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Found 61 result(s)

Global Health Data Exchange

GHDx

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The GHDx is our user-friendly and searchable data catalog for global health, demographic, and other health-related datasets. It provides detailed information about datasets ranging from censuses and surveys to health records and vital statistics, globally. It also serves as a platform for data owners to share their data with the public. The GDB Compare visualization, which allows the user to see rate of change in disease incidence, globally or by country, by age or across all ages, is especially powerful as a tool. Be sure to try adding a bottom chart, like the map, to augment the treemap that loads by default in the top chart.

eagle-i

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>>>!!!<<< The repository is no longer available. >>>!!!<<< The eagle-i National Network and eagle-i resource search at www.eagle-.net was retired on November 4, 2021.!!! Groundbreaking biomedical research requires access to cutting edge scientific resources; however such resources are often invisible beyond the laboratories or universities where they were developed. eagle-i is a discovery platform that helps biomedical scientists find previously invisible, but highly valuable, resources.

Open Tree of Life

Tree of Life - Evolution

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The tree of life links all biodiversity through a shared evolutionary history. This project will produce the first online, comprehensive first-draft tree of all 1.8 million named species, accessible to both the public and scientific communities. Assembly of the tree will incorporate previously-published results, with strong collaborations between computational and empirical biologists to develop, test and improve methods of data synthesis. This initial tree of life will not be static; instead, we will develop tools for scientists to update and revise the tree as new data come in. Early release of the tree and tools will motivate data sharing and facilitate ongoing synthesis of knowledge.

Ontology Lookup Service

OLS

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The Ontology Lookup Service (OLS) is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions. The user can browse the ontologies through the website as well as programmatically via the OLS API. The OLS provides a web service interface to query multiple ontologies from a single location with a unified output format.The OLS can integrate any ontology available in the Open Biomedical Ontology (OBO) format. The OLS is an open source project hosted on Google Code.

Host - Pathogen Interaction Database

HPIDB

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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.

RAMEDIS

Rare Metabolic Diseases Database

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The RAMEDIS system is a platform independent, web-based information system for rare metabolic diseases based on filed case reports. It was developed in close cooperation with clinical partners to allow them to collect information on rare metabolic diseases with extensive details, e.g. about occurring symptoms, laboratory findings, therapy and molecular data.

Autism Chromosome Rearrangement Database

ACRD

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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.

Health and Medical Care Archive

HMCA

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The Health and Medical Care Archive (HMCA) is the data archive of the Robert Wood Johnson Foundation (RWJF), the largest philanthropy devoted exclusively to health and health care in the United States. Operated by the Inter-university Consortium for Political and Social Research (ICPSR) at the University of Michigan, HMCA preserves and disseminates data collected by selected research projects funded by the Foundation and facilitates secondary analyses of the data. Our goal is to increase understanding of health and health care in the United States through secondary analysis of RWJF-supported data collections

Open Data Commons for Spinal Cord Injury

ODC-SCI

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A community platform to Share Data, Publish Data with a DOI, and get Citations. Advancing Spinal Cord Injury research through sharing of data from basic and clinical research.

AmoebaDB

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AmoebaDB belongs to the EuPathDB family of databases and is an integrated genomic and functional genomic database for Entamoeba and Acanthamoeba parasites. In its first iteration (released in early 2010), AmoebaDB contains the genomes of three Entamoeba species (see below). AmoebaDB integrates whole genome sequence and annotation and will rapidly expand to include experimental data and environmental isolate sequences provided by community researchers . The database includes supplemental bioinformatics analyses and a web interface for data-mining.

ARS

Antibiotika-Resistenz-Surveillance

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With ARS - Antimicrobial Resistance Surveillance in Germany - the infrastructure for a nationwide surveillance of antimicrobial resistance has been established, which covers both the inpatient medical care and the ambulatory care sector. This is intended to reliable data on the epidemiology of antimicrobial resistance in Germany and differential statements provided by structural features of the health care and by region are possible. ARS is designed as a laboratory-based surveillance system for continuous collection of resistance data from routine for the full range of clinically relevant bacterial pathogens. Project participants and thus data suppliers are laboratories that analyze samples of medical facilities and doctors' offices microbiologically.

Metlin

The original and most comprehensive MS/MS metabolite database

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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.

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.

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 !!!!! <<<<

Virus Pathogen Resource

ViPR

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<<<!!!<<< This repository is no longer available. >>>!!!>>> Migration of the data, tools, and services from IRD and ViPR to BV-BRC is complete! We are now in the sunsetting phase of the transition. Starting on October 31, 2022, launching the IRD or ViPR home pages will redirect you to the new BV-BRC home page. The current plan is to completely shut down IRD and ViPR by the end of this calendar year. Although it will still be possible to use those sites until shutdown, we strongly encourage you to start using BV-BRC now.

Genomic Data Commons

GDC

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The NCI's Genomic Data Commons (GDC) provides the cancer research community with a unified data repository that enables data sharing across cancer genomic studies in support of precision medicine. The GDC obtains validated datasets from NCI programs in which the strategies for tissue collection couples quantity with high quality. Tools are provided to guide data submissions by researchers and institutions.

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.

