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Showing 1 to 24 of 24 datasets databases. (View all databases)


1000 Genomes

Provider: 1000 Genomes
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Descriptions: 1000 Genomes: a deep catalog of human genetic variation "...is the first project to sequence the genomes of a large number of people, to provide a comprehensive resource on human genetic variation... The goal of the 1000 Genomes Project is to find most genetic variants that have frequencies of at least 1% in the populations studied." 1000 Genomes is an international endeavor, with participants from institutes, governments and universities world-wide. "DNA from the samples will be available for researchers to follow up with more detailed studies of variation in particular regions. The cell lines will allow researches to study cellular phenotypes such as gene expression, epigenetic patterns, and drug response. The extensive genotype data available on the samples, and the trio samples for some of the populations, will allow researchers to map regions of the genome computationally that affect the cellular phenotypes, and to study the heritability of these phenotypes."
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ALFRED: The Allele Frequency Database

Provider: Kenneth K. Kidd, Yale University / US National Science Foundation
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Descriptions: "ALFRED's focus is on allele frequencies in diverse anthropologically defined populations. It is not a compendium of human DNA polymorphisms but of frequencies of selected polymorphisms with an emphasis on those that have been studied in multiple populations. All of the data in ALFRED are considered to be in the public domain and available for use in research and teaching."
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Allen Brain Atlas

Provider: Allen Institute for Brain Science
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Descriptions: "A growing collection of online public resources integrating extensive gene expression and neuroanatomical data, complete with a novel suite of search and viewing tools." Images and gene expression data are available for the mouse brain and spinal cord, and human and non-human primate brains. Excellent video tutorials  provide training in the use of the atlases and the Brain Explorer 2 software.
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BioMart Bio Portal

Provider: BioMart
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Descriptions: The BioMart project provides free software and data services to the international scientific community in order to foster scientific collaboration and facilitate the scientific discovery process. The project adheres to the open source philosophy of promoting collaboration and code reuse. The majority of the contributed databases are of plant or human genomics-oriented data. Under Community, view the linked database list with descriptions and contributor names. Databases originate from the UK, USA, France, Spain, China and other countries. There are three separate portal websites-- the central "Bio" portal, a cancer portal, and one for mouse data.  Unfortunately, no link back to BioMart is provided once the user accesses one of the other portals.
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BLAST (NCBI)

Provider: National Center for Biotechnology Information
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Descriptions: The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.
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CDC Wonder

Provider: CDC (Centers for Disease Control and Prevention)
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Descriptions: CDC WONDER -- Wide-ranging Online Data for Epidemiologic Research -- is a menu-driven system that makes the information resources of the Centers for Disease Control and Prevention (CDC) available to public health professionals and the public. It provides access to a wide array of public health information. Public-use data sets about mortality , cancer incidence, HIV and AIDS, tuberculosis, vaccinations, natality, census data and many other topics are available for query, and the requested data are readily summarized and analyzed in dynamically calculated statistics, charts and maps. The data is compatible with desktop applications such as word processors, spreadsheet programs, or statistical and geographic analysis packages. File formats include plain text (ASCII), web pages (HTML), and spreadsheet files (Tab Separated Values).
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Center for Biological Sequence Analysis

Provider: Technical University of Denmark
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Descriptions: The Center does basic research in the fields of bioinformatics and systems biology. A multidisciplinary group of scientists works in ten specialist research areas (see the CBS Map) and is one of the largest such groups in European academia. Datasets, software, a publications list, and hundreds of links to other related data repositories are included here. Also includes a set of links to courses and lectures.
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dbGaP- Database of Genotypes and Phenotypes

Provider: National Center for Biotechnology Information
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Descriptions: In dbGaP, NCBI archives and distributes the results of studies investigating the interaction of genotype and phenotype. Genome-wide association studies, medical sequencing, molecular diagnostic assays, and associations between genotype and non-clinical traits are covered. dbGaP contains both open- and controlled-access data. Non-sensitive data are released on a broad scale, but sensitive data sets involving personal health information are not publicly accessible. Search by study or disease, or use Advanced Search.
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Effective Health Care Program – AHRQ

