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Found 55 result(s)

doRiNA

database of RNA interactions in post-transcriptional regulation

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doRiNA is a database of transcriptome-wide binding site data for RNA binding proteins and microRNAs

KNB Data Repository

Knowledge Network for Biocomplexity

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The KNB Data Repository is an international repository intended to facilitate ecological, environmental and earth science research in the broadest senses. For scientists, the KNB Data Repository is an efficient way to share, discover, access and interpret complex ecological, environmental, earth science, and sociological data and the software used to create and manage those data. Due to rich contextual information provided with data in the KNB, scientists are able to integrate and analyze data with less effort. The data originate from a highly-distributed set of field stations, laboratories, research sites, and individual researchers. The KNB supports rich, detailed metadata to promote data discovery as well as automated and manual integration of data into new projects. The KNB supports a rich set of modern repository services, including the ability to assign Digital Object Identifiers (DOIs) so data sets can be confidently referenced in any publication, the ability to track the versions of datasets as they evolve through time, and metadata to establish the provenance relationships between source and derived data.

CSIRO Data Access Portal

CSIRO DAP

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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.

PDBj

Protein Data Bank Japan

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PDBj (Protein Data Bank Japan) provides a centralized PDB archive of macromolecular structures, integrated tools for data retrieval, visualization, and functional characterization. PDBj is supported by JST-NBDC and Osaka University.

Environment Climate Data Sweden

ECDS

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<<<!!!<<< The repository is no longer available 2020-02-21: no more access to "Environment Climate Data Sweden" >>>!!!<<< The transfer of records from the Environment Climate Data Sweden (ECDS) database to the Swedish National Dataservice (SND) https://www.re3data.org/repository/r3d100010146 was completed in 2019. SND is a national research infrastructure with a primary function to support the accessibility, preservation, and re-use of research data and related materials. You can search the SND research data portal specifically for Natural Science or Agricultural and Veterinary Sciences datasets. Data descriptions with associated datasets, or a direct reference/URL to data, have been migrated from the ECDS portal to the SND research data portal. Previous links to these data are now automatically directed to an SND catalogue entry. Records in the ECDS catalogue that only contained metadata (ie information that data could be accessed through another portal, e.g. Pangea), now link directly to the portal in question. If you want to make one of those data descriptions searchable in SND’s catalogue, please contact SND on snd@snd.gu.se. A small number of records were neither migrated to SND nor redirected to external providers, and they redirect. Contact SND on snd@snd.gu.se if you want more information about the closing of the ECDS portal and the migration of data descriptions to SND’s research data catalogue.

National Institute of Polar Research Science Database

Polar Data Center Science Database

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The Polar Data Center (PDC) manages the Science Database among other repositories for Japanese polar research. The Science Database is the destination repository for all Japanese Antarctic Research Expedition (JARE) data as well as the Japanese contribution to the International Polar Year (IPY) 2007-2008. Metadata are in English and Japanese, and metadata records are shared with the Global Change Master Directory.

Ensembl Fungi

e!EnsemblFungi

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EnsemblFungi is a genome-centric portal for fungal species. It is a project to maintain annotation on selected genomes.

Ensembl Genomes

e!EnsemblGenomes

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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.

Ensembl Protists

e!EnsemblProtists

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EnsemblProtists is a genome-centric portal for protists species.

Ensembl Bacteria

e!EnsemblBacteria

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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.

STOREDB

Sustaining access to Tissues and data frOm Radiobiological Experiments

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STOREDB is a platform for the archiving and sharing of primary data and outputs of all kinds, including epidemiological and experimental data, from research on the effects of radiation. It also provides a directory of bioresources and databases containing information and materials that investigators are willing to share. STORE supports the creation of a radiation research commons.

Leiden Open Variation Database

LOVD

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LOVD portal provides LOVD software and access to a list of worldwide LOVD applications through Locus Specific Database list and List of Public LOVD installations. The LOVD installations that have indicated to be included in the global LOVD listing are included in the overall LOVD querying service, which is based on an API.

Ensembl Metazoa

e!EnsemblMetazoa

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Ensembl Metazoa is a genome-centric portal for metazoan species of scientific interest.

NetPath

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<<<!!!<<< 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.

Ocean Networks Canada

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Ocean Networks Canada maintains several observatories installed in three different regions in the world's oceans. All three observatories are cabled systems that can provide power and high bandwidth communiction paths to sensors in the ocean. The infrastructure supports near real-time observations from multiple instruments and locations distributed across the Arctic, NEPTUNE and VENUS observatory networks. These observatories collect data on physical, chemical, biological, and geological aspects of the ocean over long time periods, supporting research on complex Earth processes in ways not previously possible.

