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 38 result(s)

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.

Zentrale Biomaterialbank der Charité

Central Biomaterial Bank Charité

Subject(s)
Content type(s)
Country
Human biomaterial banks (short: biobanks) are collections of human body substances (i.e. blood, DNA, urine or tissue) connected with disease specific information. This allow for research of relations between deseases and underlying (molecular) modifications and paves the way for developing target-oriented therapies ("personalized medicine"). The biobank material arises from samples taken for therapeutical or diagnostic reasons or is extracted in the context of clinical trials. An approval for usage by the patient is always needed prior to any research activities.

Ningaloo Atlas

Subject(s)
Content type(s)
Country
The Ningaloo Atlas was created in response to the need for more comprehensive and accessible information on environmental and socio-economic data on the greater Ningaloo region. As such, the Ningaloo Atlas is a web portal to not only access and share information, but to celebrate and promote the biodiversity, heritage, value, and way of life of the greater Ningaloo region.

Host - Pathogen Interaction Database

HPIDB

Subject(s)
Content type(s)
Country
HPIDB is a public resource, which integrates experimental PPIs from various databases into a single database. The Host-Pathogen Interaction Database (HPIDB) is a genomics resource devoted to understanding molecular interactions between key organisms and the pathogens to which they are susceptible.

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.

NanoCommons Knowledge Base

NanoSolveIT Knowledge Base

Subject(s)
Content type(s)
Country
The NanoTox Knowlege Base provides access to Nanomaterials, their physico-chemical characterisations, toxicological assays and environmental data as well as computational model based descriptors.

Organelle Genome Megasequencing Program

OGMP

Subject(s)
Content type(s)
Country
The Organelle Genome Megasequencing Program (OGMP) provides mitochondrial, chloroplast, and mitochondrial plasmid genome data. OGMP tools allow direct comparison of OGMP and NCBI validated records. Includes GOBASE, a taxonomically broad organelle genome database that organizes and integrates diverse data related to mitochondria and chloroplasts.

Allen Brain Map

Data Portal

Subject(s)
Content type(s)
Country
The Allen Brain Atlas provides a unique online public resource integrating extensive gene expression data, connectivity data and neuroanatomical information with powerful search and viewing tools for the adult and developing brain in mouse, human and non-human primate

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.

heidICON

Die Heidelberger Bilddatenbank

Subject(s)
Content type(s)
Country
heidICON is provided by Heidelberg University Library and is the "Virtual Slide Collection" in progress of organization of Heidelberg University. In addition to record graphic material on current interest for research and teaching, the University departments and institutes can digitize and transfer their already existing slide collections.

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.

Hardwood Genomics Project

HWG

Subject(s)
Content type(s)
Country
This database serves forest tree scientists by providing online access to hardwood tree genomic and genetic data, including assembled reference genomes, transcriptomes, and genetic mapping information. The web site also provides access to tools for mining and visualization of these data sets, including BLAST for comparing sequences, Jbrowse for browsing genomes, Apollo for community annotation and Expression Analysis to build gene expression heatmaps.

HIstome

The Histone Infobase

Subject(s)
Content type(s)
Country
HIstome: The Histone Infobase is a database of human histones, their post-translational modifications and modifying enzymes. HIstome is a combined effort of researchers from two institutions, Advanced Center for Treatment, Research and Education in Cancer (ACTREC), Navi Mumbai and Center of Excellence in Epigenetics, Indian Institute of Science Education and Research (IISER), Pune.

studyforrest

Subject(s)
Content type(s)
Country
This project is an open invitation to anyone and everyone to participate in a decentralized effort to explore the opportunities of open science in neuroimaging. We aim to document how much (scientific) value can be generated from a data release — from the publication of scientific findings derived from this dataset, algorithms and methods evaluated on this dataset, and/or extensions of this dataset by acquisition and incorporation of new data. The project involves the processing of acoustic stimuli. In this study, the scientists have demonstrated an audiodescription of classic "Forrest Gump" to subjects, while researchers using functional magnetic resonance imaging (fMRI) have captured the brain activity of test candidates in the processing of language, music, emotions, memories and pictorial representations.In collaboration with various labs in Magdeburg we acquired and published what is probably the most comprehensive sample of brain activation patterns of natural language processing. Volunteers listened to a two-hour audio movie version of the Hollywood feature film "Forrest Gump" in a 7T MRI scanner. High-resolution brain activation patterns and physiological measurements were recorded continuously. These data have been placed into the public domain, and are freely available to the scientific community and the general public.