Provider: Agency for Healthcare Research and Quality (AHRQ)
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Descriptions: First funded by Congress in 2005, the Effective Health Care Program funds and synthesizes the findings of teams of researchers and clinicians across North America, to identify ways to improve the quality of health care through evidence-based decision-making. Research summaries are available for consumers (many with Spanish translations), clinicians and policy-makers. Also for patients, short videos on treatment options, helpful comparative charts on the effectiveness of different treatments for various conditions. Many resources in various formats are provided. The Program invites comments and topic research/review suggestions, and data deposit by medical professionals. Links are provided to plug-ins for viewing video content.
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F1000Research

Provider: F1000
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Descriptions: F1000Research is an open online journal based on an alternative model of scientific publishing and peer review. Peer review is open, attributed, and done post-publication, once a work has been submitted to internal review and posted. F1000 strongly encourages publication of accompanying datasets under liberal Creative Commons licensing terms. Citations contain information on the stage of refereeing and approval of references. Many Texas Medical Center faculty members are also on the distinguished international editorial staff at F1000.
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FedStats

Provider: FedStats.gov
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Descriptions: FedStats is a portal to virtually all the statistics gathered by U.S. Government agencies and bureaus. For some of these, compiling statistics is their main mission; for others, the activity supports their other work. Searches can be done by state or by topic under general subject categories-- agriculture, crime, demographics, education, energy and environment, health, labor, commerce and economics. A full list of agencies is provided, with information on the kinds of statistics they produce. International data of various kinds is also accessible here, some of it comparative.
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FlyBase: A Database of Drosophila Genes and Genomes

Provider: National Institutes of Health
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Descriptions: A visually beautiful, rich and well-organized home for Drosophila researchers, with forums, tools, links to other important sites (including Interactive Fly), high-quality images, a genome browser, and many more helpful tools and features. New FlyBase users can check under the News and link out to the explanatory article, FlyBase 101: the Basics of Navigating FlyBase. The FlyBase project is carried out by a consortium of Drosophila researchers and computer scientists from Harvard University, University of Cambridge, Indiana University and the University of New Mexico, and is funded by grants from NIH, British Medical Research Council, National Science Foundation, and Indiana University
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Gene Ontology

Provider: Gene Ontology Project
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Descriptions: "The Gene Ontology project is a major bioinformatics initiative with the aim of standardizing the representation of gene and gene product attributes across species and databases. The project provides a controlled vocabulary of terms for describing gene product characteristics and gene product annotation data from GO Consortium members, as well as tools to access and process this data."  The Ontologies describe three aspects of molecular biology- biological processes, cellular components, and molecular functions. Gene Ontology's collected tools list includes hundreds from all over the world: specialized browsers, search engines, statistical analysis and visualization tools, and many other kinds. This project began as a collaboration between three model organism databases, FlyBase (Drosophila), the Saccharomyces Genome Database  and the Mouse Genome Database  in 1998. Since then, the GO Consortium has grown to include many other databases, including several of the world's major repositories for plant, animal and microbial genomes. See the GO Consortium page for a full list of member organizations.
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GigaDB

Provider: GigaScience and BGI
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Descriptions: GigaDB is an open repository of datasets that support the research published in the open access BioMed Central bioinformatics journal, GigaScience. GigaDB provides a place from which to download supporting data and tools associated with papers published in GigaScience, thus facilitating the reproducibility of research. DataCite DOIs are assigned to these accompanying datasets, an identification device which serves to facilitate tracking and discoverability, and to provide additional credit to the authors who make their data publicly available.
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GQuery: Global Cross-database NCBI Search

Provider: National Center for Bioinformatics Information (NCBI)
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Descriptions: Integrated, text-based search and retrieval system used at the National Center for Biotechnology Information for its major databases: PubMed, Nucleotide and Protein Sequences, Protein Structures, Complete Genomes, Taxonomy, and others. GQuery integrates the scientific literature, DNA and protein sequence databases, 3D protein structure and protein domain data, population study datasets, expression data, assemblies of complete genomes, and taxonomic information into a tightly interlinked system.
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IntegromeDB

Provider: Researchers at University of California, San Diego
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Descriptions: Created by four university colleagues, IntegromeDB brings together literally hundreds of resources to provide an integrated database of genomic, proteomic, transcriptive, genetic and functional data. Featured in the database are gene function, orthology, gene expression, pathways, protein interactions, mutations and SNPs, disease relationships, and related drugs and compounds. Those not yet familiar with IntegromeDB may want to read the group's open-access article, IntegromeDB: an integrated system and biological search engine.
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KEGG (Kyoto Encyclopedia of Genes and Genomics)

