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Found 173 result(s)

TOXMAP

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<<<!!!<<< The repository is no longer available. >>>!!!>>> Selected TOXMAP data can be accesse from the following sites: U.S. EPA Toxics Release Program (TRI) (https://www.epa.gov/toxics-release-inventory-tri-program) U.S. EPA Superfund Program (https://www.epa.gov/superfund) U.S. EPA Facilities Registry System (FRS) (https://www.epa.gov/frs) U.S. EPA Clean Air Markets Program (https://www.epa.gov/airmarkets) U.S. EPA Geospatial Applications (https://www.epa.gov/geospatial/epa-geospatial-applications) U.S. NIH NCI Surveillance, Epidemiology, and End Results Program (SEER) (https://seer.cancer.gov/) Government of Canada National Pollutant Release Inventory (NPRI) (https://www.canada.ca/en/services/environment/pollution-waste-management/national-pollutant-release-inventory.html) U.S. Census Bureau (https://www.census.gov/) U.S. Nuclear Regulatory Commission (NRC) (https://www.nrc.gov/) >>>!!!>>>

International Mouse Phenotyping Consortium

IMPC

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The IMPC is a confederation of international mouse phenotyping projects working towards the agreed goals of the consortium: To undertake the phenotyping of 20,000 mouse mutants over a ten year period, providing the first functional annotation of a mammalian genome. Maintain and expand a world-wide consortium of institutions with capacity and expertise to produce germ line transmission of targeted knockout mutations in embryonic stem cells for 20,000 known and predicted mouse genes. Test each mutant mouse line through a broad based primary phenotyping pipeline in all the major adult organ systems and most areas of major human disease. Through this activity and employing data annotation tools, systematically aim to discover and ascribe biological function to each gene, driving new ideas and underpinning future research into biological systems; Maintain and expand collaborative “networks” with specialist phenotyping consortia or laboratories, providing standardized secondary level phenotyping that enriches the primary dataset, and end-user, project specific tertiary level phenotyping that adds value to the mammalian gene functional annotation and fosters hypothesis driven research; and Provide a centralized data centre and portal for free, unrestricted access to primary and secondary data by the scientific community, promoting sharing of data, genotype-phenotype annotation, standard operating protocols, and the development of open source data analysis tools. Members of the IMPC may include research centers, funding organizations and corporations.

Mouse Genome Informatics

MGI

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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

UK-AIR

Air Information Resource

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These are the UK-AIR (Air Information Resource) webpages providing in-depth information on air quality and air pollution in the UK. A range of information is available, from the latest pollution levels, pollution forecast information, a data archive, and details of the various monitoring networks.

Human Proteinpedia

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Human Proteinpedia is a community portal for sharing and integration of human protein data. This is a joint project between Pandey at Johns Hopkins University, and Institute of Bioinformatics, Bangalore. This portal allows research laboratories around the world to contribute and maintain protein annotations. Human Protein Reference Database (HPRD) integrates data, that is deposited in Human Proteinpedia along with the existing literature curated information in the context of an individual protein. All the public data contributed to Human Proteinpedia can be queried, viewed and downloaded. Data pertaining to post-translational modifications, protein interactions, tissue expression, expression in cell lines, subcellular localization and enzyme substrate relationships may be deposited.

MyTardis

Tardis

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MyTardis began at Monash University to solve the problem of users needing to store large datasets and share them with collaborators online. Its particular focus is on integration with scientific instruments, instrument facilities and research lab file storage. Our belief is that the less effort a researcher has to expend safely storing data, the more likely they are to do so. This approach has flourished with MyTardis capturing data from areas such as protein crystallography, electron microscopy, medical imaging and proteomics and with deployments at Australian institutions such as University of Queensland, RMIT, University of Sydney and the Australian Synchrotron. Data access via https://www.massive.org.au/ and https://store.erc.monash.edu.au/experiment/view/104/ and see 'remarks'.

AceView

AceView genes

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AceView provides a curated, comprehensive and non-redundant sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These experimental cDNA sequences are first co-aligned on the genome then clustered into a minimal number of alternative transcript variants and grouped into genes. Using exhaustively and with high quality standards the available cDNA sequences evidences the beauty and complexity of mammals’ transcriptome, and the relative simplicity of the nematode and plant transcriptomes. Genes are classified according to their inferred coding potential; many presumably non-coding genes are discovered. Genes are named by Entrez Gene names when available, else by AceView gene names, stable from release to release. Alternative features (promoters, introns and exons, polyadenylation signals) and coding potential, including motifs, domains, and homologies are annotated in depth; tissues where expression has been observed are listed in order of representation; diseases, phenotypes, pathways, functions, localization or interactions are annotated by mining selected sources, in particular PubMed, GAD and Entrez Gene, and also by performing manual annotation, especially in the worm. In this way, both the anatomy and physiology of the experimentally cDNA supported human, mouse and nematode genes are thoroughly annotated.

Cell Centered Database

CCDB

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>>> !!!!! The Cell Centered Database is no longer on serice. It has been merged with "Cell image library": https://www.re3data.org/repository/r3d100000023 !!!!! <<<<

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

Cancer GenomeAtlas Data Portal

Cancer Genome Atlas Data Portal

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The Cancer Genome Atlas (TCGA) Data Portal provides a platform for researchers to search, download, and analyze data sets generated by TCGA. It contains clinical information, genomic characterization data, and high level sequence analysis of the tumor genomes. The Data Coordinating Center (DCC) is the central provider of TCGA data. The DCC standardizes data formats and validates submitted data.