GWAS Catalog

NHGRI-EBI GWAS Catalog

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The GWAS Catalog is an open access repository of all human genome wide association studies. It is considered the “go-to” resource for genetic evidence of associations between common genetic variation and diseases or phenotypes, is accessed by scientists, clinicians and other users worldwide, and is integrated with numerous other resources. Association data and metadata are identified and extracted from the scientific literature by expert data curators. Submissions of full genome wide summary data can be made directly by authors, either before or after journal publication.

DataverseNO

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DataverseNO (https://dataverse.no) is a curated, FAIR-aligned national generic repository for open research data from all academic disciplines. DataverseNO commits to facilitate that published data remain accessible and (re)usable in a long-term perspective. The repository is owned and operated by UiT The Arctic University of Norway. DataverseNO accepts submissions from researchers primarily from Norwegian research institutions. Datasets in DataverseNO are grouped into institutional collections as well as special collections. The technical infrastructure of the repository is based on the open source application Dataverse (https://dataverse.org), which is developed by an international developer and user community led by Harvard University.

GiardiaDB

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Giardia lamblia is a significant, environmentally transmitted, human pathogen and an amitochondriate protist. It is a major contributor to the enormous worldwide burden of human diarrheal diseases, yet the basic biology of this parasite is not well understood. No virulence factor has been identified. The Giardia lamblia genome contains only 12 million base pairs distributed onto five chromosomes. Its analysis promises to provide insights about the origins of nuclear genome organization, the metabolic pathways used by parasitic protists, and the cellular biology of host interaction and avoidance of host immune systems. Since the divergence of Giardia lamblia lies close to the transition between eukaryotes and prokaryotes in universal ribosomal RNA phylogenies, it is a valuable, if not unique, model for gaining basic insights into genetic innovations that led to formation of eukaryotic cells. In evolutionary terms, the divergence of this organism is at least twice as ancient as the common ancestor for yeast and man. A detailed study of its genome will provide insights into an early evolutionary stage of eukaryotic chromosome organization as well as other aspects of the prokaryotic / eukaryotic divergence.

ALlele FREquency Database

ALFRED

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We are working on a new version of ALFRED web interface. The current web interface will not be available from December 15th, 2023. There will be a period where a public web interface is not available for viewing ALFRED data. Expected date for the deployment of the new ALFRED web interface with minimum functions is March 1st, 2024 --------------------------------------------- ALFRED is a free, web-accessible, curated compilation of allele frequency data on DNA sequence polymorphisms in anthropologically defined human populations. ALFRED is distinct from such databases as dbSNP, which catalogs sequence variation.

Human Protein Reference Database

HPRD

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Human Protein Reference Database (HPRD) has been established by a team of biologists, bioinformaticists and software engineers. This is a joint project between the PandeyLab at Johns Hopkins University, and Institute of Bioinformatics, Bangalore. HPRD is a definitive repository of human proteins. This database should serve as a ready reckoner for researchers in their quest for drug discovery, identification of disease markers and promote biomedical research in general. Human Proteinpedia (www.humanproteinpedia.org) is its associated data portal.

CyberCell Database

CCDB

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The CyberCell database (CCDB) is a comprehensive collection of detailed enzymatic, biological, chemical, genetic, and molecular biological data about E. coli (strain K12, MG1655). It is intended to provide sufficient information and querying capacity for biologists and computer scientists to use computers or detailed mathematical models to simulate all or part of a bacterial cell at a nanoscopic (10-9 m), mesoscopic (10-8 m).The CyberCell database CCDB actually consists of 4 browsable databases: 1) the main CyberCell database (CCDB - containing gene and protein information), 2) the 3D structure database (CC3D – containing information for structural proteomics), 3) the RNA database (CCRD – containing tRNA and rRNA information), and 4) the metabolite database (CCMD – containing metabolite information). Each of these databases is accessible through hyperlinked buttons located at the top of the CCDB homepage. All CCDB sub-databases are fully web enabled, permitting a wide variety of interactive browsing, search and display operations. and microscopic (10-6 m) level.

Nuclear Receptor Signaling Atlas

NURSA Hub

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>>> !!! the repository is offline !!! <<< More information see: https://dknet.org/about/NURSA_Archive All NURSA-biocurated transcriptomic datasets have been preserved for data mining in SPP through an enhanced and expanded version of Transcriptomine named Ominer. To access these datasets, dkNET provides users with the information of 527 transcriptomic datasets that contain data related to nuclear receptors and nuclear receptor coregulators in the NURSA Datasets table view and redirects users to the current SPP dataset page. Once users find the specific dataset of research interest, users can download the dataset by clicking DOI and then clicking the Download Dataset button at the Signaling Pathways Project webpage. See https://www.re3data.org/repository/r3d100013650

The Human Protein Atlas

HPA

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The Swedish Human Protein Atlas project has been set up to allow for a systematic exploration of the human proteome using Antibody-Based Proteomics. This is accomplished by combining high-throughput generation of affinity-purified antibodies with protein profiling in a multitude of tissues and cells assembled in tissue microarrays. Confocal microscopy analysis using human cell lines is performed for more detailed protein localization. The program hosts the Human Protein Atlas portal with expression profiles of human proteins in tissues and cells. The main objective of the resource centre is to produce specific antibodies to human target proteins using a high-throughput production method involving the cloning and protein expression of Protein Epitope Signature Tags (PrESTs). After purification, the antibodies are used to study expression profiles in cells and tissues and for functional analysis of the corresponding proteins in a wide range of platforms.