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
Found 28 result(s)

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.

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).

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.

CancerModels.Org

formerly; Patients-derived tumor xenograft finder

Subject(s)
Content type(s)
Country
Patients-derived tumor xenograft (PDX) mouse models are an important oncology research platform to study tumor evolution, drug response and personalised medicine approaches. We have expanded to organoids and cell lines and are now called CancerModels.Org

Cancer Genomics Hub

CGHub

Subject(s)
Content type(s)
Country
>>>>!!!!<<<< The Cancer Genomics Hub mission is now completed. The Cancer Genomics Hub was established in August 2011 to provide a repository to The Cancer Genome Atlas, the childhood cancer initiative Therapeutically Applicable Research to Generate Effective Treatments and the Cancer Genome Characterization Initiative. CGHub rapidly grew to be the largest database of cancer genomes in the world, storing more than 2.5 petabytes of data and serving downloads of nearly 3 petabytes per month. As the central repository for the foundational genome files, CGHub streamlined team science efforts as data became as easy to obtain as downloading from a hard drive. The convenient access to Big Data, and the collaborations that CGHub made possible, are now essential to cancer research. That work continues at the NCI's Genomic Data Commons. All files previously stored at CGHub can be found there. The Website for the Genomic Data Commons is here: https://gdc.nci.nih.gov/ >>>>!!!!<<<< The Cancer Genomics Hub (CGHub) is a secure repository for storing, cataloging, and accessing cancer genome sequences, alignments, and mutation information from the Cancer Genome Atlas (TCGA) consortium and related projects. Access to CGHub Data: All researchers using CGHub must meet the access and use criteria established by the National Institutes of Health (NIH) to ensure the privacy, security, and integrity of participant data. CGHub also hosts some publicly available data, in particular data from the Cancer Cell Line Encyclopedia. All metadata is publicly available and the catalog of metadata and associated BAMs can be explored using the CGHub Data Browser.

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

PathCards

Pathway Unification Database

Subject(s)
Content type(s)
Country
PathCards is an integrated database of human biological pathways and their annotations. Human pathways were clustered into SuperPaths based on gene content similarity. Each PathCard provides information on one SuperPath which represents one or more human pathways.

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.

BeetleBase

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

NCBI Datasets

Subject(s)
Content type(s)
Country
NCBI Datasets is a continually evolving platform designed to provide easy and intuitive access to NCBI’s sequence data and metadata. NCBI Datasets is part of the NIH Comparative Genomics Resource (CGR). CGR facilitates reliable comparative genomics analyses for all eukaryotic organisms through an NCBI Toolkit and community collaboration.

Kyoto Encyclopedia of Genes and Genomes

KEGG

Subject(s)
Content type(s)
Country
KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies

Pain Genes Database

PainGenesdb

Subject(s)
Content type(s)
Country
<<<!!!<<< The data are no longer accessible. Message: Adobe Flash Player is no longer supported >>>!!!>>>

MEROPS

Subject(s)
Content type(s)
Country
The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them.

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.

National Genomics Data Center

国家基因组科学数据中心

Subject(s)
Content type(s)
Country
The National Genomics Data Center (NGDC), part of the China National Center for Bioinformation (CNCB), advances life & health sciences by providing open access to a suite of resources, with the aim to translate big data into big discoveries and support worldwide activities in both academia and industry.

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.

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>>>!!!>>>

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.

Metlin

The original and most comprehensive MS/MS metabolite database

Subject(s)
Content type(s)
Country
METLIN represents the largest MS/MS collection of data with the database generated at multiple collision energies and in positive and negative ionization modes. The data is generated on multiple instrument types including SCIEX, Agilent, Bruker and Waters QTOF mass spectrometers.

Mouse Genome Informatics

MGI

Subject(s)
Content type(s)
Country
MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease. The projects contributing to this resource are: Mouse Genome Database (MGD) Project, Gene Expression Database (GXD) Project, Mouse Tumor Biology (MTB) Database Project, Gene Ontology (GO) Project at MGI, MouseMine Project, MouseCyc Project at MGI

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.

Screening Unit Berlin-Buch

Screening Unit Jens Peter von Kries

Subject(s)
Content type(s)
Country
The mission of the platform is to enable access for academic projects towards experiments in high-throughput without loss of IP and on a cost basis, which does not restrict access towards HTS usage. The FMP hosts the central open access technology platform of EU-OPENSCREEN, the ChemBioNet and theHelmholtz-Initiative für Wirkstoffforschung, the Screening Unit. The Unit serves for systematic screening of large compound or genome-wide RNAi libraries with state-of-the-art equipment like automated microscopes and microfluidic systems. The Screening Unit is part of the Chemical Biology Platform of the FMP also supported by the MDC. See also: https://www.mdc-berlin.de/screening-unit

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.

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.

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.