Provider: Kanehisa Laboratories, Japan
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Descriptions: KEGG is a resource purposed to facilitate understanding of the functions and utilities of the biological system--  cells, organisms and ultimately the ecosystem--  based on genomic and molecular-level information. It is a computer representation of the biological system, consisting of the molecular building blocks-- genes, proteins and chemical substances, integrated with molecular wiring diagrams of interaction, reaction and relational networks. Extensive data is available to view; ftp downloading requires a subscription. KEGG was developed in collaboration with the Bioinformatics Center, Institute for Chemical Research, Kyoto University and the Human Genome Center, Institute of Medical Science, University of Tokyo.
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National Library of Medicine: Databases, Resources and APIs

Provider: National Library of Medicine
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Descriptions: This is NLM's portal to its approximately 300 research resources, from genetics to the history of medicine, from datasets to mobile apps.  Browse the list with all descriptive information, or search by subject term, type of data or tool, or by terms related to the content or intended audience.
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NCBI (National Center for Biotechnology Information)

Provider: National Center for Biotechnology Information/National Library of Medicine
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Descriptions: The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information. NCBI provides a large number of resources for scientific research, including software and many databases.
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Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC)

Provider: NITRC,
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Descriptions: Originally funded by the NIH Blueprint for Neuroscience Research, NITRC facilitates finding and comparing neuroimaging resources for functional and structural neuroimaging analyses—tools that were once hidden in a researcher's laboratory and well-known resources. NITRC collects and points to standardized information about tools, making the task of finding and comparing them easier. This site can help researchers find the right functional or structural neuroimaging tool or resource and serve as an aid in deciding whether it will be helpful to them. 
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Protein Data Bank: An Information Portal to Biological Macromolecular Structures

Provider: RCSB (Research Collaboratory for Structural Bioinformatics)
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Descriptions:  "The RCSB (Research Collaboratory for Structural Bioinformatics) is dedicated to improving our understanding of the function of biological systems through the study of the 3-D structure of biological macromolecules. RCSB members work cooperatively and equally through joint grants and subsequently provide free public resources and publications to assist others and further the fields of bioinformatics and biology."  Protein Data Bank (PDB) curates and annotates data according to agreed-upon standards and is a member of the ww (world wide) PDB. Use this database to perform simple and advanced searches based on sequence, structure and function annotations, and to visualize, download, and analyze molecules. The database is primarily for researchers, but the site also includes an entire section (PDB101) of information quite accessible enough for educational purposes. Check out the "Molecule of the Month" feature. The extensive archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies.  As with many scientific databases, a personal log-in affords access to more features. The database is managed by Rutgers and University of California San Diego.
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PubChem

Provider: National Center for Biotechnology Information/National Library of Medicine
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Descriptions: PubChem provides information on the biological activities of small molecules and is a component of NIH's Molecular Libraries Roadmap Initiative. It includes substance information, compound structures, and bioactivity data in three primary databases: PCSubstance, PCCompound and PCBioAssay. PCSubstance contains more than 12 million records; PCCompound contains more than 7 million unique structures; and PCBioAssay contains more than 200 bioassays.
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Systematic Review Data Repository

Provider: AHRQ (Agency for Healthcare Research and Quality)
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Descriptions: In an effort to reduce the burden of conducting systematic reviews, the Evidence-based Practice Center (EPC) at Tufts Medical Center, with support from the Agency for Healthcare Research and Quality (AHRQ), developed a collaborative, web-based repository of systematic review data. This resource serves as both an archive and data extraction tool and is shared among organizations and individuals producing systematic reviews worldwide, enabling the creation of a central database of systematic review data which may be critiqued, updated, and augmented on an ongoing basis. This database is made freely accessible to facilitate evidence reviews, which in turn can improve and facilitate healthcare policy-making. To contribute comments or data, register for a free personal account.
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UniProt

Provider: UniProt Consortium
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Descriptions: "The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information."  Available material consists of: UniProtKB, a two-section protein knowledge-base consisting of SwissProt and TrEMBL; UniRef (sequence clusters;) UniParc (a sequence archive for tracking sequences and identifiers) and the supporting data (literature citations, taxonomy, keywords, nomenclature, guidelines and indexes.) A user manual and primer on annotation are provided as well. UniProt is distributed free under a Creative Commons attribution license. Updates are frequent and updated releases must be downloaded from the website. Much of UniProt's funding is provided by the NIH.
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