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 213 result(s)

Plant Transcription Factor Database

PlantTFDB

Subject(s)
Content type(s)
Country
Species included in PlantTFDB 4.0 covers the main lineages of green plants. Therefore, PlantTFDB provides genomic TF repertoires across Viridiplantae. To provide comprehensive information for the TF family, a brief introduction and key references are presented for each family. Comprehensive annotations are made for each identified TF, including functional domains, 3D structures, gene ontology (GO), plant ontology (PO), expression information, expert-curated functional description, regulation information, interaction, conserved elements, references, and annotations in various databases such as UniProt, RefSeq, TransFac, STRING, and VISTA. By inferring orthologous groups and constructing phylogenetic trees, evolutionary relationships among identified TFs were inferred. In addition, PlantTFDB has a simple and user-friendly interface to allow users to query based on combined conditions or make sequence similarity search using BLAST. The new version PlantTFDB 5.0 has been incorporated into PlantRegMap http://plantregmap.gao-lab.org/.

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.

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.

Avibase

the world bird database

Subject(s)
Content type(s)
Country
Avibase is an extensive database information system about all birds of the world, containing over 60 million records about 10,000 species and 22,000 subspecies of birds, including distribution information, taxonomy, synonyms in several languages and more. This site is managed by Denis Lepage and hosted by Bird Studies Canada, the Canadian copartner of Birdlife International. Avibase has been a work in progress since 1992 and I am now pleased to offer it as a service to the bird-watching and scientific community.

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. >>>!!!>>>

JASPAR

Subject(s)
Content type(s)
Country
JASPAR is the leading open-access database of matrix profiles describing the DNA-binding patterns of transcription factors and other proteins interacting with DNA in a sequence-specific manner.

ModelDB

Subject(s)
Content type(s)
Country
ModelDB is a curated database of published models in the broad domain of computational neuroscience. It addresses the need for access to such models in order to evaluate their validity and extend their use. It can handle computational models expressed in any textual form, including procedural or declarative languages (e.g. C++, XML dialects) and source code written for any simulation environment. The model source code doesn't even have to reside inside ModelDB; it just has to be available from some publicly accessible online repository or WWW site.

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

NOAA Antarctic UV Monitoring Network

formerly: National Science Foundation Polar Programs UV Monitoring Network

Subject(s)
Content type(s)
Country
The National Science Foundation (NSF) Ultraviolet (UV) Monitoring Network provides data on ozone depletion and the associated effects on terrestrial and marine systems. Data are collected from 7 sites in Antarctica, Argentina, United States, and Greenland. The network is providing data to researchers studying the effects of ozone depletion on terrestrial and marine biological systems. Network data is also used for the validation of satellite observations and for the verification of models describing the transfer of radiation through the atmosphere.

Old Bailey Proceedings Online

Subject(s)
Content type(s)
Country
The Old Bailey Proceedings Online makes available a fully searchable, digitised collection of all surviving editions of the Old Bailey Proceedings from 1674 to 1913, and of the Ordinary of Newgate's Accounts between 1676 and 1772. It allows access to over 197,000 trials and biographical details of approximately 2,500 men and women executed at Tyburn, free of charge for non-commercial use. In addition to the text, accessible through both keyword and structured searching, this website provides digital images of all 190,000 original pages of the Proceedings, 4,000 pages of Ordinary's Accounts, advice on methods of searching this resource, information on the historical and legal background to the Old Bailey court and its Proceedings, and descriptions of published and manuscript materials relating to the trials covered. Contemporary maps, and images have also been provided.

The Monarch Initiative

Monarch Initiative

Subject(s)
Content type(s)
Country
As with most biomedical databases, the first step is to identify relevant data from the research community. The Monarch Initiative is focused primarily on phenotype-related resources. We bring in data associated with those phenotypes so that our users can begin to make connections among other biological entities of interest. We import data from a variety of data sources. With many resources integrated into a single database, we can join across the various data sources to produce integrated views. We have started with the big players including ClinVar and OMIM, but are equally interested in boutique databases. You can learn more about the sources of data that populate our system from our data sources page https://monarchinitiative.org/about/sources.

NetPath

Subject(s)
Content type(s)
Country
<<<!!!<<< This repository is no longer available. >>>!!!>>> NetPath is currently one of the largest open-source repository of human signaling pathways that is all set to become a community standard to meet the challenges in functional genomics and systems biology. Signaling networks are the key to deciphering many of the complex networks that govern the machinery inside the cell. Several signaling molecules play an important role in disease processes that are a direct result of their altered functioning and are now recognized as potential therapeutic targets. Understanding how to restore the proper functioning of these pathways that have become deregulated in disease, is needed for accelerating biomedical research. This resource is aimed at demystifying the biological pathways and highlights the key relationships and connections between them. Apart from this, pathways provide a way of reducing the dimensionality of high throughput data, by grouping thousands of genes, proteins and metabolites at functional level into just several hundreds of pathways for an experiment. Identifying the active pathways that differ between two conditions can have more explanatory power than just a simple list of differentially expressed genes and proteins.

