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 44 result(s)

Ag Data Commons

USDA’s Open Research Data

Subject(s)
Content type(s)
Country
Ag Data Commons provides access to a wide variety of open data relevant to agricultural research. We are a centralized repository for data already on the web, as well as for new data being published for the first time. While compliance with the U.S. Federal public access and open data directives is important, we aim to surpass them. Our goal is to foster innovative data re-use, integration, and visualization to support bigger, better science and policy.

Animal Genome Size Database

Subject(s)
Content type(s)
Country
Welcome to the Animal Genome Size Database, Release 2.0, a comprehensive catalogue of animal genome size data.

Animal QTLdb

Animal Quantitative Trait Loci

Subject(s)
Content type(s)
Country
This Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house all publicly available QTL and trait mapping data (i.e. trait and genome location association data; collectively called "QTL data" on this site) on livestock animal species for easily locating and making comparisons within and between species. New database tools are continuely added to align the QTL and association data to other types of genome information, such as annotated genes, RH / SNP markers, and human genome maps. Besides the QTL data from species listed below, the QTLdb is open to house QTL/association date from other animal species where feasible. Note that the JAS along with other journals, now require that new QTL/association data be entered into a QTL database as part of their publication requirements.

AnimalGenome.ORG

BioMart AnimalGenome.ORG

Subject(s)
Content type(s)
Country
This is a animal and human genome database that uses the BioMart software.

ArkDB

Subject(s)
Content type(s)
Country
<<<!!!<<< The ArkDB is now CLOSED With apologies to anyone who still relies on the ArkDB data system or map-drawing tools, we've had to take the difficult decision to shut down the ArkDB system. We've not been funded to maintain it for many years now and have kept it in the air as best we could with the time that we had available but recent changes in personnel and continuing updates to the underpinning libraries mean that the effort required to keep it going outweighs the perceived benefits. If you feel that this is the wrong decision, please contact us to let us know and we'll see what we can do together You can always contact us on our Roslin Bioinformatics email address (roslin.bioinformatics@roslin.ed.ac.uk) The Roslin Bioinformatics Team 21st November 2018 >>>!!!>>>

Array Express

functional genomics data

Subject(s)
Content type(s)
Country
ArrayExpress is one of the major international repositories for high-throughput functional genomics data from both microarray and high-throughput sequencing studies, many of which are supported by peer-reviewed publications. Data sets are submitted directly to ArrayExpress and curated by a team of specialist biological curators. In the past (until 2018) datasets from the NCBI Gene Expression Omnibus database were imported on a weekly basis. Data is collected to MIAME and MINSEQE standards.

BeetleBase

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

Beta Cell Biology Consortium Reagent and Data Resources

BCBC Reagent and Data Resources

Subject(s)
Content type(s)
Country
>>>!!!<<< Sorry.we are no longer in operation >>>!!!<<< The Beta Cell Biology Consortium (BCBC) was a team science initiative that was established by the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK). It was initially funded in 2001 (RFA DK-01-014), and competitively continued both in 2005 (RFAs DK-01-17, DK-01-18) and in 2009 (RFA DK-09-011). Funding for the BCBC came to an end on August 1, 2015, and with it so did our ability to maintain active websites.!!! One of the many goals of the BCBC was to develop and maintain databases of useful research resources. A total of 813 different scientific resources were generated and submitted by BCBC investigators over the 14 years it existed. Information pertaining to 495 selected resources, judged to be the most scientifically-useful, has been converted into a static catalog, as shown below. In addition, the metadata for these 495 resources have been transferred to dkNET in the form of RDF descriptors, and all genomics data have been deposited to either ArrayExpress or GEO. Please direct questions or comments to the NIDDK Division of Diabetes, Endocrinology & Metabolic Diseases (DEM).

Birdbase

A database of avian genes & genomes

Subject(s)
Content type(s)
Country
<<<!!!<<< This repository is no longer available. >>>!!!>>> The sequencing of several bird genomes and the anticipated sequencing of many more provided the impetus to develop a model organism database devoted to the taxonomic class: Aves. Birds provide model organisms important to the study of neurobiology, immunology, genetics, development, oncology, virology, cardiovascular biology, evolution and a variety of other life sciences. Many bird species are also important to agriculture, providing an enormous worldwide food source worldwide. Genomic approaches are proving invaluable to studying traits that affect meat yield, disease resistance, behavior, and bone development along with many other factors affecting productivity. In this context, BirdBase will serve both biomedical and agricultural researchers.