DNA Data Bank of Japan

DDBJ

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DDBJ; DNA Data Bank of Japan is the sole nucleotide sequence data bank in Asia, which is officially certified to collect nucleotide sequences from researchers and to issue the internationally recognized accession number to data submitters.Since we exchange the collected data with EMBL-Bank/EBI; European Bioinformatics Institute and GenBank/NCBI; National Center for Biotechnology Information on a daily basis, the three data banks share virtually the same data at any given time. The virtually unified database is called "INSD; International Nucleotide Sequence Database DDBJ collects sequence data mainly from Japanese researchers, but of course accepts data and issue the accession number to researchers in any other countries.

HIstome

The Histone Infobase

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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.

International Directory Network

formerly: GCMD

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The CEOS International Directory Network (IDN) home page and search portal serve as NASA's contribution to the Committee on Earth Observation Satellites (CEOS). IDN's mission is to assist researchers, policy makers, and the public in the discovery of and access to data relevant to global change and Earth science research. The Draft Metadata Management Tool (DMMT) is a metadata authoring tool that IDN contributors can use to propose new or modified CMR records.

IFREMER-SISMER Portail de données marines

French Research Institute for Exploitation of the Sea - Scientific Information Systems for the Sea, Oceanographic Data

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SISMER (Scientific Information Systems for the Sea) is Ifremer's service in charge of managing numerous marine databases and information systems which Ifremer is responsible for implementing. The information systems managed by SISMER range from CATDS (SMOS satellite data) to geoscience data (bathymetry, seismics, geological samples), not forgetting water column data (physics and chemistry, data for operational oceanography – Coriolis - Copernicus CMEMS), fisheries data (Harmonie), coastal environment data (Quadrige 2) and deep-sea environment data (Archimède). SISMER therefore plays a pivotal role in marine database management both for Ifremer and for many national, European and international projects.

Electron Microscopy Data Bank

EMDB

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The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps of macromolecular complexes and subcellular structures. It covers a variety of techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography.

MycoBank

Fungal databases, nomenclature and species banks

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MycoBank is an on-line database aimed as a service to the mycological and scientific society by documenting mycological nomenclatural novelties (new names and combinations) and associated data, for example descriptions and illustrations. The nomenclatural novelties will each be allocated a unique MycoBank number that can be cited in the publication where the nomenclatural novelty is introduced. These numbers will also be used by the nomenclatural database Index Fungorum, with which MycoBank is associated.

EMDataResource

formerly: EMDataBank

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Cryo electron microscopy enables the determination of 3D structures of macromolecular complexes and cells from 2 to 100 Å resolution. EMDataResource is the unified global portal for one-stop deposition and retrieval of 3DEM density maps, atomic models and associated metadata, and is a joint effort among investigators of the Stanford/SLAC CryoEM Facility and the Research Collaboratory for Structural Bioinformatics (RCSB) at Rutgers, in collaboration with the EMDB team at the European Bioinformatics Institute. EMDataResource also serves as a resource for news, events, software tools, data standards, and validation methods for the 3DEM community. The major goal of the EMDataResource project in the current funding period is to work with the 3DEM community to (1) establish data-validation methods that can be used in the process of structure determination, (2) define the key indicators of a well-determined structure that should accompany every deposition, and (3) implement appropriate validation procedures for maps and map-derived models into a 3DEM validation pipeline.

World Register of Marine Species

WoRMS

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The World Register of Marine Species (WoRMS) integrates approximately 100 marine datbases to provide an authoritative and comprehensive list of marine organisms. WoRMS has an editorial system where taxonomic groups are managed by experts responsible for the quality of the information. WorMS register of marine species emerged from the European Register of Marine Species (ERMS) and the Flanders Marine Institute (VLIZ). WoRMS is a contribution to Lifewatch, Catalogue of Life, Encyclopedia of Life, Global Biodiversity Information Facility and the Census of Marine Life.

VertNet

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VertNet is a NSF-funded collaborative project that makes biodiversity data free and available on the web. VertNet is a tool designed to help people discover, capture, and publish biodiversity data. It is also the core of a collaboration between hundreds of biocollections that contribute biodiversity data and work together to improve it. VertNet is an engine for training current and future professionals to use and build upon best practices in data quality, curation, research, and data publishing. Yet, VertNet is still the aggregate of all of the information that it mobilizes. To us, VertNet is all of these things and more.

NCBI Structure

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The Structure database provides three-dimensional structures of macromolecules for a variety of research purposes and allows the user to retrieve structures for specific molecule types as well as structures for genes and proteins of interest. Three main databases comprise Structure-The Molecular Modeling Database; Conserved Domains and Protein Classification; and the BioSystems Database. Structure also links to the PubChem databases to connect biological activity data to the macromolecular structures. Users can locate structural templates for proteins and interactively view structures and sequence data to closely examine sequence-structure relationships.