doRiNA

database of RNA interactions in post-transcriptional regulation

Subject(s)
Content type(s)
Country
doRiNA is a database of transcriptome-wide binding site data for RNA binding proteins and microRNAs

bii

BioInvestigationIndex

Subject(s)
Content type(s)
Country
BioInvestigation Index database enables storing and querying functionalities of experimental biological and biomedical metadata of Leibniz Institute of Plant Biochemistry

Universal PBM Resource for Oligonucleotide Binding Evaluation

UniPROBE

Subject(s)
Content type(s)
Country
The UniPROBE (Universal PBM Resource for Oligonucleotide Binding Evaluation) database hosts data generated by universal protein binding microarray (PBM) technology on the in vitro DNA binding specificities of proteins. This initial release of the UniPROBE database provides a centralized resource for accessing comprehensive data on the preferences of proteins for all possible sequence variants ('words') of length k ('k-mers'), as well as position weight matrix (PWM) and graphical sequence logo representations of the k-mer data. In total, the database currently hosts DNA binding data for 406 nonredundant proteins from a diverse collection of organisms, including the prokaryote Vibrio harveyi, the eukaryotic malarial parasite Plasmodium falciparum, the parasitic Apicomplexan Cryptosporidium parvum, the yeast Saccharomyces cerevisiae, the worm Caenorhabditis elegans, mouse, and human. The database's web tools (on the right) include a text-based search, a function for assessing motif similarity between user-entered data and database PWMs, and a function for locating putative binding sites along user-entered nucleotide sequences

OpenWorm

Subject(s)
Content type(s)
Country
OpenWorm aims to build the first comprehensive computational model of the Caenorhabditis elegans (C. elegans), a microscopic roundworm. With only a thousand cells, it solves basic problems such as feeding, mate-finding and predator avoidance. Despite being extremely well studied in biology, this organism still eludes a deep, principled understanding of its biology. We are using a bottom-up approach, aimed at observing the worm behaviour emerge from a simulation of data derived from scientific experiments carried out over the past decade. To do so we are incorporating the data available in the scientific community into software models. We are engineering Geppetto and Sibernetic, open-source simulation platforms, to be able to run these different models in concert. We are also forging new collaborations with universities and research institutes to collect data that fill in the gaps All the code we produce in the OpenWorm project is Open Source and available on GitHub.

Animal Genome Tracks on GBrowse

Subject(s)
Content type(s)
Country
Genome track alignments using GBrowse on this site are featured with: (1) Annotated and predicted genes and transcripts; (2) QTL / SNP Association tracks; (3) OMIA genes; (4) Various SNP Chip tracks; (5) Other mapping fetures or elements that are available.

The MaxQuant DataBase

MaxQB

Subject(s)
Content type(s)
Country
MaxQB stores and displays collections of large proteomics projects and allows joint analysis and comparison. As a first dataset is contains proteome data of 11 different human cell lines. The 11 cell line proteomes together identify proteins expressed from more than half of all human genes. For each protein of interest, expression levels estimated by label-free quantification can be visualized across the cell lines. Similarly, the expression rank order and estimated amount of each protein within each proteome are plotted.

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.

Physical mapping data at Canada's Michael Smith Genome Sciences Centre - Data

Physical Mapping Data Access

Subject(s)
Content type(s)
Country
FPC Mapping data files from species that have been fingerprinted at Canada's Michael Smith Genome Sciences Centre (BCGSC).

International Long Term Ecological Research

ILTER

Subject(s)
Content type(s)
Country
ILTER is a 'network of networks', a global network of research sites located in a wide array of ecosystems that can help understand environmental change across the globe. ILTER's focus is on long-term, site-based research and monitoring.

Virtual Liver Network

VLN

Subject(s)
Content type(s)
Country
<<<!!!<<<no longer avialable>>>!!!>>>

European Nucleotide Archive

ENA

Subject(s)
Content type(s)
Country
The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. A typical workflow includes the isolation and preparation of material for sequencing, a run of a sequencing machine in which sequencing data are produced and a subsequent bioinformatic analysis pipeline. ENA records this information in a data model that covers input information (sample, experimental setup, machine configuration), output machine data (sequence traces, reads and quality scores) and interpreted information (assembly, mapping, functional annotation). Data arrive at ENA from a variety of sources. These include submissions of raw data, assembled sequences and annotation from small-scale sequencing efforts, data provision from the major European sequencing centres and routine and comprehensive exchange with our partners in the International Nucleotide Sequence Database Collaboration (INSDC). Provision of nucleotide sequence data to ENA or its INSDC partners has become a central and mandatory step in the dissemination of research findings to the scientific community. ENA works with publishers of scientific literature and funding bodies to ensure compliance with these principles and to provide optimal submission systems and data access tools that work seamlessly with the published literature.