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.

Brain-CODE

Brain-Centre for Ontario Data Exploration

Subject(s)
Content type(s)
Country
Brain-CODE is a large-scale informatics platform that manages the acquisition and storage of multidimensional data collected from participants with a variety of brain disorders.

Cancer Genome Anatomy Project

CGAP

Subject(s)
Content type(s)
Country
>>>!!!<<< Noticed 26.08.2020: The NCI CBIIT instance of the CGAP no longer exist on this website. The Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer has a new home at the NCI-funded Institute for Systems Biology Cancer Genomics Cloud available at the following location: https://mitelmandatabase.isb-cgc.org >>>!!!<<<

Combined QTL Map of Dairy Cattle Traits

Subject(s)
Content type(s)
Country
>>>!!! <<< 2021-09-01: repository is offline >>>!!!<<< Background: Many studies have been conducted to detect quantitative trait loci (QTL) in dairy cattle. However, these studies are diverse in terms of their differing resource populations, marker maps, phenotypes, etc, and one of the challenges is to be able to synthesise this diverse information. This web page has been constructed to provide an accessible database of studies, providing a summary of each study, facilitating an easier comparison across studies. However, it also highlights the need for uniform reporting of results of studies, to facilitate more direct comparisons being made. Description: Studies recorded in this database include complete and partial genome scans, single chromosome scans, as well as fine mapping studies, and contain all known reports that were published in peer-reviewed journals and readily available conference proceedings, initially up to April 2005. However, this data base is being added to, as indicated by the last web update. Note that some duplication of results will occur, in that there may be a number of reports on the same resource population, but utilising different marker densities or different statistical methodologies. The traits recorded in this map are milk yield, milk composition (protein yield, protein %, fat yield, fat %), and somatic cell score (SCS).

CorrDB

Animal Trait Correlation Database

Subject(s)
Content type(s)
Country
CorrDB has data of cattle, relating to meat production, milk production, growth, health, and others. This database is designed to collect all published livestock genetic/phenotypic trait correlation data, aimed at facilitating genetic network analysis or systems biology studies.

CSIRO Data Access Portal

CSIRO DAP

Subject(s)
Content type(s)
Country
The CSIRO Data Access Portal provides access to data published by CSIRO across a range of disciplines to facilitate sharing and reuse of data held by CSIRO.

DNASU plasmid repository

DNASU

Subject(s)
Content type(s)
Country
DNASU is a central repository for plasmid clones and collections. Currently we store and distribute over 200,000 plasmids including 75,000 human and mouse plasmids, full genome collections, the protein expression plasmids from the Protein Structure Initiative as the PSI: Biology Material Repository (PSI : Biology-MR), and both small and large collections from individual researchers. We are also a founding member and distributor of the ORFeome Collaboration plasmid collection.

eFish

Genomic Database Repository

Subject(s)
Content type(s)
Country
The project aims to examine and index the genomic diversity through the generation of complete mitochondrial and nuclear genome sequences of sharks and rays of the Pacific Rim. There is a huge diversity of elasmobranch fishes in this region, but many species are under threat because of poor management and conservation measures in many countries. It is absolutely critical that species’ identities are correct for conservation and fisheries management purposes. This project will provide this clarity of identity for both charismatic and commercially important species through the inclusion of ‘genetypes’ (ie., BioVouchers) and the application of genetic tools that utilize whole mitochondrial and nuclear genome sequences.

