plants is developed in coordination with other plant genomics and bioinformatics groups via the EBI's role in the transPLANT consortium.

Brain Transcriptome Database

BrainTx

Subject(s)
Content type(s)
Country
The Brain Transcriptome Database (BrainTx) project aims to create an integrated platform to visualize and analyze our original transcriptome data and publicly accessible transcriptome data related to the genetics that underlie the development, function, and dysfunction stages and states of the brain.

JGI MycoCosm

MycoCosm - the fungal genomics resource

Subject(s)
Content type(s)
Country
MycoCosm, the DOE JGI’s web-based fungal genomics resource, which integrates fungal genomics data and analytical tools for fungal biologists. It provides navigation through sequenced genomes, genome analysis in context of comparative genomics and genome-centric view. MycoCosm promotes user community participation in data submission, annotation and analysis.

International HapMap Project

国际人类基因组单体型图计划

Subject(s)
Content type(s)
Country
<<<!!!<<< OFFLINE >>>!!!>>> A recent computer security audit has revealed security flaws in the legacy HapMap site that require NCBI to take it down immediately. We regret the inconvenience, but we are required to do this. That said, NCBI was planning to decommission this site in the near future anyway (although not quite so suddenly), as the 1,000 genomes (1KG) project has established itself as a research standard for population genetics and genomics. NCBI has observed a decline in usage of the HapMap dataset and website with its available resources over the past five years and it has come to the end of its useful life. The International HapMap Project is a multi-country effort to identify and catalog genetic similarities and differences in human beings. Using the information in the HapMap, researchers will be able to find genes that affect health, disease, and individual responses to medications and environmental factors. The Project is a collaboration among scientists and funding agencies from Japan, the United Kingdom, Canada, China, Nigeria, and the United States. All of the information generated by the Project will be released into the public domain. The goal of the International HapMap Project is to compare the genetic sequences of different individuals to identify chromosomal regions where genetic variants are shared. By making this information freely available, the Project will help biomedical researchers find genes involved in disease and responses to therapeutic drugs. In the initial phase of the Project, genetic data are being gathered from four populations with African, Asian, and European ancestry. Ongoing interactions with members of these populations are addressing potential ethical issues and providing valuable experience in conducting research with identified populations. Public and private organizations in six countries are participating in the International HapMap Project. Data generated by the Project can be downloaded with minimal constraints. The Project officially started with a meeting in October 2002 (https://www.genome.gov/10005336/) and is expected to take about three years.

IPK Gatersleben

Leibniz Institute of Plant Genetics and Crop Plant Research

Subject(s)
Content type(s)
Country
The IPK stores a large volume of research results and information in various databases. The Institute of Plant Genetics and Crop Plant Research IPK Gatersleben, is a nonprofit research institution for crop genetics and molecular biology, and is part of the Leibniz Association. The mission of the IPK Gatersleben is to conduct basic and applied research in the area of plant genetics and crop plant research. The results of this work are not only of significant benefit to plant breeders and the agricultural industry, but also to the food, feed, and chemical industry. An additional research area, the use of renewable raw materials, is increasingly gaining in importance.

NCBI dbVar

Database of genomic structural VARiation

Subject(s)
Content type(s)
Country
The dbVar is a database of genomic structural variation containing data from multiple gene studies. Users can browse data containing the number of variant cells from each study, and filter studies by organism, study type, method and genomic variant. Organisms include human, mouse, cattle and several additional animals. ***NCBI will phase out support for non-human organism data in dbSNP and dbVar beginning on September 1, 2017 ***

Emage

e-Mouse Atlas of Gene Expression

Subject(s)
Content type(s)
Country
EMAGE (e-Mouse Atlas of Gene Expression) is an online biological database of gene expression data in the developing mouse (Mus musculus) embryo. The data held in EMAGE is spatially annotated to a framework of 3D mouse embryo models produced by EMAP (e-Mouse Atlas Project). These spatial annotations allow users to query EMAGE by spatial pattern as well as by gene name, anatomy term or Gene Ontology (GO) term. EMAGE is a freely available web-based resource funded by the Medical Research Council (UK) and based at the MRC Human Genetics Unit in the Institute of Genetics and Molecular Medicine, Edinburgh, UK.

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.

GallusReactome

Subject(s)
Content type(s)
Country
>>>!!!<<< 29.01.2020: Gallus.Reactome is offline >>>!!!<<<

Ensembl Bacteria

e!EnsemblBacteria

Subject(s)
Content type(s)
Country
This site provides access to complete, annotated genomes from bacteria and archaea (present in the European Nucleotide Archive) through the Ensembl graphical user interface (genome browser). Ensembl Bacteria contains genomes from annotated INSDC records that are loaded into Ensembl multi-species databases, using the INSDC annotation import pipeline.

Ensembl Protists

e!EnsemblProtists

Subject(s)
Content type(s)
Country
EnsemblProtists is a genome-centric portal for protists species.

cropPAL

Compendium of crop Proteins with Annotated Locations

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

Cancer Cell Line Encyclopedia

CCLE

Subject(s)
Content type(s)
Country
The Cancer Cell Line Encyclopedia project is a collaboration between the Broad Institute, and the Novartis Institutes for Biomedical Research and its Genomics Institute of the Novartis Research Foundation to conduct a detailed genetic and pharmacologic characterization of a large panel of human cancer models, to develop integrated computational analyses that link distinct pharmacologic vulnerabilities to genomic patterns and to translate cell line integrative genomics into cancer patient stratification. The CCLE provides public access to genomic data, analysis and visualization for about 1000 cell lines.

Ensembl Fungi

e!EnsemblFungi

Subject(s)
Content type(s)
Country
EnsemblFungi is a genome-centric portal for fungal species. It is a project to maintain annotation on selected genomes.

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.

Plant Genomics and Phenomics Research Data Repository

PGP Repository

Subject(s)
Content type(s)
Country
The Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) and German Plant Phenotyping Network (DPPN) has jointly initiated the Plant Genomics and Phenomics Research Data Repository (PGP) as infrastructure to comprehensively publish plant research data. This covers in particular cross-domain datasets that are not being published in central repositories because of its volume or unsupported data scope, like image collections from plant phenotyping and microscopy, unfinished genomes, genotyping data, visualizations of morphological plant models, data from mass spectrometry as well as software and documents.

Ensembl Genomes

e!EnsemblGenomes

Subject(s)
Content type(s)
Country
The Ensembl genome annotation system, developed jointly by the EBI and the Wellcome Trust Sanger Institute, has been used for the annotation, analysis and display of vertebrate genomes since 2000. Since 2009, the Ensembl site has been complemented by the creation of five new sites, for bacteria, protists, fungi, plants and invertebrate metazoa, enabling users to use a single collection of (interactive and programatic) interfaces for accessing and comparing genome-scale data from species of scientific interest from across the taxonomy. In each domain, we aim to bring the integrative power of Ensembl tools for comparative analysis, data mining and visualisation across genomes of scientific interest, working in collaboration with scientific communities to improve and deepen genome annotation and interpretation.