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.

Ensembl Metazoa

e!EnsemblMetazoa

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

Encyclopedia of Life

eol

Subject(s)
Content type(s)
Country
Our knowledge of the many life-forms on Earth - of animals, plants, fungi, protists and bacteria - is scattered around the world in books, journals, databases, websites, specimen collections, and in the minds of people everywhere. Imagine what it would mean if this information could be gathered together and made available to everyone – anywhere – at a moment’s notice. This dream is becoming a reality through the Encyclopedia of Life.

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.

DEG

Database of Essential Genes

Subject(s)
Content type(s)
Country
DEG hosts records of currently available essential genomic elements, such as protein-coding genes and non-coding RNAs, among bacteria, archaea and eukaryotes. Essential genes in a bacterium constitute a minimal genome, forming a set of functional modules, which play key roles in the emerging field, synthetic biology.

Newfoundland and Labrador Open Data

Subject(s)
Content type(s)
Country
The Newfoundland and Labrador Open Data repository increases access to government information and data.

Canadian Opinion Research Archive

CORA

Subject(s)
Content type(s)
Country
The Canadian Opinion Research Archive at Queen's University makes available commercial and independent surveys to the academic, research and journalistic communities. Founded in 1992, CORA contains hundreds of surveys including thousands of discrete items collected by major commercial Canadian firms dating back to the 1970s. CORA is continually adding new surveys and is always soliciting new data from commercial research firms, independent think tanks, research institutes, NGOs, and academic researchers. This website also includes readily accessible results from these surveys, tracking Canadian opinion over time on frequently asked survey questions, as well as tabular results from recent Canadian surveys, and more general information on polling. This material is made available as a public service by CORA and its partners.

BioStudies

Subject(s)
Content type(s)
Country
The BioStudies database holds descriptions of biological studies, links to data from these studies in other databases at EMBL-EBI or outside, as well as data that do not fit in the structured archives at EMBL-EBI. The database accepts submissions via an online tool, or in a simple tab-delimited format. It also enables authors to submit supplementary information and link to it from the publication.

Bitbucket

Atlassian Bitbucket

Subject(s)
Content type(s)
Country
Bitbucket is a web-based version control repository hosting service owned by Atlassian, for source code and development projects that use either Mercurial or Git revision control systems.

Buckeye Speech Corpus

Subject(s)
Content type(s)
Country
The Buckeye Corpus of conversational speech contains high-quality recordings from 40 speakers in Columbus OH conversing freely with an interviewer. The speech has been orthographically transcribed and phonetically labeled. The audio and text files, together with time-aligned phonetic labels, are stored in a format for use with speech analysis software (Xwaves and Wavesurfer). Software for searching the transcription files is currently being written.

HALO database

High Altitude and LOng Range database

Subject(s)
Content type(s)
Country
HALO-DB is the web platform of a data retrieval and long-term archive system. The system was established to hold and to manage a wide range of data based on observations of the HALO research aircraft and data which are related to HALO observations. HALO (High-Altitude and LOng-range aircraft) is the new German research aircraft (German Science Community (DFG)). The aircraft, a Gulfstream GV-550 Business-Jet, is strongly modified for the application as a research platform. HALO offers several advantages for scientific campaigns, such as its high range of more than 10000 km, a high maximum altitude of more than 15 km, as well as a relatively high payload.

Ocean Science Information System

OSIS

Subject(s)
Content type(s)
Country
Our system consists of a portal (portal.geomar.de), providing access to several projects with personal password. The portal offers document exchange, common or individual blogs and fora and implementation of external webpages and -services. Moreover, you can access the expedition database, that organizes data description and exchange of cruises and expeditions for each project. Expeditions are linked to KML-files (Google-Earth compatible), allowing a visualization of all stations of a cruise/expedition. We established the linkage to the publications database /repository OceanRep (EPrints), as well as the description of model-output and linkage to paper publications.

Madrigal Database

Cedar Madrigal

Subject(s)
Content type(s)
Country
The OpenMadrigal project seeks to develop and support an on-line database for geospace data. The project has been led by MIT Haystack Observatory since 1980, but now has active support from Jicamarca Observatory and other community members. Madrigal is a robust, World Wide Web based system capable of managing and serving archival and real-time data, in a variety of formats, from a wide range of ground-based instruments. Madrigal is installed at a number of sites around the world. Data at each Madrigal site is locally controlled and can be updated at any time, but shared metadata between Madrigal sites allow searching of all Madrigal sites at once from any Madrigal site. Data is local; metadata is shared.