Brain Transcriptome Database

BrainTx

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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.

InCHIANTI

The InCHIANTI Study

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<<<!!!<<< This repository is no longer available. >>>!!!>>>

Project Achilles

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Project Achilles is a systematic effort aimed at identifying and cataloging genetic vulnerabilities across hundreds of genomically characterized cancer cell lines. The project uses genome-wide genetic perturbation reagents (shRNAs or Cas9/sgRNAs) to silence or knock-out individual genes and identify those genes that affect cell survival. Large-scale functional screening of cancer cell lines provides a complementary approach to those studies that aim to characterize the molecular alterations (e.g. mutations, copy number alterations) of primary tumors, such as The Cancer Genome Atlas (TCGA). The overall goal of the project is to identify cancer genetic dependencies and link them to molecular characteristics in order to prioritize targets for therapeutic development and identify the patient population that might benefit from such targets. Project Achilles data is hosted on the Cancer Dependency Map Portal (DepMap) where it has been harmonized with our genomics and cellular models data. You can access the latest and all past datasets here: https://depmap.org/portal/download/all/

Brain-CODE

Brain-Centre for Ontario Data Exploration

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Brain-CODE is a large-scale informatics platform that manages the acquisition and storage of multidimensional data collected from participants with a variety of brain disorders.

National Database for Clinical Trials Related to Mental Illness

NDCT

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!!! >>> integrated in https://www.re3data.org/repository/r3d100012653 <<< !!! The National Database for Clinical Trials Related to Mental Illness (NDCT) is an informatics platform for the sharing of human subjects data from all clinical trials funded by the National Institute of Mental Health (NIMH).

Image Data Resource

IDR

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The IDR makes datasets that have never previously been accessible publicly available, allowing the community to search, view, mine and even process and analyze large, complex, multidimensional life sciences image data. Sharing data promotes the validation of experimental methods and scientific conclusions, the comparison with new data obtained by the global scientific community, and enables data reuse by developers of new analysis and processing tools.

BenchSCI

A.I. Driven Antibody Search

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BenchSci is a free platform designed to help biomedical research scientists quickly and easily identify validated antibodies from publications. Using various filters including techniques, tissue, cell lines, and more, scientists can find out published data along with the antibody that match specific experimental contexts within seconds. Free registration & access for academic research scientists.

Journal of Cell Biology - JCB DataViewer

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>>>!!!<<< Data originally published in the JCB DataViewer has been moved BioStudies. Please note that while the majority of data were moved, some authors opted to remove their data completely. >>>!!!<<< Migrated data can be found at https://www.ebi.ac.uk/biostudies/JCB/studies. Screen data are available in the Image Data Resource repository. http://idr.openmicroscopy.org/webclient/?experimenter=-1 >>>!!!<<< The DataViewer was decommissioned in 2018 as the journal evolved to an all-encompassing archive policy towards original source data and as new data repositories that go beyond archiving data and allow investigators to make new connections between datasets, potentially driving discovery, emerged. JCB authors are encouraged to make available all datasets included in the manuscript from the date of online publication either in a publicly available database or as supplemental materials hosted on the journal website. We recommend that our authors store and share their data in appropriate publicly available databases based on data type and/or community standard. >>>!!!<<<

GeneCorner Plasmid Collection

BCCM/GeneCorner Plasmid Collection

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The BCCM/GeneCorner Plasmid Collection accepts plasmids from and distributes plasmids to researchers worldwide. Funding by the Belgian Science Policy (Belspo) allowed BCCM/GeneCorner to evolve into a unique plasmid repository in Europe.

Bacterial and Viral Bioinformatics Resource Center

BV-BRC

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The Bacterial and Viral Bioinformatics Resource Center (BV-BRC) is an information system designed to support research on bacterial and viral infectious diseases. BV-BRC combines two long-running BRCs: PATRIC, the bacterial system, and IRD/ViPR, the viral systems.

The Cell Image Library

The Cell

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This library is a public and easily accessible resource database of images, videos, and animations of cells, capturing a wide diversity of organisms, cell types, and cellular processes. The Cell Image Library has been merged with "Cell Centered Database" in 2017. The purpose of the database is to advance research on cellular activity, with the ultimate goal of improving human health.

BIGG Database

Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions

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BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. BiGG integrates several published genome-scale metabolic networks into one resource with standard nomenclature which allows components to be compared across different organisms. BiGG can be used to browse model content, visualize metabolic pathway maps, and export SBML files of the models for further analysis by external software packages. Users may follow links from BiGG to several external databases to obtain additional information on genes, proteins, reactions, metabolites and citations of interest.

Chesapeake Bay Data Hub

Chesapeake Bay Program

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This interface provides access to several types of data related to the Chesapeake Bay. Bay Program databases can be queried based upon user-defined inputs such as geographic region and date range. Each query results in a downloadable, tab- or comma-delimited text file that can be imported to any program (e.g., SAS, Excel, Access) for further analysis. Comments regarding the interface are encouraged. Questions in reference to the data should be addressed to the contact provided on subsequent pages.

Edmond

The Open Research Data Repository of the Max Planck Society

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Edmond is the institutional repository of the Max Planck Society for public research data. It enables Max Planck scientists to create citable scientific assets by describing, enriching, sharing, exposing, linking, publishing and archiving research data of all kinds. Further on, all objects within Edmond have a unique identifier and therefore can be clearly referenced in publications or reused in other contexts.

GeneCards

The Human Gene Database

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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.