Expression Atlas

Gene Expression Atlas

Subject(s)
Content type(s)
Country
The Expression Atlas provides information on gene expression patterns under different biological conditions such as a gene knock out, a plant treated with a compound, or in a particular organism part or cell. It includes both microarray and RNA-seq data. The data is re-analysed in-house to detect interesting expression patterns under the conditions of the original experiment. There are two components to the Expression Atlas, the Baseline Atlas and the Differential Atlas. The Baseline Atlas displays information about which gene products are present (and at what abundance) in "normal" conditions (e.g. tissue, cell type). It aims to answer questions such as "which genes are specifically expressed in human kidney?". This component of the Expression Atlas consists of highly-curated and quality-checked RNA-seq experiments from ArrayExpress. It has data for many different animal and plant species. New experiments are added as they become available. The Differential Atlas allows users to identify genes that are up- or down-regulated in a wide variety of different experimental conditions such as yeast mutants, cadmium treated plants, cystic fibrosis or the effect on gene expression of mind-body practice. Both microarray and RNA-seq experiments are included in the Differential Atlas. Experiments are selected from ArrayExpress and groups of samples are manually identified for comparison e.g. those with wild type genotype compared to those with a gene knock out. Each experiment is processed through our in-house differential expression statistical analysis pipeline to identify genes with a high probability of differential expression.

FaceBase

Subject(s)
Content type(s)
Country
FaceBase is a collaborative NIDCR-funded project that houses comprehensive data in support of advancing research into craniofacial development and malformation. It serves as a community resource by curating large datasets of a variety of types from the craniofacial research community and sharing them via this website. Practices emphasize a comprehensive and multidisciplinary approach to understanding the developmental processes that create the face. The data offered spotlights high-throughput genetic, molecular, biological, imaging and computational techniques. One of the missions of this project is to facilitate cooperation and collaboration between the central coordinating center (ie, the Hub) and the craniofacial research community.

GEISHA

Gallus Expression in Situ Hybridization Analysis

Subject(s)
Content type(s)
Country
GEISHA is the online repository of in situ hybridization and corresponding metadata for genes expressed in the chicken embryo during the first six days of development.

Gemma

Tools and database for meta-analysis of functional genomics data

Subject(s)
Content type(s)
Country
Gemma is a database for the meta-analysis, re-use and sharing of genomics data, currently primarily targeted at the analysis of gene expression profiles. Gemma contains data from thousands of public studies, referencing thousands of published papers. Users can search, access and visualize co-expression and differential expression results.

GeneLab

Subject(s)
Content type(s)
Country
GeneLab is an interactive, open-access resource where scientists can upload, download, store, search, share, transfer, and analyze omics data from spaceflight and corresponding analogue experiments. Users can explore GeneLab datasets in the Data Repository, analyze data using the Analysis Platform, and create collaborative projects using the Collaborative Workspace. GeneLab promises to facilitate and improve information sharing, foster innovation, and increase the pace of scientific discovery from extremely rare and valuable space biology experiments. Discoveries made using GeneLab have begun and will continue to deepen our understanding of biology, advance the field of genomics, and help to discover cures for diseases, create better diagnostic tools, and ultimately allow astronauts to better withstand the rigors of long-duration spaceflight. GeneLab helps scientists understand how the fundamental building blocks of life itself – DNA, RNA, proteins, and metabolites – change from exposure to microgravity, radiation, and other aspects of the space environment. GeneLab does so by providing fully coordinated epigenomics, genomics, transcriptomics, proteomics, and metabolomics data alongside essential metadata describing each spaceflight and space-relevant experiment. By carefully curating and implementing best practices for data standards, users can combine individual GeneLab datasets to gain new, comprehensive insights about the effects of spaceflight on biology. In this way, GeneLab extends the scientific knowledge gained from each biological experiment conducted in space, allowing scientists from around the world to make novel discoveries and develop new hypotheses from these priceless data.

GenomeRNAi

Subject(s)
Content type(s)
Country
GenomeRNAi is a database containing phenotypes from RNA interference (RNAi) screens in Drosophila and Homo sapiens. In addition, the database provides an updated resource of RNAi reagents and their predicted quality.

GigaDB

GigaScience Database

Subject(s)
Content type(s)
Country
GigaDB primarily serves as a repository to host data and tools associated with articles published by GigaScience Press; GigaScience and GigaByte (both are online, open-access journals). GigaDB defines a dataset as a group of files (e.g., sequencing data, analyses, imaging files, software programs) that are related to and support a unit-of-work (article or study). GigaDB allows the integration of manuscript publication with supporting data and tools.

HAGR

Human Ageing Genomic Resources

Subject(s)
Content type(s)
Country
The Human Ageing Genomic Resources (HAGR) is a collection of databases and tools designed to help researchers study the genetics of human ageing using modern approaches such as functional genomics, network analyses, systems biology and evolutionary analyses.