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Found 47 result(s)

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.

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.

Estonian Biocentre Free Data

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A small genotype data repository containing data used in recent papers from the Estonian Biocentre. Most of the data pertains to human population genetics. PDF files of the papers are also freely available.

GigaDB

GigaScience Database

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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.

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.

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.

Ensembl Protists

e!EnsemblProtists

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EnsemblProtists is a genome-centric portal for protists species.

OpenNeuro

formerly: OpenfMRI

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The OpenNeuro project (formerly known as the OpenfMRI project) was established in 2010 to provide a resource for researchers interested in making their neuroimaging data openly available to the research community. It is managed by Russ Poldrack and Chris Gorgolewski of the Center for Reproducible Neuroscience at Stanford University. The project has been developed with funding from the National Science Foundation, National Institute of Drug Abuse, and the Laura and John Arnold Foundation.

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.

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.

Open PHACTS

Open Pharmacological Space

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<<<!!!<<< The Open PHACTS Linked Data API and associated infrastructure was closed down in March 2019 to allow the team to focus on the next phase. http://www.openphactsfoundation.org/open-phacts-platform-update-march-2019/ >>>!!!>>>

DAIS

Digitalni arhiv izdanja SANU

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DAIS - Digital Archive of the Serbian Academy of Sciences and Arts is a joint digital repository of the Serbian Academy of Sciences and Arts (SASA) and the research institutes under the auspices of SASA. The aim of the repository is to provide open access to publications and other research outputs resulting from the projects implemented by the SASA and its institutes. The repository uses a DSpace-based software platform developed and maintained by the Belgrade University Computer Centre (RCUB).

Barcode of Life Data Systems

BOLD Systems

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The Barcode of Life Data Systems (BOLD) provides DNA barcode data. BOLD's online workbench supports data validation, annotation, and publication for specimen, distributional, and molecular data. The platform consists of four main modules: a data portal, a database of barcode clusters, an educational portal, and a data collection workbench. BOLD is the go-to site for DNA-based identification. As the central informatics platform for DNA barcoding, BOLD plays a crucial role in assimilating and organizing data gathered by the international barcode research community. Two iBOL (International Barcode of Life) Working Groups are supporting the ongoing development of BOLD.

DataDOI

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DataDOI is an institutional research data repository managed by University of Tartu Library. DataDOI gathers all fields of research data and stands for encouraging open science and FAIR (Findable, Accessible, Interoperable, Reusable) principles. DataDOI is made for long-term preservation of research data. Each dataset is given a DOI (Digital Object Identifier) through DataCite Estonia Concortium.

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.

The International Research Institute for Climate and Society

IRI Data Library

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International Research Institute for Climate and Society (IRI) research focuses on climate, environmental monitoring, agriculture, health, water, and economic sectors in Africa, Asia and Pacific, and Latin America and Caribbean. The IRI data library is a freely accessible data repository and analysis tool. IRI allows users to view, manipulate, and download climate-related data sets through a standard web browser.

PATRIC

Pathosystems Resource Integration Center

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<<<!!!<<< This repository is no longer available. >>>!!!>>> PATRIC will go offline by mid-December2022. Here is what you need to know. As announced previously, PATRIC, the bacterial BRC, and IRD / ViPR, the viral BRCs, are being merged into the new Bacterial and Viral Bioinformatics Resource Center (BV-BRC). BV-BRC combines the data, tools, and technologies from these BRCs to provide an integrated resource for bacterial and viral genomics-based infectious disease research.

MEROPS

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

MalaCards

Human disease Database

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MalaCards is an integrated database of human maladies and their annotations, modeled on the architecture and richness of the popular GeneCards database of human genes. MalaCards mines and merges varied web data sources to generate a computerized web card for each human disease. Each MalaCard contains disease specific prioritized annotative information, as well as links between associated diseases, leveraging the GeneCards relational database, search engine, and GeneDecks set-distillation tool. As proofs of concept of the search/distill/infer pipeline we find expected elucidations, as well as potentially novel ones.

NCBI Trace Archive

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<<<!!!<<< This repository is no longer available. (Trace Archive is scheduled to retire on June 17, 2022) >>>!!!>>>

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 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.